bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling sex-specific crossover patterning in Arabidopsis
Authors: Lloyd Andrew , Jenczewski Eric 
Published: October 2018

ABSTRACTInterference is a major force governing the patterning of meiotic crossovers. A leading model describing how interference influences crossover-patterning is the beam film model, a mechanical model based on the accumulation and redistribution of crossover-promoting stress along the chromosome axis. We use the beam-film model in conjunction with a large Arabidopsis reciprocal back-cross data set to gain mechanistic insights into the differences between male and female meiosis and crossover patterning. Beam-film modelling suggests that the underlying mechanics of crossover patterning and interference are identical in the two sexes, with the large difference in recombination rates and distributions able to be entirely explained by the shorter chromosome axes in females. The modelling supports previous indications that fewer crossovers occur via the class II pathway in female meiosis and that this could be explained by reduced DNA double strand breaks in female meiosis, paralleling the observed reduction in synaptonemal complex length between the two sexes. We also demonstrate that changes in the strength of suppression of neighboring class I crossovers can have opposite effects on effective interference depending on the distance between two genetic intervals.
A confirmation bias in perceptual decision-making due to hierarchical approximate inference
Authors: Lange Richard D. , Chattoraj Ankani , Beck Jeffrey M. , Yates Jacob L. , Haefner Ralf M. 
Published: October 2018

AbstractMaking good decisions requires updating beliefs according to new evidence. This is a dynamical process that is prone to biases: in some cases, beliefs become entrenched and resistant to new evidence (leading to primacy effects), while in other cases, beliefs fade over time and rely primarily on later evidence (leading to recency effects). How and why either type of bias dominates in a given context is an important open question. Here, we study this question in classic perceptual decision-making tasks, where, puzzlingly, previous empirical studies differ in the kinds of biases they observe, ranging from primacy to recency, despite seemingly equivalent tasks. We present a new model, based on hierarchical approximate inference and derived from normative principles, that not only explains both primacy and recency effects in existing studies, but also predicts how the type of bias should depend on the statistics of stimuli in a given task. We verify this prediction in a novel visual discrimination task with human observers, finding that each observer’s temporal bias changed as the result of changing the key stimulus statistics identified by our model. By fitting an extended drift-diffusion model to our data we rule out an alternative explanation for primacy effects due to bounded integration. Taken together, our results resolve a major discrepancy among existing perceptual decision-making studies, and suggest that a key source of bias in human decision-making is approximate hierarchical inference.
Effects of Oral Domoic Acid Exposure on Maternal Reproduction and Infant Birth Characteristics in a Preclinical Nonhuman Primate Model
Authors: Burbacher Thomas M. , Grant Kimberly S. , Petroff Rebekah , Shum Sara , Crouthamel Brenda , Stanley Courtney , McKain Noelle , Jing Jing , Isoherranen Nina 
Published: October 2018

AbstractDomoic Acid (DA) is a naturally-occurring excitotoxin, produced by marine algae, which can bioaccumulate in shellfish and finfish. The consumption of seafood contaminated with DA is associated with gastrointestinal illness that, in the case of high DA exposure, can evolve into a spectrum of responses ranging from agitation to hallucinations, memory loss, seizures and coma. Because algal blooms that produce DA are becoming more widespread and very little is known about the dangers of chronic, low-dose exposure, we initiated a preclinical study focused on the reproductive and developmental effects of DA in a nonhuman primate model. To this end, 32 adult femaleMacaca fascicularismonkeys were orally exposed to 0, 0.075 or 0.15 mg/kg/day DA on a daily basis, prior to and during pregnancy. Females were bred to non-exposed males and infants were evaluated at birth. Results from this study provided no evidence of changes in DA plasma concentrations with chronic exposure. DA exposure was not associated with reproductive toxicity or adverse changes in the physical characteristics of newborns. However, in an unanticipated finding, our clinical observations battery revealed the presence of subtle neurological effects in the form of intentional tremors in the exposed adult females. While females in both dose groups displayed increased tremoring, the effect was dose-dependent and observed at a higher frequency in females exposed to 0.15 mg/kg/day. These results demonstrate that chronic, low-level exposure to DA is associated with injury to the adult CNS and suggest that current regulatory guidelines designed to protect human health may not be adequate for high-frequency shellfish consumers.Highlights1) Domoic acid acts as a tremoragen after chronic, low-dose oral exposure in adults.2) Exposure across pregnancy does not result in maternal reproductive toxicity.3) In-utero exposure does not adversely impact physical characteristics of exposed newborns.4) Current regulatory guidelines may not adequately protect high-frequency shellfish consumers from DA-induced neurological injury.
Vocal motor experiences consolidate the vocal motor circuitry and accelerate future vocal skill development
Authors: Vellema Michiel , Rocha Mariana Diales , Bascones Sabrina , Zsebők Sándor , Dreier Jes , Leitner Stefan , Van der Linden Annemie , Brewer Jonathan , Gahr Manfred 
Published: October 2018

ABSTRACTComplex motor skills take considerable time and practice to learn. Without continued practice the level of skill performance quickly degrades, posing a problem for the timely utilization of skilled motor responses. Here we quantified the recurring development of vocal motor skills and the accompanying changes in synaptic connectivity in the brain of a songbird, while manipulating skill performance by consecutively administrating and withdrawing testosterone. We demonstrate that a songbird with prior singing experience can significantly accelerate the re-acquisition of vocal performance. We further demonstrate that an increase in vocal performance is accompanied by a pronounced synaptic pruning in the forebrain vocal motor area HVC, a reduction that is not reversed when birds stop singing. These results provide evidence that lasting synaptic changes in the motor circuitry are associated with the savings of motor skills, enabling a rapid recovery of motor performance under environmental time constraints.
Discovery of allosteric non-covalent KRAS inhibitors that bind with sub-micromolar affinity and disrupt effector binding
Authors: McCarthy Michael J. , Pagba Cynthia V. , Prakash Priyanka , Naji Ali , van der Hoeven Dharini , Liang Hong , Gupta Amit K. , Zhou Yong , Cho Kwang-Jin , Hancock John F. , Gorfe Alemayehu A. 
Published: October 2018

AbstractApproximately 15% of all human tumors harbor mutant KRAS, a membrane-associated small GTPase and a notorious oncogene. Somatic mutations that render KRAS constitutively active lead to uncontrolled cell growth, survival, proliferation, and eventually cancer. KRAS is thus a critical anticancer drug target. However, despite aggressive efforts in recent years, there is no drug on the market that directly targets KRAS. In the current work, we combined molecular simulation and high-throughput virtual screening with a battery of cell-based and biophysical assays to discover a novel, pyrazolopyrimidine-based allosteric KRAS inhibitor that exhibits promising biochemical properties. The compound selectively binds to active KRAS with sub-micromolar affinity, slightly modulates exchange factor activity, disrupts effector Raf binding, significantly reduces signal transduction through mutant KRAS and inhibits cancer cell growth. Moreover, by studying two of its analogues, we identified key chemical features of the compound that are critical for affinity, effect on effector binding and mode of action. We propose a set of specific interactions with key residues at the switch regions of KRAS as critical for abrogating effector binding and reducing the rate of nucleotide exchange. Together, these findings not only demonstrate the viability of direct KRAS inhibition and offer guidance for future optimization efforts, but also show that pyrazolopyrimidine-based compounds may represent a first-in-class lead toward a clinically relevant targeting of KRAS by allosteric non-covalent inhibitors.
Dysregulated Oscillatory Connectivity in the Visual System in Autism Spectrum Disorder
Authors: Seymour R.A. , Rippon G. , Gooding-Williams G. , Schoffelen J.M. , Kessler K. 
Published: October 2018

AbstractAutism Spectrum Disorder is increasingly associated with atypical perceptual and sensory symptoms. Here we explore the hypothesis that aberrant sensory processing in Autism Spectrum Disorder could be linked to atypical intra- (local) and inter-regional (global) brain connectivity. To elucidate oscillatory dynamics and connectivity in the visual domain we used magnetoencephalography and a simple visual grating paradigm with a group of 18 adolescent autistic participants and 18 typically developing controls. Both groups showed similar increases in gamma (40-80Hz) and decreases in alpha (8-13Hz) frequency power in occipital cortex. However, systematic group differences emerged when analysing intra- and inter-regional connectivity in detail. Firstly, directed connectivity was estimated using non-parametric Granger causality between visual areas V1 and V4. Feedforward V1-to-V4 connectivity, mediated by gamma oscillations, was equivalent between Autism Spectrum Disorder and control groups, but importantly, feedback V4-to-V1 connectivity, mediated by alpha (8-13Hz) oscillations, was significantly reduced in the Autism Spectrum Disorder group. This reduction was positively correlated with autistic quotient scores, consistent with an atypical visual hierarchy in autism, characterised by reduced top-down modulation of visual input via alpha-band oscillations. Secondly, at the local level in V1, coupling of alpha-phase to gamma amplitude (alpha-gamma phase amplitude coupling, PAC) was reduced in the Autism Spectrum Disorder group. This implies dysregulated local visual processing, with gamma oscillations decoupled from patterns of wider alpha-band phase synchrony (i.e. reduced PAC), possibly due to an excitation-inhibition imbalance. More generally, these results are in agreement with predictive coding accounts of neurotypical perception and indicate that visual processes in autism are less modulated by contextual feedback information.
A wave of WNT signalling balanced by secreted inhibitors controls primitive streak formation in micropattern colonies of human embryonic stem cells
Authors: Martyn I. , Brivanlou A.H. , Siggia E.D. 
Published: October 2018

AbstractLong range signalling by morphogens and their inhibitors define embryonic patterning yet quantitative data and models are rare, especially in humans. Here we use a human embryonic stem cell “gastruloid” system to model formation of the primitive streak (PS) by WNT. In the pluripotent state E-CADHERIN (E-CAD) transduces boundary forces to focus WNT signalling to colony border. Following application of WNT ligand, E-CAD mediates a wave of epithelial-to-mesenchymal (EMT) conversion analogous to PS extension in an embryo. By knocking out the secreted WNT inhibitors active in our system, we show that DKK1 alone controls the extent and duration of patterning. The NODAL inhibitor CERBERUS1 acts downstream of WNT to refine the endoderm versus mesoderm fate choice. Our EMT wave is a generic property of a bistable system with diffusion and a single quantitative model describes both the wave and our knockout data.
Streptococcus agalactiaeinduces placental macrophages to release extracellular traps loaded with tissue remodeling enzymes via an oxidative-burst-dependent mechanism
Authors: Doster Ryan S. , Sutton Jessica A. , Rogers Lisa M. , Aronoff David M. , Gaddy Jennifer A. 
Published: October 2018

AbstractStreptococcus agalactiae, or Group BStreptococcus(GBS), is a common perinatal pathogen. GBS colonization of the vaginal mucosa during pregnancy is a risk factor for invasive infection of the fetal membranes (chorioamnionitis) and its consequences such as membrane rupture, preterm labor, stillbirth, and neonatal sepsis. Placental macrophages, or Hofbauer cells, are fetally-derived macrophages present within placental and fetal membrane tissues that perform vital functions for fetal and placental development, including supporting angiogenesis, tissue remodeling, and regulation of maternal-fetal tolerance. Although placental macrophages, as tissue-resident innate phagocytes, are likely to engage invasive bacteria such as GBS, there is limited information regarding how these cells respond to bacterial infection. Here, we demonstratein vitrothat placental macrophages release macrophage extracellular traps (METs) in response to bacterial infection. Placental macrophage METs contain proteins including histones, myeloperoxidase, and neutrophil elastase similar to neutrophil extracellular traps and are capable of killing GBS cells. MET release from these cells occurs by a process that depends on the production of reactive oxygen species. Placental macrophage METs also contain matrix metalloproteases that are released in response to GBS and could contribute to fetal membrane weakening during infection. MET structures were identified within human fetal membrane tissues infectedex vivo, suggesting that placental macrophages release METs in response to bacterial infection during chorioamnionitis.ImportanceStreptococcus agalactiae, also known as Group BStreptococcus(GBS), is a common pathogen during pregnancy where infection can result in chorioamnionitis, preterm premature rupture of membranes (PPROM), preterm labor, stillbirth, and neonatal sepsis. Mechanisms by which GBS infection results in adverse pregnancy outcomes are still incompletely understood. This study evaluated interactions between GBS and placental macrophages. The data demonstrate that in response to infection, placental macrophages release extracellular traps capable of killing GBS. Additionally, this work establishes that proteins associated with extracellular trap fibers include several matrix metalloproteinases that have been associated with chorioamnionitis. In the context of pregnancy, placental macrophage responses to bacterial infection might have beneficial and adverse consequences, including protective effects against bacterial invasion but also releasing important mediators of membrane breakdown that could contribute to membrane rupture or preterm labor.
Tibanna: software for scalable execution of portable pipelines on the cloud
Authors: Lee Soohyun , Johnson Jeremy , Vitzthum Carl , Kırlı Koray , Alver Burak H. , Park Peter J. 
Published: October 2018

AbstractSummaryWe introduce Tibanna, an open-source software tool for automated execution of bioinformatics pipelines on Amazon Web Services (AWS). Tibanna accepts reproducible and portable pipeline standards including Common Workflow Language (CWL), Workflow Description Language (WDL) and Docker. It adopts a strategy of isolation and optimization of individual executions, combined with a serverless scheduling approach. Pipelines are executed and monitored using local commands or the Python Application Programming Interface (API) and cloud configuration is automatically handled. Tibanna is well suited for projects with a range of computational requirements, including those with large and widely fluctuating loads. Notably, it has been used to process terabytes of data for the 4D Nucleome (4DN) Network.AvailabilitySource code is available on GitHub at https://github.com/4dn-dcic/tibanna.
A Multi-State Birth-Death model for Bayesian inference of lineage-specific birth and death rates
Authors: Barido-Sottani Joëlle , Vaughan Timothy G. , Stadler Tanja 
Published: October 2018

AbstractHeterogeneous populations can lead to important differences in birth and death rates across a phylogeny Taking this heterogeneity into account is thus critical to obtain accurate estimates of the underlying population dynamics. We present a new multi-state birth-death model (MSBD) that can estimate lineage-specific birth and death rates. For species phylogenies, this corresponds to estimating lineage-dependent speciation and extinction rates. Contrary to existing models, we do not require a prior hypothesis on a trait driving the rate differences and we allow the same rates to be present in different parts of the phylogeny. Using simulated datasets, we show that the MSBD model can reliably infer the presence of multiple evolutionary regimes, their positions in the tree, and the birth and death rates associated with each. We also present a re-analysis of two empirical datasets and compare the results obtained by MSBD and by the existing software BAMM. The MSBD model is implemented as a package in the Bayesian inference software BEAST2, which allows joint inference of the phylogeny and the model parameters.Significance statementPhylogenetic trees can inform about the underlying speciation and extinction processes within a species clade. Many different factors, for instance environmental changes or morphological changes, can lead to differences in macroevolutionary dynamics within a clade. We present here a new multi-state birth-death (MSBD) model that can detect these differences and estimate both the position of changes in the tree and the associated macroevolutionary parameters. The MSBD model does not require a prior hypothesis on which trait is driving the changes in dynamics and is thus applicable to a wide range of datasets. It is implemented as an extension to the existing framework BEAST2.
Adipokines contribute to central-obesity related reductions in myelin-sensitive MRI indices in the fornix
Authors: Metzler-Baddeley Claudia , Mole Jilu P. , Leonaviciute Erika , Sims Rebecca , Kidd Emma J. , Ertefai Benjamin , Kelso-Mitchell Aurora , Gidney Florence , Fasano Fabrizio , Evans John , Jones Derek K , Baddeley Roland J. 
Published: October 2018

AbstractMidlife obesity is a risk factor of late onset Alzheimer’s disease (LOAD) but why this is the case remains unknown. As systemic inflammation is involved in both conditions, one possibility is that obesity-related neuroinflammation may contribute to the development of LOAD. Neuroinflammation is closely linked to white matter myelin loss, and this can be measuredin vivowith quantitative magnetization transfer (qMT) imaging. Here, we investigated whether differences in obesity measures, i.e., in Waist Hip Ratio (WHR), abdominal visceral and subcutaneous fat volume fractions and Body Mass Index (BMI), were associated with reductions in qMT indices of apparent myelin in temporal white matter pathways involved in LOAD (i.e., the fornix, the parahippocampal cingulum and the uncinate fasciculus compared with whole brain and cortico-spinal white matter) in 166 cognitively healthy individuals (38-71 years of age). Obesity-related effects on myelin-sensitive markers were contrasted with differences in apparent axon density from dual-shell diffusion Neurite Orientation Dispersion and Density Imaging (NODDI). Differences in WHR and in visceral fat volume fractions were negatively correlated with differences in qMT estimates of apparent myelin and tissue metabolism in the fornix but not with any other microstructural components. These correlations were not explained by demographic (age, sex, education), health (hypertension, alcohol consumption, sedentary lifestyle) or genetic (APOEgenotype, family history of dementia) risk factors of LOAD. Furthermore, differences in the ratio of plasma concentrations of leptin and adiponectin were also positively correlated with differences in C-Reactive Protein concentrations, and contributed significantly to the correlations between central obesity and myelin-sensitive metrics in the fornix. These results are consistent with the view that visceral fat-related chronic inflammation may damage white matter myelin in limbic regions, known to be vulnerable to LOAD pathology.
Specificity of RNA folding and its association with evolutionarily adaptive mRNA secondary structure
Authors: Yu Gongwang , Zhu Hanbing , Chen Xiaoshu , Yang Jian-Rong 
Published: October 2018

ABSTRACTSecondary structure is a fundamental feature for both noncoding and messenger RNA. However, our understandings about the secondary structure of mRNA, especially for the coding regions, remain elusive, likely due to translation and the lack of RNA binding proteins that sustain the consensus structure, such as those bind to noncoding RNA. Indeed, mRNA has recently been found to bear pervasive alternative structures, whose overall evolutionary and functional significance remained untested. We hereby approached this problem by estimating folding specificity, the probability that a fragment of RNA folds back to the same partner once re-folded. We showed that folding specificity for mRNA is lower than noncoding RNA, and displays moderate evolutionary conservation between orthologs and between paralogs. More importantly, we found that specific rather than alternative folding is more likely evolutionarily adaptive, since it is more frequently associated with functionally important genes or sites within a gene. Additional analysis in combination with ribosome density suggests the capability of modulating ribosome movement as one potential functional advantage provided by specific folding. Our findings revealed a novel facet of RNA structome with important functional and evolutionary implications, and points to a potential way of disentangling mRNA secondary structures maintained by natural selection from molecular noise.
Artificial neural network filters for enhancing 3D optical microscopy images of neurites
Authors: Wang Shih-Luen , Kahaki Seyed M. M. , Stepanyants Armen 
Published: October 2018

ABSTRACTThe ability to extract accurate morphology of labeled neurons from microscopy images is crucial for mapping brain connectivity and for understanding changes in connectivity that underlie learning and memory formation. There are, however, two problems, specific to optical microscopy imaging of neurons, which make accurate neuron tracing exceedingly challenging: (i) neurites can appear broken due to inhomogeneous labeling and (ii) neurites can appear fused in 3D due to limited resolution. Here, we propose and evaluate several artificial neural network (NN) architectures and conventional image enhancement filters with the aim of solving both problems. To evaluate the effects of filtering, we examine the following four image quality metrics: normalized intensity in the cross-over regions between neurites, radius of neurites, coefficient of variation of intensity along neurites, and local background to neurite intensity ratio. Our results show that NN filters, trained on optimized semi-manual traces of neurites, can significantly outperform conventional filters. In particular, U-Net based filtering can virtually eliminate background intensity, while also reducing radius of neurites by 23% to nearly 1 voxel, decreasing intensity in the cross-over regions between neurites by 22%, and reducing variations in intensity along neurites by 26%. These results suggest that including a NN filtering step, which does not require much extra time or computing power, can be beneficial for neuron tracing projects.