Empowering statistical methods for cellular and molecular biologists.

We provide guidelines for using statistical methods to analyze the types of experiments reported in cellular and molecular biology journals such as Molecular Biology of the Cell. Our aim is to help experimentalists use these methods skillfully, avoid mistakes, and extract the maximum amount of information from their laboratory work. We focus on comparing the average values of control and experimental samples. A Supplemental Tutorial provides examples of how to analyze experimental data using R software

Where do uncertainties reside within environmental risk assessments? Expert opinion on uncertainty distributions for pesticide risks to surface water organisms

A reliable characterisation of uncertainties can aid uncertainty identification during environmental risk assessments (ERAs). However, typologies can be implemented inconsistently, causing uncertainties to go unidentified. We present an approach based on nine structured elicitations, in which subject-matter experts, for pesticide risks to surface water organisms, validate and assess three dimensions of uncertainty: its level (the severity of uncertainty, ranging from determinism to ignorance); nature (whether the uncertainty is epistemic or aleatory); and location (the data source or area in which the uncertainty arises). Risk characterisation contains the highest median levels of uncertainty, associated with estimating, aggregating and evaluating the magnitude of risks. Regarding the locations in which uncertainty is manifest, data uncertainty is dominant in problem formulation, exposure assessment and effects assessment. The comprehensive description of uncertainty described will enable risk analysts to prioritise the required phases, groups of tasks, or individual tasks within a risk analysis according to the highest levels of uncertainty, the potential for uncertainty to be reduced or quantified, or the types of location-based uncertainty, thus aiding uncertainty prioritisation during environmental risk assessments. In turn, it is expected to inform investment in uncertainty reduction or targeted risk management action

Where do uncertainties reside within environmental risk assessments? Testing UnISERA, a guide for uncertainty assessment

A means for identifying and prioritising the treatment of uncertainty (UnISERA) in environmental risk assessments (ERAs) is tested, using three risk domains where ERA is an established requirement and one in which ERA practice is emerging. UnISERA's development draws on 19 expert elicitations across genetically modified higher plants, particulate matter, and agricultural pesticide release and is stress tested here for engineered nanomaterials (ENM). We are concerned with the severity of uncertainty; its nature; and its location across four accepted stages of ERAs. Using an established uncertainty scale, the risk characterisation stage of ERA harbours the highest severity level of uncertainty, associated with estimating, aggregating and evaluating expressions of risk. Combined epistemic and aleatory uncertainty is the dominant nature of uncertainty. The dominant location of uncertainty is associated with data in problem formulation, exposure assessment and effects assessment. Testing UnISERA produced agreements of 55%, 90%, and 80% for the severity level, nature and location dimensions of uncertainty between the combined case studies and the ENM stress test. UnISERA enables environmental risk analysts to prioritise risk assessment phases, groups of tasks, or individual ERA tasks and it can direct them towards established methods for uncertainty treatment

Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments

BACKGROUND: Molecular evolutionary studies of noncoding sequences rely on multiple alignments. Yet how multiple alignment accuracy varies across sequence types, tree topologies, divergences and tools, and further how this variation impacts specific inferences, remains unclear. RESULTS: Here we develop a molecular evolution simulation platform, CisEvolver, with models of background noncoding and transcription factor binding site evolution, and use simulated alignments to systematically examine multiple alignment accuracy and its impact on two key molecular evolutionary inferences: transcription factor binding site conservation and divergence estimation. We find that the accuracy of multiple alignments is determined almost exclusively by the pairwise divergence distance of the two most diverged species and that additional species have a negligible influence on alignment accuracy. Conserved transcription factor binding sites align better than surrounding noncoding DNA yet are often found to be misaligned at relatively short divergence distances, such that studies of binding site gain and loss could easily be confounded by alignment error. Divergence estimates from multiple alignments tend to be overestimated at short divergence distances but reach a tool specific divergence at which they cease to increase, leading to underestimation at long divergences. Our most striking finding was that overall alignment accuracy, binding site alignment accuracy and divergence estimation accuracy vary greatly across branches in a tree and are most accurate for terminal branches connecting sister taxa and least accurate for internal branches connecting sub-alignments. CONCLUSION: Our results suggest that variation in alignment accuracy can lead to errors in molecular evolutionary inferences that could be construed as biological variation. These findings have implications for which species to choose for analyses, what kind of errors would be expected for a given set of species and how multiple alignment tools and phylogenetic inference methods might be improved to minimize or control for alignment errors

Correction: Benchmarking tools for the alignment of functional noncoding DNA

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.AbstractIn follow-up studies to this work [1], we have identified an error in a single line of code responsible for parsing BLASTZ [2] alignments that affects our previously published results for this alignment tool. This error resulted in a reduction in overall alignment coverage, with a concomitant underestimation of alignment sensitivity and overestimation of alignment specificity. As BLASTZ is an important and widely used alignment tool, we present here the revised results of our performance evaluations for BLASTZ together with previously reported results for the other alignment tools studied, which have been subsequently verified (Figures 1-4). The general conclusions presented in [1] remain unchanged, although the following sections concerning BLASTZ performance must be modified in light of our recent findings. The true overall alignment coverage for BLASTZ with and without insertion/deletion evolution and with and without blocks of constraint is shown in Figure 1, and reveals increased overall coverage in the presence of constrained blocks for intermediate to high divergence distances (Figures 1C & 1D) relative to previous results ([1] Figures 3C & 3D). As a consequence, the true overall sensitivity for BLASTZ is increased for intermediate to high divergence distances, especially in the presence of insertion/deletion evolution and constrained blocks (Figure 2D) relative to previous results ([1] Figure 4D). The most important revisions to [1] concern BLASTZ performance in interspersed blocks of constrained sequences (Figures 3, 4). Figure 3 shows that the true constraint coverage, and therefore constraint sensitivity, of BLASTZ is much improved relative to previous results for intermediate to high divergence distances ([1], Figure 5). Thus BLASTZ has increased constraint coverage relative to overall coverage (cp. Figures 1C & 1D with 3A & 3B), indicating that BLASTZ local alignments preferentially occur in constrained sequences for intermediate to high divergence distances, overturning claims on page 6 of [1] to the contrary. Likewise, the claim that BLASTZ has a "dramatic decrease in constraint sensitivity in the presence of indel evolution" on page 10 of [1] is incorrect. The increase in overall coverage, however, decreases the constraint specificity of BLASTZ for intermediate to high divergence distances (Figure 4A & 4B) relative to previous results ([1] Figure 6A & 6B). This decrease in constraint specificity requires reconsideration of the use of BLASTZ local alignments as specific detectors of constrained noncoding sequences discussed page 10 of [1]. Revised performance statistics for BLASTZ are posted along with previous results at [3]. We apologize for any misconception or inconvenience this error may have caused. References: 1. Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB: Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 2004, 5:6. 2. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W: Human-mouse alignments with BLASTZ. Genome Res 2003, 13:103-7. 3. AlignmentBenchmarking [http://rana.lbl.gov/AlignmentBenchmarking]Peer Reviewe

MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model

We introduce a method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic models of factor specificity and binding-site evolution, on which basis we compute the likelihood that putative sites are conserved and assign statistical significance to each hit. Using genomes from the genus Saccharomyces, we illustrate how the significance of real sites increases with evolutionary distance and explore the relationship between conservation and function

Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting

The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy. All three possible groupings of the species have been reported in the past, though recent multi-gene studies suggest that D. erecta and D. yakuba are sister species. Using the whole genomes of each of these species as well as the four other fully sequenced species in the subgenus Sophophora, we set out to investigate the placement of D. erecta and D. yakuba in the D. melanogaster species group and to understand the cause of the past incongruence. Though we find that the phylogeny grouping D. erecta and D. yakuba together is the best supported, we also find widespread incongruence in nucleotide and amino acid substitutions, insertions and deletions, and gene trees. The time inferred to span the two key speciation events is short enough that under the coalescent model, the incongruence could be the result of incomplete lineage sorting. Consistent with the lineage-sorting hypothesis, substitutions supporting the same tree were spatially clustered. Support for the different trees was found to be linked to recombination such that adjacent genes support the same tree most often in regions of low recombination and substitutions supporting the same tree are most enriched roughly on the same scale as linkage disequilibrium, also consistent with lineage sorting. The incongruence was found to be statistically significant and robust to model and species choice. No systematic biases were found. We conclude that phylogenetic incongruence in the D. melanogaster species complex is the result, at least in part, of incomplete lineage sorting. Incomplete lineage sorting will likely cause phylogenetic incongruence in many comparative genomics datasets. Methods to infer the correct species tree, the history of every base in the genome, and comparative methods that control for and/or utilize this information will be valuable advancements for the field of comparative genomics

Finite group actions on reductive groups and buildings and tamely-ramified descent in Bruhat-Tits theory

The purpose of the paper is to give a new approach to tamely-ramified descent in Bruhat-Tits theory. This descent was first studied by Guy Rousseau in his thesis.Comment: 28 pages. arXiv admin note: text overlap with arXiv:1611.0743

Movement Demands of Elite Under-20s and Senior International Rugby Union Players

This study compared the movement demands of elite international Under-20 age grade (U20s) and senior international rugby union players during competitive tournament match play. Forty elite professional players from an U20 and 27 elite professional senior players from international performance squads were monitored using 10Hz global positioning systems (GPS) during 15 (U20s) and 8 (senior) international tournament matches during the 2014 and 2015 seasons. Data on distances, velocities, accelerations, decelerations, high metabolic load (HML) distance and efforts, and number of sprints were derived. Data files from players who played over 60 min (n = 258) were separated firstly into Forwards and Backs, and more specifically into six positional groups; FR–Front Row (prop & hooker), SR–Second Row, BR–Back Row (Flankers & No.8), HB–Half Backs (scrum half & outside half), MF–Midfield (centres), B3 –Back Three (wings & full back) for match analysis. Linear mixed models revealed significant differences between U20 and senior teams in both the forwards and backs. In the forwards the seniors covered greater HML distance (736.4 ± 280.3 vs 701.3 ± 198.7m, p = 0.01) and severe decelerations (2.38 ± 2.2 vs 2.28 ± 1.65, p = 0.05) compared to the U20s, but performed less relative HSR (3.1 ± 1.6 vs 3.2 ± 1.5, p < 0.01), moderate (19.4 ± 10.5 vs 23.6 ± 10.5, p = 0.01) and high accelerations (2.2 ± 1.9 vs 4.3 ± 2.7, p < 0.01) and sprint•min-1 (0.11 ± 0.06 vs 0.11 ± 0.05, p < 0.01). Senior backs covered a greater relative distance (73.3 ± 8.1 vs 69.1 ± 7.6 m•min-1, p < 0.01), greater High Metabolic Load (HML) distance (1138.0 ± 233.5 vs 1060.4 ± 218.1m, p < 0.01), HML efforts (112.7 ± 22.2 vs 98.8 ± 21.7, p < 0.01) and heavy decelerations (9.9 ± 4.3 vs 9.5 ± 4.4, p = 0.04) than the U20s backs. However, the U20s backs performed more relative HSR (7.3 ± 2.1 vs 7.2 ± 2.1, p <0.01) and sprint•min-1 (0.26 ± 0.07 vs 0.25 ± 0.07, p < 0.01). Further investigation highlighted differences between the 6 positional groups of the teams. The positional groups that differed the most on the variables measured were the FR and MF groups, with the U20s FR having higher outputs on HSR, moderate & high accelerations, moderate, high & severe decelerations, HML distance, HML efforts, and sprints•min-1. For the MF group the senior players produced greater values for relative distance covered, HSR, moderate decelerations, HML distance and sprint•min-1. The BR position group was most similar with the only differences seen on heavy accelerations (U20s higher) and moderate decelerations (seniors higher). Findings demonstrate that U20s internationals appear to be an adequate ‘stepping stone’ for preparing players for movement characteristics found senior International rugby, however, the current study highlight for the first time that certain positional groups may require more time to be able to match the movement demands required at a higher playing level than others. Conditioning staff must also bear in mind that the U20s players whilst maintaining or improving match movement capabilities may require to gain substantial mass in some positions to match their senior counterparts

Datathons and Software to Promote Reproducible Research

Background: Datathons facilitate collaboration between clinicians, statisticians, and data scientists in order to answer important clinical questions. Previous datathons have resulted in numerous publications of interest to the critical care community and serve as a viable model for interdisciplinary collaboration. Objective: We report on an open-source software called Chatto that was created by members of our group, in the context of the second international Critical Care Datathon, held in September 2015. Methods: Datathon participants formed teams to discuss potential research questions and the methods required to address them. They were provided with the Chatto suite of tools to facilitate their teamwork. Each multidisciplinary team spent the next 2 days with clinicians working alongside data scientists to write code, extract and analyze data, and reformulate their queries in real time as needed. All projects were then presented on the last day of the datathon to a panel of judges that consisted of clinicians and scientists. Results: Use of Chatto was particularly effective in the datathon setting, enabling teams to reduce the time spent configuring their research environments to just a few minutes—a process that would normally take hours to days. Chatto continued to serve as a useful research tool after the conclusion of the datathon. Conclusions: This suite of tools fulfills two purposes: (1) facilitation of interdisciplinary teamwork through archiving and version control of datasets, analytical code, and team discussions, and (2) advancement of research reproducibility by functioning postpublication as an online environment in which independent investigators can rerun or modify analyses with relative ease. With the introduction of Chatto, we hope to solve a variety of challenges presented by collaborative data mining projects while improving research reproducibility