bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neural ensemble dynamics in dorsal motor cortex during speech in people with paralysis
Authors: Stavisky Sergey D. , Willett Francis R. , Murphy Brian A , Rezaii Paymon , Avansino Donald T. , Memberg William D. , Miller Jonathan P. , Kirsch Robert F. , Hochberg Leigh R , Ajiboye A. Bolu , Shenoy Krishna V. , Henderson Jaimie M. 
Published: December 2018

ABSTRACTSpeaking is a sensorimotor behavior whose neural basis is difficult to study at the resolution of single neurons due to the scarcity of human intracortical measurements and the lack of animal models. We recorded from electrode arrays in the ‘hand knob’ area of motor cortex in people with tetraplegia. Neurons in this area, which have not previously been implicated in speech, modulated during speaking and during non-speaking movement of the tongue, lips, and jaw. This challenges whether the conventional model of a ‘motor homunculus’ division by major body regions extends to the single-neuron scale. Spoken words and syllables could be decoded from single trials, demonstrating the potential utility of intracortical recordings for brain-computer interfaces (BCIs) to restore speech. Two neural population dynamics features previously reported for arm movements were also present during speaking: a large initial condition-invariant signal, followed by rotatory dynamics. This suggests that common neural dynamical motifs may underlie movement of arm and speech articulators.
Human RAD51 paralogue, SWSAP1, fosters RAD51 filament by regulating the anti-recombinase, FIGNL1 AAA+ ATPase
Authors: Matsuzaki Kenichiro , Kondo Shizuka , Ishikawa Tatsuya , Shinohara Akira 
Published: December 2018

SummaryRAD51 assembly on single-stranded (ss)DNAs is a crucial step in the homology-dependent repair of DNA damage for genomic stability. The formation of the RAD51 filament is tightly regulated by various RAD51-interacting proteins. The familial breast cancer gene, BRCA2, as well as RAD52 and six RAD51 paralogues (SWSAP1, RAD51B, RAD51C, RAD51D, XRCC2, and XRCC3) promote RAD51 assembly on ssDNAs in humans. However, the mechanisms underlying the differential control of RAD51 filament dynamics by these factors remain largely unknown. Here, we report a role for the human RAD51 paralogue, SWSAP1, as a novel regulator of RAD51 assembly. Swsap1-deficient cells show defects in DNA damage-induced RAD51 assembly during both mitosis and meiosis. Defective RAD51 assembly in SWSAP1-depleted cells is suppressed by the depletion of FIGNL1, an AAA+ ATPase, which binds to RAD51 as well as SWSAP1. Purified FIGNL1 promotes the dissociation of RAD51 from ssDNAs. The in vitro dismantling activity of FIGNL1 does not require its ATPase but depends on RAD51-binding, suggesting a novel mechanism of RAD51 filament remodelling. Purified SWSAP1 inhibits the RAD51-dismantling activity of FIGNL1. Taken together, our data suggest that SWSAP1 protects RAD51 filaments by antagonizing the anti-recombinase, FIGNL1.
Glia-neuron interactions underlie state transitions to generalized seizures
Authors: Verdugo Carmen Diaz , Myren-Svelstad Sverre , Deneubourg Celine , Pelgrims Robbrecht , Muto Akira , Kawakami Koichi , Jurisch-Yaksi Nathalie , Yaksi Emre 
Published: January 2019

SUMMARYBrain activity and connectivity alter drastically during epileptic seizures. Throughout this transition, brain networks shift from a balanced resting state to a hyperactive and hypersynchronous state, spreading across the brain. It is, however, less clear which mechanisms underlie these state transitions. By studying neuronal and glial activity across the zebrafish brain, we observed striking differences between these networks. During the preictal period, neurons displayed a small increase in synchronous activity only locally, while the entire glial network was highly active and strongly synchronized across large distances. We observed that the transition from a preictal state to a generalized seizure leads to an abrupt increase in neuronal activity and connectivity, which is accompanied by a strong functional coupling between glial and neuronal networks. Optogenetic activation of glia induced strong and transient burst of neuronal activity, emphasizing a potential role for glia-neuron connections in the generation of epileptic seizures.
Enjoy The Violence: Is appreciation for extreme music the result of cognitive control over the threat response system?
Authors: Ollivier Rosalie , Goupil Louise , Liuni Marco , Aucouturier Jean-Julien 
Published: January 2019

AbstractTraditional neurobiological theories of musical emotions explain well why extreme music such as punk, hardcore or metal, whose vocal and instrumental characteristics share much similarity with acoustic threat signals, should evoke unpleasant feelings for a large proportion of listeners. Why it doesn’t for metal music fans, however, remains a theoretical challenge: metal fans may differ from non-fans in how they process acoustic threat signals at the sub-cortical level, showing deactivated or reconditioned responses that differ from controls. Alternatively, it is also possible that appreciation for metal depends on the inhibition by cortical circuits of a normal low-order response to auditory threat. In a series of three experiments, we show here that, at a sensory level, metal fans actually react equally negatively, equally fast and even more accurately to cues of auditory threat in vocal and instrumental contexts than non-fans. Conversely, cognitive load somewhat appears to reduce fans’ appreciation of metal to the level reported by non-fans. Taken together, these results are not compatible with the idea that extreme music lovers do so because of a different low-level response to threat, but rather, highlight a critical contribution of higher-order cognition to the aesthetic experience. These results are discussed in the light of recent higher-order theories of emotional consciousness, which we argue should be generalized to the emotional experience of music across musical genres.
Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features
Authors: Andrade e Sousa Lisa Barros de , Jonkers Iris , Syx Laurène , Chaumeil Julie , Picard Christel , Foret Benjamin , Chen Chong-Jian , Lis John T. , Heard Edith , Schulz Edda G. , Marsico Annalisa 
Published: January 2019

AbstractTo initiate X-chromosome inactivation (XCI), the long non-coding RNA Xist mediates chromosome-wide gene silencing of one X chromosome in female mammals to equalize gene dosage between the sexes. The efficiency of gene silencing, however is highly variable across genes, with some genes even escaping XCI in somatic cells. A genes susceptibility to Xist-mediated silencing appears to be determined by a complex interplay of epigenetic and genomic features; however, the underlying rules remain poorly understood. We have quantified chromosome-wide gene silencing kinetics at the level of the nascent transcriptome using allele-specific Precision nuclear Run-On sequencing (PRO-seq). We have developed a Random Forest machine learning model that can predict the measured silencing dynamics based on a large set of epigenetic and genomic features and tested its predictive power experimentally. While the genomic distance to the Xist locus is the prime determinant of the speed of gene silencing, we find that also pre-marking of gene promoters with polycomb complexes is associated with fast silencing. Moreover, a series of features associated with active transcription and the O-GlcNAc transferase Ogt are enriched at rapidly silenced genes. Our machine learning approach can thus uncover the complex combinatorial rules underlying gene silencing during X inactivation.
Evidence of a Functionally Segregated Pathway from Lateral Superior Olive to Inferior Colliculus
Authors: Greene Nathaniel T. , Davis Kevin A. 
Published: January 2019

ABSTRACTNeurons in the central nucleus of the inferior colliculus (ICC) of decerebrate cats show three major response patterns when tones of different frequencies and levels are presented to the contralateral ear. The frequency response maps of type I units uniquely exhibit a narrowly tuned I-shaped area of excitation around best frequency (the most sensitive frequency) and flanking regions of inhibition at lower and higher frequencies. Type I units receive ipsilateral inhibition, and show binaural excitatory/inhibitory interactions. Lateral superior olive (LSO) principal cells display a similar receptive field organization and sensitivity to interaural level differences (ILDs) and project directly to the ICC, therefore are supposed to be the dominant source of excitatory input for type I units. To test this hypothesis, the responses of ICC units were compared before and after reversible inactivation of the LSO by injection of the non-specific excitatory amino-acid antagonist kynurenic acid. When excitatory activity within the LSO was blocked, many ICC type I units (~50%) were silenced or showed substantially decreased activitycomparable. By contrast, the responses of the other two ICC unit types were largely unaffected. With regard to the origins of unaffected ICC type I units, evidence indicates that the LSO was inactivated in an incomplete, anisotropic manner, and the monaural and binaural responses of such units are similar to those of affected type I units. Taken together, these results support the interpretation that most type I units are the midbrain components of a functionally segregated ILD processing pathway initiated by the LSO.
Embryonic signals perpetuate polar-like trophoblast stem cells and pattern the blastocyst axis
Authors: Frias-Aldeguer Javier , Kip Maarten , Vivié Judith , Li Linfeng , Alemany Anna , Korving Jeroen , Darmis Frank , van Oudenaarden Alexander , Geijsen Niels , Rivron Nicolas C. 
Published: January 2019

SummaryThe early mammalian conceptus (blastocyst) comprises an outer trophoblast globe that forms an axis originating from the inner embryonic cells. From the mouse conceptus, Trophoblast stem cells (TSCs) are derived, which are in vitro analogues of early trophoblasts. Here, we show that TSCs contain plastic subpopulations reflecting developmental states ranging from pre- to post-implantation trophoblasts. However, upon exposure to a specific combination of embryonic inductive signals, TSCs globally acquire properties of pre-implantation polar trophoblasts (gene expression, self-renewal) juxtaposing the inner embryonic cells, and an enhanced, homogeneous epithelial phenotype. These lines of polar-like TSCs (pTSCs) represent a transcriptionally earlier state that more efficiently forms blastoids, whose inner embryonic cells then induce the patterning of gene expression along the embryonic-abembryonic axis. Altogether, delineating the requirements and properties of polar trophoblasts and blastocyst axis formation in vitro provides a foundation for the precise description and dissection of early development.
Differential expression of BMP antagonists,gremlinandnogginin hydra: antagonism between Wnt and BMP pathways
Authors: Surekha Krishnapati Lakshmi , Khade Samiksha , Trimbake Diptee , Patwardhan Rohan , Nadimpalli Siva Kumar , Ghaskadbi Surendra 
Published: January 2019

AbstractMechanisms regulating BMP and Wnt signaling pathways have been widely studied in many organisms. One of the mechanisms by which these pathways are regulated is by binding of extracellular ligands. In the present study, we report studies with two BMP antagonists,gremlinandnogginfromHydra vulgarisInd-Pune and demonstrate antagonistic relationship between BMP and Wnt pathways.Gremlinwas ubiquitously expressed from the body column to head region except in the basal disc and hypostome. During budding,gremlinwas expressed predominantly in the budding region suggesting a possible role in budding; this was confirmed in polyps with different stages of buds.Noggin, on the other hand, was predominantly expressed in the endoderm of hypostome, base of the tentacles, lower body column and at the basal disc in whole polyps. During budding,nogginwas expressed at the sites of emergence of tentacles suggesting a role in tentacle formation. This was confirmed in alsterpaullone-treated polyps, which showednogginexpression as distinct spots where ectopic organizers and ectopic tentacles eventually formed. Using RT-PCR, we found that up-regulation ofWntis accompanied with down-regulation ofBMP5-8bdemonstrating antagonism between the two pathways. Down-regulation ofnogginandgremlin, however, occurred only after 24 h recovery. The data suggest that inhibition of BMP pathway by Wnt signaling in hydra does not directly involvenogginandgremlin. Our findings indicate that the BMP/Noggin antagonism evolved early for setting up and/or maintaining the head organizer while involvement of these BMP antagonists during vertebrate axial patterning are recent evolutionary acquisitions.Summary statementWe show that setting up of the Organizer by BMP/Noggin antagonism and role of BMP inhibitors in tissue patterning are evolutionarily ancient, probably arising for the first time in hydra
Optimization of the experimental parameters of the ligase cycling reaction
Authors: Schlichting Niels , Reinhardt Felix , Jager Sven , Schmidt Michael , Kabisch Johannes 
Published: January 2019

ABSTRACTThe ligase cycling reaction (LCR) is a scarless and efficient method to assemble plasmids from fragments of DNA. This assembly method is based on the hybridization of DNA fragments with complementary oligonucleotides, so-called bridging oligos (BOs), and an experimental procedure of thermal denaturation, annealing and ligation. In this study, we explore the effect of molecular crosstalk of BOs and various experimental parameters on the LCR by utilizing a fluorescence-based screening system. The results indicate an impact of the melting temperatures of BOs on the overall success of the LCR assembly. Secondary structure inhibitors, such as DMSO and betaine, are shown to negatively impact the number of correctly assembled plasmids. Adjustments of the annealing, ligation and BO-melting temperature further improved the LCR. The optimized LCR was confirmed by validation experiments. Based on these findings, a step-by-step protocol is offered within this study to ensure a routine for high efficient LCR assemblies.
Doubled haploid based parental lines are most suitable in predicting heterosis using microsatellites and in development of highly heterotic F1hybrids inBrassica oleracea
Authors: Singh Saurabh , Dey S.S. , Bhatia Reeta , Kumar Raj , Sharma Kanika , Behera T.K. 
Published: January 2019

AbstractInBrassica oleracea, heterosis is one of the most efficient tools giving impetus to hybrid vegetable industry. In this context, we presented the first report on identifying superior heterotic crosses for yield and commercial traits in cauliflower involving cytoplasmic male sterile (CMS) and doubled haploid (DH) lines as parents. We studied the suitability of SSR and EST-SSRs based genetic distance (GD) and morphological markers based phenotypic distance (PD) in prediction of heterosis when DH based genotypes are used as parents in developing F1hybrids. Overall 120 F1hybrids derived from twentyOguracybrid CMS lines and six DH based testers were evaluated for 16 phenotypic traits along with their 26 parental lines and 4 commercial standard checks, in 10 × 15 alpha lattice design. The genomic SSR and EST-SSRs based genetic structure analysis grouped 26 parental lines into 4 distinct clusters. The CMS lines Ogu118-6A, Ogu33A, Ogu34-1A were good general combiner for developing short duration hybrids. The SCA effects were significantly associated with heterosis suggesting non-additive gene effects for heterotic response of hybrids. Less than unity value of σ2A/D coupled with σ2gca/σ2scaindicated the predominance of non-additive gene action in the expression of studied traits. The genetic distance estimates among 26 parents ranged from 0.44 to 0.98 and were significantly associated with heterosis for important commercial traits, suggesting the utility of microsatellite based genetic distance in prediction of heterosis inB. oleracea.
Computational modeling of anthocyanin pathway evolution
Authors: Wheeler Lucas C. , Smith Stacey D. 
Published: January 2019

AbstractAlteration of metabolic pathways is a key component of the evolution of new phenotypes. Flower color is a striking example of the importance of metabolic evolution in a complex phenotype, wherein shifts in the activity of the underlying pathway lead to a wide range of pigments. Although experimental work has identified common classes of mutations responsible for transitions among colors, we lack a unifying model that relates pathway function and activity to the evolution of distinct pigment phenotypes. One challenge in creating such a model is the branching structure of pigment pathways, which may lead to evolutionary trade-offs due to competition for shared substrates. In order to predict the effects of shifts in enzyme function and activity on pigment production, we created a simple kinetic model of a major plant pigmentaion pathway: the anthocyanin pathway. This model describes the production of the three classes of blue, purple and red anthocyanin pigments, and accordingly, includes multiple branches and substrate competition. We first studied the general behavior of this model using a realistic, functional set of parameters. We then stochastically evolved the pathway toward a defined optimum and and analyzed the patterns of fixed mutations. This approach allowed us to quantify the probability density of trajectories through pathway state space and identify the types and number of changes. Finally, we examine whether the observed trajectories and constraints help to explain experimental observations, i.e., the predominance of mutations which change color by altering the function of branching genes in the pathway. These analyses provide a theoretical framework which can be used to predict the consequences of new mutations in terms of both pigment phenotypes and pleiotropic effects.
Dissection and validation of minor quantitative trait loci (QTLs) conferring grain size and weight in rice
Authors: Sun Ping , Zheng Yuanyuan , Li Pingbo , Ye Hong , Zhou Hao , Gao Guanjun , He Yuqing 
Published: January 2019

AbstractGrain size and weight contribute greatly to the grain yield of rice. In order to identify minor QTLs conferring grain size and weight, an F2population derived from a cross between twoindicarice lines showing small difference on grain size, Guangzhan 63-4S (GZ63-4S) and Dodda, and its derived F2:3population were developed and used for QTL analysis. Totally, 36 QTLs for grain size and weight were detected, and 7 were repeatedly detected, of which the number of beneficial alleles was contributed roughly equally by the two parents. In order to further validate effects of QTLs detected, a BC1F2population derived from a backcross of a mixture of F2lines with GZ63-4S was developed and subjected to QTL selection. Heterozygous regions of 3 QTLs,qGS3,qTGW6.2andqGT7were identified, and corresponding near-isogenic lines (NILs) of each QTL were constructed with three rounds of self-crosses. In the background of NILs,qGS3was responsible for GL, LWR, GT and TGW,qTGW6.2was for GL and TGW, andqGT7was for GT and TGW. These results have laid the foundation of further fine mapping and cloning of underlying genes, and could be of great use in breeding and improvement of rice lines with desirable size and yield.
Differential expression feature extraction (DEFE) and its application in RNA-seq data analysis
Authors: Pan Youlian , Li Yifeng , Liu Ziying , Surendra Anuradha , Wang Lipu , Foroud Nora A. , Goyal Ravinder K. , Ouellet Thérèse , Fobert Pierre R. 
Published: January 2019

AbstractIn differential gene expression data analysis, one objective is to identify groups of co-expressed genes from a large dataset to detect the association between such a group of genes and a phenotypic trait. This is often done through a clustering approach, such as k-means or bipartition hierarchical clustering, based on particular similarity measures in the grouping process. In such a dataset, the gene differential expression itself is an innate attribute that can be used in the feature extraction process. For example, in a dataset consisting of multiple treatments versus their controls, the expression of a gene in each treatment would have three possible behaviors, up-, down- regulated, or unchanged. We propose here a differential expression feature extraction (DEFE) method by using a string consisting of three numerical values at each character to denote such behavior, i.e. 1=up, 2=down, and 0=unchanged, which results in up to 3B differential expression patterns across all B comparisons. This approach has been successfully applied in many datasets, of which we present in this study two sets of RNA-sequencing (RNA-seq) data on wheat challenged with stress related phytohormones or Fusarium graminearum, the causal agent of fusarium head blight (FHB), a devastating wheat disease to illustrate the algorithm. Combinations of multiple schemes of DEFE patterns revealed groups of genes putatively associated with resistance or susceptibility to FHB. DEFE enabled discovery of genes closely associated with defense related signaling molecules such as JAZ10, shikimate and chorismate biosynthesis pathway and groups of wheat genes with differential effects between more or less virulent strains of Fusarium graminearum.
Reachable domain of spacecraft with a single normal impulse
Authors: Zhang Junhua , Yuan Jianping , Wang Wei , Wang Jiao 
Published: January 2019

Purpose
The purpose of this paper is to obtain the reachable domain (RD) for spacecraft with a single normal impulse while considering both time and impulse constraints.

Design/methodology/approach
The problem of RD is addressed in an analytical approach by analyzing for either the initial maneuver point or the impulse magnitude being arbitrary. The trajectories are considered lying in the intersection of a plane and an ellipsoid of revolution, whose family can be determined analytically. Moreover, the impulse and time constraints are considered while formulating the problem. The upper bound of impulse magnitude, “high consumption areas” and the change of semi-major axis and eccentricity are discussed.

Findings
The equations of RD with a single normal impulse are analytically obtained. The equations of three scenarios are obtained. If normal impulse is too large, the RD cannot be obtained. The change of the semi-major axis and eccentricity with large normal impulse is more obvious. For long-term missions, the change of semi-major axis and eccentricity leaded by multiple normal impulses should be considered.

Practical implications
The RD gives the pre-defined region (all positions accessible) for a spacecraft under a given initial orbit and a normal impulse with certain magnitude.

Originality/value
The RD for spacecraft with normal impulse can be used for non-coplanar orbital transfers, emergency evacuation after failure of rendezvous and docking and collision avoidance.