bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct neural systems for the production of communicative vocal behaviors
Authors: Agnew ZK , Ward L. , McGettigan C. , Josephs O. , Scott SK. 
Published: February 2017

AbstractVocalizations are the production of sounds by the coordinated activity of up to eighty respiratory and laryngeal muscles. Whilst voiced acts, modified by the upper vocal tract (tongue, jaw, lip and palate) are central to the production of human speech, they are also central to the production of emotional vocalizations such as sounds of disgust, anger, laughter and crying. Evidence suggests that the speech and emotional vocalizations may comprise distinct classes of vocal movements: patients with speech production deficits are often able to produce emotional vocalizations. In addition to this, the ontogeny of the two articulations is largely distinct, with some culturally universal emotional vocalizations emerging soon after birth and human speech being a culture specific, highly learnt motor act, which must develop to some degree before a critical period in development. Here we investigate the motor pathways underlying these two classes of vocal movements for the first time by directly comparing BOLD responses during production of speech and non-speech vocal movements. Using functional magnetic resonance imaging, we report distinct patterns of activity in both subcortical and cortical regions (putamen and bilateral inferior frontal and parietal cortices) during the production of emotional vocalizations compared to speech production. In contrast we show that responses in primary sensorimotor regions do not differ during the production of speech and emotional vocalizations, suggesting partially overlapping, and partially non-overlapping neural structures for the motor control of these two classes of movement. In addition to this we report that responses in auditory cortices are distinct during the production of speech and non-speech vocalizations, suggesting that feedback control of speech and emotional vocalizations are distinct. These data provide novel evidence for the presence of dual pathways for the neural control of complex articulatory movements in humans. These findings are discussed in relation to the clinical and primate literature of vocal motor control.Significance StatementThis work marks the first evidence in healthy humans for dual routes to vocal behaviors. Clinical evidence suggests that patients unable to produce speech may still be able to produce other vocal behaviors that employ the same set of effectors. Here we demonstrate that the production of different classes of vocal behavior is associated with overlapping and distinct networks of activity. Moreover, we show that auditory processing that occurs during the production of these movements may be distinct, suggesting that feedback may be used differently for these distinct classes of vocal movement.
The erratic and contingent progression of research on territoriality: a case study
Authors: Kamath Ambika , Losos Jonathan 
Published: February 2017

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

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

AbstractBackgroundThe outcome from the analysis of high through-put genomics experiments is commonly a list of genes. The most basic measure of association is whether the genes in the list have ever been cocited together.ResultsThe web applicationgene-cociteaccepts a list of genes and returns a list of the papers which cocite any two or more of the genes. The proportion of the genes which are cocited with at least one other gene is given, and thep-value for the probability of this proportion of cocitations occurring by chance from a random list of genes of the same length calculated. An interactive graph with links to papers is displayed, showing how the genes in the list are related to each other by publications.Conclusionsgene-cocite (http://sysbio.mrc-bsu.cam.ac.uk/gene-cocite) is designed to be an easy to use first step for biological researchers investigating the background of their list of genes.
Age-related changes in spatial and temporal features of resting state fMRI
Authors: Vij Shruti G. , Nomi Jason S. , Dajani Dina R. , Uddin Lucina Q. 
Published: February 2017

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

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

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

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

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

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

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

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

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

AbstractLarge-scale studies such as the ​Arabidopsis thaliana1001 Genomes Project aim to understand genetic variation in populations and link it to phenotypic variation. Such studies require routine genotyping of stocks to avoid sample contamination and mix-ups. To genotype samples efficiently and economically, sequencing must be inexpensive a​nd data processing simple. Here we present SNPmatch, a tool which identifies the most likely strain (inbred line, or “accession”) from a SNP database. We tested the tool by performing low-coverage sequencing of over 2000 strains. SNPmatch could readily genotype samples correctly from 1-fold coverage sequencing data, and could also identify the parents of F1 or F2 individuals. SNPmatch can be run either on the command line or through AraGeno (https://arageno.gmi.oeaw.ac.at), a web interface that permits sample genotyping from a user-uploaded VCF or BED file.Availability and implementation:https://github.com/Gregor-Mendel-Institute/SNPmatch.git
Optogenetic Control of RhoA Reveals Zyxin-mediated Elasticity of Stress Fibers
Authors: Oakes Patrick W. , Wagner Elizabeth , Brand Christoph A. , Probst Dimitri , Linke Marco , Schwarz Ulrich S. , Glotzer Michael , Gardel Margaret L. 
Published: February 2017

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