bluuebunny/crossref_metadata_2025 huggingface dataset:
CropSurveyor: a scalable open-source experiment management system for distributed plant phenotyping and IoT-based crop management
Authors: Reynolds Daniel , Ball Joshua , Bauer Alan , Griffiths Simon , Zhou Ji
Published: October 2018

Background:

High-quality plant phenotyping and climate data lay the foundation of phenotypic analysis as well as genotype-by-environment interactions, which is important biological evidence not only to understand the dynamics between crop performance, genotypes, and environmental factors, but also for agronomists and farmers to monitor crops in fluctuating agricultural conditions. With the rise of Internet of Things technologies in recent years, many IoT-based remote sensing devices have been applied to phenotyping and crop monitoring that generate big plant-environment datasets every day; however, it is still technically challenging to calibrate, annotate, and aggregate big data effectively, especially when they were generated in multiple locations, and often at different scales.

Findings:

CropSurveyor is a PHP and SQL based server platform, which provides automated data collation, storage, device and experiment management through IoT-based sensors and distributed plant phenotyping workstations. It provides a two-component solution for monitoring biological experiments and networked devices, with interfaces specifically designed for distributed IoT devices and centralised data servers. Data transfer is performed automatically though an HTTP accessible RESTful API installed on both device-side and server-side of the CropSurveyor system, which synchronise daily representative crop growth images for quick and visual-based crop assessment, as well as detailed microclimate readings for GxE studies. CropSurveyor also supports the comparison of historical and ongoing crop performance whilst different experiments are being conducted.

Conclusions:

As an open-source experiment and data management system, CropSurveyor can be used to maintain and collate important crop performance and microclimate datasets captured by IoT sensors and distributed phenotyping installations. It provides near real-time environmental and crop growth monitoring in addition to historical and current data comparison through a single cloud-ready server system. Accessible both locally in the field through smart devices and remotely in an office using a PC, CropSurveyor has been used in wheat field experiments for prebreeding since 2016 and has the potential to enable scalable crop management and IoT-style agricultural practices in the near future.
Perfect Counterfactuals for Epidemic Simulations
Authors: Kaminsky Joshua , Keegan Lindsay T. , E. Metcalf C. Jessica , Lessler Justin
Published: October 2018

Simulation studies are often used to predict the expected impact of control measures in infectious disease outbreaks. Typically, two independent sets of simulations are conducted, one with the intervetnion, and one without, and epidemic sizes (or some related metric) are compared to estimate the effect of the intervention. Since it is possible that controlled epidemics are larger than uncontrolled ones if there is substantial stochastic variation between epidemics, uncertainty intervals from this approach can include a negative effect even for an effective intervention. To more precisely estimate the number of cases an intervention will prevent within a single epidemic, here we develop a ‘single world’ approach to matching simulations of controlled epidemics to their exact uncontrolled counterfac-tual. Our method borrows concepts from percolation approaches prune out possible epidemic histories and create potential epidemic graph that can be ‘realized’ to create perfectly matched controlled and uncontrolled epidemics. We present an implementation of this method for a common class of compartmental models, and its application in a simple SIR model. Results illustrate how, at the cost of some computation time, this method substantially narrows confidence intervals and avoids non-sensical inferences.
Genomic basis of transcriptome dynamics in rice under field conditions
Authors: Kashima Makoto , Sakamoto Ryota L. , Saito Hiroki , Ohkubo Satoshi , Tezuka Ayumi , Deguchi Ayumi , Hashida Yoichi , Kurita Yuko , Iwayama Koji , Adachi Shunsuke , Nagano Atsushi J.
Published: October 2018

How genetic variations affect gene expression dynamics of field-grown plants remains unclear. Using statistical analysis of large-scale time-series RNA-sequencing of field-grown rice from chromosome segment substitution lines (CSSLs), we identified 1675 expression dynamics quantitative trait loci (edQTLs) leading to polymorphisms in expression dynamics under field conditions. Based on the edQTL and environmental information, we successfully predicted gene expression under environments different from training environments, and in rice cultivars with more complex genotypes than the CSSLs. Overall, edQTL’ identification helped understanding the genetic architecture of expression dynamics under field conditions, which is difficult to assess with laboratory experiments1.The prediction of expression based on edQTL and environmental information will contribute to crop breeding by increasing the accuracy of trait prediction under diverse conditions.
Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation
Authors: He Shengbo , Vickers Martin , Zhang Jingyi , Feng Xiaoqi
Published: October 2018

Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation.
Novel genome-wide associations for suicidality in UK Biobank, genetic correlation with psychiatric disorders and polygenic association with completed suicide
Authors: Strawbridge Rona J. , Ward Joey , Ferguson Amy , Graham Nicholas , Shaw Richard J , Cullen Breda , Pearsall Robert , Lyall Laura M. , Johnston Keira J.A. , Niedzwiedz Claire L. , Pell Jill P. , Mackay Daniel , Martin Julie Langan , Lyall Donald M. , Bailey Mark E.S. , Smith Daniel J.
Published: October 2018

Background: Suicide is a major issue for global public health. ‘Suicidality’ describes a broad clinical spectrum of thoughts and behaviours, some of which are common in the general population.

Methods: UK Biobank recruited ∼0·5 million middle age individuals from the UK, of whom 157,000 completed an assessment of suicidality. Mutually exclusive groups were assessed in an ordinal genome-wide association study of suicidality: ‘no suicidality’ controls (N=83,557); ‘thoughts that life was not worth living’ (N=21,063); ‘ever contemplated self-harm’ (N=13,038); ‘an act of deliberate self-harm in the past’ (N=2,498); and ‘a previous suicide attempt’ (N=2,666). Linkage of UK Biobank to death certification records identified a small sub-group of ‘completed suicide’ (N=137).

Outcomes: We identified three novel genome-wide significant loci for suicidality (on Chromosomes 9, 11 and 13) and moderate-to-strong genetic correlations between suicidality and a range of psychiatric disorders, most notably depression (rg 0·81). Higher polygenic risk scores for suicidality were associated with increased risk of completed suicide relative to controls in an independent sub-group (N=137 vs N=5,330, OR 1·23, 95%CI 1·06 to 1·41, p=0.03). Rs598046-G (chromosome 11) demonstrated a similar effect size and direction (p=0·05) within a Danish suicidality study.

Interpretation: These findings have significant implications for our understanding of genetic vulnerability to suicidal thoughts and behaviours. Future work should assess the extent to which polygenic risk scores for suicidality, in combination with non-genetic risk factors, may be useful for stratified approaches to suicide prevention at a population level.

Funding: UKRI Innovation-HDR-UK Fellowship (MR/S003061/1). MRC Mental Health Data Pathfinder Award (MC_PC_17217).
Baseline corticosterone does not reflect iridescent plumage traits in female tree swallows
Authors: Sarpong Keneth , Madliger Christine L. , Harris Christopher M. , Love Oliver P. , Doucet Stéphanie M. , Bitton Pierre-Paul
Published: October 2018

The production of high quality secondary sexual traits can be constrained by trade-offs in the allocation of energy and nutrients with other metabolic activities, and is mediated by physiological processes. In birds, the factors influencing male plumage quality have been well studied; however, factors affecting female plumage quality are poorly understood. Furthermore, it remains uncertain which physiological traits mediate the relationship between body condition and ornaments. In this three-year study of after-second-year female tree swallows (Tachycineta bicolor), we investigated (1) the relationship between baseline corticosterone near the end of the brood-rearing period (CORTBR) and feather colour characteristics (hue, saturation, brightness) the following year, and (2) the relationship between baseline corticosterone measured during incubation (CORTI) and brood rearing (CORTBR), and feather colour in the same year. To control for reproductive effort, we included reproductive parameters as covariates in all analyses. In this first study between CORT and the plumage colour characteristics of a species bearing iridescent feathers, we did not find any relationship between CORTBRand the colour of subsequently-produced feathers, nor did we find any relationship between CORTIand the colour of feathers displayed during that breeding season. If CORT levels at the end of breeding carry over to influence the immediately subsequent moult period as we expect, our results generally indicate that structural plumage quality may not be as sensitive to circulating CORT levels compared to carotenoid-based colouration. Future studies, particularly those employing experimental manipulations of CORT during moult in species with iridescent traits, are necessary to fully determine the role glucocorticoids play in mediating the quality of secondary sexual characteristics.
Phytoplankton thermal responses adapt in the absence of hard thermodynamic constraints
Authors: Kontopoulos Dimitrios - Georgios , van Sebille Erik , Lange Michael , Yvon-Durocher Gabriel , Barraclough Timothy G. , Pawar Samraat
Published: October 2018

To better predict how populations and communities respond to climatic temperature variation, it is necessary to understand how the shape of the response of fitness-related traits to temperature evolves (the thermal performance curve). Currently, there is disagreement about the extent to which the evolution of thermal performance curves is constrained. One school of thought has argued for the prevalence of thermodynamic constraints through enzyme kinetics, whereas another argues that adaptation can—at least partly—overcome such constraints. To shed further light on this debate, we perform a phylogenetic meta-analysis of the thermal performance curves of growth rate of phytoplankton—a globally important functional group—, controlling for environmental effects (habitat type and thermal regime). We find that thermodynamic constraints have a minor influence on the shape of the curve. In particular, we detect a very weak increase of maximum performance with the temperature at which the curve peaks, suggesting a weak “hotter-is-better” constraint. Also, instead of a constant thermal sensitivity of growth across species, as might be expected from strong constraints, we find that all aspects of the thermal performance curve evolve along the phylogeny. Our results suggest that phytoplankton thermal performance curves adapt to thermal environments largely in the absence of hard thermodynamic constraints.
Topographical cuescontrol the morphology and dynamics of migrating cortical interneurons
Authors: Leclech Claire , Renner Marianne , Villard catherine , Métin Christine
Published: October 2018

In mammalian embryos, cortical interneurons travel long distances among complex three-dimensional tissues before integrating into cortical circuits. Several molecular guiding cues involved in this migration process have been identified, but the influence of physical parameters remains poorly understood. In the present study, we have investigatedin vitrothe influence of the topography of the microenvironment on the migration of primary cortical interneurons released from mouse embryonic explants.

We found that arrays of 10 μm-sized PDMS micro-pillars, either round or square, influenced both the morphology and the migratory behavior of interneurons. Strikingly, most interneurons exhibited a single and long leading process oriented along the diagonals of the square pillared array, whereas leading processes of interneurons migrating in-between round pillars were shorter, often branched and oriented in all available directions. Accordingly, dynamic studies revealed that growth cone divisions were twice more frequent in round than in square pillars. Both soma and leading process tips presented forward directed movements within square pillars, contrasting with the erratic trajectories and more dynamic movements observed among round pillars. In support of these observations, long interneurons migrating in square pillars displayed tight bundles of stable microtubules aligned in the direction of migration.

Overall, our results show that micron-sized topography provides global spatial constraints promoting the establishment of two different morphological and migratory states. Remarkably, both states belong to the natural range of migratory behaviors of cortical interneurons, highlighting the potential importance of topographical cues in the guidance of these embryonic neurons, and more generally in brain development.
Resistance diagnostics as a public health tool to combat antibiotic resistance: A model-based evaluation
Authors: McAdams David , Waldetoft Kristofer Wollein , Tedijanto Christine , Lipsitch Marc , Brown Sam P.
Published: October 2018

Rapid point-of-care resistance diagnostics (POC-RD) are a key tool in the fight against antibiotic resistance. By tailoring drug choice to infection genotype, doctors can improve treatment efficacy while limiting costs of inappropriate antibiotic prescription. Here we combine epidemiological theory and data to assess the potential of RD innovations in a public health context, as a means to limit or even reverse selection for antibiotic resistance. POC-RD can be used to impose a non-biological fitness cost on resistant strains, by enabling diagnostic-informed treatment and targeted interventions that reduce resistant strains’ opportunities for transmission. We assess this diagnostic-imposed fitness cost in the context of a spectrum of bacterial population biologies, and find that the expected impact varies from selection against resistance for obligate pathogens to marginal public health improvements for opportunistic pathogens with high ‘bystander’ antibiotic exposure during asymptomatic carriage (e.g. the pneumococcus). We close by generalizing the notion of RD-informed strategies to incorporate carriage surveillance information, and illustrate that coupling transmission-control interventions to the discovery of resistant strains in carriage can potentially select against resistance in a broad range of opportunistic pathogens.
Hippocampal theta bursting and waveform shape reflect CA1 spiking patterns
Authors: Cole Scott , Voytek Bradley
Published: October 2018

Brain rhythms are nearly always analyzed in the spectral domain in terms of their power, phase, and frequency. While this conventional approach has uncovered spike-field coupling, as well as correlations to normal behaviors and pathological states, emerging work has highlighted the physiological and behavioral importance of multiple novel oscillation features. Oscillatory bursts, for example, uniquely index a variety of cognitive states, and the nonsinusoidal shape of oscillations relate to physiological changes, including Parkinson’s disease. Open questions remain regarding how bursts and nonsinusoidal features relate to circuit-level processes, and how they interrelate. By analyzing unit and local field recordings in the rodent hippocampus, we uncover a number of significant relationships between oscillatory bursts, nonsinusoidal waveforms, and local inhibitory and excitatory spiking patterns. Bursts of theta oscillations are surprisingly related to a decrease in pyramidal neuron synchrony, and have no detectable effect on firing sequences, despite significant increases in neuronal firing rates during periods of theta bursting. Theta burst duration is predicted by the asymmetries of its first cycle, and cycle asymmetries relate to firing rate, synchrony, and sequences of pyramidal neurons and interneurons. These results provide compelling physiological evidence that time-domain features, of both nonsinusoidal hippocampal theta waveform and the theta bursting state, reflects local circuit properties. These results point to the possibility of inferring circuit states from local field potential features in the hippocampus and perhaps other brain regions with other rhythms.
Irregular chromatin: packing density, fiber width and occurrence of heterogeneous clusters
Authors: Bajpai Gaurav , Padinhateeri Ranjith
Published: October 2018

How chromatin is folded in the lengthscale of a gene is an open question. Recent experiments have suggested that, in vivo, chromatin is folded in an irregular manner and not as an ordered fiber with a width of 30 nm expected from theories of higher order packaging. Using computational methods, we examine how the interplay between DNA-bending non histone proteins, histone tails, intra-chromatin electrostatic and other interactions decide the nature of packaging of chromatin. We show that while the DNA-bending non histone proteins make the chromatin irregular, they may not alter the packing density and size of the fiber. We find that the length of the interacting region and intra-chromatin electrostatic interactions influence the packing density, clustering of nucleosomes, and the width of the chromatin fiber. Our results suggest that the actively maintained heterogeneity in the interaction pattern will play an an important role in deciding the nature of packaging of chromatin.
How non-veridical perception drives actions in healthy humans - Evidence from Synaesthesia
Authors: Luise Schreiter Marie , Chmielewski Witold X. , Ward Jamie , Beste Christian
Published: October 2018

We continually perform actions driven by our perception and it is commonly held that only objectively perceived changes within the ‘real’ world affect behaviour. Exceptions are usually only made for clinical conditions associated with hallucinations, where objectively non-existent percepts can influence behavior. Using synaesthesia as a model condition, we show that even in healthy populations irrelevant non-veridical precepts exert an effect on action. By non-veridical we refer to stimulus dimensions that are only subjectively perceived to be there. Applying electrophysiological (EEG) methods, we show that although these examined peculiarities are perceptual in nature, not primarily perceptual processes underlie the effects of irrelevant non-veridical perceptions on actions. Rather, high-order processes linking perceptions and motor control in medial frontal cortices reflect the underlying mechanism how irrelevant non-veridical perceptions modulate behaviour. Our results challenge assumptions about the determinants of healthy human behaviour but can be embedded within existing frameworks detailing perception action interactions.
SKA: Split Kmer Analysis Toolkit for Bacterial Genomic Epidemiology
Authors: Harris S. R.
Published: October 2018

Genome sequencing is revolutionising infectious disease epidemiology, providing a huge step forward in sensitivity and specificity over more traditional molecular typing techniques. However, the complexity of genome data often means that its analysis and interpretation requires high-performance compute infrastructure and dedicated bioinformatics support. Furthermore, current methods have limitations that can differ between analyses and are often opaque to the user, and their reliance on multiple external dependencies makes reproducibility difficult. Here I introduce SKA, a toolkit for analysis of genome sequence data from closely-related, small, haploid genomes. SKA uses split kmers to rapidly identify variation between genome sequences, making it possible to analyse hundreds of genomes on a standard home computer. Tests on publicly available simulated and real-life data show that SKA is both faster and more efficient than the gold standard methods used today while retaining similar levels of accuracy for epidemiological purposes. SKA can take raw read data or genome assemblies as input and calculate pairwise distances, create single linkage clusters and align genomes to a reference genome or using a reference-free approach. SKA requires few decisions to be made by the user, which, along with its computational efficiency, allows genome analysis to become accessible to those with only basic bioinformatics training. The limitations of SKA are also far more transparent than for current approaches, and future improvements to mitigate these limitations are possible. Overall, SKA is a powerful addition to the armoury of the genomic epidemiologist. SKA source code is available from Github (https://github.com/simonrharris/SKA).
Predictive coding with neural transmission delays: a real-time temporal alignment hypothesis
Authors: Hogendoorn Hinze , Burkitt Anthony N
Published: October 2018

Hierarchical predictive coding is an influential model of cortical organization, in which sequential hierarchical layers are connected by feedback connections carrying predictions, as well as feedforward connections carrying prediction errors. To date, however, predictive coding models have neglected to take into account that neural transmission itself takes time. For a time-varying stimulus, such as a moving object, this means that feedback predictions become misaligned with new sensory input. We present an extended model implementing both feed-forward and feedback extrapolation mechanisms that realigns feedback predictions to minimize prediction error. This realignment has the consequence that neural representations across all hierarchical stages become aligned in real-time. Using visual motion as an example, we show that the model is neurally plausible, that it is consistent with evidence of extrapolation mechanisms throughout the visual hierarchy, that it predicts several known motion-position illusions, and that it provides a solution to the temporal binding problem.
Detection of low-density Plasmodium falciparum infections using amplicon deep sequencing
Authors: Early Angela M. , Daniels Rachel F. , Farrell Timothy M. , Grimsby Jonna , Volkman Sarah K. , Wirth Dyann F. , MacInnis Bronwyn L. , Neafsey Daniel E.
Published: October 2018

Background

Deep sequencing of targeted genomic regions is becoming a common tool for understanding the dynamics and complexity of Plasmodium infections, but its lower limit of detection is currently unknown. Here, a new amplicon analysis tool, the Parallel Amplicon Sequencing Error Correction (PASEC) pipeline, is used to evaluate the performance of amplicon sequencing on low-density Plasmodium DNA samples. Illumina-based sequencing of two P. falciparum genomic regions (CSP and SERA2) was performed on two types of samples: in vitro DNA mixtures mimicking low-density infections (1-200 genomes/μl) and extracted blood spots from a combination of symptomatic and asymptomatic individuals (44-653,080 parasites/μl). Three additional analysis tools—DADA2, HaplotypR, and SeekDeep—were applied to both datasets and the precision and sensitivity of each tool were evaluated.

Results

Amplicon sequencing can contend with low-density samples, showing reasonable detection accuracy down to a concentration of 5 Plasmodium genomes/μl. Due to increased stochasticity and background noise, however, all four tools showed reduced sensitivity and precision on samples with very low parasitemia (<5 copies/μl) or low read count (<100 reads per amplicon). PASEC could distinguish major from minor haplotypes with an accuracy of 90% in samples with at least 30 Plasmodium genomes/μl, but only 61% at low Plasmodium concentrations (<5 genomes/μl) and 46% at very low read counts (<25 reads per amplicon). The four tools were additionally used on a panel of extracted parasite-positive blood spots from natural malaria infections. While all four identified concordant patterns of complexity of infection (COI) across four sub-Saharan African countries, the COI values obtained for individual samples differed in some cases.

Conclusions

Amplicon deep sequencing can be used to determine the complexity and diversity of low-density Plasmodium infections. Despite differences in their approach, four state-of-the-art tools resolved known haplotype mixtures with similar sensitivity and precision. Researchers can therefore choose from multiple robust approaches for analyzing amplicon data, however, error filtration approaches should not be uniformly applied across samples of varying parasitemia. Samples with very low parasitemia and very low read count have higher false positive rates and call for read count thresholds that are higher than current recommendations.
HLA*PRG:LA – HLA typing from linearly projected graph alignments
Authors: Dilthey Alexander T , Mentzer Alexander J , Carapito Raphael , Cutland Clare , Cereb Nezih , Madhi Shabir A. , Rhie Arang , Koren Sergey , Bahram Seiamak , McVean Gil , Phillippy Adam M
Published: October 2018

HLA*PRG:LA implements a new graph alignment model for HLA type inference, based on the projection of linear alignments onto a variation graph. It enables accurate HLA type inference from whole-genome (99% accuracy) and whole-exome (93% accuracy) Illumina data; from long-read Oxford Nanopore and Pacific Biosciences data (98% accuracy for whole-genome and targeted data); and from genome assemblies. Computational requirements for a typical sample vary between 0.7 and 14 CPU hours per sample.

Availability and Implementation:

HLA*PRG:LA is implemented in C++ and Perl and freely available from https://github.com/DiltheyLab/HLA-PRG-LA (GPL v3).

Contact:

alexander.dilthey@med.uni-duesseldorf.de

Supplementary information

Supplementary data are available online.
DNA motifs are not general predictors of recombination in twoDrosophilasister species
Authors: Howie James M. , Mazzucco Rupert , Taus Thomas , Nolte Viola , Schlötterer Christian
Published: October 2018

Meiotic recombination is crucial for chromosomal segregation, and facilitates the spread of beneficial and removal of deleterious mutations. Recombination rates frequently vary along chromosomes andDrosophila melanogasterexhibits a remarkable pattern. Recombination rates gradually decrease towards centromeres and telomeres, with dramatic impact on levels of variation in natural populations. Two close sister species,D. simulansandD. mauritianado not only have higher recombination rates, but also exhibit a much more homogeneous recombination rate that only drops sharply close to centromeres and telomeres. Because certain sequence motifs are associated with recombination rate variation inD. melanogaster, we tested whether the difference in recombination landscape betweenD. melanogasterandD. simulanscan be explained by the genomic distribution of recombination-rate associated sequence motifs. We constructed the first high resolution recombination map forD. simulans, and searched for motifs linked with high recombination in both sister species. We identified five consensus motifs, present in either species. While the association between motif density and recombination is strong and positive inD. melanogaster, the results are equivocal inD. simulans. Despite the strong association inD. melanogaster, we do not find a decreasing density of these repeat motifs towards centromeres and telomeres. We conclude that the density of recombination-associated repeat motifs cannot explain the large-scale recombination landscape inD. melanogaster, nor the differences toD. simulans. The strong association seen for the sequence motifs inD. melanogasterlikely reflects their impact influencing local differences in recombination rates along the genome.
RNA polymerase clamp movement aids dissociation from DNA but is not required for RNA release at intrinsic terminators
Authors: Bellecourt Michael J , Ray-Soni Ananya , Harwig Alex , Mooney Rachel Anne , Landick Robert
Published: October 2018

In bacteria, disassembly of elongating transcription complexes (ECs) can occur at intrinsic terminators in a 2-3 nucleotide window after transcription of multiple kilobase pairs of DNA. Intrinsic terminators trigger pausing on weak RNA-DNA hybrids followed by formation of a strong, GC-rich stem-loop in the RNA exit channel of RNA polymerase (RNAP), inactivating nucleotide addition and inducing dissociation of RNA and RNAP from DNA. Although the movements of RNA and DNA during intrinsic termination have been studied extensively leading to multiple models, the effects of RNAP conformational changes remain less well-defined. RNAP contains a clamp domain that closes around the nucleic-acid scaffold during transcription initiation and can be displaced by either swiveling or opening motions. Clamp opening is proposed to promote termination by releasing RNAP-nucleic acid contacts. We developed a cysteine-crosslinking assay to constrain clamp movements and study effects on intrinsic termination. We found that biasing the clamp into different conformations perturbed termination efficiency, but that perturbations were due primarily to changes in elongation rate, not the competing rate at which ECs commit to termination. After commitment, however, inhibiting clamp movements slowed release of DNA but not of RNA from the EC. We also found that restricting trigger-loop movements with the RNAP inhibitor microcin J25 prior to commitment inhibits termination, in agreement with a recently proposed multistate-multipath model of intrinsic termination. Together our results support views that termination commitment and DNA release are separate steps and that RNAP may remain associated with DNA after termination.

Highlights

Disulfide bond crosslinks probe the role of the RNAP clamp domain in termination

RNA but not DNA can release at terminators when the RNAP clamp is closed

Restricting RNAP clamp movement affects elongation rate more than termination rate

Inhibiting TL conformational flexibility impairs both RNA and DNA release
Evolution of resilience in protein interactomes across the tree of life
Authors: Zitnik Marinka , Sosič Rok , Feldman Marcus W. , Leskovec Jure
Published: October 2018

Phenotype robustness to environmental fluctuations is a common biological phenomenon. Although most phenotypes involve multiple proteins that interact with each other, the basic principles of how such interactome networks respond to environmental unpredictability and change during evolution are largely unknown. Here we study interactomes of 1,840 species across the tree of life involving a total of 8,762,166 protein-protein interactions. Our study focuses on the resilience of interactomes to network failures and finds that interactomes become more resilient during evolution, meaning that interactomes become more robust to network failures over time. In bacteria, we find that a more resilient interactome is in turn associated with the greater ability of the organism to survive in a more complex, variable and competitive environment. We find that at the protein family level, proteins exhibit a coordinated rewiring of interactions over time and that a resilient interactome arises through gradual change of the network topology. Our findings have implications for understanding molecular network structure both in the context of evolution and environment.
Inductive determination of allele frequency spectrum probabilities in structured populations
Authors: Uyenoyama Marcy K. , Takebayashi Naoki , Kumagai Seiji
Published: October 2018

We present a method for inductively determining exact allele frequency spectrum (AFS) probabilities for samples derived from a population comprising two demes under the infinite-allele model of mutation. This method builds on a labeled coalescent argument to extend the Ewens sampling formula (ESF) to structured populations. A key departure from the panmictic case is that the AFS conditioned on the number of alleles in the sample is no longer independent of the scaled mutation rate (θ). In particular, biallelic site frequency spectra, widely-used in explorations of genome-wide patterns of variation, depend on the mutation rate in structured populations. Variation in the rate of substitution across loci and through time may contribute to apparent distortions of site frequency spectra exhibited by samples derived from structured populations.
Climate drives spatial variation in Zika epidemics in Latin America
Authors: Harris Mallory , Caldwell Jamie M. , Mordecai Erin A.
Published: October 2018

Between 2015 and 2017, Zika virus spread rapidly through populations in the Americas with no prior exposure to the disease. Although climate is a known determinant of many Aedes-transmitted diseases, it is currently unclear whether climate was a major driver the of Zika epidemic and how climate might have differentially impacted outbreak intensity across locations within Latin America. Here, we estimated force of infection for Zika over time and across provinces in Latin America using a time-varying Susceptible Infectious Recovered model. Climate factors explained less than 5% of the variation in weekly transmission intensity in a spatiotemporal model of force of infection by province over time, suggesting that week to week transmission within provinces may be too stochastic to predict. By contrast, climate and population factors were highly predictive of spatial variation in the presence and intensity of Zika transmission among provinces, with pseudo R2 values between 0.33 and 0.60. Temperature, temperature range, rainfall, and population size were the most important predictors of where Zika transmission occurred, while rainfall, relative humidity, and a nonlinear effect of temperature were the best predictors of Zika intensity and burden. Surprisingly, force of infection was greatest in locations with temperatures near 24°C, much lower than previous estimates from mechanistic models, potentially suggesting that existing vector control programs and/or prior exposure to other mosquito-borne diseases may have limited transmission in locations most suitable for Aedes aegypti, the main vector of Zika, dengue, and chikungunya viruses in Latin America.
Sex allocation conflict and sexual selection throughout the lifespan of eusocial colonies
Authors: Avila Piret , Fromhage Lutz , Lehmann Laurent
Published: October 2018

Models of sex allocation conflict are central to evolutionary biology but have mostly assumed static decisions, where resource allocation strategies are constant over colony lifespan. Here, we develop a model to study how the evolution of dynamic resource allocation strategies is affected by the queen-worker conflict in annual eusocial insects. We demonstrate that the time of dispersal of sexuals affects the sex allocation ratio through sexual selection on males. Furthermore, our model provides three predictions that depart from established results of classic static allocation models. First, we find that the queen wins the sex allocation conflict, while the workers determine the maximum colony size and colony productivity. Second, male-biased sex allocation and protandry evolve if sexuals disperse directly after eclosion. Third, when workers are more related to new queens, then the proportional investment into queens is expected to be lower, which results from the interacting effect of sexual selection (selecting for protandry) and sex allocation conflict (selecting for earlier switch to producing sexuals). Overall, we find that colony ontogeny crucially affects the outcome of sex-allocation conflict because of the evolution of distinct colony growth phases, which decouples how queens and workers affect allocation decisions and can result in asymmetric control.
Bacteriophages dynamically modulate the gut microbiota and metabolome
Authors: Hsu Bryan B. , Gibson Travis E. , Yeliseyev Vladimir , Liu Qing , Bry Lynn , Silver Pamela A. , Gerber Georg K.
Published: October 2018

The human gut microbiome is comprised of densely colonizing micro-organisms in dynamic interaction with each other and the host. While the bacterial component of the microbiome is under intense investigation, far less is known about how bacteriophages impact bacterial communities in the gut. We investigated the dynamic effects of phages on a model microbiome using gnotobiotic mice colonized by commensal bacteria that colonize the human infant gut, and found that phage predation not only directly impacts susceptible bacteria but also leads to cascading effects on other bacterial speciesviainter-bacterial interactions. Using metabolomic profiling, we also found that the shifts in the microbiome caused by phage predation have a direct consequence on the gut metabolome. Our work provides insight into the ecological importance of phages as modulators of bacterial colonization, and additionally suggests the potential impact of gut phages on the host with implications for the use of phages as therapeutic tools to rationally and precisely modulate the microbiome.
Targeted synthesis of a polypyridyl polyoxometalate coordination complex using microwave-assisted reaction conditions
Authors: Xu Jingjing , Gable Robert W. , Ritchie Chris
Published: October 2018

In this article, we build upon our recent efforts that have focused on demonstrating the value of microwave-assisted synthesis in polyoxometalate (POM) chemistry. Herein, we report for the first time a microwave-assisted approach that enabled the facile preparation and crystallization of a large POM-containing coordination complex. The judicious selection and reaction of a sparingly water-soluble transition-metal-substituted polyanion (TMSP) salt with the tritopic ligand 2,4,6-tris(4-pyridyl)-1,3,5-triazine (TPT) in a mixed solvent system under moderately forcing conditions yields Ba9[(BIIIWVI
11O39CoIII)3(C18H12N6)]·38H2O in moderate yield. Crystallographic analysis reveals significant intermolecular interactions between the organic ligand and neighbouring polyanions, predominantly C—H...O(water) in nature; meanwhile, the solvated regions of the crystal show significant disorder. To supplement the crystallographic study, combustion analysis, and IR and 1H NMR spectroscopic analyses were conducted, revealing good bulk purity and the stability of the complex in aqueous media.
(Z)-1,2-Bis(3-bromophenyl)diazene 1-oxide
Authors: Goswami Shailesh K. , Hanton Lyall R. , McAdam C. John , Moratti Stephen C. , Simpson Jim
Published: October 2018

The title compound C12H8Br2N2O, lies on an inversion centre in the space group P21/n. Doubts are cast on the report of a polymorph of this structure in the non-centrosymmetric space group P21 [Zhu, R.-T., Liu, J.-C., Jin, S., Liu, B. & Guo J.-P. (2006). Hecheng Huaxue (Chin. J. Synth. Chem.) 14, 591] as ADDSYM alerts point strongly to a centrosymmetric structure. In the crystal, C—H...O and C—H...Br hydrogen bonds together with offset π–π interactions stack the molecules along the a-axis direction.
Safety management systems: an opportunity and a challenge for military aviation organisations
Authors: Chatzi Anna V.
Published: October 2018

Purpose

Most military aviation organisations today have not evolved their safety management approach towards harmonising with civil aviation. Safety culture is the base for any civil aviation organisation, enabling employees to communicate effectively and be fully aware and extrovert on safety. Just culture and reporting culture both are related to safety culture. Both are parts of the awareness process, enhancing safety promotion. These distinct elements and the safety management systems (SMS) can serve well the military aviation. This paper aims to present and discuss the SMS philosophy, structure and elements as a solution for military aviation organisations.

Design/methodology/approach

The feature of civil aviation SMSs are presented and discussed, with reference to the applicable frameworks and regulations governing the SMS operation. A discussion on the challenges faced within the military aviation organisations, with a brief examination of a European Union military aviation organisation, is presented.

Findings

The European Military Airworthiness Requirements, which are based on the European Aviation Safety Agency set of rules, can act the basis for establishing military aviation SMSs. A civil-based approach, blended, as necessary, with military culture is workable, as this is the case for many defence forces that have adopted such aviation safety systems.

Originality/value

This viewpoint paper discusses the opportunities and challenges associated with the adoption of SMS by military aviation organisations. This is the first time that this issue is openly discussed and presented to the wider aviation community, outside military aviation.
The health and social care of people with disabilities in Germany
Authors: Elstner Samuel , Theil Michael-Mark
Published: October 2018

Purpose

The purpose of this paper is to present information on the health care system in Germany with the focus on mental health care in people with intellectual disabilities (ID).

Design/methodology/approach

The paper is descriptive providing an overview of the general structure of the German health care system with historical and economic background. The paper also provides further information on the general social and health care in Germany for people with ID and medical education in the field of ID is used.

Findings

There is a highly developed health care infrastructure in Germany but health care for people with ID is not co-ordinated or universal. Mental health care for people with ID is predominantly in in-patient services. Only in recent years, out-patient services for people with ID have been developed. There is a little emphasis in medical education on the health care needs of people with ID.

Originality/value

The value of this paper is its description of health care in Germany and services for people with ID.
Determinants of operational efficiency in the oil and gas sector
Authors: Al-Qubaisi Salama S. , Ajmal Mian
Published: October 2018

Purpose

There is limited research that indicates the relation between knowledge management practices (KMPs), organizational culture (OC) and operational efficiency performance (OE) by using Balanced scorecards (BSC) specifically in oil and gas sector. This relationship is not yet acknowledged through empirical tests. The purpose of this paper is to fill this gap by providing a better understanding of that relationship and its importance with regard to business outcomes.

Design/methodology/approach

In order to examine the relationship between OC and OE, this research takes a BSC perspective with the mediating impact of KMPs. Three hypotheses were developed using literature review and tested through the application of confirmatory factor analysis in structural equation modeling. Altogether, 568 valid responses were collected from one of the biggest oil and gas companies in the UAE.

Findings

All KMPs were found to have significant relationship with OE and OC. Also, KMPs mediate the relationship between OC and OE. In addition, the results show that the standardized coefficients of these paths and the loadings of the indicators on their factors are significant. Pearson’s correlations indicate strong evidences of the joint impact of OC and KM practices on OE, with a possible mediator impact of KM practices on OE.

Research limitations/implications

One of research limitations is the type of organization. Future research may include other industries such as manufacturing and construction. Only the operational variable is evaluated and there is no consideration of other dimensions such as leadership type, organizational structure and technology.

Originality/value

This paper is the first in the UAE and the region to examine the relationship between OC and KMPs by considering OE from a BSC perspective with the mediating impact of KMPs.
Kit preparation for mixed-model assembly: efficiency impact of confirmation methods
Authors: Fager Patrik
Published: October 2018

Purpose

Confirmations are applied in kit preparation for mixed-model assembly to promote quality, but research that explains the impact on time efficiency has been lacking. The purpose of this paper is to determine the extent to which the type of confirmation method relates to time-efficient kit preparation when order batching is applied.

Design/methodology/approach

An industrially relevant laboratory experiment is applied, simulating kit preparation with order batching for mixed-model assembly. The time efficiency is studied as associated with four confirmation methods – barcode ring scanner, button presses, voice commands and RFID-reading wristbands – when applied as pick-from and place-to confirmation. Furthermore, the paper also considers the quality outcome.

Findings

Efficiency is promoted by methods that minimise interrupting the picker’s motions when performing pick-from confirmations and with methods that allow each hand to place components and perform place-to confirmations simultaneously – here represented by button presses and RFID-reading wristbands. Moreover, combining various methods for the tasks of pick-from or place-to confirmation can benefit efficiency.

Research limitations/implications

Pickers at an early stage of the learning curve (one shift of training) were considered.

Practical implications

The findings promote the customised applications of picking information systems in industry.

Social implications

Combining various methods for the tasks of pick-from and place-to confirmation can provide more fitting applications that better align with the picker’s preferences.

Originality/value

Combinations of various methods when applied as either pick-from or place-to confirmation, or both, are studied.