bluuebunny/crossref_metadata_2025_split huggingface dataset:
High similarity among ChEC-seq datasets
Authors: Mittal Chitvan , Rossi Matthew J. , Pugh B. Franklin 
Published: February 2021

AbstractChEC-seq is a method used to identify protein-DNA interactions across a genome. It involves fusing micrococcal nuclease (MNase) to a protein of interest. In principle, specific genome-wide interactions of the fusion protein with chromatin result in local DNA cleavages that can be mapped by DNA sequencing. ChEC-seq has been used to draw conclusions about broad gene-specificities of certain protein-DNA interactions. In particular, the transcriptional regulators SAGA, TFIID, and Mediator are reported to generally occupy the promoter/UAS of genes transcribed by RNA polymerase II in yeast. Here we compare published yeast ChEC-seq data performed with a variety of protein fusions across essentially all genes, and find high similarities with negative controls. We conclude that ChEC-seq patterning for SAGA, TFIID, and Mediator differ little from background at most promoter regions, and thus cannot be used to draw conclusions about broad gene specificity of these factors.
Focused X-ray Luminescence Computed Tomography using a Continuous Scanning Scheme
Authors: Lun Michael C. , Fang Yile , Li Changqing 
Published: February 2021

AbstractX-ray luminescence computed tomography (XLCT) imaging is a hybrid molecular imaging modality combining the merits of both conventional x-ray imaging (high spatial resolution) and optical imaging (high measurement sensitivity). The narrow x-ray beam based XLCT imaging has been shown to be promising. However due to the selective excitation scheme, the imaging speed is slow thus limiting its practical applications forin vivoimaging. In this work, we have introduced a continuous scanning scheme to acquire data for each angular projection in one motion, eliminating the previous stepping scheme and reducing the data acquisition time, which makes it feasible for multiple transverse scans for three-dimensional (3D) imaging. We have introduced a high accuracy vertical stage to our focused x-ray beam based XLCT imaging system to perform high-resolution and 3D XLCT imaging. We have also included a scintillator crystal coupled to a PMT to act as a single-pixel detector for boundary detection purposes to replace our previous flat panel x-ray detector. We have verified the feasibility of our proposed scanning scheme and imaging system by performing phantom experimental studies. A phantom was embedded with a set of cylindrical targets with 200 µm edge-to-edge distance and was scanned in our imaging system with the proposed method. To test the feasibility for 3D scanning, we took measurements from 4 transverse slices with a vertical step size of 1 mm. The results of the experiments verified the feasibility of our proposed method to perform 3D XLCT imaging using a narrow x-ray beam in a reasonable time.
Practical selection of representative sets of RNA-seq samples using a hierarchical approach
Authors: Tung Laura H. , Kingsford Carl 
Published: February 2021

AbstractDespite numerous RNA-seq samples available at large databases, most RNA-seq analysis tools are evaluated on a limited number of RNA-seq samples. This drives a need for methods to select a representative subset from all available RNA-seq samples to facilitate comprehensive, unbiased evaluation of bioinformatics tools. In sequence-based approaches for representative set selection (e.g. a k-mer counting approach that selects a subset based on k-mer similarities between RNA-seq samples), because of the huge number of available RNA-seq samples and the large number of k-mers/sequences in each sample, computing the full similarity matrix between all samples using k-mers/sequences for the entire set of RNA-seq samples in a large database (e.g. the SRA) has memory and runtime challenges, making direct representative set selection infeasible with limited computing resources. Therefore, we developed a novel computational method called “hierarchical representative set selection” to handle this challenge. Hierarchical representative set selection is a divide-and-conquer-like algorithm that breaks the representative set selection into sub-selections and hierarchically selects representative samples through multiple levels. We demonstrate that hierarchical representative set selection can achieve performance close to that of direct representative set selection, while largely reducing the runtime and memory requirements of computing the full similarity matrix (up to 8.4X runtime reduction and 4.7X memory reduction for 10000 samples that could be practically run with direct subset selection). We show that hierarchical representative set selection substantially outperforms random sampling on the entire SRA set of RNA-seq samples, making it a practical solution to representative set selection on large databases such as the SRA.
On the robustness of inference of association with the gut microbiota in stool, swab and mucosal tissue samples
Authors: Sun Shan , Zhu Xiangzhu , Huang Xiang , Murff Harvey J. , Ness Reid M. , Seidner Douglas L. , Sorgen Alicia , Blakley Ivory , Yu Chang , Dai Qi , Azcarate-Peril M. Andrea , Shrubsole Martha J. , Fodor Anthony A. 
Published: February 2021

AbstractThe gut microbiota plays an important role in human health and disease. Stool, swab and mucosal tissue samples have been used in individual studies to survey the microbial community but the consequences of using these different sample types are not completely understood. We previously reported differences in microbial community composition with 16S rRNA amplicon sequencing between stool, swab and mucosal tissue samples. Here, we extended the previous study to a larger cohort and performed shotgun metagenome sequencing of 1,397 stool, swab and mucosal tissue samples from 240 participants. Consistent with previous results, taxonomic composition of stool and swab samples was distinct, but still more similar to each other than mucosal tissue samples, which had a substantially different community composition, characterized by a high relative abundance of the mucus metabolizersBacteroidesandSubdoligranulum,as well as bacteria with higher tolerance for oxidative stress such asEscherichia. As has been previously reported, functional profiles were more uniform across sample types than taxonomic profiles with differences between stool and swab samples smaller, but mucosal tissue samples remained distinct from the other two types. When the taxonomic and functional profiles of different sample types were used for inference in association with host phenotypes of age, sex, body mass index (BMI), antibiotics or non-steroidal anti-inflammatory drugs (NSAIDs) use, hypothesis testing using either stool or swab gave broadly similar results, but inference performed on mucosal tissue samples gave results that were generally less consistent with either stool or swab. Our study represents an important resource for the experimental design of studies aimed to understand microbiota perturbations specific to defined micro niches within the human intestinal tract.
SARS-CoV-2 ORF7b: is a bat virus protein homologue a major cause of COVID-19 symptoms?
Authors: Fogeron Marie-Laure , Montserret Roland , Zehnder Johannes , Nguyen Minh-Ha , Dujardin Marie , Brigandat Louis , Cole Laura , Ninot-Pedrosa Marti , Lecoq Lauriane , Meier Beat H , Böckmann Anja 
Published: February 2021

AbstractORF7b is an accessory protein of SARS-CoV-2, the virus behind the COVID-19 pandemic. Using cell-free synthesized ORF7b, we experimentally show that ORF7b assembles into stable multimers. The ORF7b sequence shows a transmembrane segment, which multimerizes through a leucine zipper. We hypothesize that ORF7b has the potential to interfere with important cellular processes that involve leucine-zipper formation, and present two particularly striking examples. First, leucine zippers are central in heart rhythm regulation through multimerization of phospholamban in cardiomyocytes. Second, epithelial cell-cell adhesion relies on E-cadherins, which dimerize using a transmembrane leucine zipper. Most common symptoms of SARS-CoV-2 infection, including heart arrythmias, odor loss, impaired oxygen uptake and intestinal problems, up to multiorgan failure, can be rationalized by a possible interference of ORF7b with the functions of these proteins. We ask whether this is pure coincidence, or whether our observations point to disruption by ORF7b of vital processes in COVID-19.
Caprin-1 binding to the critical stress granule protein G3BP1 is regulated by pH
Authors: Schulte Tim , Panas Marc D. , Williams Lucy , Kedersha Nancy , Fleck Jonas Simon , Tan Timothy J.C. , Olsson Anders , Morro Ainhoa Moliner , Hanke Leo , Nilvebrant Johan , Giang Kim Anh , Nygren Per-Åke , Anderson Paul , Achour Adnane , McInerney Gerald M. 
Published: February 2021

AbstractG3BP is the central hub within the protein-RNA interaction network of stress-induced bio-molecular condensates known as stress granules (SG). The SG-associated proteins Caprin-1 and USP10 exhibit mutually exclusive binding to the structured NTF2-domain of G3BP1, thereby regulating G3BP1-mediated condensation, but with opposite effects: Caprin-1 promotes but USP10 inhibits SG formation. Herein, we present the crystal structure of G3BP1-NTF2 in complex with a Caprin-1 derived short linear motif (SLiM), which provides a molecular understanding for the mutually exclusive binding of USP10 and Caprin-1 to G3BP1. Caprin-1 but not USP10 contacts two G3BP1-NTF2 histidine residues, which was confirmed using biochemical, biophysical and cellular biological binding assays. G3BP1/Caprin-1 interactions disrupted via point mutations resulted in fewer and smaller SG condensates. In addition, biochemical binding assays demonstrated reduced binding of Caprin-1 to G3BP1 at lower pH values. Finally, ratiometric pH sensitive measurements of SGs revealed a substantial drop in pH compared to the adjacent cytosol, suggesting that reduced pH can fine-tune and regulate the G3BP1-mediated interaction network via a NTF2-mediated pH-sensitive SLiM-selection mechanism.
Collaboration between the Fab and Fc contribute to maximal protection against SARS-CoV-2 in nonhuman primates following NVX-CoV2373 subunit vaccine with Matrix-M™ vaccination
Authors: Gorman Matthew J , Patel Nita , Guebre-Xabier Mimi , Zhu Alex , Atyeo Caroline , Pullen Krista M. , Loos Carolin , Goez-Gazi Yenny , Carrion Ricardo , Tian Jing-Hui , Yaun Dansu , Bowman Kathryn , Zhou Bin , Maciejewski Sonia , McGrath Marisa E. , Logue James , Frieman Matthew B. , Montefiori David , Mann Colin , Schendel Sharon , Amanat Fatima , Krammer Florian , Saphire Erica Ollmann , Lauffenburger Douglas , Greene Ann M. , Portnoff Alyse D. , Massare Michael J. , Ellingsworth Larry , Glenn Gregory , Smith Gale , Alter Galit 
Published: February 2021

AbstractRecently approved vaccines have already shown remarkable protection in limiting SARS-CoV-2 associated disease. However, immunologic mechanism(s) of protection, as well as how boosting alters immunity to wildtype and newly emerging strains, remain incompletely understood. Here we deeply profiled the humoral immune response in a cohort of non-human primates immunized with a stable recombinant full-length SARS-CoV-2 spike (S) glycoprotein (NVX-CoV2373) at two dose levels, administered as a single or two-dose regimen with a saponin-based adjuvant Matrix-M™. While antigen dose had some effect on Fc-effector profiles, both antigen dose and boosting significantly altered overall titers, neutralization and Fc-effector profiles, driving unique vaccine-induced antibody fingerprints. Combined differences in antibody effector functions and neutralization were strongly associated with distinct levels of protection in the upper and lower respiratory tract, pointing to the presence of combined, but distinct, compartment-specific neutralization and Fc-mechanisms as key determinants of protective immunity against infection. Moreover, NVX-CoV2373 elicited antibodies functionally target emerging SARS-CoV-2 variants, collectively pointing to the critical collaborative role for Fab and Fc in driving maximal protection against SARS-CoV-2. Collectively, the data presented here suggest that a single dose may prevent disease, but that two doses may be essential to block further transmission of SARS-CoV-2 and emerging variants.HighlightsNVX-CoV2373 subunit vaccine elicits receptor blocking, virus neutralizing antibodies, and Fc-effector functional antibodies.The vaccine protects against respiratory tract infection and virus shedding in non-human primates (NHPs).Both neutralizing and Fc-effector functions contribute to protection, potentially through different mechanisms in the upper and lower respiratory tract.Both macaque and human vaccine-induced antibodies exhibit altered Fc-receptor binding to emerging mutants.
Small in size, big on taste: metabolomics analysis of flavor compounds from Philippine garlic
Authors: Molino Ralph John Emerson J. , Rellin Klidel Fae B. , Nellas Ricky B. , Junio Hiyas A. 
Published: February 2021

AbstractPhilippine garlic (Allium sativum L.) is arguably known to pack flavor and aroma in smaller bulbs compared to imported varieties saturating the local market. In this study, ethanolic extracts of Philippine garlic cultivars were profiled using ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF). γ-Glu dipeptides, oligosaccharides and lipids were determined in Philippine garlic cultivars through bioinformatics analysis in GNPS Molecular Networking Platform and fragmentation analysis. Multivariate statistical analysis using XCMS Online showed the abundance of γ-Glu allyl cysteine in Batanes-sourced garlic while γ-Glu propenyl cysteine, γ-Glu methyl cysteine, and alliin are enriched in the Ilocos cultivar. Principal component analysis showed that the γ-Glu dipeptides found in local garlic influenced their distinct separation across PC1 from imported varieties. This presence of high levels of γ-Glu dipeptides and probiotic oligosaccharides may potentially contribute to the superior flavor and nutritional benefits of Philippine garlic.
The impacts of hydropower on freshwater macroinvertebrate richness: A global meta-analysis
Authors: Trottier Gabrielle , Turgeon Katrine , Boisclair Daniel , Bulle Cécile , Margni Manuele 
Published: February 2021

AbstractHydroelectric dams and their reservoirs have been suggested to affect freshwater biodiversity. However, studies investigating the consequences of hydroelectric dams and reservoirs on macroinvertebrate richness have reached opposite conclusions. We carried out a meta-analysis devised to elucidate the effects of hydropower dams and their reservoirs on macroinvertebrates richness while accounting for the potential role played by moderators such as biomes, impact types, study designs, sampling seasons and gears. We used a random and mixed effect model, combined with robust variance estimation, to conduct the meta-analysis on 72 pairs of observations (i.e., impacted versus reference) extracted from 17 studies (more than one observation per study). We observed a large range of effect sizes, from very negative to very positive impacts of hydropower. However, according to this meta-analysis, hydropower dams and their reservoirs did not have an overall clear, directional and statistically significant effect on macroinvertebrate richness. We tried to account for the large variability in effect sizes using moderators, but none of the moderators included in the meta-analysis had statistically significant effect. This suggests that some other moderators, which were unavailable for the 17 studies included in this meta-analysis, might be important (e.g., temperature, granulometry, wave disturbance and macrophytes) and that macroinvertebrate richness may be driven by local, smaller scale processes. As new studies become available, it would be interesting to keep enriching this meta-analysis, as well as collecting local habitat variables, to see if we could finally draw statistically significant conclusions about the impacts of hydropower on macroinvertebrate richness.
Furin cleavage of the SARS-CoV-2 spike is modulated by O-glycosylation
Authors: Zhang Liping , Mann Matthew , Syed Zulfeqhar , Reynolds Hayley M. , Tian E , Samara Nadine L. , Zeldin Darryl C. , Tabak Lawrence A. , Ten Hagen Kelly G. 
Published: February 2021

AbstractThe SARS-CoV-2 coronavirus responsible for the global pandemic contains a unique furin cleavage site in the spike protein (S) that increases viral infectivity and syncytia formation. Here, we show that O-glycosylation near the furin cleavage site is mediated by specific members of the GALNT enzyme family and is dependent on the novel proline at position 681 (P681). We further demonstrate that O-glycosylation of S decreases furin cleavage. Finally, we show that GALNT family members capable of glycosylating S are expressed in human respiratory cells that are targets for SARS-CoV-2 infection. Our results suggest that O-glycosylation may influence viral infectivity/tropism by modulating furin cleavage of S and provide mechanistic insight into the potential role of P681 mutations in the recently identified, highly transmissible B.1.1.7 variant.
Performance measurement in-fourth party reverse logistics
Authors: Öz Halil Hilmi , Özyörük Bahar 
Published: February 2021

Purpose
This paper aims to develop a performance measurement (PM) system for fourth-party reverse logistics (RL). In this regard, it proposes simultaneous utilization of a procedural approach and hybrid use of existing performance frameworks.

Design/methodology/approach
The paper first describes fundamentals of RL and PM approaches in literature to build a basis for further discussion. It then carries out a systematic review of the literature on PM in RL to highlight current trends and approaches in this regard. At last, it develops a PM system for fourth-party RL by exploring relevant performance frameworks and by defining a procedure in detail.

Findings
The paper identifies the ongoing interest in development PM in RL, and the gap and the need for the development of comprehensive PM system for fourth-party RL. It also identifies the best approach is to use existing performance frameworks in literature and a procedural approach together as they complement each other rather than contradicting.

Research limitations/implications
The paper fills a gap in literature by developing a comprehensive PM framework for the fourth-party RL. The presented procedure is well suited to be used as part of strategic management process in any fourth-party RL organization. It forces users a top-down approach, from strategies to measures, so that a strong linkage is established in the process. When used together with the proposed PM framework, it guarantees a comprehensive and balanced PM system.

Practical implications
The paper identifies the need for the development of a PM framework as well as a measurement system for the fourth-party RL in the literature. In this regard, it develops a PM framework first, and then a procedure on how to implement it. As a result, users can effectively use them as a part of strategic management process of their organizations.

Social implications
The fourth-party RL is growing and very promising mode of RL for well-being of society, by offering a strong path to sustainable development in the midst of diminishing resources in the world. The existence of a well measurement system is crucial for the healthy operations and development of fourth-party RL organizations. The paper is offering a strong PM model in this regard.

Originality/value
The paper fulfills an identified need to study how to develop a PM system for fourth-party RL.
Personality and pace‐of‐life: Ecological lessons learnt from free‐ranging lemon sharks
Authors: Dingemanse Niels J. 
Published: February 2021

AbstractIn Focus: Dhellemmes, F., Finger J.S., Smukall M.J., Gruber S.H., Guttridge T.L., Laskowski K.L., & J. Krause. (2020) Personality‐driven life‐history trade‐offs differ in two subpopulations of free‐ranging predators. Journal of Animal Ecology, 90, 260–272. Life‐history theory predicts that explorative individuals live‐fast‐but‐die‐young as they take risks to rapidly accumulate resources. Dhellemmes et al. (2020) show that fast‐exploring sharks forage in risky habitats, where they grow‐fast‐but‐die‐young. In higher risk environments, however, this personality‐related pace‐of‐life‐syndrome does not exist because neither fast‐ nor slow‐exploring types venture out into risky areas. The study thereby reveals the key role of ecology as a mediator of personality‐related pace‐of‐life‐syndromes in the wild.
Genetic relationship between tetraploids and pentaploids in the agamospermous species Taraxacum albidum Dahlst., clarified by enzyme electrophoresis
Authors: Morita Tatsuyoshi , Misawa Kyoko , Nishino Takako 
Published: February 2021

AbstractIn order to reveal the genetic relationship of tetraploids and pentaploids in the agamospermous species Taraxacum albidum Dahlst., an allozyme study was carried out. Approximately 200 plants putatively identified as T. albidum were collected mainly from the Kyushu Island of Japan, and analyzed by enzyme electrophoresis. Two multilocus genotypes at 14 presumptive loci of nine enzymes, Type A and Type B, were detected. Most of the sample plants showed uniclonal Type A, which corresponds to “T. albidum” as reported in our previous paper. Type B, which is also uniclonal, was found at fewer localities and was clearly different from Type A in the allele composition of pgi‐2 and pgm‐1, as well as in the allele dosage at mdh and sod‐1. By means of flow cytometry and chromosome count, the ploidy levels of Type A and Type B were shown to be pentaploid and tetraploid, respectively. A comparison of the allele composition suggests a hybrid origin of pentaploid T. albidum (Type A) from an unreduced gamete of Type B and a reduced gamete of any diploid Taraxacum species.
Current state of athalassohaline deep‐sea hypersaline anoxic basin research—recommendations for future work and relevance to astrobiology
Authors: Fisher Luke A. , Pontefract Alexandra , M. Som Sanjoy , Carr Christopher E. , Klempay Benjamin , E. Schmidt Britney , S. Bowman Jeff , Bartlett Douglas H. 
Published: February 2021

SummaryDeep‐sea hypersaline anoxic basins (DHABs) are uniquely stratified polyextreme environments generally found in enclosed seas. These environments select for elusive and widely uncharacterized microbes that may be living below the currently recognized window of life on Earth. Still, there is strong evidence of highly specialized active microbial communities in the Kryos, Discovery, and Hephaestus basins located in the Eastern Mediterranean Sea; the only known athalassohaline DHABs. Life is further constrained in these DHABs as near‐saturated concentrations of magnesium chloride significantly reduces water activity (aw) and exerts extreme chaotropic stress, the tendency of a solution to disorder biomolecules. In this review, we provide an overview of microbial adaptations to polyextremes focusing primarily on chaotropicity, summarize current evidence of microbial life within athalassohaline DHABs and describe the difficulties of life detection approaches and sampling within these environments. We also reveal inconsistent measurements of chaotropic activity in the literature highlighting the need for a new methodology. Finally, we generate recommendations for future investigations and discuss the importance of athalassohaline DHAB research to help inform extraterrestrial life detection missions.