bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bifocal tACS Enhances Visual Motion Discrimination by Modulating Phase Amplitude Coupling Between V1 and V5 Regions
Authors: Salamanca-Giron Roberto F. , Raffin Estelle , Zandvliet Sarah Bernardina , Seeber Martin , Michel Christoph M. , Sauseng Paul , Huxlin Krystel R. , Hummel Friedhelm C. 
Published: November 2020

ABSTRACTVisual motion discrimination involves reciprocal interactions in the alpha band between the primary visual cortex (V1) and the mediotemporal area (V5/MT). We investigated whether modulating alpha phase synchronization using individualized multisite transcranial alternating current stimulation (tACS) over V5 and V1 regions would improve motion discrimination. We tested 3 groups of healthy subjects: 1) an individualized In-Phase V1alpha-V5alphatACS (0° lag) group, 2) an individualized Anti-Phase V1alpha-V5alphatACS (180° lag) group and 3) a sham tACS group. Motion discrimination and EEG activity were compared before, during and after tACS. Performance significantly improved in the Anti-Phase group compared to that in the In-Phase group at 10 and 30 minutes after stimulation. This result could be explained by changes in bottom-up alpha-V1 gamma-V5 phase-amplitude coupling. Thus, Anti-Phase V1alpha-V5alphatACS might impose an optimal phase lag between stimulation sites due to the inherent speed of wave propagation, hereby supporting optimized neuronal communication.IMPACT STATEMENTAlpha multisite (V1 and V5) tACS influences global motion discrimination and integrationPhase-amplitude coupling is associated with visual performanceMultisite Anti-Phase stimulation of strategic visual areas (V1 and V5) is associated with connectivity changes in the visual cortex and thus, associated with changes in direction acuity
Reinforcing neuron extraction and spike inference in calcium imaging using deep self-supervised learning
Authors: Li Xinyang , Zhang Guoxun , Wu Jiamin , Zhang Yuanlong , Zhao Zhifeng , Lin Xing , Qiao Hui , Xie Hao , Wang Haoqian , Fang Lu , Dai Qionghai 
Published: November 2020

ABSTRACTCalcium imaging is inherently susceptible to detection noise especially when imaging with high frame rate or under low excitation dosage. We developed DeepCAD, a self-supervised learning method for spatiotemporal enhancement of calcium imaging without requiring any high signal-to-noise ratio (SNR) observations. Using this method, detection noise can be effectively suppressed and the imaging SNR can be improved more than tenfold, which massively improves the accuracy of neuron extraction and spike inference and facilitate the functional analysis of neural circuits.
Photostimulation of lymphatic clearance of red blood cells from the mouse brain after intraventricular hemorrhage
Authors: Li Dong-Yu , Liu Shao-Jun , Yu Ting-Ting , Liu Zhang , Sun Si-Lin , Bragin Denis , Navolokin Nikita , Kurths Jürgen , Glushkovskaya-Semyachkina Oxana , Zhu Dan 
Published: November 2020

AbstractIntraventricular hemorrhage (IVH) is the most fatal form of brain injury, yet a therapy directed at ameliorating intraventricular clot is very limited. There is accumulating evidence that an augmentation of the meningeal lymphatic (MLVs) functions might be a promising therapeutic target for IVH. In particular, the photostimulation (PS) of MLVs could be promising for non-invasive therapy of IVH via PS of clearance of red blood cells (RBCs) from the brain via MLVs. Indeed, we uncover that PS has therapeutic effects on IVH in mice reducing the mortality, improving the emotional status, accelerating the RBCs evacuation from the ventricles and increasing the ICP recovery. Our findings strongly suggest that the PS-mediated stimulation of drainage and clearing functions of MLVs can be a novel bedside, readily applicable and commercially viable technologies for treatment of IVH. These pilot results open new horizons in a non-invasive therapy of IVH via PS stimulation of regenerative lymphatic mechanisms.
MegaGO: a fast yet powerful approach to assess functional similarity across meta-omics data sets
Authors: Verschaffelt Pieter , Van Den Bossche Tim , Gabriel Wassim , Burdukiewicz Michał , Soggiu Alessio , Martens Lennart , Renard Bernhard Y. , Schiebenhoefer Henning , Mesuere Bart 
Published: November 2020

AbstractThe study of microbiomes has gained in importance over the past few years, and has led to the fields of metagenomics, metatranscriptomics and metaproteomics. While initially focused on the study of biodiversity within these communities the emphasis has increasingly shifted to the study of (changes in) the complete set of functions available in these communities. A key tool to study this functional complement of a microbiome is Gene Ontology (GO) term analysis. However, comparing large sets of GO terms is not an easy task due to the deeply branched nature of GO, which limits the utility of exact term matching. To solve this problem, we here present MegaGO, a user-friendly tool that relies on semantic similarity between GO terms to compute functional similarity between two data sets. MegaGO is highly performant: each set can contain thousands of GO terms, and results are calculated in a matter of seconds. MegaGO is available as a web application athttps://megago.ugent.beand installable via pip as a standalone command line tool and reusable software library. All code is open source under the MIT license, and is available athttps://github.com/MEGA-GO/.
The reward-complexity trade-off in schizophrenia
Authors: Gershman Samuel J. , Lai Lucy 
Published: November 2020

AbstractAction selection requires a policy that maps states of the world to a distribution over actions. The amount of memory needed to specify the policy (the policy complexity) increases with the state-dependence of the policy. If there is a capacity limit for policy complexity, then there will also be a trade-off between reward and complexity, since some reward will need to be sacrificed in order to satisfy the capacity constraint. This paper empirically characterizes the trade-off between reward and complexity for both schizophrenia patients and healthy controls. Schizophrenia patients adopt lower complexity policies on average, and these policies are more strongly biased away from the optimal reward-complexity trade-off curve compared to healthy controls. How-ever, healthy controls are also biased away from the optimal trade-off curve, and both groups appear to lie on the same empirical trade-off curve. We explain these findings using a cost-sensitive actor-critic model. Our empirical and theoretical results shed new light on cognitive effort abnormalities in schizophrenia.
Tysserand - Fast and accurate reconstruction of spatial networks from bioimages
Authors: Coullomb Alexis , Pancaldi Vera 
Published: November 2020

AbstractSummaryNetworks provide a powerful framework to analyze spatial omics experiments. However, we lack tools that integrate several methods to easily reconstruct networks for further analyses with dedicated libraries. In addition, choosing the appropriate method and parameters can be challenging.We proposetysserand, a Python library to reconstruct spatial networks from spatially resolved omics experiments. It is intended as a common tool to which the bioinformatics community can add new methods to reconstruct networks, choose appropriate parameters, clean resulting networks and pipe data to other libraries.Availability and implementationtysserandsoftware and tutorials with a Jupyter notebook to reproduce the results are available athttps://github.com/VeraPancaldiLab/tysserandSupplementary informationSupplementary data are available atBioarxivonline.
Mandibular morphology, task specialization, and bite mechanics inPheidoleants (Hymenoptera: Formicidae)
Authors: Klunk C.L. , Argenta M.A. , Casadei-Ferreira A. , Economo E.P. , Pie M.R. 
Published: November 2020

AbstractThe remarkable ecological and evolutionary success of ants was associated with the evolution of reproductive division of labor, in which sterile workers perform most colony tasks whereas reproductives become specialized in reproduction. In some lineages, the worker force became further subdivided into morphologically distinct subcastes (e.g. minor vs. major workers), allowing for the differential performance of particular roles in the colony. However, the functional and ecological significance of morphological differences between subcastes is not well understood. Here, we applied Finite Element Analysis (FEA) to explore the functional differences between major and minor ant worker mandibles. Analyses were carried out on mandibles of twoPheidolespecies, a dimorphic ant genus. In particular, we test whether major mandibles evolved to minimize stress when compared to minors using combinations of tooth and masticatory margin bites under strike and pressure conditions. Majors performed better in pressure conditions yet, contrary to our expectations, minors performed better in strike bite scenarios. Moreover, we demonstrate that even small morphological differences in ant mandibles might lead to substantial differences in biomechanical responses to bite loading. These results also underscore the potential of FEA to uncover biomechanical consequences of morphological differences within and between ant worker castes.
Simplified and unified access to cancer proteogenomic data
Authors: Lindgren Caleb M. , Adams David W. , Kimball Benjamin , Boekweg Hannah , Tayler Sadie , Pugh Samuel L. , Payne Samuel H. 
Published: November 2020

AbstractComprehensive cancer datasets recently generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) offer great potential for advancing our understanding of how to combat cancer. These datasets include DNA, RNA, protein, and clinical characterization for tumor and normal samples from large cohorts in many different cancer types. The raw data are publicly available at various Cancer Research Data Commons. However, widespread re-use of these datasets is also facilitated by easy access to the processed quantitative data tables. We have created a Python package,cptac, which is a data API that distributes the finalized processed CPTAC datasets in a consistent, up-to-date format. This consistency makes it easy to integrate the data with common graphing, statistical, and machine learning packages for advanced analysis. Additionally, consistent formatting across all cancer types promotes the investigation of pan-cancer trends. The data API structure of directly streaming data within a programming environment enhances reproducibility. Finally, with the accompanying tutorials, this package provides a novel resource for cancer research education.
ION-Decoding: A Single-channel Interactive Offline Neural Decoding Algorithm for a large number of neurons
Authors: Rastegari Mohsen , Marateb Hamid Reza 
Published: November 2020

AbstractResearchers have widely used extracellular recordings as a technique of paramount importance due to its wide usage in cognitive studies, health technologies, and prosthetics and orthotics research. To extract the required information from this technique, a critical and crucial step, called spike sorting, must be performed on the recorded signal. By this method, it is possible to analyze a single neuron (single-unit activity) and investigate its specifications, such as the firing rates and the number of action potentials (spikes) of an individual neuron. Here we introduce a novel idea of a user-friendly interactive, offline, and unsupervised algorithm called ION-Decoding. This platform extracts and aligns the spikes using a high-resolution alignment method, and the clusters can be atomically identified and manually edited. The entire procedure is performed using the minimum number of adjustable parameters, and cluster merging was performed in a smart, intuitive way. The ION-Decoding algorithm was evaluated by a benchmark dataset, including 95 simulations of two to twenty neurons from 10 minutes simulated extracellular recordings. There was not any significant relationship between the number of missed clusters with the quality of the signal (i.e., the signal-to-noise ratio (SNR)) by controlling the number of neurons in each signal (p_value=0.103). Moreover, the number of extra clusters was not significantly dependent on the parameter SNR (p_value=0.400). The accuracy of the classification method was significantly associated with the decomposability index (DI) (p_value<0.001). A number of 77% of the neurons with the DI higher than 20 had the classification accuracy higher than 80%. The ION-Decoding algorithm significantly outperformed Wave_Clus in terms of the number of hits (p_value=0.017). However, The Wave_Clus algorithm significantly outperformed the ION-Decoding algorithm when the false-positive error (FP) was considered (p_value=0.001). The ION-Decoding is thus a promising single-channel spike sorting algorithm. However, our future focuses on the improvement of the cluster representative identification and FP error reduction.
The gut bacteria of an invasive amphibian respond to the dual challenges of range-expansion and parasite attack
Authors: Zhou Jia , Nelson Tiffanie Maree , Rodriguez Lopez Carlos , Zhou Shao Jia , Ward-Fear Georgia , Stuart Katarina C. , Shine Richard , Rollins Lee Ann 
Published: November 2020

AbstractGut bacterial communities influence, and are influenced by, the behaviour and ecology of their hosts. Those interactions have been studied primarily in humans and model organisms, but we need field research to understand the relationship between an organism’s gut bacteria and its ecological challenges, such as those imposed by rapid range expansion (as in invasive species) and the presence of host-manipulating parasites. Cane toads (Rhinella marina) provide an excellent model system in this respect, because the species’ ongoing colonization of Australia has enforced major changes in phenotypic traits (including behaviour), and lungworm parasites (Rhabdias pseudosphaerocephala) modify host gut function in ways that enhance the viability of lungworm larvae. We collected female toads from across the species’ invasive range and studied their morphology, behaviour, parasite infection status and gut bacterial community. Range-coreversusrange-edge toads differed in morphology, behaviour, gut bacterial composition and predicted gut bacterial function but did not differ in the occurrence of parasite infection nor in the intensity of infection. Toads infected with lungworms differed from uninfected conspecifics in gut bacterial composition and diversity. Our study demonstrates strong associations between gut bacterial community and host ecology and behaviour.
Probing the aggregated effects of purifying selection per individual on 1,380 medical phenotypes in the UK biobank
Authors: Vy Ha My T. , Jordan Daniel M. , Balick Daniel J. , Do Ron 
Published: November 2020

AbstractUnderstanding the relationship between natural selection and phenotypic variation has been a long-standing challenge in human population genetics. With the emergence of biobank-scale datasets, along with new statistical metrics to approximate strength of purifying selection at the variant level, it is now possible to correlate a proxy of individual relative fitness with a range of medical phenotypes. We calculated a per-individual deleterious load score by summing the total number of derived alleles per individual after incorporating a weight that approximates strength of purifying selection. We assessed four methods for the weight, including GERP, phyloP, CADD, and fitcons. By quantitatively tracking each of these scores with the site frequency spectrum, we identified phyloP as the most appropriate weight. The phyloP-weighted load score was then calculated across 15,129,142 variants in 335,161 individuals from the UK Biobank and tested for association on 1,380 medical phenotypes. After accounting for multiple test correction, we observed a strong association of the load score amongst coding sites only on 27 traits including body mass, adiposity and metabolic rate. We further observed that the association signals were driven by common variants (derived allele frequency > 5%) with high phyloP score (phyloP > 2). Finally, through permutation analyses, we showed that the load score amongst coding sites had an excess of nominally significant associations on many medical phenotypes. These results suggest a broad impact of deleterious load on medical phenotypes and highlight the deleterious load score as a tool to disentangle the complex relationship between natural selection and medical phenotypes.Author summaryThis study aims to augment our understanding between the complex relation between natural selection and human phenotypic variation. We developed a load score to approximate the relative fitness of an individual and correlate it with a set of medical phenotypes. Association tests between the load score amongst coding sites and 1,380 phenotypes in a sample of 335,161 individuals from the UK Biobank showed a strong association with 27 traits including body mass, adiposity and metabolic rate. Furthermore, an excess of nominal associations at suggestive levels was observed between the load score amongst coding sites and medical phenotypes than would be expected under a null model. These results suggest that the aggregate effect of deleterious mutations as measured by the load score has a broad effect on human phenotypes.
TheRhinolophus affinisbat ACE2 and multiple animal orthologs are functional receptors for bat coronavirus RaTG13 and SARS-CoV-2
Authors: Li Pei , Guo Ruixuan , Liu Yan , Zhang Yintgtao , Hu Jiaxin , Ou Xiuyuan , Mi Dan , Chen Ting , Mu Zhixia , Han Yelin , Cui Zhewei , Zhang Leiliang , Wang Xinquan , Wu Zhiqiang , Wang Jianwei , Jin Qi , Qian Zhaohui 
Published: November 2020

AbstractBat coronavirus (CoV) RaTG13 shares the highest genome sequence identity with SARS-CoV-2 among all known coronaviruses, and also uses human angiotensin converting enzyme 2 (hACE2) for virus entry. Thus, SARS-CoV-2 is thought to have originated from bat. However, whether SARS-CoV-2 emerged from bats directly or through an intermediate host remains elusive. Here, we found thatRhinolophus affinisbat ACE2 (RaACE2) is an entry receptor for both SARS-CoV-2 and RaTG13, although RaACE2 binding to the receptor binding domain (RBD) of SARS-CoV-2 is markedly weaker than that of hACE2. We further evaluated the receptor activities of ACE2s from additional 16 diverse animal species for RaTG13, SARS-CoV, and SARS-CoV-2 in terms of S protein binding, membrane fusion, and pseudovirus entry. We found that the RaTG13 spike (S) protein is significantly less fusogenic than SARS-CoV and SARS-CoV-2, and seven out of sixteen different ACE2s function as entry receptors for all three viruses, indicating that all three viruses might have broad host rages. Of note, RaTG13 S pseudovirions can use mouse, but not pangolin ACE2, for virus entry, whereas SARS-CoV-2 S pseudovirions can use pangolin, but limited for mouse, ACE2s enter cells. Mutagenesis analysis revealed that residues 484 and 498 in RaTG13 and SARS-CoV-2 S proteins play critical roles in recognition of mouse and human ACE2. Finally, two polymorphousRhinolophous sinicusbat ACE2s showed different susceptibilities to virus entry by RaTG13 and SARS-CoV-2 S pseudovirions, suggesting possible coevolution. Our results offer better understanding of the mechanism of coronavirus entry, host range, and virus-host coevolution.
Elephant endotheliotropic herpesvirus is omnipresent in elephants in European zoos and an Asian elephant range country
Authors: Hoornweg Tabitha E. , Schaftenaar Willem , Maurer Gilles , van den Doel Petra B. , Molenaar Fieke M. , Chamouard-Galante Alexandre , Vercammen Francis , Rutten Victor P.M.G. , de Haan Cornelis A.M. 
Published: November 2020

AbstractElephant endotheliotropic herpesviruses (EEHVs) are a group of evolutionary divergent herpesviruses that may cause acute, often lethal, hemorrhagic disease (EEHV-HD) in young elephants. Although EEHV was first discovered over 20 years ago, its prevalence in different elephant populations is still largely unknown, partially due to the lack of readily available, sensitive serological assays. In order to improve diagnostic tools for the detection of EEHV infections and to obtain insight in its spread among elephants, we developed novel ELISAs focusing on EEHV1A gB and gH/gL as antigens. Performance of the ELISAs was assessed using sera taken from 41 European zoo elephants and 69 semi-captive elephants from Laos, one of the Asian elephant range countries. Sera from all (sub)adult animals tested (≥5 years of age) showed high reactivity with both gB and gH/gL, whereas reactivity towards the antigens was generally lower for sera of juvenile animals (1 > 5 years). Only one (juvenile) animal, which was sampled directly after succumbing to EEHV-HD, was found to be seronegative for EEHV. The two other EEHV-HD cases tested showed low antibody levels, suggesting that all three cases died upon a primary EEHV infection. Direct comparison with another EEHV-specific ELISA previously used in two large serosurveys, showed that EEHV prevalence was underestimated before, likely due to aberrant folding of the antigen used. In conclusion, our study suggests that essentially all (semi-)captive (sub)adult elephants in European zoos and in Laos carry EEHV, and that young elephants with low antibody levels are at risk of dying from EEHV-HD.ImportanceOver the last 30 years, nearly 20% of all Asian elephants born in Western zoos succumbed to acute hemorrhagic disease caused by elephant endotheliotropic herpesvirus (EEHV-HD). Yet, the prevalence of EEHV in captive and wild elephant populations is still largely unknown, mainly due to the lack of readily available, sensitive serological assays. For this study two highly sensitive EEHV-specific ELISAs were developed. Using these assays, it was shown that nearly all elephants tested were seropositive for EEHV, with highest antibody levels detected in (sub)adult elephants. In contrast, antibody levels in EEHV-HD cases were very low or non-detectable. Lack of antibodies may thus be a risk factor for developing severe disease. As the novel ELISAs are low-tech in nature, these assays may easily be disseminated to local laboratories in zoos and elephant range countries in order to determine EEHV serostatus of individual animals or complete herds and (wild) populations.
A LAMP-based microfluidic chip for rapid detection of pathogen in Cryptococcal meningitis
Authors: Tian Yueru , Zhang Tong , Guo Jian , Lu Huijun , Yao Yuhan , Chen Xi , Zhang Xinlian , Sui Guodong , Guan Ming 
Published: November 2020

AbstractCryptococcal meningitis (CM) is a global threat with significant attributable morbidity and mortality. Information on integrated detection for CM diagnosis is still limited. This is mainly due to the presence of a large polysaccharide capsule and the tough cell wall ofCryptococcus, which makes it difficult to extract nucleic acids on the chip. In this study, we developed a LAMP-based microfluidic chip for rapid detection of pathogen in CM. We adopted 4 duplicate filtration membrane structures to improve target capture and simplify the enrichment process, and combined lyticase digestion and thermal alkaline lysisto optimize the nucleic acid extraction ofCryptococcuson the chip, and selected a portable UVA flashlight to shine the LAMP products to obtain the visual detection results which could be observed by the naked eye. This microfluidic chip, integrating sampleCryptococcusenrichment, nucleic acid extraction and LAMP detection unit, streamlined the operation process and reduced the exposure risk of directly handling cryptococcal samples. It did not require any additional instruments and demonstrated a rapid, reliable, as well as high-efficiency approach. It truly realized the “sample-to-answer” application and could be easily used for clinical cryptococcal prediagnosis.