bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organ-specific NLR resistance gene expression varies with plant symbiotic status
Authors: Munch David , Gupta Vikas , Bachmann Asger , Busch Wolfgang , Kelly Simon , Mun Terry , Andersen Stig Uggerhøj 
Published: May 2017

AbstractNucleotide-binding site leucine-rich repeat resistance genes (NLRs) allow plants to detect microbial effectors. We hypothesized that NLR expression patterns would reflect organ-specific differences in effector challenge and tested this by carrying out a meta-analysis of expression data for 1,235 NLRs from 9 plant species. We found stable NLR root/shoot expression ratios within species, suggesting organ-specific hardwiring of NLR expression patterns in anticipation of distinct challenges. Most monocot and dicot plant species preferentially expressed NLRs in roots. In contrast,Brassicaceaespecies, including oilseed rape and the model plantArabidopsis thaliana, were unique in showing NLR expression skewed towards the shoot across multiple phylogenetically distinct groups of NLRs. TheBrassicaceaeNLR expression shift coincides with loss of the endomycorrhization pathway, which enables intracellular root infection by symbionts. We propose that its loss offer two likely explanations for the unusualBrassicaceaeNLR expression pattern: loss of NLR-guarded symbiotic components and elimination of constraints on general root defences associated with exempting symbionts from targeting. This hypothesis is consistent with the existence ofBrassicaceae-specific receptors for conserved microbial molecules and suggests thatBrassicaceaespecies are rich sources of unique antimicrobial root defences.
Oxidative-phosphorylation genes from the mitochondrial and nuclear genomes co-express in all human tissues except for the ancient brain
Authors: Barshad Gilad , Blumberg Amit , Mishmar Dan 
Published: May 2017

AbstractIn humans, oxidative phosphorylation (OXPHOS), the cellular energy producer, harbors ∼90 nuclear DNA (nDNA)- and mitochondrial DNA (mtDNA)-encoded subunits. Although nDNA- and mtDNA-encoded OXPHOS proteins physically interact, their transcriptional regulation profoundly diverges, thus questioning their co-regulation. To address mtDNA-nDNA gene co-expression, we analyzed ∼8,500 RNA-seq Gene-Tissue-Expression (GTEx) experiments encompassing 48 human tissues. We found overall positive cross-tissue mtDNA-nDNA OXPHOS gene co-expression. Nevertheless, alternatively-spliced variants, as well as certain OXPHOS genes, did not converge into the main OXPHOS gene cluster, suggesting tissue-specific flavor of OXPHOS gene expression. Finally, unlike non-brain body sites, and neocortex and cerebellum (‘mammalian’ brain), negative mito-nuclear expression correlation was found in the hypothalamus, basal ganglia and amygdala (‘ancient brain’). Analyses of co-expression, DNase-seq and ChIP-seq experiments identified candidate RNA-binding genes and CEBPb as best explaining this phenomenon. We suggest that evolutionary convergence of the ‘mammalian’ brain into positive mtDNA-nDNA OXPHOS co-expression reflects adjustment to novel bioenergetics needs.
No compelling evidence that preferences for facial masculinity track changes in women’s hormonal status
Authors: Jones Benedict C , Hahn Amanda C , Fisher Claire I , Wang Hongyi , Kandrik Michal , Han Chengyang , Fasolt Vanessa , Morrison Danielle , Lee Anthony J , Holzleitner Iris J , O’Shea Kieran J , Roberts Craig , Little Anthony C , DeBruine Lisa M 
Published: May 2017

AbstractAlthough widely cited as strong evidence that sexual selection has shaped human facial attractiveness judgments, evidence that preferences for masculine characteristics in men’s faces are related to women’s hormonal status is equivocal and controversial. Consequently, we conducted the largest ever longitudinal study of the hormonal correlates of women’s preferences for facial masculinity (N=584). Analyses showed no compelling evidence that preferences for facial masculinity were related to changes in women’s salivary steroid hormone levels. Furthermore, both within-subject and between-subject comparisons showed no evidence that oral contraceptive use decreased masculinity preferences. However, women generally preferred masculinized over feminized versions of men’s faces, particularly when assessing men’s attractiveness for short-term, rather than long-term, relationships. Our results do not support the hypothesized link between women’s preferences for facial masculinity and their hormonal status.
Mapping Tumor-Specific Expression QTLs in Impure Tumor Samples
Authors: Wilson Douglas R. , Sun Wei , Ibrahim Joseph G. 
Published: May 2017

AbstractThe study of gene expression quantitative trait loci (eQTL) is an effective approach to illuminate the functional roles of genetic variants. Computational methods have been developed for eQTL mapping using gene expression data from microarray or RNA-seq technology. Application of these methods for eQTL mapping in tumor tissues is problematic because tumor tissues are composed of both tumor and infiltrating normal cells (e.g. immune cells) and eQTL effects may vary between tumor and infiltrating normal cells. To address this challenge, we have developed a new method for eQTL mapping using RNA-seq data from tumor samples. Our method separately estimates the eQTL effects in tumor and infiltrating normal cells using both total expression and allele-specific expression (ASE). We demonstrate that our method controls type I error rate and has higher power than some alternative approaches. We applied our method to study RNA-seq data from The Cancer Genome Atlas and illustrated the similarities and differences of eQTL effects in tumor and normal cells.
ELEMENT-FREE MULTISCALE MODELING OF LARGE DEFORMATION BEHAVIOR OF RED BLOOD CELL MEMBRANE WITH MALARIA INFECTION
Authors: Ademiloye A.S. , Zhang L.W. , Liew K.M. 
Published: May 2017

SUMMARYIn normal physiological and healthy conditions, red blood cells (RBCs) deform readily as they pass through the microcapillaries and the spleen. In this paper, we examine the effects ofPlasmodium falciparuminfection and maturation on the large deformation behavior of malaria-infected red blood cells (iRBCs) by means of a three-dimensional (3D) multiscale meshfree method. We numerically simulated the optical tweezers experiment and observed the force-displacement response of the iRBC membrane as malaria infection progresses. Our simulation results agree well with experimental data and confirm that the deformability of malaria-infected cells decreases significantly as malaria infection progresses.
Eyeballs on science: Impact is not just citations, but how big is readership?
Authors: Winker Kevin 
Published: May 2017

AbstractA full evaluation of the impact of scientific publications needs to count readers who don’t generate citations. But this is very difficult to do. I set up a scholarly foraging experiment to try to estimate readership for my own body of work: a personal web site with ‘reprint’ pdf files available for downloading and a web statistics program engaged to count these downloads. (I made the site topically rather than author-oriented to increase potential audience size.) Despite this, human users are difficult to count. There are a lot of bots, spiders, and other web programs that increasingly mimic human behavior (e.g., with IP- and chrono-camouflage), and humans’ own behaviors are changing (e.g., reading papers online many times). From four years of data, after culling both automated activity (a fascinating ecosystem) and humans reading repeatedly online, my papers receive ∼4000-8000 downloads per year, about an order of magnitude higher than the number of citations they receive annually. This is a conservative minimum, because these publications can be obtained from other sources as well. On average, this body of work may be being read at an approximately 10:1 download-to-citation ratio. At a more granular scale, downloads do not correlate with citations; there are some papers being downloaded at about a 100:1 ratio, and it turns out these are exactly how they were meant to be used (e.g., an instruction manual). How intensively someone reads a paper is of course highly variable, but this exercise gives us an idea of how broad our publications’ impacts actually are. Citations alone don’t come close to measuring it.
Genome-wide characterization of differential transcript usage inArabidopsis thaliana
Authors: Vaneechoutte Dries , Estrada April R. , Lin Ying-Chen , Loraine Ann E. , Vandepoele Klaas 
Published: May 2017

SUMMARYAlternative splicing and the usage of alternate transcription start- or stop sites allows a single gene to produce multiple transcript isoforms. Most plant genes express certain isoforms at a significantly higher level than others, but under specific conditions this expression dominance can change, resulting in a different set of dominant isoforms. These events of Differential Transcript Usage (DTU) have been observed for thousands ofArabidopsis thaliana,Zea maysandVitis viniferagenes and have been linked to development and stress response. However, the characteristics of these genes, nor the implications of DTU on their protein coding sequences or functions, are currently well understood. Here we present a dataset of isoform dominance and DTU for all genes in the AtRTD2 reference transcriptome based on a protocol that was benchmarked on simulated data and validated through comparison with a published RT-PCR panel. We report DTU events for 8,148 genes across 206 public RNA-Seq samples and find that protein sequences are affected in 22% of the cases. The observed DTU events show high consistency across replicates and reveal reproducible patterns in response to treatment and development. We also demonstrate that genes with different evolutionary ages, expression breadths, and functions show large differences in the frequency at which they undergo DTU and in the effect that these events have on their protein sequences. Finally, we showcase how the generated dataset can be used to explore DTU events for genes of interest or to find genes with specific DTU in samples of interest.SIGNIFICANCE STATEMENTDifferential transcript usage through alternative splicing has been reported for thousands of genes in plants, yet genome-wide datasets to study the implications for gene functions are thus far not available. Here we present the first reference dataset of isoform dominance and differential transcript usage forArabidopsis thalianabased on 206 public RNA-Seq samples and provide insights in the occurrence and functional consequences of alternative splicing.
Crosstalk between diverse synthetic protein degradation tags inEscherichia coli
Authors: Butzin Nicholas C. , Mather William H. 
Published: May 2017

AbstractRecently, a synthetic circuit inE. colidemonstrated that two proteins engineered with LAA tags targeted to the native protease ClpXP are susceptible to crosstalk due to competition for degradation between proteins. To understand proteolytic crosstalk beyond the single protease regime, we investigated inE. colia set of synthetic circuits designed to probe the dynamics of existing and novel degradation tags fused to fluorescent proteins. These circuits were tested using both microplate reader and single-cell assays. We first quantified the degradation rates of each tag in isolation. We then tested if there was crosstalk between two distinguishable fluorescent proteins engineered with identical or different degradation tags. We demonstrated that proteolytic crosstalk was indeed not limited to the LAA degradation tag, but was also apparent between other diverse tags, supporting the complexity of theE. coliprotein degradation system.
Sensorimotor processing in the basal ganglia leads to transient beta oscillations during behavior
Authors: Mirzaei Amin , Kumar Arvind , Leventhal Daniel , Mallet Nicolas , Aertsen Ad , Berke Joshua , Schmidt Robert 
Published: May 2017

AbstractBrief epochs of beta oscillations have been implicated in sensorimotor control in the basal ganglia of task-performing healthy animals. However, which neural processes underlie their generation and how they are affected by sensorimotor processing remains unclear. To determine the mechanisms underlying transient beta oscillations in the local field potential (LFP), we combined computational modeling of the subthalamo-pallidal network for the generation of beta oscillations with realistic stimulation patterns derived from single unit data. The single unit data were recorded from different basal ganglia subregions in rats performing a cued choice task. In the recordings we found distinct firing patterns in the striatum, globus pallidus and subthalamic nucleus related to sensory and motor events during the behavioral task. Using these firing patterns to generate realistic inputs to our network model lead to transient beta oscillations with the same time course as the rat LFP data. In addition, our model can account for further non-intuitive aspects of beta modulation, including beta phase resets following sensory cues and correlations with reaction time. Overall, our model can explain how the combination of temporally regulated sensory responses of the subthalamic nucleus, ramping activity of the subthalamic nucleus, and movement-related activity of the globus pallidus, leads to transient beta oscillations during behavior.Significance StatementTransient beta oscillations emerge in the normal functioning cortico-basal ganglia loop during behavior. In this work we employ a unique approach connecting a computational model closely with experimental data. In this way we achieve a simulation environment for our model that mimics natural input patterns in awake behaving animals. Using this approach we demonstrate that a computational model for beta oscillations in Parkinson’s disease can also account for complex patterns of transient beta oscillations in healthy animals. Therefore, we propose that transient beta oscillations in healthy animals share the same mechanism with pathological beta oscillations in Parkinson’s disease. This important result connects functional and pathological roles of beta oscillations in the basal ganglia.
A confidence-based reinforcement learning model for perceptual learning
Authors: Guggenmos Matthias , Sterzer Philipp 
Published: May 2017

AbstractIt is well established that learning can occur without external feedback, yet normative reinforcement learning theories have difficulties explaining such instances of learning. Recently, we reported on a confidence-based reinforcement learn-ing model for the model case of perceptual learning (Guggenmos, Wilbertz, Hebart, & Sterzer, 2016), according to which the brain capitalizes on internal monitoring processes when no external feedback is available. In the model, internal confidence prediction errors – the difference between current confidence and expected confidence – serve as teaching signals to guide learning. In the present paper, we explore an extension to this idea. The main idea is that the neural information processing pathways activated for a given sensory stimulus are subject to fluctuations, where some pathway configurations lead to higher confidence than others. Confidence prediction errors strengthen pathway configurations for which fluctuations lead to above-average confidence and weaken those that are associated with below-average con-fidence. We show through simulation that the model is capable of self-reinforced perceptual learning and can benefit from exploratory network fluctuations. In addition, by simulating different model parameters, we show that the ideal confidence-based learner should (i) exhibit high degrees of network fluctuation in the initial phase of learning, but re-duced fluctuations as learning progresses, (ii) have a high learning rate for network updates for immediate performance gains, but a low learning rate for long-term maximum performance, and (iii) be neither too under-nor too overconfident. In sum, we present a model in which confidence prediction errors strengthen favorable network fluctuations and enable learning in the absence of external feedback. The model can be readily applied to data of real-world perceptual tasks in which observers provided both choice and confidence reports.
Quantitative Protein Topography Measurements by High Resolution Hydroxyl Radical Protein Footprinting Enable Accurate Molecular Model Selection
Authors: Xie Boer , Sood Amika , Woods Robert J. , Sharp Joshua S. 
Published: May 2017

AbstractWe report an integrated workflow that allows mass spectrometry-based high-resolution hydroxyl radical protein footprinting (HR-HRPF) measurements to accurately measure the absolute average solvent accessible surface area (<SASA>) of amino acid side chains. This approach is based on application of multi-point HR-HRPF, electron-transfer dissociation (ETD) tandem MS (MS/MS) acquisition, measurement of effective radical doses by radical dosimetry, and proper normalization of the inherent reactivity of the amino acids. The accuracy of the resulting <SASA> measurements was tested by using well-characterized protein models. Moreover, we demonstrated the ability to use <SASA> measurements from HR-HRPF to differentiate molecular models of high accuracy (< 3Å backbone RMSD) from models of lower accuracy (> 4Å backbone RMSD). The ability of <SASA> data from HR-HRPF to differentiate molecular model quality was found to be comparable to that of <SASA> data obtained from X-ray crystal structures, indicating the accuracy and utility of HR-HRPF for evaluating the accuracy of computational models.
Identifying core biological processes distinguishing human eye tissues with precise systems-level gene expression analyses and weighted correlation networks
Authors: Bryan John M , Fufa Temesgen D , Bharti Kapil , Brooks Brian P , Hufnagel Robert B , McGaughey David M 
Published: May 2017

AbstractThe human eye is built from several specialized tissues which direct, capture, and pre-process information to provide vision. The gene expression of the different eye tissues has been extensively profiled with RNA-seq across numerous studies. Large consortium projects have also used RNA-seq to study gene expression patterning across many different human tissues, minus the eye. There has not been an integrated study of expression patterns from multiple eye tissues compared to other human body tissues. We have collated all publicly available healthy human eye RNA-seq datasets as well as dozens of other tissues. We use this fully integrated dataset to probe the biological processes and pan expression relationships between the cornea, retina, RPE-choroid complex, and the rest of the human tissues with differential expression, clustering, and GO term enrichment tools. We also leverage our large collection of retina and RPE-choroid tissues to build the first human weighted gene correlation networks and use them to highlight known biological pathways and eye gene disease enrichment. We also have integrated publicly available single cell RNA-seq data from mouse retina into our framework for validation and discovery. Finally, we make all these data, analyses, and visualizations available via a powerful interactive web application (https://eyeintegration.nei.nih.gov/).
Priming in a permissive type I-C CRISPR-Cas system reveals distinct dynamics of spacer acquisition and loss
Authors: Rao Chitong , Chin Denny , Ensminger Alexander W. 
Published: May 2017

AbstractCRISPR-Cas is a bacterial and archaeal adaptive immune system that uses short, invader-derived sequences termed spacers to target invasive nucleic acids. Upon recognition of previously encountered invaders, the system can stimulate secondary spacer acquisitions, a process known as primed adaptation. Previous studies of primed adaptation have been complicated by intrinsically high interference efficiency of most systems againstbona fidetargets. As such, most primed adaptation to date has been studied within the context of imperfect sequence complementarity between spacers and targets. Here, we take advantage of a native type I-C CRISPR-Cas system inLegionella pneumophilathat displays robust primed adaptation even within the context of a perfectly matched target. Using next-generation sequencing to survey acquired spacers, we observe strand bias and positional preference that are consistent with a 3′ to 5′ translocation of the adaptation machinery. We show that spacer acquisition happens in a wide range of frequencies across the plasmid, including a remarkable hotspot that predominates irrespective of the priming strand. We systematically characterize protospacer sequence constraints in both adaptation and interference and reveal extensive flexibilities regarding the protospacer adjacent motif in both processes. Lastly, in a strain with a genetically truncated CRISPR array, we observe greatly increased interference efficiency coupled with a dramatic shift away from spacer acquisition towards spacer loss. Based on these observations, we propose that theLegionellatype I-C system represents a powerful model to study primed adaptation and the interplay between CRISPR interference and adaptation.
Gaussian curvature directs the distribution of spontaneous curvature on bilayer membrane necks
Authors: Chabanon Morgan , Rangamani Padmini 
Published: May 2017

ABSTRACTFormation of membrane necks is crucial for fission and fusion in lipid bilayers. In this work, we seek to answer the following fundamental question: what is the relationship between protein-induced spontaneous mean curvature and the Gaussian curvature at a membrane neck? Using an augmented Helfrich model for lipid bilayers to include membrane-protein interaction, we solve the shape equation on catenoids to find the field of spontaneous curvature that satisfies mechanical equilibrium of membrane necks. In this case, the shape equation reduces to a variable coefficient Helmholtz equation for spontaneous curvature, where the source term is proportional to the Gaussian curvature. We show how this latter quantity is responsible for non-uniform distribution of spontaneous curvature in minimal surfaces. We then explore the energetics of catenoids with different spontaneous curvature boundary conditions and geometric asymmetries to show how heterogeneities in spontaneous curvature distribution can couple with Gaussian curvature to result in membrane necks of different geometries.