bluuebunny/crossref_metadata_2025_split huggingface dataset:
Timely lagging strand maturation relies on Ubp10-mediated PCNA dissociation from replicating chromatin
Authors: Zamarreño Javier , Muñoz Sofía , Alonso Esmeralda , Alcalá Macarena , Bermejo Rodrigo , Sacristán María P. , Bueno Avelino 
Published: January 2024

AbstractSynthesis and maturation of Okazaki Fragments is an incessant and highly efficient metabolic process completing the synthesis of the lagging strands at replication forks during S phase. Accurate Okazaki fragment maturation (OFM) is crucial to maintain genome integrity and, therefore, cell survival in all living organisms. In eukaryotes, OFM involves the consecutive action of DNA polymerase Pol ∂, 5’ Flap endonuclease Fen1 and DNA ligase I, and constitutes the best example of a sequential process coordinated by the sliding clamp PCNA. For OFM to occur efficiently, cooperation of these enzymes with PCNA must be highly regulated. Here, we present evidence of a role for the PCNA-deubiquitylase Ubp10 in the maturation of Okazaki fragments in the budding yeastSaccharomyces cerevisiae. We show that Ubp10 associates with lagging-strand DNA synthesis machineries on replicating chromatin to ensure timely ligation of Okazaki fragments by promoting an Elg1ATAD5-independent PCNA unloading mechanism.This document was written without the use of AI.
The origin, deployment, and evolution of a plant-parasitic nematode effectorome
Authors: Molloy Beth , Shin Dio S. , Long Jonathan , Pellegrin Clement , Senatori Beatrice , Vieira Paulo , Thorpe Peter , Damm Anika , Ahmad Mariam , Vermeulen Kerry , Derevnina Lida , Wei Siyuan , Sperling Alexis , Estévez Estefany Reyes , Bruty Samuel , Moura de Souza Victor Hugo , Kranse Olaf Prosper , Maier Tom , Baum Thomas , Eves-van den Akker Sebastian 
Published: January 2024

AbstractPlant-parasitic nematodes constrain global food security. During parasitism, they secrete effectors into the host plant from two types of pharyngeal gland cells. These effectors elicit profound changes in host biology to suppress immunity and establish a unique feeding organ from which the nematode draws nutrition. Despite the importance of effectors in nematode parasitism, there has been no comprehensive identification and characterisation of the effector repertoire of any plant-parasitic nematode.To address this, we advance techniques for gland cell isolation and transcriptional analysis to define a stringent annotation of putative effectors for the cyst nematodeHeterodera schachtiiat three key life-stages. We define 659 effector gene loci: 293 “known” high-confidence homologs of plant-parasitic nematode effectors, and 366 “novel” effectors with high gland cell expression. In doing so we define a comprehensive “effectorome” of a plant-parasitic nematode.Using this effector definition, we provide the first systems-level understanding of the origin, deployment and evolution of a plant-parasitic nematode effectorome. The robust identification of the comprehensive effector repertoire of a plant-parasitic nematode will underpin our understanding of nematode pathology, and hence, inform strategies for crop protection.
MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography
Authors: Lamm Lorenz , Zufferey Simon , Righetto Ricardo D. , Wietrzynski Wojciech , Yamauchi Kevin A. , Burt Alister , Liu Ye , Zhang Hanyi , Martinez-Sanchez Antonio , Ziegler Sebastian , Isensee Fabian , Schnabel Julia A. , Engel Benjamin D. , Peng Tingying 
Published: January 2024

AbstractMemBrain v2 is a deep learning-enabled program aimed at the efficient analysis of membranes in cryo-electron tomography (cryo-ET). The final v2 release of MemBrain will comprise three main modules: 1) MemBrain-seg, which provides automated membrane segmentation, 2) MemBrain-pick, which provides automated picking of particles along segmented membranes, and 3) MemBrain-stats, which provides quantitative statistics of particle distributions and membrane morphometrics.This initial version of the manuscript is focused on the beta release of MemBrain-seg, which combines iterative training with diverse data and specialized Fourier-based data augmentations. These augmentations are specifically designed to enhance the tool’s adaptability to a variety of tomographic data and address common challenges in cryo-ET analysis. A key feature of MemBrain-seg is the implementation of the Surface-Dice loss function, which improves the network’s focus on membrane connectivity and allows for the effective incorporation of manual annotations from different sources. This function is beneficial in handling the variability inherent in membrane structures and annotations. Our ongoing collaboration with the cryo-ET community plays an important role in continually improving MemBrain v2 with a wide array of training data. This collaborative approach ensures that MemBrain v2 remains attuned to the field’s needs, enhancing its robustness and generalizability across different types of tomographic data.The current version of MemBrain-seg is available athttps://github.com/teamtomo/membrain-seg, and the predecessor of MemBrain-pick (also called MemBrain v1) is deposited athttps://github.com/CellArchLab/MemBrain. This preprint will be updated concomitantly with the code until the three integrated modules of MemBrain v2 are complete.
Pathogen infection induces sickness behaviors by recruiting neuromodulatory systems linked to stress and satiety inC. elegans
Authors: Pradhan Sreeparna , Madan Gurrein K. , Kang Di , Bueno Eric , Atanas Adam A. , Kramer Talya S. , Dag Ugur , Lage Jessica D. , Gomes Matthew A. , Lu Alicia Kun-Yang , Park Jungyeon , Flavell Steven W. 
Published: January 2024

SUMMARYWhen animals are infected by a pathogen, peripheral sensors of infection signal to the brain to coordinate a set of adaptive behavioral changes known as sickness behaviors. While the pathways that signal from the periphery to the brain have been intensively studied in recent years, how central circuits are reconfigured to elicit sickness behaviors is not well understood. Here we find that neuromodulatory systems linked to stress and satiety are recruited upon infection to drive sickness behaviors inC. elegans. Upon chronic infection by the bacteriumPseudomonas aeruginosaPA14,C. elegansdecrease their feeding behavior, then display reversible bouts of quiescence, and eventually die. The ALA neuron and its neuropeptides FLP-7, FLP-24, and NLP-8, which control stress-induced sleep in uninfected animals, promote the PA14-induced feeding reduction. However, the ALA neuropeptide FLP-13 instead acts to delay quiescence and death in infected animals. Cell-specific genetic perturbations show that the neurons that release FLP-13 to delay quiescence in infected animals are distinct from ALA. A brain-wide imaging screen reveals that infection-induced quiescence involves ASI and DAF-7/TGF-beta, which control satiety-induced quiescence in uninfected animals. Our results suggest that a common set of neuromodulators are recruited across different physiological states, acting from distinct neural sources and in distinct combinations to drive state-dependent behaviors.
A basally active cGAS-STING pathway limits SARS-CoV-2 replication in a subset of ACE2 positive airway cell models
Authors: Puray-Chavez Maritza , Eschbach Jenna E. , Xia Ming , LaPak Kyle M. , Zhou Qianzi , Jasuja Ria , Pan Jiehong , Xu Jian , Zhou Zixiang , Mohammed Shawn , Wang Qibo , Lawson Dana Q. , Djokic Sanja , Hou Gaopeng , Ding Siyuan , Brody Steven L. , Major Michael B. , Goldfarb Dennis , Kutluay Sebla B. 
Published: January 2024

ABSTRACTHost factors that define the cellular tropism of SARS-CoV-2 beyond the cognate ACE2 receptor are poorly defined. Here we report that SARS-CoV-2 replication is restricted at a post-entry step in a number of ACE2-positive airway-derived cell lines due to tonic activation of the cGAS-STING pathway mediated by mitochondrial DNA leakage and naturally occurring cGAS and STING variants. Genetic and pharmacological inhibition of the cGAS-STING and type I/III IFN pathways as well as ACE2 overexpression overcome these blocks. SARS-CoV-2 replication in STING knockout cell lines and primary airway cultures induces ISG expression but only in uninfected bystander cells, demonstrating efficient antagonism of the type I/III IFN-pathway in productively infected cells. Pharmacological inhibition of STING in primary airway cells enhances SARS-CoV-2 replication and reduces virus-induced innate immune activation. Together, our study highlights that tonic activation of the cGAS-STING and IFN pathways can impact SARS-CoV-2 cellular tropism in a manner dependent on ACE2 expression levels.
A Functional Analysis of a Resorbable Citrate-based Composite Tendon Anchor
Authors: Thirumaran Arun , Poudel Anup , Sankar Magesh , Doulgkeroglou Meletios , Easley Jeremiah , Gadomski Ben , Biggs Manus 
Published: January 2024

AbstractOrthopaedic fixation seeks solutions to the challenges of non-union, reconstructive surgery, and soft tissue injuries by providing stability and tissue alignment during the healing process. Risks associated with fixation devices such as peri-implant resorption, implant loosening and sub-optimal device resorption remain a significant challenge in the development of transient fixation devices. Osteomimetic biomaterials, and in particular, bio-resorbable polymer composites designed to match the mineral phase content of native bone have been shown to exhibit osteoinductive and osteoconductive propertiesin vivoand have been used in bone fixation for the past 2 decades. However, the specific signalling pathways driving the osteogenic response to these biomaterials remain largely unknown.In this study a resorbable, bioactive, and mechanically robust citrate-based composite, formulated from poly(octamethylene citrate) (POC) and hydroxyapatite (HA) (POC-HA) was investigated as a potential orthopedic biomaterial.In vitroanalysis with human Mesenchymal Stem Cells (hMSCs) indicated that POC-HA composite materials supported cell adhesion, growth, and proliferation and increased calcium deposition, alkaline phosphatase production, the expression of osteogenic specific genes and activation of canonical pathways leading to osteoinduction and osteoconduction. Furtherin vivoevaluation of a POC-HA tendon fixation device in a sheep metaphyseal model indicated the regenerative and remodelling potential of this citrate-based composite material in orthopedic applications.
Phago-mixotrophy of small eukaryotic phytoplankton might alleviate iron limitation in HNLC Southern Ocean
Authors: Ong Denise Rui Ying , Gutiérrez-Rodríguez Andrés , Safi Karl A. , Marie Dominique , Selph Karen E. , Stukel Michael R. , Décima Moira , Lopes dos Santos Adriana 
Published: January 2024

AbstractSmall phytoplankton, consisting of pico and nano size fractions, are diverse in size and taxonomy. Yet, the differences in their productivity and taxonomic diversity are poorly described. Here, we measured the cell-specific carbon fixation rates of picocyanobacteriaSynechococcus, picoeukaryote and nanoeukaryote populations while unveiling their taxonomic composition in oligotrophic subtropical (ST) and high-nutrient low-chlorophyll subantarctic (SA) waters. We coupled 24 h in-situ radiolabelled14C incubations to flow cytometry sorting (FCM-sorting) and DNA metabarcoding from the same incubated samples, offering a direct account of the community associated with the carbon fixation rates measured. In both water masses, nanoeukaryotes had the highest cell-specific carbon fixation rate, followed by picoeukaryotes andSynechococcus(2.24±29.99, 2.18±2.08 and 0.78±0.55 fgC cell-1h-1, respectively). The cell-specific carbon fixation rates and growth rates ofSynechococcuswere 3-fold higher in ST compared to SA waters, while the rates of picoeukaryotes and nanoeukaryotes had no significant difference between the biogeochemically-contrasting water masses. Despite significant differences in their taxonomic composition, the FCM-sorted picoeukaryote and nanoeukaryote populations in SA waters were dominated by taxa with reported phago-mixotrophic strategies (Chrysophyceae, Dinophyceae and Prymnesiophyceae), suggesting phago-mixotrophy might alleviate nutrient stress in iron-limited conditions for discrete small photosynthetic eukaryote populations.
Early survival in Atlantic salmon is associated with parental genotypes at loci linked to timing of maturation
Authors: Aykanat Tutku , McLennan Darryl , Metcalfe Neil B. , Prokkola Jenni M. 
Published: January 2024

AbstractLarge effects loci often contain genes with critical developmental functions with potentially broad effects across life-stages. However, the life-stage-specific fitness consequences are rarely explored. In Atlantic salmon, variation in two large-effect loci,six6andvgll3, is linked to age at maturity, and several physiological and behavioural traits in early life. By genotyping the progeny of wild Atlantic salmon that were planted into natural streams with nutrient manipulations, we tested if genetic variation in these loci is associated with survival in early life. We found that higher early life survival was linked to the genotype associated with late maturation in thevgll3, but with early maturation in thesix6locus. These effects were significant in high-nutrient, but not in in low-nutrient streams. The differences in early survival were not explained by additive genetic effects in the offspring generation, but by maternal genotypes in thesix6locus, and by both parents’ genotypes in thevgll3locus. Our results suggest that indirect genetic effects by large-effect loci can be significant determinants of offspring fitness. This study demonstrates an intriguing case of how large-effect loci can exhibit complex fitness associations across life stages in the wild and indicates that predicting evolutionary dynamics is difficult.
BLADE-ON-PETIOLE interacts with CYCLOIDEA to fine-tuneCYCLOIDEA-mediated flower symmetry in Monkeyflowers (Mimulus)
Authors: Gao Yuan , Li Jingjian , He Jiayue , Yu Yaqi , Qian Zexin , Geng Zhiqiang , Yang Liuhui , Zhang Yumin , Ke Yujie , Lin Qiaoshan , Wang Jing , Chen Sumei , Chen Fadi , Yuan Yao-Wu , Ding Baoqing 
Published: January 2024

AbstractMorphological novelties, or key innovations, are instrumental to the diversification of the organisms. In plants, one such innovation is the evolution of zygomorphic flowers, which is thought to promote outcrossing and increases flower morphological diversity. We isolated three allelic mutants from twoMimulusspecies displaying altered floral symmetry and identified the causal gene as the orthologue ofArabidopsis BLADE-ON-PETIOLE. We found that MlBOP and MlCYC2a physically interact and this BOP-CYC interaction module is highly conserved across the angiosperms. Furthermore, MlBOP self-ubiquitinates and suppressesMlCYC2aself- activation. MlCYC2a, in turn, impedes MlBOP ubiquitination. Thus, this molecular tug-of-war between MlBOP and MlCYC2a fine-tunes the expression ofMlCYC2a, contributing to the formation of bilateral symmetry flowers, a key trait in angiosperm evolution.One Sentence SummaryMolecular tug-of-war between MlBOP and MlCYC2a fine-tunes the expression ofMlCYC2a, contributing to the bilateral flower symmetry formation.
Illuminating the dark corners: a qualitative examination of cryptocurrency’s risk
Authors: Mehta Kriti , Chawla Sonia 
Published: January 2024

Purpose
The study provides a comprehensive understanding of the issues and illegal activities related to cryptocurrencies and their negative repercussions. This study aims to identify and classify cryptocurrency downsides using grounded theory and in-depth interviews. The study also analysed investors’ reluctance to invest in cryptocurrency. This pioneering qualitative study illuminates a deep and multifaceted criminal aspect of cryptocurrency.

Design/methodology/approach
The study conducted in-depth interviews with respondents who have experience and knowledge of cryptocurrency investments. The interviews were recorded and transcribed. The analysis was performed using the NVivo 14 software in the study.

Findings
The study specified two major types of cryptocurrency’s negative aspects: barriers and illegal usage. Barriers to cryptocurrency investment include technological, security, trust, market-related and regulatory reasons. Terrorist funding, money laundering, fraud and ransom payments are all examples of illegal usage. The results of the word cloud analysis are consistent with the overall findings of the survey, which highlighted illegal usage as a prominent negative element of cryptocurrencies. It is a key reason why cryptocurrency is not included in investing portfolios by investors.

Originality/value
The study’s findings provide useful insights for policymakers to develop better methods for successfully mitigating risks and ensuring responsible and sustainable usage of cryptocurrencies. In addition, the study could serve as a stepping stone for more cryptocurrency-related studies, contributing to the development of a more complete and nuanced comprehension of this emergent technology and its societal effects.
Reactions to gender-(counter)normative behavior online in the United States: attraction and hiring implications
Authors: Badawy Rebecca , Brouer Robyn , Stefanone Michael 
Published: January 2024

PurposeResearch indicates that inconsistent gender norm presentations are met with backlash, which is particularly damaging to women. With social media use in selection rising, it is important to understand if this remains consistent for job applicants on social media.Design/methodology/approachIn two experiments, this study investigates hiring managers' reactions to job applicant (in)consistent gender norm-based communication on Facebook (n = 197) and YouTube (n = 203). Participants located in the United States were asked to review social media materials, reported perceptions of task and social attraction, and make hiring recommendations.FindingsInconsistent with work on backlash in face-to-face settings, results demonstrated that masculine communication styles on social media may be detrimental to job seekers, and this was more pronounced for male job seekers. Feminine presentation styles had more favorable results.Practical implicationsThe findings challenge the long-held understanding that men have more leeway to behave in agentic ways in job seeking contexts. While this may remain true in face-to-face settings, these findings suggest that social media, lacking media richness, may be a context in which males experience backlash for agentic behavior.Originality/valueThe research offers a novel perspective investigating traditional gender expectations in the digital realm, paving the way for a more comprehensive understanding of gender in employment contexts. This study contributes to the growing body of research on online behavior and expands understanding of how hiring managers react to gender norms in the era of social media.
Examining the boundary conditions of tokenism: within-occupation gender wage gaps and female representation in the Canadian labor market
Authors: Stephenson Amber L. , Yerger David B. 
Published: January 2024

PurposeThe purpose of this study was to examine the boundary conditions of Kanter's (1977) tokenism theory as applied to the gender wage gap. The authors aimed to discover if there was a point where the relationship between the percentage of women in a job category and the gender wage gap changed, and, if so, where the threshold was located and what was the nature of the shift in relationship.Design/methodology/approachThe authors used the Andrews’ (1993) threshold effects technique. Using 22 separate years of publicly available Canadian wage data, they examined the relationship between the percentage of females in 40 unique occupational categories and the female-to-male earnings ratio (for a total of 880 observations).FindingsThe results showed the existence of a threshold point, and that early gains in percent female within an occupation, up to approximately 14% female in the occupation, associate with strong gains in the female-to-male wage ratio. However, beyond that point, further gains in percent female associate with smaller improvements in the female-to-male wage ratio.Practical implicationsThe findings are useful in understanding the dynamics of occupational group gender composition, potential theoretical reasons for the nuances in relationship, as well as opportunities that may facilitate more equitable outcomes.Originality/value The results show that, though improvements were made above and below the threshold point, enhancements in the wage gap are actually larger when there are less women in the job category (e.g. tokens).
Academic motivation and academic satisfaction: a moderated mediation model of academic engagement and academic self-efficacy
Authors: Pham Thi Thuy Hang , Ho Thi Truc Quynh , Nguyen Be Thi Ngoc , Nguyen Hung Thanh , Nguyen Thi Ha 
Published: January 2024

PurposeThis study aims to investigate the conditional indirect effect of academic self-efficacy in the interplay between academic motivation and academic satisfaction through academic engagement among university students.Design/methodology/approachA cross-sectional study was performed on 1,638 Vietnamese university students (31.9% males and 68.1% females) aged 16 to 36 (Mean = 20.06, SD = 1.428). The participants filled out a questionnaire with the Vietnam versions of the General Self-Efficacy Scale, Academic Motivation Scale, Academic Life Satisfaction Scale and Academic Engagement Scale. Model 4 and Model 7 in the PROCESS macro were used for the mediation analysis and the moderated mediation analysis.FindingsResults showed that the indirect effect of academic engagement on the academic motivation-academic satisfaction link was significant. Furthermore, academic self-efficacy moderated this indirect effect. The indirect effect was stronger among students with high academic self-efficacy and weaker among students with low academic self-efficacy.Originality/valueThis study’s findings contribute to educational research on academic satisfaction and can be used by institutions of higher education and educators to enhance academic satisfaction among university students.
Dancing with the devil: the use and perceptions of academic journal ranking lists in the management field
Authors: Serenko Alexander , Bontis Nick 
Published: January 2024

Purpose This study explores the use and perceptions of scholarly journal ranking lists in the management field based on stakeholders’ lived experience.Design/methodology/approach The results are based on a survey of 463 active knowledge management and intellectual capital researchers.Findings Journal ranking lists have become an integral part of contemporary management academia: 33% and 37% of institutions and individual scholars employ journal ranking lists, respectively. The Australian Business Deans Council (ABDC) Journal Quality List and the UK Academic Journal Guide (AJG) by the Chartered Association of Business Schools (CABS) are the most frequently used national lists, and their influence has spread far beyond the national borders. Some institutions and individuals create their own journal rankings.Practical implications Management researchers employ journal ranking lists under two conditions: mandatory and voluntary. The forced mode of use is necessary to comply with institutional pressure that restrains the choice of target outlets. At the same time, researchers willingly consult ranking lists to advance their personal career, maximize their research exposure, learn about the relative standing of unfamiliar journals, and direct their students. Scholars, academic administrators, and policymakers should realize that journal ranking lists may serve as a useful tool when used appropriately, in particular when individuals themselves decide how and for what purpose to employ them to inform their research practices.Originality/value The findings reveal a journal ranking lists paradox: management researchers are aware of the limitations of ranking lists and their deleterious impact on scientific progress; however, they generally find journal ranking lists to be useful and employ them.