bluuebunny/crossref_metadata_2025_split huggingface dataset:
polymapR – linkage analysis and genetic map construction from F1 populations of outcrossing polyploids
Authors: Bourke Peter M. , van Geest Geert , Voorrips Roeland E. , Jansen Johannes , Kranenburg Twan , Shahin Arwa , Visser Richard G. F. , Arens Paul , Smulders Marinus J. M. , Maliepaard Chris 
Published: December 2017

AbstractMotivationPolyploid species carry more than two copies of each chromosome, a condition found in many of the world’s most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realise all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops.ResultspolymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops.Availability and ImplementationpolymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) athttp://cran.r-project.org/packages=polymapR.ContactChris Maliepaard chris.maliepaard@wur.nl or Roeland E. Voorrips roeland.voorrips@wur.nl
Dynamic copy number evolution of X- and Y-linked ampliconic genes in human populations
Authors: Lucotte Elise A. , Skov Laurits , Coll Macià Moisès , Munch Kasper , Schierup Mikkel H. 
Published: December 2017

AbstractAmpliconic genes are good candidates for speciation genes: they are testis-expressed, multicopy and localized on sex chromosomes. Moreover, copy number variation in a specific ampliconic gene pair (SlxandSly) is involved in hybrid incompatibilities betweenM. musculusandM. domesticus. However, we know little about the distribution of the ampliconic genes copy number and their turnover in human populations. Here we explore the evolution of human X- and Y-linked ampliconic genes by investigating copy number variation (CNV) and coding variation between populations using the Simons Genome Diversity Project. We develop a method to assess CNVs using the read-depth on modified X and Y chromosome targets containing only one repetition of each ampliconic gene. Our results reveal extensive standing variation in copy number both within and between human populations for several ampliconic genes. For the Y chromosome, we can infer multiple independent amplifications and losses of these gene copies even within closely related Y haplogroups, that diversified less than 50,000 years ago. For the X chromosome, we also find high copy number and coding diversity within populations. While we cannot rule out that neutral processes are at the origin of this high diversity, this study gives insights on the distribution of copy number within human populations, and demonstrates an extremely fast turnover in copy number of these regions.
Complete mitochondrial genome of Glomeridesmus spelaeus (Diplopoda), a troglobitic species from Carajás iron-ore caves (Pará, Brazil)
Authors: Nunes Gisele Lopes , Oliveira Renato Renison Moreira , Pires Eder Soares , Vasconcelos Santelmo , Pietrobon Thadeu , Prous Xavier , Oliveira Guilherme 
Published: December 2017

AbstractWe report the complete mitochondrial genome sequence of Glomeridesmus spelaeus, the first sequenced genome of the order Gomeridesmida. The genome is 14,825 pb in length and encodes 37 mitochondrial (13 PCGs, 2 rRNA genes, 22 tRNA) genes and contains a typical AT-rich region. The base composition of the genome was A (40.1%), T (36.4%), C (15.8%), and G (7.6%), with an AT content of 76.5%. Our results indicated that Glomeridesmus spelaeus only distantly related to the other Diplopoda species with available mitochondrial genomes in the public databases. The publication of the mitogenome of G. spelaeus will contribute to the identification of troglobitic invertebrates, a very significant advance for the conservation of the troglofauna.
Suppressed sensory response to predictable object stimuli throughout the ventral visual stream
Authors: Richter David , Ekman Matthias , de Lange Floris P. 
Published: December 2017

AbstractPrediction plays a crucial role in perception, as prominently suggested by predictive coding theories. However, the exact form and mechanism of predictive modulations of sensory processing remain unclear, with some studies reporting a downregulation of the sensory response for predictable input, while others observed an enhanced response. In a similar vein, downregulation of the sensory response for predictable input has been linked to either sharpening or dampening of the sensory representation, which are opposite in nature. In the present study we set out to investigate the neural consequences of perceptual expectation of object stimuli throughout the visual hierarchy, using fMRI in human volunteers. Participants (n=24) were exposed to pairs of sequentially presented object images in a statistical learning paradigm, in which the first object predicted the identity of the second object. Image transitions were not task relevant; thus all learning of statistical regularities was incidental. We found strong suppression of neural responses to expected compared to unexpected stimuli throughout the ventral visual stream, including primary visual cortex (V1), lateral occipital complex (LOC), and anterior ventral visual areas. Expectation suppression in LOC, but not V1, scaled positively with image preference, lending support to the dampening account of expectation suppression in object perception.Significance StatementStatistical regularities permeate our world and help us to perceive and understand our surroundings. It has been suggested that the brain fundamentally relies on predictions and constructs models of the world in order to make sense of sensory information. Previous research on the neural basis of prediction has documented expectation suppression, i.e. suppressed responses to expected compared to unexpected stimuli. In the present study we queried the presence and characteristics of expectation suppression throughout the ventral visual stream. We demonstrate robust expectation suppression in the entire ventral visual pathway, and underlying this suppression a dampening of the sensory representation in object-selective visual cortex, but not in primary visual cortex. Taken together, our results provide novel evidence in support of theories conceptualizing perception as an active inference process, which selectively dampens cortical representations of predictable objects. This dampening may support our ability to automatically filter out irrelevant, predictable objects.
The ventral visual pathway represents animal appearance over animacy, unlike human behavior and deep neural networks
Authors: Bracci Stefania , Kalfas Ioannis , de Beeck Hans Op 
Published: December 2017

AbstractRecent studies showed agreement between how the human brain and neural networks represent objects, suggesting that we might start to understand the underlying computations. However, we know that the human brain is prone to biases at many perceptual and cognitive levels, often shaped by learning history and evolutionary constraints. Here we explore one such bias, namely the bias to perceive animacy, and used the performance of neural networks as a benchmark. We performed an fMRI study that dissociated object appearance (how an object looks like) from object category (animate or inanimate) by constructing a stimulus set that includes animate objects (e.g., a cow), typical inanimate objects (e.g., a mug), and, crucially, inanimate objects that look like the animate objects (e.g., a cow-mug). Behavioral judgments and deep neural networks categorized images mainly by animacy, setting all objects (lookalike and inanimate) apart from the animate ones. In contrast, activity patterns in ventral occipitotemporal cortex (VTC) were strongly biased towards object appearance: animals and lookalikes were similarly represented and separated from the inanimate objects. Furthermore, this bias interfered with proper object identification, such as failing to signal that a cow-mug is a mug. The bias in VTC to represent a lookalike as animate was even present when participants performed a task requiring them to report the lookalikes as inanimate. In conclusion, VTC representations, in contrast to neural networks, fail to veridically represent objects when visual appearance is dissociated from animacy, probably due to a biased processing of visual features typical of animate objects.
Visual recency bias is explained by a mixture model of internal representations
Authors: Kalm Kristjan , Norris Dennis 
Published: December 2017

AbstractHuman bias towards more recent events is a common and well-studied phenomenon. Recent studies in visual perception have shown that this recency bias persists even when past events contain no information about the future. Reasons for this suboptimal behaviour are not well understood and the internal model that leads people to exhibit recency bias is unknown. Here we use a well-known orientation estimation task to frame the human recency bias in terms of incremental Bayesian inference. We show that the only Bayesian model capable of explaining the recency bias relies on a weighted mixture of past states. Furthermore, we suggest that this mixture model is a consequence of participants’ failure to infer a model for data in visual short term memory, and reflects the nature of the internal representations used in the task.
Bioinformatics analysis quantifies neighborhood preferences of cancer cells in Hodgkin lymphoma
Authors: Scheidel Jennifer , Schäefer Hendrik , Ackermann Jöerg , Hebel Marie , Schäfer Tim , Döering Claudia , Hartmann Sylvia , Hansmann Martin-Leo , Koch Ina 
Published: December 2017

AbstractMotivationHodgkin lymphoma is a tumor of the lymphatic system and represents one of the most frequent lymphoma in the Western world. It is characterized by Hodgkin cells and Reed-Sternberg cells, which exhibit a broad morphological spectrum. The cells are visualized by immunohistochemical staining of tissue sections. In pathology, tissue images are mainly manually evaluated, relying on the expertise and experience of pathologists. Computational quantification methods become more and more essential to evaluate tissue images. In particular, the distribution of cancer cells is of great interest.ResultsHere, we systematically quantified and investigated cancer cell properties and their spatial neighborhood relations by applying statistical analyses to whole slide images of Hodgkin lymphoma and lymphadenitis, which describes a non-cancerous inflammation of the lymph node. We differentiated cells by their morphology and studied the spatial neighborhood relation of more than 400,000 immunohistochemically stained cells. We found that, according to their morphological features, the cells exhibited significant preferences for and aversions to cells of specific profiles as nearest neighbor. We quantified differences between Hodgkin lymphoma and lymphadenitis concerning the neighborhood relations of cells and the sizes of cells. The approach can easily be applied to other cancer types.Contactina.koch@bioinformatik.uni-frankfurt.de
Organisation of the transcriptional regulation of genes involved in protein transactions in yeast
Authors: Dikicioglu Duygu , Nightingale Daniel J H , Wood Valerie , Lilley Kathryn S , Oliver Stephen G 
Published: December 2017

AbstractThe topological analyses of many large-scale molecular interaction networks often provide only limited insights into network function or evolution. In this paper, we argue that the functional heterogeneity of network components, rather than network size, is the main factor limiting the utility of topological analysis of large cellular networks. We have analysed large epistatic, functional, and transcriptional regulatory networks of genes that were attributed to the following biological process groupings: protein transactions, gene expression, cell cycle, and small molecule metabolism. Control analyses were performed on networks of randomly selected genes. We identified novel biological features emerging from the analysis of functionally homogenous biological networks irrespective of their size. In particular, direct regulation by transcription as an underrepresented feature of protein transactions. The analysis also demonstrated that the regulation of the genes involved in protein transactions at the transcriptional level was orchestrated by only a small number of regulators. Quantitative proteomic analysis of nuclear- and chromatin-enriched sub-cellular fractions of yeast provided supportive evidence for the conclusions generated by network analyses.
A quantitative model for characterizing the evolutionary history of mammalian gene expression
Authors: Chen Jenny , Swofford Ross , Johnson Jeremy , Cummings Beryl B. , Rogel Noga , Lindblad-Toh Kerstin , Haerty Wilfried , di Palma Federica , Regev Aviv 
Published: December 2017

AbstractCharacterizing the evolutionary history of a gene’s expression profile is a critical component for understanding the relationship between genotype, expression, and phenotype. However, it is not well-established how best to distinguish the different evolutionary forces acting on gene expression. Here, we use RNA-seq across 7 tissues from 17 mammalian species to show that expression evolution across mammals is accurately modeled by the Ornstein-Uhlenbeck (OU) process. This stochastic process models expression trajectories across time as Gaussian distributions whose variance is parameterized by the rate of genetic drift and strength of stabilizing selection. We use these mathematical properties to identify expression pathways under neutral, stabilizing, and directional selection, and quantify the extent of selective pressure on a gene’s expression. We further detect deleterious expression levels outside expected evolutionary distributions in expression data from individual patients. Our work provides a statistical framework for interpreting expression data across species and in disease.One Sentence SummaryWe demonstrate the power of a stochastic model for quantifying selective pressure on expression and estimating evolutionary distributions of optimal gene expression.
Longitudinal standards for mid-life cognitive performance: Identifying abnormal within-person changes in the Wisconsin Registry for Alzheimer’s Prevention
Authors: Koscik Rebecca L. , Jonaitis Erin M. , Clark Lindsay R. , Mueller Kimberly D. , Allison Samantha L. , Gleason Carey E. , Chappell Richard , Hermann Bruce P. , Johnson Sterling C. 
Published: December 2017

AbstractObjectiveA major challenge in cognitive aging is differentiating preclinical disease-related cognitive decline from changes associated with normal aging. Neuropsychological test authors typically publish single time-point norms, referred to here asunconditionalstandards or reference values. However, detecting significant change requires longitudinal, orconditionalXSreference values, created by modeling cognition as a function of prior performance. Our objectives were to create, depict, and examine preliminary validity of unconditional and conditional reference values for ages 40-75 on neuropsychological tests of memory and executive function.MethodWe used quantile regression to create growth-curve-like models of performance on tests of memory and executive function using participants from the Wisconsin Registry for Alzheimer’s Prevention. Unconditional and conditional models accounted for age, sex, education, and verbal ability/literacy; conditional models also included past performance on and number of prior exposures to the test. Models were then used to estimate individuals’ unconditional and conditional percentile ranks for each test. We then examined how low performance on each test (operationalized as <7th percentile) related to consensus-conference-determined cognitive statuses, and subjective impairment.ResultsParticipants with low performance according to the reference values were more likely to receive an abnormal cognitive diagnosis at the current visit (but not later visits). Low performance was also linked to subjective and informant reports of worsening memory function.ConclusionsMethods are needed to identify significant within-person cognitive change. The unconditional and conditional reference-development methods described here have many potential uses in research and clinical settings.
RodZ modulates geometric localization of the bacterial actin MreB to regulate cell shape
Authors: Colavin Alexandre , Shi Handuo , Huang Kerwyn Casey 
Published: December 2017

AbstractIn the rod-shaped bacteriumEscherichia coli, the actin-like protein MreB localizes in a curvature-dependent manner and spatially coordinates cell-wall insertion to maintain cell shape across changing environments, although the molecular mechanism by which cell width is regulated remains unknown. Here, we demonstrate that the bitopic membrane protein RodZ regulates the biophysical properties of MreB and alters the spatial organization ofE. colicell-wall growth. The relative expression levels of MreB and RodZ changed in a manner commensurate with variations in growth rate and cell width. We carried out single-cell analyses to determine that RodZ systematically alters the curvature-based localization of MreB and cell width in a manner dependent on the concentration of RodZ. Finally, we identified MreB mutants that we predict using molecular dynamics simulations to alter the bending properties of MreB filaments at the molecular scale similar to RodZ binding, and showed that these mutants rescued rod-like shape in the absence of RodZ alone or in combination with wild-type MreB. Together, our results show thatE. colicontrols its shape and dimensions by differentially regulating RodZ and MreB to alter the patterning of cell-wall insertion, highlighting the rich regulatory landscape of cytoskeletal molecular biophysics.
Do social conflicts at work affect employees’ job satisfaction?
Authors: Hagemeister Alexandra , Volmer Judith 
Published: December 2017

PurposeThe purpose of this study is to examine social conflicts with co-workers (SCCWs) as a predictor of job satisfaction with co-workers (JSCWs) on a daily basis. Moreover, dispositional emotion regulation (ER) was suggested to moderate the within-person relationship between daily conflicts at work and JSCWs.Design/methodology/approachNinety-eight employees from German civil service agencies completed surveys across five consecutive work days. Dispositional variables and controls were assessed in a general survey which was completed before the start of the daily surveys.FindingsHierarchical linear modeling showed that SCCWs at noon were significantly related to employees’ JSCWs in the evening and that dispositional ER moderated this relationship, indicating that people with high abilities of ER reported higher levels of job satisfaction with their co-workers than people with low abilities of ER after experiencing SCCWs.Originality/valueThe present study links conflict research with organizational and personality research. The findings broaden the understanding of social conflicts in an organizational context and further highlight ER as an important factor which can buffer the negative effects of workplace conflicts.
Exploring future models of primary care for Texas
Authors: Kash Bita A. , Ogden Paul , Popp Elizabeth , Shaffer Melissa , Bolin Jane 
Published: December 2017

PurposeThe purpose of this study is to identify best practices for innovative primary care models and to describe a potential future primary care (PC) model for Texas to address the burden of chronic disease in a population-based approach.Design/methodology/approachA systematic literature review was conducted and identified 1,880 published records through PubMed using 26 search terms. After abstract and full-text review, 70 articles remained as potential models.FindingsAlthough there is already a severe shortage of physicians in Texas, emerging practice patterns and choices among physicians are likely to erode access to primary care services in the state. Health-care leaders are encouraged to consider models such as complex adaptive systems for team-based care, pharmacist hypertension care management program and combined nurse-led care management with group visit structure.Research limitations/implicationsAs with any study, this research has its limitations; for example, models that might work in one state, or under a unique state-funded academic medical center, might not be “do-able” in another state within the nuances of a different funding mechanism.Practical implicationsResults of this research provide a model for implementing IPCM for the state of Texas first and will guide IPCM planning and implementation in other states.Originality/valueThis study is “land grant-centric” and focused on carrying out the mission of a major, top-tier research university with an emerging college of medicine at an academic medical center.
Intelligent grasping with natural human-robot interaction
Authors: Zhou Yuliang , Chen Mingxuan , Du Guanglong , Zhang Ping , Liu Xin 
Published: December 2017

Purpose
The aim of this paper is to propose a grasping method based on intelligent perception for implementing a grasp task with human conduct.

Design/methodology/approach
First, the authors leverage Kinect to collect the environment information including both image and voice. The target object is located and segmented by gesture recognition and speech analysis and finally grasped through path teaching. To obtain the posture of the human gesture accurately, the authors use the Kalman filtering (KF) algorithm to calibrate the posture use the Gaussian mixture model (GMM) for human motion modeling, and then use Gaussian mixed regression (GMR) to predict human motion posture.

Findings
In the point-cloud information, many of which are useless, the authors combined human’s gesture to remove irrelevant objects in the environment as much as possible, which can help to reduce the computation while dividing and recognizing objects; at the same time to reduce the computation, the authors used the sampling algorithm based on the voxel grid.

Originality/value
The authors used the down-sampling algorithm, kd-tree algorithm and viewpoint feature histogram algorithm to remove the impact of unrelated objects and to get a better grasp of the state.