bluuebunny/crossref_metadata_2025_split huggingface dataset:
NeuroWRAP: integrating, validating, and sharing neurodata analysis workflows
Authors: Bowen Zac , Magnusson Gudjon , Diep Madeline , Ayyangar Ujjwal , Smirnov Aleksandr , Losert Wolfgang 
Published: October 2022

AbstractMultiphoton calcium imaging is one of the most powerful tools in modern neuroscience. However, multiphoton data require significant pre-processing of images and post-processing of extracted signals. As a result, many algorithms and pipelines have been developed for the analysis of multiphoton data, particularly two-photon imaging data. Most current studies use one of several algorithms and pipelines that are published and publicly available, and add customized upstream and downstream analysis elements to fit the needs of individual researchers. The vast differences in algorithm choices, parameter settings, pipeline composition, and data sources combine to make collaboration difficult, and raise questions about the reproducibility and robustness of experimental results. We present our solution, called NeuroWRAP, which is a tool that wraps multiple published algorithms together, and enables integration of custom algorithms. It enables development of collaborative, shareable custom workflows and reproducible data analysis for multiphoton calcium imaging data enabling easy collaboration between researchers. NeuroWRAP implements an approach to evaluate the sensitivity and robustness of the configured pipelines. When this sensitivity analysis is applied to a crucial step of image analysis, cell segmentation, we find a substantial difference between two popular workflows, CaImAn and Suite2p. NeuroWRAP harnesses this difference by introducing consensus analysis, utilizing two workflows in conjunction to significantly increase the trustworthiness and robustness of cell segmentation results.
Variability of the urinary and blood steroid profiles in healthy women
Authors: Moreillon Basile , Salamin Olivier , Krumm Bastien , Iannella Loredana , Molaioni Francesco , Kuuranne Tiia , Nicoli Raul , Saugy Jonas J. , Botrè Francesco , Faiss Raphael 
Published: October 2022

AbstractThe steroidal module of the Athlete Biological Passport (ABP) targets the use of exogenous androgenous anabolic steroids (EAAS) in elite sport by monitoring urinary steroid profiles.Urine and blood samples were collected weekly during two consecutive OCP cycles (8 weeks) in 15 physically active women to investigate the low urinary steroid concentrations and putative confounding effect of OCP.In urine, testosterone (T) and/or epitestosterone (E) were below the limit of quantification of 1 ng/mL in 62% of the samples. Biomarkers’ variability ranged between 31% and 41%, with a significantly lesser variability for ratios (with the exception of T/E (41%)): 20% for androsterone/etiocholanolone (p < 0.001) and 25% for 5α-androstane-3α,17β-diol/5ß-androstane-3α,17β-diol (p < 0.001).In serum, variability for testosterone (T; 24%), androstenedione (A4; 23%), dihydrotestosterone (DHT; 19%) and T/A4 (16%) was significantly lower than urinary biomarkers (p < 0.001). Urinary A/Etio increased by > 18% after the first two weeks (p < 0.05) following blood loss. In contrast, T (0.98 nmol/L during the first week), and T/A4 (0.34 the first week) decreased significantly by more than 25% and 17% (p<0.05), respectively in the following weeks.Our results outline steroidal variations during the OCP cycle highlighting exogenous hormonal preparations as confounder for steroid concentrations in blood. Low steroid levels in urine samples have a clear detrimental impact on the subsequent interpretation of steroidal variations for the ABP. With a greater analytical sensitivity and lesser variability for steroids in serum vs. urine in healthy active women, serum represents a complementary matrix to urine in the ABP steroidal module.
Benefits and costs of a global cooperative surveillance strategy to control trans-boundary crop pathogens
Authors: Radici Andrea , Martinetti Davide , Bevacqua Daniele 
Published: October 2022

AbstractTrans-boundary diseases are extremely complex to control and can cause global socioeconomic damages. In the context of crop protection, surveillance strategies are usually designed according to administrative boundaries. In this study, we investigate to which extent this geographical scale of surveillance is suitable for long-distance dispersed pathogens. We lever on a global epidemic network, presented in a previous work, describing worldwide potential transport ofP. graminis, the causal agent of stem rust of wheat. We conceive two surveillance strategies: “Country-based” and “Cooperative” and we compare their performances, in terms of minimizing the number of sentinels deployed, to achieve given surveillance targets, both at the global and country level. As expected, we find that a “Cooperative” strategy is more efficient at the global scale, and this is particularly true for intermediate targets of surveillance. However, costs and benefits of adopting a “Cooperative” strategy are not equally distributed among countries. Medium size countries in central Europe and Asia are those that would benefit most from a cooperative strategy. On the other hand, Greece and Finland, having a small wheat production but placed in importantPucciniapathways, are those that should deploy, in the global interest, more sentinels than they would place in the national interest. Among the major wheat producers, China is the only country that would have a cost from a cooperative strategy, while India, Russia, United States, France and Ukraine would have the most benefits. It follows that the acknowledgement of these discrepancies could help to achieve general stakeholder support for a global international cooperative surveillance system.
RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches
Authors: Xu Xiaoming , Yin Zekun , Yan Lifeng , Zhang Hao , Xu Borui , Wei Yanjie , Niu Beifang , Schmidt Bertil , Liu Weiguo 
Published: October 2022

AbstractWe present RabbitTClust, a fast and memory-efficient genome clustering tool based on sketch-based distance estimation. Our approach enables efficient processing of large-scale datasets by combining dimensionality reduction techniques with streaming and parallelization on modern multi-core platforms. 113,674 complete bacterial genome sequences (RefSeq: 455 GB in FASTA format) can be clustered within less than 6 minutes and 1,009,738 GenBank assembled bacterial genomes (4.0 TB in FASTA format) within only 34 minutes on a 128-core workstation. Our results further identify 1,269 repetitive genomes (identical nucleotide content) in RefSeq bacterial genomes.
St2cell: Reconstruction of in situ single-cell spatial transcriptomics by integrating high-resolution histological image
Authors: Hou Siyu , Tian Kuan , Yang Sen , Xiang Jinxi , Yang Wei , Zhang Jun , Han Xiao 
Published: October 2022

AbstractSpatially resolved transcriptomics (SRT) has greatly expanded our understanding of the spatial patterns of gene expression in histological tissue sections. However, most currently available platforms could not provide in situ single-cell spatial transcriptomics, limiting their biological applications. Here, to in silico reconstruct SRT at the single-cell resolution, we propose St2cell which combines deep learning-based frameworks with a novel convex quadratic programming (CQP)-based model. St2cell can thoroughly leverage information in high-resolution (HR) histological images, enabling the accurate segmentation of in situ single cells and identification of their transcriptomics. Applying St2cell on various SRT datasets, we demonstrated the reliability of reconstructed transcriptomics. The single-cell resolution provided by our proposed method greatly promoted the detection of elaborate spatial architectures and further facilitated the integration with single-cell RNA-sequencing data. Moreover, in a breast cancer tissue, St2cell identified general spatial structures and co-occurrence patterns of cell types in the tumor microenvironment. St2cell is also computationally efficient and easily accessible, making it a promising tool for SRT studies.
Accurate detection of shared genetic architecture from GWAS summary statistics in the small-sample context
Authors: Willis Thomas W. , Wallace Chris 
Published: October 2022

AbstractAssessment of the genetic similarity between two phenotypes can provide insight into a common genetic aetiology and inform the use of pleiotropy-informed, cross-phenotype analytical methods to identify novel genetic associations. The genetic correlation is a well-known means of quantifying and testing for genetic similarity between traits, but its estimates are subject to comparatively large sampling error. This makes it unsuitable for use in a small-sample context. We discuss the use of a nonparametric test of genetic similarity first introduced by Li et al. for application to GWAS summary statistics. We establish that the null distribution of the test statistic is modelled better by an extreme value distribution than a transformation of the standard exponential distribution as originally recommended by Li and colleagues. We show with simulation studies and real data from GWAS of 18 phenotypes from the UK Biobank that the test is to be preferred for use with small sample sizes, particularly when genetic effects are few and large, outperforming the genetic correlation and another nonparametric statistical test of independence. We find the test suitable for the detection of genetic similarity in the rare disease context.Author summaryThe genome-wide association study (GWAS) is a method used to identify genetic variants which contribute to the risk of developing disease. These genetic variants are frequently shared between conditions, such that the study of the genetic basis of one disease can be informed by knowledge of another, similar disease. This approach can be productive where the disease in question is rare such that a GWAS has less power to associate variants with the disease, but there exist larger GWAS of similar diseases. Existing methods do not measure genetic similarity precisely when patients are few. Here we assess a previously published method of testing for genetic similarity between pairs of diseases using GWAS data, the ‘GPS’ test, against three other methods with the use of real and simulated data. We present a new computational procedure for carrying out the test and show that the GPS test is superior to its comparators in identifying genetic similarity when the sample size is small and when the genetic similarity signal is less strong. Use of the test will enable accurate detection of genetic similarity and the study of rarer conditions using data from better-characterised diseases.
Targeted memory reactivation during post-learning sleep does not enhance motor memory consolidation in older adults
Authors: Nicolas Judith , Carrier Julie , Swinnen Stephan P. , Doyon Julien , Albouy Geneviève , King Bradley R. 
Published: October 2022

AbstractTargeted memory reactivation (TMR) during sleep enhances memory consolidation in young adults by modulating electrophysiological markers of neuroplasticity. Interestingly, older adults exhibit deficits in motor memory consolidation, an impairment that has been linked to age-related degradations in the same sleep features sensitive to TMR. We hypothesized that TMR would enhance consolidation in older adults via the modulation of these markers. Seventeen older participants were trained on a motor task involving two auditory-cued sequences. During a post-learning nap, two auditory cues were played: one associated to a learned (i.e., reactivated) sequence and one control. Performance during two delayed retests did not differ between reactivated and non-reactivated sequences. Moreover, both associated and control sounds modulated brain responses, yet there were no consistent differences between the auditory cue types. Our results collectively demonstrate that older adults do not benefit from specific reactivation of a motor memory trace by an associated auditory cue during post-learning sleep. It is possible, however, that auditory stimulation during post-learning sleep boosts motor memory consolidation in a non-specific manner.
Entropy predicts sensitivity of pseudo-random seeds
Authors: Maier Benjamin Dominik , Sahlin Kristoffer 
Published: October 2022

AbstractIn sequence similarity search applications such as read mapping, it is desired that seeds match between a read and reference in regions with mutations or read errors (seed sensitivity).K-mers are likely the most well-known and used seed construct in bioinformatics, and many studies on,e.g., spacedk-mers aim to improve sensitivity overk-mers. Spacedk-mers are highly sensitive when substitutions largely dominate the mutation rate but quickly deteriorate when indels are present. Recently, we developed a pseudo-random seeding construct, strobemers, which were empirically demonstrated to have high sensitivity also at high indel rates. However, the study lacked a deeper understanding of why. In this study, we demonstrate that a seed’s entropy (randomness) is a good predictor for seed sensitivity. We propose a model to estimate the entropy of a seed and find that seeds with high entropy, according to our model, in most cases have high match sensitivity. We also present three new strobemer seed constructs, mixedstrobes, altstrobes, and multistrobes. We use both simulated and biological data to demonstrate that our new seed constructs improve sequence-matching sensitivity to other strobemers. We implement strobemers into minimap2 and observe slightly faster alignment time and higher accuracy than usingk-mers at various error rates.Our discovered seed randomness-sensitivity relationship explains why some seeds perform better than others, and the relationship provides a framework for designing even more sensitive seeds. In addition, we show that the three new seed constructs are practically useful. Finally, in cases where our entropy model does not predict the observed sensitivity well, we explain why and how to improve the model in future work.
Inferring transmission routes for foot-and-mouth disease virus within a cattle herd using approximate Bayesian computation
Authors: Ellis John , Brown Emma , Colenutt Claire , Schley David , Gubbins Simon 
Published: October 2022

AbstractTo control an outbreak of an infectious disease it is essential to understand the different routes of transmission and how they contribute to the overall spread of the pathogen. With this information, policy makers can choose the most efficient methods of detection and control during an outbreak. Here we demonstrate a method for assessing the contribution of different routes of transmission using approximate Bayesian computation with sequential Monte Carlo sampling (ABC-SMC). We apply this to infer parameters of an individual based model of within-herd transmission of foot-and-mouth disease virus (FMDV), incorporating transmission through direct contact and via environmental contamination. Additionally, we use ABC-SMC for model selection to assess the plausibility of either transmission route alone being responsible for all infections. We show that direct transmission likely contributes the majority of infections during an outbreak of FMD but there is an accumulation of environmental contamination that can cause infections within a farm and also have the potential to spread between farms via fomites.
Aneuploidy in human embryos is associated with a maternal age-independent increase in mitochondrial DNA content and an enrichment of ultra-rare mitochondrial DNA variants
Authors: Ri Maxim , Ree Natalia , Oreshkov Sergey , Tofilo Maria , Zvereva Irina , Kirillova Anastasia , Gunbin Konstantin , Yurov Valerian , Salumets Andres , Woods Dori C. , Khrapko Konstantin , Fellay Jacques , Tilly Jonathan L. , Mazunin Ilya , Popadin Konstantin 
Published: October 2022

ABSTRACTUsing low-coverage, whole-genome sequences of trophectoderm biopsies from 11,610 human blastocyst-stage embryos, we analyzed the relationship between chromosomal abnormalities and mitochondrial (mt) DNA dynamics. Comparing 6,208 aneuploid and 5,402 euploid embryos in cohort studies, we found that mtDNA content in aneuploid embryos was significantly higher than that in euploid embryos. This outcome was confirmed through intrafamilial analyses of embryos with matched parents andin vitrofertilization cycles, and it occurred independent of maternal age. Additional human population-based studies uncovered a higher abundance of ultra-rare mtDNA variants located in never-altered positions in the human population in aneuploid compared to euploid embryos in both cohort- and family-based analyses. This maternal age-independent association of increased mtDNA content and aneuploidy in human embryos may reflect a novel mechanism of purifying selection against potentially deleterious mtDNA variants, which arise from germline or early developmental mtDNA damaging events, that occurs in human embryos prior to implantation.
TWO DISULFIDE-REDUCING PATHWAYS ARE REQUIRED FOR THE MATURATION OF PLASTIDC-TYPE CYTOCHROMES INCHLAMYDOMONAS REINHARDTII
Authors: Das Ankita , Subrahmanian Nitya , Gabilly Stéphane T. , Andrianova Ekaterina P. , Zhulin Igor B. , Motohashi Ken , Hamel Patrice Paul 
Published: October 2022

AbstractIn plastids, conversion of light energy into ATP relies on cytochromef, a key electron carrier with a heme covalently attached to a CXXCH motif. Covalent heme attachment requires reduction of the disulfide bonded CXXCH motif by CCS5 and CCS4, a protein of unknown function. CCS5 receives electrons from the oxido-reductase CCDA at the thylakoid membrane. InChlamydomonas reinhardtii, loss of CCS4 or CCS5 function yields a partial cytochromefassembly defect. Here we report that the Δccs4ccs5double mutant displays a synthetic photosynthetic defect due to a complete loss of holocytochromefassembly, a phenotype that can be chemically corrected by reducing agents. In Δccs4, the CCDA protein accumulation is decreased, indicating that one function of CCS4 is to stabilize CCDA. Dominant suppressor mutations mapping to theCCS4gene were identified in photosynthetic revertants of the Δccs4ccs5mutants. The suppressor mutations correspond to changes in the stroma-facing domain of CCS4 and restore holocytochromefassembly above the residual levels detected in Δccs5. Because disulfide reduction via CCS5 no longer takes place in Δccs5, we hypothesize the suppressor mutations enhance the supply of reducing power independently of CCS5, uncovering the participation of CCS4 in a distinct redox pathway. CCS4-like proteins occur in the green lineage and are related to mitochondrial COX16, a protein involved in a disulfide reducing pathway. We discuss the operation of two pathways controlling the redox status of the heme-binding cysteines of apocytochromefand the possible function of CCS4 as a shared component between the two pathways.Abstract FigureGraphical abstract.The Δccs4ccs5mutant exhibits a photosynthetic growth defect due to a complete loss of cytochromecassembly.Reduction of apocytochromefin the thylakoid lumen requires the provision of reducing power through two different pathways, pathway 1 and 2. CCDA and CCS5, components of pathway 1, deliver electrons from stroma to apocytochromefvia thiol – disulfide exchange. CCS4 is involved in pathway 1 by stabilizing CCDA, but also functions through a CCS5 – independent pathway (pathway 2). In the absence of CCS5, gain – of – function mutations in the C terminus of CCS4 (indicated by a yellow star) enhance the delivery of reducing power either via CCDA or independently of CCDA to yet-to-be-discovered reductases
Anti-glutamatergic effects of three lignan compounds: arctigenin, matairesinol and trachelogenin - An ex vivo study on rat brain slices
Authors: Koech Peter Kiplangat , Jócsák Gergely , Boldizsár Imre , Moldován Kinga , Borbély Sándor , Világi Ildikó , Dobolyi Arpád , Varró Petra 
Published: October 2022

AbstractArctigenin is a bioactive dibenzylbutyrolactone-type lignan exhibiting various pharmacological activities. The neuroprotective effects of arctigenin were demonstrated to be mediated via inhibition of AMPA/KA type glutamate receptors in the somatosensory cortex of the rat brain. The aim of this study was to compare the effects of arctigenin with matairesinol and trachelogenin on synaptic activity inex vivorat brain slices. Arctigenin, matairesinol and trachelogenin were isolated fromArctium lappa, Centaurea scabiosaandCirsium arvense, respectively, and applied on brain slices via perfusion medium at the concentration range of 0.5-40 μM. The effects of the lignans were examined in the CA1 hippocampus and the somatosensory cortex by recording electrically evoked field potentials. Arctigenin and trachelogenin caused a significant dose-dependent decrease in the amplitude of hippocampal population spikes (POPS) and the slope of excitatory postsynaptic potentials (EPSPs), whereas matairesinol (1 μM and 10 μM) decreased EPSP slope but had no effect on POPS amplitude. Trachelogenin effect (0.5 μM, 10 μM, 20 μM) was comparable to arctigenin (1 μM, 20 μM, 40 μM) (p > 0.05). In the neocortex, arctigenin (10 μM, 20 μM) and trachelogenin (10 μM) significantly decreased the amplitude of evoked potential early component, while matairesinol (1 μM and 10 μM) had no significant effect (p>0.05). The results suggest that trachelogenin and arctigenin act via inhibition of AMPA/KA receptors in the brain and trachelogenin has a higher potency than arctigenin. Thus, trachelogenin and arctigenin could serve as lead compounds in the development of alternative neuroprotective drugs.
Human-Sloth Bear (Melursus ursinus) Conflicts in Nawada Forest Division, Nawada, Bihar, India
Authors: Kumar Gourav , Paul Dilip kumar , Kumari Deepa 
Published: October 2022

ABSTRACTSloth bears (Melursus ursinus) are endemic to the Indian subcontinent and frequently come into conflict with human. Both in Rajauli Wildlife Sanctuary(RWLS) and Kauwkol Forest Range (KFR), sand mining operations create heavy noise during the summer for stone crushing which could be the cause of disturbance in the sloth bear territory and sloth bear attacks during the summer and winter. During the study period of 2016 to 2018, a total of 16 sloth bear attacks were incidently reported in various ranges of NFD. There was a marked seasonal variation in human casualties by sloth bear in the study area. Out of 16 cases, highest number of casualties were observed in monsoon (n=8, 50%) as compared to casualties in Summer (n=5, 31.25%) and winter (n=3, 18.75%) season. Most of the attacks were reported during 4.01-8.00 hours (n=6, 37.5%), followed by incidences occurred during evening time, 16.01-20.00 hours (n=4, 25%), 8.01-12.00 hrs (n=3, 18.75%) and 12.01-16.00 (n=2, 12.5%). Moreover, males (n=10) were shown to have a 62 percent attack rate compared to females (n=6; 38 percent). The data also shows that the frequency of attacks on victims engaged in various activities were related to their intensity of usage of specific habitats. It is reported that highest incidences of HSBC occurred when the victims were engaged in NTFP collection (37.5%), followed by victims engaged in walking (25%), farming (18.75%), defection (12.5%) and cattle grazing (6.25%) activities. We recommend education programs among the people to reduce human injury through mitigation techniques.