MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'EURASIP Journal on Bioinformatics and Systems Biology' source. Thu, 09 Feb 2012 22:12:28 +0100 http://www.medworm.com/index.php?rid=5521039&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fpm%2F2011%2F931342%2F Interstitial lung disease (ILD) represents a severe manifestation in connective tissue diseases (CTD), with an overall incidence of 15%, and it is still a challenge for clinicians evaluation and management. ILD is the most common manifestation of lung involvement in Rheumatoid Arthritis (RA), observed in up to 80% of biopsies, 50% of chest Computed Tomography (CT) and only 5% of chest radiographs. Histopatological patterns of ILD in RA may present with different patterns, such as: usual interstitial pneumonia, non specific interstitial pneumonia, desquamative interstitial pneumonia, organizing pneumonia, and eosinophilic infiltration. The incidence of ILD in RA patients is not only related to the disease itself, many drugs may be in fact associated with the development ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5521039 Tue, 20 Dec 2011 15:07:57 +0100 5521039 http://www.medworm.com/index.php?rid=5521038&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Famet%2F2011%2F924516%2F Monthly averaged tropospheric ozone residual (TOR) data from TOMS and OMI during the period 1979–2009 are used to study the spatial distribution of tropospheric column ozone within the landmass of the Indian subcontinent, the Tibetan plateau in the north and the Bay of Bengal in the south. The climatological mean shows seasonal maxima in spring and minima in winter in all the regions. The oceanic regions exhibit broad summer maximum and the maximum to minimum ratio is the lowest for these regions. The concentration of tropospheric column ozone is found to be highest in North Eastern India (NE) and the Indo Gangetic plains (IGP). NE ozone concentration exceeds that of IGP during spring whereas in post monsoon and winter reverse is the case. In the monsoon season, O3 levels in the two ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5521038 Tue, 20 Dec 2011 15:07:57 +0100 5521038 http://www.medworm.com/index.php?rid=5521037&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fecam%2F2012%2F417267%2F Conclusions. Supplementation with standardised Echinacea tablets, if taken before and during travel, may have preventive effects against the development of respiratory symptoms during travel involving long-haul flights. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5521037 Tue, 20 Dec 2011 15:07:57 +0100 5521037 http://www.medworm.com/index.php?rid=5521036&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fijsa%2F2011%2F543590%2F We consider an agent who wants to liquidate an asset with unknown drift. The agent believes that the drift takes one of two given values and has initially an estimate for the probability of either of them. As time goes by, the agent observes the asset price and can therefore update his beliefs about the probabilities for the drift distribution. We formulate an optimal stopping problem that describes the liquidation problem, and we demonstrate that the optimal strategy is to liquidate the first time the asset price falls below a certain time-dependent boundary. Moreover, this boundary is shown to be monotonically increasing, continuous and to satisfy a nonlinear integral equation. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5521036 Tue, 20 Dec 2011 15:07:57 +0100 5521036 http://www.medworm.com/index.php?rid=5521035&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fcrim%2Fophmed%2F2011%2F942946%2F We describe a 40-year-old man who presented to our clinic complaining of foreign body sensation and irritation in his left eye which lasted several months. The patient history was positive for bilateral rhegmatogenous retinal detachment which was treated with sclera buckling. Upon presentation the left eye demonstrated phthisis and an exposed and infected sclera buckle and explant in the lower quadrants. The explant was removed, and the patient was treated with antibiotics. This case suggests that wide encircling sclera element might erode through the conjunctiva of eyes undergoing phthisis. Integrity of the conjunctiva overlying episcleral implant should be evaluated during routine follow-up exams to exclude exposure of the implant particularly in eyes undergoing phthisis. (Source: EURASI... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5521035 Tue, 20 Dec 2011 15:07:57 +0100 5521035 http://www.medworm.com/index.php?rid=5521034&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fcrim%2Fophmed%2F2011%2F549270%2F We report a 45-year-old male, HBV+, HIV+, with a past history of a liver transplant for ELSD (end-stage liver disease) with hepatocellular carcinoma and recurrent HCC, who presented with proptosis and diplopia of the left eye. CT scans of the head revealed a large, irregular mass in the left orbit causing superior and lateral destruction of the orbital bone. Biopsy specimens of the orbital tumor showed features of metastatic foci of hepatocellular carcinoma. Only 16 other cases of HCC metastasis to the orbit have been described in literature, and this is the first case in a previously transplanted HIV+, HBV+ patient. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5521034 Tue, 20 Dec 2011 15:07:57 +0100 5521034 http://www.medworm.com/index.php?rid=5521033&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjar%2F2011%2F682470%2F Conclusion. Members of the general public may serve as an alternative to patients and caregivers in the elicitation of health-related quality of life in AD. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5521033 Tue, 20 Dec 2011 15:07:57 +0100 5521033 http://www.medworm.com/index.php?rid=5521032&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fijpg%2F2011%2F261975%2F The most commonly applied strategies for identifying genes with a common response profile are based on clustering algorithms. These methods have no explicit rules to define the appropriate number of groups of genes. Usually the number of clusters is decided on heuristic criteria or through the application of different methods proposed to assess the number of clusters in a data set. The purpose of this paper is to compare the performance of seven of these techniques, including traditional ones, and some recently proposed. All of them produce underestimations of the true number of clusters. However, within this limitation, the gDGC algorithm appears to be the best. It is the only one that explicitly states a rule for cutting a dendrogram on the basis of a testing hypothesis framework, allowi... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5521032 Tue, 20 Dec 2011 15:07:57 +0100 5521032 http://www.medworm.com/index.php?rid=5521031&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjtran%2F2011%2F581485%2F Conclusion. RTx using TIP in HCV-positive patients is a viable option with acceptable outcome. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5521031 Tue, 20 Dec 2011 15:07:57 +0100 5521031 http://www.medworm.com/index.php?rid=5521030&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fapm%2F2011%2F353207%2F This study examined the factors affecting the intention to be vaccinated against the swine flu among students in Israel. Questionnaires were distributed in December 2009 among 387 students at higher-education institutions. The research questionnaire included sociodemographic characteristics and Health Belief Model principles. The results show that the factors positively affecting the intention to take the swine flu vaccine were past experience with seasonal flu shot and three HBM categories: higher levels of perceived susceptibility for catching the illness, perceived seriousness of illness, and lower levels of barriers. We conclude that offering the vaccine at workplaces may raise the intention to take the vaccine among young people in Israel. (Source: EURASIP Journal on Bioinformatics an... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5521030 Tue, 20 Dec 2011 15:07:57 +0100 5521030 http://www.medworm.com/index.php?rid=5521029&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbcri%2F2011%2F809259%2F Caveolin-2 is one of the major protein components of cholesterol- and glycosphingolipid-rich flask-shaped invaginations of plasma membrane caveolae. A new body of evidence suggests that caveolin-2 plays an important, and often more direct, role than caveolin-1 in regulating signaling and function in a cell- and tissue type-specific manner. The purpose of this paper is to primarily focus on discussing how these recent discoveries may help better understand the specific contribution of caveolin-2 to lipid raft- and caveolae-regulated cell/tissue-specific signaling and functions. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5521029 Tue, 20 Dec 2011 15:07:57 +0100 5521029 http://www.medworm.com/index.php?rid=5521028&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fmpe%2F2011%2F145692%2F This paper proposes a robust design optimization methodology under design uncertainties of an aerospace vehicle propulsion system. The approach consists of 3D geometric design coupled with complex internal ballistics, hybrid optimization, worst-case deviation, and efficient statistical approach. The uncertainties are propagated through worst-case deviation using first-order orthogonal design matrices. The robustness assessment is measured using the framework of mean-variance and percentile difference approach. A parametric sensitivity analysis is carried out to analyze the effects of design variables variation on performance parameters. A hybrid simulated annealing and pattern search approach is used as an optimizer. The results show the objective function of optimizing the mean performanc... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5521028 Tue, 20 Dec 2011 15:07:57 +0100 5521028 http://www.medworm.com/index.php?rid=5521027&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fcrim%2Fophmed%2F2011%2F850919%2F We report an unusual case where the dislocated cataractous lens firmly adherent to the corneal endothelium evoked a cellular reaction similar to phacolytic glaucoma but clinically appeared like a deep corneal abscess. The 73-year-old lady presented with severe photophobia, pain, and redness in the left eye for two months despite being on antibiotics and antifungals. Anterior chamber wash revealed a cataractous lens buried within the infiltrate, which was removed and sent for histopathological examination. Postoperatively she was treated with topical ofloxacin, homatropine, dorzolamide, timolol, and tapering dose of steroids. Histological confirmation of inflammation, histiocytic response, and giant cells around the lens material confirmed the ongoing phacolytic process. Photophobia, pain, ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5521027 Tue, 20 Dec 2011 15:07:57 +0100 5521027 http://www.medworm.com/index.php?rid=5513110&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjsc%2F2011%2F614097%2F Ubiquitin and ubiquitin-related proteins posttranslationally modify substrates, and thereby alter the functions of their targets. The ubiquitination process is involved in various physiological responses, and dysregulation of components of the ubiquitin system has been linked to many diseases including skin cancer. The ubiquitin pathways activated among skin cancers are highly diverse and may reflect the various characteristics of the cancer type. Basal cell carcinoma and squamous cell carcinoma, the most common types of human skin cancer, are instances where the involvement of the deubiquitination enzyme CYLD has been recently highlighted. In basal cell carcinoma, the tumor suppressor protein CYLD is repressed at the transcriptional levels through hedgehog signaling pathway. Downregulatio... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5513110 Sat, 17 Dec 2011 15:37:59 +0100 5513110 http://www.medworm.com/index.php?rid=5501866&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjpath%2F2011%2F947218%2F Proteinases secreted by the oomycete Phytophthora infestans (Mont.) de Bary, Rhizoctonia solani, and Fusarium culmorum belonging to different families of fungi have been studied to determine if the exoenzyme secretion depends on the environmental conditions and the phylogenetic position of the pathogen. The substrate specificity of the extracellular proteinases of F. culmorum, R. solani, and P. infestans and their sensitivity to the action of synthetic and protein inhibitors suggest that they contain trypsin-like and subtilisin-like enzymes regardless of culture medium composition. The relation of trypsin-like and subtilisin-like enzymes is dependent on the culture medium composition, especially on the form of nitrogen nutrition, particularly in the case of the exoenzymes secreted by R. so... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5501866 Wed, 14 Dec 2011 17:08:27 +0100 5501866 http://www.medworm.com/index.php?rid=5501865&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fecam%2F2012%2F519084%2F We have investigated effect of Moringa oleifera leaf and fruit extracts on markers of oxidative stress, its toxicity evaluation, and correlation with antioxidant properties using in vitro and in vitro assays. The aqueous extract of leaf was able to increase the GSH and reduce MDA level in a concentration-dependent manner. The ethanolic extract of fruit showed highest phenolic content, strong reducing power and free radical scavenging capacity. The antioxidant capacity of ethanolic extract of both fruit and leaf was higher in the in vitro assay compared to aqueous extract which showed higher potential in vivo. Safety evaluation studies showed no toxicity of the extracts up to a dose of 100 mg/kg body weight. Our results support the potent antioxidant activity of aqueous and ethanolic... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5501865 Wed, 14 Dec 2011 17:08:27 +0100 5501865 http://www.medworm.com/index.php?rid=5501864&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjcnc%2F2011%2F707592%2F This paper proposes a new replica placement algorithm that expands the exhaustive search limit with reasonable calculation time. It combines a new type of parallel data-flow processor with an architecture tuned for fast calculation. The replica placement problem is to find a replica-server set satisfying service constraints in a content delivery network (CDN). It is derived from the set cover problem which is known to be NP-hard. It is impractical to use exhaustive search to obtain optimal replica placement in large-scale networks, because calculation time increases with the number of combinations. To reduce calculation time, heuristic algorithms have been proposed, but it is known that no heuristic algorithm is assured of finding the optimal solution. The proposed algorithm suits parallel... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5501864 Wed, 14 Dec 2011 17:08:27 +0100 5501864 http://www.medworm.com/index.php?rid=5501863&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fat%2F2011%2F178943%2F Friction plots of polymers sliding on smooth metal surfaces are generally characterized by two regions of distinct dependency on the normal load, with low sensitivity at low stress levels followed by a sharp change in the rate of decrease of friction with increasing pressure at levels above the plastic flow limit of the polymer. A simplified model is proposed to describe this behavior which accounts for the effect of the normal load on the growth of the real contact area and the shear stress at the interface between the polymer and the mating surface. The model has a wide generality when expressed in terms of dimensionless variables, allowing to rationalize the friction behavior of different polymers within a single framework. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5501863 Wed, 14 Dec 2011 17:08:27 +0100 5501863 http://www.medworm.com/index.php?rid=5501862&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fcrim%2Fophmed%2F2011%2F507073%2F Conclusion. This is the first case report of travoprost causing granulomatous anterior uveitis. The uveitis recurred with a rechallenge. Changing the prostaglandin analogue to another topical treatment may be adequate to cease the inflammation. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5501862 Wed, 14 Dec 2011 17:08:27 +0100 5501862 http://www.medworm.com/index.php?rid=5501861&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcrim%2F2011%2F948328%2F Gastric neuroendocrine carcinomas are rare and have a poor prognosis, and the diagnostic criteria for this disease have recently changed. We herein report a case of sporadic gastric neuroendocrine carcinoma. A 75-year-old man was referred to our hospital with epigastric pain. Endoscopic examination revealed a localized ulcerative lesion (diameter, 4 cm) at the upper stomach. The diagnosis on biopsy was neuroendocrine carcinoma. Total gastrectomy with D2 lymphadenectomy, splenectomy, and cholecystectomy was performed. Pathologically, the tumor infiltrated the subserosal layer, and 6/49 lymph nodes were involved. The tumor was uniform in shape and arranged in a rosette-like structure to form solid nests, with medium-sized, round-to-cuboid-shaped tumor cells and intense mitosis 46/10 H... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5501861 Wed, 14 Dec 2011 17:08:27 +0100 5501861 http://www.medworm.com/index.php?rid=5501860&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbca%2F2011%2F429241%2F A new mononuclear Pt(II) complex, [Pt(DMP)(DIP)]Cl2.H2O, in which DMP is 4,4-dimethyl-2,2-bipyridine and DIP is 4,7-diphenyl-1,10-phenantroline, has been synthesized and characterized by physicochemical and spectroscopic methods. The binding interaction of this complex with calf thymus DNA (CT-DNA) was investigated using fluorimetry, spectrophotometry, circular dichroism, viscosimetry and cyclic voltametry (CV). UV-VIS spectrum showed 4 nm bathochromic shift of the absorption band at 280 nm along with significant hypochromicity for the absorption band of the complex. The intrnisic binding constant (Kb=2×104 M-1) is more in keeping with intercalators and suggests this binding mode. The viscosity measurements showed that the complex-DNA interaction can be hydrop... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5501860 Wed, 14 Dec 2011 17:08:27 +0100 5501860 http://www.medworm.com/index.php?rid=5454550&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fijeco%2F2011%2F870853%2F Assessing the viability of reintroduced animal populations is a complicated task. Reintroductions are usually carried out with a small number of individuals, thereby, limiting the possibilities for monitoring because of the possible negative effects of intensive monitoring on survival and reproduction. Moreover, reintroduction studies are part of a socioeconomic interplay of forces, thereby, also limiting monitoring possibilities. Also, knowledge of population demography and abundance can be incomplete or unattainable. Here, we illustrate how we combined traditional telemetry and novel non-invasive genetic methodology to construct a detailed life table of a small reintroduced otter population in The Netherlands. Combining an appropriate capture-mark-recapture framework with a matrix modell... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5454550 Tue, 29 Nov 2011 15:59:43 +0100 5454550 http://www.medworm.com/index.php?rid=5454549&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fcrim%2Fpediatrics%2F2011%2F414693%2F Spondylolysis, a fracture of the pars interarticularis, is a common source back pain in children and adolescents. While the incidence is significantly higher in Asian and Inuit populations, it is never seen in nonambulatory children and is most commonly associated with athletic activities that involve extension or rotational deformity about the spine suggesting a functional component. Given that the associated pain is typically insidious in onset, lacks preceding trauma, and is accompanied by muscular spasm, prompt diagnosis requires a high index of suspicion, familiarity with provocative testing, and knowledge of the appropriate radiographic evaluation. Treatment requires cessation of athletic activity, bracing, and rest for a minimum of four to six weeks, or until symptomatic and radiogr... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5454549 Tue, 29 Nov 2011 15:59:43 +0100 5454549 http://www.medworm.com/index.php?rid=5454548&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fmse%2F2011%2F496732%2F The main aim of this work is to show that such a powerful optimizing tool like evolutionary algorithms (EAs) can be in reality used for the simulation and optimization of a nonlinear system. A nonlinear mathematical model is required to describe the dynamic behaviour of batch process; this justifies the use of evolutionary method of the EAs to deal with this process. Four algorithms from the field of artificial intelligent—differential evolution (DE), self-organizing migrating algorithm (SOMA), genetic algorithm (GA), and simulated annealing (SA)—are used in this investigation. The results show that EAs are used successfully in the process optimization. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5454548 Tue, 29 Nov 2011 15:59:43 +0100 5454548 http://www.medworm.com/index.php?rid=5454547&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcrp%2F2011%2F341521%2F Conclusion. Inflammation seems to be more active in symptomatic BrS. C-reactive protein concentrations ≥ 2 mg/L might be associated with the previous symptoms in BrS. The value of inflammation as a risk factor of arrhythmic events in BrS needs to be studied. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5454547 Tue, 29 Nov 2011 15:59:43 +0100 5454547 http://www.medworm.com/index.php?rid=5454546&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fije%2F2011%2F715370%2F In conclusion, serum FT4 determines REE in euthyroid patients with GH treated with BRT. Twelve weeks after BRT cessation, BW and energy homeostasis are unaltered. However, as serum FT3/FT4 ratio increases after cessation of BRT, which is a positive determinant of changes in REE, a longer term BW decrease is likely to occur. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5454546 Tue, 29 Nov 2011 15:59:43 +0100 5454546 http://www.medworm.com/index.php?rid=5428677&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2011%2F212146%2F Accurate and efficient splicing is of crucial importance for highly-transcribed intron-containing genes (ICGs) in rapidly replicating unicellular eukaryotes such as the budding yeast Saccharomyces cerevisiae. We characterize the 5′ and 3′ splice sites (ss) by position weight matrix scores (PWMSs), which is the highest for the consensus sequence and the lowest for splice sites differing most from the consensus sequence and used PWMS as a proxy for splicing strength. HAC1, which is known to be spliced by a nonspliceosomal mechanism, has the most negative PWMS for both its 5′ ss and 3′ ss. Several genes under strong splicing regulation and requiring additional splicing factors for their splicing also have small or negative PWMS values. Splicing strength is higher f... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5428677 Sun, 20 Nov 2011 15:42:17 +0100 5428677 http://www.medworm.com/index.php?rid=5428676&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjamop%2F2011%2F573179%2F We present a systematic treatment of the bound state structure of a short-range attractive interatomic potential in one, two, and three dimensions as its range approaches zero. This allows the evaluation of the utility of delta function potentials in the modeling of few-body systems such as nuclei, atoms, and clusters. The relation to scattering by delta function potentials is also discussed. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5428676 Sun, 20 Nov 2011 15:42:17 +0100 5428676 http://www.medworm.com/index.php?rid=5428675&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Faps%2F2011%2F740687%2F Effects of GSE and vitamins C and E on aspirin- and ethanol-induced gastric ulcer and associated increases of lipid peroxidation in rats were compared. Two experiments were conducted. Rats were randomized into eight groups: a negative control and seven groups that received aspirin or ethanol for ulcer induction: one positive control (vehicle) and six with VC, VE, or GSE (25 and 250 mg/kg). Ulcer indexes and gastric levels of malondialdehyde (MDA) were quantified. VC, VE, and GSE (25 and 250 mg/kg) decreased aspirin, and ethanol-induced ulcers and MDA values compared with positive control group. The magnitude of aspirin ulcer reduction was comparable for all treatments, and MDA decrease with GSE was higher than with VC and tended to be greater, albeit none significantly, than ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5428675 Sun, 20 Nov 2011 15:42:17 +0100 5428675 http://www.medworm.com/index.php?rid=5428674&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fcrim%2Fid%2F2011%2F525841%2F We report a patient who developed during HIV primary infection a symptomatic mixed cryoglobulinemia. The patient suffered from arthralgias, vascular purpura of the legs, and proteinuria. Cryoglobulinemia progressively disappeared in several months after HAART. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5428674 Sun, 20 Nov 2011 15:42:17 +0100 5428674 http://www.medworm.com/index.php?rid=5428673&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fsrcm%2F2011%2F289673%2F Conclusion. Nine percent of STS patients in our cohort developed significant (grade≥2) lymphoedema. Tumor size>5 cm and deep tumors were associated with an increased occurrence of lymphoedema but not radiation dosage. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5428673 Sun, 20 Nov 2011 15:42:17 +0100 5428673 http://www.medworm.com/index.php?rid=5428672&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fijqsr%2F2011%2F379129%2F Reliability studies for coding contributing factors of incident reports in high hazard industries are rarely conducted and reported. Although the Human Factors Analysis and Classification System (HFACS) appears to have a larger number of such studies completed than most other systems doubt exists as the accuracy and comparability of results between studies due to aspects of methodology and reporting. This paper reports on a trial conducted on HFACS to determine its reliability in the context of military air traffic control (ATC). Two groups participated in the trial: one group comprised of specialists in the field of human factors, and the other group comprised air traffic controllers. All participants were given standardized training via a self-paced workbook and then read 14 incident rep... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5428672 Sun, 20 Nov 2011 15:42:17 +0100 5428672 http://www.medworm.com/index.php?rid=5428671&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Faans%2F2011%2F751908%2F We used five years of global solar radiation data to estimate the monthly average of daily global solar irradiation on a horizontal surface based on a single parameter, sunshine hours, using the artificial neural network method. The station under the study is located in Kampala, Uganda at a latitude of 0.19°N, a longitude of 32.34°E, and an altitude of 1200 m above sea level. The five-year data was split into two parts in 2003–2006 and 2007-2008; the first part was used for training, and the latter was used for testing the neural network. Amongst the models tested, the feed-forward back-propagation network with one hidden layer (65 neurons) and with the tangent sigmoid as the transfer function emerged as the more appropriate model. Results obtained using the propose... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5428671 Sun, 20 Nov 2011 15:42:17 +0100 5428671 http://www.medworm.com/index.php?rid=5428670&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fecam%2F2012%2F383608%2F Acute lung injury (ALI), instilled by lipopolysaccharide (LPS), is a severe illness with excessive mortality and has no specific treatment strategy. Luteolin is an anti-inflammatory flavonoid and widely distributed in the plants. Pretreatment with luteolin inhibited LPS-induced histological changes of ALI and lung tissue edema. In addition, LPS-induced inflammatory responses, including increased vascular permeability, tumor necrosis factor (TNF)-α and interleukin (IL)-6 production, and expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2), were also reduced by luteolin in a concentration-dependent manner. Furthermore, luteolin suppressed activation of NFκB and its upstream molecular factor, Akt. These results suggest that the protection mechanism of ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5428670 Sun, 20 Nov 2011 15:42:17 +0100 5428670 http://www.medworm.com/index.php?rid=5428669&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fcrim%2Fophmed%2F2011%2F232986%2F A 40 year old man was admitted with a 2 weeks history of headache, blurred vision and bilateral optic neuritis. During the 6 months period prior to admission he had treated with infliximab infusions for prsoriasis arthritis. He had 0.2 vision in right eye and 0.5 in left Fundoscopy showed moderate disc swelling more on the right than on the left side and right-sided splinter heamorrhages at the disc margin. The intracranial pressure was normal. He was treated with oral methylprednisolone, 100 mg daily for 1 week. His vision improved gradually and when seen 10 weeks later his visual acuity was 1.0 in both eyes and he had normal visual fields. Optic neuritis is a rare but well recognized serious adverse effect of treatments with tumor necrosis factor (TNF) antagonists. This case repo... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5428669 Sun, 20 Nov 2011 15:42:17 +0100 5428669 http://www.medworm.com/index.php?rid=5428668&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fah%2F2011%2F473709%2F The first mature cells to arise in the developing mammalian embryo belong to the erythroid lineage. This highlights the immediacy of the need for red blood cells during embryogenesis and for survival. Linked with this pressure is the necessity of the embryo to obtain and transport iron, synthesize hemoglobin, and then dispose of the potentially toxic heme via the stress-induced protein heme oxygenase-1 (HO-1, encoded by Hmox1 in the mouse). Null mutation of Hmox1 results in significant embryonic mortality as well as anemia and defective iron recycling. Here, we discuss the interrelated nature of this critical enzyme with iron trafficking, erythroid cell function, and embryonic survival. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5428668 Sun, 20 Nov 2011 15:42:17 +0100 5428668 http://www.medworm.com/index.php?rid=5404989&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjnm%2F2011%2F454730%2F In the current research, an easy and inexpensive method is used to synthesize highly crystalline gallium nitride (GaN) nanowires (NWs) on two different substrates [i.e., porous zinc oxide (PZnO) and porous gallium nitride (PGaN)] on Si (111) wafer by thermal evaporation without any catalyst. Microstructural studies by scanning electron microscopy and transmission electron microscope measurements reveal the role of the substrates in the nucleation and alignment of the GaN NWs. Further structural and optical characterizations were performed using high-resolution X-ray diffraction, energy-dispersive X-ray spectroscopy, and photoluminescence spectroscopy. Results indicate that the NWs have a single-crystal hexagonal GaN structure and growth direction in the (0001) plane. The quality and densit... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5404989 Mon, 14 Nov 2011 14:34:22 +0100 5404989 http://www.medworm.com/index.php?rid=5404988&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Faaa%2F2011%2F259796%2F It is shown that a univalent function f belongs to QK if and only if sup a∈𝔻∫01M∞2(r,f∘φa-f(a))K′(log (1/r))dr<∞, where φa(z)=(a-z)/(1-a¯z), provided K satisfies certain regularity conditions. It is also shown that under these conditions QK contains all univalent Bloch functions if and only if ∫01(log ((1+r)/(1-r)))2K′(log (1/r))dr<∞. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5404988 Mon, 14 Nov 2011 14:34:22 +0100 5404988 http://www.medworm.com/index.php?rid=5404987&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fstni%2F2011%2F284274%2F The paper describes one of the variants of mathematical models of a fluid dynamics process inside the containment, which occurs in the conditions of operation of spray systems in severe accidents at nuclear power plant. The source of emergency emissions in this case is the leak of the coolant or rupture at full cross-section of the main circulating pipeline in a reactor building. Leak or rupture characteristics define the localization and the temporal law of functioning of a source of emergency emission (or accrued operating) of warmed up hydrogen and steam in the containment. Operation of this source at the course of analyzed accident models should be described by the assignment of the relevant Dirichlet boundary conditions. Functioning of the passive autocatalytic recombiners of hydrogen... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5404987 Mon, 14 Nov 2011 14:34:22 +0100 5404987 http://www.medworm.com/index.php?rid=5404986&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fat%2F2011%2F974065%2F The surface degradation of metals in boiler tubes and turbines in high-temperature corrosive environments causes severe problems in fuel combustion power plant systems. High-temperature resistant materials have been recently developed using a thermal barrier coating (TBC) and high-chromium alloys. Oxide films or coatings formed on metal surfaces at high temperatures can sometimes decrease the corrosion rate. However, the damage to the material is often accelerated by the mechanical removal of corrosion products from the material surface. It is therefore very important to investigate the mechanical and adhesive properties of the oxide films or coatings on metal surfaces used in high-temperature environments. This paper introduces a tribological method that uses a single spherical projectile... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5404986 Mon, 14 Nov 2011 14:34:22 +0100 5404986 http://www.medworm.com/index.php?rid=5344153&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjmb%2F2011%2F193759%2F The composition and distribution of the main associations of submerged macrobenthos of Bahía Málaga (Colombian pacific coast), were studied in relation to the distribution of hard and soft substrates and some abiotic factors. Eight localities were sampled during six months: three in the external border of the estuary and five in the inner part. In total, 728 organisms were registered, belonging to 207 species, 132 genera, 86 families, and 14 orders of six invertebrate groups (Porifera, Cnidaria, Polychaeta, Mollusca, Crustacea, and Echinodermata). The submerged bottoms presented soft and hard substrates, with rocks and thick sand in five sites, soft bottoms with fine sand in one, and soft bottoms with slime and clay in two. The temperature and salinity values were higher in the e... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5344153 Mon, 24 Oct 2011 13:11:48 +0100 5344153 http://www.medworm.com/index.php?rid=5344152&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fmpe%2F2011%2F890901%2F Structure of data set is of critical importance in identifying clusters, especially the density difference feature. In this paper, we present a clustering algorithm based on density consistency, which is a filtering process to identify same structure feature and classify them into same cluster. This method is not restricted by the shapes and high dimension data set, and meanwhile it is robust to noises and outliers. Extensive experiments on synthetic and real world data sets validate the proposed the new clustering algorithm. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5344152 Mon, 24 Oct 2011 13:11:48 +0100 5344152 http://www.medworm.com/index.php?rid=5344151&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fijae%2F2011%2F874375%2F Improvement of ductility at room temperature has been a major concern on processing and application of Ti aluminides over the years. Modifications in alloy chemistry of binary alloy (Ti48 Al) and processing conditions were suggested through experimental studies with limited success. Using the reported data, the present paper aims to optimize the experimental conditions through computational modeling using artificial neural network (ANN). Ductility database were prepared, and three parameters, namely, alloy type, grain size, and heat treatment cycle were selected for modeling. Additionally, ductility data were generated from the literature for training and validation of models on the basis of linearity and considering the primary effect of these three parameters. Model was trained and teste... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5344151 Mon, 24 Oct 2011 13:11:48 +0100 5344151 http://www.medworm.com/index.php?rid=5344150&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjam%2F2011%2F409181%2F Rough set theory is a powerful tool for dealing with uncertainty, granularity, and incompleteness of knowledge in information systems. This paper discusses five types of existing neighborhood-based generalized rough sets. The concepts of minimal neighborhood description and maximal neighborhood description of an element are defined, and by means of the two concepts, the properties and structures of the third and the fourth types of neighborhood-based rough sets are deeply explored. Furthermore, we systematically study the covering reduction of the third and the fourth types of neighborhood-based rough sets in terms of the two concepts. Finally, two open problems proposed by Yun et al. (2011) are solved. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5344150 Mon, 24 Oct 2011 13:11:48 +0100 5344150 http://www.medworm.com/index.php?rid=5344149&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjamop%2F2011%2F217020%2F We numerically investigate the optical transmission through a compound spherical stack with conventional and metamaterial (MM) layers and also embedded MM defect. A formation of extremely narrow resonant peak with nearly complete transmittance in area of a band gap is found. We demonstrate that photon fields of certain frequencies can be strongly confined by a left-handed (LH) defect. The influence of a random deviation in the width of compound spherical layers as well the transit to the whispering gallery mode (WGM) is also discussed. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5344149 Mon, 24 Oct 2011 13:11:48 +0100 5344149 http://www.medworm.com/index.php?rid=5344148&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fcrim%2Fsurgery%2F2011%2F572454%2F We present our surgical approach to a case with significant stenosis and kinking of internal carotid artery. We performed a 6-mm-PTFE graft interposition between common and internal carotid artery and resection of the kinking segment. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5344148 Mon, 24 Oct 2011 13:11:48 +0100 5344148 http://www.medworm.com/index.php?rid=5344147&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fijelc%2F2011%2F386023%2F A hybrid polynuclear nickel hexacyanoferrate (NiHCFe)/graphitized mesoporous carbon- (GMC-) modified glassy carbon electrode (GCE/NiHCFe@GMC) has been prepared by a sequential method using electrodeposited Ni on a GMC-modified glassy carbon electrode (GCE/Ni@GMC) as a template and [Fe(CN)6]3− as an in-situ chemical precipitant, without any additional interlinking agent. Physicochemical and electrochemical characterizations reveal the presence of NiHCFe units within the porous sites of the GMC. The GCE/NiHCFe@GMC electrode showed highly stable and well-defined redox behaviors with surface-confined electron-transfer mechanism in a pH 7 phosphate buffer solution. The GCE/NiHCFe@GMC showed about 20 times enhancement in hydrazine oxidation peak current along with 500 mV reduction ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5344147 Mon, 24 Oct 2011 13:11:48 +0100 5344147 http://www.medworm.com/index.php?rid=5344146&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fcrim%2Fcardiology%2F2011%2F762873%2F We report a case of an unusual giant right atrium in context of rheumatic stenosis and severe tricuspid regurgitation in a 58-year-old woman. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5344146 Mon, 24 Oct 2011 13:11:48 +0100 5344146 http://www.medworm.com/index.php?rid=5344145&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Farch%2F2011%2F716456%2F It is becoming clear that the regulation of gas vesicle biogenesis in Halobacterium salinarum NRC-1 is multifaceted and appears to integrate environmental and metabolic cues at both the transcriptional and posttranscriptional levels. The mechanistic details underlying this process, however, remain unclear. In this manuscript, we quantify the contribution of light scattering made by both intracellular and released gas vesicles isolated from Halobacterium salinarum NRC-1, demonstrating that each form can lead to distinct features in growth curves determined by optical density measured at 600 nm (OD600). In the course of the study, we also demonstrate the sensitivity of gas vesicle accumulation in Halobacterium salinarum NRC-1 on small differences in growth conditions and reevaluate pu... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5344145 Mon, 24 Oct 2011 13:11:48 +0100 5344145 http://www.medworm.com/index.php?rid=5344144&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjs%2F2011%2F609758%2F The synthesis and characterization of novel N-arylhydroxylamine-based molecular wires are described for use in the site-directed covalent immobilization of whole IgG antibodies onto gold electrode surfaces. The hydroxylamine, electrochemically generated in situ from reduction of the corresponding nitrobenzene, is stable under a wide range of solution conditions and reacts selectively with carbohydrate away from the antibody-binding site to allow the development of immunosensors with maximal activity. Cyclic voltammetric responses have shown a direct correlation between the structure and length of the molecular wire and its stability and concentration at the electrode surface. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5344144 Mon, 24 Oct 2011 13:11:48 +0100 5344144 http://www.medworm.com/index.php?rid=5331527&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjar%2F2011%2F721390%2F Conclusions. This study provides the first evidence that poor sleep quality explains significant variation in LTL, a marker of cellular aging. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331527 Thu, 20 Oct 2011 11:29:32 +0100 5331527 http://www.medworm.com/index.php?rid=5331526&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fijz%2F2011%2F308469%2F Troop takeover is common in one-male primate groups, but there are few reports in multimale groups. Japanese macaques (Macaca fuscata) form multimale groups and males commonly join troops at the bottom rank. On Yakushima island, however, where group size is relatively small, entrance into groups at the alpha position is also observed. This paper reports on the general features of troop takeover, on the predictors of takeover events, and on the reproductive success of takeover males. Troop takeovers occurred only in the mating season; nontroop males (NTMs) did not cooperate with each other; former alpha males were rarely expelled from the troop; new alpha males did not commit infanticide; new alpha male tenure in the group was usually less than two years. Logistic regression analysis showed... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331526 Thu, 20 Oct 2011 11:29:32 +0100 5331526 http://www.medworm.com/index.php?rid=5331525&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fmi%2F2011%2F785265%2F This study examined the activities of the NF-κB signaling pathway in the brain of autistic subjects and their age-matched controls. The NF-κB activation is also determined in the brain of BTBR mice, which is a promising animal model for study of pathogenic mechanisms responsible for autism. Our results showed that the level of IKKα kinase, which phosphorylates the inhibitory subunit IκBα, is significantly increased in the cerebellum of autistic subjects. However, the expression and phosphorylation of IκBα are not altered. In addition, our results demonstrated that the expression of NF-κB (p65), and the phosphorylation/activation of NF-κB (p65) at Ser536 are not significantly changed in the cerebellum and cortex of both... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331525 Thu, 20 Oct 2011 11:29:32 +0100 5331525 http://www.medworm.com/index.php?rid=5331524&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Faess%2F2011%2F237071%2F Long-term mining activities in the mountains around Creede, Colorado have resulted in significant contamination in soils and water in the Willow Creek floodplain. Total major and trace were determined for soils and water and sequential chemical extraction for soils. Objectives were to determine concentrations and potential reactivity of trace elements and investigate their relationship with other soil and water properties. Water trace elements showed significant variability among sites, ranging from 347 to 12108 μg/L. Relative trend showed (Zn > Sr > Ba) > (Mn > W > Cd) > (Sn > V ≈ Ni ≈ Cu > Co) > (Ag). Soil trace elements showed significant short-range spatial variability, ranging from 2819 to 19274 mg/kg. Rela... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331524 Thu, 20 Oct 2011 11:29:32 +0100 5331524 http://www.medworm.com/index.php?rid=5331523&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fijol%2F2011%2F203805%2F The LCOT is a self-administered test designed to assess olfactory deficits. Altogether, 525 subjects contributed to the validation. Elderly participants were well represented in this sample. In a validation study (study 1), 407 healthy and 17 anosmic volunteers between 15 and 91 years of age underwent threshold, supraliminal detection, and identification testing. Cutoff values for normosmia and hyposmia were calculated and applied in a second study in a group of patients with smell complaints and in a group of Alzheimer patients with age-matched controls. Incidence of smell deficit was estimated at 5.6% in the healthy population of study 1, and at 16% in the elderly control group of study 2. Assessment of the ability of each subtest to discriminate between groups showed that LCOT is re... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331523 Thu, 20 Oct 2011 11:29:32 +0100 5331523 http://www.medworm.com/index.php?rid=5331522&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fame%2F2011%2F103502%2F This study encompassed the Reynolds number (Re) ranging from 3400 to 27600, longitudinal pitch of the obstacle (Pl/e) varied from 3/2 to 11/2, and relative obstacle height (e/H) varied from 0.25 to 0.75. The relative obstacle transverse pitch (Pt/b)=7/3 and the angle of attack of flow on obstacle = 90° are kept constant during the whole experimentation. By comparing the heat transfer data obtained from the obstacle-mounted duct with that of smooth duct under similar geometrical and flow conditions, the obstacle-mounted duct enhances the heat transfer by 3.6-times at Re=7276.82, Pl/e=3/2, and e/H=0.75. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331522 Thu, 20 Oct 2011 11:29:32 +0100 5331522 http://www.medworm.com/index.php?rid=5331521&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjaa%2F2011%2F424501%2F The peptide-signaling molecules (<50 amino acid residues) occur in a wide variety of invertebrate and vertebrate organisms, playing pivotal roles in physiological, endocrine, and developmental processes. While some of these peptides display similar structures in mammals and invertebrates, others differ with respect to their structure and function in a species-specific manner. Such a conservation of basic structure and function implies that many peptide-signaling molecules arose very early in the evolutionary history of some taxa, while species-specific characteristics led us to suggest that they also acquire the ability to evolve in response to specific environmental conditions. In this paper, we describe GLWamide-family peptides that function as signaling molecules in the process o... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331521 Thu, 20 Oct 2011 11:29:32 +0100 5331521 http://www.medworm.com/index.php?rid=5331520&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjpr%2F2011%2F341535%2F Prevalence of bat ectoparasites on sympatric Myotis lucifugus and M. septentrionalis was quantitatively characterized in Nova Scotia and New Brunswick by making systematic collections at swarming sites. Six species of ectoparasite were recorded, including Myodopsylla insignis, Spinturnix americanus, Cimex adjunctus, Macronyssu scrosbyi, Androlaelap scasalis, and an unknown species of the genus Acanthophthirius. Male M. lucifugus and M. septentrionalis had similar prevalence of any ectoparasite (22% and 23%, resp.). Female M. lucifugus and M. septentrionalis had 2-3 times higher prevalence than did conspecific males (68% and 44%, resp.). Prevalence of infection of both genders of young of the year was not different from one another and the highest prevalence of any ectoparasite (M. lucifugu... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331520 Thu, 20 Oct 2011 11:29:32 +0100 5331520 http://www.medworm.com/index.php?rid=5331519&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fcrim%2Fobgyn%2F2011%2F426127%2F We describe the sixth case of posterior uterine rupture, with intact lower segment scar, and the first neonatal survival after expulsion into the abdominal cavity with posterior rupture. Case Presentation. A multiparous woman underwent prostaglandin induction of labour for postmaturity, after one previous caesarean section. Emergency caesarean section for bradycardia revealed a complete posterior uterine rupture, with fetal and placental expulsion. Upon delivery, the baby required inflation breaths only. The patient required a subtotal hysterectomy but returned home on day 5 postnatally with her healthy baby. Discussion. Vaginal birth after caesarean section constitutes a trial of labour, and the obstetrician must be reactive to labour events. Posterior uterine rupture is extremely rare an... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331519 Thu, 20 Oct 2011 11:29:32 +0100 5331519 http://www.medworm.com/index.php?rid=5331518&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fijht%2F2011%2F701029%2F Conclusion. Silent hypertension was high in Iraq. Salt-free diet noncompliance was high in both groups; drug noncompliance was significantly higher in patients with myocardial infarction. Angiotensin 11 receptor blocker use was associated significantly with myocardial infarction more than in stroke. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331518 Thu, 20 Oct 2011 11:29:32 +0100 5331518 http://www.medworm.com/index.php?rid=5331517&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fcrim%2Fophmed%2F2011%2F405838%2F Conclusions. Malignant form of idiopathic intracranial hypertension must be kept in mind in selected patients to avoid irreversible visual loss. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331517 Thu, 20 Oct 2011 11:29:32 +0100 5331517 http://www.medworm.com/index.php?rid=5331516&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjece%2F2011%2F154040%2F Wireless, power line communication (PLC), fiber optic, Ethernet, and so forth are among the communication technologies on which smart grid communication infrastructure is envisioned to be built. Among these, wireless and PLC-based solutions are attractive considering the cost of initial deployment. Wireless communication deployment in smart grid covers a variety of environments such as indoor, outdoor, and electric-power-system facilities. Similar diversity is expected in PLC deployment as well covering low voltage (LV), medium voltage (MV), and high voltage (HV) segments of the grid. In spite of being attractive, wireless and PLC channels are very harsh posing great challenges to performance of communication systems. In proposing solutions to smart grid communication needs, two approaches... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331516 Thu, 20 Oct 2011 11:29:32 +0100 5331516 http://www.medworm.com/index.php?rid=5331515&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fijso%2F2011%2F415219%2F Large, locally advanced cutaneous malignancy of the head and neck region is rare. However, when present, they impart a significant reconstructive challenge. These cancers have a tendency to invade peripheral tissues covering a large surface area as well as expose deeper structures such as skull, dura, orbit, and sinus after resection. Complicating the reconstructive dilemma is the high incidence of individuals who have undergone previous surgery in the region as well as adjuvant radiation therapy, which may preclude the use of local flaps or skin graft. Free tissue transfer provides a reconstructive surgeon the ability to provide well-vascularized tissue with adequate volume not limited by arc of rotation. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331515 Thu, 20 Oct 2011 11:29:32 +0100 5331515 http://www.medworm.com/index.php?rid=5331514&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fcrim%2Fobgyn%2F2011%2F181034%2F Following one year of secondary fertility, a couple conceived with a quadruplet after transfer of three embryos through IVF-ICSI. At 36 weeks and 2 days of gestation, the mother developed gestational induced hypertension and delivered the next day by caesarean section. Pathology confirmed the zygosity to be trichorionic quadramniotic and all four babies were discharged home with their mother on postoperative day 3. Herein, we describe a successfully managed high-risk pregnancy case. A review of the literature was conducted and to our knowledge no other cases with similar criteria ever reached such advanced gestational age. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331514 Thu, 20 Oct 2011 11:29:32 +0100 5331514 http://www.medworm.com/index.php?rid=5331513&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fijps%2F2011%2F731708%2F This study comprises a detailed morphological study of cold-drawn polyethylene monofilaments by Raman spectroscopy, differential scanning calorimetry (DSC) and X-ray measurements. The structure of the three-phase morphology of the linear low-density polyethylene monofilaments was investigated by combining these measurements. It was found that the most important structure variation was found in the intermediate or rigid amorphous phase, whereby the amounts of crystalline and amorphous phases were nearly constant and almost independent of the cold-draw ratio. The intermediate third phase contains gauche and transmolecules, and the amount of transmolecules was increased with the cold-draw ratio and was directly related to this cold-draw ratio. It was found that the two peaks in the Raman spec... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331513 Thu, 20 Oct 2011 11:29:32 +0100 5331513 http://www.medworm.com/index.php?rid=5331512&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fmpe%2F2011%2F402943%2F Inside a chiral nihility slab which is backed by perfect electromagnetic conductor, all valid fractional dual solutions are determined using the fractional curl operator. Fractional dual solutions may be regarded as intermediate step between the original and dual to the original solution. Corresponding fields outside the nihility slab for each case are also determined and analyzed. It is noted that only for one out of three cases the corresponding field outside chiral nihility slab is also fractional dual, while for other two cases, corresponding fields are not fractional dual. It is noted that time average power density vanishes inside the PEC-backed chiral nihility slab, while it exists outside the nihility slab. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331512 Thu, 20 Oct 2011 11:29:32 +0100 5331512 http://www.medworm.com/index.php?rid=5331511&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fcrim%2Fdentistry%2F2011%2F190592%2F We report a case of peripheral ossifying fibroma overlying the mandibular alveolar ridge of a 55-year-old female. MR scans showed a large exophytic soft tissue mass overlying mandibular alveolar ridge. The tumor revealed peripheral calcifications with slight erosion of adjacent cortical plate. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331511 Thu, 20 Oct 2011 11:29:32 +0100 5331511 http://www.medworm.com/index.php?rid=5331510&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fmpe%2F2011%2F570980%2F We investigate a H1-Galerkin mixed finite element method for nonlinear viscoelasticity equations based on H1-Galerkin method and expanded mixed element method. The existence and uniqueness of solutions to the numerical scheme are proved. A priori error estimation is derived for the unknown function, the gradient function, and the flux. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5331510 Thu, 20 Oct 2011 11:29:32 +0100 5331510 http://www.medworm.com/index.php?rid=5302107&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fddns%2F2011%2F431840%2F We study the polytopic-k-step Fibonacci sequences, the polytopic-k-step Fibonacci sequences modulo m, and the polytopic-k-step Fibonacci sequences in finite groups. Also, we examine the periods of the polytopic-k-step Fibonacci sequences in semidihedral group SD2m. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5302107 Mon, 10 Oct 2011 15:49:40 +0100 5302107 http://www.medworm.com/index.php?rid=5302106&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fcrim%2Frheumatology%2F2011%2F124940%2F We report the case of a 64-year-old male who presented with isolated cutaneous leukocytoclastic vasculitis that was initially attributed to essential mixed cryoglobulinemia after thorough diagnostic evaluation. A lack of adequate clinical response to therapy prompted further investigation, including cryoprecipitate electrophoresis and immunofixation, which revealed an IgM kappa monoclonal gammopathy consistent with type 1 cryoglobulinemia. A renewed search for an underlying malignancy led to the discovery of early Waldenstrom's macroglobulinemia. Although leukocytoclastic vasculitis is more characteristic of mixed cryoglobulinemia, it can be a presenting manifestation of type 1 cryoglobulinemia. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5302106 Mon, 10 Oct 2011 15:49:40 +0100 5302106 http://www.medworm.com/index.php?rid=5302105&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Farch%2F2011%2F693253%2F Extreme environments, generally characterized by atypical temperatures, pH, pressure, salinity, toxicity, and radiation levels, are inhabited by various microorganisms specifically adapted to these particular conditions, called extremophiles. Among these, the microorganisms belonging to the Archaea domain are of significant biotechnological importance as their biopolymers possess unique properties that offer insights into their biology and evolution. Particular attention has been devoted to two main types of biopolymers produced by such peculiar microorganisms, that is, the extracellular polysaccharides (EPSs), considered as a protection against desiccation and predation, and the endocellular polyhydroxyalkanoates (PHAs) that provide an internal reserve of carbon and energy. Here, we repor... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5302105 Mon, 10 Oct 2011 15:49:40 +0100 5302105 http://www.medworm.com/index.php?rid=5302104&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbcri%2F2011%2F901572%2F Hsp27 oligomer is reported to interact with F-actin as a barbed-end-capping protein. The present study determined the binding strength and stoichiometry of the interaction using fluorescence of probes attached to Hsp27 cysteine-137. The fluorescence of acrylodan attached to Hsp27 increased 4-5-fold upon interaction with F-actin. Titration of the fluorescence with F-actin yielded a weak binding constant (KDapp=5.3 μM) with an actin/Hsp27 stoichiometry between < 1 and 6. This stoichiometry is inconsistent with an F-actin end-capping protein. Pyrene attached to Hsp27 exhibited a large excimer fluorescence, in agreement with the known proximity of the cysteine-137's in the Hsp27 oligomer. Upon interaction with F-actin the pyrene-Hsp27 excimer fluorescence was largely... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5302104 Mon, 10 Oct 2011 15:49:40 +0100 5302104 http://www.medworm.com/index.php?rid=5302103&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fmpe%2F2011%2F282696%2F Establishment of three-dimensional finite-element model of the whole auditory system includes external ear, middle ear, and inner ear. The sound-solid-liquid coupling frequency response analysis of the model was carried out. The correctness of the FE model was verified by comparing the vibration modes of tympanic membrane and stapes footplate with the experimental data. According to calculation results of the model, we make use of the least squares method to fit out the distribution of sound pressure of external auditory canal and obtain the sound pressure function on the tympanic membrane which varies with frequency. Using the sound pressure function, the pressure distribution on the tympanic membrane can be directly derived from the sound pressure at the external auditory canal opening. ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5302103 Mon, 10 Oct 2011 15:49:40 +0100 5302103 http://www.medworm.com/index.php?rid=5302102&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjece%2F2011%2F604647%2F This paper presents an algorithm for camera localization using trajectory estimation (CLUTE) in a distributed network of nonoverlapping cameras. The algorithm recovers the extrinsic calibration parameters, namely, the relative position and orientation of the camera network on a common ground plane coordinate system. We first model the observed trajectories in each camera's field of view using Kalman filtering, then we use this information to estimate the missing trajectory information in the unobserved areas by fusing the results of a forward and backward linear regression estimation from adjacent cameras. These estimated trajectories are then filtered and used to recover the relative position and orientation of the cameras by analyzing the estimated and observed exit and entry points ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5302102 Mon, 10 Oct 2011 15:49:40 +0100 5302102 http://www.medworm.com/index.php?rid=5194846&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Faor%2F2011%2F269239%2F We study empirically and analytically growth and fluctuation of firm size distribution. An empirical analysis is carried out on a US data set on firm size, with emphasis on one-time distribution as well as growth-rate probability distribution. Both Pareto's law and Gibrat's law are often used to study firm size distribution. Their theoretical relationship is discussed, and it is shown how they are complementable with a bimodal distribution of firm size. We introduce economic mechanisms that suggest a bimodal distribution of firm size in the long run. The mechanisms we study have been known in the economic literature since long. Yet, they have not been studied in the context of a dynamic decision problem of the firm. Allowing for these mechanism thus will give rise to heterogeneity ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5194846 Mon, 05 Sep 2011 13:30:15 +0100 5194846 http://www.medworm.com/index.php?rid=5156761&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fisrn%2Falgebra%2F2011%2F282940%2F We determine the second to fourth largest (resp. the second smallest) signless Laplacian spectral radii and the second to fourth largest signless Laplacian spreads together with the corresponding graphs in the class of unicyclic graphs with n vertices. Moreover, we prove that one class of unicyclic graphs are determined by their signless Laplacian spectra. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5156761 Thu, 25 Aug 2011 10:24:54 +0100 5156761 http://www.medworm.com/index.php?rid=5156760&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fisrn%2Fpharmaceutics%2F2011%2F237501%2F The main purpose of the present study was to develop ocuserts of Fluconazole β-CD (beta-cyclodextrin) complex and to evaluate both in vitro and in vivo. Fluconazole was made complex with β-CD, and the release rate was controlled by HPMC K4M and ethyl cellulose polymers using dibutyl Phthalate as permeability enhancer. Drug-polymer interactions were studied by Fourier transform infrared spectroscopic studies. The formulated ocuserts were tested for physicochemical parameters of in vitro release and in vivo permeation in rabbits. The optimized formulations (F-5 and F-8) were subjected to stability studies. The formulated ocuserts were found to have good physical characters, thickness, diameter, uniformity in weight, folding endurance, less moisture absorption, and controlled rele... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5156760 Thu, 25 Aug 2011 10:24:54 +0100 5156760 http://www.medworm.com/index.php?rid=5156759&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fijqsr%2F2011%2F681210%2F This paper deals with the Bayes prediction of the future failures of a deteriorating repairable mechanical system subject to minimal repairs and periodic overhauls. To model the effect of overhauls on the reliability of the system a proportional age reduction model is assumed and the 2-parameter Engelhardt-Bain process (2-EBP) is used to model the failure process between two successive overhauls. 2-EBP has an advantage over Power Law Process (PLP) models. It is found that the failure intensity of deteriorating repairable systems attains a finite bound when repeated minimal repair actions are combined with some overhauls. If such a data is analyzed through models with unbounded increasing failure intensity, such as the PLP, then pessimistic estimates of the system reliability will arise and... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5156759 Thu, 25 Aug 2011 10:24:54 +0100 5156759 http://www.medworm.com/index.php?rid=5156758&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcrim%2F2011%2F896396%2F Conclusions. Three-dimensional technique is a reliable diagnostic modality for preoperative assessment of an ovarian teratoma as it can be performed during the first trimester of pregnancy. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5156758 Thu, 25 Aug 2011 10:24:54 +0100 5156758 http://www.medworm.com/index.php?rid=5117920&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fijped%2F2011%2F217564%2F Conclusion. Complete or partial clot resolution in neonatal thrombosis occurred in both the treated group and nontreated group. Randomized controlled trials are warranted to determine the optimal management in neonatal thrombosis. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5117920 Thu, 11 Aug 2011 18:33:30 +0100 5117920 http://www.medworm.com/index.php?rid=5068860&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fpri%2F2011%2F780652%2F Lung cancers account for a huge percentage of death in industrialized countries, and hence there is an increasing call for the development of novel treatments. These malignancies are caused by a combination of environmental factors, principally cigarette smoking and genetic alterations. MicroRNAs (miRNAs) are a recently discovered class of regulatory noncoding small RNAs with a significance in numerous biological processes. Strong evidence links miRNA impaired expression profiles and pathways to the etiology of several diseases, including neoplasia. This paper focuses on the emerging role of miRNA function in lung cancer development with particular highlighting on the use of miRNA profiles and polymorphisms for the molecular and biological characterization of tumor pulmonary growth and pro... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=5068860 Wed, 27 Jul 2011 16:28:21 +0100 5068860 http://www.medworm.com/index.php?rid=4828362&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Faurt%2F2011%2F398636%2F Autism spectrum disorders (ASDs) have become increasingly common in recent years. The discovery of single-nucleotide polymorphisms and accompanying copy number variations within the genome has increased our understanding of the architecture of the disease. These genetic and genomic alterations coupled with epigenetic phenomena have pointed to a neuroimmunopathological mechanism for ASD. Model animal studies, developmental biology, and affective neuroscience laid a foundation for dissecting the neural pathways impacted by these disease-generating mechanisms. The goal of current autism research is directed toward a systems biological approach to find the most basic genetic and environmental causes to this severe developmental disease. It is hoped that future genomic and neuroimmunological re... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4828362 Tue, 17 May 2011 10:00:38 +0100 4828362 http://www.medworm.com/index.php?rid=4828361&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fam%2F2011%2F421820%2F The earth mover's distance (EMD) is a measure of the distance between two distributions, and it has been widely used in multimedia information retrieval systems, in particular, in content-based image retrieval systems. When the EMD is applied to image problems based on color or texture, the EMD reflects the human perceptual similarities. However, its computations are too expensive to use in large-scale databases. In order to achieve efficient computation of the EMD during query processing, we have developed “fastEMD,” a library for high-speed feature-based similarity retrievals in large databases. This paper introduces techniques that are used in the implementation of the fastEMD and performs extensive experiments to demonstrate its efficiency. (Source: EURASIP Journal on Bioin... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4828361 Tue, 17 May 2011 10:00:38 +0100 4828361 http://www.medworm.com/index.php?rid=4828360&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fijvt%2F2011%2F439074%2F We propose an approach for vehicle localization in dense urban environments using a stereoscopic system and a GPS sensor. Stereoscopic system is used to capture the stereo video flow, to recover the environments, and to estimate the vehicle motion based on feature detection, matching, and triangulation from every image pair. A relative depth constraint is applied to eliminate the tracking couples which are inconsistent with the vehicle ego-motion. Then the optimal rotation and translation between the current and the reference frames are computed using an RANSAC based minimization method. Meanwhile, GPS positions are obtained by an on-board GPS receiver and periodically used to adjust the vehicle orientations and positions estimated by stereovision. The proposed method is tested with two re... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4828360 Tue, 17 May 2011 10:00:38 +0100 4828360 http://www.medworm.com/index.php?rid=4828359&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjnm%2F2011%2F919853%2F Ternary Sn88Ag5Cu7, Sn93Ag4Cu3, Sn58Ag18Cu24, Sn78Ag16Cu6, Sn90Ag4Cu6, Sn87Ag4Cu9 alloy nanowires were produced at various values of deposition potential by dc electrodeposition on highly ordered porous anodic alumina oxide (AAO) templates. During the deposition process some parameters, such as ion content, deposition time, pH, and temperature of the solution, were kept constant. The diameter and length of regular Sn93Ag4Cu3 nanowires electrodeposited at −1 V were determined by scanning electron microscopy (SEM) to be approximately 200–250 nm and 7-8 μm, respectively. Differential scanning calorimetry (DSC) results indicate that the melting onset temperature of Sn93Ag4Cu3 nanowires is about 204°C. (Source: EURASIP Journal on Bioinformatics an... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4828359 Tue, 17 May 2011 10:00:38 +0100 4828359 http://www.medworm.com/index.php?rid=4669801&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fisrn%2Furology%2F2011%2F343850%2F Stress urinary incontinence (SUI) affects 10–20% of women in the general population. Surgery for stress incontinence has been performed on women for over a century, but with the advent of new urogynaecological sling procedures for its management, urological surgeons are having to deal with an increasing number of patients presenting with associated complications. With no clarity on the full range of possible complications or certain consensus on their optimal management, the ideal treatment remains a decision for the individual surgeon. In view of this, we felt it of common interest to review the literature for the history of sling procedures, present commonly arising complications, and seek to answer the question in the title. (Source: EURASIP Journal on Bioinformatics and Syste... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4669801 Sun, 03 Apr 2011 14:49:39 +0100 4669801 http://www.medworm.com/index.php?rid=4669800&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fijsa%2F2011%2F489386%2F The object of this paper is to study the stability behaviours of the deterministic and stochastic versions of a two-species symmetric competition model. The logistic parameters of the competitive species are perturbed by colored noises or Ornstein-Uhlenbeck processes due to random environment. The Fokker-Planck equation has been used to obtain probability density functions. Here, we have also discussed the relationship between stability behaviours of this model in a deterministic environment and the corresponding model in a stochastic environment. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4669800 Sun, 03 Apr 2011 14:49:39 +0100 4669800 http://www.medworm.com/index.php?rid=4669799&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fijd%2F2011%2F405139%2F This study was undertaken to evaluate the effect of oral administration of lactoferrin (LF) and lactoperoxidase-(LPO-)containing tablet on periodontal condition. Seventy-two individuals with chronic periodontitis were randomly assigned to take either bovine LF and LPO-containing tablets (test group, n=37) or control tablets (control group, n=35) every day for 12 weeks. Periodontal parameters and levels of subgingival plaque bacteria, human and bovine LF, and endotoxin in gingival crevicular fluid (GCF) were evaluated at baseline, 1 week, 4 weeks, and 12 weeks. Significant differences were observed in GCF levels of bovine LF between the test and control groups throughout the study (P<.05). However, clinical and bacteriological parameter values proved comparable between the two groups... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4669799 Sun, 03 Apr 2011 14:49:39 +0100 4669799 http://www.medworm.com/index.php?rid=4669798&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fjpr%2F2011%2F824162%2F Effects of water flooding on the oviposition capacity of engorged adult females and hatchability of eggs of Rhipicephalus sanguineus and Haemaphysalis leachi leachi under laboratory conditions were investigated. The durations of time of water flooding were 1, 2, 4, 6, 12, 24, 48, 72, 96, and 120 hours. Engorged females of R. sanguineus and H. leachi leachi did not oviposit after being flooded for more than 48 and 6 hours, respectively. The preoviposition periods of both species were longer than those of their controls. The number of eggs laid were significantly lower (P<.05) and higher (P<.05) than their controls, respectively, for R. sanguineus and H. leachi leachi flooded for 1–4 hours. The hatchability of eggs of both species decreased as flooding time increased. The... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4669798 Sun, 03 Apr 2011 14:49:39 +0100 4669798 http://www.medworm.com/index.php?rid=4535736&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fijog%2F2011%2F465810%2F Upper ocean conditions in the Caribbean Sea are studied for long-term variability and trends using filtered surface observations and ocean model reanalysis fields. A principal component analysis is made, and trends in the leading mode are extracted. Sea surface temperature shows an accelerating upward trend while air pressure exhibits quasidecadal fluctuations. Sea surface height and subsurface temperature rise linearly while subsurface salinity exhibits fresher upper and saltier lower layers. The amplitude of warming is highest in the southern Caribbean east of 75°W near 150 m and lowest near the surface, indicating little role for a top-down process such as air-sea exchange. The freshening surface layer does not appear connected to river discharge or regional rainfall, so c... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4535736 Wed, 02 Mar 2011 13:05:35 +0100 4535736 http://www.medworm.com/index.php?rid=4293536&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2010%2F814127.html In this study, the scoring method was applied to potential translation initiation sites in Drosophila to compute Translation Relative Individual Information (TRII) scores. The weight matrix at the core of the scoring method was optimized based on high-confidence translation initiation sites identified by using a progressive partitioning approach. Comparing the distributions of TRII scores for sites of interest with those for high-confidence translation initiation sites and random sequences provides a new methodology for assessing the quality of translation initiation sites. The optimized weight matrices can also be used to describe the consensus at translation initiation sites, providing a quantitative measure of preferred and avoided nucleotides at each position. (Source: EURASIP Journal ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4293536 Wed, 29 Dec 2010 04:32:21 +0100 4293536 http://www.medworm.com/index.php?rid=4060024&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2010%2F947564.html Bayesian network models are commonly used to model gene expression data. Some applications require a comparison of the network structure of a set of genes between varying phenotypes. In principle, separately fit models can be directly compared, but it is difficult to assign statistical significance to any observed differences. There would therefore be an advantage to the development of a rigorous hypothesis test for homogeneity of network structure. In this paper, a generalized likelihood ratio test based on Bayesian network models is developed, with significance level estimated using permutation replications. In order to be computationally feasible, a number of algorithms are introduced. First, a method for approximating multivariate distributions due to Chow and Liu (1968) is adapted, pe... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4060024 Wed, 13 Oct 2010 01:02:45 +0100 4060024 http://www.medworm.com/index.php?rid=4040150&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2007%2F070561.abs.html Microarray data acquired during time-course experiments allow the temporal variations in gene expression to be monitored. An original postprandial fasting experiment was conducted in the mouse and the expression of 200 genes was monitored with a dedicated macroarray at 11 time points between 0 and 72 hours of fasting. The aim of this study was to provide a relevant clustering of gene expression temporal profiles. This was achieved by focusing on the shapes of the curves rather than on the absolute level of expression. Actually, we combined spline smoothing and first derivative computation with hierarchical and partitioning clustering. A heuristic approach was proposed to tune the spline smoothing parameter using both statistical and biological considerations. Clusters are illustrated a pos... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4040150 Thu, 07 Oct 2010 21:57:04 +0100 4040150 http://www.medworm.com/index.php?rid=4040149&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2007%2F064628.abs.html Gene expression profiling has been widely used to study molecular signatures of many diseases and to develop molecular diagnostics for disease prediction. Gene selection, as an important step for improved diagnostics, screens tens of thousands of genes and identifies a small subset that discriminates between disease types. A two-step gene selection method is proposed to identify informative gene subsets for accurate classification of multiclass phenotypes. In the first step, individually discriminatory genes (IDGs) are identified by using one-dimensional weighted Fisher criterion (wFC). In the second step, jointly discriminatory genes (JDGs) are selected by sequential search methods, based on their joint class separability measured by multidimensional weighted Fisher criterion (wFC). The p... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4040149 Thu, 07 Oct 2010 21:57:04 +0100 4040149 http://www.medworm.com/index.php?rid=4040148&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2007%2F046150.abs.html Two computational methods for estimating the cell cycle phase distribution of a budding yeast (Saccharomyces cerevisiae) cell population are presented. The first one is a nonparametric method that is based on the analysis of DNA content in the individual cells of the population. The DNA content is measured with a fluorescence-activated cell sorter (FACS). The second method is based on budding index analysis. An automated image analysis method is presented for the task of detecting the cells and buds. The proposed methods can be used to obtain quantitative information on the cell cycle phase distribution of a budding yeast S. cerevisiae population. They therefore provide a solid basis for obtaining the complementary information needed in deconvolution of gene expression data. As a case stud... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4040148 Thu, 07 Oct 2010 21:57:04 +0100 4040148 http://www.medworm.com/index.php?rid=4040147&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2007%2F023054.abs.html This study further demonstrated that microarray-based transcriptional evidence would facilitate genome-wide gene finding, and is also the first report concerning intergenic expression in M. tuberculosis genome. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4040147 Thu, 07 Oct 2010 21:57:04 +0100 4040147 http://www.medworm.com/index.php?rid=4040146&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2007%2F038473.abs.html The aim of many microarray experiments is to build discriminatory diagnosis and prognosis models. Given the huge number of features and the small number of examples, model validity which refers to the precision of error estimation is a critical issue. Previous studies have addressed this issue via the deviation distribution (estimated error minus true error), in particular, the deterioration of cross-validation precision in high-dimensional settings where feature selection is used to mitigate the peaking phenomenon (overfitting). Because classifier design is based upon random samples, both the true and estimated errors are sample-dependent random variables, and one would expect a loss of precision if the estimated and true errors are not well correlated, so that natural questions arise as ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4040146 Thu, 07 Oct 2010 21:57:04 +0100 4040146 http://www.medworm.com/index.php?rid=4040145&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2007%2F028576.abs.html The exponential growth in the volume of publications in the biomedical domain has made it impossible for an individual to keep pace with the advances. Even though evidence-based medicine has gained wide acceptance, the physicians are unable to access the relevant information in the required time, leaving most of the questions unanswered. This accentuates the need for fast and accurate biomedical question answering systems. In this paper we introduce INDOC—a biomedical question answering system based on novel ideas of indexing and extracting the answer to the questions posed. INDOC displays the results in clusters to help the user arrive the most relevant set of documents quickly. Evaluation was done against the standard OHSUMED test collection. Our system achieves high accuracy and m... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4040145 Thu, 07 Oct 2010 21:57:04 +0100 4040145 http://www.medworm.com/index.php?rid=4040144&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2007%2F053096.abs.html Several natural language processing tools, both commercial and freely available, are used to extract protein interactions from publications. Methods used by these tools include pattern matching to dynamic programming with individual recall and precision rates. A methodical survey of these tools, keeping in mind the minimum interaction information a researcher would need, in comparison to manual analysis has not been carried out. We compared data generated using some of the selected NLP tools with manually curated protein interaction data (PathArt and IMaps) to comparatively determine the recall and precision rate. The rates were found to be lower than the published scores when a normalized definition for interaction is considered. Each data point captured wrongly or not picked up by the to... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4040144 Thu, 07 Oct 2010 21:57:04 +0100 4040144 http://www.medworm.com/index.php?rid=4040143&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2007%2F025250.abs.html The regulation of IκB, NF-κB is of foremost interest in biology as the transcription factor NF-κB has multiple target genes. We have modeled a previously published model by Hoffmann et al. (2002) of IκB, NF-κB mathematically as discrete reaction systems. We have used stochastic algorithm to compare the results when there are large and small numbers of molecules available in a finite volume for each protein. Our results for small number of molecules show that with continuous presence of stimulation, nuclear NF-κB oscillates continuously in every individual cell rather than damping, which was observed in cell population results. This characteristic of the system is missed when averaged behavior is studied. (Source: EURASIP Journal on Bioinformatics a... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4040143 Thu, 07 Oct 2010 21:57:04 +0100 4040143 http://www.medworm.com/index.php?rid=4040142&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2008%2F482090.html The Boolean network paradigm is a simple and effective way to interpret genomic systems, but discovering the structure of these networks remains a difficult task. The minimum description length (MDL) principle has already been used for inferring genetic regulatory networks from time-series expression data and has proven useful for recovering the directed connections in Boolean networks. However, the existing method uses an ad hoc measure of description length that necessitates a tuning parameter for artificially balancing the model and error costs and, as a result, directly conflicts with the MDL principle's implied universality. In order to surpass this difficulty, we propose a novel MDL-based method in which the description length is a theoretical measure derived from a universal normali... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4040142 Thu, 07 Oct 2010 21:57:04 +0100 4040142 http://www.medworm.com/index.php?rid=4040141&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2008%2F342746.html Structured information provided by manual annotation of proteins with Gene Ontology concepts represents a high-quality reliable data source for the research community. However, a limited scope of proteins is annotated due to the amount of human resources required to fully annotate each individual gene product from the literature. We introduce a novel method for automatic identification of GO terms in natural language text. The method takes into consideration several features: (1) the evidence for a GO term given by the words occurring in text, (2) the proximity between the words, and (3) the specificity of the GO terms based on their information content. The method has been evaluated on the BioCreAtIvE corpus and has been compared to current state of the art methods. The precision reached ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4040141 Thu, 07 Oct 2010 21:57:04 +0100 4040141 http://www.medworm.com/index.php?rid=4040140&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2008%2F231950.html We propose a method for improving the quality of signal from DNA microarrays by using several scans at varying scanner sen-sitivities. A Bayesian latent intensity model is introduced for the analysis of such data. The method improves the accuracy at which expressions can be measured in all ranges and extends the dynamic range of measured gene expression at the high end. Our method is generic and can be applied to data from any organism, for imaging with any scanner that allows varying the laser power, and for extraction with any image analysis software. Results from a self-self hybridization data set illustrate an improved precision in the estimation of the expression of genes compared to what can be achieved by applying standard methods and using only a single scan. (Source: EURASIP Journ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4040140 Thu, 07 Oct 2010 21:57:04 +0100 4040140 http://www.medworm.com/index.php?rid=4040139&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2008%2F297945.html Is it better to design a classifier and estimate its error on the full sample or to design a classifier on a training subset and estimate its error on the holdout test subset? Full-sample design provides the better classifier; nevertheless, one might choose holdout with the hope of better error estimation. A conservative criterion to decide the best course is to aim at a classifier whose error is less than a given bound. Then the choice between full-sample and holdout designs depends on which possesses the smaller expected bound. Using this criterion, we examine the choice between holdout and several full-sample error estimators using covariance models and a patient-data model. Full-sample design consistently outperforms holdout design. The relation between the two designs is revealed via ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4040139 Thu, 07 Oct 2010 21:57:04 +0100 4040139 http://www.medworm.com/index.php?rid=4012183&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2010%2F268513.html To study chromosomal aberrations that may lead to cancer formation or genetic diseases, the array-based Comparative Genomic Hybridization (aCGH) technique is often used for detecting DNA copy number variants (CNVs). Various methods have been developed for gaining CNVs information based on aCGH data. However, most of these methods make use of the log-intensity ratios in aCGH data without taking advantage of other information such as the DNA probe (e.g., biomarker) positions/distances contained in the data. Motivated by the specific features of aCGH data, we developed a novel method that takes into account the estimation of a change point or locus of the CNV in aCGH data with its associated biomarker position on the chromosome using a compound Poisson process. We used a Bayesian approach to ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=4012183 Wed, 29 Sep 2010 21:22:49 +0100 4012183 http://www.medworm.com/index.php?rid=3902661&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2010%2F210685.html In recent years, Boolean-network-model-based approaches to dynamical analysis of complex biological networks such as gene regulatory networks have been extensively studied. One of the fundamental problems in control theory of such networks is the problem of determining whether a given substance quantity can be arbitrarily controlled by operating the other substance quantities, which we call the controllability problem. This paper proposes a polynomial-time algorithm for solving this problem. Although the algorithm is based on a sufficient condition for controllability, it is easily computable for a wider class of large-scale biological networks compared with the existing approaches. A key to this success in our approach is to give up computing Boolean operations in a rigorous way and to ex... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=3902661 Thu, 26 Aug 2010 09:47:40 +0100 3902661 http://www.medworm.com/index.php?rid=3710221&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2010%2F107036.html We propose an image computing-based method for quantitative analysis of continuous physiological processes that can be sensed by medical imaging and demonstrate its application to the analysis of morphological alterations of the bone structure, which correlate with the progression of osteoarthritis (OA). The purpose of the analysis is to quantitatively estimate OA progression in a fashion that can assist in understanding the pathophysiology of the disease. Ultimately, the texture analysis will be able to provide an alternative OA scoring method, which can potentially reflect the progression of the disease in a more direct fashion compared to the existing clinically utilized classification schemes based on radiology. This method can be useful not just for studying the nature of OA, but also... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=3710221 Wed, 30 Jun 2010 07:41:25 +0100 3710221 http://www.medworm.com/index.php?rid=3702844&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2010%2F746021.html The central purpose of this study is to further evaluate the quality of the performance of a new algorithm. The study provides additional evidence on this algorithm that was designed to increase the overall efficiency of the original k-means clustering technique—the Fast, Efficient, and Scalable k-means algorithm (FES-k-means). The FES-k-means algorithm uses a hybrid approach that comprises the k-d tree data structure that enhances the nearest neighbor query, the original k-means algorithm, and an adaptation rate proposed by Mashor. This algorithm was tested using two real datasets and one synthetic dataset. It was employed twice on all three datasets: once on data trained by the innovative MIL-SOM method and then on the actual untrained data in order to evaluate its competence. This... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=3702844 Mon, 28 Jun 2010 07:37:51 +0100 3702844 http://www.medworm.com/index.php?rid=3331012&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F878013.html Reconstruction of gene regulatory networks based on experimental data usually relies on statistical evidence, necessitating the choice of a statistical threshold which defines a significant biological effect. Approaches to this problem found in the literature range from rigorous multiple testing procedures to ad hoc P-value cut-off points. However, when the data implies graphical structure, it should be possible to exploit this feature in the threshold selection process. In this article we propose a procedure based on this principle. Using coding theory we devise a measure of graphical structure, for example, highly connected nodes or chain structure. The measure for a particular graph can be compared to that of a random graph and structure inferred on that basis. By varying the statistica... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=3331012 Thu, 04 Mar 2010 18:22:46 +0100 3331012 http://www.medworm.com/index.php?rid=3321944&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F504069.html Many missing-value (MV) imputation methods have been developed for microarray data, but only a few studies have investigated the relationship between MV imputation and classification accuracy. Furthermore, these studies are problematic in fundamental steps such as MV generation and classifier error estimation. In this work, we carry out a model-based study that addresses some of the issues in previous studies. Six popular imputation algorithms, two feature selection methods, and three classification rules are considered. The results suggest that it is beneficial to apply MV imputation when the noise level is high, variance is small, or gene-cluster correlation is strong, under small to moderate MV rates. In these cases, if data quality metrics are available, then it may be helpful to consi... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=3321944 Tue, 02 Mar 2010 17:48:20 +0100 3321944 http://www.medworm.com/index.php?rid=2894065&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F484601.html Computational gene regulation models provide a means for scientists to draw biological inferences from time-course gene expression data. Based on the state-space approach, we developed a new modeling tool for inferring gene regulatory networks, called time-delayed Gene Regulatory Networks (tdGRNs). tdGRN takes time-delayed regulatory relationships into consideration when developing the model. In addition, a priori biological knowledge from genome-wide location analysis is incorporated into the structure of the gene regulatory network. tdGRN is evaluated on both an artificial dataset and a published gene expression data set. It not only determines regulatory relationships that are known to exist but also uncovers potential new ones. The results indicate that the proposed tool is effective i... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2894065 Thu, 15 Oct 2009 15:17:27 +0100 2894065 http://www.medworm.com/index.php?rid=2616582&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F386853.html Circadian rhythms are ubiquitous in all eukaryotes and some prokaryotes. Several computational models with or without time delays have been developed for circadian rhythms. Exact stochastic simulations have been carried out for several models without time delays, but no exact stochastic simulation has been done for models with delays. In this paper, we proposed a detailed and a reduced stochastic model with delays for circadian rhythms in Drosophila based on two deterministic models of Smolen et al. and employed exact stochastic simulation to simulate circadian oscillations. Our simulations showed that both models can produce sustained oscillations and that the oscillation is robust to noise in the sense that there is very little variability in oscillation period although there are signifi... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2616582 Mon, 20 Jul 2009 12:13:10 +0100 2616582 http://www.medworm.com/index.php?rid=2506222&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F601068.html The objective of the present study is to propose and test a method that addresses these three issues. The model we employ is a mixture of factor analyzers, in which the latent variables correspond to different transcription factors, grouped into complexes or modules. We pursue inference in a Bayesian framework, using the Variational Bayesian Expectation Maximization (VBEM) algorithm for approximate inference of the posterior distributions of the model parameters, and estimation of a lower bound on the marginal likelihood for model selection. We have evaluated the performance of the proposed method on three criteria: activity profile reconstruction, gene clustering, and network inference. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2506222 Thu, 25 Jun 2009 08:57:40 +0100 2506222 http://www.medworm.com/index.php?rid=2506221&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F617281.html Reverse engineering of gene regulatory networks has been an intensively studied topic in bioinformatics since it constitutes an intermediate step from explorative to causative gene expression analysis. Many methods have been proposed through recent years leading to a wide range of mathematical approaches. In practice, different mathematical approaches will generate different resulting network structures, thus, it is very important for users to assess the performance of these algorithms. We have conducted a comparative study with six different reverse engineering methods, including relevance networks, neural networks, and Bayesian networks. Our approach consists of the generation of defined benchmark data, the analysis of these data with the different methods, and the assessment of algorith... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2506221 Thu, 25 Jun 2009 08:57:40 +0100 2506221 http://www.medworm.com/index.php?rid=2506220&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F714985.html (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2506220 Thu, 25 Jun 2009 08:57:40 +0100 2506220 http://www.medworm.com/index.php?rid=2468738&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2008%2F235451.html This paper presents a novel feature vector based on physicochemical property of amino acids for prediction protein structural classes. The proposed method is divided into three different stages. First, a discrete time series representation to protein sequences using physicochemical scale is provided. Later on, a wavelet-based time-series technique is proposed for extracting features from mapped amino acid sequence and a fixed length feature vector for classification is constructed. The proposed feature space summarizes the variance information of ten different biological properties of amino acids. Finally, an optimized support vector machine model is constructed for prediction of each protein structural class. The proposed approach is evaluated using leave-one-out cross-validation tests on... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468738 Wed, 10 Jun 2009 05:47:05 +0100 2468738 http://www.medworm.com/index.php?rid=2468737&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2008%2F620767.html A key objective of gene network modeling is to develop intervention strategies to alter regulatory dynamics in such a way as to reduce the likelihood of undesirable phenotypes. Optimal stationary intervention policies have been developed for gene regulation in the framework of probabilistic Boolean networks in a number of settings. To mitigate the possibility of detrimental side effects, for instance, in the treatment of cancer, it may be desirable to limit the expected number of treatments beneath some bound. This paper formulates a general constraint approach for optimal therapeutic intervention by suitably adapting the reward function and then applies this formulation to bound the expected number of treatments. A mutated mammalian cell cycle is considered as a case study. (Source: EURAS... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468737 Wed, 10 Jun 2009 05:47:05 +0100 2468737 http://www.medworm.com/index.php?rid=2468736&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2008%2F248747.html Recent advances in high-throughput DNA microarrays and chromatin immunoprecipitation (ChIP) assays have enabled the learning of the structure and functionality of genetic regulatory networks. In light of these heterogeneous data sets, this paper proposes a novel approach for reconstruction of genetic regulatory networks based on the posterior probabilities of gene regulations. Built within the framework of Bayesian statistics and computational Monte Carlo techniques, the proposed approach prevents the dichotomy of classifying gene interactions as either being connected or disconnected, thereby it reduces significantly the inference errors. Simulation results corroborate the superior performance of the proposed approach relative to the existing state-of-the-art algorithms. A genetic regulat... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468736 Wed, 10 Jun 2009 05:47:05 +0100 2468736 http://www.medworm.com/index.php?rid=2468735&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2008%2F769293.html Time series microarray measurements of gene expressions have been exploited to discover genes involved in cell cycles. Due to experimental constraints, most microarray observations are obtained through irregular sampling. In this paper three popular spectral analysis schemes, namely, Lomb-Scargle, Capon and missing-data amplitude and phase estimation (MAPES), are compared in terms of their ability and efficiency to recover periodically expressed genes. Based on in silico experiments for microarray measurements of Saccharomyces cerevisiae, Lomb-Scargle is found to be the most efficacious scheme. 149 genes are then identified to be periodically expressed in the Drosophila melanogaster data set. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468735 Wed, 10 Jun 2009 05:47:05 +0100 2468735 http://www.medworm.com/index.php?rid=2468734&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2008%2F253894.html The inference of gene regulatory network from expression data is an important area of research that provides insight to the inner workings of a biological system. The relevance-network-based approaches provide a simple and easily-scalable solution to the understanding of interaction between genes. Up until now, most works based on relevance network focus on the discovery of direct regulation using correlation coefficient or mutual information. However, some of the more complicated interactions such as interactive regulation and coregulation are not easily detected. In this work, we propose a relevance network model for gene regulatory network inference which employs both mutual information and conditional mutual information to determine the interactions between genes. For this purpose, we ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468734 Wed, 10 Jun 2009 05:47:05 +0100 2468734 http://www.medworm.com/index.php?rid=2468733&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2008%2F172840.html Two-level gene regulatory networks consist of the transcription factors (TFs) in the top level and their regulated genes in the second level. The expression profiles of the regulated genes are the observed high-throughput data given by experiments such as microarrays. The activity profiles of the TFs are treated as hidden variables as well as the connectivity matrix that indicates the regulatory relationships of TFs with their regulated genes. Factor analysis (FA) as well as other methods, such as the network component algorithm, has been suggested for reconstructing gene regulatory networks and also for predicting TF activities. They have been applied to E. coli and yeast data with the assumption that these datasets consist of identical and independently distributed samples. Thus, the mai... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468733 Wed, 10 Jun 2009 05:47:05 +0100 2468733 http://www.medworm.com/index.php?rid=2468732&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2008%2F780541.html The inference of genetic regulatory networks from global measurements of gene expressions is an important problem in computational biology. Recent studies suggest that such dynamical molecular systems are poised at a critical phase transition between an ordered and a disordered phase, affording the ability to balance stability and adaptability while coordinating complex macroscopic behavior. We investigate whether incorporating this dynamical system-wide property as an assumption in the inference process is beneficial in terms of reducing the inference error of the designed network. Using Boolean networks, for which there are well-defined notions of ordered, critical, and chaotic dynamical regimes as well as well-studied inference procedures, we analyze the expected inference error relativ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468732 Wed, 10 Jun 2009 05:47:05 +0100 2468732 http://www.medworm.com/index.php?rid=2468731&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2008%2F521407.html A Boolean network (BN) is a mathematical model of genetic networks. We propose several algorithms for control of singleton attractors in BN. We theoretically estimate the average-case time complexities of the proposed algorithms, and confirm them by computer experiments. The results suggest the importance of gene ordering. Especially, setting internal nodes ahead yields shorter computational time than setting external nodes ahead in various types of algorithms. We also present a heuristic algorithm which does not look for the optimal solution but for the solution whose computational time is shorter than that of the exact algorithms. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468731 Wed, 10 Jun 2009 05:47:05 +0100 2468731 http://www.medworm.com/index.php?rid=2468730&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F147157.html We propose a network structure-based model for heterosis, and investigate it relying on metabolite profiles from Arabidopsis. A simple feed-forward two-layer network model (the Steinbuch matrix) is used in our conceptual approach. It allows for directly relating structural network properties with biological function. Interpreting heterosis as increased adaptability, our model predicts that the biological networks involved show increasing connectivity of regulatory interactions. A detailed analysis of metabolite profile data reveals that the increasing-connectivity prediction is true for graphical Gaussian models in our data from early development. This mirrors properties of observed heterotic Arabidopsis phenotypes. Furthermore, the model predicts a limit for increasing hybrid vigor with i... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468730 Wed, 10 Jun 2009 05:47:05 +0100 2468730 http://www.medworm.com/index.php?rid=2468729&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F362309.html Two major approaches are known in the field of stochastic dynamics of intracellular biochemical networks. The first one places the focus of attention on the fact that many biochemical constituents vitally important for the network functionality may be present only in small quantities within the cell, and therefore the regulatory process is essentially discrete and prone to relatively big fluctuations. The second approach treats the regulatory process as essentially continuous. Complex pseudostochastic behavior in such processes may occur due to multistability and oscillatory motions within limit cycles. In this paper we outline the third scenario of stochasticity in the regulatory process. This scenario is only conceivable in high-dimensional highly nonlinear systems. In particular, we sh... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468729 Wed, 10 Jun 2009 05:47:05 +0100 2468729 http://www.medworm.com/index.php?rid=2468728&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F327503.html Differential equation models for biological oscillators are often not robust with respect to parameter variations. They are based on chemical reaction kinetics, and solutions typically converge to a fixed point. This behavior is in contrast to real biological oscillators, which work reliably under varying conditions. Moreover, it complicates network inference from time series data. This paper investigates differential equation models for biological oscillators from two perspectives. First, we investigate the effect of time delays on the robustness of these oscillator models. In particular, we provide sufficient conditions for a time delay to cause oscillations by destabilizing a fixed point in two-dimensional systems. Moreover, we show that the inclusion of a time delay also stabilizes osc... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468728 Wed, 10 Jun 2009 05:47:05 +0100 2468728 http://www.medworm.com/index.php?rid=2468727&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2008%2F308623.html Modelling in systems biology often involves the integration of component models into larger composite models. How to do this systematically and efficiently is a significant challenge: coupling of components can be unidirectional or bidirectional, and of variable strengths. We adapt the waveform relaxation (WR) method for parallel computation of ODEs as a general methodology for computing systems of linked submodels. Four test cases are presented: (i) a cascade of unidirectionally and bidirectionally coupled harmonic oscillators, (ii) deterministic and stochastic simulations of calcium oscillations, (iii) single cell calcium oscillations showing complex behaviour such as periodic and chaotic bursting, and (iv) a multicellular calcium model for a cell plate of hepatocytes. We conclude that W... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468727 Wed, 10 Jun 2009 05:47:05 +0100 2468727 http://www.medworm.com/index.php?rid=2468726&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F195272.html Nested effects models (NEMs) are a class of probabilistic models that were designed to reconstruct a hidden signalling structure from a large set of observable effects caused by active interventions into the signalling pathway. We give a more flexible formulation of NEMs in the language of Bayesian networks. Our framework constitutes a natural generalization of the original NEM model, since it explicitly states the assumptions that are tacitly underlying the original version. Our approach gives rise to new learning methods for NEMs, which have been implemented in the R/Bioconductor package nem. We validate these methods in a simulation study and apply them to a synthetic lethality dataset in yeast. (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468726 Wed, 10 Jun 2009 05:47:05 +0100 2468726 http://www.medworm.com/index.php?rid=2468725&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F308959.html The reverse engineering of transcription regulatory networks from expression data is gaining large interest in the bioinformatics community. An important family of inference techniques is represented by algorithms based on information theoretic measures which rely on the computation of pairwise mutual information. This paper aims to study the impact of the entropy estimator on the quality of the inferred networks. This is done by means of a comprehensive study which takes into consideration three state-of-the-art mutual information algorithms: ARACNE, CLR, and MRNET. Two different setups are considered in this work. The first one considers a set of 12 synthetically generated datasets to compare 8 different entropy estimators and three network inference algorithms. The two methods emerging... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468725 Wed, 10 Jun 2009 05:47:05 +0100 2468725 http://www.medworm.com/index.php?rid=2468724&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F162824.html Compressive sensing microarrays (CSMs) are DNA-based sensors that operate using group testing and compressive sensing (CS) principles. In contrast to conventional DNA microarrays, in which each genetic sensor is designed to respond to a single target, in a CSM, each sensor responds to a set of targets. We study the problem of designing CSMs that simultaneously account for both the constraints from CS theory and the biochemistry of probe-target DNA hybridization. An appropriate cross-hybridization model is proposed for CSMs, and several methods are developed for probe design and CS signal recovery based on the new model. Lab experiments suggest that in order to achieve accurate hybridization profiling, consensus probe sequences are required to have sequence homology of at least 80% with all... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468724 Wed, 10 Jun 2009 05:47:05 +0100 2468724 http://www.medworm.com/index.php?rid=2468723&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F616234.html Various methods have been recently employed to characterise the structure of biological networks. In particular, the concept of network motif and the related one of coloured motif have proven useful to model the notion of a functional/evolutionary building block. However, algorithms that enumerate all the motifs of a network may produce a very large output, and methods to decide which motifs should be selected for downstream analysis are needed. A widely used method is to assess if the motif is exceptional, that is, over- or under-represented with respect to a null hypothesis. Much effort has been put in the last thirty years to derive P-values for the frequencies of topological motifs, that is, fixed subgraphs. They rely either on (compound) Poisson and Gaussian approximations for the mot... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468723 Wed, 10 Jun 2009 05:47:05 +0100 2468723 http://www.medworm.com/index.php?rid=2468722&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F630695.html In recent work, attempts have been made to link the structure of biochemical networks to their complex dynamics. It was shown that structurally stable network motifs are enriched in such networks. In this work, we investigate to what extent these findings apply to metabolic networks. To this end, we extend a previously proposed method by changing the null model for determining motif enrichment, by using interaction types directly obtained from structural interaction matrices, by generating a distribution of partial derivatives of reaction rates and by simulating enzymatic regulation on metabolic networks. Our findings suggest that the conclusions drawn in previous work cannot be extended to metabolic networks, that is, structurally stable network motifs are not enriched in metabolic networ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468722 Wed, 10 Jun 2009 05:47:05 +0100 2468722 http://www.medworm.com/index.php?rid=2468721&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F535869.html Gene-Gene dependency plays a very important role in system biology as it pertains to the crucial understanding of different biological mechanisms. Time-course microarray data provides a new platform useful to reveal the dynamic mechanism of gene-gene dependencies. Existing interaction measures are mostly based on association measures, such as Pearson or Spearman correlations. However, it is well known that such interaction measures can only capture linear or monotonic dependency relationships but not for nonlinear combinatorial dependency relationships. With the invocation of hidden Markov models, we propose a new measure of pairwise dependency based on transition probabilities. The new dynamic interaction measure checks whether or not the joint transition kernel of the bivariate state var... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468721 Wed, 10 Jun 2009 05:47:05 +0100 2468721 http://www.medworm.com/index.php?rid=2468720&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F717136.html While microarrays make it feasible to rapidly investigate many complex biological problems, their multistep fabrication has the proclivity for error at every stage. The standard tactic has been to either ignore or regard erroneous gene readings as missing values, though this assumption can exert a major influence upon postgenomic knowledge discovery methods like gene selection and gene regulatory network (GRN) reconstruction. This has been the catalyst for a raft of new flexible imputation algorithms including local least square impute and the recent heuristic collateral missing value imputation, which exploit the biological transactional behaviour of functionally correlated genes to afford accurate missing value estimation. This paper examines the influence o... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468720 Wed, 10 Jun 2009 05:47:05 +0100 2468720 http://www.medworm.com/index.php?rid=2468719&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F618502.html To accomplish adaptability, all living organisms are constructed of regulatory networks on different levels which are capable to differentially respond to a variety of environmental inputs. Structure of regulatory networks determines their phenotypical plasticity, that is, the degree of detail and appropriateness of regulatory replies to environmental or developmental challenges. This regulatory network structure is encoded within the genotype. Our conceptual simulation study investigates how network structure constrains the evolution of networks and their adaptive abilities. The focus is on the structural parameter network size. We show that small regulatory networks adapt fast, but not as good as larger networks in the longer perspective. Selection leads to an optimal network size depend... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468719 Wed, 10 Jun 2009 05:47:05 +0100 2468719 http://www.medworm.com/index.php?rid=2468718&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F570456.html We propose two strategies to characterize organisms with respect to their metabolic capabilities. The first, investigative, strategy describes metabolic networks in terms of their capability to utilize different carbon sources, resulting in the concept of carbon utilization spectra. In the second, predictive, approach minimal nutrient combinations are predicted from the structure of the metabolic networks, resulting in a characteristic nutrient profile. Both strategies allow for a quantification of functional properties of metabolic networks, allowing to identify groups of organisms with similar functions. We investigate whether the functional description reflects the typical environments of the corresponding organisms by dividing all species into disjoint groups based on whether they are ... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468718 Wed, 10 Jun 2009 05:47:05 +0100 2468718 http://www.medworm.com/index.php?rid=2468717&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F545176.html Gene expression time course data can be used not only to detect differentially expressed genes but also to find temporal associations among genes. The problem of reconstructing generalized logical networks to account for temporal dependencies among genes and environmental stimuli from transcriptomic data is addressed. A network reconstruction algorithm was developed that uses statistical significance as a criterion for network selection to avoid false-positive interactions arising from pure chance. The multinomial hypothesis testing-based network reconstruction allows for explicit specification of the false-positive rate, unique from all extant network inference algorithms. The method is superior to dynamic Bayesian network modeling in a simulation study. Temporal gene expression data from... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468717 Wed, 10 Jun 2009 05:47:05 +0100 2468717 http://www.medworm.com/index.php?rid=2468716&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F713248.html Based on gene expression profiles, genes can be partitioned into clusters, which might be associated with biological processes or functions, for example, cell cycle, circadian rhythm, and so forth. This paper proposes a novel clustering preprocessing strategy which combines clustering with spectral estimation techniques so that the time information present in time series gene expressions is fully exploited. By comparing the clustering results with a set of biologically annotated yeast cell-cycle genes, the proposed clustering strategy is corroborated to yield significantly different clusters from those created by the traditional expression-based schemes. The proposed technique is especially helpful in grouping genes participating in time-regulated processes. (Source: EURASIP Journal on Bio... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468716 Wed, 10 Jun 2009 05:47:05 +0100 2468716 http://www.medworm.com/index.php?rid=2468715&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F924601.html Many studies of biological sequence data have examined sequence structure in terms of periodicity, and various methods for measuring periodicity have been suggested for this purpose. This paper compares two such methods, autocorrelation and the Fourier transform, using synthetic periodic sequences, and explains the differences in periodicity estimates produced by each. A hybrid autocorrelation—integer period discrete Fourier transform is proposed that combines the advantages of both techniques. Collectively, this representation and a recently proposed variant on the discrete Fourier transform offer alternatives to the widely used autocorrelation for the periodicity characterization of sequence data. Finally, these methods are compared for various tetramers of interest in C. elegans c... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468715 Wed, 10 Jun 2009 05:47:05 +0100 2468715 http://www.medworm.com/index.php?rid=2468714&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F491074.html When aligning RNAs, it is important to consider both the secondary structure similarity and primary sequence similarity to find an accurate alignment. However, algorithms that can handle RNA secondary structures typically have high computational complexity that limits their utility. For this reason, there have been a number of attempts to find useful alignment constraints that can reduce the computations without sacrificing the alignment accuracy. In this paper, we propose a new method for finding effective alignment constraints for fast and accurate structural alignment of RNAs, including pseudoknots. In the proposed method, we use a profile-HMM to identify the “seed” regions that can be aligned with high confidence. We also estimate the position range of the aligned bases tha... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468714 Wed, 10 Jun 2009 05:47:05 +0100 2468714 http://www.medworm.com/index.php?rid=2468713&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F360864.html An approximate representation for the state space of a context-sensitive probabilistic Boolean network has previously been proposed and utilized to devise therapeutic intervention strategies. Whereas the full state of a context-sensitive probabilistic Boolean network is specified by an ordered pair composed of a network context and a gene-activity profile, this approximate representation collapses the state space onto the gene-activity profiles alone. This reduction yields an approximate transition probability matrix, absent of context, for the Markov chain associated with the context-sensitive probabilistic Boolean network. As with many approximation methods, a price must be paid for using a reduced model representation, namely, some loss of optimality relative to using the full state spa... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468713 Wed, 10 Jun 2009 05:47:05 +0100 2468713 http://www.medworm.com/index.php?rid=2468712&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F683463.html Based on time series gene expressions, cyclic genes can be recognized via spectral analysis and statistical periodicity detection tests. These cyclic genes are usually associated with cyclic biological processes, for example, cell cycle and circadian rhythm. The power of a scheme is practically measured by comparing the detected periodically expressed genes with experimentally verified genes participating in a cyclic process. However, in the above mentioned procedure the valuable prior knowledge only serves as an evaluation benchmark, and it is not fully exploited in the implementation of the algorithm. In addition, partial data sets are also disregarded due to their nonstationarity. This paper proposes a novel algorithm to identify cyclic-process-involved genes by integrating the prior kn... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468712 Wed, 10 Jun 2009 05:47:05 +0100 2468712 http://www.medworm.com/index.php?rid=2468711&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F158368.html There has been considerable interest recently in the application of bagging in the classification of both gene-expression data and protein-abundance mass spectrometry data. The approach is often justified by the improvement it produces on the performance of unstable, overfitting classification rules under small-sample situations. However, the question of real practical interest is whether the ensemble scheme will improve performance of those classifiers sufficiently to beat the performance of single stable, nonoverfitting classifiers, in the case of small-sample genomic and proteomic data sets. To investigate that question, we conducted a detailed empirical study, using publicly-available data sets from published genomic and proteomic studies. We observed that, under t-test and RELIEF filt... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468711 Wed, 10 Jun 2009 05:47:05 +0100 2468711 http://www.medworm.com/index.php?rid=2468710&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F195712.html A method for gene clustering from expression profiles using shape information is presented. The conventional clustering approaches such as K-means assume that genes with similar functions have similar expression levels and hence allocate genes with similar expression levels into the same cluster. However, genes with similar function often exhibit similarity in signal shape even though the expression magnitude can be far apart. Therefore, this investigation studies clustering according to signal shape similarity. This shape information is captured in the form of normalized and time-scaled forward first differences, which then are subject to a variational Bayes clustering plus a non-Bayesian (Silhouette) cluster statistic. The statistic shows an improved ability to identify the correct numbe... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468710 Wed, 10 Jun 2009 05:47:05 +0100 2468710 http://www.medworm.com/index.php?rid=2468709&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fbsb%2F2009%2F250306.html (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2468709 Wed, 10 Jun 2009 05:47:05 +0100 2468709 http://www.medworm.com/index.php?rid=2364092&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2009%2F195712 A method for gene clustering from expression profiles using shape information is presented. The conventional clustering approaches such as K-means assume that genes with similar functions have similar expression levels and hence allocate genes with similar expression levels into the same cluster. However, genes with similar function often exhibit similarity in signal shape even though the expression magnitude can be far apart. Therefore, this investigation studies clustering according to signal shape similarity. This shape information is captured in the form of normalized and time-scaled forward first differences, which then are subject to a variational Bayes clustering plus a non-Bayesian (Silhouette) cluster statistic. The statistic shows an improved ability to identify the correct numbe... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2364092 Fri, 24 Apr 2009 19:15:40 +0100 2364092 http://www.medworm.com/index.php?rid=2364091&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2009%2F250306 (Source: EURASIP Journal on Bioinformatics and Systems Biology) EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2364091 Fri, 24 Apr 2009 19:15:40 +0100 2364091 http://www.medworm.com/index.php?rid=2341259&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2009%2F713248 Based on gene expression profiles, genes can be partitioned into clusters, which might be associated with biological processes or functions, for example, cell cycle, circadian rhythm, and so forth. This paper proposes a novel clustering preprocessing strategy which combines clustering with spectral estimation techniques so that the time information present in time series gene expressions is fully exploited. By comparing the clustering results with a set of biologically annotated yeast cell-cycle genes, the proposed clustering strategy is corroborated to yield significantly different clusters from those created by the traditional expression-based schemes. The proposed technique is especially helpful in grouping genes participating in time-regulated processes. (Source: EURASIP Journal on Bio... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2341259 Sat, 18 Apr 2009 19:56:05 +0100 2341259 http://www.medworm.com/index.php?rid=2341258&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2009%2F924601 Many studies of biological sequence data have examined sequence structure in terms of periodicity, and various methods for measuring periodicity have been suggested for this purpose. This paper compares two such methods, autocorrelation and the Fourier transform, using synthetic periodic sequences, and explains the differences in periodicity estimates produced by each. A hybrid autocorrelation—integer period discrete Fourier transform is proposed that combines the advantages of both techniques. Collectively, this representation and a recently proposed variant on the discrete Fourier transform offer alternatives to the widely used autocorrelation for the periodicity characterization of sequence data. Finally, these methods are compared for various tetramers of interest in C. elegans c... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2341258 Sat, 18 Apr 2009 19:56:05 +0100 2341258 http://www.medworm.com/index.php?rid=2341257&cid=s_37040_79_f&fid=37040&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2009%2F491074 When aligning RNAs, it is important to consider both the secondary structure similarity and primary sequence similarity to find an accurate alignment. However, algorithms that can handle RNA secondary structures typically have high computational complexity that limits their utility. For this reason, there have been a number of attempts to find useful alignment constraints that can reduce the computations without sacrificing the alignment accuracy. In this paper, we propose a new method for finding effective alignment constraints for fast and accurate structural alignment of RNAs, including pseudoknots. In the proposed method, we use a profile-HMM to identify the “seed” regions that can be aligned with high confidence. We also estimate the position range of the aligned bases tha... EURASIP Journal on Bioinformatics and Systems Biology journals http://www.medworm.com/rss/comments.php?id=2341257 Sat, 18 Apr 2009 19:56:05 +0100 2341257