bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Newcastle disease virus (NDV) expressing membrane-anchored spike as a cost-effective inactivated SARS-CoV-2 vaccine
Authors: Sun Weina , McCroskery Stephen , Liu Wen-Chun , Leist Sarah R. , Liu Yonghong , Albrecht Randy A. , Slamanig Stefan , Oliva Justine , Amanat Fatima , Schäfer Alexandra , Dinnon Kenneth H. , Innis Bruce L. , García-Sastre Adolfo , Krammer Florian , Baric Ralph S. , Palese Peter 
Published: August 2020

AbstractA successful SARS-CoV-2 vaccine must be not only safe and protective but must also meet the demand on a global scale at low cost. Using the current influenza virus vaccine production capacity to manufacture an egg-based inactivated Newcastle disease virus (NDV)/SARS-CoV-2 vaccine would meet that challenge. Here, we report pre-clinical evaluations of an inactivated NDV chimera stably expressing the membrane-anchored form of the spike (NDV-S) as a potent COVID-19 vaccine in mice and hamsters. The inactivated NDV-S vaccine was immunogenic, inducing strong binding and/or neutralizing antibodies in both animal models. More importantly, the inactivated NDV-S vaccine protected animals from SARS-CoV-2 infections or significantly attenuated SARS-CoV-2 induced disease. In the presence of an adjuvant, antigen-sparing could be achieved, which would further reduce the cost while maintaining the protective efficacy of the vaccine.
Validation and Application of a Bench Top Cell Sorter in a BSL-3 Containment Setting
Authors: Roberts Lydia M , Anderson Rebecca , Carmody Aaron , Bosio Catharine M 
Published: August 2020

AbstractRigorous assessment of the cellular and molecular changes during infection typically requires isolation of specific immune cell subsets for downstream application. While there are numerous options for enrichment/isolation of cells from tissues, fluorescent activated cell sorting (FACS) is accepted as a method that results in superior purification of a wide variety of cell types. Flow cytometry requires extensive fluidics and aerosol droplets can be generated during collection of target cells. Pathogens such asFrancisella tularensis,Mycobacterium tuberculosis,Yersinia pestis, and SARS-CoV-2 require manipulation at biosafety level-3 (BSL-3). Due to the concern of potential aerosolization of these pathogens, use of flow cytometric-based cell sorting in these laboratory settings requires placement of the equipment in dedicated biosafety cabinets within the BSL-3. For many researchers, this is often not possible due to expense, space, or expertise available. Here we describe the safety validation and utility of a completely closed cell sorter that results in gentle, rapid, high purity, and safe sorting of cells on the benchtop at BSL-3. We also provide data demonstrating the need for cell sorting versus bead purification and the applicability of this technology for BSL-3 and potentially BSL-4 related infectious disease projects. Adoption of this technology will significantly expand our ability to uncover important features of the most dangerous infectious diseases leading to faster development of novel vaccines and therapeutics.
Intrinsic neural timescales related to sensory processing: Evidence from abnormal behavioural states
Authors: Zilio Federico , Gomez-Pilar Javier , Cao Shumei , Zhang Jun , Zang Di , Qi Zengxin , Tan Jiaxing , Hiromi Tanigawa , Wu Xuehai , Fogel Stuart , Huang Zirui , Hohmann Matthias R. , Fomina Tatiana , Synofzik Matthis , Grosse-Wentrup Moritz , Owen Adrian M. , Northoff Georg 
Published: August 2020

AbstractThe brain exhibits a complex temporal structure which translates into a hierarchy of distinct neural timescales. An open question is how these intrinsic timescales are related to sensory or motor information processing and whether these dynamics have common patterns in different behavioural states. We address these questions by investigating the brain’s intrinsic timescales in healthy controls, motor (amyotrophic lateral sclerosis, locked-in syndrome), sensory (anaesthesia, unresponsive wakefulness syndrome), and progressive reduction of sensory processing (from awake states over N1, N2, N3). We employed a combination of measures from EEG resting-state data: auto-correlation window (ACW), power spectral density (PSD), and power-law exponent (PLE). Prolonged neural timescales accompanied by a shift towards slower frequencies were observed in the conditions with sensory deficits, but not in conditions with motor deficits. Our results establish that the spontaneous activity’s intrinsic neural timescale is related to specifically sensory rather than motor information processing in the healthy brain.HighlightsEEG resting-state shows a hierarchy of intrinsic neural timescales.Sensory deficits as in disorders of consciousness lead to prolonged intrinsic neuraltimescales.Clinical conditions with motor deficits do not show changes in intrinsic neural timescales.20Graphical Abstract
Estimating Genetic Similarity Matrices using Phylogenies
Authors: Wang Shijia , Ge Shufei , Colijn Caroline , Biller Priscila , Wang Liangliang , Elliott Lloyd T 
Published: August 2020

AbstractGenetic similarity is a measure of the genetic relatedness among individuals. The standard method for computing these matrices involves the inner product of observed genetic variants. Such an approach is inaccurate or impossible if genotypes are not available, or not densely sampled, or of poor quality (for example, genetic analysis of extinct species). We provide a new method for computing genetic similarities among individuals using phylogenetic trees. Our method can supplement (or stand in for) computations based on genotypes. We provide simulations suggesting that the genetic similarity matrices computed from trees are consistent with those computed from genotypes. With our methods, quantitative analysis on genetic traits and analysis of heritability and co-heritability can be conducted directly using genetic similarity matrices and so in the absence of genotype data, or under uncertainty in the phylogenetic tree. We use simulation studies to demonstrate the advantages of our method, and we provide applications to data.
dadi.CUDA: Accelerating population genetic inference with Graphics Processing Units
Authors: Gutenkunst Ryan N. 
Published: August 2020

AbstractExtracting insight from population genetic data often demands computationally intensive modeling. dadi is a popular program for fitting models of demographic history and natural selection to such data. Here, I show that running dadi on a Graphics Processing Unit (GPU) can speed computation by orders of magnitude compared to the CPU implementation, with minimal user burden. This speed increase enables the analysis of more complex models, which motivated the extension of dadi to four- and five-population models. Remarkably, dadi performs almost as well on inexpensive consumer-grade GPUs as on expensive server-grade GPUs. GPU computing thus offers large and accessible benefits to the community of dadi users. This functionality is available in dadi version 2.1.0,https://bitbucket.org/gutenkunstlab/dadi/.
Genome fractionation and loss of heterozygosity in hybrids and polyploids: mechanisms, consequences for selection, and link to gene function
Authors: Janko Karel , Bartoš Oldřich , Kočí Jan , Roslein Jan , Drdová Edita Janková , Kotusz Jan , Eisner Jan , Štefková-Kašparová Eva 
Published: August 2020

Abstract:Hybridization and genome duplication have played crucial roles in the evolution of many animal and plant taxa. During their evolution, the subgenomes of parental species undergo considerable changes in hybrids and polyploids, which often selectively eliminate segments of one subgenome. However, the mechanisms underlying these changes are not well understood, particularly when the hybridization is linked with asexual reproduction that may enforce specific evolutionary pathways.We studied the genome evolution in asexual diploid and polyploid hybrids between fish from the genusCobitis. Comparing exome sequencing with published cytogenetic and RNAseq data revealed that clonal genomes remain static on chromosome-scale levels but undergo considerable small-scale restructurations owing to two major processes; hemizygous deletions and gene conversions. Interestingly, polyploids were much more tolerant to accumulating deletions than diploid asexuals where gene conversions prevailed. The genomic restructurations accumulated preferentially in genes characterized by high transcription levels, relatively strong purifying selection and some specific functions such as interacting with intracellular membranes. The likelihood of an ortholog’s retention or loss correlated with its parental-species ancestry, GC content, and expression. Furthermore, all hybrids showed a strong bias towards the retention of one parental subgenome. Contrary to expectations, however, the preferentially retained subgenome was not transcriptionally dominant as all hybrids were phenotypically more similar to the other parent.The present study demonstrated that the fate of subgenomes in asexual hybrids and polyploids depends on the complex interplay of selection and several molecular mechanisms whose impact depends on ploidy, sequence composition, gene expression as well as parental ancestry.
CoCoNet: Boosting RNA contact prediction by convolutional neural networks
Authors: Zerihun Mehari B. , Pucci Fabrizio , Schug Alexander 
Published: August 2020

AbstractPhysics-based co-evolutionary models such as direct coupling analysis (DCA) in combination with machine learning (ML) techniques based on deep neural networks are able to predict protein contact maps with astonishing accuracy. Such contacts can be used as constraints in structure prediction and massively increase prediction accuracy. Unfortunately, the same ML methods cannot readily be applied to RNA as they rely on large structural datasets only available for proteins but not for RNAs. Here, we demonstrate how the small amount of data available for RNA can be used to significantly improve prediction of RNA contact maps. We introduce an algorithm calledCoCoNetthat is based on a combination of aCoevolutionary model and a shallowConvolutional NeuralNetwork. Despite its simplicity and the small number of trained parameters, the method boosts the contact prediction accuracy by about 70% with respect to straightforward DCA as tested by cross-validation on a dataset of about sixty RNA structures. Both our extensive robustness tests and the limited number of parameters allow the generalization properties of our model. Finally, applications to other RNAs highlight the power of our approach. CoCoNet is freely available and can be found athttps://github.com/KIT-MBS/coconet.
Towards understanding how we pay attention in naturalistic visual search settings
Authors: Turoman Nora , Tivadar Ruxandra I. , Retsa Chrysa , Murray Micah M. , Matusz Pawel J. 
Published: August 2020

AbstractResearch on attentional control has largely focused on single senses and the importance of behavioural goals in controlling attention. However, everyday situations are multisensory and contain regularities, both likely influencing attention. We investigated how visual attentional capture is simultaneously impacted by top-down goals, the multisensory nature of stimuli,andthe contextual factors of stimuli’s semantic relationship and temporal predictability. Participants performed a multisensory version of the Folk et al. (1992) spatial cueing paradigm, searching for a target of a predefined colour (e.g. a red bar) within an array preceded by a distractor. We manipulated: 1) stimuli’s goal-relevance via distractor’s colour (matching vs. mismatching the target), 2) stimuli’s multisensory nature (colour distractors appearing alone vs. with tones), 3) the relationship between the distractor sound and colour (arbitrary vs. semantically congruent) and 4) the temporal predictability of distractor onset. Reaction-time spatial cueing served as a behavioural measure of attentional selection. We also recorded 129-channel event-related potentials (ERPs), analysing the distractor-elicited N2pc component both canonically and using a multivariate electrical neuroimaging framework. Behaviourally, arbitrary target-matching distractors captured attention more strongly than semantically congruent ones, with no evidence for context modulating multisensory enhancements of capture. Notably, electrical neuroimaging of surface-level EEG analyses revealed context-based influences on attention to both visual and multisensory distractors, in how strongly they activated the brain and type of activated brain networks. For both processes, the context-driven brain response modulations occurred long before the N2pc time-window, with topographic (network-based) modulations at ~30ms, followed by strength-based modulations at ~100ms post-distractor onset. Our results reveal that both stimulus meaning and predictability modulate attentional selection, and they interact while doing so. Meaning, in addition to temporal predictability, is thus a second source of contextual information facilitating goal-directed behaviour. More broadly, in everyday situations, attention is controlled by an interplay between one’s goals, stimuli’s perceptual salience, meaning and predictability. Our study calls for a revision of attentional control theories to account for the role of contextual and multisensory control.
Rapid Online Assessment of Reading Ability
Authors: Yeatman Jason D. , Tang Kenny An , Donnelly Patrick M. , Yablonski Maya , Ramamurthy Mahalakshmi , Karipidis Iliana I. , Caffarra Sendy , Takada Megumi E. , Kanopka Klint , Ben-Shachar Michal , Domingue Benjamin W. 
Published: August 2020

AbstractAn accurate model of the factors that contribute to individual differences in reading ability depends on data collection in large, diverse and representative samples of research participants. However, that is rarely feasible due to the constraints imposed by standardized measures of reading ability which require test administration by trained clinicians or researchers. Here we explore whether a simple, two-alternative forced choice, time limited lexical decision task (LDT), self-delivered through the web-browser, can serve as an accurate and reliable measure of reading ability. We found that performance on the LDT is highly correlated with scores on standardized measures of reading ability such as the Woodcock-Johnson Letter Word Identification test (r = 0.91, disattenuated r = 0.94). Importantly, the LDT reading ability measure is highly reliable (r = 0.97). After optimizing the list of words and pseudowords based on item response theory, we found that a short experiment with 76 trials (2-3 minutes) provides a reliable (r = 0.95) measure of reading ability. Thus, the self-administered, Rapid Online Assessment of Reading ability (ROAR) developed here overcomes the constraints of resource-intensive, in-person reading assessment, and provides an efficient and automated tool for effective online research into the mechanisms of reading (dis)ability.
Triploidy affects standard and postprandial metabolism in brook charr,Salvelinus fontinalis
Authors: Daigle Nicole J. , Sacobie Charles F.D. , Verhille Christine E. , Benfey Tillmann J. 
Published: August 2020

AbstractThe use of sterile triploids in aquaculture is currently limited because of reduced performance in situations of aerobic stress such as high temperature, hypoxia, and exhaustive exercise. Many studies have therefore attempted to find underlying metabolic differences between triploids and their diploid counterparts to improve triploid rearing protocols. This study investigated the effects of triploidy on postprandial metabolism (and therefore also pre-feeding standard metabolic rate; SMR) by measuring oxygen uptake and total ammonia nitrogen (TAN) excretion at 14-15°C of previously fasted (for eight days) diploid and triploid brook charr,Salvelinus fontinalis, from 48h before to 48h after being fed a single ration of 0.4% body mass. Triploids had significantly lower SMRs and higher postprandial metabolic rates (i.e., specific dynamic action) and net TAN excretion than diploids. While this greater cost of processing a meal may not represent a major diversion of metabolic reserves for triploids, it could affect their growth and survival when simultaneously faced with oxygen-limiting conditions.
Genetic structure of the Coconut Rhinoceros Beetle (Oryctes rhinoceros) population and the incidence of its biocontrol agent (Oryctes rhinoceros nudivirus) in the South Pacific Islands
Authors: Etebari Kayvan , Hereward James , Sailo Apenisa , Ahoafi Emeline M. , Tautua Robert , Tsatsia Helen , Jackson Grahame V , Furlong Michael J. 
Published: August 2020

AbstractIncursions of the Coconut rhinoceros beetle (CRB),Oryctes rhinoceros, have been detected in several countries of the south west Pacific in recent years, resulting in an expansion of the pest’s geographic range. It has been suggested that this resurgence is related to anO. rhinocerosmitochondrial lineage (previously referred to as the CRB-G “biotype”) that is reported to show reduced susceptibility to the well-established classical biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). We investigatedO. rhinocerospopulation genetics and the OrNV status of adult specimens collected in the Philippines and seven different South Pacific island countries (Fiji, New Caledonia, Papua New Guinea (PNG), Samoa, Solomon Islands, Tonga, and Vanuatu). Based on the presence of single nucleotide polymorphisms (snps) in the mitochondrial Cytochrome C Oxidase subunit I (CoxI) gene, we found three major mitochondrial lineages (CRB-G, a PNG lineage (CRB-PNG) and the South Pacific lineage (CRB-S)) across the region. Haplotype diversity varied considerably between and within countries. TheO. rhinocerospopulation in most countries was monotypic and all individuals tested belonged to a single mitochondrial lineage (Fiji, CRB-S; Tonga, CRB-S; Vanuatu, CRB-PNG; PNG (Kimbe), CRB-PNG; New Caledonia CRB-G; Philippines, CRB-G). However, in Samoa we detected CRB-S and CRB-PNG and in Solomon Islands we detected all three haplotype groups. Genotyping-by-Sequencing (GBS) methods were used to genotype 10,000snps from 230 insects across the Pacific and showed genetic differentiation in theO. rhinocerosnuclear genome among different geographical populations. The GBS data also provided evidence for gene flow and admixture between different haplotypes in Solomon Islands. Therefore, contrary to earlier reports, CRB-G is not solely responsible for damage to the coconut palms reported since the pest was first recorded in Solomon Islands in 2015. We also PCR-screened a fragment of OrNV from 260 insects and detected an extremely high prevalence of viral infection in all three haplotypes in the region. We conclude that the haplotype groups CRB-G, CRB-S, and PNG, do not represent biotypes, subspecies, or cryptic species, but simply represent different invasions ofO. rhinocerosacross the Pacific. This has important implications for management, especially biological control, of Coconut rhinoceros beetle in the region.
The histidine phosphotransfer AHP4 plays a negative role inArabidopsisplant response to drought
Authors: Van Ha Chien , Nguyen Kien Huu , Mostofa Mohammad Golam , Tran Cuong Duy , Watanabe Yasuko , Li Weiqiang , Osakabe Yuriko , Sato Mayuko , Toyooka Kiminori , Tanaka Maho , Seki Motoaki , Burritt David J. , Anderson Cheyenne , Zhang Ru , Phan Tran Lam-Son 
Published: August 2020

ABSTRACTCytokinin plays an important role in plant stress responses via a multistep signaling pathway, involving the histidine phosphotransfer proteins (HPs). InArabidopsis thaliana, the AHP2, AHP3 and AHP5 proteins are known to impact drought responses; however, the role of AHP4 in drought adaptation remains undetermined. In the present study, using a loss-of-function approach we showed that AHP4 possesses a negative regulatory role inArabidopsis’s response to drought. This is evidenced by both higher survival rates ofahp4than wild-type (WT) plants under drought conditions, and the down-regulatedAHP4expression in WT during periods of dehydration. Comparative transcriptome analysis ofahp4and WT plants revealed AHP4-mediated expression of several dehydration- and/or abscisic acid (ABA)-responsive genes involved in regulation of various physiological and biochemical processes important for plant drought acclimation. In comparison with WT,ahp4plants showed increased wax crystal accumulation in stems, thicker cuticles in leaves, greater sensitivity to exogenous ABA at germination, narrow stomatal apertures, heightened leaf temperatures during dehydration, and longer root length under osmotic stress. Additionally,ahp4plants showed greater photosynthetic efficiency, lower levels of reactive oxygen species (ROS), reduced electrolyte leakage and lipid peroxidation, and increased anthocyanin contents under drought, when compared with WT. These differences displayed inahp4plants are likely due to up-regulation of genes that encode enzymes involved in ROS-scavenging and non-enzymatic antioxidant metabolism. The role of AHP4 in negative regulation of multiple protective mechanisms associated with drought tolerance could make editing ofAHP4a promising approach for the production of drought-tolerant crop plants.Significance statementLoss-of-function analysis of the cytokinin signaling member AHP4 revealed its function inArabidopsisadaptation to drought as a negative regulator, affecting various physiological and biochemical processes by modulating the expression of a large set of genes potentially in a crosstalk with ABA.AHP4and its homologs are promising candidates for gene editing to develop drought-tolerant crop cultivars.
MacaquePose: A novel ‘in the wild’ macaque monkey pose dataset for markerless motion capture
Authors: Labuguen Rollyn , Matsumoto Jumpei , Negrete Salvador , Nishimaru Hiroshi , Nishijo Hisao , Takada Masahiko , Go Yasuhiro , Inoue Ken-ichi , Shibata Tomohiro 
Published: August 2020

AbstractVideo-based markerless motion capture permits quantification of an animal’s pose and motion, with a high spatiotemporal resolution in a naturalistic context, and is a powerful tool for analyzing the relationship between the animal’s behaviors and its brain functions. Macaque monkeys are excellent non-human primate models, especially for studying neuroscience. Due to the lack of a dataset allowing training of a deep neural network for the macaque’s markerless motion capture in the naturalistic context, it has been challenging to apply this technology for macaques-based studies. In this study, we created MacaquePose, a novel open dataset with manually labeled body part positions for macaques in naturalistic scenes, consisting of >13,000 images, refined by researchers. We show that the pose estimation performance of an artificial neural network trained with the dataset is close to that of a human-level. The MacaquePose will provide a platform for innovative behavior analysis for non-human primate.