bluuebunny/crossref_metadata_2025_split huggingface dataset:
A sparse negative binomial mixture model for clustering RNA-seq count data
Authors: Li Yujia , Rahman Tanbin , Ma Tianzhou , Tang Lu , Tseng George C 
Published: June 2021

SummaryClustering with variable selection is a challenging yet critical task for modern small-n-large-p data. Existing methods based on sparse Gaussian mixture models or sparse $K$-means provide solutions to continuous data. With the prevalence of RNA-seq technology and lack of count data modeling for clustering, the current practice is to normalize count expression data into continuous measures and apply existing models with a Gaussian assumption. In this article, we develop a negative binomial mixture model with lasso or fused lasso gene regularization to cluster samples (small $n$) with high-dimensional gene features (large $p$). A modified EM algorithm and Bayesian information criterion are used for inference and determining tuning parameters. The method is compared with existing methods using extensive simulations and two real transcriptomic applications in rat brain and breast cancer studies. The result shows the superior performance of the proposed count data model in clustering accuracy, feature selection, and biological interpretation in pathways.
Exploratory Study of the Resettlement Experiences of Burmese Refugees Children in the USA
Authors: Tonsing Jenny C 
Published: June 2021

Abstract
The purpose of this study is to explore the educational and resettlement experiences of Burmese refugee children in the USA. Transition and migration in itself are a difficult task for refugees due to the demands associated with adjustment to a new way of life in a different environment, and even more so for children, as the events co-occur with the developmental changes they experience. The study has employed qualitative research methods in the form of in-depth interviews to examine the subjective experiences of the participants. Using the purposive sampling method, twenty-eight Burmese refugee children participated in a one-on-one in-depth interview. Respondents ranged in age from ten to seventeen years, with the majority being girls (53.6 per cent). The average length of time in the USA was 5.8 years. Analysis of the data revealed three key themes that relate to school experience, bi-cultural dynamics and changing role expectations, and future hopes and aspirations. Implications for practice and future research are discussed.
Response Inhibitory Control Varies with Different Sensory Modalities
Authors: Ikarashi Koyuki , Sato Daisuke , Fujimoto Tomomi , Edama Mutsuaki , Baba Yasuhiro , Yamashiro Koya 
Published: June 2021

AbstractResponse inhibition plays an essential role in preventing anticipated and unpredictable events in our daily lives. It is divided into proactive inhibition, where subjects postpone responses to an upcoming signal, and reactive inhibition, where subjects stop an impending movement based on the presentation of a signal. Different types of sensory input are involved in both inhibitions; however, differences in proactive and reactive inhibition with differences in sensory modalities remain unclear. This study compared proactive and reactive inhibitions induced by visual, auditory, and somatosensory signals using the choice reaction task (CRT) and stop-signal task (SST). The experiments showed that proactive inhibitions were significantly higher in the auditory and somatosensory modalities than in the visual modality, whereas reactive inhibitions were not. Examining the proactive inhibition-associated neural processing, the auditory and somatosensory modalities showed significant decreases in P3 amplitudes in Go signal-locked event-related potentials (ERPs) in SST relative to those in CRT; this might reflect a decreasing attentional resource on response execution in SST in both modalities. In contrast, we did not find significant differences in the reactive inhibition-associated ERPs. These results suggest that proactive inhibition varies with different sensory modalities, whereas reactive inhibition does not.
Evaluating corticosterone as a biomarker for amphibians exposed to increased salinity and ambient corticosterone
Authors: Tornabene Brian J , Hossack Blake R , Crespi Erica J , Breuner Creagh W 
Published: June 2021

Abstract
Physiological biomarkers are commonly used to assess the health of taxa exposed to natural and anthropogenic stressors. Glucocorticoid (GC) hormones are often used as indicators of physiological stress in wildlife because they affect growth, reproduction and survival. Increased salinity from human activities negatively influences amphibians and their corticosterone (CORT; the main amphibian GC) physiology; therefore, CORT could be a useful biomarker. We evaluated whether waterborne CORT could serve as a biomarker of salt stress for three free-living amphibian species that vary in their sensitivity to salinity: boreal chorus frogs (Pseudacris maculata), northern leopard frogs (Rana pipiens) and barred tiger salamanders (Ambystoma mavortium). Across a gradient of contamination from energy-related saline wastewaters, we tested the effects of salinity on baseline and stress-induced waterborne CORT of larvae. Stress-induced, but not baseline, CORT of leopard frogs increased with increasing salinity. Salinity was not associated with baseline or stress-induced CORT of chorus frogs or tiger salamanders. Associations between CORT and salinity were also not related to species-specific sensitivities to salinity. However, we detected background environmental CORT (ambient CORT) in all wetlands and spatial variation was high within and among wetlands. Higher ambient CORT was associated with lower waterborne CORT of larvae in wetlands. Therefore, ambient CORT likely confounded associations between waterborne CORT and salinity in our analysis and possibly influenced physiology of larvae. We hypothesize that larvae may passively take up CORT from their environment and downregulate endogenous CORT. Although effects of some hormones (e.g. oestrogen) and endocrine disruptors on aquatic organisms are well described, studies investigating the occurrence and effects of ambient CORT are limited. We provide suggestions to improve collection methods, reduce variability and avoid confounding effects of ambient CORT. By making changes to methodology, waterborne CORT could still be a promising, non-invasive conservation tool to evaluate effects of salinity on amphibians.
Comparison of recent ceramide-based coronary risk prediction scores in cardiovascular disease patients
Authors: Leiherer Andreas , Mündlein Axel , Laaksonen Reijo , Lääperi Mitja , Jylhä Antti , Fraunberger Peter , Drexel Heinz 
Published: June 2021

AbstractAimCholesterol-based risk prediction is often insufficient in cardiovascular disease (CVD) patients. Ceramides are a new kind of biomarkers for CVD. The Coronary Event Risk Test (CERT) is a validated cardiovascular risk predictor that uses only circulating ceramide levels, determined by coupled liquid chromatography–mass spectrometry, to allocate patients into one of four risk categories. This test has recently been modified (CERT2) by additionally including phosphatidylcholine levels.Methods and resultsIn this observational cohort study, we have recruited 999 Austrian patients with CVD and followed them for up to 13 years. We found that CERT and CERT2 both predicted cardiovascular events, cardiovascular mortality, and overall mortality. CERT2 had the higher performance compared to CERT and also to the recent cardiovascular risk score of the ESC/EAS guidelines (Systematic COronary Risk Evaluation (SCORE)) for low-risk European countries. Combining CERT2 with the ESC/EAS-SCORE, predictive capacity was further increased leading to a hazard ratio of 3.58 (2.02–6.36; P &lt; 0.001) for cardiovascular events, 11.60 (2.72–49.56; P = 0.001) for cardiovascular mortality, and 9.86 (4.23–22.99; P &lt; 0.001) for overall mortality when patients with very high risk (category 4) were compared to those with low risk (category 1). The use of the combined score instead of the ESC/EAS-SCORE significantly improved the predictive power according to the integrated discrimination improvement index (P = 0.004).ConclusionWe conclude that CERT and CERT2 are powerful predictors of cardiovascular events, cardiovascular mortality, and overall mortality in CVD patients. Including phosphatidylcholine to a ceramide-based score increases the predictive performance and is best in combination with classical risk factors as used in the ESC/EAS-SCORE.
Evidence for nutrient-dependent regulation of the COPII coat by O-GlcNAcylation
Authors: Bisnett Brittany J , Condon Brett M , Linhart Noah A , Lamb Caitlin H , Huynh Duc T , Bai Jingyi , Smith Timothy J , Hu Jimin , Georgiou George R , Boyce Michael 
Published: June 2021

AbstractO-linked β-N-acetylglucosamine (O-GlcNAc) is a dynamic form of intracellular glycosylation common in animals, plants and other organisms. O-GlcNAcylation is essential in mammalian cells and is dysregulated in myriad human diseases, such as cancer, neurodegeneration and metabolic syndrome. Despite this pathophysiological significance, key aspects of O-GlcNAc signaling remain incompletely understood, including its impact on fundamental cell biological processes. Here, we investigate the role of O-GlcNAcylation in the coat protein II complex (COPII), a system universally conserved in eukaryotes that mediates anterograde vesicle trafficking from the endoplasmic reticulum. We identify new O-GlcNAcylation sites on Sec24C, Sec24D and Sec31A, core components of the COPII system, and provide evidence for potential nutrient-sensitive pathway regulation through site-specific glycosylation. Our work suggests a new connection between metabolism and trafficking through the conduit of COPII protein O-GlcNAcylation.
Karyopherin-βs play a key role as a phase separation regulator
Authors: Yoshizawa Takuya , Guo Lin 
Published: June 2021

AbstractRecent studies have revealed that cells utilize liquid–liquid phase separation (LLPS) as a mechanism in assembly of membrane-less organelles, such as RNP granules. The nucleus is a well-known membrane-bound organelle surrounded by the nuclear envelope; the nuclear pore complex on the nuclear envelope likely applies LLPS in the central channel to facilitate selective biological macromolecule exchange. Karyopherin-β family proteins exclusively pass through the central channel with cargos by dissolving the phase separated hydrogel formed by the phenylalanine-glycine (FG) repeats-containing nucleoporins. Karyopherin-βs also exhibit dissolution activity for the phase separation of cargo proteins. Many cargos, including RNA-binding proteins containing intrinsically disordered regions (IDRs), undergo phase separation; however, aberrant phase separation is linked to fatal neurodegenerative diseases. Multiple weak interactions between karyopherin-βs and phase separation-prone proteins, such as FG repeats-containing nucleoporins or IDR-containing karyopherin-β cargos, are likely to be important for passing through the nuclear pore complex and maintaining the soluble state of cargo, respectively. In this review, we discuss how karyopherin-βs regulate phase separation to function.
Fragments of Quasi-Nelson: The Algebraizable Core
Authors: Rivieccio Umberto 
Published: June 2021

Abstract
This is the second of a series of papers that investigate fragments of quasi-Nelson logic (QNL) from an algebraic logic standpoint. QNL, recently introduced as a common generalization of intuitionistic and Nelson’s constructive logic with strong negation, is the axiomatic extension of the substructural logic $FL_{ew}$ (full Lambek calculus with exchange and weakening) by the Nelson axiom. The algebraic counterpart of QNL (quasi-Nelson algebras) is a class of commutative integral residuated lattices (a.k.a. $FL_{ew}$-algebras) that includes both Heyting and Nelson algebras and can be characterized algebraically in several alternative ways. The present paper focuses on the algebraic counterpart (a class we dub quasi-Nelson implication algebras, QNI-algebras) of the implication–negation fragment of QNL, corresponding to the connectives that witness the algebraizability of QNL. We recall the main known results on QNI-algebras and establish a number of new ones. Among these, we show that QNI-algebras form a congruence-distributive variety (Cor. 3.15) that enjoys equationally definable principal congruences and the strong congruence extension property (Prop. 3.16); we also characterize the subdirectly irreducible QNI-algebras in terms of the underlying poset structure (Thm. 4.23). Most of these results are obtained thanks to twist representations for QNI-algebras, which generalize the known ones for Nelson and quasi-Nelson algebras; we further introduce a Hilbert-style calculus that is algebraizable and has the variety of QNI-algebras as its equivalent algebraic semantics.
Root mass carbon costs to acquire nitrogen are determined by nitrogen and light availability in two species with different nitrogen acquisition strategies
Authors: Perkowski Evan A , Waring Elizabeth F , Smith Nicholas G 
Published: June 2021

Abstract
Plant nitrogen acquisition requires carbon to be allocated belowground to build roots and sustain microbial associations. This carbon cost to acquire nitrogen varies by nitrogen acquisition strategy; however, the degree to which these costs vary due to nitrogen availability or demand has not been well tested under controlled conditions. We grew a species capable of forming associations with nitrogen-fixing bacteria (Glycine max) and a species not capable of forming such associations (Gossypium hirsutum) under four soil nitrogen levels to manipulate nitrogen availability and four light levels to manipulate nitrogen demand in a full-factorial greenhouse experiment. We quantified carbon costs to acquire nitrogen as the ratio of total root carbon to whole-plant nitrogen within each treatment combination. In both species, light availability increased carbon costs due to a larger increase in root carbon than whole-plant nitrogen, while nitrogen fertilization generally decreased carbon costs due to a larger increase in whole-plant nitrogen than root carbon. Nodulation data indicated that G. max shifted relative carbon allocation from nitrogen fixation to direct uptake with increased nitrogen fertilization. These findings suggest that carbon costs to acquire nitrogen are modified by changes in light and nitrogen availability in species with and without associations with nitrogen-fixing bacteria.
Particle diffusion and acceleration in magnetorotational instability turbulence
Authors: Sun Xiaochen , Bai Xue-Ning 
Published: June 2021

ABSTRACT
Hot accretion flows contain collisionless plasmas that are believed to be capable of accelerating particles to very high energies, as a result of turbulence generated by the magnetorotational instability (MRI). We conduct unstratified shearing-box simulations of the MRI turbulence in ideal magnetohydrodynamic (MHD), and inject energetic relativistic test particles in simulation snapshots to conduct a detailed investigation on particle diffusion and stochastic acceleration. We consider different amount of net vertical magnetic flux, with sufficiently high resolution to resolve the gyro-radii (Rg) of most particles. Particles with large Rg (≳ 0.03 disc scale height H) show spatial diffusion coefficients of ∼30 and ∼5 times Bohm values in the azimuthal and poloidal directions, respectively. We further measure particle momentum diffusion coefficient D(p) by applying the Fokker–Planck equation, finding that contribution from turbulent fluctuations scales as D(p) ∝ p, and shear acceleration takes over when Rg ≳ 0.1H, characterized by D(p) ∝ p3. For particles with smaller Rg (≲ 0.03H), their spatial diffusion coefficients roughly scale as ∼p−1, and show evidence of D(p) ∝ p2 scaling in momentum diffusion but with large uncertainties. We find that multiple effects contribute to stochastic acceleration/deceleration, and the process is likely affected by intermittency in the MRI turbulence. We also discuss the potential of accelerating PeV cosmic rays in hot accretion flows around supermassive black holes.
Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination
Authors: Elkrewi Marwan , Moldovan Mikhail A , Picard Marion A L , Vicoso Beatriz 
Published: June 2021

Abstract
Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group.
Keywords: sex chromosomes, evolutionary strata, W-linked gene, sex determining gene, schistosome parasites.
Molecular characterization of both transesterification reactions of the group II intron circularization pathway
Authors: LaRoche-Johnston Félix , Monat Caroline , Verreault Erika , Cousineau Benoit 
Published: June 2021

Abstract
Group II introns can self-splice from RNA transcripts through branching, hydrolysis and circularization, being released as lariats, linear introns and circles, respectively. In contrast to branching, the circularization pathway is mostly based on assumptions and has been largely overlooked. Here, we address the molecular details of both transesterification reactions of the group II intron circularization pathway in vivo. We show that free E1 is recruited by the intron through base pairing interactions and that released intron circles can generate free E1 by the spliced exon reopening reaction. The first transesterification reaction was found to be induced inaccurately by the 3′OH of the terminal residue of free E1 at the 3′ splice site, producing circularization intermediates with heterogeneous 3′ ends. Nevertheless, specific terminal 3′OH, selected by a molecular ruler, was shown to precisely attack the 5′ splice site and release intron circles with 3′–5′ rather than 2′–5′ bonds at their circularization junction. Our work supports a circularization model where the recruitment of free E1 and/or displacement of cis-E1 induce a conformational change of the intron active site from the pre-5′ to the pre-3′ splice site processing conformation, suggesting how circularization might initiate at the 3′ instead of the 5′ splice site.
Detrital Chromite from Jack Hills, Western Australia: Signatures of Metamorphism and Constraints on Provenance
Authors: Staddon Leanne G , Parkinson Ian J , Cavosie Aaron J , Elliott Tim , Valley John W , Fournelle John , Kemp Anthony I S , Shirey Steven B 
Published: June 2021

Abstract
Detrital chromites are commonly reported within Archean metasedimentary rocks, but have thus far garnered little attention for use in provenance studies. Systematic variations of Cr–Fe spinel mineral chemistry with changing tectonic setting have resulted in the extensive use of chromite as a petrogenetic indicator, and so detrital chromites represent good candidates to investigate the petrogenesis of eroded Archean mafic and ultramafic crust. Here, we report the compositions of detrital chromites within fuchsitic (Cr-muscovite rich) metasedimentary rocks from the Jack Hills, situated within the Narryer Terrane, Yilgarn Craton, Western Australia, which are geologically renowned for hosting Hadean (&gt;4000 Ma) zircons. We highlight signatures of metamorphism, including highly elevated ZnO and MnO, coupled with lowered Mg# in comparison with magmatic chromites, development of pitted domains, and replacement of primary inclusions by phases that are part of the metamorphic assemblages within host metasedimentary rocks. Oxygen isotope compositions of detrital chromites record variable exchange with host metasedimentary rocks. The variability of metamorphic signatures between chromites sampled only meters apart further indicates that modification occurred in situ by interaction of detrital chromites with metamorphic fluids and secondary mineral assemblages. Alteration probably occurred during upper greenschist to lower amphibolite facies metamorphism and deformation of host metasedimentary rocks at ∼2650 Ma. Regardless of metamorphic signatures, sampling location or grain shape, chromite cores yield a consistent range in Cr#. Although other key petrogenetic indices, such as Fe2O3 and TiO2 contents, are complicated in Jack Hills chromites by mineral non-stoichiometry and secondary mobility within metasedimentary rocks, we demonstrate that the Cr# of chromite yields significant insights into their provenance. Importantly, moderate Cr# (typically 55–70) precludes a komatiitic origin for the bulk of chromites, reflecting a dearth of komatiites and intrusive equivalents within the erosional catchment of the Jack Hills metasedimentary units. We suggest that the Cr# of Jack Hills chromite fits well with chromites derived from layered intrusions, and that a single layered intrusion may account for the observed chemical compositions of Jack Hills detrital chromites. Where detailed characterization of key metamorphic signatures is undertaken, detrital chromites preserved within Archean metasedimentary rocks may therefore yield valuable information on the petrogenesis and geodynamic setting of poorly preserved mafic and ultramafic crust.