bluuebunny/crossref_metadata_2025 huggingface dataset:
Microbe Profile: Escherichia coli O157 : H7 – notorious relative of the microbiologist’s workhorse
Authors: Gally David L. , Stevens Mark P.
Published: February 2017

Escherichia coli O157 : H7 is a zoonotic diarrhoeal pathogen of worldwide importance. It belongs to a subset of Shiga toxin-producing E. coli that can form attaching and effacing lesions on intestinal epithelia via the action of a type 3 secretion system that injects bacterial effectors into enterocytes. Infections in humans often arise from contaminated food or direct environmental exposure and can involve life-threatening Shiga toxin-dependent sequelae. In the three decades since E. coli O157 : H7 was first recognized intensive research has helped to unravel the basis of pathogenesis, but few effective options for prevention and treatment of infections exist.
Laboratory cultivation of acidophilic nanoorganisms. Physiological and bioinformatic dissection of a stable laboratory co-culture
Authors: Krause Susanne , Bremges Andreas , Münch Philipp C. , McHardy Alice C. , Gescher Johannes
Published: February 2017

This study describes the laboratory cultivation of ARMAN (Archaeal Richmond Mine Acidophilic Nanoorganisms). After 2.5 years of successive transfers in an anoxic medium containing ferric sulfate as an electron acceptor, a consortium was attained that is comprised of two members of the orderThermoplasmatales, a member of a proposed ARMAN group, as well as a fungus. The 16S rRNA of one archaeon is only 91.6% identical toThermogymnomonas acidicolaas most closely related isolate. Hence, this organism is the first member of a new genus. The enrichment culture is dominated by this microorganism and the ARMAN. The third archaeon in the community seems to be present in minor quantities and has a 100% 16S rRNA identity to the recently isolatedCuniculiplasma divulgatum. The enriched ARMAN species is most probably incapable of sugar metabolism because the key genes for sugar catabolism and anabolism could not be identified in the metagenome. Metatranscriptomic analysis suggests that the TCA cycle funneled with amino acids is the main metabolic pathway used by the archaea of the community. Microscopic analysis revealed that growth of the ARMAN is supported by the formation of cell aggregates. These might enable cross feeding by other community members to the ARMAN.
Distinct neural systems for the production of communicative vocal behaviors
Authors: Agnew ZK , Ward L. , McGettigan C. , Josephs O. , Scott SK.
Published: February 2017

Vocalizations are the production of sounds by the coordinated activity of up to eighty respiratory and laryngeal muscles. Whilst voiced acts, modified by the upper vocal tract (tongue, jaw, lip and palate) are central to the production of human speech, they are also central to the production of emotional vocalizations such as sounds of disgust, anger, laughter and crying. Evidence suggests that the speech and emotional vocalizations may comprise distinct classes of vocal movements: patients with speech production deficits are often able to produce emotional vocalizations. In addition to this, the ontogeny of the two articulations is largely distinct, with some culturally universal emotional vocalizations emerging soon after birth and human speech being a culture specific, highly learnt motor act, which must develop to some degree before a critical period in development. Here we investigate the motor pathways underlying these two classes of vocal movements for the first time by directly comparing BOLD responses during production of speech and non-speech vocal movements. Using functional magnetic resonance imaging, we report distinct patterns of activity in both subcortical and cortical regions (putamen and bilateral inferior frontal and parietal cortices) during the production of emotional vocalizations compared to speech production. In contrast we show that responses in primary sensorimotor regions do not differ during the production of speech and emotional vocalizations, suggesting partially overlapping, and partially non-overlapping neural structures for the motor control of these two classes of movement. In addition to this we report that responses in auditory cortices are distinct during the production of speech and non-speech vocalizations, suggesting that feedback control of speech and emotional vocalizations are distinct. These data provide novel evidence for the presence of dual pathways for the neural control of complex articulatory movements in humans. These findings are discussed in relation to the clinical and primate literature of vocal motor control.

Significance Statement

This work marks the first evidence in healthy humans for dual routes to vocal behaviors. Clinical evidence suggests that patients unable to produce speech may still be able to produce other vocal behaviors that employ the same set of effectors. Here we demonstrate that the production of different classes of vocal behavior is associated with overlapping and distinct networks of activity. Moreover, we show that auditory processing that occurs during the production of these movements may be distinct, suggesting that feedback may be used differently for these distinct classes of vocal movement.
The erratic and contingent progression of research on territoriality: a case study
Authors: Kamath Ambika , Losos Jonathan
Published: February 2017

Our understanding of animal mating systems has changed dramatically with the advent of molecular methods to determine individuals’ reproductive success. But why are older behavioral descriptions and newer genetic descriptions of mating systems often seemingly inconsistent? We argue that a potentially important reason for such inconsistencies is a research trajectory rooted in early studies that were equivocal and overreaching, followed by studies that accepted earlier conclusions at face value and assumed, rather than tested, key ideas about animal mating systems. We illustrate our argument usingAnolislizards, whose social behavior has been studied for nearly a century. A dominant view emerging from this behavioral research was that anoles display strict territorial polygyny, where females mate with just the one male in whose territory they reside. However, all genetic evidence suggests that females frequently mate with multiple males. We trace this mismatch to early studies that concluded that anoles are territorial based on limited data. Subsequent research assumed territoriality implicitly or explicitly, resulting in studies that were unlikely to uncover or consider important any evidence of anoles’ departures from strict territorial polygyny. Thus, descriptions of anole behavior were largely led away from predicting a pattern of female multiple mating. We end by considering the broader implications of such erratic trajectories for the study of animal mating systems, and posit that precise definitions, renewed attention to natural history, and explicitly questioning assumptions made while collecting behavioral observations will allow us to move towards a fuller understanding of animal mating systems.
Analysis of the Quality of Macromolecular Structures
Authors: Salunke Dinakar M.
Published: February 2017

Structure determination utilizing X-ray crystallography involves collection of diffraction data, determination of initial phases followed by iterative rounds of model building and crystallographic refinement to improve the phases and minimize the differences between calculated and observed structure factors. At each of these stages, a variety of statistical filters exist to ensure appropriate validation. Biologically important observations often come from interpretations of signals that need to be carefully deciphered from noise and therefore human intervention is as important as the automated filters. Currently, all structural data are deposited in the Protein Data Bank and this repository is continuously evolving to incorporate possible new improvements in macromolecular crystallography. The journals that publish data arising from structural studies modulate their policies to take cognizance of new improved methodologies. The PDB and journals have evolved an accepted protocol to ensure the integrity of crystallographic results. As a result, the quality of available data and interpretations are becoming better over the years. However, there have been periodic efforts by some individuals who misuse validation mechanisms to selectively target published research through spurious challenges. These actions do more harm to the field of structural biology and runs counter to their claim to cleanse the system. The scientific systems in structural biology are robust and capable of self-correction and unwarranted vigilantism is counterproductive.
gene-cocite: a web application for extracting, visualising and assessing the cocitations of a list of genes
Authors: Newton Richard , Wernisch Lorenz
Published: February 2017

Background

The outcome from the analysis of high through-put genomics experiments is commonly a list of genes. The most basic measure of association is whether the genes in the list have ever been cocited together.

Results

The web applicationgene-cociteaccepts a list of genes and returns a list of the papers which cocite any two or more of the genes. The proportion of the genes which are cocited with at least one other gene is given, and thep-value for the probability of this proportion of cocitations occurring by chance from a random list of genes of the same length calculated. An interactive graph with links to papers is displayed, showing how the genes in the list are related to each other by publications.

Conclusions

gene-cocite (http://sysbio.mrc-bsu.cam.ac.uk/gene-cocite) is designed to be an easy to use first step for biological researchers investigating the background of their list of genes.
Age-related changes in spatial and temporal features of resting state fMRI
Authors: Vij Shruti G. , Nomi Jason S. , Dajani Dina R. , Uddin Lucina Q.
Published: February 2017

Development and aging are associated with functional changes in the brain across the lifespan. These changes can be detected in spatial and temporal features of resting state functional MRI (rs-fMRI) data. Independent vector analysis (IVA) is a whole-brain multivariate approach that can be used to comprehensively assess these changes in spatial and temporal features. We present a multi-dimensional approach to assessing age-related changes in spatial and temporal features of statistically independent components identified by IVA in a cross-sectional lifespan sample (ages 6-85 years). We show that while large-scale brain network configurations remain consistent throughout the lifespan, changes continue to occur in both local organization and in the spectral composition of these functional networks. We show that the spatial extent of functional networks decreases with age, but with no significant change in the peak functional loci of these networks. Additionally, we show differential age-related patterns across the frequency spectrum; lower frequency correlations decrease across the lifespan whereas higher-frequency correlations increase. These changes indicate an increasing stability of networks with age. In addition to replicating results from previous studies, the current results uncover new aspects of functional brain network changes across the lifespan that are frequency band-dependent.
Darker eggs resist more to desiccation: the case of melanin inAedes,AnophelesandCulexmosquito vectors
Authors: Farnesil Luana C , Vargas Helena C M , Valle Denise , Rezende Gustavo L
Published: February 2017

Mosquito vectors lay their eggs in the aquatic milieu. During early embryogenesis water passes freely through the transparent eggshell, composed of exochorion and endochorion. Within two hours the endochorion darkens via melanization but even so eggs shrink and perish if removed from moisture. However, during mid-embryogenesis, cells of the extraembryonic serosa secretes the serosal cuticle, localized right below the endochorion, which greatly reduces water flow and allows the egg to survive outside the water. The degree of egg resistance to desiccation (ERD) at late embryogenesis varies among different species:Aedes aegypti, Anopheles aquasalisandCulex quinquefasciatuseggs can survive in a dry environment for ≥ 72, 24 and 5 hours, respectively. In some adult insects, darker-body individuals show greater resistance to desiccation than lighter ones. We asked if melanization enhances serosal cuticle-dependent ERD. Species with higher ERD at late embryogenesis exhibit more melanized eggshells. The melanization-ERD hypothesis was confirmed employing twoAnopheles quadrimaculatusstrains, the wild type and the mutant GORO, with a dark-brown and a golden eggshell, respectively. In all cases, serosal cuticle formation is fundamental for the establishment of an efficient ERD but egg viability outside the water is much higher in mosquitoes with darker eggshells than in those with lighter ones. The finding that pigmentation influences egg water balance is relevant to understand the evolutionary history of insect coloration. Since eggshell and adult cuticle pigmentation ensure insect survivorship in some cases, they should be considered regarding species fitness and novel approaches for vector or pest insects control.
Proper experimental design requires randomization/balancing of molecular ecology experiments
Authors: Bálint Miklós , Márton Orsolya , Schatz Marlene , Düring Rolf-Alexander , Grossart Hans-Peter
Published: February 2017

Properly designed (randomized and/or balanced) experiments are standard in ecological research. Molecular methods are increasingly used in ecology, but studies generally do not report the detailed design of sample processing in the laboratory. This may strongly influence the interpretability of results if the laboratory procedures do not account for the confounding effects of unexpected laboratory events. We demonstrate this with a simple experiment where unexpected differences in laboratory processing of samples would have biased results if randomization in DNA extraction and PCR steps do not provide safeguards. We emphasize the need for proper experimental design and reporting of the laboratory phase of molecular ecology research to ensure the reliability and interpretability of results.
High-confidence Coding and Noncoding Transcriptome Maps
Authors: You Bo-Hyun , Yoon Sang-Ho , Nam Jin-Wu
Published: February 2017

The advent of high-throughput RNA-sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic genomes. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed based on RNA-seq reads that lack their orientations (known as unstranded reads) and certain boundary information. Methods to expand the usability of unstranded RNA-seq data by predetermining the orientation of the reads and precisely determining the boundaries of assembled transcripts could significantly benefit the quality of the resulting transcriptome maps. Here, we present a high-performing transcriptome assembly pipeline, called CAFE, that significantly improves the original assemblies, respectively assembled with stranded and/or unstranded RNA-seq data, by orienting unstranded reads using the maximum likelihood estimation and by integrating information about transcription start sites and cleavage and polyadenylation sites. Applying large-scale transcriptomic data comprising ninety-nine billion RNAs-seq reads from the ENCODE, human BodyMap projects, The Cancer Genome Atlas, and GTEx, CAFE enabled us to predict the directions of about eighty-nine billion unstranded reads, which led to the construction of more accurate transcriptome maps, comparable to the manually curated map, and a comprehensive lncRNA catalogue that includes thousands of novel lncRNAs. Our pipeline should not only help to build comprehensive, precise transcriptome maps from complex genomes but also to expand the universe of non-coding genomes.
Simulating retinal encoding: factors influencing Vernier acuity
Authors: Jiang Haomiao , Cottaris Nicolas , Golden James , Brainard David , Farrell Joyce E. , Wandell Brian A.
Published: February 2017

Humans resolve the spatial alignment between two visual stimuli at a resolution that is substantially finer than the spacing between the foveal cones. In this paper, we analyze the factors that limit the information at the cone photoreceptors that is available to make these acuity judgments (Vernier acuity). We use open-source software, ISETBIO1to quantify the stimulus and encoding stages in the front-end of the human visual system, starting with a description of the stimulus spectral radiance and a computational model that includes the physiological optics, inert ocular pigments, eye movements, photoreceptor sampling and absorptions. The simulations suggest that the visual system extracts the information available within the spatiotemporal pattern of photoreceptor absorptions within a small spatial (0.12 deg) and temporal (200 ms) regime. At typical display luminance levels, the variance arising from the Poisson absorptions and small eye movements (tremors and microsaccades) both appear to be critical limiting factors for Vernier acuity.
Early Archean origin of Photosystem II
Authors: Cardona Tanai , Sánchez-Baracaldo Patricia , Rutherford A. William , Larkum Anthony W. D.
Published: February 2017

Photosystem II is a photochemical reaction center that catalyzes the light-driven oxidation of water to molecular oxygen. Water oxidation is the distinctive photochemical reaction that permitted the evolution of oxygenic photosynthesis and the eventual rise of Eukaryotes. At what point during the history of life an ancestral photosystem evolved the capacity to oxidize water still remains unknown. Here we study the evolution of the core reaction center proteins of Photosystem II using sequence and structural comparisons in combination with Bayesian relaxed molecular clocks. Our results indicate that a homodimeric photosystem with sufficient oxidizing power to split water had already appeared in the early Archean about a billion years before the most recent common ancestor of all described Cyanobacteria capable of oxygenic photosynthesis, and well before the diversification of some of the known groups of anoxygenic photosynthetic bacteria. Based on a structural and functional rationale we hypothesize that this early Archean photosystem was capable of water oxidation and had already evolved some level of protection against the formation of reactive oxygen species, which would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.
Studies in Particle Sorting by Paramecium Cilia Arrays
Authors: Mayne Richard , Whiting James , Wheway Gabrielle , Melhuish Chris , Adamatzky Andrew
Published: February 2017

Motile cilia are cell-surface organelles whose purposes, in ciliated protists and certain ciliated vertebrate epithelia, include generating fluid flow, chemosensation, mechanosensation and substance uptake. Certain properties of cilia arrays, such as beating synchronisation and manipulation of external proximate particulate matter, are considered emergent, but remain incompletely characterised despite these phenomena having being the subject of extensive modelling. This study constitutes a laboratory experimental characterisation of one of the emergent properties of motile cilia; microparticle manipulation. The work demonstrates through automated videomicrographic particle tracking that interactions between microparticles and somatic cilia arrays of the ciliated model organismParamecium caudatumconstitute a form of rudimentary ‘sorting’. Small particles are drawn into the organism’s proximity by cilia-induced fluid currents at all times, whereas larger particles may be held immobile at a distance from the cell margin when the cell generates characteristic feeding currents in the surrounding media. These findings can contribute to the design and fabrication of biomimetic cilia, with potential applications to the study of ciliopathies.
Toxicity and applications of internalised magnetite nanoparticles within liveParamecium caudatumcells
Authors: Mayne Richard , Whiting James , Melhuish Chris , Adamatzky Andrew
Published: February 2017

The nanotechnology revolution has allowed us to speculate on the possibilities of hybridising nanoscale materials with live substrates, yet significant doubt still remains pertaining to the effects of nanomaterials on biological matter. In this investigation we cultivate the ciliated protistic pond-dwelling microorganismParamecium caudatumin the presence of excessive quantities of magnetite nanoparticles in order to assess both potential beneficial applications for this technique as well as any deleterious effects on the organisms’ health. Our findings indicate that these nanoparticles are well-tolerated by paramecia, who were observed to consume in quantities exceeding 10% of their body volume: cultivation in the presence of magnetite nanoparticles does not alterP. caudatumcell volume, swim speed, growth rate or peak colony density and cultures may persist in nanoparticle-contaminated medium for many weeks. We demonstrate thatP. caudatumcells ingest starch coated magnetite nanoparticles which facilitates their being magnetically immobilised whilst maintaining apparently normal ciliary dynamics, thus demonstrating that nanoparticle biohybridisation is a viable alternative to conventional forms of ciliate quieting. Ingested magnetite nanoparticle deposits appear to aggregate, suggesting that (a) the process of being internalised concentrates and therefore detoxifies nanomaterial suspensions in aquatic environments and (b)P. caudatumis a candidate organism for programmable nanomaterial manipulation and delivery.
Strategies for analyzing bisulfite sequencing data
Authors: Wreczycka Katarzyna , Gosdschan Alexander , Yusuf Dilmurat , Grüening Björn , Assenov Yassen , Akalin Altuna
Published: February 2017

DNA methylation is one of the main epigenetic modifications in the eukaryotic genome; it has been shown to play a role in cell-type specific regulation of gene expression, and therefore cell-type identity. Bisulfite sequencing is the gold-standard for measuring methylation over the genomes of interest. Here, we review several techniques used for the analysis of high-throughput bisulfite sequencing. We introduce specialized short-read alignment techniques as well as pre/post-alignment quality check methods to ensure data quality. Furthermore, we discuss subsequent analysis steps after alignment. We introduce various differential methylation methods and compare their performance using simulated and real bisulfite sequencing datasets. We also discuss the methods used to segment methylomes in order to pinpoint regulatory regions. We introduce annotation methods that can be used for further classification of regions returned by segmentation and differential methylation methods. Finally, we review software packages that implement strategies to efficiently deal with large bisulfite sequencing datasets locally and we discuss online analysis workflows that do not require any prior programming skills. The analysis strategies described in this review will guide researchers at any level to the best practices of bisulfite sequencing analysis.
Verification ofArabidopsisstock collections using SNPmatch - an algorithm for genotyping high-plexed samples
Authors: Pisupati Rahul , Reichardt Ilka , Seren Ümit , Korte Pamela , Nizhynska Viktoria , Kerdaffrec Envel , Uzunova Kristina , Rabanal Fernando , Filiault Daniele , Nordborg Magnus
Published: February 2017

Large-scale studies such as the ​Arabidopsis thaliana1001 Genomes Project aim to understand genetic variation in populations and link it to phenotypic variation. Such studies require routine genotyping of stocks to avoid sample contamination and mix-ups. To genotype samples efficiently and economically, sequencing must be inexpensive a​nd data processing simple. Here we present SNPmatch, a tool which identifies the most likely strain (inbred line, or “accession”) from a SNP database. We tested the tool by performing low-coverage sequencing of over 2000 strains. SNPmatch could readily genotype samples correctly from 1-fold coverage sequencing data, and could also identify the parents of F1 or F2 individuals. SNPmatch can be run either on the command line or through AraGeno (https://arageno.gmi.oeaw.ac.at), a web interface that permits sample genotyping from a user-uploaded VCF or BED file.

Availability and implementation:https://github.com/Gregor-Mendel-Institute/SNPmatch.git
Optogenetic Control of RhoA Reveals Zyxin-mediated Elasticity of Stress Fibers
Authors: Oakes Patrick W. , Wagner Elizabeth , Brand Christoph A. , Probst Dimitri , Linke Marco , Schwarz Ulrich S. , Glotzer Michael , Gardel Margaret L.
Published: February 2017

The mechanics of the actin cytoskeleton regulates cell morphogenesis during essential physiological processes. While cellular contractility is known to be largely RhoA-dependent, the process by which localized biochemical signals are translated into cell-level responses is not well understood. Here we combine optogenetic control of RhoA in space and time, live cell imaging and traction force microscopy to investigate the dynamics of actomyosin-based force generation in adherent fibroblasts. Local activation of RhoA not only stimulates local recruitment of actin and myosin, but also leads to increased traction forces outside the activation region that rapidly propagate across the cell via stress fibers and drive actin flow towards the region of heightened RhoA. Surprisingly, the flow reverses direction when local RhoA activation stops. We identify zyxin as a regulator of stress fiber mechanics, as stress fibers are fluid-like without flow reversal in its absence. These experimental data are used to constrain a physical model, which demonstrates that stress fibers are elastic-like, even at time scales exceeding turnover of constituent proteins. Such molecular control of actin mechanics likely plays critical roles in regulation of morphogenic events.
Modeling allele-specific gene expression by single-cell RNA sequencing
Authors: Jiang Yuchao , Zhang Nancy R , Li Mingyao
Published: February 2017

Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing (scRNA-seq) allows the comparison of expression distribution between the two alleles of a diploid organism and thus the characterization of allele-specific bursting. We propose SCALE to analyze genome-wide allele-specific bursting, with adjustment of technical variability. SCALE detects genes exhibiting allelic differences in bursting parameters, and genes whose alleles burst non-independently. We apply SCALE to mouse blastocyst and human fibroblast cells and find that, globally,ciscontrol in gene expression overwhelmingly manifests as differences in burst frequency.
MinE recruits, stabilizes, releases, and inhibits MinD interactions with membrane to drive oscillation
Authors: Vecchiarelli Anthony G. , Li Min , Mizuuchi Michiyo , Ivanov Vassili , Mizuuchi Kiyoshi
Published: February 2017

The MinD and MinE proteins ofEscherichia coliself-organize into a standing-wave oscillator on the membrane to help align division at mid-cell. When unleashed from cellular confines, we find that MinD and MinE form a wide spectrum of patterns on artificial bilayers - static amoebas, traveling waves, traveling mushrooms, and bursts with standing-wave dynamics. We recently focused our cell-free studies on bursts because their dynamics closely resemble those foundin vivo. The data unveiled a patterning mechanism largely governed by MinE regulation of MinD interaction with membrane. We proposed that the MinD to MinE ratio on the membrane acts as a toggle switch between MinE-stimulated recruitment or release of MinD from the membrane. Here we provide data that further refines and extends our model that explains the remarkable spectrum of patterns supported by these two ‘simple’ proteins.
Relational uncertainty in service dyads
Authors: Kreye Melanie E.
Published: February 2017

Purpose

Relational uncertainty determines how relationships develop because it enables the building of trust and commitment. However, relational uncertainty has not been explored in an inter-organisational setting. The purpose of this paper is to investigate how organisations experience relational uncertainty in service dyads and how they resolve it through suitable organisational responses to increase the level of service quality.

Design/methodology/approach

The author applies the overall logic of organisational information-processing theory and presents empirical insights from two industrial case studies collected via semi-structured interviews and secondary data.

Findings

The findings suggest that relational uncertainty is caused by the partner’s unresolved organisational uncertainty, i.e. their lacking capabilities to deliver or receive (parts of) the service. Furthermore, the author found that resolving the relational uncertainty increased the functional quality while resolving the partner’s organisational uncertainty increased the technical quality of the delivered service.

Originality/value

The author makes two contributions: first,the author introduces relational uncertainty to the OM literature as the inability to predict and explain the actions of a partnering organisation due to a lack of knowledge about their abilities and intentions; and second, the author presents suitable organisational responses to relational uncertainty and their effect on service quality.
High‐resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils
Authors: Narrowe Adrienne B. , Angle Jordan C. , Daly Rebecca A. , Stefanik Kay C. , Wrighton Kelly C. , Miller Christopher S.
Published: February 2017

Despite being key contributors to biogeochemical processes, archaea are frequently outnumbered by bacteria, and consequently are underrepresented in combined molecular surveys. Here, we demonstrate an approach to concurrently survey the archaea alongside the bacteria with high‐resolution 16S rRNA gene sequencing, linking these community data to geochemical parameters. We applied this integrated analysis to hydric soils sampled across a model methane‐emitting freshwater wetland. Geochemical profiles, archaeal communities, and bacterial communities were independently correlated with soil depth and water cover. Centimeters of soil depth and corresponding geochemical shifts consistently affected microbial community structure more than hundreds of meters of lateral distance. Methanogens with diverse metabolisms were detected across the wetland, but displayed surprising OTU‐level partitioning by depth. Candidatus Methanoperedens spp. archaea thought to perform anaerobic oxidation of methane linked to iron reduction were abundant. Domain‐specific sequencing also revealed unexpectedly diverse non‐methane‐cycling archaeal members. OTUs within the underexplored Woesearchaeota and Bathyarchaeota were prevalent across the wetland, with subgroups and individual OTUs exhibiting distinct occupancy and abundance distributions aligned with environmental gradients. This study adds to our understanding of ecological range for key archaeal taxa in a model freshwater wetland, and links these taxa and individual OTUs to hypotheses about processes governing biogeochemical cycling.
Cold adaptation of the Antarctic haloarchaea Halohasta litchfieldiae and Halorubrum lacusprofundi
Authors: Williams Timothy J. , Liao Yan , Ye Jun , Kuchel Rhiannon P. , Poljak Anne , Raftery Mark J. , Cavicchioli Ricardo
Published: February 2017

Halohasta litchfieldiae represents ∼ 44% and Halorubrum lacusprofundi ∼ 10% of the hypersaline, perennially cold (≥ −20°C) Deep Lake community in Antarctica. We used proteomics and microscopy to define physiological responses of these haloarchaea to growth at high (30°C) and low (10 and 4°C) temperatures. The proteomic data indicate that both species responded to low temperature by modifying their cell envelope including protein N‐glycosylation, maintaining osmotic balance and translation initiation, and modifying RNA turnover and tRNA modification. Distinctions between the two species included DNA protection and repair strategies (e.g. roles of UspA and Rad50), and metabolism of glycerol and pyruvate. For Hrr. lacusprofundi, low temperature led to the formation of polyhydroxyalkanoate‐like granules, with granule formation occurring by an unknown mechanism. Hrr. lacusprofundi also formed biofilms and synthesized high levels of Hsp20 chaperones. Hht. litchfieldiae was characterized by an active CRISPR system, and elevated levels of the core gene expression machinery, which contrasted markedly to the decreased levels of Hrr. lacusprofundi. These findings greatly expand the understanding of cellular mechanisms of cold adaptation in psychrophilic archaea, and provide insight into how Hht. litchfieldiae gains dominance in Deep Lake.
Equity Ownership in Cross‐border Mergers and Acquisitions by British Firms: An Analysis of Real Options and Transaction Cost Factors
Authors: Ahammad Mohammad F. , Leone Vitor , Tarba Shlomo Y. , Glaister Keith W. , Arslan Ahmad
Published: February 2017

The authors investigate the factors influencing the share of equity ownership sought in cross‐border mergers and acquisitions (CBM&As). Drawing on real options theory and transaction cost economics (TCE), they address and hypothesize key factors linked to commitment under exogenous uncertainty and the separation of desired and non‐desired assets’ influence on share of equity sought by acquiring firms in CBM&As. Empirical analysis based on 1872 CBM&As undertaken by British firms in both developed and emerging economies shows that British MNEs are more likely to pursue a partial acquisition in a target foreign firm when those foreign firms are from culturally distant countries. Further, findings support the view that the high cost of separating desired assets from non‐desired assets motivates firms to make a partial acquisition rather than acquire the target completely. This is one of the first studies to use real options theory to address the cost of commitment under exogenous uncertainty, as well as TCE logic to address the separation of desired and non‐desired assets in the target firm while analysing equity ownership sought in CBM&As. Empirically, this paper contributes by examining CBM&As by British firms in both developed and emerging markets.
Examining Facilitative Configurations of Entrepreneurially Oriented Growth: An Information Processing Perspective
Authors: Kearney Claudine , Soleimanof Sohrab , Wales William J.
Published: February 2017

This study examines how the relationship between entrepreneurial orientation and firm growth is shaped by learning orientation in technologically sophisticated environments. We draw upon an information processing perspective that emphasizes alignment between information processing demands and support mechanisms. Using data from 116 small to medium‐sized enterprises in the Netherlands, we observe that the ability of entrepreneurial orientation to drive firm growth greatly depends on the joint consideration of technological sophistication and learning orientation. Our findings contribute to a better understanding of how configurations of strategic orientations and environmental considerations work in concert to influence the efficacy of organizational entrepreneurial efforts dramatically.
Inter‐level Trust in a Multilevel Political System
Authors: Karlsson David
Published: February 2017

The aim of this article is to study political representatives in a multilevel government system and their level of political trust in relation to institutions in their own and other tiers of government. The results show that two factors are essential for understanding variations in their trust: Representatives tend to trust institutions in other tiers less than those in their own tier (the tier‐association effect), and they trust institutions more where their own party is in a governing position (the home‐team effect). Of the two, the home‐team effect is by far the most dominant factor. Multiple mandates serve to increase inter‐level trust, but divided loyalties possibly make representatives with multiple mandates less trusting towards political institutions in their own tiers than more partisan single mandate representatives. The study builds on data from surveys conducted among all elected representatives in Sweden in 2012 (local and regional councillors) and 2014 (national MPs).
The 22 July Terrorist Attacks in Norway: Impact on Public Attitudes towards Counterterrorist Authorities
Authors: Christensen Dag Arne , Aars Jacob
Published: February 2017

Did the terrorist attacks in Norway affect citizens’ attitudes to security‐related institutions and policies? To answer this question this study pools two cross‐sectional surveys, collected shortly before and after the 2011 terrorist attacks, to determine the attacks’ effects on people's attitudes. One important finding is that general support for the institutions responsible for security increased slightly, whereas specific support for government agencies capability to prevent and cope with crises decreased markedly. A second important finding concerns the potential for politicisation of crises: On issues of security, the distance between right‐wing voters and other party voters increased after the attack. Irrespective of party attachment, Norwegians have become less satisfied with governmental policies on security‐related issues, but dissatisfaction has increased significantly more among right‐wing than among left‐wing voters. Thus, even in a country where politicians responded to the crisis with an appeal to togetherness and common values, citizens’ attitudes on security policies were politicised.
An evaluation of the effectiveness of a computer‐assisted reading intervention
Authors: Messer David , Nash Gilly
Published: February 2017

Background

A cost‐effective method to address reading delays is to use computer‐assisted learning, but these techniques are not always effective.

Methods

We evaluated a commercially available computer system that uses visual mnemonics, in a randomised controlled trial with 78 English‐speaking children (mean age 7 years) who their schools identified as needing reading support. School‐based individual tutorials usually took place 2–3 times/week. Only the experimental group received the intervention in the first 10 months; thereafter, both the experimental and control groups received the intervention for 6 months.

Results

After 10 months, the experimental group had significantly higher standardised scores than the waiting list control group of decoding, phonological awareness, naming speed, phonological short‐term memory and executive loaded working memory.

Conclusions

The computer‐assisted intervention was effective, and this suggests that this medium can be used for reading interventions with English‐speaking children.

What is already known about this topic

There are comparatively few randomised controlled trial evaluations of computer‐based reading interventions.

Meta‐analyses report small positive effect sizes for such interventions with English‐speaking children.

The use of visual mnemonics to improve reading has rarely been investigated.

What this paper adds

The findings suggest that computer‐based interventions for English‐speaking, struggling readers can be effective.

The effects extended beyond the targeted abilities, and a longer intervention was more effective than a shorter one.

Apart from spelling, the mean reading and reading related standardised scores for children at the end of the intervention were above or just below 100.

Implications for theory, policy or practice

Computer‐based interventions can be used to support English‐speaking, struggling readers, and their effects can go beyond targeted abilities.

The use of visual mnemonics and the development of the intervention programme over a number of years could have contributed to this success.

The role of visual mnemonics as a help for struggling readers deserves further investigation.
Serous tubal intraepithelial carcinomas associated with high‐grade serous ovarian carcinomas: a systematic review
Authors: Chen F , Gaitskell K , Garcia MJ , Albukhari A , Tsaltas J , Ahmed AA
Published: February 2017

Background

Serous tubal intraepithelial carcinomas (STICs) have been documented in high‐grade serous ovarian carcinomas (HGSOCs). However, the rate of association between STICs and HGSOCs and, therefore, the fraction of HGSOCs that are likely to have originated from the fallopian tube (FT), has remained unclear.

Objective

To appraise the literature describing the association between STICs and established HGSOCs.

Search strategy

Ovid MEDLINE and EMBASE were searched.

Selection criteria

Studies were included if they evaluated the frequency of STICs in HGSOCs, and were published in an English peer‐reviewed journal.

Data collection and analysis

Appropriate studies were evaluated for their compliance with the ‘Strengthening and Reporting of Observational Studies in Epidemiology (STROBE)’ criteria.

Main results

Ten articles met the study selection criteria. The reported coexistence between STICs and HGSOCs ranged from 11% to 61% (mean: 31%, 95% CI: 17–46%). STICs were rarely found in other gynaecological cancers. Small sample size, lack of objective criteria to identify STICs and the retrospective nature of the studies contributed to the variability in reporting the rate of the association.

Conclusions

STICs were identified commonly in the FTs of women with HGSOC. Finding the true rate of association between STICs and HGSOCs will require further investigations. While there is evidence that a fraction of HGSOCs arise from the FTs, an accurate estimate of that fraction remains to be determined. The lack of an accurate estimate of the association makes it difficult to evaluate the potential magnitude of reduction of HGSOCs following prophylactic salpingectomy.

Tweetable abstract

A systematic review of the incidence of STICs in HGSOCs identifies significant methodological inconsistencies.
Identifying Primary Care Pathways from Quality of Care to Outcomes and Satisfaction Using Structural Equation Modeling
Authors: Ricci‐Cabello Ignacio , Stevens Sarah , Dalton Andrew R. H. , Griffiths Robert I. , Campbell John L. , Valderas Jose M.
Published: February 2017

Objective

To study the relationships between the different domains of quality of primary health care for the evaluation of health system performance and for informing policy decision making.

Data Sources

A total of 137 quality indicators collected from 7,607 English practices between 2011 and 2012.

Study Design

Cross‐sectional study at the practice level. Indicators were allocated to subdomains of processes of care (“quality assurance,” “education and training,” “medicine management,” “access,” “clinical management,” and “patient‐centered care”), health outcomes (“intermediate outcomes” and “patient‐reported health status”), and patient satisfaction. The relationships between the subdomains were hypothesized in a conceptual model and subsequently tested using structural equation modeling.

Principal Findings

The model supported two independent paths. In the first path, “access” was associated with “patient‐centered care” (β = 0.63), which in turn was strongly associated with “patient satisfaction” (β = 0.88). In the second path, “education and training” was associated with “clinical management” (β = 0.32), which in turn was associated with “intermediate outcomes” (β = 0.69). “Patient‐reported health status” was weakly associated with “patient‐centered care” (β = −0.05) and “patient satisfaction” (β = 0.09), and not associated with “clinical management” or “intermediate outcomes.”

Conclusions

This is the first empirical model to simultaneously provide evidence on the independence of intermediate health care outcomes, patient satisfaction, and health status. The explanatory paths via technical quality clinical management and patient centeredness offer specific opportunities for the development of quality improvement initiatives.
Home Health Care: Nurse–Physician Communication, Patient Severity, and Hospital Readmission
Authors: Pesko Michael F. , Gerber Linda M. , Peng Timothy R. , Press Matthew J.
Published: February 2017

Objective

To evaluate whether communication failures between home health care nurses and physicians during an episode of home care after hospital discharge are associated with hospital readmission, stratified by patients at high and low risk of readmission.

Data Source/Study Setting

We linked Visiting Nurse Services of New York electronic medical records for patients with congestive heart failure in 2008 and 2009 to hospitalization claims data for Medicare fee‐for‐service beneficiaries.

Study Design

Linear regression models and a propensity score matching approach were used to assess the relationship between communication failure and 30‐day readmission, separately for patients with high‐risk and low‐risk readmission probabilities.

Data Collection/Extraction Methods

Natural language processing was applied to free‐text data in electronic medical records to identify failures in communication between home health nurses and physicians.

Principal Findings

Communication failure was associated with a statistically significant 9.7 percentage point increase in the probability of a patient readmission (32.6 percent of the mean) among high‐risk patients.

Conclusions

Poor communication between home health nurses and physicians is associated with an increased risk of hospital readmission among high‐risk patients. Efforts to reduce readmissions among this population should consider focusing attention on this factor.
CEO Inside Debt Incentives and Corporate Tax Sheltering
Authors: CHI SABRINA , HUANG SHAWN X. , SANCHEZ JUAN MANUEL
Published: February 2017

This paper examines the relation between CEO inside debt holdings (pension benefits and deferred compensation) and corporate tax sheltering. Because inside debt holdings are generally unsecured and unfunded liabilities of the firm, CEOs are exposed to risk similar to that faced by outside creditors. As such, theory (Jensen and Meckling [1976]) suggests that inside debt holdings negatively impact CEO risk‐appetite. To the extent that corporate tax shelters are likely to result in high cash flow volatility in the future, we expect that inside debt holdings will curb CEOs from engaging in tax shelter transactions. Consistent with the prediction, we document a negative association between CEO inside debt holdings and tax sheltering. Additional analyses suggest that the effect of inside debt on tax sheltering is more (less) pronounced in the presence of high default risk and liquidity threats (cash‐out options in pension packages). Overall, our results highlight the importance of investigating the implication of CEO debt‐like compensation for corporate tax policies.