bluuebunny/crossref_metadata_2025_split huggingface dataset:
Static and Dynamic Aspects of Cerebro-Cerebellar Functional Connectivity are Associated with Self-reported Measures of Impulsivity: A Resting-State fMRI Study
Authors: Abdallah Majd , Farrugia Nicolas , Chirokoff Valentine , Chanraud Sandra 
Published: January 2020

AbstractConverging evidence from human and animal studies predict a possible role of the cerebellum in impulsivity. However, this hypothesis has not been thoroughly investigated within the framework of functional connectivity (FC). To address this issue, we employed resting-state fMRI data and two self-reports of impulsivity (UPPS-P and BIS/BAS) from a large group of healthy young individuals (N=134). We identified cerebral and cerebellar resting-state networks, and evaluated the association of static (strength) and dynamic (temporal variability) aspects of cerebro-cerebellar FC with different elements of self-reported impulsivity. Our results revealed that the behavioral inhibition and approach systems (BIS/BAS) were inversely associated with basal ganglia-cerebellar and fronto-cerebellar FC strength, respectively. In addition, we found that lack of premeditation was inversely associated with the temporal variability of FC between the cerebellum and top-down control networks that included sub-regions of the prefrontal cortex, precuneus, and posterior cingulate cortex. Moreover, we found that sensation seeking was associated with the temporal variability of FC between the cerebellum and networks that included cortical control regions and sub-cortical reward regions: the basal ganglia and the thalamus. Together, these findings indicate that the cerebellum may contribute to different forms of impulsivity through its connections to large-scale control and reward networks.
Tick-Borne bacterial and protozoan animal pathogens shape the native microbiome withinHyalomma anatolicum anatolicumandRhipicephalus microplustick vectors
Authors: Adegoke Abdulsalam , Kumar Deepak , Rashid Muhammad Imran , Durrani Aneela Zameer , Sajid Muhammad Sohail , Karim Shahid 
Published: January 2020

AbstractBackgroundTicks vector a variety of bacterial, viral, and protozoan pathogens of public and animal health significance. Ticks also harbor a diverse community of microbes linked with their biological processes like hematophagy and hence vector competence. The interactions between bacterial and/or protozoan pathogens and their tick vector microbiome are yet to be investigated. In lieu of this, this study was designed to define the microbial composition of uninfected and infectedHyalomma (H.) anatolicum anatolicumandRhipicephalus (R.) microplustick species.Methodology/Principal findingsA total of 320H. anatolicumandR. micropluswere screened for the presence of the protozoan (Theileriasp.), and bacterial (Anaplasma marginale) pathogens by PCR. Subsequently, the microbiome of uninfected and infected individualH. anatolicumandR. micropluswere analyzed. The highly conserved V1-V3 region of the 16S rRNA gene was sequenced using the MiSeq Illumina platform. The microbiome of femaleH. anatolicum anatolicumticks was dominated by the endosymbiontCandidatus Midichloria mitochondrii(CMM) andFrancisella-like endosymbiont (FLE) which were not affected by pathogen infection.Ehrlichiaspecies was detected inA. marginale-infected maleH. anatolicum anatolicum(6.2%) as opposed to theTheileriasp.-infected femaleH. anatolicum anatolicum.Coxiellasp. was also detected in uninfected (2.96%) andA. marginale-infected (4.25%), but not inTheileriasp.-infectedR. microplusticks. Analysis of the eukaryote composition in the respectively ticks also revealed the presence of operational taxonomic units (OTUs) belonging toPlasmodium (P.) falciparuminTheileriasp.-infectedH. a. anatolicumandR. microplusticks, whileHepatozoon americanumdetected fromTheileriasp.-infected and uninfectedH. a. anatolicum.Conclusion and SignificanceThis study establishes the extent of the diversity of microbial community of two important tick species from Pakistan and also revealed the presence ofTheileriaandA. marginaleand additional pathogenic bacteria that could be of public health significance. We hypothesized that infection with either a protozoan or bacterial pathogen will alter the microbial composition within these tick species. Interestingly, we reported the detection of the malarial parasite (P. falciparum) from ticks infected with the protozoan pathogen (Theileriasp.). Further validation experiments are required on endosymbionts and pathogens of ticks to investigate how they could be important in the epidemiology of human and animal pathogens.
Tree diversity and the temporal stability of mountain forest productivity: testing the effect of species composition, through asynchrony and overyielding
Authors: Jourdan Marion , Piedallu Christian , Baudry Jonas , Morin Xavier 
Published: January 2020

ABSTRACTClimate change modifies ecosystem processes directly through its effect on environmental conditions, but also indirectly by changing community composition. Theoretical studies and grassland experiments suggest that diversity may increase and stabilize communities’ productivity over time. Few recent studies on forest ecosystems suggested the same pattern but with a larger variability between the results. In this paper, we aimed to test stabilizing diversity effect for two kinds of mixtures (Fagus sylvatica-Quercus pubescensandFagus sylvatica-Abies alba), and to assess how climate may affect the patterns. We used tree ring data from forest plots distributed along a latitudinal gradient across French Alps. We found that diversity effect on stability in productivity varies with stand composition. Most beech–fir stands showed a greater stability in productivity over time than monocultures, while beech–oak stands showed a less stable productivity. Considering non-additive effects, no significant trends were found, regardless the type of mixed stands considered. We further highlighted that these patterns could be partially explained by asynchrony between species responses to annual climatic conditions (notably to variation in temperature or precipitation), overyielding, and climatic conditions. We also showed that the intensity of the diversity effect on stability varies along the ecological gradient, consistently with the stress gradient hypothesis for beech-oak forests, but not for beech-fir forests. This study showed the importance of the species identity on the relationships between diversity, climate and stability of forest productivity. Better depicting diversity and composition effects on forest ecosystem functioning appears to be crucial for forest managers to promote forest adaptation and maintain timber resource in the context of on-going climate change.
Control tools to selectively produce purple bacteria for microbial protein in raceway reactors
Authors: Alloul Abbas , Cerruti Marta , Adamczyk Damian , Weissbrodt David G. , Vlaeminck Siegfried E. 
Published: January 2020

AbstractPurple non-sulfur bacteria (PNSB) show potential for microbial protein production on wastewater as animal feed. They offer good selectivity (i.e. uneven community with high abundance of one species) when grown anaerobically in the light. However, the cost of a closed anaerobic photobioreactor (PBR) is prohibitive for protein production. While open raceway reactors are cheaper, their feasibility to selectively grow PNSB is thus far unexplored. This study developed tools to boost PNSB abundance in the biomass of a raceway reactor fed with volatile fatty acids as carbon source. For oxygen availability as tool, not stirring in the night (i.e. reduced oxygen supply) elevated the PNSB abundance from 8% to 20%. For light availability as tool, a 24-h illumination increased the PNSB abundance from 8% to 31% compared to a 12-h light/12-h dark regime. A reactor run at 2-d sludge retention time at the highest surface-to-volume ratio (10 m2m-3increased light availability) showed productivities up to 0.2 g protein L-1d-1and the highest PNSB abundance (78%). The estimated production cost is €1.9 kg-1dry weight (vs. PBR €11.4 kg-1dry weight). This study pioneered in PNSB-based microbial protein production in raceways, yielding cost efficiency along with high selectivity when avoiding the combined availability of oxygen, COD and darkness.Graphical abstract
Spatial receptive field structure of double-opponent cells in macaque V1
Authors: De Abhishek , Horwitz Gregory D. 
Published: January 2020

ABSTRACTThe spatial processing of color is important for visual perception. Double-opponent (DO) cells likely contribute to this processing by virtue of their spatially opponent and cone-opponent receptive fields (RFs). However, the representation of visual features by DO cells in the primary visual cortex of primates is unclear because the spatial structure of their RFs has not been fully characterized. To fill this gap, we mapped the RFs of DO cells in awake macaques with colorful, dynamic white noise patterns. The spatial RF of each neuron was fitted with a Gabor function and a Difference of Gaussians (DoG) function. The Gabor function provided the more accurate description for most DO cells, a result that is incompatible with the traditionally assumed center-surround RF organization. A slightly modified (non-concentric) DoG function, in which the RFs have a circular center and a crescent-shaped surround, performed nearly as well as the Gabor model. For comparison, we also measured the RFs of simple cells. We found that the superiority of the Gabor fits over DoG fits was slightly more decisive for simple cells than for DO cells. The implications of these results on biological image processing and visual perception are discussed.
A genome-wide association study finds genetic variants associated with neck or shoulder pain in UK Biobank
Authors: Meng Weihua , Chan Brian W , Harris Cameron , Freidin Maxim B , Hebert Harry L , Adams Mark J , Campbell Archie , Hayward Caroline , Zheng Hua , Zhang Xianwei , Colvin Lesley A , Hales Tim G , Palmer Colin NA , Williams Frances MK , McIntosh Andrew , Smith Blair H 
Published: January 2020

ABSTRACTBackgroundCommon types of musculoskeletal conditions include pain in the neck and shoulder areas. This study seeks to identify the genetic variants associated with neck or shoulder pain based on a genome-wide association approach using 203,309 subjects from the UK Biobank cohort and look for replication evidence from the Generation Scotland: Scottish Family Health Study (GS:SFHS) and TwinsUK.MethodsCases in the UK Biobank were determined by a question which asked the participants if they had experienced pain in the neck or shoulder in the previous month influencing daily activities. Controls were the UK Biobank participants who reported no pain anywhere in the last month. A genome-wide association study was performed adjusting for age, sex, BMI and 9 population principal components. Significant and independent genetic variants were then sent to GS:SFHS and TwinsUK for replication.ResultsWe identified 3 genetic loci that were associated with neck or shoulder pain in the UK Biobank samples. The most significant locus was in an intergenic region in chromosome 17, rs12453010, havingP= 1.66 × 10-11. The second most significant locus was located in theFOXP2gene in chromosome 7 withP= 2.38 × 10-10for rs34291892. The third locus was located in theLINC01572gene in chromosome 16 withP= 4.50 × 10-8for rs62053992. In the replication stage, among 4 significant and independent genetic variants, rs2049604 in theFOXP2gene and rs62053992 in theLINC01572gene were weakly replicated in GS:SFHS (P =0.0240 andP= 0.0202, respectively). None of the single nucleotide polymorphisms (SNPs) were replicated in the TwinsUK cohort (P> 0.05).ConclusionsWe have identified 3 loci associated with neck or shoulder pain in the UK Biobank cohort, two of which were weakly supported in a replication cohort. Further evidence is needed to confirm their roles in neck or shoulder pain.SignificanceThis is the first genome-wide association study on neck or shoulder pain. We have identified 3 genetic loci (an intergenic region in chromosome 17, theFOXP2gene in chromosome 7, and theLINC01572gene in chromosome 16) that are associated with neck or shoulder pain using the UK Biobank cohort, among which theFOXP2gene and theLINC01572gene were weakly replicated by the Generation Scotland: Scottish Family Health Study (P< 0.05). The SNP heritability was 0.11, indicating neck or shoulder pain is a heritable trait. The tissue expression analysis suggested that neck or shoulder pain was related to multiple brain tissues, indicating the involvement of neuron function. The results will inform further research in the characterisation of the mechanisms of neck or shoulder pain.
A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data
Authors: Vavoulis Dimitrios V. , Cutts Anthony , Taylor Jenny C. , Schuh Anna 
Published: January 2020

ABSTRACTTumours are composed of genotypically and phenotypically distinct cancer cell populations (clones), which are subject to a process of Darwinian evolution in response to changes in their local micro-environment, such as drug treatment. In a cancer patient, this process of continuous adaptation can be studied through next-generation sequencing of multiple tumour samples combined with appropriate bioinformatics and statistical methodologies. One family of statistical methods for clonal deconvolution seeks to identify groups of mutations and estimate the prevalence of each group in the tumour, while taking into account its purity and copy number profile. These methods have been used in the analysis of cross-sectional data, as well as for longitudinal data by discarding information on the timing of sample collection. Two key questions are how (in the case of longitudinal data) can we incorporate such information in our analyses and if there is any benefit in doing so. Regarding the first question, we incorporated information on the temporal spacing of longitudinally collected samples into standard non-parametric approaches for clonal deconvolution by modelling the time dependence of the prevalence of each clone as aGaussian process. This permitted reconstruction of the temporal profile of the abundance of each clone continuously from several sparsely collected samples and without any strong prior assumptions on the functional form of this profile. Regarding the second question, we tested various model configurations on a range of whole genome, whole exome and targeted sequencing data from patients with chronic lymphocytic leukaemia, on liquid biopsy data from a patient with melanoma and on synthetic data. We demonstrate that incorporating temporal information in our analysis improves model performance, as long as data of sufficient volume and complexity are available for estimating free model parameters. We expect that our approach will be useful in cases where collecting a relatively long sequence of tumour samples is feasible, as in the case of liquid cancers (e.g. leukaemia) and liquid biopsies. The statistical methodology presented in this paper is freely available atgithub.com/dvav/clonosGP.
Deciphering cattle temperament measures derived from a four-platform standing scale using genetic factor analytic modeling
Authors: Yu Haipeng , Morota Gota , Celestino Elfren F. , Dahlen Carl R. , Wagner Sarah A. , Riley David G. , Hanna Lauren L. Hulsman 
Published: January 2020

AbstractThe animal’s reaction to human handling (i.e., temperament) is critical for work safety, productivity, and welfare. Subjective phenotyping methods have been traditionally used in beef cattle production. Even so, subjective scales rely on the evaluator’s knowledge and interpretation of temperament, which may require substantial experience. Selection based on such subjective scores may not precisely change temperament preferences in cattle. The objectives of this study were to investigate the underlying genetic interrelationships among temperament measurements using genetic factor analytic modeling and validate a movement-based objective method (four-platform standing scale, FPSS) as a measure of temperament. Relationships among subjective methods of docility score (DS), temperament score (TS), 12 qualitative behavior assessment (QBA) attributes and objective FPSS including the standard deviation of total weight on FPSS over time (SSD) and coefficient of variation of SSD (CVSSD) were investigated using 1,528 calves at weaning age. An exploratory factor analysis (EFA) identified two latent variables account for TS and 12 QBA attributes, termeddifficultandeasyfrom their characteristics. Inclusion of DS in EFA was not a good fit because it was evaluated under restraint and other measures were not. A Bayesian confirmatory factor analysis inferred thedifficultandeasyscores discovered in EFA. This was followed by fitting a pedigree-based Bayesian multi-trait model to characterize the genetic interrelationships amongdifficult,easy, DS, SSD, and CVSSD. Estimates of heritability ranged from 0.18 to 0.4 with the posterior standard deviation averaging 0.06. The factors ofdifficultandeasyexhibited a large negative genetic correlation of −0.92. Moderate genetic correlation was found between DS anddifficult(0.36),easy(−0.31), SSD (0.42), and CVSSD (0.34) as well as FPSS withdifficult(CVSSD: 0.35; SSD: 0.42) andeasy(CVSSD: −0.35; SSD: −0.4). Correlation coefficients indicate selection could be performed with either and have similar outcomes. We contend that genetic factor analytic modeling provided a new approach to unravel the complexity of animal behaviors and FPSS-like measures could increase the efficiency of genetic selection by providing automatic, objective, and consistent phenotyping measures that could be an alternative of DS, which has been widely used in beef production.
The zinc cluster transcription factor Rha1 is a positive filamentation regulator inCandida albicans
Authors: Omran Raha Parvizi , Law Chris , Dumeaux Vanessa , Morschhäuser Joachim , Whiteway Malcolm 
Published: January 2020

AbstractZinc cluster transcription factors are essential fungal specific regulators of gene expression. In the dimorphic pathogenCandida albicans,they control processes ranging from metabolism and stress adaptation to mating, virulence, and antifungal resistance. Here, we have identified the geneCaORF19.1604as encoding a zinc cluster transcription factor that acts as a regulator of filament development. Hyperactivation ofCaORF19.1604, which we have namedRHA1forRegulator ofHyphalActivity, leads to a wrinkled colony morphology under non-hyphal growth conditions, to pseudohyphal growth and filament formation, to invasiveness and enhanced biofilm formation.  Cells with activated Rha1 are sensitive to cell wall modifying agents such as Congo red and the echinocandin drug caspofungin but show normal sensitivity to fluconazole. RNA-sequencing-based transcriptional profiling of the activated Rha1 strain reveals the up-regulation of genes for core filamentation and cell-wall-adhesion-related proteins such as Als1, Als3, Ece1, and Hwp1. Upregulation is also seen for the genes for the hyphal-inducing transcription factors Brg1 and Ume6 and genes encoding several enzymes involved in arginine metabolism, while downregulation is seen for the hyphal repressor Nrg1. The deletion ofBRG1blocks the filamentation caused by activated Rha1, while null mutants ofUME6result in a partial block. Deletion ofRHA1can partially reduce healthy hyphal development triggered by environmental conditions such as Spider medium or serum at 37°C.In contrast to the limited effect of either single mutant, the doublerha1 ume6deletion strain is totally defective in both serum and Spider medium stimulated hyphal development. While the loss of Brg1 function blocks serum-stimulated hyphal development, this block can be significantly bypassed by Rha1 hyperactivity, and the combination of Rha1 hyperactivity and serum addition can generate significant polarization in evenbrg1 ume6double mutants. Our results thus suggest that in response to external signals, Rha1 functions to facilitate the switch from an Nrg1 controlled yeast state to a Brg1/Ume6 regulated hyphal state.Author SummaryCandida albicansis the predominant human fungal pathogen, generating a mortality rate of 40% in systemically infected patients. The ability ofCandida albicansto change its morphology is a determinant of its tissue penetration and invasion in response to variant host-related stimuli. The regulatory mechanism for filamentation includes a complex network of transcription factors that play roles in regulating hyphae associated genes. We identify here a new regulator of filamentation from the zinc cluster transcription factor family. We present evidence suggesting that this transcription factor assists the Nrg1/Brg1 switch regulating hyphal development.
Reduced function of the glutathione S-transferase S1 suppresses behavioral hyperexcitability inDrosophilaexpressing a mutant voltage-gated sodium channel
Authors: Chen Hung-Lin , Kasuya Junko , Lansdon Patrick , Kaas Garrett , Tang Hanxi , Sodders Maggie , Kitamoto Toshihiro 
Published: January 2020

ABSTRACTVoltage-gated sodium (Nav) channels play a central role in the generation and propagation of action potentials in excitable cells such as neurons and muscles. To determine how the phenotypes of Nav-channel mutants are affected by other genes, we performed a forward genetic screen for dominant modifiers of the seizure-prone, gain-of-functionDrosophila melanogasterNav-channel mutant,paraShu. Our analyses using chromosome deficiencies, gene-specific RNA interference, and single-gene mutants revealed that a null allele ofglutathione S-transferase S1(GstS1) dominantly suppressesparaShuphenotypes. ReducedGstS1function also suppressed phenotypes of other seizure-prone Nav-channel mutants,paraGEFS+andparabss. Notably,paraShumutants expressed 50% lessGstS1than wild-type flies, further supporting the notion thatparaShuandGstS1interact functionally. Introduction of a loss-of-functionGstS1mutation into aparaShubackground led to up- and down-regulation of various genes, with those encoding cytochrome P450 (CYP) enzymes most significantly over-represented in this group. BecauseGstS1is a fly ortholog of mammalian hematopoietic prostaglandin D synthase, and in mammals CYPs are involved in the oxygenation of polyunsaturated fatty acids including prostaglandins, our results raise the intriguing possibility that bioactive lipids play a role inGstS1-mediated suppression ofparaShuphenotypes.
Single-cell metabolic dynamics of early activated CD8 T cells during the primary immune response to infection
Authors: Levine Lauren S. , Hiam Kamir J. , Marquez Diana M. , Tenvooren Iliana , Contreras Diana C. , Rathmell Jeffrey C. , Spitzer Matthew H. 
Published: January 2020

AbstractMemory T cells conventionally rely on oxidative phosphorylation and short-lived effector T cells on glycolysis. Here, we investigate how T cells arrive at these states during an immune response. In order to understand the metabolic state of rare, early activated T cells, we adapted mass cytometry to quantify metabolic regulators at single-cell resolution in parallel with cell signaling, proliferation, and effector function. We interrogated CD8 T cell activation in vitro as well as the trajectory of CD8 T cells responding toListeria monocytogenesinfection, a well-characterizedin vivomodel for studies of T cell differentiation. This approach revealed a unique metabolic state in early activated T cells characterized by maximal expression of glycolytic and oxidative metabolic proteins. Peak utilization of both pathways was confirmed by extracellular flux analysis. Cells in this transient state were most abundant five days post-infection before rapidly downregulating metabolic protein expression. This approach should be useful for mechanistic investigations of metabolic regulation of immune responses.