bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional diversity among sensory neurons from efficient coding principles
Authors: Gjorgjieva Julijana , Meister Markus , Sompolinsky Haim 
Published: April 2017

AbstractIn many sensory systems the neural signal is coded by the coordinated response of heterogeneous populations of neurons. What computational benefit does this diversity confer on information processing? We derive an efficient coding framework assuming that neurons have evolved to communicate signals optimally given natural stimulus statistics and metabolic constraints. Incorporating nonlinearities and realistic noise, we study optimal population coding of the same sensory variable using two measures: maximizing the mutual information between stimuli and responses, and minimizing the error incurred by the optimal linear decoder of responses. Our theory is applied to a commonly observed splitting of sensory neurons into ON and OFF that signal stimulus increases or decreases, and to populations of monotonically increasing responses of the same type, ON. Depending on the optimality measure, we make different predictions about how to optimally split a population into ON and OFF, and how to allocate the firing thresholds of individual neurons given realistic stimulus distributions and noise, which accord with certain biases observed experimentally.
wft4galaxy: A Workflow Tester for Galaxy
Authors: Piras Marco Enrico , Pireddu Luca , Zanetti Gianluigi 
Published: April 2017

ABSTRACTMotivationWorkflow managers for scientific analysis provide a high-level programming platform facilitating standardization, automation, collaboration and access to sophisticated computing resources. The Galaxy workflow manager provides a prime example of this type of platform. As compositions of simpler tools, workflows effectively comprise specialized computer programs implementing often very complex analysis procedures. To date, no simple way exists to automatically test Galaxy workflows and ensure their correctness has appeared in the literature.ResultsWithwft4galaxywe offer a tool to bring automated testing to Galaxy workflows, making it feasible to bring continuous integration to their development and ensuring that defects are detected promptly.wft4galaxycan be easily installed as a regular Python program or launched directly as a Docker container – the latter reducing installation effort to a minimum.Availabilitywft4galaxyis available online athttps://github.com/phnmnl/wft4galaxyunder the Academic Free License v3.0.Supplementary informationSupplementary information is available athttp://wft4galaxy.readthedocs.io.
Real-time observation of light-controlled transcription in living cells
Authors: Rademacher Anne , Erdel Fabian , Trojanowski Jorge , Rippe Karsten 
Published: April 2017

AbstractGene expression is a tightly controlled process that is coordinated in space and time. To dissect its dynamic regulation with high temporal resolution, we introduce an optogenetic tool termed BLInCR (Blue Light-Induced Chromatin Recruitment) that combines rapid and reversible light-dependent recruitment of effector proteins with a real-time readout for transcription. We used BLInCR to control the activity of a reporter gene cluster in the human osteosarcoma cell line U2OS by reversibly recruiting the viral transactivator VP16. RNA production was detectable ∼2 minutes after VP16 recruitment and readily decreased when VP16 dissociated from the cluster in the absence of light. Quantitative assessment of the activation process revealed biphasic activation kinetics with a pronounced early phase in cells treated with the histone deacetylase inhibitor SAHA. Comparison with kinetic models for transcription activation suggests that the gene cluster undergoes a maturation process when activated. BLInCR will facilitate the study of transcription dynamics in living cells.
N-(3-oxododecanoyl)-L-homoserine lactone interactions in the breast tumor microenvironment: implications for breast cancer viability and proliferationin vitro
Authors: Balhouse Brittany N. , Patterson Logan , Schmelz Eva M. , Slade Daniel J. , Verbridge Scott S. 
Published: April 2017

AbstractIt is well documented that the tumor microenvironment profoundly impacts the etiology and progression of breast cancer, yet the contribution of the resident microbiome within breast tissue remains poorly understood. Tumor microenvironmental conditions, such as hypoxia and dense tumor stroma, predispose progressive phenotypes and therapy resistance, however the role of bacteria in this interplay remains uncharacterized. We hypothesized that the effect of individual bacterial secreted molecules on breast cancer viability and proliferation would be modulated by these tumor-relevant stressors differentially for cells at varying stages of progression. To test this, we incubated human breast adenocarcinoma cells (MDA-MB-231,MCF-DCIS.com) and non-malignant breast epithelial cells (MCF-10A) with N-(3-oxododecanoyl)-L-homoserine lactone (OdDHL), a quorum-sensing molecule fromPseudomonas aeruginosathat regulates bacterial stress responses. This molecule was selected becausePseudomonaswas recently characterized as a significant fraction of the breast tissue microbiome and OdDHL is documented to impact mammalian cell viability. After OdDHL treatment, we demonstrated the greatest decrease in viability with the more malignant MDAMB-231 cells and an intermediateMCF-DCIS.com(ductal carcinomain situ) response. The responses were also culture condition (i.e. microenvironment) dependent. These results contrast the MCF-10A response, which demonstrated no change in viability in any culture condition. We further determined that the observed trends in breast cancer viability were due to modulation of proliferation for both cell types, as well as the induction of necrosis for MDA-MB-231 cells in all conditions. Our results provide evidence that bacterial quorum-sensing molecules interact with the host tissue environment to modulate breast cancer viability and proliferation, and that the effect of OdDHL is dependent on both cell type as well as microenvironment. Understanding the interactions between bacterial signaling molecules and the host tissue environment will allow for future studies that determine the contribution of bacteria to the onset, progression, and therapy response of breast cancer.
MicroRNA regulation of the MRN complex impacts DNA damage, cellular senescence and angiogenic signaling
Authors: Espinosa-Diez Cristina , Wilson RaeAnna , Chatterjee Namita , Hudson Clayton , Ruhl Rebecca , Hipfinger Christina , Helms Erin , Khan Omar F. , Anderson Daniel G. , Anand Sudarshan 
Published: April 2017

AbstractMicroRNAs contribute to biological robustness by buffering cellular processes from external perturbations. Here we report an unexpected link between DNA damage response and angiogenic signaling that is buffered by two distinct microRNAs. We demonstrate that genotoxic stress-induced miR-494 and miR-99b inhibit the DNA repair machinery by targeting the MRE11a-RAD50-NBN (MRN) complex. Functionally, gain and loss of function experiments show that miR-494 and miR-99b affect telomerase activity, activate p21 and Rb pathways and diminish angiogenic sproutingin vitroandin vivo. Genetic and pharmacological disruption of VEGFR-2 signaling and the MRN complex reveal a surprising co-dependency of these pathways in regulating endothelial senescence and proliferation. Vascular-targeted delivery of miR-494 decreases both growth factor-induced and tumor angiogenesis in mouse models. Mechanistically, disruption of the MRN complex induced CD44, a known driver of senescence and regulator of VEGF signaling in addition to suppressing IL-13 a stimulator of VEGF signaling. Our work identifies a putative miR-facilitated mechanism by which endothelial cells can be insulated against VEGF signaling to facilitate the onset of senescence and highlight the potential of targeting DNA repair to disrupt pathological angiogenesis.
A horizontally transferred autonomous Helitron became a full polydnavirus segment inCotesia vestalis
Authors: Heringer Pedro , Dias Guilherme B. , Kuhn Gustavo C. S. 
Published: May 2017

ABSTRACTBracoviruses associate symbiotically with thousands of parasitoid wasp species in the family Braconidae, working as virulence gene vectors, and allowing the development of wasp larvae within hosts. These viruses are composed by multiple DNA circles that are packaged into infective particles and injected together with wasp's eggs during parasitization. One of the viral segments ofCotesia vestalisbracovirus contains a gene that has been previously described as a helicase of unknown origin. Here we demonstrate that this gene is a Rep/Helicase from an intact Helitron transposable element that covers the viral segment almost entirely. We also provide evidence that this element underwent at least two horizontal transfers, which appear to have occurred consecutively: first from a Drosophila host ancestor to the genome of the parasitoid waspCotesia vestalisand its bracovirus, and then fromC. vestalisto a lepidopteran host (Bombyx mori). Our results reinforce the idea of parasitoid wasps as frequent agents of horizontal transfers in eukaryotes. Additionally, this Helitron-bracovirus segment is the first example of a transposable element that effectively became a whole viral circle.
Caterpillars lack a resident gut microbiome
Authors: Hammer Tobin J. , Janzen Daniel H. , Hallwachs Winnifred , Jaffe Samuel L. , Fierer Noah 
Published: May 2017

AbstractMany animals are inhabited by microbial symbionts that influence their hosts’ development, physiology, ecological interactions, and evolutionary diversification. However, firm evidence for the existence and functional importance of resident microbiomes in larval Lepidoptera (caterpillars) is lacking, despite the fact that these insects are enormously diverse, major agricultural pests, and dominant herbivores in many ecosystems. Using 16S rRNA gene sequencing and quantitative PCR, we characterized the gut microbiomes of wild leaf-feeding caterpillars in the United States and Costa Rica, representing 124 species from 16 families. Compared with other insects and vertebrates assayed using the same methods, the microbes we detected in caterpillar guts were unusually low-density and highly variable among individuals. Furthermore, the abundance and composition of leaf-associated microbes were reflected in the feces of caterpillars consuming the same plants. Thus, microbes ingested with food are present (though possibly dead or dormant) in the caterpillar gut, but host-specific, resident symbionts are largely absent. To test whether transient microbes might still contribute to feeding and development, we conducted an experiment on field-collected caterpillars of the model speciesManduca sexta. Antibiotic suppression of gut bacterial activity did not significantly affect caterpillar weight gain, development, or survival. The high pH, simple gut structure, and fast transit times that typify caterpillar digestive physiology may prevent microbial colonization. Moreover, host-encoded digestive and detoxification mechanisms likely render microbes unnecessary for caterpillar herbivory. Caterpillars illustrate the potential ecological and evolutionary benefits of independence from symbionts, a lifestyle which may be widespread among animals.
Accurate estimation of acoustic impedance based on spectral inversion
Authors: Liu Jie , Zhang Jianzhong , Huang Zhong‐lai 
Published: May 2017

ABSTRACTAcoustic impedance is one of the best attributes for seismic interpretation and reservoir characterisation. We present an approach for estimating acoustic impedance accurately from a band‐limited and noisy seismic data. The approach is composed of two stages: inverting for reflectivity from seismic data and then estimating impedance from the reflectivity inverted in the first stage. For the first stage, we achieve a two‐step spectral inversion that locates the positions of reflection coefficients in the first step and determines the amplitudes of the reflection coefficients in the second step under the constraints of the positions located in the first step. For the second stage, we construct an iterative impedance estimation algorithm based on reflectivity. In each iteration, the iterative impedance estimation algorithm estimates the absolute acoustic impedance based on an initial acoustic impedance model that is given by summing the high‐frequency component of acoustic impedance estimated at the last iteration and a low‐frequency component determined in advance using other data. The known low‐frequency component is used to restrict the acoustic impedance variation tendency in each iteration. Examples using one‐ and two‐dimensional synthetic and field seismic data show that the approach is flexible and superior to the conventional spectral inversion and recursive inversion methods for generating more accurate acoustic impedance models.
Effects of crown architecture and stand structure on light absorption in mixed and monospecificFagus sylvaticaandPinus sylvestrisforests along a productivity and climate gradient through Europe
Authors: Forrester David Ian , Ammer Christian , Annighöfer Peter J. , Barbeito Ignacio , Bielak Kamil , Bravo‐Oviedo Andrés , Coll Lluis , del Río Miren , Drössler Lars , Heym Michael , Hurt Václav , Löf Magnus , den Ouden Jan , Pach Maciej , Pereira Mário Gonzalez , Plaga Benjamin N. E. , Ponette Quentin , Skrzyszewski Jerzy , Sterba Hubert , Svoboda Miroslav , Zlatanov Tzvetan M. , Pretzsch Hans 
Published: April 2017

AbstractWhen tree‐species mixtures are more productive than monocultures, higher light absorption is often suggested as a cause. However, few studies have quantified this effect and even fewer have examined which light‐related interactions are most important, such as the effects of species interactions on tree allometric relationships and crown architecture, differences in vertical or horizontal canopy structure, phenology of deciduous species or the mixing effects on tree size and stand density.In this study, measurements of tree sizes and stand structures were combined with a detailed tree‐level light model (Maestra) to examine the contribution of each light‐related interaction on tree‐ and stand‐level light absorption at 21 sites, each of which contained a triplet of plots including a mixture and monocultures ofFagus sylvaticaandPinus sylvestris(63 plots). These sites were distributed across the current distribution of these species within Europe.Averaged across all sites, the light absorption of mixtures was 14% higher than the mean of the monocultures. At the whole community level, this positive effect of mixing on light absorption increased as canopy volume or site productivity increased, but was unrelated to climate. At the species population or individual tree levels, the mixing effect on light absorption resulted from light‐related interactions involving vertical canopy structure, stand density, the presence of a deciduous species (F. sylvatica), as well as the effects of mixing on tree size and allometric relationships between diameter and height, crown diameter and crown length.The mixing effects on light absorption were only correlated with the mixing effects on growth forP. sylvestris, suggesting that the mixing effects on this species were driven by the light‐related interactions, whereas mixing effects onF. sylvaticaor whole community growth were probably driven by non‐light‐related interactions.Synthesis. The overall positive effect of mixing on light absorption was the result of a range of light‐related interactions. However, the relative importance of these interactions varied between sites and is likely to vary between other species combinations and as stands develop.
Do traumatic events have more impact on the development of dental anxiety than negative, non‐traumatic events?
Authors: De Jongh Ad , van Eeden Astrid , van Houtem Caroline M. H. H. , van Wijk Arjen J. 
Published: April 2017

The importance of exposure to traumatic events for the development of dental anxiety has not been investigated. The aim of the present study was to test the hypotheses that individuals who reported having been exposed to a traumatic event [that is, fulfilling Criterion A of the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition (DSM‐5), for post‐traumatic stress disorder (PTSD)] as the cause of their dental anxiety would report significantly higher levels of dental anxiety, typical trauma‐related (PTSD) symptoms, and greater disturbance of memories involving these events than those who reported being exposed to non‐traumatic events. Patients of a specialized dental fear clinic (n = 90) were divided into those who reported a traumatic event that initiated their dental trait anxiety and those who did not. The two groups did not differ in their severity of dental anxiety and number of PTSD symptoms, but the memories of those who had been exposed to traumatic events were significantly more vivid than the memories of those in the reference group. Length of time since the event took place did not play a role. Hence, traumatic events are remembered more vividly, but do not seem to initiate more severe forms of dental anxiety than other events.
Telling friend from foe: Environmental cues improve detection accuracy of individuals with hostile intentions
Authors: Wijn Remco , van der Kleij Rick , Kallen Victor , Stekkinger Michael , de Vries Peter 
Published: April 2017

PurposeDetecting deviant behaviours that precede and are related to crimes can help prevent these crimes. Research suggests that the psychological mindset of wrongdoers may differ from others, such that they are more anxious, self‐focussed, and vigilant. As a result, their responses to environmental cues, specifically those that signal risk of exposure, may differ.MethodIn two randomized controlled trials, participants with high (vs. low) cognitive load walked a pre‐defined route to carry out a hostile or non‐hostile task. En route, participants were exposed to a strong (vs. mild) cue from a security officer (Study 1), or a cue (vs. no cue) resembling police walkie‐talkie static noise (Study 2). Participants filled out a questionnaire measuring psychological constructs. Reactions during the task were recorded and presented to independent observers to determine the participants’ intent.ResultsParticipants with high (vs. low) cognitive load who were exposed to a strong (vs. mild or no) cue while carrying out their task were more often correctly identified by observers as either innocent or hostile based on their behaviour. Analysis of the questionnaire revealed that the experience of hostile intentions is related to anxiety, inhibitory control of anxiety, activation control of normal behaviour, and to other relevant constructs which may explain why cues that signal risk of exposure can improve the detection accuracy of individuals with hostile intentions.ConclusionThese studies show that cues that signal risk of exposure can improve the detection of wrongdoers and the role of self‐regulation in the suppression of anxiety and deviant behaviours.
On the role of asymmetric frontal cortical activity in approach and withdrawal motivation: An updated review of the evidence
Authors: Harmon‐Jones Eddie , Gable Philip A. 
Published: May 2017

AbstractWe review conceptual arguments and research on the role of asymmetric frontal cortical activity in emotional and motivational processes. The current article organizes and reviews research on asymmetrical frontal cortical activity by focusing on research that has measured trait (baseline) frontal asymmetry and related it to other individual differences measures related to motivation (e.g., anger, bipolar disorder). The review also covers research that has measured state frontal asymmetry in response to situational manipulations of motivation and emotion and as an intervening variable in motivation‐cognition interactions. This review concludes that much research supports the view that greater left than right frontal cortical activity is associated with greater positively or negatively valenced approach motivation. The view that greater right than left frontal cortical activity is associated with withdrawal motivation, although supported, has received less empirical attention. In addition to reviewing research on the emotive functions of asymmetric frontal cortical activity, the reviewed research illustrates the need to consider motivational direction as separate from affective valence in conceptual models of emotional space.
Transoral approach for ventral tympanic bulla osteotomy in the dog: A descriptive cadaveric study*
Authors: Manou Maria , Moissonnier Pierre H. M. , Jardel Nicolas , Tissier Aymeric , Vallefuoco Rosario 
Published: May 2017

AbstractObjectiveTo describe a transoral approach for tympanic bulla osteotomy in the dog.Study designAnatomic cadaveric study.Sample populationFifteen canine cadavers (n = 29 tympanic bullae), including mesaticephalic, dolichocephalic, and brachycephalic breeds.Materials and methodsThe oral surface of the tympanic bulla was identified during an anatomical study (3 canine cadavers) and the ventral approach to the tympanic bulla was described (3 canine cadavers). The safety of the technique was assessed (9 canine cadavers, n = 17 bullae) during further anatomical dissections, where a complete approach and drilling of the tympanic bulla were performed.ResultsIn all cases, tympanic bulla osteotomy was performed without damaging the inner ear, the epitympanic recess contents, and the neurovascular structures. The oral approach to the tympanic bulla was easier in mesaticephalic and dolichocephalic dogs than in brachycephalic breeds.ConclusionThis study defines anatomical landmarks for transoral bulla osteotomy, without a high risk of damage to neurovascular and anatomical structures within and/or surrounding the tympanic cavity. This minimally invasive approach to the tympanic bulla is performed via a natural opening, and does not require simultaneous access through the ear canal. In vivo evaluation of this technique is required to verify its safety in clinical cases prior to large scale application.
Effect of stem sizing and position on short‐term complications with canine press fit cementless total hip arthroplasty
Authors: Townsend Sarah , Kim Stanley E. , Pozzi Antonio 
Published: May 2017

AbstractObjectiveTo determine the influence of stem sizing and positioning with early subsidence and stem complications with cementless (BFX) total hip arthroplasty (THA).Study designRetrospective case series.AnimalsFifty‐five dogs; 58 THAs.MethodsEighty cobalt‐chromium BFX THAs were reviewed, 58 met inclusion criteria. Implant size, positioning, and major complications within 12 months of surgery were recorded. Femoral canal flare (FCF), canal fill, stem angle, and subsidence at 3 months were measured from postoperative radiographs. Appropriateness of final stem size was assessed with digital templates. Odds ratios for associations were calculated.ResultsMean ± SD coronal canal fill (Fillcor) was 75% ± 6, FCF was 2.0 ± 0.3, and subsidence was 1.7 mm ± 2.6. Stem angulation ranged from 7° varus to 6° valgus, and 7° cranial to 3° caudal. Appropriately sized stems (n = 45) had a mean Fillcor of 78%. Major stem complications occurred in 12% of THAs. Femora with subsidence > 3 mm were 45.3 times more likely to develop postoperative stem complications (P = .02). Stems with varus angulation ≥ 5° were 12.5 times more likely to sustain intraoperative fissures (P = .03). Stems considered undersized based on postoperative digital templating were 5.6 times more likely to develop stem complications (P = .04) and 5.7 times more likely to subside > 3 mm (P = .03).ConclusionVarus stem angulation should be avoided to prevent fissures. Canal fill is a poor indicator of optimal stem size and the current recommendation of >85% is unnecessarily high. Postoperative templating may be useful for assessing appropriateness of stem size.