Limitations and potentials of current motif discovery algorithms

Computational methods for de novo identification of gene regulation elements, such as transcription factor binding sites, have proved to be useful for deciphering genetic regulatory networks. However, despite the availability of a large number of algorithms, their strengths and weaknesses are not sufficiently understood. Here, we designed a comprehensive set of performance measures and benchmarked five modern sequence-based motif discovery algorithms using large datasets generated from Escherichia coli RegulonDB. Factors that affect the prediction accuracy, scalability and reliability are characterized. It is revealed that the nucleotide and the binding site level accuracy are very low, while the motif level accuracy is relatively high, which indicates that the algorithms can usually capture at least one correct motif in an input sequence. To exploit diverse predictions from multiple runs of one or more algorithms, a consensus ensemble algorithm has been developed, which achieved 6–45% improvement over the base algorithms by increasing both the sensitivity and specificity. Our study illustrates limitations and potentials of existing sequence-based motif discovery algorithms. Taking advantage of the revealed potentials, several promising directions for further improvements are discussed. Since the sequence-based algorithms are the baseline of most of the modern motif discovery algorithms, this paper suggests substantial improvements would be possible for them

Climate change and habitat fragmentation drive the occurrence of Borrelia burgdorferi, the agent of Lyme disease, at the northeastern limit of its distribution

Lyme borreliosis is rapidly emerging in Canada, and climate change is likely a key driver of the northern spread of the disease in North America. We used field and modeling approaches to predict the risk of occurrence of Borrelia burgdorferi, the bacteria causing Lyme disease in North America. We combined climatic and landscape variables to model the current and future (2050) potential distribution of the black-legged tick and the white-footed mouse at the northeastern range limit of Lyme disease and estimated a risk index for B. burgdorferi from these distributions. The risk index was mostly constrained by the distribution of the white-footed mouse, driven by winter climatic conditions. The next factor contributing to the risk index was the distribution of the black-legged tick, estimated from the temperature. Landscape variables such as forest habitat and connectivity contributed little to the risk index. We predict a further northern expansion of B. burgdorferi of approximately 250-500 km by 2050 - a rate of 3.5-11 km per year - and identify areas of rapid rise in the risk of occurrence of B. burgdorferi. Our results will improve understanding of the spread of Lyme disease and inform management strategies at the most northern limit of its distribution.Julie A. Simon, Robby R. Marrotte, Nathalie Desrosiers, Jessica Fiset, Jorge Gaitan, Andrew Gonzalez, Jules K. Koffi, Francois-Joseph Lapointe, Patrick A. Leighton, Lindsay R. Lindsay, Travis Logan, Francois Milord, Nicholas H. Ogden, Anita Rogic, Emilie Roy-Dufresne, Daniel Suter, Nathalie Tessier, and Virginie Millie

The Insulin-Mediated Modulation of Visually Evoked Magnetic Fields Is Reduced in Obese Subjects

BACKGROUND: Insulin is an anorexigenic hormone that contributes to the termination of food intake in the postprandial state. An alteration in insulin action in the brain, named "cerebral insulin resistance", is responsible for overeating and the development of obesity. METHODOLOGY/PRINCIPAL FINDINGS: To analyze the direct effect of insulin on food-related neuronal activity we tested 10 lean and 10 obese subjects. We conducted a magnetencephalography study during a visual working memory task in both the basal state and after applying insulin or placebo spray intranasally to bypass the blood brain barrier. Food and non-food pictures were presented and subjects had to determine whether or not two consecutive pictures belonged to the same category. Intranasal insulin displayed no effect on blood glucose, insulin or C-peptide concentrations in the periphery; however, it led to an increase in the components of evoked fields related to identification and categorization of pictures (at around 170 ms post stimuli in the visual ventral stream) in lean subjects when food pictures were presented. In contrast, insulin did not modulate food-related brain activity in obese subjects. CONCLUSIONS/SIGNIFICANCE: We demonstrated that intranasal insulin increases the cerebral processing of food pictures in lean whereas this was absent in obese subjects. This study further substantiates the presence of a "cerebral insulin resistance" in obese subjects and might be relevant in the pathogenesis of obesity

Empirical comparison of cross-platform normalization methods for gene expression data

<p>Abstract</p> <p>Background</p> <p>Simultaneous measurement of gene expression on a genomic scale can be accomplished using microarray technology or by sequencing based methods. Researchers who perform high throughput gene expression assays often deposit their data in public databases, but heterogeneity of measurement platforms leads to challenges for the combination and comparison of data sets. Researchers wishing to perform cross platform normalization face two major obstacles. First, a choice must be made about which method or methods to employ. Nine are currently available, and no rigorous comparison exists. Second, software for the selected method must be obtained and incorporated into a data analysis workflow.</p> <p>Results</p> <p>Using two publicly available cross-platform testing data sets, cross-platform normalization methods are compared based on inter-platform concordance and on the consistency of gene lists obtained with transformed data. Scatter and ROC-like plots are produced and new statistics based on those plots are introduced to measure the effectiveness of each method. Bootstrapping is employed to obtain distributions for those statistics. The consistency of platform effects across studies is explored theoretically and with respect to the testing data sets.</p> <p>Conclusions</p> <p>Our comparisons indicate that four methods, DWD, EB, GQ, and XPN, are generally effective, while the remaining methods do not adequately correct for platform effects. Of the four successful methods, XPN generally shows the highest inter-platform concordance when treatment groups are equally sized, while DWD is most robust to differently sized treatment groups and consistently shows the smallest loss in gene detection. We provide an R package, CONOR, capable of performing the nine cross-platform normalization methods considered. The package can be downloaded at <url>http://alborz.sdsu.edu/conor</url> and is available from CRAN.</p

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma

Follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL) are the two most common non-Hodgkin lymphomas (NHLs). Here we sequenced tumour and matched normal DNA from 13 DLBCL cases and one FL case to identify genes with mutations in B-cell NHL. We analysed RNA-seq data from these and another 113 NHLs to identify genes with candidate mutations, and then re-sequenced tumour and matched normal DNA from these cases to confirm 109 genes with multiple somatic mutations. Genes with roles in histone modification were frequent targets of somatic mutation. For example, 32% of DLBCL and 89% of FL cases had somatic mutations in MLL2, which encodes a histone methyltransferase, and 11.4% and 13.4% of DLBCL and FL cases, respectively, had mutations in MEF2B, a calcium-regulated gene that cooperates with CREBBP and EP300 in acetylating histones. Our analysis suggests a previously unappreciated disruption of chromatin biology in lymphomagenesis

Overview of cattle diseases listed under category C, D or E in the animal health law for wich control programmes are in place within Europe

13 páginas, 5 figuras, 3 tablas.The COST action “Standardising output-based surveillance to control non-regulated diseases of cattle in the European Union (SOUND control),” aims to harmonise the results of surveillance and control programmes (CPs) for non-EU regulated cattle diseases to facilitate safe trade and improve overall control of cattle infectious diseases. In this paper we aimed to provide an overview on the diversity of control for these diseases in Europe. A non-EU regulated cattle disease was defined as an infectious disease of cattle with no or limited control at EU level, which is not included in the European Union Animal health law Categories A or B under Commission Implementing Regulation (EU) 2020/2002. A CP was defined as surveillance and/or intervention strategies designed to lower the incidence, prevalence, mortality or prove freedom from a specific disease in a region or country. Passive surveillance, and active surveillance of breeding bulls under Council Directive 88/407/EEC were not considered as CPs. A questionnaire was designed to obtain country-specific information about CPs for each disease. Animal health experts from 33 European countries completed the questionnaire. Overall, there are 23 diseases for which a CP exists in one or more of the countries studied. The diseases for which CPs exist in the highest number of countries are enzootic bovine leukosis, bluetongue, infectious bovine rhinotracheitis, bovine viral diarrhoea and anthrax (CPs reported by between 16 and 31 countries). Every participating country has on average, 6 CPs (min–max: 1–13) in place. Most programmes are implemented at a national level (86%) and are applied to both dairy and non-dairy cattle (75%). Approximately one-third of the CPs are voluntary, and the funding structure is divided between government and private resources. Countries that have eradicated diseases like enzootic bovine leukosis, bluetongue, infectious bovine rhinotracheitis and bovine viral diarrhoea have implemented CPs for other diseases to further improve the health status of cattle in their country. The control of non-EU regulated cattle diseases is very heterogenous in Europe. Therefore, the standardising of the outputs of these programmes to enable comparison represents a challenge.Peer reviewe

Analytical validation of the iSED automated analyzer for erythrocyte sedimentation rate

Introduction: iSED is an alternate automated analyzer for erythrocyte sedimentation rate (ESR) based on photometric rheology technology that estimates ESR by measuring rouleaux formation. The aim was to evaluate the analytical performance of the iSED analyzer and compare the results with the Westergren method and another alternate ESR analyzer, TEST1. Methods: Validation was performed at two study sites according to the recommendations by the International Council for Standardization in Haematology and included determination of intrarun precision and inter-run precision, bias, carryover, and method comparison, which was further assessed for samples with normal and low hematocrit, as well as per low, middle, and upper third of the analytical range. Results: Intrarun coefficients of variation (CVs) with commercial controls were 4.0% and 1.8%, while inter-run CVs 7.5% and 0.7%, for the normal and pathological range, respectively. Intrarun CVs obtained with patient samples were 19.9%, 9.9%, 10.3%, and 9.4%, the highest being for the lowest ESR value. Correlation coefficients for the comparison between iSED and Westergren were 0.862 (Site-1) and 0.916 (Site-2). While proportional difference with a positive bias was revealed at Site-1, comparison at Site-2 showed both constant and proportional difference and a negligible negative bias. Higher correlation was obtained for samples with low than normal hematocrit. Comparison between iSED and TEST1 yielded a correlation coefficient of 0.986, constant and proportional difference, and positive bias. Carryover was 3.2%. Conclusion: This study proved the analytical validity of the iSED analyzer, despite minor discrepancies to the Westergren method that can be attributed to methodological differences

An international study of how laboratories handle and evaluate patient samples after detecting an unexpected APTT prolongation

PubMed ID: 26023801Background: An unexpectedly detected prolonged activated partial thromboplastin time (APTT) can be a harmless laboratory finding, but can also reflect a thrombotic tendency or a bleeding disorder. The assistance of laboratory professionals in the interpretation of an unexpectedly detected prolonged APTT (uAPTT) is often required. The way in which uAPTTs are evaluated in laboratories was assessed in this international study with the aim of determining whether laboratory professionals are able to fulfill this need. Methods: Postanalytical practices after uAPTT were investigated and the mixing study methodology (if used) was studied by circulating a case report with a questionnaire to staff in the invited laboratories. In addition, the interpretations of those staff regarding the presence or absence of inhibitors in three APTT mixing study scenarios were examined. Results: Large within- and between-country variations were detected in both postanalytical practices and mixing study methodologies among the 990 responding laboratories, 90% of which were in 13 countries. Shortcomings regarding the investigation of uAPTTs leading to potentially incorrect or delayed clinical diagnoses were found in 88% of the laboratories. Of the laboratories to which the interpretative questions were sent, 49% interpreted all mixing study scenarios correctly. uAPTTs were investigated appropriately and all mixing study scenarios interpreted correctly in parallel in only 9.6% of the participating laboratories. Conclusions: The clinical requirement for the assistance of laboratory professionals in the interpretation of uAPTTs cannot be met at most of the participating laboratories. Laboratory professionals should be trained in the evaluation of ordinary laboratory tests, such as that for uAPTTs. © 2015 by De Gruyter.Acknowledgments: We thank all of the staff at the participating laboratories who responded to our survey. We are also thankful for EQALM and its member organizations for distributing invitations for this study to the participants. We thank especially those External Quality Assessment organizers who assisted this project in countries providing more than 20 responses each, which were as follows: Ö QUASTA (Austrian Society for Quality Assurance and Standardization of Medical Laboratory Tests), Vienna, Austria; CSMBLM (Croatian Society of Medical Biochemistry and Laboratory Medicine, CROQALM Programme), Zagreb, Croatia; DEKS (Danish Institute for External Quality Assurance for Laboratories in Health Care) Herlev, Denmark; CTCB (Centre Toulousain pour le Contrô le de qualité en Biologie clinique), Toulouse, France; RfB (Reference Institute for Bioanalytics), Bonn, Germany; Qualicont (In Vitro Diagnostic Quality Control Nonprofit Public Utility Ltd.), Szeged, Hungary; IEQAS (Irish EQA Scheme), Dublin, Ireland; Centro di Ricerca Biomedica of Veneto Region, Padova, Italy; NKK (Norwegian Clinical Chemistry EQA Program), Bergen, Norway; PNAEQ (Programa Nacional de Avalia ç ã o Externa da Qualidade), Lisbon, Portugal; CSCQ (Quality Control Center Switzerland), Ch ê ne-Bourg, Switzerland; SEKK, Pardubice, Czech Republic; SKML (Dutch Foundation for Quality Assessment in Medical Laboratories, Section Coagulation), Nijmegen in liason with ECAT Foundation, Voorschoten, The Netherlands. We are also grateful for Joseph Watine for his useful comments during the project and to Csilla P á l and S á ndor Kecskem é ti for their excellent technical assistance. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission. Financial support: None declared. Employment or leadership: None declared. Honorarium: None declared. Competing interests: The funding organization(s) played no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the report for publication. -