bluuebunny/crossref_metadata_2025_split huggingface dataset:
LIONS: Analysis Suite for Detecting and Quantifying Transposable Element Initiated Transcription from RNA-seq
Authors: Babaian Artem , Thompson Richard , Lever Jake , Gagnier Liane , Karimi Mohammad M. , Mager Dixie L. 
Published: June 2017

AbstractSummaryTransposable Elements (TEs) influence the evolution of novel transcriptional networks yet the specific and meaningful interpretation of how TE-initiation events contribute to the transcriptome has been marred by computational and methodological deficiencies. We developedLIONSfor the analysis of paired-end RNA-seq data to specifically detect and quantify TE-initiated transcripts.AvailabilitySource code, container, test data and instruction manual are freely available atwww.github.com/ababaian/LIONS.Contactababaian@bccrc.caormahdi.karimi@lms.mrc.ac.ukordmager@bccrc.ca.Supplementary informationSupplementary data are available at Bioinformatics online.
Simultaneous spike-time locking to multiple frequencies
Authors: Sinz Fabian H. , Sachgau Carolin , Henninger Jörg , Benda Jan , Grewe Jan 
Published: June 2017

AbstractPhase locking of neural firing is ubiquitously observed in the brain and occurs when neurons fire at a particular phase of a periodic signal. Here we study in detail how spikes of single neurons can simultaneously lock to multiple distinct frequencies at the example of p-type electroreceptor afferents in the electrosensory system of the Gymnotiform weakly electric fishApteronotus leptorhynchus. We identify key elements for multiple frequency locking, study its determining factors and limits, and provide concise mathematical models reproducing our main findings. Our findings provide another example how rate and temporal codes can coexist and complement each other in single neurons, and demonstrate that sensory coding in p-type electroreceptor afferents provides a much richer representation of the sensory environment than commonly assumed. Since the underlying mechanisms are not specific to the electrosensory system, our results could provide the basis for studying multiple-frequency locking in other systems.
Neural stem cells induce the formation of their physical niche during organogenesis
Authors: Seleit Ali , Krämer Isabel , Riebesehl Bea , Ambrosio Elizabeth M. , Stolper Julian S. , Dross Nicolas , Lischik Colin Q. , Centanin Lazaro 
Published: June 2017

AbstractMost organs rely on stem cells to maintain homeostasis during post-embryonic life. Typically, stem cells of independent lineages work coordinately within mature organs to ensure proper ratios of cell types. Little is known, however, on how these different stem cells locate to forming organs during development. Here we show that neuromasts of the posterior lateral line in medaka are composed of two independent life-long lineages with different embryonic origins. Clonal analysis and 4D imaging revealed a hierarchical organisation with instructing and responding roles: an inner, neural lineage induces the formation of an outer, border cell lineage (nBC) from the skin epithelium. Our results demonstrate that the neural lineage is necessary and sufficient to generate nBCs highlighting self-organisation principles at the level of the entire embryo. We hypothesise that transformation of surrounding tissues plays a major role during the establishment of vertebrate stem cell niches.
Stability-based sorting: The forgotten process behind (not only) biological evolution
Authors: Flegr Jaroslav , Toman Jan 
Published: June 2017

AbstractNatural selection is considered to be the main process that drives biological evolution. It requires selected entities to originate dependent upon one another by the means of reproduction or copying, and for the progeny to inherit the qualities of their ancestors. However, natural selection is a manifestation of a more generalpersistence principle, whose temporal consequences we propose to name “stability-based sorting” (SBS). Sorting based onstatic stability, i.e., SBS in its strict sense and usual conception, favours characters that increase the persistence of their holders and act on all material and immaterial entities. Sorted entities could originate independently from each other, are not required to propagate and need not exhibit heredity. Natural selection is a specific form of SBS—sorting based ondynamic stability. It requires some form of heredity and is based on competition for the largest difference between the speed of generating its own copies and their expiration. SBS in its strict sense and selection thus have markedly different evolutionary consequences that are stressed in this paper. In contrast to selection, which is opportunistic, SBS is able to accumulate even momentarily detrimental characters that are advantageous for the long-term persistence of sorted entities. However, it lacks the amplification effect based on the preferential propagation of holders of advantageous characters. Thus, it works slower than selection and normally is unable to create complex adaptations. From a long-term perspective, SBS is a decisive force in evolution—especially macroevolution. SBS offers a new explanation for numerous evolutionary phenomena, including broad distribution and persistence of sexuality, altruistic behaviour, horizontal gene transfer, patterns of evolutionary stasis, planetary homeostasis, increasing ecosystem resistance to disturbances, and the universal decline of disparity in the evolution of metazoan lineages. SBS acts on all levels in all biotic and abiotic systems. It could be the only truly universal evolutionary process, and an explanatory framework based on SBS could provide new insight into the evolution of complex abiotic and biotic systems.
Inferring synteny between genome assemblies: a systematic evaluation
Authors: Liu Dang , Hunt Martin , Tsai Isheng. J. 
Published: June 2017

AbstractIdentification of synteny between genomes of closely related species is an important aspect of comparative genomics. However, it is unknown to what extent draft assemblies lead to errors in such analysis. To investigate this, we fragmented genome assemblies of model nematodes to various extents and conducted synteny identification and downstream analysis. We first show that synteny between species can be underestimated up to 40% and find disagreements between popular tools that infer synteny blocks. This inconsistency and further demonstration of erroneous gene ontology enrichment tests throws into question the robustness of previous synteny analysis when gold standard genome sequences remain limited. In addition, determining the true evolutionary relationship is compromised by assembly improvement using a reference guided approach with a closely related species. Annotation quality, however, has minimal effect on synteny if the assembled genome is highly contiguous. Our results highlight the need for gold standard genome assemblies for synteny identification and accurate downstream analysis.Author summaryGenome assemblies across all domains of life are currently produced routinely. Initial analysis of any new genome usually includes annotation and comparative genomics. Synteny provides a framework in which conservation of homologous genes and gene order is identified between genomes of different species. The availability of human and mouse genomes paved the way for algorithm development in large-scale synteny mapping, which eventually became an integral part of comparative genomics. Synteny analysis is regularly performed on assembled sequences that are fragmented, neglecting the fact that most methods were developed using complete genomes. Here, we systematically evaluate this interplay by inferring synteny in genome assemblies with different degrees of contiguation. As expected, our investigation reveals that assembly quality can drastically affect synteny analysis, from the initial synteny identification to downstream analysis. Importantly, we found that improving a fragmented assembly using synteny with the genome of a related species can be dangerous, as thisa prioriassumes a potentially false evolutionary relationship between the species. The results presented here re-emphasize the importance of gold standard genomes to the science community, and should be achieved given the current progress in sequencing technology.
Kin competition accelerates experimental range expansion in an arthropod herbivore
Authors: Van Petegem Katrien , Moerman Felix , Dahirel Maxime , Fronhofer Emanuel A. , Vandegehuchte Martijn L. , Van Leeuwen Thomas , Wybouw Nicky , Stoks Robby , Bonte Dries 
Published: June 2017

AbstractWith ongoing global change, life is continuously forced to move to novel areas, which leads to dynamically changing species ranges. As dispersal is central to range dynamics, factors promoting fast and distant dispersal are key to understanding and predicting species ranges. During range expansions, genetic variation is depleted at the expanding front. Such conditions should reduce evolutionary potential, while increasing kin competition. Organisms able to recognise relatives may be able to assess increased levels of relatedness at expanding range margins and to increase their dispersal in a plastic manner. Using individual-based simulations and experimental range expansions of a spider mite, we demonstrate that plastic responses to kin structure can be at least as important as evolution in driving range expansion speed. Because recognition of kin or kind is increasingly documented across the tree of life, we anticipate it to be a highly important but neglected driver of range expansions.
Bayesian Comparison of Explicit and Implicit Causal Inference Strategies in Multisensory Heading Perception
Authors: Acerbi Luigi , Dokka Kalpana , Angelaki Dora E. , Ma Wei Ji 
Published: June 2017

AbstractThe precision of multisensory heading perception improves when visual and vestibular cues arising from the same cause, namely motion of the observer through a stationary environment, are integrated. Thus, in order to determine how the cues should be processed, the brain must infer the causal relationship underlying the multisensory cues. In heading perception, however, it is unclear whether observers follow the Bayesian strategy, a simpler non-Bayesian heuristic, or even perform causal inference at all. We developed an efficient and robust computational framework to perform Bayesian model comparison of causal inference strategies, which incorporates a number of alternative assumptions about the observers. With this framework, we investigated whether human observers’ performance in anexplicitcause attribution and animplicitheading discrimination task can be modeled as a causal inference process. In the explicit inference task, all subjects accounted for cue disparity when reporting judgments of common cause, although not necessarily all in a Bayesian fashion. By contrast, but in agreement with previous findings, data from the heading discrimination task only could not rule out that several of the same observers were adopting a forced-fusion strategy, whereby cues are integrated regardless of disparity. Only when we combined evidence from both tasks we were able to rule out forced-fusion in the heading discrimination task. Crucially, findings were robust across a number of variants of models and analyses. Our results demonstrate that our proposed computational framework allows researchers to ask complex questions within a rigorous Bayesian framework that accounts for parameter and model uncertainty.
Underwater hyperspectral classification of deep sea corals exposed to 2-methylnaphthalene
Authors: Letnes Paul Anton , Hansen Ingrid Myrnes , Sandvik Aas Lars Martin , Eide Ingvar , Pettersen Ragnhild , Tassara Luca , Receveur Justine , Floch Stephane le , Guyomarch Julien , Camus Lionel , Bytingsvik Jenny 
Published: June 2017

AbstractCoral reefs around the world are under threat due to anthropogenic impacts on the environment. It is therefore important to develop methods to monitor the status of the reefs and detect changes in the health condition of the corals at an early stage before severe damage occur. In this work, we evaluate underwater hyperspectral imaging as a method to detect changes in health status of both orange and white color morphs of the coral speciesLophelia pertusa.Differing health status was achieved by exposing 66 coral samples to the toxic compound 2-methylnaphthalene in concentrations of 0 mg L−1to 3.5 mg L−1. A machine learning model was utilized to classify corals according to lethal concentration (LC) levels LC5 (5 % mortality) and LC25 (25 % mortality), solely based on their reflectance spectra. All coral samples were classified to correct concentration group. This is a first step towards developing a remote sensing technique able to assess environmental impact on deep-water coral habitats over larger areas.
Parent of Origin Effects on Quantitative Phenotypes in a Founder Population
Authors: Mozaffari Sahar V. , DeCara Jeanne M. , Shah Sanjiv J. , Lang Roberto M. , Nicolae Dan L. , Ober Carole 
Published: June 2017

ABSTRACTThe impact of the parental origin of associated alleles in GWAS has been largely ignored. Yet sequence variants could affect traits differently depending on whether they are inherited from the mother or the father. To explore this possibility, we studied 21 quantitative phenotypes in a large Hutterite pedigree. We first identified variants with significant single parent (maternal-only or paternal-only) effects, and then used a novel statistical model to identify variants with opposite parental effects. Overall, we identified parent of origin effects (POEs) on 11 phenotypes, most of which are risk factors for cardiovascular disease. Many of the loci with POEs have features of imprinted regions and many of the variants with POE are associated with the expression of nearby genes. Overall, our results indicate that POEs, which are often opposite in direction, are relatively common in humans, have potentially important clinical effects, and will be missed in traditional GWAS.
Evolution and genetics of precocious burrowing behavior inPeromyscusmice
Authors: Metz Hillery C. , Bedford Nicole L. , Pan Linda , Hoekstra Hopi E. 
Published: June 2017

SummaryA central challenge in biology is to understand how innate behaviors evolve between closely related species. One way to elucidate how differences arise is to compare the development of behavior in species with distinct adult traits. Here, we report thatPeromyscus polionotusis strikingly precocious with regard to burrowing behavior, but not other behaviors, compared to its sister speciesP. maniculatus. InP. polionotus, burrows were excavated as early as 17 days of age, whileP. maniculatusdid not build burrows until 10 days later. Moreover, the well-known differences in burrow architecture between adults of these species—P. polionotusadults excavate long burrows with an escape tunnel, whileP. maniculatusdig short, single-tunnel burrows—were intact in juvenile burrowers. To test whether this juvenile behavior is influenced by early-life environment, pups of both species were reciprocally cross-fostered. Fostering did not alter the characteristic burrowing behavior of either species, suggesting these differences are genetic. In backcross F2hybrids, we show that precocious burrowing and adult tunnel length are genetically correlated, and that a singleP. polionotusallele in a genomic region linked to adult tunnel length is predictive of precocious burrow construction. The co-inheritance of developmental and adult traits indicates the same genetic region—either a single gene with pleiotropic effects, or closely linked genes— acts on distinct aspects of the same behavior across life stages. Such genetic variants likely affect behavioral drive (i.e. motivation) to burrow, and thereby affect both the development and adult expression of burrowing behavior.HighlightsJuvenileP. polionotusconstruct burrows precociously compared to its sister speciesP. maniculatusCross-fostering does not alter species-specific burrowing behaviorA QTL linked to adult tunnel length predicts developmental onset of burrow construction in hybridsPleiotropic genetic variant(s) may affect behavioral drive across life stages
An alternative model of pre-hospital care for 999 patients who require non-emergency medical assistance
Authors: Blodgett Joanna M. , Robertson Duncan , Ratcliffe David , Rockwood Kenneth 
Published: June 2017

Purpose
With the increasing demand on ambulance services, paramedics are tasked to arrange as much out of hospital care as possible, to develop integrated systems of care and work with hundreds of different providers – all in the 15 minutes allocated for assessment. A UK ambulance trust is navigating and leading much of this work as one of the first trusts to implement a general practitioner referral policy as an alternate to direct conveyance. The paper aims to discuss this issue.

Design/methodology/approach
Here the authors discuss the referral scheme, examine the limited evidence available and discuss what is needed to influence prospective success of implementing this scheme in other trusts.

Findings
Limited evidence for these schemes are described, however there is a clear gap in critical appraisal and methodologically rigorous evidence needed to implement these schemes in other ambulance schemes.

Originality/value
In order to facilitate collaboration of healthcare services and to minimize the burden of increasing numbers of patients, communication and discussion of alternate routes of care is crucial. This viewpoint piece is one of the first to emphasize the potential benefits of such schemes.
An exploration of violence against paramedics, burnout and post-traumatic symptoms in two Australian ambulance services
Authors: Wongtongkam Nualnong 
Published: June 2017

Purpose
Violence directed at ambulance paramedics has attracted increasing public attention because of its major negative impact on the physical and psychological well-being of victims and productivity of organisations. The purpose of this paper is to explore the prevalence of violent incidents, contributing factors, burnout and post-traumatic symptoms among paramedics.

Design/methodology/approach
A cross-sectional survey was distributed in two ambulance services in Tasmania and South Australia, with self-administered instruments completed online. In total, 48 respondents completed questionnaires.

Findings
There were no significant differences between sites in timing of violent incidents, consequences of traumatic events or organisation provision. Surprisingly, over 90 per cent of paramedics had not been pushed, slapped, beaten, scratched or spat on in the previous month. There was a statistically significant difference between genders for being yelled at or verbally abused (p=0.02). When considering burnout, female paramedics showed significantly higher levels of emotional exhaustion t(37)=–2.32, p=0.02 and lower levels of career satisfaction than their male counterparts, t(37)=3.32, p=0.00.

Originality/value
Although prevalence rates of violent incidents seemed lower than expected, policy interventions to encourage female paramedics to display their professional identities and steps to enhance well-being and safety while on duty should be considered.
Effects of different temperature regimes on survival of Diaphorina citri and its endosymbiotic bacterial communities
Authors: Hussain Mubasher , Akutse Komivi Senyo , Ravindran Keppanan , Lin Yongwen , Bamisile Bamisope Steve , Qasim Muhammad , Dash Chandra Kanta , Wang Liande 
Published: June 2017

AbstractThe Asian citrus psyllid, Diaphorina citri, is a major pest of citrus and vector of citrus greening (huanglongbing) in Asian. In our field‐collected psyllid samples, we discovered that Fuzhou (China) and Faisalabad (Pakistan), populations harbored an obligate primary endosymbiont Candidatus Carsonella (gen. nov.) with a single species, Candidatus Carsonella ruddii (sp. nov.) and a secondary endosymbiont, Wolbachia surface proteins (WSP) which are intracellular endosymbionts residing in the bacteriomes. Responses of these symbionts to different temperatures were examined and their host survival assessed. Diagnostic PCR assays showed that the endosymbionts infection rates were not significantly reduced in both D. citri populations after 24 h exposure to cold or heat treatments. Although quantitative PCR assays showed significant reduction of WSP relative densities at 40°C for 24 h, a substantial decrease occurred as the exposure duration increased beyond 3 days. Under the same temperature regimes, Ca. C. ruddii density was initially less affected during the first exposure day, but rapidly reduced at 3–5 days compared to WSP. However, the mortality of the psyllids increased rapidly as exposure time to heat treatment increased. The responses of the two symbionts to unfavorable temperature regimes highlight the complex host‐symbionts interactions between D. citri and its associated endosymbionts.
Grazing of leaf‐associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function
Authors: Flues Sebastian , Bass David , Bonkowski Michael 
Published: June 2017

SummaryPreferential food selection in protists is well documented, but we still lack basic understanding on how protist predation modifies the taxonomic and functional composition of bacterial communities. We conducted feeding trials using leaf‐associated cercomonad Cercozoa by incubating them on a standardized, diverse bacterial community washed from plant leaves. We used a shotgun metagenomics approach to investigate the taxonomic and functional changes of the bacterial community after five days protist predation on bacteria. Predation‐induced shifts in bacterial community composition could be linked to phenotypic protist traits. Protist reproduction rate, morphological plasticity and cell speed were most important in determining bacterial community composition. Analyses of co‐occurrence patterns showed less complex correlations between bacterial taxa in the protist‐grazed treatments with a higher proportion of positive correlations than in non‐grazed controls, suggesting that predation reduced the influence of strong competitors. Protist predation influenced 14 metabolic core functions including membrane transport from which type VI secretion systems were in particular upregulated. In view of the functional importance of bacterial communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of predator‐prey interactions, changes in microbial composition and function, and subsequent repercussions on plant performance are clearly required.