MultiPhyl: a high-throughput phylogenomics webserver using distributed computing

With the number of fully sequenced genomes increasing steadily, there is greater interest in performing large-scale phylogenomic analyses from large numbers of individual gene families. Maximum likelihood (ML) has been shown repeatedly to be one of the most accurate methods for phylogenetic construction. Recently, there have been a number of algorithmic improvements in maximum-likelihood-based tree search methods. However, it can still take a long time to analyse the evolutionary history of many gene families using a single computer. Distributed computing refers to a method of combining the computing power of multiple computers in order to perform some larger overall calculation. In this article, we present the first high-throughput implementation of a distributed phylogenetics platform, MultiPhyl, capable of using the idle computational resources of many heterogeneous non-dedicated machines to form a phylogenetics supercomputer. MultiPhyl allows a user to upload hundreds or thousands of amino acid or nucleotide alignments simultaneously and perform computationally intensive tasks such as model selection, tree searching and bootstrapping of each of the alignments using many desktop machines. The program implements a set of 88 amino acid models and 56 nucleotide maximum likelihood models and a variety of statistical methods for choosing between alternative models. A MultiPhyl webserver is available for public use at: http://www.cs.nuim.ie/distributed/multiphyl.php

Generalizability of achievement goal profiles across five cultural groups : more similarities than differences

Previous results have shown possible cultural differences in students’ achievement goals endorsement and in their relations with various predictors and outcomes. In this person-centered study, we sought to identify achievement goal profiles and to assess the extent to which these configurations and their associations with predictors and outcomes generalize across cultures. We used a new statistical approach to assess latent profile similarities across adolescents from five cultural backgrounds (N = 2643, including Non-Indigenous Australians, Indigenous Australians, Indigenous American, Middle Easterners, and Asians). Our results supported the cross-cultural generalizability of the profiles, their predictors, and their outcomes. Five similar profiles were identified in each cultural group, but their relative frequency differed across cultures. The results revealed advantages of exploring multidimensional goal profiles

Formate Formation and Formate Conversion in Biological Fuels Production

Biomethanation is a mature technology for fuel production. Fourth generation biofuels research will focus on sequestering CO2 and providing carbon-neutral or carbon-negative strategies to cope with dwindling fossil fuel supplies and environmental impact. Formate is an important intermediate in the methanogenic breakdown of complex organic material and serves as an important precursor for biological fuels production in the form of methane, hydrogen, and potentially methanol. Formate is produced by either CoA-dependent cleavage of pyruvate or enzymatic reduction of CO2 in an NADH- or ferredoxin-dependent manner. Formate is consumed through oxidation to CO2 and H2 or can be further reduced via the Wood-Ljungdahl pathway for carbon fixation or industrially for the production of methanol. Here, we review the enzymes involved in the interconversion of formate and discuss potential applications for biofuels production

Revitalising audit and feedback to improve patient care

Healthcare systems face challenges in tackling variations in patient care and outcomes. Audit and feedback aim to improve patient care by reviewing clinical performance against explicit standards and directing action towards areas not meeting those standards. It is a widely used foundational component of quality improvement, included in around 60 national clinical audit programmes in the United Kingdom. Ironically, there is currently a gap between what audit and feedback can achieve and what they actually deliver, whether led locally or nationally. Several national audits have been successful in driving improvement and reducing variations in care, such as for stroke and lung cancer, but progress is also slower than hoped for in other aspects of care (table 1). Audit and feedback have a chequered past.6 Clinicians might feel threatened rather than supported by top-down feedback and rightly question whether rewards outweigh efforts invested in poorly designed audit. Healthcare organisations have limited resources to support and act on audit and feedback. Dysfunctional clinical and managerial relationships undermine effective responses to feedback, particularly when it is not clearly part of an integrated approach to quality assurance and improvement. Unsurprisingly, the full potential of audit and feedback has not been realised

Syntrophomonas zehnderi sp. nov., an anaerobe that degrades long-chain fatty acids in co-culture with Methanobacterium formicicum

An anaerobic, mesophilic, syntrophic fatty-acid-oxidizing bacterium, designated strain OL-4T, was isolated as a co-culture with Methanobacterium formicicum DSM 1535NT from an anaerobic expanded granular sludge bed reactor used to treat an oleate-based effluent. Strain OL-4T degraded oleate, a mono-unsaturated fatty acid, and straight-chain fatty acids C4 : 0–C18 : 0 in syntrophic association with Methanobacterium formicicum DSM 1535NT. Even-numbered fatty acids were degraded to acetate and methane whereas odd-numbered fatty acids were degraded to acetate, propionate and methane. Branched-chain fatty acids were not degraded. The bacterium could not grow axenically with any other substrate tested and therefore is considered to be obligately syntrophic. Fumarate, sulfate, thiosulfate, sulfur and nitrate could not serve as electron acceptors for strain OL-4T to degrade oleate or butyrate. Cells of strain OL-4T were curved rods, formed spores and showed a variable response to Gram staining. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain OL-4T was most closely related to the fatty-acid-oxidizing, syntrophic bacterium Syntrophomonas sp. TB-6 (95% similarity), Syntrophomonas wolfei subsp. wolfei DSM 2245T (94% similarity) and Syntrophomonas erecta DSM 16215T (93% similarity). In addition to this moderate similarity, phenotypic and physiological characteristics, such as obligate syntrophy, spore formation and utilization of a broader substrate range, differentiated strain OL-4T from these Syntrophomonas species. Therefore strain OL-4T represents a novel species, for which the name yntrophomonas zehnderi sp. nov. is proposed. The type strain is OL-4T (=DSM 17840T=JCM 13948T).Fundação para a Ciência e a Tecnologia (FCT)( Fundo Social Europeu (FSE); Wageningen Institute for Environmental and Climate Research (WIMEK)

Modal Codon Usage: Assessing the Typical Codon Usage of a Genome

Most genomes are heterogeneous in codon usage, so a codon usage study should start by defining the codon usage that is typical to the genome. Although this is commonly taken to be the genomewide average, we propose that the mode—the codon usage that matches the most genes—provides a more useful approximation of the typical codon usage of a genome. We provide a method for estimating the modal codon usage, which utilizes a continuous approximation to the number of matching genes and a simplex optimization. In a survey of bacterial and archaeal genomes, as many as 20% more of the genes in a given genome match the modal codon usage than the average codon usage. We use the mode to examine the evolution of the multireplicon genomes of Agrobacterium tumefaciens C58 and Borrelia burgdorferi B31. In A. tumefaciens, the circular and linear chromosomes are characterized by a common “chromosome-like” codon usage, whereas both plasmids share a distinct “plasmid-like” codon usage. In B. burgdorferi, in addition to different codon-usage biases on the leading and lagging strands of DNA replication found by McInerney (McInerney JO. 1998. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc Natl Acad Sci USA. 95:10698–10703), we also detect a codon-usage similarity between linear plasmid lp38 and the leading strand of the chromosome and a high similarity among the cp32 family of plasmids

Teachers' commitment and psychological well-being : Implications of self-beliefs for teaching in Hong Kong

Despite ample research on commitment in industrial settings, there has been no systematic attempt to investigate outcomes associated with teacher commitment. Therefore, the aim of this study was to examine the relationship between teacher commitment and psychological well-being in the work place using questionnaires. Hong Kong teachers (N = 857) participated. Hierarchical regression analyses were used to investigate how the three aspects of commitment pertaining to the organisation and occupation predicted relevant outcomes. Results showed that affective and normative commitment positively predicted psychological well-being in the work place: interpersonal fit at work, thriving at work, feeling of competency, perceived recognition at work, desire for involvement at work and job satisfaction. Continuance commitment was a negative predictor of some outcomes. Results of the current study provide support to Meyer’s 3 × 2 factor model of commitment. Findings are discussed in relation to the situation of teachers in the Hong Kong context

Toward Open Science at the European Scale: Geospatial Semantic Array Programming for Integrated Environmental Modelling

[Excerpt] Interfacing science and policy raises challenging issues when large spatial-scale (regional, continental, global) environmental problems need transdisciplinary integration within a context of modelling complexity and multiple sources of uncertainty. This is characteristic of science-based support for environmental policy at European scale, and key aspects have also long been investigated by European Commission transnational research. Approaches (either of computational science or of policy-making) suitable at a given domain-specific scale may not be appropriate for wide-scale transdisciplinary modelling for environment (WSTMe) and corresponding policy-making. In WSTMe, the characteristic heterogeneity of available spatial information and complexity of the required data-transformation modelling (D-TM) appeal for a paradigm shift in how computational science supports such peculiarly extensive integration processes. In particular, emerging wide-scale integration requirements of typical currently available domain-specific modelling strategies may include increased robustness and scalability along with enhanced transparency and reproducibility. This challenging shift toward open data and reproducible research (open science) is also strongly suggested by the potential - sometimes neglected - huge impact of cascading effects of errors within the impressively growing interconnection among domain-specific computational models and frameworks. Concise array-based mathematical formulation and implementation (with array programming tools) have proved helpful in supporting and mitigating the complexity of WSTMe when complemented with generalized modularization and terse array-oriented semantic constraints. This defines the paradigm of Semantic Array Programming (SemAP) where semantic transparency also implies free software use (although black-boxes - e.g. legacy code - might easily be semantically interfaced). A new approach for WSTMe has emerged by formalizing unorganized best practices and experience-driven informal patterns. The approach introduces a lightweight (non-intrusive) integration of SemAP and geospatial tools - called Geospatial Semantic Array Programming (GeoSemAP). GeoSemAP exploits the joint semantics provided by SemAP and geospatial tools to split a complex D-TM into logical blocks which are easier to check by means of mathematical array-based and geospatial constraints. Those constraints take the form of precondition, invariant and postcondition semantic checks. This way, even complex WSTMe may be described as the composition of simpler GeoSemAP blocks. GeoSemAP allows intermediate data and information layers to be more easily and formally semantically described so as to increase fault-tolerance, transparency and reproducibility of WSTMe. This might also help to better communicate part of the policy-relevant knowledge, often diffcult to transfer from technical WSTMe to the science-policy interface. [...

Practical approaches to produce high-quality probabilistic predictions and improve risk-based design making

Conference theme 'Digital Water.'Probabilistic predictions provide crucial information regarding the uncertainty of hydrological predictions, which are a key input for risk-based decision-making. High-quality probabilistic predictions provide reliable estimates of water resource system risks – avoiding a false sense of security. However, probabilistic predictions are not widely used in hydrological modelling applications because they are perceived to be difficult to construct and interpret. We present a software tool that provides an easy-to-use and simple approach to produce high-quality probabilistic streamflow predictions. The approach integrates the recommendations from multiple research papers over multiple years to provide guidance on selection of robust descriptions of uncertainty (residual error models) for a wide range of hydrological applications. This guidance includes the choice of transformation to handle common features of residual errors (heteroscedasticity, skewness, persistence) and techniques that handles a wide range of common objective functions. A case study illustrating the practical benefits of uncertainty analysis for risk-based decision- making is provided. The case study evaluates fish health in two catchments (Mt. McKenzie and Upper Jacobs) in Barossa Valley, South Australia. The streamflow predictions of environmental flow metrics are combined with a simplified environmental response model to estimate fish health. The outcomes obtained using deterministic streamflow predictions are contrasted to the outcomes obtained from probabilistic predictions. In general, probabilistic predictions provide greater confidence in the predictions of fish health because the uncertainty ranges recognise the differences at the two sites between the quality of hydrological predictions. The uncertainty ranges were generally high, in the range 40-60% (Mt McKenzie) or 4-20% (Upper Jacobs) for predictions of the frequency of years with poor (or worse) fish health. This analysis provides a richer source of information for risk averse decision-makers than the single values provided by deterministic predictions.Mark Thyer, David McInerney, Dmitri Kavetski, Jason Hunte

High-quality probabilistic predictions for existing hydrological models with common objective functions

Conference theme 'Digital Water.'Probabilistic predictions describe the uncertainty in modelled streamflow, which is a critical input for many environmental modelling applications. A residual error model typically produces the probabilistic predictions in tandem with a hydrological model that predicts the deterministic streamflow. However, many objective functions that are commonly used to calibrate the parameters of the hydrological model make (implicit) assumptions about the errors that do not match the properties (e.g. of heteroscedasticity and skewness) of those errors. The consequence of these assumptions is often low-quality probabilistic predictions of errors, which reduces the practical utility of probabilistic modelling. Our study has two aims: Firstly, to evaluate the impact of objective function inconsistency on the quality of probabilistic predictions; Secondly, to demonstrate how a simple enhancement to a residual error model can rectify the issues identified with inconsistent objective functions in Aim 1, and thereby improve probabilistic predictions in a wide range of scenarios. Our findings show that the enhanced error model enables high-quality probabilistic predictions to be obtained for a range of catchments and objective functions, without requiring any changes to the hydrological modelling or calibration process. This advance has practical benefits that are aimed at increasing the uptake of probabilistic predictions in real-world applications, in that the methods are applicable to existing hydrological models that are already calibrated, simple to implement, easy to use and fast. Finally, these methods are available as an open-source R-shiny application and an R-package function.Jason Hunter, Mark Thyer, David McInerney, Dmitri Kavetsk