bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population modeling with machine learning can enhance measures of mental health - Open-Data Replication
Authors: Easley Ty , Chen Ruiqi , Hannon Kayla , Dutt Rosie , Bijsterbosch Janine 
Published: April 2022

AbstractEfforts to predict trait phenotypes based on functional MRI data from large cohorts have been hampered by low prediction accuracy and/or small effect sizes. Although these findings are highly replicable, the small effect sizes are somewhat surprising given the presumed brain basis of phenotypic traits such as neuroticism and fluid intelligence. We aim to replicate previous work and additionally test multiple data manipulations that may improve prediction accuracy by addressing data pollution challenges. Specifically, we added additional fMRI features, averaged the target phenotype across multiple measurements to obtain more accurate estimates of the underlying trait, balanced the target phenotype’s distribution through undersampling of majority scores, and identified data-driven subtypes to investigate the impact of between-participant heterogeneity. Our results replicated prior results from Dadi et a (2021) in a larger sample. Each data manipulation further led to small but consistent improvements in prediction accuracy, which were largely additive when combining multiple data manipulations. Combining data manipulations (i.e., extended fMRI features, averaged target phenotype, balanced target phenotype distribution) led to a three-fold increase in prediction accuracy for fluid intelligence compared to prior work. These findings highlight the benefit of several relatively easy and low-cost data manipulations, which may positively impact future work.
Changing patterns of SARS-CoV-2 infection through Delta and Omicron waves by vaccination status, previous infection and neighbourhood deprivation: A cohort analysis of 2.7M people
Authors: Green Mark A. , Hungerford Daniel J. , Hughes David M. , Garcia-Fiñana Marta , Turtle Lance , Cheyne Christopher , Ashton Matthew , Leeming Gary , Semple Malcolm G. , Singleton Alex , Buchan Iain 
Published: April 2022

AbstractObjectiveTo examine if SARS-CoV-2 infections vary by vaccination status, if an individual had previously tested positive and by neighbourhood socioeconomic deprivation across the Delta and Omicron epidemic waves of SARS-CoV-2.DesignCohort study using electronic health recordsSettingCheshire and Merseyside, England (3rd June 2021 to 1st March 2022)Participants2.7M residentsMain Outcome measureRegistered positive test for SARS-CoV-2ResultsSocial inequalities in registered positive tests were dynamic during the study. Originally higher SARS-CoV-2 rates in the most socioeconomically deprived neighbourhoods changed to being higher in the least deprived neighbourhoods from the 1st September 2021. While the introduction of Omicron initially reset inequalities, they continued to be dynamic and inconsistent. Individuals who were fully vaccinated (two doses) were associated with fewer registered positive tests (e.g., between 1st September and 27th November 2021: (i) individuals engaged in testing – Hazards Ratio (HR) = 0.48, 95% Confidence Intervals (CIs) = 0.47-0.50; (ii) individuals engaged with healthcare - HR = 0.34, 95% CIs = 0.33-0.34). Individuals with a previous registered positive test were also less likely to have a registered positive test (e.g., between 1st September and 27th November 2021: (i) individuals engaged in testing - HR = 0.16, 95% CIs = 0.15-0.18; (ii) individuals engaged with healthcare - HR = 0.14, 95% CIs = 0.13-0.16). However, Omicron is disrupting these associations due to immune escape resulting in smaller effect sizes for both measures.ConclusionsChanging patterns of SARS-CoV-2 infections during the Delta and Omicron waves reveals a dynamic pandemic that continues to affect diverse communities in sometimes unexpected ways.
Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool
Authors: Trébeau Céline , de Monvel Jacques Boutet , Altay Gizem , Tinevez Jean-Yves , Etournay Raphaël 
Published: April 2022

AbstractEfficient tools allowing the extraction of 2D surfaces from 3D-microscopy data are essential for studies aiming to decipher the complex cellular choreography through which epithelium morphogenesis takes place during development. Most existing methods allow for the extraction of a single and smooth manifold of sufficiently high signal intensity and contrast, and usually fail when the surface of interest has a rough topography or when its localization is hampered by other surrounding structures of higher contrast. Multiple surface segmentation entails laborious manual annotations of the various surfaces separately. As automating this task is critical in studies involving tissue-tissue or tissue-matrix interaction, we developed the Zellige software, which allows the extraction of a non-prescribed number of surfaces of varying inclination, contrast, and texture from a 3D image. The tool requires the adjustment of a small set of control parameters, for which we provide an intuitive interface implemented as a Fiji plugin. As a proof of principle of the versatility of Zellige, we demonstrate its performance and robustness on synthetic images and on four different types of biological samples, covering a wide range of biological contexts.
Time series analysis of SARS-CoV-2 genomes and correlations among highly prevalent mutations
Authors: Periwal Neha , Rathod Shravan B. , Sarma Sankritya , Singh Gundeep , Jain Avantika , Barnwal Ravi P. , Srivastava Kinsukh R. , Kaur Baljeet , Arora Pooja , Sood Vikas 
Published: April 2022

AbstractThe efforts of the scientific community to tame the recent SARS-CoV-2 pandemic seems to have been diluted by the emergence of new viral strains. Therefore, it becomes imperative to study and understand the effect of mutations on viral evolution, fitness and pathogenesis. In this regard, we performed a time-series analysis on 59541 SARS-CoV-2 genomic sequences from around the world. These 59541 genomes were grouped according to the months (January 2020-March 2021) based on the collection date. Meta-analysis of this data led us to identify highly significant mutations in viral genomes. Correlation and Hierarchical Clustering of the highly significant mutations led us to the identification of sixteen mutation pairs that were correlated with each other and were present in >30% of the genomes under study. Among these mutation pairs, some of the mutations have been shown to contribute towards the viral replication and fitness suggesting the possible role of other unexplored mutations in viral evolution and pathogenesis. Additionally, we employed various computational tools to investigate the effects of T85I, P323L, and Q57H mutations in Non-structural protein 2 (Nsp2), RNA-dependent RNA polymerase (RdRp) and Open reading frame 3a (ORF3a) respectively. Results show that T85I in Nsp2 and Q57H in ORF3a mutations are deleterious and destabilize the parent protein whereas P323L in RdRp is neutral and has a stabilizing effect. The normalized linear mutual information (nLMI) calculations revealed the significant residue correlation in Nsp2 and ORF3a in contrast to reduce correlation in RdRp protein.
Lichen speciation is sparked by a substrate requirement shift and reproduction mode differentiation
Authors: Kantelinen Annina , Printzen Christian , Poczai Péter , Myllys Leena 
Published: April 2022

SummaryWe show that obligate lignicoles in lichenizedMicareaare predominately asexual whereas most facultative lignicoles reproduce sexually. Our 3 loci phylogenetic analyses (ITS, mtSSU,Mcm7) together with ancestral state reconstruction show that the shift in reproduction mode has evolved independently several times within the group and that facultative and obligate lignicoles are sister species. The analyses support the assumption that the ancestor of these species was a facultative lignicole. We hypotezise that a shift in substrate requirement from bark to wood leads to differentiation in reproduction mode and becomes a driver of speciation. This is the first example of lichenized fungi where reproduction mode is linked to substrate requirement. This is also the first example where such a linkage is demonstrated to spark lichen speciation. Our main hypothesis is that obligate species on dead wood need to colonize new suitable substrata relatively fast and asexual reproduction is more effective a strategy for successful colonization. Our main hypothesis for explaining the discovered phenomenon involves the species’ life cycle: species on decaying wood face a significant challenge because the ecological properties of their substratum change relatively fast. When this happens, species need to colonize new suitable substrata. This may set a time limit, where asexual reproduction is a faster and more effective strategy for successful colonization.
Potential impact of TE-derived sRNA on gene regulation in the grassBrachypodium distachyon
Authors: Wyler Michele , Keller Bettina , Roulin Anne C 
Published: April 2022

AbstractIn plants, the transcriptional and post-transcriptional repression of TEs involved the production of small interfering RNAs (siRNAs) that guide thede novomethylation and transcriptional silencing of TEs. Because siRNAs act via sequence complementarity, they indiscriminately target TEs and possible non-TE transcripts. TEs and their derived siRNAs might thus provide a reservoir for long-distance gene regulation. To test this hypothesis, we infectedBrachypodium distachyonwithMangnaporte oryzae, the agent of Rice Blast. The infection caused the differential expression of multiple TE copies as well as a global change in gene expression. By sequencing the small RNA fraction, we identified TE-derived sRNA that are identical in sequence to motifs contained in the UTR region of differentially expressed genes. Our study opens new avenues of research to further investigate to what extent TEs may serve as a source for in trans gene regulation.
Obstacles to inferring mechanistic similarity using Representational Similarity Analysis
Authors: Dujmović Marin , Bowers Jeffrey S , Adolfi Federico , Malhotra Gaurav 
Published: April 2022

AbstractRepresentational Similarity Analysis (RSA) is an innovative approach used to compare neural representations across individuals, species and computational models. Despite its popularity within neuroscience, psychology and artificial intelligence, this approach has led to difficult-to-reconcile and contradictory findings, particularly when comparing primate visual representations with deep neural networks (DNNs). Here, we demonstrate how such contradictory findings could arise due to incorrect inferences about mechanism when comparing complex systems processing high-dimensional stimuli. In a series of studies comparing computational models, primate cortex and human cortex we find two problematic phenomena: a “mimic effect”, where confounds in stimuli can lead to high RSA-scores between provably dissimilar systems, and a “modulation effect”, where RSA- scores become dependent on stimuli used for testing. Since our results bear on a number of influential findings, we provide recommendations to avoid these pitfalls and sketch a way forward to a more solid science of representation in cognitive systems.
Reduced injury risk links sociality to survival in a group-living primate
Authors: Pavez-Fox Melissa A. , Kimock Clare M. , Rivera-Barreto Nahiri , Negron-Del Valle Josue E. , Phillips Daniel , Ruiz-Lambides Angelina , Snyder-Mackler Noah , Higham James P. , Siracusa Erin R. , Brent Lauren J.N. 
Published: April 2022

AbstractAffiliative social relationships and high social status predict longer lifespans in many mammal species, including humans. Yet, the mechanisms by which these components of sociality influence survival are still largely unknown. Using 10 years of data and over 1000 recorded injuries from a free-ranging population of rhesus macaques (Macaca mulatta), we investigated two possible mechanisms that could underpin the relationship between sociality and survival: sociality (1) reduces injury risk; and/or (2) increases the probability of survival after an injury. We found that sociality can affect an individual’s survival by influencing their risk of injury, but had no effect on the probability of injured individuals dying. Individuals with more affiliative partners experienced fewer injuries compared to less socially integrated. Social status was also associated with lower risk of injury, particularly for older high-ranking individuals. These results represent the first demonstration of a link between social integration and fatal injury risk in a group-living species, and are the first to link social status, injury risk and survival outside of humans. Collectively, our results offer insights into a mechanism that can mediate the well-known benefits of sociality on an individual’s fitness.
Membrane interactions of mitochondrial lipid transfer proteins
Authors: Sadeqi Fereshteh , Stroh Kai , Vache Marian , Riedel Dietmar , Janshoff Andreas , Risselada Herre Jelger , Meinecke Michael 
Published: April 2022

AbstractThe mitochondrial inner membrane is an integral part of the cellular lipid biosynthesis network. Intramitochondrial lipid transfer shuttles specific lipid species between the two mitochondrial membranes. This pathway is facilitated by designated protein complexes in the intermembrane space. A hetero-dimeric complex of Ups1 and Mdm35 has been identified in yeast to transfer phosphatidic acid from the outer to the inner membrane. Here, we define pH and lipid charge dependency of Ups1 membrane interaction. We show that Ups1 interacts with membranes in a membrane curvature dependent manner. Ups1 predominantly binds to membrane domains of positive curvature. Desorption of phosphatidic acid from positively curved membranes is energetically favorable over flat or negatively curved membranes. Hence, our results demonstrate that Ups1 specifically binds to membrane regions where extraction and insertion of lipids is enhanced.
QuasiFlow: a bioinformatic tool for genetic variability analysis from next generation sequencing data
Authors: Seoane Pedro , Díaz-Martínez Luis , Viguera Enrique , Claros M. Gonzalo , Grande-Pérez Ana 
Published: April 2022

ABSTRACTPopulations of RNA and ssDNA viruses within their hosts contain a heterogeneous collection of variant genomes known as quasispecies. Large variability in mitochondrial DNA has also been found within the same organism, drawing an interesting parallel between the two situations. The advent of next-generation sequencing technologies facilitated studying genetic variation, but many open-source bioinformatic tools have to be combined in a non-trivial approach. Here it is presented QuasiFlow, a workflow based on well-stablished software that extracts reliable mutations and recombinations, even at low frequencies (~10-4), provided that at least 250 million nucleotides are analysed. Accurate prediction of mutations and recombinations has been demonstrated with synthetic reads and with in vitro rolling-circle amplification of a plant geminivirus. An in-depth analysis of viral quasispecies was performed and QuasiFlow revealed the coexistence in the plant of three virus genomes and distinct recombinations between some of them. Human mitochondrial variants were also investigated and high level of heteroplasmy (75%) was confirmed, and the relation between low-frequency heteroplasmy (0.1- 0.2%) and some human diseases, regardless of sex, was established. Hence, we propose that QuasiFlow may find use with known and emerging viruses to reveal evolutionary jumps and co-infections, with mitochondrial DNA to detect relevant heteroplasmy would otherwise be elusive, or even in other population studies such as those considering single cell sequencing.
Efficient Permutation-based Genome-wide Association Studies for Normal and Skewed Phenotypic Distributions
Authors: John Maura , Ankenbrand Markus J , Artmann Carolin , Freudenthal Jan A , Korte Arthur , Grimm Dominik G 
Published: April 2022

AbstractMotivationGenome-wide Association Studies (GWAS) are an integral tool for studying the architecture of complex genotype and phenotype relationships. Linear Mixed Models (LMMs) are commonly used to detect associations between genetic markers and the trait of interest, while at the same time allowing to account for population structure and cryptic relatedness. Assumptions of LMMs include a normal distribution of the residuals and that the genetic markers are independent and identically distributed - both assumptions are often violated in real data. Permutation-based methods can help to overcome some of these limitations and provide more realistic thresholds for the discovery of true associations. Still, in practice they are rarely implemented due to its high computational complexity.ResultsWe propose permGWAS, an efficient linear mixed model reformulation based on 4D-tensors that can provide permutation-based significance thresholds. We show that our method outperforms current state-of-the-art LMMs with respect to runtime and that a permutation-based threshold has a lower false discovery rate for skewed phenotypes compared to the commonly used Bonferroni threshold. Furthermore, using permGWAS we re-analysed more than 500 Arabidopsis thaliana phenotypes with 100 permutations each in less than eight days on a single GPU. Our re-analyses suggest that applying a permutation-based threshold can improve and refine the interpretation of GWAS results.AvailabilitypermGWAS is open-source and publicly available on GitHub for download: https://github.com/grimmlab/permGWAS.
Nucleoporins facilitate ORC loading onto chromatin
Authors: Richards Logan , Lord Christopher L. , Benton Mary Lauren , Capra John A. , Nordman Jared T. 
Published: April 2022

SUMMARYThe origin recognition complex (ORC) binds throughout the genome to initiate DNA replication. In metazoans, it is still unclear how ORC is targeted to specific loci to facilitate helicase loading and replication initiation. Here, we performed immunoprecipitations coupled with mass spectrometry for ORC2 in Drosophila embryos. Surprisingly, we found that ORC2 associates with multiple subunits of the Nup107-160 subcomplex of the nuclear pore. Bioinformatic analysis revealed that, relative to all modENCODE factors, nucleoporins are among the most enriched factors at ORC2 binding sites. Critically, depletion of the nucleoporin Elys, a member of the Nup107-160 complex, results in decreased ORC2 loading onto chromatin. Depleting Elys also sensitized cells to replication fork stalling, which could reflect a defect in establishing dormant replication origins. Our work reveals a new connection between ORC, replication initiation and nucleoporins, highlighting a previously unrecognized function of nucleoporins in metazoan replication initiation.
Antibody Resistance of SARS-CoV-2 Omicron BA.1, BA.1.1, BA.2 and BA.3 Sub-lineages
Authors: Ai Jingwen , Wang Xun , He Xinyi , Zhao Xiaoyu , Zhang Yi , Jiang Yuchao , Li Minghui , Cui Yuchen , Chen Yanjia , Qiao Rui , Li Lin , Yang Lulu , Li Yi , Hu Zixin , Zhang Wenhong , Wang Pengfei 
Published: April 2022

AbstractThe SARS-CoV-2 Omicron variant has been partitioned into four sub-lineages designated BA.1, BA.1.1, BA.2 and BA.3, with BA.2 becoming dominant worldwide recently by outcompeting BA.1 and BA.1.1. We and others have reported the striking antibody evasion of BA.1 and BA.2, but side-by-side comparison of susceptibility of all the major Omicron sub-lineages to vaccine-elicited or monoclonal antibody (mAb)-mediated neutralization are urgently needed. Using VSV-based pseudovirus, we found that sera from individuals vaccinated by two doses of inactivated whole-virion vaccines (BBIBP-CorV) showed very weak to no neutralization activity, while a homologous inactivated vaccine booster or a heterologous booster with protein subunit vaccine (ZF2001) markedly improved the neutralization titers against all Omicron variants. The comparison between sub-lineages indicated that BA.1.1, BA.2 and BA.3 had comparable or even greater antibody resistance than BA.1. We further evaluated the neutralization profile of a panel of 20 mAbs, including 10 already authorized or approved, against these Omicron sub-lineages as well as viruses with different Omicron spike single or combined mutations. Most mAbs lost their neutralizing activity completely or substantially, while some demonstrated distinct neutralization patterns among Omicron sub-lineages, reflecting their antigenic difference. Taken together, our results suggest all four Omicron sub-lineages threaten the efficacies of current vaccines and antibody therapeutics, highlighting the importance of vaccine boosters to combat the emerging SARS-CoV-2 variants.
Impact of green human resource practices on hotel environmental performance: the moderating effect of environmental knowledge and individual green values
Authors: Raza Syed Ali , Khan Komal Akram 
Published: April 2022

PurposeGreen management initiatives are an influential factor for forward-thinking corporations across the globe. Human resource (HR) practitioners find incorporating sustainable development into HR practices a significant challenge, but green initiatives enhance environmental quality. This study aims to analyze the impact of green human resources management (GHRM) practices on hotel environmental performance (HEP) by incorporating environmental knowledge (EK) and individual green values (IGV) as a moderator.Design/methodology/approachThe software Smart PLS has been used for data analysis, and partial least square-structural equation modeling has been used to assess measurement and structural models. Data was gathered from 329 white-collar employees of Pakistan’s guest service hotels.FindingsThe results reveal that GHRM practices positively correlate with employees’ affective commitment (EAC) and eco-friendly behavior. Also, employees’ eco-friendly behavior increases HEP, but EAC shows an insignificant association. Moreover, EK does not strengthen the relationship between GHRM practices and EAC and eco-friendly behavior. However, IGV strengthen the relationship between affective commitment and HEP.Practical implicationsThe research suggests that management should embrace GHRM practices for better environmental performance. Hotels should ensure that all GHRM attributes, such as green recruitment, training and compensation, are rightly executed. They can help acquire and retain committed and eco-friendly employees whose environmental values and objectives are compatible with the organization.Originality/valueIt will provide insight into the role of the GHRM in fostering EAC and eco-friendly behavior that, in turn, influence environmental performance. Also, the theory of social identity has been incorporated to inspect employees’ behavior along with the moderating role of EK and IGV. It is crucial to understand two essential aspects in a developing country like Pakistan so that the hospitality sector can implement them efficiently in the future: how hotels protect the environment through their green practices and whether employees of a developing country depict eco-friendly behavior and affective commitment on the basis of GHRM.