ALBERT

Description: Background: The objective of the research was to evaluate the current effectiveness of Ciprofloxacin on the uropathogens prevalent in infected urines of a cross-section of patients in Karachi, Pakistan.FindingsAn observational study conducted in a private diagnostic laboratory and its branches in key areas of Karachi City from February 2010 to July 2011. A total of 2963 consecutive urine samples were cultured on chocolate agar, CLED medium and selective EMB agar. Growth of possible uropathogens was noted, and compared retrospectively with earlier lab data of suggestive urine cultures (n = 1997) recorded during January 2009 and December 2009. The isolates were identified using routine procedures and the API 20 system and evaluated for their sensitivity to ciprofloxacin by Kirby-Bauer disk diffusion method. Data was subjected to statistical analysis on SPSS version 16. Out of the present-day culture-positive urines, 2409 (80.4%) yielded gram-negative rods, and 554 (18.5%) gram-positive cocci. E.coli (43.1%) was most frequent, followed by Klebsiella pneumoniae (22.4%) and Staphylococcus aureus (15.5%). 57.2% of the Gram-negative bacteria and 48.7% of the Gram-positive isolates were resistant to ciprofloxacin. In the earlier (2009) screening, 39% of Gram-negative rods and 48% of Gram-positive cocci were indifferent to the drug. Conclusions: A decrease in bacterial susceptibility of uropathogens to ciprofloxacin, a commonly prescribed drug in our population, is underlined, occurring possibly due to overuse pressure. Empirical initial treatment with ciprofloxacin would be inadequate in more than half of UTI cases, thereby counseling increased C/S testing of urines to provide existing sensitivity data for apt drug prescription.

Description: Background: Data accuracy and completeness are crucial for ensuring both the correctness and epidemiological relevance of a given data set. In this study we evaluated a clinical register in the administrative district of Marburg-Biedenkopf, Germany, for these criteria. Methods: The register contained data gathered from a comprehensive integrated breast-cancer network from three hospitals that treated all included incident cases of malignant breast cancer in two distinct time periods from 1996--97 (N=389) and 2003--04 (N=488). To assess the accuracy of this data, we compared distributions of risk, prognostic, and predictive factors with distributions from established secondary databases to detect any deviations from these [prime][prime]true[prime][prime] population parameters. To evaluate data completeness, we calculated epidemiological standard measures as well as incidence-mortality-ratios (IMRs). Results: In total, 12% (13 of 109) of the variables exhibited inaccuracies: 9% (5 out of 56) in 1996--97 and 15% (8 out of 53) in 2003--04. In contrast to raw, unstandardized incidence rates, (in-) directly age-standardized incidence rates showed no systematic deviations. Our final completeness estimates were IMR=36% (1996--97) and IMR=43% (2003--04). Conclusion: Overall, the register contained accurate, complete, and correct data. Regional differences accounted for detected inaccuracies. Demographic shifts occurred. Age-standardized measures indicate an acceptable degree of completeness. The IMR method of measuring completeness was inappropriate for incidence-based data registers. For the rising number of population-based health-care networks, further methodological advancements are necessary. Correct and epidemiologically relevant data are crucial for clinical and health-policy decision-making.

Description: Background: Patients increasingly turn to the Internet for information on medical conditions, including clinical news and treatment options. In recent years, an online patient community has arisen alongside the rapidly expanding world of social media, or "Web 2.0." Twitter provides real-time dissemination of news, information, personal accounts and other details via a highly interactive form of social media, and has become an important online tool for patients. This medium is now considered to play an important role in the modern social community of online, "wired" cancer patients. Results: Fifty-one highly influential "power accounts" belonging to cancer patients were extracted from a dataset of 731 Twitter accounts with cancer terminology in their profiles. In accordance with previously established methodology, "power accounts" were defined as those Twitter accounts with 500 or more followers. We extracted data on the cancer patient (female) with the most followers to study the specific relationships that existed between the user and her followers, and found that the majority of the examined tweets focused on greetings, treatment discussions, and other instances of psychological support. These findings went against our hypothesis that cancer patients' tweets would be centered on the dissemination of medical information and similar "newsy" details. Conclusions: At present, there exists a rapidly evolving network of cancer patients engaged in information exchange via Twitter. This network is valuable in the sharing of psychological support among the cancer community.

Description: Background: Exposure to early adverse events can result in the development of later psychopathology, and is often associated with cognitive impairment. This may be due to accelerated cell aging, which can be catalogued by attritioned telomeres. Exercise enhances neurogenesis and has been proposed to buffer the effect of psychological stress on telomere length. This study aimed to investigate the impact of early developmental stress and voluntary exercise on telomere length in the ventral hippocampus (VH) and prefrontal cortex (PFC) of the rat. Forty-five male Sprague--Dawley rats were categorised into four groups: maternally separated runners (MSR), maternally separated non-runners (MSnR), non-maternally separated runners (nMSR) and non-maternally separated non-runners (nMSnR). Behavioural analyses were conducted to assess anxiety-like behaviour and memory performance in the rats, after which relative telomere length was measured using qPCR. Results: Maternally separated (MS) rats exhibited no significant differences in either anxiety levels or memory performance on the elevated-plus maze and the open field compared to non-maternally separated rats at 49 days of age. Exercised rats displayed increased levels of anxiety on the day that they were removed from the cages with attached running wheels, as well as improved spatial learning and temporal recognition memory compared to non-exercised rats. Exploratory post-hoc analyses revealed that maternally separated non-exercised rats exhibited significantly longer telomere length in the VH compared to those who were not maternally separated; however, exercise appeared to cancel this effect since there was no difference in VH telomere length between maternally separated and non-maternally separated runners. Conclusions: The increased telomere length in the VH of maternally separated non-exercised rats may be indicative of reduced cellular proliferation, which could, in turn, indicate hippocampal dysfunction. This effect on telomere length was not observed in exercised rats, indicating that voluntary exercise may buffer against the progressive changes in telomere length caused by alterations in maternal care early in life. In future, larger sample sizes will be needed to validate results obtained in the present study and obtain a more accurate representation of the effect that psychological stress and voluntary exercise have on telomere length.

Description: Background: RNA interference (RNAi) becomes an increasingly important and effective genetic tool to study the function of target genes by suppressing specific genes of interest. This system approach helps identify signaling pathways and cellular phase types by tracking intensity and/or morphological changes of cells. The traditional RNAi screening scheme, in which one siRNA is designed to knockdown one specific mRNA target, needs a large library of siRNAs and turns out to be time-consuming and expensive. Results: In this paper, we propose a conceptual model, called compressed sensing RNAi (csRNAi), which employs the unique combination of group of small interfering RNAs (siRNAs) to knockdown a much larger size of genes. This strategy is based on the fact that one gene can be partially bound with several small interfering RNAs (siRNAs) and conversely, one siRNA can bind to a few genes with distinct binding affinity. This model constructs a multi-to-multi correspondence between siRNAs and their targets, with siRNAs much fewer than mRNA targets, compared with the conventional scheme. Mathematically this problem involves an underdetermined system of equations (linear or nonlinear), which is ill-posed in general. However, the recently developed compressed sensing (CS) theory can solve this problem. We present a mathematical model to describe the csRNAi system based on both CS theory and biological concerns. To build this model, we first search nucleotide motifs in a target gene set. Then we propose a machine learning based method to find the effective siRNAs with novel features, such as image features and speech features to describe an siRNA sequence. Numerical simulations show that we can reduce the siRNA library to one third of that in the conventional scheme. In addition, the features to describe siRNAs outperform the existing ones substantially. Conclusions: This csRNAi system is very promising in saving both time and cost for large-scale RNAi screening experiments which may benefit the biological research with respect to cellular processes and pathways.

Description: Background: Copy number variations (CNVs) are genomic structural variants that are found in healthy populations and have been observed to be associated with disease susceptibility. Existing methods for CNV detection are often performed on a sample-by-sample basis, which is not ideal for large datasets where common CNVs must be estimated by comparing the frequency of CNVs in the individual samples. Here we describe a simple and novel approach to locate genome-wide CNVs common to a specific population, using human ancestry as the phenotype. Results: We utilized our previously published Genome Alteration Detection Analysis (GADA) algorithm to identify common ancestry CNVs (caCNVs) and built a caCNV model to predict population structure. We identified a 73 caCNV signature using a training set of 225 healthy individuals from European, Asian, and African ancestry. The signature was validated on an independent test set of 300 individuals with similar ancestral background. The error rate in predicting ancestry in this test set was 2% using the 73 caCNV signature. Among the caCNVs identified, several were previously confirmed experimentally to vary by ancestry. Our signature also contains a caCNV region with a single microRNA (MIR270), which represents the first reported variation of microRNA by ancestry. Conclusions: We developed a new methodology to identify common CNVs and demonstrated its performance by building a caCNV signature to predict human ancestry with high accuracy. The utility of our approach could be extended to large case--control studies to identify CNV signatures for other phenotypes such as disease susceptibility and drug response.

Description: Background: HIV/AIDS has several means of transmission. Exposure to blood and other body fluids is a very important means of transmission. Healthcare workers are exposed to this disease mainly due to the nature of their work. This is an exploration of the perceptions of healthcare workers of the University of Gondar Hospital. Methods: Based on purposive sampling seven healthcare workers were selected from different departments in the hospital so that they could reflect on their perceptions. The selected healthcare workers were asked about the risks related to their work, their experience of HIV related hazards and their general views on the transmission of HIV. The main themes were identified for analysis and the views were summarized under the themes. Results: All the respondents were aware of the risk of acquiring HIV in healthcare settings. Some had experienced accidents that made them take post-exposure prophylaxis, and most witnessed accidents like needle-stick injuries to their colleagues. They also expressed their feelings that their workplace was not the best place to work at. Conclusion: Health professionals are well aware of the possibility of HIV transmission associated with their practice. Accidents like needle stick injuries are apparently common; and at the same time, the practice of healthcare workers towards using universal precautions looks poor.

Description: Background: Health control beliefs were postulated to be associated with health behaviour. However, the results of studies assessing these associations suggest that they might not be universal. Among young adults associations have been reported, but, the evidence is limited. The objective of this analysis was to re-examine these associations in a sample of university students in Germany.FindingsData from a multicentre cross-sectional study among university students in North Rhine-Westphalia, Germany was used (N=3,306). The Multidimensional Health Locus of Control Scale with three dimensions (one internal and two external) and six aspects of health behaviour (smoking habits, alcohol use, drug consumption, being over-/ or underweight, physical activity, and importance of healthy nutrition) were evaluated. Students with stronger internal locus of control scores paid more attention to healthy nutrition and displayed a higher level of physical activity. Individuals with a stronger belief in health professionals were less likely to use drugs and paid more attention to healthy nutrition. Furthermore, higher scores in the second external locus of control dimension (beliefs in luck or chance) were associated with a higher likelihood of current smoking, lower physical activity and less attention to healthy nutrition. Conclusions: Students engaged more strongly in unhealthy behaviour if they believed that luck determines health. In contrast, believing in having control over one's own health was associated with more healthy behaviour. These findings support the need to consider health control beliefs while designing preventive strategies in this specific population.

Description: Background: Accumulation of extracellular matrix (ECM) and increased matrix metalloproteinase (MMP) activity are hallmarks of liver fibrosis. The aim of the present study was to develop a model of liver fibrosis combining ex vivo tissue culture of livers from CCl4 treated animals with an ELISA detecting a fragment of type III collagen generated in vitro by MMP-9 (C3M), known to be associated with liver fibrosis and to investigate cAMP modulation of MMP activity and liver tissue turnover in this model.FindingsIn vivo: Rats were treated for 8 weeks with CCl4/Intralipid. Liver slices were cultured for 48 hours. Levels of C3M were determined in the supernatants of slices cultured without treatment, treated with GM6001 (positive control) or treated with IBMX (phosphodiesterase inhibitor). Enzymatic activity of MMP-2 and MMP-9 were studied by gelatin zymography.Ex vivo: The levels of serum C3M increased 77% in the CCl4-treated rats at week 8 (p 〈 0.01); Levels of C3M increased significantly by 100% in fibrotic liver slices compared to controls after 48 hrs (p 〈 0.01). By adding GM6001 or IBMX to the media, C3M was restored to control levels. Gelatin zymography demonstrated CCl4-treated animals had highly increased MMP-9, but not MMP-2 activity, compared to slices derived from control animals. Conclusions: We have combined an ex vivo model of liver fibrosis with measurement of a biochemical marker of collagen degradation in the condition medium. This technology may be used to evaluate the molecular process leading to structural fibrotic changes, as collagen species are the predominant structural part of fibrosis. These data suggest that modulation of cAMP may play a role in regulation of collagen degradation associated with liver fibrosis.

Description: Background: A measles outbreak was detected at Ndanga Hospital in Zaka district Masvingo Province on the 5th of May 2010 and there were five deaths. Source of infection was not known and an investigation was carried out to determine factors associated with contracting measles in Zaka district.Materials and methodsA 1:1 unmatched case control study was conducted. A case was a person residing in Zaka district who developed signs and symptoms of measles or tested IgM positive from 06 May 2010 to 30 August 2010. A control was a person residing in the same community who did not have history of signs and symptoms of measles during the same period. A structured interviewer administered questionnaire (translated into shona) was used to solicit information from cases and controls. Ethical consideration like written consent from all participants, respect and confidentiality were observed. Permission to carry out the study was obtained from the medical research Council of Zimbabwe and the provincial Medical Directors Masvingo. Epi info was used to calculate frequencies, odds ratios and perform logistic regression to control for confounding variables.FindingsA total of 110 cases and 110 controls were recruited. Most cases (63.03%) were from the apostolic sect while 44.7% of controls were from orthodox churches. Contact with a measles case [AOR= 41.14, 95% CI (7.47-226.5)],being unvaccinated against measles [AOR= 3.96, 95%CI (2.58-6.08)] and not receiving additional doses of measles vaccine [AOR 5.48, 95% CI (2.16-11.08)] were independent risk factor for contracting measles . Measles vaccination coverage for Zaka district was 75%. The median duration for seeking treatment after onset of illness was three days (Q1=2; Q3=7). There were no emergency preparedness plans in place. Conclusion: This outbreak occurred due to a large number of unvaccinated children and a boarding school that facilitated person to person transmission. We recommend mandatory vaccination for all children before enrolling into schools. As a result of the study one day training on outbreak management and surveillance was done with all District Nursing Officers and Environmental Health Officers in personnel in the province.

Description: Background: The localized scleroderma (LS) known as morphea, presents a variety of clinical manifestations that can include systemic involvement. Current classification schemes divide morphea into categories based solely on cutaneous morphology, without reference to systemic disease or autoimmune phenomena. This classification is likely incomplete. Autoimmune phenomena such as vitiligo and Hashimoto thyroiditis associated with LS have been reported in some cases suggesting an autoimmune basis. To our knowledge this is the first case of a morphea forming part of a multiple autoimmune syndrome (MAS) and presenting simultaneously with autoimmune thrombocytopenic purpura and central nervous system vasculitis.Case presentationWe report an uncommon case of a white 53 year old female patient with LS as part of a multiple autoimmune syndrome associated with pneumonitis, autoimmune thrombocytopenic purpura and central nervous system vasculitis presenting a favorable response with thrombopoietin receptor agonists, pulses of methylprednisolone and cyclophosphamide. Conclusion: Is likely that LS have an autoimmune origin and in this case becomes part of MAS, which consist on the presence of three or more well-defined autoimmune diseases in a single patient.

Description: Background: Extensive research effort has advanced our understanding of Caenorhabditis as a model system, but its natural association with bacteria remains to be explored in an ecological context. Explored associations vary vastly from mutualistic to parasitic. Serratia marcescens has been shown to be pathogenic to Caenorhabditis with a fitness cost. The recent isolation of an entomopathogenic Caenorhabditis briggsae KT0001/S. marcescens SCBI association from the wild has allowed us to examine under laboratory conditions whether such an association poses a serious cost to Caenorhabditis as previously surmised for other Serratia. Results: A fecundity table of Caenorhabditis briggsae KT0001 fed on S. marcescens SCBI and the control fed on E. coli OP50 is presented. We found no significant difference in survivorship or total fecundity between the S. marcescens SCBI fed and E. coli OP50 fed Caenorhabditis briggsae KT0001. Only the mean onset of reproduction was significantly different between the two groups with E. coli fed C. briggsae maturing earlier (2.12 days) than those fed on Serratia (2.42 days). Conclusion: S. marcescens SCBI is not highly pathogenic to C. briggsae KT0001 indicating that the entomopathogenicity reported for this association may be beneficial for both the nematode and bacteria. In light of the fact that hitherto conducted experimental tests conform to widely held view that Serratia are highly pathogenic to Caenorhabditis, the absence of a high fitness cost for C. briggsae we report here may indicate that this entomopathogenic association is non-transient suggesting nematode/bacterial associations in the wild may vary greatly. Consequently, broad generalizations about nematode/bacterial associations should be interpreted with care.

Description: Background The robust identification of isotope patterns originating from peptides being analyzed through mass spectrometry (MS) is often significantly hampered by noise artifacts and the interference of overlappingpatterns arising e.g. from post-translational modifications. As the classification of the recorded data points into either 'noise' or 'signal' lies at the very root of essentially every proteomic application, the quality of the automated processing of mass spectra can significantly influence the way the data might be interpreted within a given biological context.Results We propose non-negative least squares/non-negative least absolute deviation regression to fit a raw spectrum by templates imitating isotope patterns. In a carefully designed validation scheme, we show that the method exhibits excellent performance in pattern picking. It is demonstrated that the method is able to disentangle complicated overlaps of patterns. Conclusions: We find that regularization is not necessary to prevent overfitting and that thresholding is an effective and user-friendly way to perform feature selection. The proposed method avoids problems inherent in regularization-based approaches, comes with a set of well-interpretable parameters whose default configuration is shown to generalize well without the need for fine-tuning, and is applicable to spectra of different platforms. The R package IPPD implements the method and is available from the Bioconductor platform (http://bioconductor.fhcrc.org/help/bioc-views/devel/bioc/html/IPPD.html).

Description: Background: Hyperelastosis cutis is an inherited autosomal recessive connective tissue disorder. Affected horses are characterized by hyperextensible skin, scarring, and severe lesions along the back. The disorder is caused by a mutation in cyclophilin B. Results: The crystal structures of both wild-type and mutated (Gly6-〉Arg) horse cyclophilin B are presented. The mutation neither affects the overall fold of the enzyme nor impairs the catalytic site structure. Instead, it locally rearranges the flexible N-terminal end of the polypeptide chain and also makes it more rigid. Conclusions: Interactions of the mutated cyclophilin B with a set of endoplasmic reticulum-resident proteins must be affected.

Description: Background: In plants, a large family of calmodulin (CaM) and CaM-like (CML) proteins transduce the increase in cytosolic Ca2+ concentrations by binding to and altering the activities of target proteins, and thereby affecting the physiological responses to a vast array of stimuli. Here, transcript expression analysis of Cam and CML gene family members in rice (Oryza sativa L.) was extensively examined. Results: Cam and CML genes in rice exhibited differential expression patterns in tissues/organs. Under osmotic stress and salt stress, expression of OsCam1-1, OsCML4, 5, 8, and 11 was induced with different kinetics and magnitude. OsCML4 and 8 mRNA levels significantly increased by 3 h after treatment and remained elevated for at least 24 h while expression of OsCam1-1, OsCML5 and 11 was up-regulated as early as 1--3 h before rapidly returning to normal levels. Several cis-acting elements in response to abiotic stresses, including DREs (important promoter elements responsive to drought, high salt, and cold stress), were detected in the 5[prime] upstream regions of these genes. The observed induction of the GUS activity of transgenic rice plants via the OsCam1-1 promoter appeared to be biphasic and dependent on the severity of salt stress. Conclusions: Large OsCam and OsCML gene family members likely play differential roles as signal transducers in regulating various developmental processes and represent important nodes in the signal transduction and transcriptional regulation networks in abiotic stresss responses mediated by the complex Ca2+ signals in plants, which are rich in both spatial and temporal information.

Description: Background: The inference of homologies among DNA sequences, that is, positions in multiple genomes that share a common evolutionary origin, is a crucial, yet difficult task facing biologists. Its computational counterpart is known as the multiple sequence alignment problem. There are various criteria and methods available to perform multiple sequence alignments, and among these, the minimization of the overall cost of the alignment on a phylogenetic tree is known in combinatorial optimization as the Tree Alignment Problem. This problem typically occurs as a subproblem of the Generalized Tree Alignment Problem, which looks for the tree with the lowest alignment cost among all possible trees. This is equivalent to the Maximum Parsimony problem when the input sequences are not aligned, that is, when phylogeny and alignments are simultaneously inferred. Results: For large data sets, a popular heuristic is Direct Optimization (DO). DO provides a good tradeoff between speed, scalability, and competitive scores, and is implemented in the computer program POY. All other (competitive) algorithms have greater time complexities compared to DO. Here, weintroduce and present experiments a new algorithm Affine-DO to accommodate the indel (alignment gap) models commonly used in phylogenetic analysis of molecular sequence data. Affine-DO has the same time complexity as DO, but is correctly suited for the affine gap edit distance. We demonstrateits performance with more than 330,000 experimental tests. These experiments show that the solutions of Affine-DO are close to the lower bound inferred from a linear programming solution. Moreover, iterating over a solution produced using Affine-DO shows little improvement. Conclusions: Our results show that Affine-DO is likely producing near-optimal solutions, with approximations within 10% for sequences with small divergence, and within 30% for random sequences, for which Affine-DO produced the worst solutions. The Affine-DO algorithm has the necessary scalability andoptimality to be a significant improvement in the real-world phylogenetic analysis of sequence data.

Description: Background: Breast cancer is one of the leading causes of cancer morbidity and mortality worldwide. In Cameroon, breast cancer causes as many as 10.7 deaths per 100,000 women making it the second cause of cancer mortality. Better documenting women's knowledge and practices on breast cancer and breast self-exam (BSE) would be useful in the design of interventions aimed at preventing breast cancer. This study sought to 1. describe Cameroonian women's knowledge of breast self-examination (BSE); 2. assess their impression on the practice of BSE and 3. describe their perceptions on the causes, risk factors and prevention of breast cancer. Methods: A cross-sectional survey was conducted in a volunteer sample of 120 consenting women in Buea, Cameroon. Data were collected using a structured questionnaire self-administered by study participants. Results: The sample was fairly educated with close to three quarters (70.83%) having completed high school. Nearly three quarters (74.17%) of participants had previously heard about BSE, however as many as 40% had never done a BSE. Although 95% of participants believed that breast cancer could be prevented, only 36.67% recognized breast examination as a prevention method. A substantial 13.33% thought that breast cancer could be prevented with a vaccine while 45% thought that dieting or exercising would prevent breast cancer. Similarly, 70% of participants thought that breast cancer could be treated, with 35.83% thinking that it could be treated medically while 34.17% thought it could be treated traditionally or spiritually. Conclusions: The practice of BSE while perceived as being important is not frequent in these women in Buea, Cameroon. Health education campaigns are imperative to elucidate the public on the causes, risk factors and prevention of breast cancer. Further studies need to explore what interventions could be best used to improve the uptake and practice of BSE.

Description: BMC Research Notes recently published a research article regarding the use of ligated DNA extracted from formalin-fixed paraffin embedded (FFPE) tissue on the Illumina Infinium methylation platform - "Interpretation of genome-wide infinium methylation data from ligated DNA in formalin-fixed, paraffin-embedded paired tumor and normal tissue" Jasmine et al. BMC Research Notes 2012, 5:117. This article repeatedly refers to our previous work and concludes that methylation data obtained from ligated FFPE extracted DNA should be used with great caution. In this Discussion we review the data analysis performed in Jasmine et al's paper and suggest limitations which subsequently lead the authors to draw what we believe are incorrect conclusions. Moreover, we continue to analyse genome-wide methylation data from DNA extracted from FFPE tissue successfully on both the HumMeth27 and 450K arrays.

Description: Background: Time-course gene expression data such as yeast cell cycle data may be periodically expressed. To cluster such data,currently used Fourier series approximations of periodic gene expressions have been found not to be sufficientlyadequate to model the complexity of the time-course data, partly due to their ignoring the dependence between theexpression measurements over time and the correlation among gene expression profiles. We further investigatethe advantages and limitations of available models in the literature and propose a new mixture model withautoregressive random effects of the first order for the clustering of time-course gene-expression profiles. Somesimulations and real examples are given to demonstrate the usefulness of the proposed models. Results: We illustrate the applicability of our new model using synthetic and real time-course datasets. We show that ourmodel outperforms existing models to provide more reliable and robust clustering of time-course data. Our modelprovides superior results when genetic profiles are correlated. It also gives comparable results when the correlationbetween the gene profiles is weak. In the applications to real time-course data, relevant clusters of co-regulatedgenes are obtained, which are supported by gene-function annotation databases. Conclusions: Our new model under our extension of the EMMIX-WIRE procedure is more reliable and robust for clusteringtime-course data because it adopts a random effects model that allows for the correlation among observations atdifferent time points. It postulates gene-specific random effects with an auto-correlation variance structure thatmodels coregulation within the clusters The developed R package is flexible in its specification of the randomeffectsthrough user-input parameters that enables improved modelling and consequent clustering of time-coursedata.

Description: Background: Transforming growth factor-beta (TGF-beta) is a multi-factorial peptide growth factor that has a vital role in the regulation of cell growth, differentiation, inflammation, and tissue repair. Quantification of biologically active TGF-beta levels in tissues is crucial to illustrate mechanisms involved in various physiological and pathological processes, but direct measurement of bioactive TGF-beta level in the tissue has been hampered by lack of reliable methods. Here, we introduced mink lung epithelial cell bioassay to quantify both active and total TGF-beta levels in serum and protein lysates from solid organs in the mouse model.FindingsMink lung epithelial cells were stably transfected with plasminogen activator inhibitor-1 promoter/luciferase construct, in which bioactive TGF-beta level was represented by luciferase activity. Serum total TGF-beta levels were comparable between the bioassay and enzyme-linked immunosorbent assay (ELISA), but active TGF-beta levels measured by ELISA were significantly lower than those obtained by the bioassay. Active and total TGF-beta levels in the solid organs including heart, liver, and kidney were also measured. Total TGF-beta levels were relatively comparable among these organs, but active TGf-beta levels were slightly higher in hearts and kidneys than in livers. Positive luciferase activities in the bioassay were almost completely inhibited by adding pan-TGF-beta neutralizing antibodies, suggesting its high specificity to bioactive TGF-beta. We also measured myocardial TGF-beta levels after myocardial infarction and sham control by the bioassay, and compared the values with those obtained by ELISA. The bioassay demonstrated that both active and total tissue TGF-beta levels were significantly higher in post-myocardial infarction than in sham myocardium. ELISA was markedly less sensitive in detecting both active and total TGF-beta levels than our bioassay and failed to show any statistically significant difference in TGF-beta levels between myocardial infarction and sham myocardium. Conclusions: Our data suggested that the bioassay was significantly more sensitive than ELISA in detecting active TGF-beta in serum and both active and total TGF-beta in solid organ tissues. The bioassay will be useful in investigating TGF-beta profile in various solid organs in physiological and pathological conditions. (332 words)

Description: Background: The genus Eucalyptus consists of approximately 600 species and subspecies and has a physiological plasticity that allows some species to propagate in different regions of the world. Eucalyptus is a major source of cellulose for paper manufacturing, and its cultivation is limited by weather conditions, particularly water stress and low temperatures. Gene expression studies using quantitative reverse transcription polymerase chain reaction (qPCR) require reference genes, which must have stable expression to facilitate the comparison of the results from analyses using different species, tissues, and treatments. Such studies have been limited in eucalyptus. Results: Eucalyptus globulus Labill, Eucalyptus urograndis (hybrid from Eucalyptus urophylla S.T. Blake X Eucalyptus grandis Hill ex-Maiden) and E. uroglobulus (hybrid from E. urograndis X E. globulus) were subjected to different treatments, including water deficiency and stress recovery, low temperatures, presence or absence of light, and their respective controls. Except for treatment with light, which examined the seedling hypocotyl or apical portion of the stem, the expression analyses were conducted in the apical and basal parts of the stem. To select the best pair of genes, the bioinformatics tools GeNorm and NormFinder were compared. Comprehensive analyses that did not differentiate between species, treatments, or tissue types, showed that IDH (isocitrate dehydrogenase), SAND (SAND protein), ACT (actin), and A-Tub (alpha-tubulin) genes were the most stable. IDH was the most stable gene in all of the treatments. Conclusion: Comparing these results with those of other studies on eucalyptus, we concluded that five genes are stable in different species and experimental conditions: IDH, SAND, ACT, A-Tub, and UBQ (ubiquitin). It is usually recommended a minimum of two reference genes is expression analysis; therefore, we propose that IDH and two others genes among the five identified genes in this study should be used as reference genes for a wide range of conditions in eucalyptus.

Description: Background: 454 pyrosequencing is a commonly used massively parallel DNA sequencing technology with a wide variety of application fields such as epigenetics, metagenomics and transcriptomics. A well-known problem of this platform is its sensitivity to base-calling insertion and deletion errors, particularly in the presence of long homopolymers. In addition, the base-call quality scores are not informative with respect to whether an insertion or a deletion error is more likely. Surprisingly, not much effort has been devoted to the development of improved base-calling methods and more intuitive quality scores for this platform. Results: We present HPCall, a 454 base-calling method based on a weighted Hurdle Poisson model. HPCall uses a probabilistic framework to call the homopolymer lengths in the sequence by modeling well-known 454 noise predictors. Base-calling quality is assessed based on estimated probabilities for each homopolymer length, which are easily transformed to useful quality scores. Conclusions: Using a reference data set of the Escherichia coli K-12 strain, we show that HPCall produces superior quality scores that are very informative towards possible insertion and deletion errors, while maintaining a base-calling accuracy that is better than the current one. Given the generality of the framework, HPCall has the potential to also adapt to other homopolymer-sensitive sequencing technologies.

Description: Background: Our previous study on ripe apples from a progeny of a cross between the apple cultivars 'Prima' and 'Fiesta' showed a hotspot of mQTLs for phenolic compounds at the top of LG16, both in peel and in flesh tissues. In order to find the underlying gene(s) of this mQTL hotspot, we investigated the expression profiles of structural and putative transcription factor genes of the phenylpropanoid and flavonoid pathways during different stages of fruit development in progeny genotypes. Results: Only the structural gene leucoanthocyanidin reductase (MdLAR1) showed a significant correlation between transcript abundance and content of metabolites that mapped on the mQTL hotspot. This gene is located on LG16 in the mQTL hotspot. Progeny that had inherited one or two copies of the dominant MdLAR1 alleles (Mm, MM) showed a 4.4- and 11.8-fold higher expression level of MdLAR1 respectively, compared to the progeny that had inherited the recessive alleles (mm). This higher expression was associated with a four-fold increase of procyanidin dimer II as one representative metabolite that mapped in the mQTL hotspot. Although expression level of several structural genes were correlated with expression of other structural genes and with some MYB and bHLH transcription factor genes, only expression of MdLAR1 was correlated with metabolites that mapped at the mQTL hotspot.MdLAR1 is the only candidate gene that can explain the mQTL for procyanidins and flavan-3-ols. However, mQTLs for other phenylpropanoids such as phenolic esters, dihydrochalcones and flavonols, that appear to map at the same locus, have so far not been considered to be dependent on LAR, as their biosynthesis does not involve LAR activity. An explanation for this phenomenon is discussed. Conclusions: Transcript abundances and genomic positions indicate that the mQTL hotspot for phenolic compounds at the top of LG16 is controlled by the MdLAR1 gene. The dominant allele of the MdLAR1 gene, causing increased content of metabolites that are potentially health beneficial, could be used in marker assisted selection of current apple breeding programs and for cisgenesis.

Description: Background: Despite benefits of adherence, little is known about the degree to which patients will express their perceptions of medications as more or less important to take as prescribed. We determined the frequency with which Veteran patients would explicitly identify one of their medications as "most important" or "least important."FindingsWe conducted a retrospective cohort study of patients from ambulatory clinics at VA Boston from April 2010-July 2011. Patients answered two questions: "Which one of your medicines, if any, do you think is the most important? (if none, please write 'none')" and "Which one of your medicines, if any, do you think is the least important? (if none, please write 'none')." We determined the prevalence of response categories for each question. Our cohort of 104 patients was predominantly male (95%), with a mean of 9 medications (SD 5.7). Regarding their most important medication, 41 patients (39%) identified one specific medication; 26 (25%) selected more than one; 21 (20%) wrote "none"; and 16 (15%) did not answer the question. For their least important medication, 31 Veterans (30%) chose one specific medication; two (2%) chose more than one; 51 (49%) wrote "none"; and 20 (19%) did not directly answer the question. Conclusions: Thirty-five percent of patients did not identify a most important medication, and 68% did not identify a least important medication. Better understanding of how patients prioritize medications and how best to elicit this information will improve patient-provider communication, which may in turn lead to better adherence.

Description: Background: While an increased prevalence of cystic fibrosis (CF) in patients with jejunal atresia and ileal atresia (JIA) has been described previously, it still may not be a practice routine to indicate a sweat test or DNA test for CFTR mutations in newborns presenting with JIA. Leading textbooks do not mention JIA as a possible presenting clinical feature of CF. We describe two cases of JIA with a delayed diagnosiis of CF (4 months [post mortem] and 19 months). This led to a retrospective review of all patients with JIA in our hospital. We hypothesised that also in the past although indicated further testing for CF had not always been performed. Methods: Over an 18-year period from January 1991 until December 2008, all cases of JIA in our centre were reviewed (n=50). We compared patients who have been tested for CF (n=18) with patients who have not been tested for CF (n=32), with respect to their patient characteristics, either by logistic regression analysis or a nonparametric test (p

Description: Background: Multivariate approaches have been successfully applied to genome wide association studies. Recently, a Partial Least Squares (PLS) based approach was introduced for mapping yeast genotype-phenotype relations, where background information such as gene function classification, gene dispensability, recent or ancient gene copy number variations and the presence of premature stop codons or frameshift mutations in reading frames, were used post hoc to explain selected genes. One of the latest advancement in PLS named L-Partial Least Squares (L-PLS), where 'L' presents the used data structure, enables the use of background information at the modeling level. Here, a modification of L-PLS with variable importance on projection (VIP) was implemented using a stepwise regularized procedure for gene and background information selection. Results werecompared to PLS-based procedures, where no background information was used. Results: Applying the proposed methodology to yeast Saccharomyces cerevisiae data, we found the relationship between genotype-phenotype to have improved understandability. Phenotypic variations were explained by the variations of relatively stable genes and stable background variations. The suggested procedure provides an automatic way for genotype-phenotype mapping. The selected phenotype influencing genes were evolving 29% faster than non-influential genes, and the current results are supported by a recently conducted study. Further power analysis on simulated data verified that the proposed methodology selects relevant variables. Conclusions: A modification of L-PLS with VIP in a stepwise regularized elimination procedure can improve the understandability and stability of selected genes and background information. The approach is recommended for genome wide association studies where background information is available.

Description: Background: Biomarker panels derived separately from genomic and proteomic data and with a variety of computational methods have demonstrated promising classification performance in various diseases. An open question is how to create effective proteo-genomic panels. The framework of ensemble classifiers has been applied successfully in various analytical domains to combine classifiers so that the performance of the ensemble exceeds the performance of individual classifiers. Using blood-based diagnosis of acute renal allograft rejection as a case study, we address the following question in this paper: Can acute rejection classification performance be improved by combining individual genomic and proteomic classifiers in an ensemble? Results: The first part of the paper presents a computational biomarker development pipeline for genomic and proteomic data. The pipeline begins with data acquisition (e.g., from bio-samples to microarray data), quality control, statistical analysis and mining of the data, and finally various forms of validation. The pipeline ensures that the various classifiers to be combined later in an ensemble are diverse and adequate for clinical use. Five mRNA genomic and five proteomic classifiers were developed independently using single time-point blood samples from 11 acute-rejection and 22 non-rejection renal transplant patients. The second part of the paper examines five ensembles ranging in size from two to 10 individual classifiers. Performance of ensembles is characterized by area under the curve (AUC), sensitivity, and specificity, as derived from the probability of acute rejection for individual classifiers in the ensemble in combination with one of two aggregation methods: (1) Average Probability or (2) Vote Threshold. One ensemble demonstrated superior performance and was able to improve sensitivity and AUC beyond the best values observed for any of the individual classifiers in the ensemble, while staying within the range of observed specificity. The Vote Threshold aggregation method achieved improved sensitivity for all 5 ensembles, but typically at the cost of decreased specificity. Conclusion: Proteo-genomic biomarker ensemble classifiers show promise in the diagnosis of acute renal allograft rejection and can improve classification performance beyond that of individual genomic or proteomic classifiers alone. Validation of our results in an international multicenter study is currently underway.

Description: Background: Plant resistance genes, which encode R-proteins, constitute one of the most important and widely investigated gene families. Thanks to the use of both genetic and molecular approaches, more than 100 R genes have been cloned so far. Analysis of resistance proteins and investigation of domain properties may afford insights into their role and function. Moreover, genomic experiments and availability of high-throughput sequence data are very useful for discovering new R genes and establish hypotheses about R-genes architecture.Result: We surveyed the PRGdb dataset to provide valuable information about hidden R-protein features. Through an in silico approach 4409 putative R-proteins belonging to 33 plant organisms were analysed for domain associations frequency. The proteins showed common domain associations as well as previously unknown classes. Interestingly, the number of proteins falling into each class was found inversely related to domain arrangement complexity. Out of 31 possible theoretical domain combinations, only 22 were found. Proteins retrieved were filtered to highlight, through the visualization of a Venn diagram, candidate classes able to exert resistance function. Detailed analyses performed on conserved profiles of those strong putative R proteins revealed interesting domain features. Finally, several atypical domain associations were identified. Conclusion: The effort made in this study allowed us to approach the R-domains arrangement issue from a different point of view, sorting through the vast diversity of R proteins. Overall, many protein features were revealed and interesting new domain associations were found. In addition, insights on domain associations meaning and R domains modelling were provided.

Description: Background: Co-expression measures are often used to define networks among genes. Mutual information (MI) is often used as a generalized correlation measure. It is not clear how much MI adds beyond standard (robust) correlation measures or regression model based association measures. Further, it is important to assess what transformations of these and other co-expression measures lead to biologically meaningful modules (clusters of genes). Results: We provide a comprehensive comparison between mutual information and several correlation measures in 8 empirical data sets and in simulations. We also study different approaches for transforming an adjacency matrix, e.g. using the topological overlap measure. Overall, we confirm close relationships between MI and correlation in all data sets which reflects the fact that most gene pairs satisfy linear or monotonic relationships. We discuss rare situations when the two measures disagree. We also compare correlation and MI based approaches when it comes to defining co-expression network modules. We show that a robust measure of correlation (the biweight midcorrelation transformed via the topological overlap transformation) leads to modules that are superior to MI based modules and maximal information coefficient (MIC) based modules in terms of gene ontology enrichment. We present a function that relates correlation to mutual information which can be used to approximate the mutual information from the corresponding correlation coefficient. We propose the use of polynomial or spline regression models as an alternative to MI for capturing non-linear relationships between quantitative variables. Conclusions: The biweight midcorrelation outperforms MI in terms of elucidating gene pairwise relationships. Coupled with the topological overlap matrix transformation, it often leads to more significantly enriched co-expression modules. Spline and polynomial networks form attractive alternatives to MI in case of non-linear relationships. Our results indicate that MI networks can safely be replaced by correlation networks when it comes to measuring co-expression relationships in stationary data.

Description: Background: Illumina BeadArray technology includes non specific negative control features that allow a precise estimation of the background noise. As an alternative to the background subtraction proposed in BeadStudio which leads to an important loss of information by generating negative values, a background correction method modeling the observed intensities as the sum of the exponentially distributed signal and normally distributed noise has been developed. Nevertheless, Wang and Ye (2012) display a kernel-based estimator of the signal distribution on Illumina BeadArrays and suggest that a gamma distribution would represent a better modeling of the signal density. Hence, the normal-exponential modeling may not be appropriate for Illumina data and background corrections derived from this model may lead to wrong estimation. Results: We propose a more flexible modeling based on a gamma distributed signal and a normal distributed background noise and develop the associated background correction, implemented in the R-package NormalGamma. Our model proves to be markedly more accurate to model Illumina BeadArrays: on the one hand, it is shown on two types of Illumina BeadChips that this model offers a more correct fit of the observed intensities. On the other hand, the comparison of the operating characteristics of several background correction procedures on spike-in and on normal-gamma simulated data shows high similarities, reinforcing the validation of the normal-gamma modeling. The performance of the background corrections based on the normal-gamma and normal-exponential models are compared on two dilution data sets, through testing procedures which represent various experimental designs. Surprisingly, we observe that the implementation of a more accurate parametrisation in the model-based background correction does not increase the sensitivity. These results may be explained by the operating characteristics of the estimators: the normal-gamma background correction offers an improvement in terms of bias, but at the cost of a loss in precision. Conclusions: This paper addresses the lack of fit of the usual normal-exponential model by proposing a more flexible parametrisation of the signal distribution as well as the associated background correction. This new model proves to be considerably more accurate for Illumina microarrays, but the improvement in terms of modeling does not lead to a higher sensitivity in differential analysis. Nevertheless, this realistic modeling makes way for future investigations, in particular to examine the characteristics of pre-processing strategies.

Description: Background: Laparoscopic gastrectomy is a new and technically challenging surgical procedure with potential benefit. The objective of this study was to investigate clinical and para-clinical consequences following Roux-en-Y and Jejunal Loop interposition reconstructive techniques for subtotal gastrectomy using laparoscopic assisted surgery. Results: Following resection of the stomach attachments through a laparoscopic approach, stomach was removed and reconstruction was performed with either standard Roux-en-Y (n = 5) or Jejunal Loop interposition (n = 5) methods. Weight changes were monitored on a daily basis and blood samples were collected on Days 0, 7 and 21 post surgery. A fecal sample was collected on Day 28 after surgery to evaluate fat content. One month post surgery, positive contrast radiography was conducted at 5, 10, 20, 40, 60 and 90 minutes after oral administration of barium sulfate, to evaluate the postoperative complications. There was a gradual decline in body weight in both experimental groups after surgery (P 〈 0.05). There was no difference in blood parameters at any time after surgery between the two methods (P 〉 0.05). Fecal fat content increased in the Roux-en-Y compared to the Jejunal loop interposition technique (P 〈 0.05). No major complications were found in radiographs and gastric emptying time was similar between the two groups (P 〉 0.05). Conclusion: Roux-en-Y and Jejunal loop interposition techniques might be considered as suitable approaches for reconstructing gastro-intestinal tract following gastrectomy in dogs. The results of this study warrant further investigation with a larger number of animals.

Description: Background: Corneal lacerations mostly affect younger children, commonly males, who will constitute the majority of the workforce. Clinical outcomes are reviewed and compared so that measures to reduce their occurrence and improve outcome can be proffered. Methods: Records of all children between the ages of 1-18 yrs, who presented with penetrating eye injuries at the eye clinic of the University of Port Harcourt teaching Hospital, Rivers state, Nigeria between January 2002 and December 2009 were included. Information retrieved -patient's Bio data, presenting symptoms, presenting visual acuity (VA), source of injury, surgical intervention and outcome using VA. All data analysed with EPI Info version 6 with the aid of a statistician. Results: Folders of thirty-six children (36 eyes) between the ages of 0--18 years diagnosed with corneal laceration over a period of 8 years out of 65 cases managed within that period available. Other folders reported as missing. Male female ratio 3:1, the mean age is 8.7 years (SD +/- 3.67). Only one presented within 24 hours. Objects causing injury mainly missiles with stones/catapult injuries (n = 8, 22.2%). Presenting VAs in those that could be measured, ranged from 6/24 to 6/60 (n = 4, 11%) to no light perception (NLP) (n = 5, 13.9%). Associated injuries include lid laceration, cataract, vitreous haemorrhage and retinal detachment. Twenty one patients had primary corneal repair (58.3%) carried out within 7 days of presentation. Four had endophthalmitis. After 3 months follow up, VA of 6/60 and better was achieved in 11 of 18 eyes left in follow up (6/60-6/24 in 8 eyes (22.2%), 6/18 and better in 3 eyes (8.3%).) Conclusion: Most eye injuries in children are preventable. In this study, the prognosis was better in those whose injuries were confined to a peripheral part of the cornea, with no other associated injury, who presented within 5 days and who did not have any intraocular infection at the time of presentation. The importance of health education, adult supervision of play and application of appropriate measures that is necessary for reducing the incidence and severity of trauma is emphasized.

Description: Background: Preterm prelabor rupture of membrane (PPROM) causes maternal and neonatal complications. Prophylactic antiobiotics were used in the management of PPROM. The objectives of this retrospective study were to compare clinical course and outcome of PPROM managed expectantly with prophylactic antibiotics and antenatal corticosteroids with those without prophylactic antibiotics and antenatal corticosteroids. Results: A total of 170 cases of singleton pregnant women with gestational age between 28--34 weeks suffering from PROM during January 1998 to December 2009 were included; 119 cases received prophylactic antibiotics and antenatal corticosteroids while 51 cases did not received prophylactic antibiotics and antenatal corticosteroids. Median latency period in the study group was significantly longer than in the control group (89.8 vs. 24.3 hours, P 〈 0.001). The percentage of patients who did not deliver within 48 hours and within 7 days in the study group were also significantly higher than in control group (64.7 vs. 31.4%, P 〈 0.001 and 29.4 vs. 7.8%, P = 0.002, respectively). Maternal infectious morbidity was comparable between groups (17.6% vs. 13.7%, P = 0.52). Neonatal infectious morbidity was significantly lesser in study group than control group (21% vs. 35.3%, p = 0.04). Conclusions: Latency period of PPROM after using prophylactic antibiotics and antenatal corticosteroids increased while neonatal infectious morbidity was low. But maternal infectious morbidity was not increased. This retrospective study confirms the benefit of prophylactic antibiotics and antenatal corticosteroids in management of PPROM.

Description: Background: Hepatocyte Growth Factor (HGF) enhances cytotoxicity of paclitaxel (PTX) and cisplatin (CDDP) in human ovarian cancer cells. Because of potential pitfalls of HGF exogenous administration, we investigated whether HGF serum concentration might be alternatively raised in vivo by administering low molecular weight heparin (LMWH). Methods: The main HGF pharmacokinetic parameters were evaluated following acute and chronic LMWH treatment. First, women, operated on for gynaecological tumors, were treated with a single dose of calcium nadroparin and studied for 12 hours. Next, women operated on for benign or malignant gynaecological tumors were treated daily with calcic nadroparin for one month. Subsequently, the biological activity of the measured HGF serum levels was tested in assays of ovarian cancer cell sensitization to drugs. Results: In the short-term treated group, median HGF AUCss, Cmax and Caverage were about four-fold that of the control group, whereas Cmin was three-fold. In the patients treated chronically median HGF serum levels rose about six-fold in the first week, and decreased but remained significantly higher after one month. The pharmacokinetic of nadroparin-dependent HGF increase were similar in the two groups. The HGF concentrations measured after both acute and chronic treatment were found to be effective in sensitising ovarian cancer cells to chemotherapeutics. Conclusions: This study raises the possibility of using LMWH to increase HGF serum concentration and to take advantage of its biological activities. In particular, nadroparin might be used as a chemo-potentiating agent in epithelial cell ovarian carcinoma through its action on HGF serum concentration.Trial registrationClinicalTrials.gov ID: NCT01523652

Description: Background: Biologists are elucidating complex collections of genetic regulatory data for multiple organisms. Software is needed for such regulatory network data. Results: The Pathway Tools software provides a comprehensive environment for manipulating molecular regulatory interactions that integrates regulatory data with an organism's genome and metabolic network. The Pathway Tools regulation ontology captures transcriptional and translational regulation, substrate-level regulation of enzyme activity, post-translational modifications, and regulatory pathways. Curated collections of regulatory data are available for Escherichia coli, Bacillus subtilis, and Shewanella oneidensis. Regulatory visualizations include a novel diagram that sum- marizes all regulatory influences on a gene; a transcription-unit diagram, and an interactive visualization of a full transcriptional regulatory network that can be painted with gene expression data to probe correlations between gene expression and regulatory mechanisms. We introduce a novel type of enrichment analysis that asks whether a gene-expression dataset is over-represented for known regulators. We present algorithms for ranking the degree of regulatory influence of genes , and for computing the net positive and negative regulatory influences on a gene.

Description: Background: Inverted repeat genes encode precursor RNAs characterized by hairpin structures. These RNA hairpins are then metabolized by biosynthetic pathways to produce functional small RNAs. In eukaryotic genomes, short non-autonomous transposable elements can have similar size and hairpin structures as non-coding precursor RNAs. This resemblance leads to problems annotating small RNAs.MethodWe mapped all microRNA precursors from miRBASE to several genomes and studied the repetition and dispersion of the corresponding loci. We then searched for repetitive elements overlapping these loci. Results: We developed an automatic method called ncRNAclassifier to classify pre-ncRNAs according to their relationship with transposable elements (TEs). We show there is a correlation between the number of scattered occurrences of ncRNA precursor candidates is correlated with the presence of TEs. We applied ncRNAclassifier on six chordate genomes and report our findings. Among the 1,426 human and 721 mouse pre-miRNAs of miRBase, we identified 235 and 68 mis-annotated pre-miRNAs respectively corresponding completely to TEs. Conclusions: We provide a tool enabling the identification of repetitive elements in precursor ncRNA sequences. ncRNAclassifier is available at http://EvryRNA.ibisc.univ-evry.fr

Description: Background: Childhood overweight and obesity have increased progressively in developing countries and nowadays they are considered as a global epidemic.The aim of the present study was to determine prevalence of overweight and obesity in 2-5 year-old children in kindergartens of Birjand in 2008.FindingsThis cross- sectional and descriptive- analytical study was conducted on 500 children, who were 2-5 years-old, in kindergartens of Birjand selected through census. It was found that prevalence of overweight was 10.6% (11.7% in females and 9.6% in males) and obesity 7.6% (6.3% in females and 9.6% in males).Prevalence of overweight and obesity were statistically significant regarding birth weight, mother's occupation and father's level of education. Conclusion: Prevalence of overweight and obesity in pre-schoolchildren is more than that of 7-18 year-old group in Birjand, but it is less than the result of similar studies in Tehran and most studies in other countries. Further studies are recommended to identify risk factors in obese children. Periodic studies are necessary to compare the changes in prevalence of obesity in children in future.

Description: Background: Highly infectious diseases (HIDs) are defined as being transmissible from person to person, causing life-threatening illnesses and presenting a serious public health hazard. The sampling, handling and transport of specimens from patients with HIDs present specific bio-safety concerns.FindingsThe European Network for HID project aimed to record, in a cross-sectional study, the infection control capabilities of referral centers for HIDs across Europe and assesses the level of achievement to previously published guidelines. In this paper, we report the current diagnostic capabilities and bio-safety measures applied to diagnostic procedures in these referral centers. Overall, 48 isolation facilities in 16 European countries were evaluated. Although 81% of these referral centers are located near a biosafety level 3 laboratory, 11% and 31% of them still performed their microbiological and routine diagnostic analyses, respectively, without bio-safety measures. Conclusions: The discrepancies among the referral centers surveyed between the level of practices and the European Network of Infectious Diseases (EUNID) recommendations have multiple reasons of which the interest of the individuals in charge and the investment they put in preparedness to emerging outbreaks. Despite the fact that the less prepared centers can improve by just updating their practice and policies any support to help them to achieve an acceptable level of biosecurity is welcome.

Description: Background: Pregnancy in adolescents is a worldwide health problem and has been mostly common in poor populations. It is not clear if socioeconomic or biological factors are the main determinants of perinatal adverse outcomes in pregnant adolescents. Adolescents under 15 years old may present a high growth rate which may contribute to impair fetal growth. Our aim is to compare perinatal characteristics among early (aged 10 to 14 years) and late (aged 15 to 19 years) pregnant adolescents. Methods: A cross-sectional study was performed using data from Pernambuco State 2009, obtained from DATASUS/SISNAC, a Brazilian Government, open-access public health database. Maternal and neonatal outcomes were compared between early (aged 10--14 years) and late (aged 15--19 years) pregnant adolescents. Family income was compared between early and late pregnant adolescents using a sample of 412 subjects evaluated at Instituto de Medicina Integral Prof. Fernando Figueira (IMIP) during 2011. Statistical comparisons were made using the chi-square test was used with a significant level of 0.05; bivariate and multivariate analysis were performed. This project received was approved by the Institutional Ethics Review Board. Results: Data from 31,209 pregnant adolescents were analyzed. 29,733 (95.2 %) were aged 15 to 19 years and 1,476 (4.7 %) were aged 10 to 14 years. There were significant differences with respect to marital status, education level and number of prenatal visits of mothers aged 10 to 14 years compared to 15 to 19 years. Of importance, early adolescents had a greater rate of neonates born premature and with low birth weight. Prematurity and low birth weight remained statistically significant after multivariate analysis. Conclusions: Early aged adolescents may have an increased risk of prematurity and low birth weight. These findings highlight the potential role of biological factors in newborn outcomes in pregnant adolescents.

Description: Background: For several decades, overcrowding in emergency departments (EDs) has been intensifying due to the increased number of patients seeking care in EDs. Demand growth is partly due to misuse of EDs by patients who seek care for nonurgent problems. This study explores the reasons why people with nonurgent complaints choose to come to EDs, and how ED health professionals perceive the phenomenon of "nonurgency." Results: Semi-structured interviews were conducted in 10 EDs with 87 nonurgent patients and 34 health professionals. Interviews of patients revealed three themes: (1) fulfilled health care needs, (2) barriers to primary care providers (PCPs), and (3) convenience. Patients chose EDs as discerning health consumers: they preferred EDs because they had difficulties obtaining a rapid appointment. Access to technical facilities in EDs spares the patient from being overwhelmed with appointments with various specialists. Four themes were identified from the interviews of health professionals: (1) the problem of defining a nonurgent visit, (2) explanations for patients' use of EDs for nonurgent complaints, (3) consequences of nonurgent visits, and (4) solutions to counter this tendency. Conclusions: Studies on the underlying reasons patients opt for the ED, as well as on their decision-making process, are lacking. The present study highlighted discrepancies between the perceptions of ED patients and those of health professionals, with a special focus on patient behaviour. To explain the use of ED, health professionals based themselves on the acuity and urgency of medical problems, while patients focused on rational reasons to initiate care in the ED (accessibility to health care resources, and the context in which the medical problem occurred). In spite of some limitations due to the slightly outdated nature of our data, as well as the difficulty of categorizing nonurgent situations, our findings show the importance of conducting a detailed analysis of the demand for health care. Understanding it is crucial, as it is the main determining factor in the utilization of health care resources, and provides promising insights into the phenomenon of ED usage increase. For reforms to be successful, the process of decision-making for unscheduled patients will have to be thoroughly investigated.

Description: Background: Mode of delivery has been reported to affect the cord blood glucose level of newborns. Vaginally delivered (VD) newborns were found to have relatively increased concentration of cord blood glucose than those delivered by cesarean section (CS). The aim of this study is thus to determine whether the difference in cord blood glucose concentration among VD and CS newborns is necessitating partitioned reference intervals (RIs) for the laboratory diagnosis of neonatal hypoglycemia. Methods: A total of 60 newborns were included from Tikur Anbessa Specialized Hospital (TASH). Cord blood samples were collected and analyzed for glucose by Glucose-oxidase (GOD-PAP) method in TASH laboratory using HumaStar 300 from November 2010 to April 2011. All pre-analytical, analytical and post-analytical aspects were thoroughly controlled. A robust method was used for the determination of reference intervals using MedCalc(R) software Version 11.6.1. Results: VD newborns accounted for 71.7% (n = 43) while the CS newborns accounted for 28.3% (n = 17). No statistically significant difference was noted in the studied demographic variables among VD and CS newborns except for blood glucose level. The RIs were then determined to be 2.46-6.85 mmol/l and 2.46-5.04 mmol/l for VD and CS newborns respectively. The combined RI was 2.24-6.48 mmol/l. Conclusion: Combined RI better be used for the interpretation of cord blood glucose values in VD and CS newborns. Cord blood glucose concentrations of 2.24 mmol/l can be used as statistical estimates of cut off points for neonatal hypoglycemia in newborns irrespective of their mode of deliveries.

Description: Background: Tuberculosis (TB) still remains one of the most deadly infectious diseases in the world. Mycobacterium tuberculosis beta-ketoacyl-ACP Reductase (MabA) is a member of the fatty acid elongation system type II, providing precursors of mycolic acids that are essential to the bacterial cell growth and survival. MabA has been shown to be essential for M. tuberculosis survival and to play a role in intracellular signal transduction of bacilli.FindingsHere we describe site-directed mutagenesis, recombinant protein expression and purification, steady-state kinetics, fluorescence spectroscopy, and molecular modeling for S140T and S140A mutant MabA enzymes. No enzyme activity could be detected for S140T and S140A. Although the S140T protein showed impaired NADPH binding, the S140A mutant could bind to NADPH. Computational predictions for NADPH binding affinity to WT, S140T and S140A MabA proteins were consistent with fluorescence spectroscopy data. Conclusions: The results suggest that the main role of the S140 side chain of MabA is in catalysis. The S140 side chain appears to also play an indirect role in NADPH binding. Interestingly, NADPH titrations curves shifted from sigmoidal for WT to hyperbolic for S140A, suggesting that the S140 residue may play a role in displacing the pre-existing equilibrium between two forms of MabA in solution. The results here reported provide a better understanding of the mode of action of MabA that should be useful to guide the rational (function-based) design of inhibitors of MabA enzyme activity which, hopefully, could be used as lead compounds with anti-TB action.

Description: Background: Coiled-coils are found in different proteins like transcription factors, myosin tail domain, tropomyosin, leucine zippers and kinesins. Analysis of various structures containing coiled-coils has revealed the importance of electrostatic and hydrophobic interactions. In such domains, regions of different strength of interactions need to be identified since they could be biologically relevant.FindingsWe have updated our coiled-coil validation webserver, now called COILCHECK+, where new features were added to efficiently identify the strength of interaction at the interface region and measure the density of charged residues and hydrophobic residues. We have examined charged residues and hydrophobic ladders, using a new algorithm called CHAHO, which is incorporated within COILCHECK + server. CHAHO permits the identification of spatial charged residue patches and the continuity of hydrophobic ladder which stabilizes and destabilizes the coiled-coil structure. Conclusions: The availability of such computational tools should be useful to understand the importance of spatial clustering of charged residues and the continuity of hydrophobic residues at the interface region of coiled-coil dimers. COILCHECK + is a structure based tool to validate coiled-coil stability; it can be accessed at http://caps.ncbs.res.in/coilcheckplus

Description: Background: Current research in network reverse engineering for genetic or metabolic networks very often does not include a proper experimental and/or input design. In this paper we address this issue in more detail and suggest a method that includes an iterative design of experiments based, on the most recent data that become available. The presented approach allows a reliable reconstruction of the network and addresses an important issue, i.e., the analysis and the propagation of uncertainties as they exist in both the data and in our own knowledge. These two types of uncertainties have their immediate ramifications for the uncertainties in the parameter estimates and, hence, are taken into account from the very beginning of our experimental design.FindingsThe method is demonstrated for two small networks that include a genetic network for mRNA synthesis and degradation and an oscillatory network describing a molecular network underlying adenosine 3'-5' cyclic monophosphate (cAMP) as observed in populations of Dyctyostelium cells. In both cases a substantial reduction in parameter uncertainty was observed. Extension to larger scale networks is possible but needs a more rigorous parameter estimation algorithm that includes sparsity as a constraint in the optimization procedure. Conclusion: We conclude that a careful experiment design very often (but not always) pays off in terms of reliability in the inferred network topology. For large scale networks a better parameter estimation algorithm is required that includes sparsity as an additional constraint. These algorithms are available in the literature and can also be used in an adaptive optimal design setting as demonstrated in this paper.

Description: Background: Despite evidence suggesting that the Liverpool Care Pathway for the Dying Patient is a structured and proficient means of supporting care delivery in the last hours or days of life, discrepancies in uptake are widespread. This exploratory study sought to understand why patients dying of cancer in oncology wards of one hospital trust were, or were not, supported by the LCP. A purposive qualitative case study design was used; each case represented a patient who had died and their most involved nurse and doctor. In-depth interviews explored both recollections of the 'case' and wider experiences of using the Pathway in end-of-life care. Eleven healthcare professionals were interviewed about their involvement in the end-of-life care of six patients. For four of these patients care was supported by the LCP.FindingsAlthough doctors and nurses reported they preferred to use the Pathway to ensure comfortable death, an important factor influencing their decisions was time of death. Access to timely senior review was regarded as an essential preliminary to placing patients on the Pathway but delayed access 'out of hours' was commonly experienced and tensions arose from balancing conflicting priorities. Consequently, the needs of dying patients sometimes failed to compete with those receiving curative treatment. Conclusions: This study suggests that greater attention should be focused on 'out of hours' care in hospitals to ensure regular senior review of all patients at risk of dying and to support front line staff to communicate effectively and make contingency plans focused on patients' best interests.

Description: Background: Urinary catheters are associated, commonly with bacteriuria and frequently with urinary tract infection. Tamm-Horsfall Protein (THP) is urine's most abundant protein and is known to bind to uropathogenic bacteria. The role of THP in the pathogenesis of catheter associated urinary tract infection (CAUTI) is not clear. We examined the role of THP in facilitating bacterial binding to urinary catheters in vivo and in vitro.FindingsTwenty one urinary catheters were obtained from 20 hospitalized patients. THP was eluted from the catheter surface and catheter segments were cultured. Additional studies were performed in vitro on unused silicone and latex catheters to determine the binding of THP, and the effect of THP on the binding of Escherichia coli (E. coli) and Pseudomonas aeruginosa (P. aeruginosa), to the catheter surface.On catheters obtained from patients, the THP deposition was significantly more on culture positive catheters than on culture negative catheters. In the in vitro studies, THP bound to both silicone and latex catheters, and THP enhanced the adherence of E. coli and P. aeruginosa to both types of catheters. Conclusion: THP binds to urinary catheters and facilitates the binding of uropathogenic bacteria to catheters.

Description: Background: Scar sarcoidosis is a rare and uncommon but specific cutaneous manifestation of sarcoidosis. In general it arises in pre-existing scars deriving from mechanical traumas. As most surgeons dealing with scars might not be aware of cutaneous sarcoidosis and its different types of appearance the appropriate staging and treatment might be missed or at least delayed. To our knowledge this is the first case in literature of scar sarcoidosis on a finger.Case presentationWe present a case of a 33-year-old carpenter who developed scar sarcoidosis on his right index finger 4 years after the tendon of the long digital flexor got accidentally cut by an angle grinder. He was referred due to a swelling of the finger suspected to be a malignant soft tissue tumour. The circumference of the affected finger had almost doubled, adding up to 94 mm. Incision biopsy revealed typical noncaseating granulomas. Further investigation showed a systemic extent of the disease with involvement of the lung. A systemic treatment with oral steroids led to an almost full regression of the swelling with restoration of function and resolution of lung infiltrates. Conclusion: In case of a suspicious and/or progressive swelling a definite diagnosis should be achieved by biopsy within a short time to enable a proper treatment. If scar sarcoidosis is proven further investigation is necessary to exclude a systemical involvement. A surgical treatment of the swelling is not indicated.

Description: Background: Plantar fibromatosis is a benign disease creating nodules on the medial plantar side of affected patients. While surgical removal is regarded as the therapeutic mainstay, recurrence rates and impairment of daily activities remains substantial. High-energy focussed extracorporeal shockwave therapy has been suggested to be potentially effective in plantar fibromatosis in terms of pain reduction.HypothesisHigh-energy focussed extracorporeal shockwave therapy reduces pain in plantar fibromatosis.FindingsA total number of six patients (5 males, 58+/-4 years) were included with plantar fibromatosis (Ledderhose's disease) associated with pain. Three patients were operated on previously, one had concomitant Dupuytren's contracture. High-energy focussed ESWT was applied using a Storz Duolith SD1 (2000 impulses, 3 Hz, 1.24mJ/mm2) in two sessions with 7 days between. Pain was 6+/-2 at baseline, 2+/-1 after 14 days and 1+/-1 after 3 months. Softening of the nodules was noted by all patients. No adverse effects were noted. Conclusions: High-energy focussed extracorporeal shockwave energy reduces pain in painful plantar fibromatosis (Morbus Ledderhose). Further large-scale prospective trials are warranted to elucidate the value of high-energy focussed extracorporeal shockwave therapy (ESWT) in plantar fibromatosis in terms of recurrence and efficacy.

Description: Background: The Ay allele at the agouti locus causes obesity and promotes linear growth in mice. The effect of the Ay allele on obesity has been extensively investigated, whereas its effect on body length is only poorly analyzed. To gain insight into the genetic control of body length, quantitative trait locus (QTL) analysis was performed in F2 female mice produced by crossing C57BL/6 J females and DDD.Cg-Ay males. A congenic DDD.Cg-Ay strain was established by introgressing the Ay allele from the B6.Cg-Ay strain by backcrossing for 12 generations. DDD.Cg-Ay females were longer than B6.Cg-Ay females; therefore, QTLs that interact with the Ay allele may be identified for body length. In addition, QTL analysis was also performed for plasma insulin-like growth factor 1 (IGF1) levels because IGF1 is known to play essential roles in growth and development. If QTLs for IGF1 levels coincide with those for body length, we can gain endocrinological insight into the QTLs for body length. Results: Correlations between body length and IGF1 levels were statistically significant in F2 populations. For body length, two significant QTLs were identified on chromosomes 15 and 17. For IGF1 levels, three significant QTLs were identified on chromosomes 10, 12, and 19. QTLs on chromosomes 12 and 19 appeared to be novel, and the latter interacted with the Ay allele. Conclusion: QTLs for body length and IGF1 levels contained candidate genes that were components of the growth hormone/insulin-like growth factor axis. However, there was no overlap between QTLs for these two traits. Contrary to our expectations, QTLs that interacted with the Ay allele were identified not for body length but for IGF1 levels. Body length and IGF1 levels were, thus, controlled by different sets of genes.

Description: Background: Dislocation remains a difficult problem in total hip arthroplasty. Large-diameter femoral heads may lower the incidence of dislocation by enhancing the jump distance and decreasing impingement, but their performance against small-diameter heads has not been assessed. This study compared the mid-term radiographic and functional outcomes of two matched cohorts of patients undergoing total hip arthroplasty who had a high pre-operative risk for dislocation and who received either small-diameter (26- or 28-millimeters) or large-diameter (〉=36-millimeters) femoral heads. Methods: All patients who received large-diameter heads (〉=36-millimeter) between 2002 and 2005, and who had pre-operative risk factors for dislocation, were identified in the institution's joint registry. Forty-one patients (52 hips) who received large-diameter heads were identified, and these patients were matched to 48 patients (52 hips) in the registry who received small-diameter femoral heads. Results: At mean final follow-up of 62 months (range, 49 to 101 months), both groups achieved excellent functional outcomes as measured by Harris Hip scores, with slightly better final scores in the large-diameter group (90 vs. 83 points). No patient showed any radiographic signs of loosening. No patient dislocated in the large-diameter femoral head group; the smaller-diameter group had a greater rate of dislocation (3.8%, 2 out of 52). Conclusions: Large-diameter femoral head articulations may reduce dislocation rates in patients who have a high pre-operative risk for dislocation while providing the same functional improvements and safety as small-diameter bearings.

Description: Background: Primary myelofibrosis is a myeloproliferative disorder characterized by bone marrow fibrosis, abnormal cytokine expression, splenomegaly and anemia. The activation of JAK2 and the increased levels of circulating proinflammatory cytokines seem to play an important role in the pathogenesis of myelofibrosis. Novel therapeutic agents targeting JAKs have been developed for the treatment of myeloproliferative disorders. Ruxolitinib (INCB018424) is the most recent among them.Case presentationTo our knowledge, there is no evidence from clinical trials of an increased risk of tuberculosis during treatment with JAK inhibitors. Here we describe the first case of tuberculosis in a patient treated with Ruxolitinib, a male with a 12-year history of chronic idiopathic myelofibrosis admitted to our Institute because of fever, night sweats, weight loss and an enlarging mass in the left inguinal area for two months. Conclusion: Treatment with Ruxolitinib may have triggered the reactivation of latent tuberculosis because of an inhibition of Th1 response. Our case highlights the importance of an accurate screening for latent tuberculosis before starting an anti-JAK 2 treatment.

Description: Background: Although laparoscopy is rapidly becoming the abdominal surgical modality of choice in adults, there are obstacles to its use in children. We analyzed our experience with pediatric laparoscopic surgery over the past 5 years, with particular emphasis on emergency procedures.FindingsWe retrospectively evaluated the records of patients aged

Description: Background: New computational resources are needed to manage the increasing volume of biological data from genome sequencing projects. One fundamental challenge is the ability to maintain a complete and current catalog of protein diversity. We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences. Results: We implemented fully automated and high-throughput procedures to de novo cluster proteins into families based upon global alignment similarity. Our approach employs an iterative clustering strategy in which homologs of known families are sifted out of the search for new families. The resulting reduction in computational complexity enables us to rapidly identify novel protein families found in new genomes and to perform efficient, automated updates that keep pace with genome sequencing. We refer to protein families identified through this approach as "Sifting Families," or SFams. Our analysis of ~10.5 million protein sequences from 2,928 genomes identified 436,360 SFams, many of which are not represented in other protein family databases. We validated the quality of SFam clustering through statistical as well as network topology--based analyses. Conclusions: We describe the rapid identification of SFams and demonstrate how they can be used to annotate genomes and metagenomes. The SFam database catalogs protein-family quality metrics, multiple sequence alignments, hidden Markov models, and phylogenetic trees. Our source code and database are publicly available and will be subject to frequent updates (http://edhar.genomecenter.ucdavis.edu/sifting_families/).

Description: Background: Interest in cellulose degrading enzymes has increased in recent years due to the expansion of the cellulosic biofuel industry. The rumen is a highly adapted environment for the degradation of cellulose and a promising source of enzymes for industrial use. To identify cellulase enzymes that may be of such use we have undertaken a functional metagenomic screen to identify cellulase enzymes from the bacterial community in the rumen of a grass-hay fed dairy cow. Results: Twenty five clones specifying cellulose activity were identified. Subcloning and sequence analysis of a subset of these hydrolase-positive clones identified 10 endoglucanase genes. Preliminary characterization of the encoded cellulases was carried out using crude extracts of each of the subclones. Zymogram analysis using carboxymethylcellulose as a substrate showed a single positive band for each subclone, confirming that only one functional cellulase gene was present in each. One cellulase gene, designated Cel14b22, was expressed at a high level in Escherichia coli and purified for further characterization. The purified recombinant enzyme showed optimal activity at pH 6.0 and 50 [degree sign]C. It was stable over a broad pH range, from pH 4.0 to 10.0. The activity was significantly enhanced by Mn2+ and dramatically reduced by Fe3+ or Cu2+. The enzyme hydrolyzed a wide range of beta-1,3-, and beta-1,4-linked polysaccharides, with varying activities. Activities toward microcrystalline cellulose and filter paper were relatively high, while the highest activity was toward Oat Gum. Conclusion: The present study shows that a functional metagenomic approach can be used to isolate previously uncharacterized cellulases from the rumen environment.

Description: Background: Y-Short Tandem Repeats (Y-STR) data consist of many similar and almost similar objects. This characteristic of Y-STR data causes two problems with partitioning: non-unique centroids and local minima problems. As a result, the existing partitioning algorithms produce poor clustering results. Results: Our new algorithm, called k-Approximate Modal Haplotypes (k-AMH), obtains the highest clustering accuracy scores for five out of six datasets, and produces an equal performance for the remaining dataset. Furthermore, clustering accuracy scores of 100% are achieved for two of the datasets. The k-AMH algorithm records the highest mean accuracy score of 0.93 overall, compared to that of other algorithms: k-Population (0.91), k-Modes-RVF (0.81), New Fuzzy k-Modes (0.80), k-Modes (0.76), k-Modes-Hybrid 1 (0.76), k-Modes-Hybrid 2 (0.75), Fuzzy k-Modes (0.74), and k-Modes-UAVM (0.70). Conclusions: The partitioning performance of the k-AMH algorithm for Y-STR data is superior to that of other algorithms, owing to its ability to solve the non-unique centroids and local minima problems. Our algorithm is also efficient in terms of time complexity, which is recorded as O(km(n-k)) and considered to be linear.

Description: Background: Chromosome conformation capture experiments result in pairwise proximity measurements between chromosome locations in a genome, and they have been used to construct three-dimensional models of genomic regions, chromosomes, and entire genomes. These models can be used to understand long-range gene regulation, chromosome rearrangements, and the relationships between sequence and spatial location. However, it is unclear whether these pairwise distance constraints provide sufficient information to embed chromatin in three dimensions. A priori, it is possible that an infinite number of embeddings are consistent with the measurements due to a lack of constraints between some regions. It is therefore necessary to separate regions of the chromatin structure that are sufficiently constrained from regions with measurements that do not provide enough information to reconstruct the embedding. Results: We present a new method based on graph rigidity to assess the suitability of experiments for constructingplausible three-dimensional models of chromatin structure. Underlying this analysis is a new, efficient, andaccurate algorithm for finding sufficiently constrained (rigid) collections of constraints in three dimensions, aproblem for which there is no known efficient algorithm. Applying the method to four recent chromosomeconformation experiments, we find that, for even stringently filtered constraints, a large rigid component spansmost of the measured region. Filtering highlights higher-confidence regions, and we find that the organizationof these regions depends crucially on short-range interactions. Conclusions: Without performing an embedding or creating a frequency-to-distance mapping, our proposed approachestablishes which substructures are supported by a sufficient framework of interactions. It also establishes thatinteractions from recent highly filtered genome-wide chromosome conformation experiments provide anadequate set of constraints for embedding. Pre-processing experimentally observed interactions with thismethod before relating chromatin structure to biological phenomena will ensure that hypothesized correlationsare not driven by the arbitrary choice of a particular unconstrained embedding. The software for identifyingrigid components is GPL-Licensed and available for download at http://cbcb.umd.edu/kingsford-group/starfish.

Description: Background: Experimental determination of protein 3D structures is expensive, time consuming and sometimes impossible. A gap between number of protein structures deposited in the World Wide Protein Data Bank and the number of sequenced proteins constantly broadens. Computational modeling is deemed to be one of the ways to deal with the problem. Although protein 3D structure prediction is a difficult task, many tools are available. These tools can model it from a sequence or partial structural information, e.g. contact maps. Consequently, biologists have the ability to generate automatically a putative 3D structure model of any protein. However, the main issue becomes evaluation of the model quality, which is one of the most important challenges of structural biology. Results: GOBA - Gene Ontology-Based Assessment is a novel Protein Model Quality Assessment Program. It estimates the compatibility between a model-structure and its expected function. GOBA is based on the assumption that a high quality model is expected to be structurally similar to proteins functionally similar to the prediction target. Whereas DALI is used to measure structure similarity, protein functional similarity is quantified using standardized and hierarchical description of proteins provided by Gene Ontology combined with Wang's algorithm for calculating semantic similarity. Two approaches are proposed to express the quality of protein model-structures. One is a single model quality assessment method, the other is its modification, which provides a relative measure of model quality. Exhaustive evaluation is performed on data sets of model-structures submitted to the CASP8 and CASP9 contests. Conclusions: The validation shows that the method is able to discriminate between good and bad model-structures. The best of tested GOBA scores achieved 0.74 and 0.8 as a mean Pearson correlation to the observed quality of models in our CASP8 and CASP9-based validation sets. GOBA also obtained the best result for two targets of CASP8, and one of CASP9, compared to the contest participants. Consequently, GOBA offers a novel single model quality assessment program that addresses the practical needs of biologists. In conjunction with other Model Quality Assessment Programs (MQAPs), it would prove useful for the evaluation of single protein models.

Description: Background: The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. A simple application programming interface (API) in a scripting language aimed at the biologist was however not yet available. Here, we present the Ruby UCSC API, a library to access the UCSC genome database using Ruby. Results: The API is designed as a BioRuby plug-in and built on the ActiveRecord 3 framework for the object-relational mapping, making writing SQL statements unnecessary. The current version of the API supports databases of all organisms in the UCSC genome database including human, mammals, vertebrates, deuterostomes, insects, nematodes, and yeast.The API uses the bin index---if available---when querying for genomic intervals. The API also supports genomic sequence queries using locally downloaded *.2bit files that are not stored in the official MySQL database. The API is implemented in pure Ruby and is therefore available in different environments and with different Ruby interpreters (including JRuby). Conclusions: Assisted by the straightforward object-oriented design of Ruby and ActiveRecord, the Ruby UCSC API will facilitate biologists to query the UCSC genome database programmatically. The API is available through the RubyGem system. Source code and documentation are available at https://github.com/misshie/bioruby-ucsc-api/ under the Ruby license. Feedback and help is provided via the website at http://rubyucscapi.userecho.com/.

Description: Background: Ulcerative colitis (UC) is uncommon in the tropics and sub-tropics. We report a case of UC in a 7 year old girl whose parents were both Nigerians. This report is to alert healthcare professionals in sub-Saharan Africa that UC is not a rare health problem, especially in children.Case presentationThe patient presented with frequent passage of blood stained stool, abdominal pain and significant weight loss. The diagnosis was entertained after she was investigated for common causes of chronic diarrhea in our setting and the findings were negative. The patient symptoms abated after she was commenced on steroid therapy. Conclusion: Under-diagnosis and misdiagnosis may account for a dearth of information on UC in African children.

Description: Background: Infections due to nontyphoidal Salmonella have increased worldwide over the last couple of decades. Salmonella enterica serotype Blockley (Salmonella Blockley) infections is associated with chickens and is a rarely isolated serotype in human infections in most countries.Case presentationWe report a case of human infections due to Salmonella Blockley in KwaZulu-Natal, South Africa in 2011. Three African males (aged 4, 14 and 16) presented to a clinic with diarrhoea, stomach cramps and headache. They started experiencing signs of illness a day after they consumed a common meal, consisting of meat, rice and potatoes. Stool specimens from the patients cultured Salmonella Blockley. The strains showed an indistinguishable pulsed-field gel electrophoresis pattern. Conclusion: This is the first recorded case of human infections due to Salmonella Blockley in South Africa.

Description: Background: To assess the efficacy, clinical outcomes, visual acuity (VA), incidence of adverse effects, and complications of peripheral iris fixation of 3-piece acrylic IOLs in eyes lacking capsular support. Thirteen patients who underwent implantation and peripheral iris fixation of a 3-piece foldable acrylic PC IOL for aphakia in the absence of capsular support were followed after surgery. Clinical outcomes and macular SD-OCT (Cirrus OCT; Carl Zeiss Meditec, Germany) were analyzed.FindingsThe final CDVA was 20/40 or better in 8 eyes (62%), 20/60 or better in 12 eyes (92%), and one case of 20/80 due to corneal astigmatism and mild persistent edema. No intraoperative complications were reported. There were seven cases of medically controlled ocular hypertension after surgery due to the presence of viscoelastic in the AC. There were no cases of cystoid macular edema, chronic iridocyclitis, IOL subluxation, pigment dispersion, or glaucoma. Macular edema did not develop in any case by means of SD-OCT. Conclusions: We think that this technique for iris suture fixation provides safe and effective results. Patients had substantial improvements in UDVA and CDVA. This surgical strategy may be individualized however; age, cornea status, angle structures, iris anatomy, and glaucoma are important considerations in selecting candidates for an appropriate IOL fixation method.

Description: Background: With today's rapid advances in technology and understanding of disease, more screening and diagnostic tests have become available in a variety of sociodemographic and clinical settings. This analysis quantifies the impact of varying prevalence rates on test performance for given sensitivity and specificity values. Methods: Using a worked example of latent tuberculosis infection, we compared true-positive (TP) and false-positive (FP) results when varying prevalence and test sensitivity and specificity. We used estimates from published literature to estimate two tests' sensitivity (81%, QuantiFERON(R)-TB Gold In-Tube; 88%, T-SPOT(R).TB) and specificity (99%; 88%), and we used World Health Organization data to estimate disease prevalence in five countries. Results: Varying sensitivity impacted outcomes most in high-prevalence settings; change in specificity had greater impact in low-prevalence settings. In switching from QuantiFERON-TB to T-SPOT.TB (higher sensitivity, lower specificity), trade-offs between increasing case identification (TPs) and decreasing unnecessary treatments (FPs) varied dramatically with prevalence. Lower-prevalence settings paid a greater "price" of more FPs for each TP gained, with 37.7 FPs per TP in the United States (5% prevalence) versus 2.5 in the Ivory Coast (55% prevalence). Conclusions: Prevalence affects test performance for given sensitivity and specificity values. To optimize test performance, disease prevalence should be incorporated in testing decisions, and sensitivity and specificity should be set locally not globally. In lower-prevalence settings, using highly specific assays may optimize outcomes.

Description: Background: In 2006, the Dutch government initiated Hello World, an email-based program promoting healthy lifestyles among pregnant women through quizzes with pregnancy-related questions. In 2008, an updated version was released.The present study aimed to (1) examine the reach of Hello World and the representativeness of its users for all pregnant women in the Netherlands, (2) explore the relationship between program engagement and lifestyle characteristics, and (3) explore the relationship between the program content participants accessed (content on smoking, physical activity, and nutrition) and their lifestyle characteristics. Methods: Data from 4,363 pregnant women were included. After registration, women received an online questionnaire with demographic and lifestyle questions. To evaluate their representativeness, their demographic characteristics were compared with existing data for Dutch (pregnant) women. Women were classified on the following lifestyle characteristics: smoking, nutrition, physical activity, and pre-pregnancy weight status. Program use was tracked and the relationships between lifestyle characteristics, program engagement, and the percentage of smoking, physical activity, and nutrition questions accessed after opening a quiz were explored using Mann--Whitney U tests and Kruskal-Wallis tests. Results: Hello World reached +/-4% of its target population. Ten percent of participants were low educated and 22% immigrants. On average, women received 6.1 (SD:2.8) quiz emails and opened 32% of the associated quizzes (2.0, SD:2.1). A significant positive association was found between the number of quizzes opened and the number of healthy lifestyle characteristics. After opening a quiz, women accessed most smoking, nutrition, and physical activity questions. Significant relationships were found between several lifestyle characteristics and the percentage of smoking, physical activity, and nutrition questions accessed. However, between-group differences were small, quiz topics were largely unrelated to their lifestyle characteristics, and inconsistencies were found regarding the directions of these associations. Conclusions: Hello World reached +/-4% of its target population, which is lower than the reach of its previous version (+/-8%). Relatively few low educated and immigrant women registered for the program. Active participation in the program was positively associated with the number of healthy behaviours participants engaged in. The program content participants chose to access was largely unrelated to their lifestyle characteristics.

Description: Background: Double chambered right ventricle (DCRV) is a relatively rare congenital heart disease, characterized by the abnormal division of the right ventricle into a high-pressure inlet and low-pressure outlet by anomalous muscle bundles. Extra-cardiac right-to-left shunts may present with clinical symptoms in adulthood and should be sought in patients with previous cavo-pulmonary shunt procedures.Case presentationWe report a case of DCRV in a 29 year old Caucasian male presenting in adulthood with a right-to-left shunt secondary to venous collaterals, following cavopulmonary anastomosis for congenital pulmonary atresia and hypoplastic right ventricle. Conclusion: Multimodality cardiac imaging using echocardiography, cardiac CT, cardiac MRI and cardiac catheterization is often required for complete characterization of complex congenital heart anomalies in adulthood.

Description: Background: Sporadic Amyotrophic Lateral Sclerosis (sALS) is a devastating, complex disease of unknown etiology. We studied this disease with microarray technology to capture as much biological complexity as possible. The Affymetrix-focused BaFL pipeline takes into account problems with probes that arise from physical and biological properties, so we adapted it to handle the long-oligonucleotide probes on our arrays (hence LO-BaFL). The revised method was tested against a validated array experiment and then used in a meta-analysis of peripheral white blood cells from healthy control samples in two experiments. We predicted differentially expressed (DE) genes in our sALS data, combining the results obtained using the TM4 suite of tools with those from the LO-BaFL method. Those predictions were tested using qRT-PCR assays. Results: LO-BaFL filtering and DE testing accurately predicted previously validated DE genes in a published experiment on coronary artery disease (CAD). Filtering healthy control data from the sALS and CAD studies with LO-BaFL resulted in highly correlated expression levels across many genes. After bioinformatics analysis, twelve genes from the sALS DE gene list were selected for independent testing using qRT-PCR assays. High-quality RNA from six healthy Control and six sALS samples yielded the predicted differential expression for 7 genes: TARDBP, SKIV2L2, C12orf35, DYNLT1, ACTG1, B2M, and ILKAP. Four of the seven have been previously described in sALS studies, while ACTG1, B2M and ILKAP appear in the context of this disease for the first time. Supplementary material can be accessed at: http://webpages.uncc.edu/~cbaciu/LO-BaFL/supplementary_data.html Conclusion: LO-BaFL predicts DE results that are broadly similar to those of other methods. The small healthy control cohort in the sALS study is a reasonable foundation for predicting DE genes. Modifying the BaFL pipeline allowed us to remove noise and systematic errors, improving the power of this study, which had a small sample size. Each bioinformatics approach revealed DE genes not predicted by the other; subsequent PCR assays confirmed seven of twelve candidates, a relatively high success rate.

Description: Background: Theoretical models suggest that DNA degradation would sharply limit the PCR-based detection of both eukaryotic and prokaryotic DNA within ancient specimens. However, the relative extent of decay of eukaryote and prokaryote DNA over time is a matter of debate. In this study, the murine macrophage cell line J774, alone or infected with Mycobacterium smegmatis bacteria, were killed after exposure to 90[degree sign]C dry heat for intervals ranging from 1 to 48 h in order to compare eukaryotic cells, extracellular bacteria and intracellular bacteria. The sizes of the resulting mycobacterial rpoB and murine rpb2 homologous gene fragments were then determined by real-time PCR and fluorescent probing.FindingsThe cycle threshold (Ct) values of PCR-amplified DNA fragments from J774 cells and the M. smegmatis negative controls (without heat exposure) varied from 26--33 for the J774 rpb2 gene fragments and from 24--29 for M. smegmatis rpoB fragments. After 90[degree sign]C dry heat incubation for up to 48 h, the Ct values of test samples increased relative to those of the controls for each amplicon size. For each dry heat exposure time, the Ct values of the 146-149-bp fragments were lower than those of 746-747-bp fragments. During the 4- to 24-h dry heat incubation, the non-infected J774 cell DNA was degraded into 597-bp rpb2 fragments. After 48 h, however, only 450-bp rpb2 fragments of both non-infected and infected J774 cells could be amplified. In contrast, the 746-bp rpoB fragments of M. smegmatis DNA could be amplified after the 48-h dry heat exposure in all experiments. Infected and non-infected J774 cell DNA was degraded more rapidly than M. smegmatis DNA after dry heat exposure (ANOVA test, p 〈 0.05). Conclusion: In this study, mycobacterial DNA was more resistant to dry-heat stress than eukaryotic DNA. Therefore, the detection of large, experimental, ancient mycobacterial DNA fragments is a suitable approach for paleomicrobiological studies.

Description: Background: With the advent of next-generation sequencing (NGS) technologies, full cDNA shotgun sequencing has become a major approach in the study of transcriptomes, and several different protocols in 454 sequencing have been invented. As each protocol uses its own short DNA tags or adapters attached to the ends of cDNA fragments for labeling or sequencing, different contaminants may lead to mis-assembly and inaccurate sequence products. Results: We have designed and implemented a new program for raw sequence cleaning in a graphical user interface and a batch script. The cleaning process consists of several modules including barcode trimming, sequencing adapter trimming, amplification primer trimming, poly-A tail trimming, vector screening and low quality region trimming. These modules can be combined based on various sequencing applications. Conclusions: ESTclean is a software package not only for cleaning cDNA sequences, but also for helping to develop sequencing protocols by providing summary tables and figures for sequencing quality control in a graphical user interface. It outperforms in cleaning read sequences from complicated sequencing protocols which use barcodes and multiple amplification primers.

Description: Background: While the genetics of diploid inheritance are well studied and software for linkage mapping, haplotyping and QTL analysis are available, for tetraploids the available tools are limited. In order to develop such tools it would be helpful if simulated populations based on a variety of models of the tetraploid meiosis would be available. Results: Here we present PedigreeSim, a software package that simulates meiosis in both diploid and tetraploid species and uses this to simulate pedigrees and cross populations. For tetraploids a variety of models can be used, including both bivalent and quadrivalent formation, varying degrees of preferential pairing of hom(oe)ologous chromosomes, different quadrivalent configurations and more. Simulation of quadrivalent meiosis results as expected in double reduction and recombination between more than two hom(oe)ologous chromosomes. The results are shown to match theoretical predictions. Conclusions: This is the first simulation software that implements all features of meiosis in tetraploids. It allows to generate data for tetraploid and diploid populations, and to investigate different models of tetraploid meiosis. The software and manual are available from http://www.plantbreeding.wur.nl/UK/software_pedigreeSim.html and as Additional files 1, 2, 3 and 4 with this publication.

Description: Background: A higher prevalence of coeliac disease has recently been reported among patients with HCV-related chronic hepatitis. Moreover, development of clinically overt coeliac disease has been described in a number of HCV-related chronic hepatitis patients during alpha-interferon therapy. This prospective study was designed to evaluate 1) the prevalence of coeliac disease in patients with HCV-related chronic hepatitis; 2) the prevalence of HCV infection in patients with coeliac disease; 3) whether PEG interferon-alpha treatment might favour the development of coeliac disease in patients with chronic hepatitis C.Materials and methodsTwo hundred-ten consecutive patients (M/F = 140/70, range of age 35--58 years, median age 46.5 years) with biopsy proven chronic hepatitis C underwent serological screening for antiendomysial and tissue transglutaminase IgA antibodies. One hundred ninety-four coeliac patients (M/F = 52/142, range of age 18--74 years, median age 34 years) were screened for HCV antibodies. Positivity for HCV antibodies in coeliac disease patients was confirmed by detection of serum HCV-RNA by RT-PCR. This work was carried out in accordance to ethical guidelines of Declaration of Helsinki and was approved by Institutional Ethics Committee of the Second University of Naples. All patients gave informed written consent. Results: 1) none of the 210 HCV-related chronic hepatitis patients were positive for coeliac disease serologic screening; 2) prevalence of HCV infection among coeliac patients was 1.54% (3/194) which is comparable to that reported in the Southern Italy population; 3) PEG interferon-alpha treatment was not associated with development of coeliac disease either clinical or serological. Conclusions: 1) coeliac disease is not associated with HCV infection; 2) PEG interferon-alpha does not trigger celiac disease.

Description: Background: Among the working population, unemployed and temporary agency workers with psychological problems are a particularly vulnerable group, at risk for sickness absence and prolonged work disability. There is a need for the development of a new protocol for this group, because the existing return to work (RTW) interventions, including practice guidelines, do not address the situation when there is no workplace to return to. The purpose of this study was to [1] describe the adaptations needed in the practice guideline for employed workers to enable its use by insurance physicians (IPs) for counselling of sick-listed unemployed and temporary agency workers with minor psychological problems; and [2] evaluate the experiences of IPs when using the new guidance document for minor psychological problems (MPP guidance document). Methods: The MPP guidance document for unemployed and temporary agency workers was developed through discussions with nine IPs and with the help of an expert. Semi-structured interviews with five IPs were then held to evaluate the IPs' field experience using the MPP guidance document, in terms of (a) feasibility and (b) perceived usefulness of the MPP guidance document. Results: The main adaptation introduced in the guideline is that interaction with the workplace, which is absent in this population, needed to be established in an alternative way, i.e., through the involvement of vocational rehabilitation agencies and labour experts. Overall, the guideline required minimal changes. In total, nineteen sick-listed workers were counselled using the MPP guidance document. The overall experience of the IPs was that the MPP guidance document was feasible and useful for the IP, while they had mixed responses on its usefulness for the sick-listed worker, in part due to the follow-up period of this study. Conclusions: An existing practice guideline for employed workers was adapted for use as a guidance document for unemployed and temporary agency workers with minor psychological problems. IPs were positive about applying the MPP guidance document. The guidance document provides opportunities for RTW counselling for unemployed and temporary agency workers with minor psychological problems.

Description: Background: Peripartum cardiomyopathy (PPCM) is a rare cardiac disorder characterized by the development of heart failure in the last month of pregnancy or up to 5 months postpartum in women without other identifiable causes of cardiac failure. The combination of left ventricular (LV) systolic dysfunction and hypercoaguability can cause thromboembolic complications including intra-cardiac thrombi.Case presentationA 25-year-old Caucasian female with PPCM demonstrated multiple thrombi in the LV on transthoracic echocardiography. Following anticoagulation with parenteral heparin, a cardiac MRI four days later demonstrated near resolution of the thrombi. Conclusion: We review the presentation, diagnosis and management of LV thrombi in the clinical setting of PPCM.

Description: Background: Metabolic and morphological changes associated with excessive abdominal fat, after the introduction of Antiretroviral Therapy, increase the risk of cardiovascular disease in people living with HIV/AIDS(PLWHA). Accurate methods for body composition analysis are expensive and the use of anthropometric indices is an alternative. However the investigations about this subject in PLWHA are rare, making this research very important for clinical purpose and to advance scientific knowledge. The aim of this study is to correlate results of anthropometric indices of evaluation of body fat distribution with the results obtained by Dual-energy X-Ray Absorptiometry(DEXA), in people living with HIV/AIDS. Methods: The sample was of 67 PLWHA(39 male and 28 female), aged 43.6+7.9 years. Body mass index, conicity index, waist/hip ratio, waist/height ratio and waist/thigh were calculated. Separated by sex, each index/ratio was plotted in a scatter chart with linear regression fit and their respective Pearson correlation coefficients. Analyses were performed using Prism statistical program and significance was set at 5%. Results: The waist/height ratio presented the highest correlation coefficient, for both male (r=0.80, p

Description: Background: Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement. Results: The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDB's) e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components. Conclusions: VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity.

Description: Background: We consider the problem of finding the maximum frequent agreement subtrees (MFASTs) in a collection ofphylogenetic trees. Existing methods for this problem often do not scale beyond datasets with around 100taxa. Our goal is to address this problem for datasets with over a thousand taxa and hundreds of trees. Results: We develop a heuristic solution that aims to find MFASTs in sets of many, large phylogenetic trees. Ourmethod works in multiple phases. In the first phase, it identifies small candidate subtrees from the set of inputtrees which serve as the seeds of larger subtrees. In the second phase, it combines these small seeds to buildlarger candidate MFASTs. In the final phase, it performs a post-processing step that ensures that we find afrequent agreement subtree that is not contained in a larger frequent agreement subtree. We demonstrate thatthis heuristic can easily handle data sets with 1000 taxa, greatly extending the estimation of MFASTs beyondcurrent methods. Conclusions: Although this heuristic does not guarantee to find all MFASTs or the largest MFAST, it found the MFAST inall of our synthetic datasets where we could verify the correctness of the result. It also performed well on largeempirical data sets. Its performance is robust to the number and size of the input trees. Overall, this methodprovides a simple and fast way to identify strongly supported subtrees within large phylogenetic hypotheses.

Description: Background: Currently, there is no open-source, cross-platform and scalable framework for coalescent analysis in population genetics. There is no scalable GUI based user application either. Such a framework and application would not only drive the creation of more complex and realistic models but also make them truly accessible. Results: As a first attempt, we built a framework and user application for the domain of exact calculations in coalescent analysis. The framework provides an API with the concepts of model, data, statistic, phylogeny, gene tree and recursion. Infinite-alleles and infinite-sites models are considered. It defines pluggable computations such as counting and listing all the ancestral configurations and genealogies and computing the exact probability of data. It can visualize a gene tree, trace and visualize the internals of the recursion algorithm for further improvement and attach dynamically a number of output processors. The user application defines jobs in a plug-in like manner so that they can be activated, deactivated, installed or uninstalled on demand. Multiple jobs can be run and their inputs edited. Job inputs are persisted across restarts and running jobs can be cancelled where applicable. Conclusions: Coalescent theory plays an increasingly important role in analysing molecular population genetic data. Models involved are mathematically difficult and computationally challenging. An open-source, scalable framework that lets users immediately take advantage of the progress made by others will enable exploration of yet more difficult and realistic models. As models become more complex and mathematically less tractable, the need for an integrated computational approach is obvious. Object oriented designs, though has upfront costs, are practical now and can provide such an integrated approach.

Description: Background: On-line provision of information during the transition phase after treatment carries great promise in meeting shortcomings in post-treatment care for breast cancer survivors and their partners. The objectives of this study are to describe the development and process evaluation of a tailored informative website and to assess which characteristics of survivors and partners, participating in the feasibility study, are related to visiting the website. Methods: The development process included quantitative and qualitative assessments of survivors' and partners' care needs and preferences. Participants' use and evaluation of the website were explored by conducting baseline and post-measurements. During the intervening 10--12 weeks 57 survivors and 28 partners were granted access to the website. Results: Fifty-seven percent (n=21) of survivors who took part in the post-measurement indicated that they had visited the website. Compared to non-visitors (n=16), they were more likely to have a partner and a higher income, reported higher levels of self-esteem and had completed treatment for a longer period of time. Partners who consulted the on-line information (42%, n=8) were younger and reported lower levels of social support compared to partners who did not visit the website (n=11). Visitors generally evaluated the content and lay-out positively, yet some believed the information was incomplete and impersonal. Conclusions: The website reached only about half of survivors and partners, yet was mostly well-received. Besides other ways of providing information and support, a website containing clear-cut and tailored information could be a useful tool in post-treatment care provision.

Description: Background: Hyphema is a complication that can occur after glaucoma filtering surgery. Biomicroscopic examination of the anterior segment is commonly used to diagnose it and gonioscopy may provide a useful support to find the source of the haemorrhage. Unfortunately, when the blood hides the structure of the anterior segment the gonioscopic examination fails. In this case we performed ultrabiomiscroscopy with 50--80 MHz probes to overcome the limits of gonioscopy. The use of this technique to study the anterior segment of the eye has previously been reported in literature, but we illustrates its importance for performing a correct diagnosis in a specific case of hyphema.Case presentationWe report a case of a sixty-year-old caucasian male with recurrent hyphema in the left eye. The episodes of hyphema were four in two years and the patient came to the hospital for the first time in the last occasion. The past episodes were managed with topical corticosteroids and mydriatic drops. He referred surgical trabeculectomy in both eyes 5 years before the first symptoms and no specific eye trauma before the first episode. The examination of the anterior segment revealed a 2 mm hyphema in the left eye due to blood leakage through the superior iridectomy. Gonioscopy could not identify the source of the haemorrhage. B-scan ultrasound and ultrabiomiscroscopy, with 50--80 MHz probes, were performed. Ultrabiomiscroscopy, mainly with the probe of 80 MHz, provided images of high resolution of the structures of the anterior segment and it allowed the visualization of an abnormal vessel at the inner margin of the trabeculectomy opening, probably responsible of the recurrent hyphema. Conclusion: Ultrabiomicroscopy proved to be a useful diagnostic technique for identifying the cause of the recurrent hyphema when other examination techniques are not applicable.

Description: Background: Clinical Bioinformatics is currently growing and is based on the integration of clinical and omics data aiming at the development of personalized medicine. Thus the introduction of novel technologies able to investigate the relationship among clinical states and biological machineries may help the development of this field. For instance the Affymetrix DMET platform (drug metabolism enzymes and transporters) is able to study the relationship among the variation of the genome of patients and drug metabolism, detecting SNPs (Single Nucleotide Polymorphism) ongenes related to drug metabolism. This may allow for instance to find genetic variants in patients which present different drug responses, in pharmacogenomics and clinical studies. Despite this, there is currently a lack in the development of open-source algorithms and tools for the analysis of DMET data. Existing software tools for DMET data generally allow only the preprocessing of binary data (e.g. the DMET-Console provided by Affymetrix) and simple data analysis operations, but do not allow to test the association of the presence of SNPs with the response to drugs. Results: We developed DMET-Analyzer a tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The proposed system allows: (i) to automatize the workflow of analysis of DMET-SNP data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaGKB, a major knowledge base for pharmacogenomic studies. DMET-Analyzer has a simple graphical user interface that allows users (doctors/biologists) to upload and analyse DMET files produced by Affymetrix DMET-Console in an interactive way. The effectiveness and easy use of DMET Analyzer is demonstrated through different case studies regarding the analysis of clinical datasets produced in the University Hospital of Catanzaro, Italy. Conclusion: DMET Analyzer is a novel tool able to automatically analyse data produced by the DMET-platform in case-control association studies. Using such tool user may avoid wasting time in the manual execution of multiple statistical tests avoiding possible errors and reducing the amount of time needed for a whole experiment. Moreover annotations and the direct link to external databases may increase the biological knowledge extracted. The system is freely available for academic purposes at: https://sourceforge.net/projects/dmetanalyzer/files/

Description: Background: Spatial gene expression quantification is required for modeling gene regulation in developing organisms. The fruit fly Drosophila melanogaster is the model system most widely applied for spatial gene expression analysis due to its unique embryonic properties: the shape does not change significantly during its early cleavage cycles and most genes are differentially expressed along a straight axis. This system of development is quite exceptional in the animal kingdom.In the sea anemone Nematostella vectensis the embryo changes its shape during early development; there are cell divisions and cell movement, like in most other metazoans. Nematostella is an attractive case study for spatial gene expression since its transparent body wall makes it accessible to various imaging techniques.FindingsOur new quantification method produces standardized gene expression profiles from raw or annotated Nematostella in situ hybridizations by measuring the expression intensity along its cell layer. The procedure is based on digital morphologies derived from high-resolution fluorescence pictures. Additionally, complete descriptions of nonsymmetric expression patterns have been constructed by transforming the gene expression images into a three-dimensional representation. Conclusions: We created a standard format for gene expression data, which enables quantitative analysis of in situ hybridizations from embryos with various shapes in different developmental stages. The obtained expression profiles are suitable as input for optimization of gene regulatory network models, and for correlation analysis of genes from dissimilar Nematostella morphologies. This approach is potentially applicable to many other metazoan model organisms and may also be suitable for processing data from three-dimensional imaging techniques.

Description: Background: Microsatellites, or simple sequence repeats (SSRs), are DNA sequences that include tandem copies of specific sequences no longer than six bases. SSRs are ubiquitous in all genomes and highly mutable.Presentation of the hypothesisResults from previous studies suggest that flanking regions of SSR are exhibit high stability in a wide range of organisms. We hypothesized that the SSRs ability to discard weak DNA polymerases could be responsible for this unusual stability. . When the weak polymerases are being decayed over SSRs, the flanking sequences would have higher opportunity to be replicated by more stable DNA polymerases. We present evidence of the molecular basis of our hypothesis.Testing the hypothesisThe hypothesis could be tested by examining the activity of DNA polymerase during and after a number of PCRs. The PCR reactions should be run with the same SSR locus possessing differences in the SSR length. The hypothesis could also be tested by comparing the mutational rate of a transferred gene between two transformations. The first one has a naked T-DNA (transferred DNA), while the second one has the same T-DNA flanked with two SSRs.Implications of the hypothesisIn any transformation experiment, flanking the T-DNA fragment with SSR sequences would result in more stably transferred genes. This process would decrease the unpredictable risks that may occur because of the mutational pressure on this foreign segment.

Description: Background: The Hedgehog Signaling Pathway is one of signaling pathways that are very important toembryonic development. The participation of inhibitors in the Hedgehog Signal Pathway cancontrol cell growth and death, and searching novel inhibitors to the functioning of thepathway are in a great demand. As the matter of fact, effective inhibitors could provideefficient therapies for a wide range of malignancies, and targeting such pathway in cellsrepresents a promising new paradigm for cell growth and death control. Current researchmainly focuses on the syntheses of the inhibitors of cyclopamine derivatives, which bindspecifically to the Smo protein, and can be used for cancer therapy. While quantitativelystructure-activity relationship (QSAR) studies have been performed for these compounds among different cell lines, none of them have achieved acceptable results in the prediction ofactivity values of new compounds. In this study, we proposed a novel collaborative QSARmodel for inhibitors of the Hedgehog Signaling Pathway by integration the information frommultiple cell lines. Such a model is expected to substantially improve the QSAR ability fromsingle cell lines, and provide useful clues in developing clinically effective inhibitors andmodifications of parent lead compounds for target on the Hedgehog Signaling Pathway. Results: In this study, we have presented: (1) a collaborative QSAR model, which is used to integrateinformation among multiple cell lines to boost the QSAR results, rather than only a singlecell line QSAR modeling. Our experiments have shown that the performance of our model issignificantly better than single cell line QSAR methods; and (2) an efficient feature selectionstrategy under such collaborative environment, which can derive the commonly importantfeatures related to the entire given cell lines, while simultaneously showing their specificcontributions to a specific cell-line. Based on feature selection results, we have proposedseveral possible chemical modifications to improve the inhibitor affinity towards multipletargets in the Hedgehog Signaling Pathway. Conclusions: Our model with the feature selection strategy presented here is efficient, robust, and flexible,and can be easily extended to model large-scale multiple cell line/QSAR data. The data andscripts for collaborative QSAR modeling are available in the Additional file 1.

Description: Background: Primary immunodeficiency (PID) is a cluster of serious disorders that requires special alertness on the part of the medical staff for prompt diagnosis and management of the patient. This study explored PID knowledge and experience among pediatricians of wide educational backgrounds, practicing in the United Arab Emirates (UAE).MethodA self-administered questionnaire was used to determine the competency of pediatricians in their knowledge of PID disorders. This study questionnaire included questions on PID signs and symptoms, syndromes associated with immunodeficiency, screening tests, interpreting laboratory tests and case management. The participants were 263 pediatricians of diverse education working in the 27 governmental hospitals in all regions of UAE. Results: The overall performance of the pediatricians did not differ based on their age, gender, origin of certification, rank, or years of experience. Of the 50 questions, 20% of pediatricians answered correctly 80% of the questions. Seventeen of the 19 PID signs and symptoms were identified by 55 to 97%. Four of 5 syndromes associated with immunodeficiency were identified by 50 to 90%. Appropriate screening tests were chosen by 64 to 96%. Attention to the laboratory reference range values as function of patient age was notably limited. Conclusions: There was a noteworthy deficiency in PID work-up. Therefore, implementing effective educational strategies is needed to improve the competency of pediatricians to diagnose and mange PID disorders

Description: Background: Refugees as "People Living in Highly Stressful Situation" are particularly vulnerable to mental ill-health as a result of the trauma experienced pre- and post-migration. The lack of information on the mental health disparities of refugees and non-refugees in West Africa is what this study aimed to bridge.A cross-sectional study design was employed using a cluster sampling technique. Interviewer-administered structured questionnaires consisting of the Mini-International Neuropsychiatric Interview (MINI), WHO quality of life (WHOQOL-BREF) and the Community Quality of Life (CQoL) were used for data collection. Data were analyzed with SPSS version 17. Logistic regression analysis was used to determine the predictors of mental health status and QoL. Results: Respondents consisted of 444(45.7%) refugees and 527(54.3%) non-refugees. Two-thirds 292 (66%) of the refugees were Liberians. Mean age: refugees - 34.8+/-12.8 years versus non-refugees - 33.3+/- 8.1 years (p

Description: Background: Phytohormones mediate plant defense responses to pests and pathogens. In particular, the hormones jasmonic acid, ethylene, salicylic acid, and abscisic acid have been shown to dictate and fine-tune defense responses, and identification of the phytohormone components of a particular defense response is commonly used to characterize it. Identification of phytohormone regulation is particularly important in transcriptome analyses. Currently there is no computational tool to determine the relative activity of these hormones that can be applied to transcriptome analyses in soybean.FindingsWe developed a pathway analysis method that provides a broad measure of the activation or suppression of individual phytohormone pathways based on changes in transcript expression of pathway-related genes. The magnitude and significance of these changes are used to determine a pathway score for a phytohormone for a given comparison in a microarray experiment. Scores for individual hormones can then be compared to determine the dominant phytohormone in a given defense response. To validate this method, it was applied to publicly available data from previous microarray experiments that studied the response of soybean plants to Asian soybean rust and soybean cyst nematode. The results of the analyses for these experiments agreed with our current understanding of the role of phytohormones in these defense responses. Conclusions: This method is useful in providing a broad measure of the relative induction and suppression of soybean phytohormones during a defense response. This method could be used as part of microarray studies that includes individual transcript analysis, gene set analysis, and other methods for a comprehensive defense response characterization.

Description: Background: Accurate gene structure annotation is a fundamental but somewhat elusive goal of genome projects, as witnessed by the fact that (model) genomes typically undergo several cycles of re-annotation.In many cases, it is not only different versions of annotations that need to be compared but also different sources of annotation of the same genome, derived from distinct gene prediction workflows.Such comparisons are of interest to annotation providers, prediction software developers, and end-users, who all need to assess what is common and what is different among distinct annotation sources.We developed ParsEval, a software application for pairwise comparison of sets of gene structure annotations.ParsEval calculates several statistics that highlight the similarities and differences between the two sets of annotations provided.These statistics are presented in an aggregate summary report, with additional details provided as individual reports specific to non-overlappinng, gene-model-centric genomic loci.Genome browser styled graphics embedded in these reports help visualize the genomic context of the annotations.Output from ParsEval is both easily read and parsed, enabling systematic identification of problematic gene models for subsequent focused analysis. Results: ParsEval is capable of analyzing annotations for large eukaryotic genomes on typical desktop or laptop hardware.In comparison to existing methods, ParsEval exhibits a considerable performance improvement, both in terms of runtime and memory consumption.Reports from ParsEval can provide relevant biological insights into the gene structure annotations being compared. Conclusions: Implemented in C, ParseEval provides the quickest and most feature-rich solution for genome annotation comparison to date.The source code is freely available (under an ISC license) at http://parseval.sourceforge.net/.

Description: Background: Respiratory disease can impose a significant burden on the health of rural populations. The Saskatchewan Rural Health Study (SRHS) is a new large prospective cohort study of ages 6 and over currently being conducted in farming and non-farming communities to evaluate potential health determinants associated with respiratory outcomes in rural populations. In this article, we describe the rationale and methodology for the adult component. Methods: The study is being conducted over 5 years (2009-15) in two phases, baseline and longitudinal. The baseline survey consists of two components, adults and children. The adult component consists of a questionnaire-based evaluation of individual and contextual factors of importance to respiratory health in two sub populations (a Farm Cohort and a Small Town Cohort) of rural families in Saskatchewan Rural Municipalities (RMs). Clinical studies of lung function and allergy tests are being conducted on selected sub-samples of the two cohorts based on the positive response to the last question on the baseline questionnaire: "Would you be willing to be contacted about having breathing and/or allergy tests at a nearby location?". We adopted existing population health theory to evaluate individual factors, contextual factors, and principal covariates on the outcomes of chronic bronchitis, chronic obstructive pulmonary disease, asthma and obstructive sleep apnea.FindingsOf the RMs selected to participate, 32 (89%) out of 36 RMs and 15 (94%) out of 16 small towns within the RMs agreed to participate. Using the mail out survey method developed by Dillman, we obtained completed questionnaires from 4264 households (8261 individuals). We obtained lung function measurements on 1609 adults, allergy skin test information on 1615 adults; both measurements were available on 1549 adults. We observed differences between farm and non-farm rural residents with respect to individual, contextual factors and covariates.DiscussionThere are differences between farm and non-farm rural residents with respect to individual and contextual factors and other variables of importance. The findings of the SRHS will improve knowledge of respiratory disease etiology, assist in the development and targeting of prevention programs, and in planning health services with farm and small town populations.

Description: Background: RNA-based gene duplicates (retrocopies) played pivotal roles in many physiological processes. Nowadays, functional retrocopies have been systematically identified in several mammals, fruit flies, plants, zebrafish and other chordates, etc. However, studies about this kind of duplication in Caenorhabditis nematodes have not been reported.FindingsWe identified 43, 48, 43, 9, and 42 retrocopies, of which 6, 15, 18, 3, and 13 formed chimeric genes in C. brenneri, C. briggsae, C. elegans, C. japonica, and C. remanei, respectively. At least 5 chimeric types exist in Caenorhabditis species, of which retrocopy recruiting both N and C terminus is the commonest one. Evidences from different analyses demonstrate many retrocopies and almost all chimeric genes may be functional in these species. About half of retrocopies in each species has coordinates in other species, and we suggest that retrocopies in closely related species may be helpful in identifying retrocopies for one certain species. Conclusions: A number of retrocopies and chimeric genes exist in Caenorhabditis genomes, and some of them may be functional. The evolutionary patterns of these genes may correlate with their genomic features, such as the activity of retroelements, the high rate of mutation and deletion rate, and a large proportion of genes subject to trans-splicing.

Description: Background: In overhead sports like volleyball, the onset of a rotator cuff tendinopathy due to functional overload is a common observation. An angiofibroblastic etiopathogenesis has been hypothesized, whereby a greater anaerobic metabolism occurs in critical zones of the tendon with a lower degree of vascularization; this would induce collagen and extracellular matrix degradation, that could then trigger a compensatory neovascularization response.We performed a clinical observational study of 80 elite volleyball players, monitoring the perfusion values of the rotator cuff tendons by oximetry. Results: No statistically significant differences were found between the oximetry data and age, sex or years of sports activity, nor when comparing the right and left arm or the dominant and non-dominant arm. A statistically significant difference was found for the dominant arm values in relation to the competitive role, higher values being obtained in outside hitters (62.7%) middle hitters (53.7%), opposite hitters (55.5%) and libero players (54.4%) (p 0.05). Conclusions: The different tendon vascularization values found in players with different roles in the team may be attributed to a response to the specific biomechanical demands posed by the different overhead throwing roles.

Description: Background: Sickle cell disease is a genetic abnormality involving the haemoglobin. Although, it is primarily a red cell disorders, the white blood cells and platelets are also affected by the mutation. The consequent haemoglobin S causes polymerization of haemoglobin resulting in haemolysis and anaemia. This study aims to provide baseline haematological values in sickle cell disease patients in steady state and compare the deviation from haemoglobin phenotype AA control values. Methods: A case-control study was conducted amongst homozygous sickle cell patients attending the sickle cell clinics of Lagos State University Teaching Hospital Ikeja and haemoglobin phenotype AA controls. About 4.5mls of blood sample was collected from each participant for full blood count analysis. All blood samples were screened for HIV and haemoglobin phenotypes confirmed using cellulose acetate haemoglobin electrophoresis at pH 8.6. Results: A total of 103 cases and 98 controls were enrolled. The overall mean haemoglobin concentration for cases was 7.93+/-1.47 g/dl, packed cell volume 24.44+/-4.68%, mean cell volume 81.52+/-7.89fl, and mean cell haemoglobin 26.50+/-3.20 pg. While for controls, mean haemoglobin concentration was 13.83+/-1.32g/dl, packed cell volume 43.07+/-3.95%, mean cell volume 86.90+/-4.69 fl, and mean cell haemoglobin 28.50+/-1.34pg. The overall mean white blood cell counts for the cases was 10.27+/-3.94 *103/mul and platelet counts of 412.71+/-145.09*103/mul. While white blood cell count for the controls was 5.67+/-1.59*103/mul and platelet counts of 222.82+/-57.62*103/mul. Conclusion: Homozygous sickle cell disease patients have lower values of red cell parameters, but higher values of white cell and platelets counts compared to haemoglobin phenotype AA controls.KeywordsHaematological values; homozygous sickle cell disease; steady state; haemoglobin phenotype AA.

Description: Background: The chemotherapeutic agent paclitaxel arrests cell division by binding to the hetero-dimeric protein tubulin. Subtle differences in tubulin sequences, across eukaryotes and among beta-tubulin isotypes, can have profound impact on paclitaxel-tubulin binding. To capture the experimentally observed paclitaxel-resistance of human betaIII tubulin isotype and yeast beta-tubulin, within a common theoretical framework, we have performed structural principal component analyses of beta-tubulin sequences across eukaryotes. Results: The paclitaxel-resistance of human betaIII tubulin isotype and yeast beta-tubulin uniquely mapped on to the lowest two principal components, defining the paclitaxel-binding site residues of beta-tubulin. The molecular mechanisms behind paclitaxel-resistance, mediated through key residues, were identified from structural consequences of characteristic mutations that confer paclitaxel-resistance. Specifically, Ala277 in betaIII isotype was shown to be crucial for paclitaxel-resistance. Conclusions: The present analysis captures the origin of two apparently unrelated events, paclitaxel-insensitivity of yeast tubulin and human betaIII tubulin isotype, through two common collective sequence vectors.

Description: Background: Brief family intervention may have a positive impact on family caregivers to patients with mental disorders. We aimed to assess the effectiveness of a group psycho-educational program on family caregivers to patients with schizophrenia and mood disorders.MethodThis randomized controlled trial was performed on 100 caregivers to patients with mental disorders attending Isfahan Behavioral Sciences Research Center, Isfahan, Iran. 100 family caregivers of patients with schizophrenia (n=50) and mood disorders (n=50) were selected and assigned randomly to either a psycho-educational group intervention or routine care in each diagnosis category. The caregivers were followed up for a period of 3 months. Caregiver burden was assessed using the Zarit Burden Interview. Results: The burden decreased significantly in the group that participated in the psycho-educational program. The mean scores of the Zarit caregiver burden scale decreased, while scores in the control group did not change significantly. Conclusion: This group intervention program was effective for the Iranian studied population to reduce the caregiver burden in both categories of mental disorder. It may potentially improve the quality of life of both patients and caregivers by improving the standards of care giving.

Description: Background: Web-based synteny visualization tools are important for sharing data and revealing patterns of complicated genome conservation and rearrangements. Such tools should allow biologists to upload genomic data for their own analysis. This requirement is critical because individual biologists are generating large amounts of genomic sequences that quickly overwhelm any centralized web resources to collect and display all those data. Recently, we published a web-based synteny viewer, GSV, which was designed to satisfy the above requirement. However, GSV can only compare two genomes at a given time. Extending the functionality of GSV to visualize multiple genomes is important to meet the increasing demand of the research community. Results: We have developed a multi-Genome Synteny Viewer (mGSV). Similar to GSV, mGSV is a web-based tool that allows users to upload their own genomic data files for visualization. Multiple genomes can be presented in a single integrated view with an enhanced user interface. Users can navigate through all the selected genomes in either pairwise or multiple viewing mode to examine conserved genomic regions as well as the accompanying genome annotations. Besides serving users who manually interact with the web server, mGSV also provides Web Services for machine-to-machine communication to accept data sent by other remote resources. The entire mGSV package can also be downloaded for easy local installation. Conclusions: mGSV significantly enhances the original functionalities of GSV. A web server hosting mGSV is provided at http://cas-bioinfo.cas.unt.edu/mgsv.

Description: Background: Increasingly, biologists and biochemists use computational tools to design experiments to probe the function of proteins and/or to engineer them for a variety of different purposes. The most effective strategies rely on the knowledge of the three-dimensional structure of the protein of interest. However it is often the case that an experimental structure is not available and that models of different quality are used instead. On the other hand, the relationship between the quality of a model and its appropriate use is not easy to derive in general, and so far it has been analyzed in detail only for specific application Results: This paper describes a database and related software tools that allow testing of a given structure based methods on models of a protein representing different levels of accuracy. The comparison of the results of a computational experiment on the experimental structure and on a set of its decoy models will allow developers and users to assess which is the specific threshold of accuracy required to perform the task effectively. Conclusions: The ModelDB server automatically builds decoy models of different accuracy for a given protein of known structure and provides a set of useful tools for their analysis. Pre-computed data for a non-redundant set of deposited protein structures are available for analysis and download in the ModelDB database.

Description: Background: Gene expression profiling (GEP) in cells obtained from peripheral blood has shown that this is a very useful approach for biomarker discovery and for studying molecular pathogenesis of prevalent diseases. While there is limited literature available on gene expression markers associated with Chronic Obstructive Pulmonary Disease (COPD), the transcriptomic picture associated with critical respiratory illness in this disease is not known at the present moment.FindingsBy using Agilent microarray chips, we have profiled gene expression signatures in the whole blood of 28 COPD patients hospitalized with different degrees of respiratory compromise.12 of them needed of admission to the ICU, whilst 16 were admitted to the Respiratory Medicine Service. GeneSpring GX 11.0 software was used for performing statistical comparisons of transcript levels between ICU and non-ICU patients. Ingenuity pathway analysis 8.5 (IPA) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to select, annotate and visualize genes by function and pathway (gene ontology). T-test showed evidence of 1501 genes differentially expressed between ICU and non-ICU patients. IPA and KEGG analysis of the most representative biological functions revealed that ICU patients had increased levels of neutrophil gene transcripts, being [cathepsin G (CTSG)], [elastase, neutrophil expressed (ELANE)], [proteinase 3 (PRTN3)], [myeloperoxidase (MPO)], [cathepsin D (CTSD)], [defensin, alpha 3, neutrophil-specific (DEFA3)], azurocidin 1 (AZU1)], and [bactericidal/permeability-increasing protein (BPI)] the most representative ones. Proteins codified by these genes form part of the azurophilic granules of neutrophils and are involved in both antimicrobial defence and tissue damage. This "neutrophil signature" was paralleled by the necessity of advanced respiratory and vital support, and the presence of bacterial infection. Conclusion: Study of transcriptomic signatures in blood suggests an essential role of neutrophil proteases in COPD patients with critical respiratory illness. Measurement and modulation of the expression of these genes could present an option for clinical monitoring and treatment of severe COPD exacerbations.

Description: Background: Postnatal regulation of the small intestinal mucus layer is potentially important in the development of adult gut functionality. We hypothesized that the nature of bacterial colonization affects mucus gene regulation in early life.We thus analyzed the influence of the presence of a conventional microbiota as well as two selected monocolonizing bacterial strains on the transcription of murine genes involved in mucus layer development during the first week of life.Mouse pups (N=8/group) from differently colonized dams: Germ-free (GF), conventional specific pathogen free (SPF), monocolonized with either Lactobacillus acidophilus NCFM (Lb) or Escherichia coli Nissle (Ec) were analyzed by qPCR on isolated ileal tissue sections from postnatal days 1 and 6 (PND1, PND6) after birth with respect to: (i) transcription of specific genes involved in mucus production (Muc1-4, Tff3) and (ii) amounts of 16S rRNA of Lactobacillus and E. coli. Quantification of 16S rRNA genes was performed to obtain a measure for amounts of colonized bacteria. Results: We found a microbiota-independent transcriptional increase of all five mucus genes from PND1 to PND6. Furthermore, the relative level of transcription of certain mucus genes on PND1 was increased by the presence of bacteria. This was observed for Tff3 in the SPF, Ec, and Lb groups; for Muc2 in SPF; and for Muc3 and Muc4 in Ec and Lb, respectively.Detection of bacterial 16S rRNA genes levels above the qPCR detection level occurred only on PND6 and only for some of the colonized animals. On PND6, we found significantly lower levels of Muc1, Muc2 and Muc4 gene transcription for Lb animals with detectable Lactobacillus levels as compared to animals with Lactobacillus levels below the detection limit. Conclusions: In summary, our data show that development of the expression of genes encoding secreted (Muc2/Tff3) and membrane-bound (Muc1/Muc3/Muc4) mucus regulatory proteins, respectively, is distinct and that the onset of this development may be accelerated by specific groups of bacteria present or absent at the mucosal site.

Description: Background: Protein-protein, cell-signaling, metabolic, and transcriptional interaction networks are useful for identifying connections between lists of experimentally identified genes/proteins. However, besides physical or co-expression interactions there are many ways in which pairs of genes, or their protein products, can be associated. By systematically incorporating knowledge on shared properties of genes from diverse sources to build functional association networks (FANs), researchers may be able to identify additional functional interactions between groups of genes that are not readily apparent. Results: Genes2FANs is a web based tool and a database that utilizes 14 carefully constructed FANs and a large-scale protein-protein interaction (PPI) network to build subnetworks that connect input lists of human and mouse genes. The FANs are created from mammalian gene set libraries where mouse genes are converted to their human orthologs. The tool takes as input a list of human or mouse Entrez gene symbols to produce a subnetwork and a ranked list of intermediate genes that are used to connect the query input list. In addition, users can enter any PubMed search term and then the system automatically converts the returned results to gene lists using GeneRIF. This gene list is then used as input to generate a subnetwork from the user's PubMed query. As a case study, we applied Genes2FANs to connect disease genes from 90 well studied disorders. We find an inverse correlation between the counts of links connecting disease genes through PPI and links connecting diseases genes through FANs separating diseases into two categories. Conclusions: Genes2FANs is a useful tool for interpreting the relationships between gene/protein lists in the context of their various functions and networks. Combining functional association interactions with physical PPIs can be useful for revealing new biology and help form hypotheses for further experimentation. Our finding that disease genes in many cancers are mostly connected through PPIs whereas other complex diseases, such as autism and type-2 diabetes, are mostly connected through FANs without PPIs, can guide better strategies for disease gene discovery. Genes2FANs is available at: http://actin.pharm.mssm.edu/genes2FANs.

Description: Background: Due to hybridization events in evolution, studying two different genes of a set of species may yieldtwo related but different phylogenetic trees for the set of species. In this case, we want to combine the two phylogenetic trees into a hybridization network with the fewest hybridization events. This leads to three computational problems, namely, the problem of computing the minimum size of a hybridization network, the problem of constructing one minimum hybridization network, and the problem of enumerating a representative set of minimum hybridization networks. The previously best software tools for these problems (namely, Chen and Wang's HybridNet and Albrecht et al.'s Dendroscope 3) run very slowly for large instances that cannot be reduced to relatively small instances. Indeed, when the minimum size of a hybridization network of two given trees are larger than 23 and the problem for the trees cannot be reduced to relatively smaller independent subproblems, then HybridNet almost always takes longer than 1 day and Dendroscope 3 often fails to complete. Thus, a faster software tool for the problems is in need. Results: We develop a software tool in ANSI C, named FastHN, for the following problems: Computing the minimum size of a hybridization network, constructing one minimum hybridization network, and enumerating a representative set of minimum hybridization networks. We obtain FastHN by refining HybridNet with three ideas. The first idea is to preprocess the input trees so that the trees become smaller or the problem becomes to solve two or more relatively smaller independent subproblems. The second idea is to use a fast algorithm for computing rSPR distance of two given phylognetic trees to cut more branches of the search tree in the exhaustive-search stage of the algorithm. The third idea is that during the exhaustive-search stage of the algorithm, we find two sibling leaves in one of the two forests (obtained from the given trees by cutting some edges) such that they are as far as possible in the other forest. As the result, FastHN always runs much faster than HybridNet. Unlike Dendroscope 3, FastHN is a single-threaded program. Despite this disadvantage, our experimental data shows that FastHN runs substantially faster than the multi-threaded Dendroscope 3 on a PC with multiple cores. Indeed, FastHN can finish within 16 minutes (on average on a Windows-7 (x64) desktop PC with i7-2600 CPU) even if the minimum size of a hybridization network of two given trees is about 25, the trees each have 100 leaves, and the problem for the input trees cannot be reduced to two or more independent subproblems via cluster reductions. It is also worth mentioning that like HybridNet, FastHN does not use much memory (indeed, the amount of memory is at most quadratic in the input size). In contrast, Dendroscope 3 uses a huge amount of memory. Executables of FastHN for Windows XP (x86), Windows 7 (x64), Linux, and Mac OS are available. Conclusions: For both biological datasets and simulated datasets, our experimental results show that FastHN runs substantially faster than HybridNet and Dendroscope 3. The superiority of FastHN in speed over the previous tools becomes more significant as the hybridization number becomes larger. In addition, FastHN uses much less memory than Dendroscope 3 and uses the same amount of memory as HybridNet.

Description: Background: Many consensus-based and Position Weight Matrix-based methods for recognizing transcription factor binding sites (TFBS) are not well suited to the variability in the lengths of binding sites. Besides, many methods discard known binding sites while building the model. Moreover, the impact of Information Content (IC) and the positional dependence of nucleotides within an aligned set of TFBS has not been well researched for modeling variable-length binding sites. In this paper, we propose ML-Consensus (Mixed-Length Consensus): a consensus model for variable-length TFBS which does not exclude any reported binding sites. We consider Pairwise Score (PS) as a measure of positional dependence of nucleotides within an alignment of TFBS. We investigate how the prediction accuracy of ML-Consensus is affected by the incorporation of IC and PS with a particular binding site alignment strategy. We perform cross-validations for datasets of six species from the TRANSFAC public database, and analyze the results using ROC curves and the Wilcoxon matched-pair signed-ranks test. Results: We observe that the incorporation of IC and PS in ML-Consensus results in statistically significant improvement in the prediction accuracy of the model. Moreover, the existence of a core region among the known binding sites (of any length) is witnessed by the pairwise coexistence of nucleotides within the core length. Conclusions: These observations suggest the possibility of an efficient multiple sequence alignment algorithm for aligning TFBS, accommodating known binding sites of any length, for optimal (or near-optimal) TFBS prediction. However, designing such an algorithm is a matter of further investigation. Availability: All source codes (C#), results, supporting evidence, supplementary data and figures are available from http://biogrid.engr.uconn.edu/mlconsensus/

Description: Background: Ongoing innovation in phylogenetics and evolutionary biology has been accompanied by a proliferation of software tools, data formats, analytical techniques and web servers. This brings with it the challenge of integrating phylogenetic and other related biological data found in a wide variety of formats, and underlines the need for reusable software that can read, manipulate and transform this information into the various forms required to build computational pipelines. Results: We built a Python software library for working with phylogenetic data that is tightly integrated with Biopython, a broad-ranging toolkit for computational biology. Our library, Bio.Phylo, is highly interoperable with existing libraries, tools and standards, and is capable of parsing common file formats for phylogenetic trees, performing basic transformations and manipulations, attaching rich annotations, and visualizing trees. We unified the modules for working with the standard file formats Newick, NEXUS and phyloXML behind a consistent and simple API, providing a common set of functionality independent of the data source. Conclusions: Bio.Phylo meets a growing need in bioinformatics for working with heterogeneous types of phylogenetic data. By supporting interoperability with multiple file formats and leveraging existing Biopython features, this library simplifies the construction of phylogenetic workflows. We also provide examples of the benefits of building a community around a shared open-source project. Bio.Phylo is included with Biopython, available through the Biopython website, http://biopython.org.

Description: Background: The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need todetermine whether a set of gene trees significantly deviate from the phylogenetic patterns of other genes.Such unusual gene trees may have been influenced by other evolutionary processes such as selection, geneduplication, or horizontal gene transfer. Results: Motivated by this problem we propose a nonparametric goodness-of-fit test for two empirical distributionsof gene trees, and we developed the software GeneOut to estimate a p-value for the test. Our approachmaps trees into a multi-dimensional vector space and then applies support vector machines (SVMs) tomeasure the separation between two sets of pre-defined trees. We use a permutation test to assess thesignificance of the SVM separation. To demonstrate the performance of GeneOut, we applied it to thecomparison of gene trees simulated within different species trees across a range of species tree depths.Applied directly to sets of simulated gene trees with large sample sizes, GeneOut was able to detect verysmall differences between two set of gene trees generated under different species trees. Our statistical testcan also include tree reconstruction into its test framework through a variety of phylogenetic optimalitycriteria. When applied to DNA sequence data simulated from different sets of gene trees, results in the formof receiver operating characteristic (ROC) curves indicated that GeneOut performed well in the detectionof differences between sets of trees with different distributions in a multi-dimensional space. Furthermore, itcontrolled false positive and false negative rates very well, indicating a high degree of accuracy. Conclusions: The non-parametric nature of our statistical test provides fast and efficient analyses, and makes it anapplicable test for any scenario where evolutionary or other factors can lead to trees with differentmulti-dimensional distributions. The software GeneOut is freely available under the GNU public license.