bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disruption of Hepatic Mitochondrial Pyruvate and Amino Acid Metabolism Impairs Gluconeogenesis and Endurance Exercise Capacity in Mice
Authors: Martino Michael R. , Habibi Mohammad , Ferguson Daniel , Brookheart Rita T. , Thyfault John P. , Meyer Gretchen A. , Lantier Louise , Hughey Curtis C. , Finck Brian N. 
Published: August 2023

ABSTRACTExercise robustly increases the glucose demands of skeletal muscle. This demand is met not only by muscle glycogenolysis, but also by accelerated liver glucose production from hepatic glycogenolysis and gluconeogenesis to fuel mechanical work and prevent hypoglycemia during exercise. Hepatic gluconeogenesis during exercise is dependent on highly coordinated responses within and between muscle and liver. Specifically, exercise increases the rate at which gluconeogenic precursors such as pyruvate/lactate or amino acids are delivered from muscle to the liver, extracted by the liver, and channeled into glucose. Herein, we examined the effects of interrupting gluconeogenic efficiency and capacity on exercise performance by deleting hepatic mitochondrial pyruvate carrier 2 (MPC2) and/or alanine transaminase 2 (ALT2) in mice. We found that deletion of MPC2 or ALT2 alone did not significantly affect time to exhaustion or post-exercise glucose concentrations in treadmill exercise tests, but mice lacking both MPC2 and ALT2 in liver (DKO) reached exhaustion faster and exhibited lower circulating glucose during and after exercise. Use of ²H/¹³C metabolic flux analyses demonstrated that DKO mice exhibited lower endogenous glucose production owing to decreased glycogenolysis and gluconeogenesis at rest and during exercise. The decreased gluconeogenesis was accompanied by lower anaplerotic, cataplerotic, and TCA cycle fluxes. Collectively, these findings demonstrate that the transition of the liver to the gluconeogenic mode is critical for preventing hypoglycemia and sustaining performance during exercise. The results also illustrate the need for interorgan crosstalk during exercise as described by the Cahill and Cori cycles.
The genome of a globally invasive passerine, the common myna (Acridotheres tristis)
Authors: Stuart Katarina C. , Johnson Rebecca N. , Major Richard , Atsawawaranunt Kamolphat , Ewart Kyle M. , Rollins Lee A. , Santure Anna W. , Whibley Annabel 
Published: August 2023

AbstractIn an era of global climate change and massive environmental disturbance, biodiversity conservation is receiving increased attention. Conservation efforts are being greatly aided by genetic tools and approaches, which seek to understand patterns of genetic diversity and how they impact species health and ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions around adaptive potential, with a particular focus on how changes in genetic diversity and effective population size interact with the novel selection regime of the invaded range to drive rapid evolution. The common myna (Acridotheres tristis) is a globally invasive passerine, which has undergone multiple concurrent and sequential bottlenecks across its globally invasive range, and yet has established itself across a diverse array of ecological conditions. It is therefore an excellent model species for research both into the persistence of low-diversity populations and the mechanics of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna, assembled using a backbone of Oxford Nanopore Technologies long reads, alongside an RNA-seq based transcriptome and genome annotation. To provide genomic context for future studies, we describe the genomic landscape of this species, including genome wide allelic diversity, methylation, repeats, and recombination rate, as well as an examination of gene family expansions and contractions. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, but also reveal artefactual impacts of genetic bottlenecks on demographic analysis.
Evaluating single-cell variability in proteasomal decay
Authors: Das Sukanya , Singh Abhyudai , Shah Premal 
Published: August 2023

AbstractGene expression is a stochastic process that leads to variability in mRNA and protein abundances even within an isogenic population of cells grown in the same environment. This variation, often called gene-expression noise, has typically been attributed to transcriptional and translational processes while ignoring the contributions of protein decay variability across cells. Here we estimate the single-cell protein decay rates of two degron GFPs inSaccharomyces cerevisiaeusing time-lapse microscopy. We find substantial cell-to-cell variability in the decay rates of the degron GFPs. We evaluate cellular features that explain the variability in the proteasomal decay and find that the amount of 20s catalytic beta subunit of the proteasome marginally explains the observed variability in the degron GFP half-lives. We propose alternate hypotheses that might explain the observed variability in the decay of the two degron GFPs. Overall, our study highlights the importance of studying the kinetics of the decay process at single-cell resolution and that decay rates vary at the single-cell level, and that the decay process is stochastic. A complex model of decay dynamics must be included when modeling stochastic gene expression to estimate gene expression noise.
The resting and ligand-bound states of the membrane-embedded human T-cell receptor–CD3 complex
Authors: Notti Ryan Q. , Yi Fei , Heissel Søren , Bush Martin W. , Molvi Zaki , Das Pujita , Molina Henrik , Klebanoff Christopher A. , Walz Thomas 
Published: August 2023

AbstractThe T-cell receptor (TCR) initiates T-lymphocyte activation, but mechanistic questions remain(1–4). Here, we present cryogenic electron microscopy structures for the unliganded and human leukocyte antigen (HLA)-bound human TCR–CD3 complex in nanodiscs that provide a native-like lipid environment. Distinct from the “open and extended” conformation seen in detergent(5–8), the unliganded TCR–CD3 in nanodiscs adopts two related “closed and compacted” conformations that represent its physiologic resting statein vivo. By contrast, the HLA-bound complex adopts the open and extended conformation, and conformation-locking disulfide mutants show that ectodomain opening is necessary for maximal ligand-dependent T-cell activation. Together, these results reveal allosteric conformational change during TCR activation and highlight the importance of native-like lipid environments for membrane protein structure determination.
Spectral decomposition unlocks ascidian morphogenesis
Authors: Dokmegang Joel , Faure Emmanuel , Lemaire Patrick , Munro Ed , Mani Madhav 
Published: August 2023

AbstractDescribing morphogenesis generally consists in aggregating the multiple high resolution spatiotemporal processes involved into reproducible low dimensional morphological processes consistent across individuals of the same species or group. In order to achieve this goal, biologists often have to submit movies issued from live imaging of developing embryos either to a qualitative analysis or to basic statistical analysis. These approaches, however, present noticeable drawbacks, as they can be time consuming, hence unfit for scale, and often lack standardisation and a firm foundation. In this work, we leverage the power of a continuum mechanics approach and flexibility of spectral decompositions to propose a standardised framework for automatic detection and timing of morphological processes. First, we quantify whole-embryo scale shape changes in developing ascidian embryos by statistically estimating the strain-rate tensor field of its time-evolving surface without the requirement of cellular segmentation and tracking. We then apply to this data spectral decomposition in space using spherical harmonics and in time using wavelets transforms. These transformations result in the identification of the principal dynamical modes of ascidian embryogenesis and the automatic unveiling of its blueprint in the form of scalograms that tell the story of development in ascidian embryos.
Pharmaceutical pollution alters the cost of bacterial infection and its relationship to pathogen load
Authors: Aulsebrook Lucinda C. , Wong Bob B.M. , Hall Matthew D. 
Published: August 2023

AbstractThe relationship between pathogen proliferation and the cost of infection experienced by a host drives the ecology and evolution of host-pathogen dynamics. While environmental factors can shape this relationship, there is currently limited knowledge on the consequences of emerging contaminants, such as pharmaceutical pollutants, for the commonly observed trade-off between a pathogen’s growth within the host and the damage it causes, termed its virulence. Here, we investigated how exposure to fluoxetine (Prozac), a commonly detected psychoactive pollutant, could alter this key relationship using the water fleaDaphnia magnaand its bacterial pathogenPasteuria ramosaas a model system. Across a variety of fluoxetine concentrations, we found that fluoxetine shaped the damage a pathogen caused, such as the reduction in fecundity or intrinsic growth experienced by infected individuals, but with minimal change in average pathogen spore loads. Instead, fluoxetine modified the relationship between the degree of pathogen proliferation and its virulence, with both the strength of this trade-off and the component of host fitness most affected varying by fluoxetine concentration and host genotype. Our study underscores the potential for pharmaceutical pollution to modify the virulence of an invading pathogen, as well as the fundamental trade-off between host and pathogen fitness, even at the trace amounts increasingly found in natural waterways.
Unravelling cancer subtype-specific driver genes in single-cell transcriptomics data with CSDGI
Authors: Huang Meng , Ma Jiangtao , An Guangqi , Ye Xiucai 
Published: August 2023

AbstractCancer is known as a heterogeneous disease.Cancerdrivergenes (CDGs) need to be inferred for understanding tumor heterogeneity in cancer. However, the existing computational methods have identified many common CDGs. A key challenge exploring cancer progression is to infer cancer subtype-specific driver genes (CSDGs), which provides guidane for the diagnosis, treatment and prognosis of cancer. The significant advancements in single-cell RNA-sequencing (scRNA-seq) technologies have opened up new possibilities for studying human cancers at the individual cell level. In this study, we develop a novel unsupervised method,CSDGI(CancerSubtype-specificDriverGeneInference), which applies Encoder-Decoder-Framework consisting of low-rank residual neural networks to inferring driver genes corresponding to potential cancer subtypes at single-cell level. To infer CSDGs, we applyCSDGIto the tumor single-cell transcriptomics data. To filter the redundant genes before driver gene inference, we perform the differential expression genes (DEGs). The experimental results demonstrateCSDGIis effective to infer driver genes that are cancer subtype-specific. Functional and disease enrichment analysis shows these inferred CSDGs indicate the key biological processes and disease pathways.CSDGIis the first method to explore cancer driver genes at the cancer subtype level. We believe that it can be a useful method to understand the mechanisms of cell transformation driving tumours.Author summaryCancer is recognized as a complex disease with diverse characteristics. In order to comprehend the diversity within tumors, it is essential to infer cancer subtype-specific driver genes (CSDGs), which offer valuable insights for investigating cancer progression and treatment. The remarkable progress made in single-cell RNA-sequencing (scRNA-seq) technologies has ushered in new prospects for studying human cancers at the cellular level. Cancer Subtype-specific Driver Gene Inference (CSDGI) is a novel unsupervised method proposed. In our study, we use Encoder-Decoder-Framework to infer driver genes specific to cancer subtypes in the CSDGI. We apply CSDGI to three tumor single-cell transcriptomics data. The experimental results have shown the effectiveness of CSDGI. Furthermore, functional and disease enrichment analyses illustrate that these inferred CSDGs shed light on crucial biological processes and disease pathways. Our collection of driver genes will serve as a valuable resource in unraveling the mechanisms driving cell transformation in tumors.
Targeted mutagenesis of Medicago truncatula Nodule-specific Cysteine-rich (NCR) genes using the Agrobacterium rhizogenes-mediated CRISPR/Cas9 system
Authors: Güngör Berivan , Biró János Barnabás , Domonkos Ágota , Horváth Beatrix , Kaló Péter 
Published: August 2023

AbstractThe host-produced nodule specific cysteine-rich (NCR) peptides control the terminal differentiation of endosymbiotic rhizobia in the nodules of IRLC legumes. Although the Medicago truncatula genome encodes about 700 NCR peptides, only few of them have been proved to be crucial for nitrogen-fixing symbiosis. In this study, we applied the CRISPR/Cas9 gene editing technology to generate knock-out mutants of NCR genes for which no genetic or functional data were previously available. We have developed a workflow to analyse the mutation and the symbiotic phenotype of individual nodules formed on Agrobacterium rhizogenes-mediated transgenic hairy roots. The selected NCR genes were successfully edited by the CRISPR/Cas9 system and nodules formed on knockout hairy roots showed wild type phenotype indicating that peptides NCR068, NCR089, NCR128 and NCR161 are not essential for symbiosis between M. truncatula Jemalong and Sinorhizobium medicae WSM419. We regenerated stable mutants edited for the NCR068 from hairy roots obtained from A. rhizogenes-mediated transformation. The analysis of the symbiotic phenotype of stable ncr068 mutants showed that peptide NCR068 is not required for symbiosis with S. meliloti strains 2011 and FSM-MA either. Our study reports that gene editing can help to elicit the role of particular NCRs in symbiotic nitrogen fixation.
A key to recovery for working mothers? Psychological detachment and the roles of relaxation, mastery and control on boundary violations
Authors: Trzebiatowski Tiffany 
Published: August 2023

PurposeThis study aims to incorporate theory on effort-recovery and stressor-detachment models to examine the roles of relaxation, mastery and types of control on the relationship between psychological detachment from work and boundary violations at home.Design/methodology/approachThis study analyzes data from two time points using a sample of 348 working mothers recruited from Prolific.FindingsWorking moms who psychologically detach from work have less work boundary violations at home. There are mixed findings on whether and when the other types of recovery experiences moderate the relationship between psychological detachment and boundary violations at home. Relaxation, control after work and job autonomy do not moderate the effect while mastery and boundary control do. Specifically, psychological detachment is more effective as reducing boundary violations at home for working moms who have (1) low levels of mastery and (2) high levels of boundary control.Practical implicationsWorking mothers juggle multiple roles and often have increased stress and less time to manage the two domains. The findings of this study illustrate whether and when psychological detachment from work acts as a key to recovery from work-based stressors.Originality/valueMuch of the research on recovery experiences is based on employees without consideration of motherhood status. Further, scholars have not examined the combinative potential of recovery experiences. Finally, examining control over both domains (vs. one domain) adds precision to the literature.
An investigation of linked data catalogue features in libraries, archives, and museums: a checklist approach
Authors: Chen Ya-Ning 
Published: August 2023

Purpose
In this study, the distinctive functional features of linked data (LD) catalogues were investigated to contrast with existing online public access catalogues (OPACs) and discovery systems using a checklist approach. The checklist was derived from a literature review and is composed of 10 items as follows: self-descriptive and dynamic content for resource description, linkage to external LD sources and online services, aggregation of knowledge contexts into knowledge graphs (KGs), URI-based link discovery, representation and query of LD relationships, URI-based serendipitous discovery, keyword recommendation, faceted limitation and browsing, visualization and openness of data.

Design/methodology/approach
Ten functional features derived from the literature were checked against existing LD catalogues offered by libraries, archives and museums (LAMs). The LD catalogues were regarded as qualified subjects if they offered functional features that were distinct from current OPACs and discovery systems through URI-based enrichment and aggregation from various LD sources. In addition to individual organizations, LD union catalogues were also included. However, LD hubs, such as ISNI, OCLC WorldCat Entities, VIAF and Wikidata, were excluded. In total, six LD catalogues from LAMs were selected as subjects for examination.

Findings
First, LD catalogues provide similar KG information through URI combination, and KGs also facilitate information serendipity, including social-document, intellectual, conceptual, spatial and temporal contexts and networks of corporate bodies, persons and families (CPFs). Second, LD catalogues have transformed the “seek first and browse later” paradigm into a “seek or browse” paradigm by refreshing the browsing function of traditional card catalogues with preview and new options to facilitate LD identification and discovery. Third, LD catalogues have refined keyword recommendation with the addition of the following fields: person’s title, CPF relationships, entity type and LD source. Lastly, a virtual union LD catalogue is offered.

Research limitations/implications
The proposed checklist revealed the unique/improved functional features of LD catalogues, allowing further investigation and comparison. More cases from the fields of medicine, engineering science and so on will be required to make revisions to fine-tune the proposed checklist approach.

Originality/value
To the best of the author’s knowledge, this is the first study to propose a checklist of functional features for LD catalogues and examine what the results and features of LD catalogues have achieved and are supported by from ontologies across LAMs. The findings suggest that LD provides a viable alternative to catalogues. The proposed checklist and results pave the way for the future development of LD catalogues and next-generation catalogues and also provide a basis for the future study of LD catalogues from other fields to refine the proposed checklist.
Students' core self-evaluations and academic burnout: the mediating role of personal resources
Authors: Paloș Ramona 
Published: August 2023

PurposeAlthough many studies emphasize the need to design programs to help students manage post-pandemic burnout, few address personal resources' mediating role in the relationship between positive self-evaluation and experienced academic burnout. The present study aims to investigate the mediating role of two personal resources (i.e. psychological capital and proactive coping) on the relationship between core self-evaluations and academic burnout.Design/methodology/approachThe research was carried out in the first part of 2022, at the end of two years of online teaching. The sample consisted of 183 Romanian university students who voluntarily filled in four questionnaires that measured core self-evaluations, academic burnout, psychological capital and proactive coping. To verify the hypotheses, a mediation analysis using the PROCESS 4.0 macro in SPSS 23.0, Model 6 was conducted. The indirect effect was tested based on a bias-corrected bootstrapping procedure with 5,000 samples, and a bootstrap confidence interval (95% CI).FindingsResults showed that students with a high level of core self-evaluations report a low level of burnout. Also, students with positive core self-evaluations are more likely to use their psychological resources (i.e. psychological capital) and act proactively (i.e. proactive coping) in dealing with challenging situations, which can increase their burnout. However, the overall effect of the core self-evaluations on burnout was lower in the case of mediation by students' personal resources.Originality/valueThese research findings highlight the role of personal resources in coping with a challenging context, being among the few studies that have focused on student burnout in the immediate post-pandemic period. Furthermore, by working with malleable personal resources that can be enhanced through instruction, this research underlines how students can be taught to assess and develop these resources to cope with a highly demanding educational context.
Isolation and chemistry of plant pigments
Authors: Naharwal Pankaj , Meena Mahesh , Somani Charul , Kumari Neetu , Yadav Dinesh Kumar 
Published: August 2023

Purpose
This paper aims to critically review the isolation and chemistry of plant pigments.

Design/methodology/approach
A literature survey from 1974 to 2022 was carried out and studied thoroughly. The authors reviewed literature in various areas such as isolation methods and catalytic properties of pigments.

Findings
With vast growing research in the field of catalytic activities of various pigments like chlorophyll, anthocyanin and flavonoids, there is still scope for further research for the pigments such as Lycopene, carotenoids and xanthophyll as there has not been any significant work in this area.

Research limitations/implications
Plant pigments may be used as an ecofriendly catalyst for chemical reactions.

Practical implications
One can get the direction of pigment research.

Social implications
Plant pigments are natural and ecofriendly catalyst which can reduce the pollution.

Originality/value
This is an original work. This paper precisely depicts the advantages as well as disadvantages of the isolation techniques of pigments. This study also presents the chemistry of plant pigments.

Graphical abstract