bluuebunny/crossref_metadata_2025_split huggingface dataset:
Misregulation of mitochondrial 6mA promotes the propagation of mutant mtDNA and causes aging inC. elegans
Authors: Hahn Anne , Hung Grace Ching Ching , Ahier Arnaud , Forde Brian M. , Dai Chuan-Yang , Lee Rachel Shin Yie , Campbell Daniel , Onraet Tessa , Kirmes Ina , Zuryn Steven 
Published: March 2023

AbstractIn virtually all eukaryotes, the mitochondrial genome (mitochondrial DNA, mtDNA) encodes proteins necessary for oxidative phosphorylation (OXPHOS) and the RNA machinery required for their synthesis inside the mitochondria. Appropriate regulation of mtDNA copy number and expression is essential for ensuring the correct stoichiometric formation of OXPHOS complexes assembled from both nuclear- and mtDNA-encoded subunits. The mechanisms of mtDNA regulation are not completely understood but are essential to organismal viability and lifespan. Here, using multiple approaches, we identify the presence of N6-methylation (6mA) on the mtDNA of diverse animal and plant species. Importantly, we also demonstrate that this modification is regulated inC. elegansby the DNA methyltransferase DAMT-1, and DNA demethylase ALKB-1, which localize to mitochondria. Misregulation of mtDNA 6mA through targeted overexpression of these enzymatic activities inappropriately alters mtDNA copy number and expression, impairing OXPHOS function and producing increased oxidative stress, as well as a shortened lifespan. Compounding defects in mtDNA regulation, reductions in mtDNA 6mA methylation promote the propagation of a deleterious mitochondrial genome across generations. Together, these results reveal that mtDNA 6mA is highly conserved among eukaryotes and regulates lifespan by influencing mtDNA copy number, expression, and heritable mutation levelsin vivo.
Genetic diversity and evidence of recombination ofHorsegram yellow mosaic virusinfecting pole bean (Phaseolus vulgarisL.) from South India
Authors: Bindu J , Kumar H. D. Vinay , Hiremath Shridhar , Muttappagol Mantesh , Nandan M. , Devaraj  , Basha C. R. Jahir , Shankarappa K. S. , Venkataravanappa V. , Reddy C. N. Lakshminarayana 
Published: March 2023

AbstractThe yellow mosaic disease (YMD) caused by begomoviruses is a major constraint for the production of pole bean (Phaseolus vulgarisL.) in India. Survey was carried out in the eastern dry zone of Karnataka during 2019-20 to record the incidence of yellow mosaic disease in pole bean which revealed the ubiquitous prevalence of YMD in pole bean ranging from 6.02 to 80.74 per cent. Leaf samples collected (symptomatic and asymptomatic) were subjected for begomovirus detection using specific primers. Twelve samples, representing all the 12 taluks in the surveyed region were considered for full genome amplification by RCA, cloned and sequenced. Genome length of 12 current isolates ranged from 2718 – 2744 and 2668 – 2671 nucleotides for DNA-A and DNA-B, respectively. Sequence analysis using Sequence Demarcation Tool (SDT) showed >91 per cent nucleotide identity of current isolates (DNA-A) with other horsegram yellow mosaic virus (HgYMV) isolates available in the GenBank. As per existing ICTV criteria, all the current isolates can be considered as strains of HgYMV. Further, DNA-B associated with all the 12 isolates also shared >91 per cent nucleotide identity with DNA-B of HgYMV isolates, indicating absence of component re-assortment in HgYMV. Variation in the pairwise nucleotide identity and phylogenetic analysis confirmed the existence of new strains within the current HgYMV isolates. GC plot analysis reveals potential recombination in the low GC rich regions. Further, recombination breakpoint analysis indicated intra-species recombination in both DNA-A and DNA-B, which might have driven the origin of new strains in HgYMV. This is the first comprehensive study on begomoviruses ioslates associated with the yellow mosaic disease of pole bean based on complete genome sequencing in the world.
SARS-CoV-2 accessory proteins involvement in inflammatory and profibrotic processes through IL11 signaling
Authors: López-Ayllón Blanca Dies , de Lucas-Rius Ana , Mendoza-García Laura , García-García Tránsito , Fernández-Rodríguez Raúl , Suárez-Cárdenas José M. , Santos Fátima Milhano , Corrales Fernando , Redondo Natalia , Pedrucci Federica , Zaldívar-López Sara , Jiménez-Marín Ángeles , Garrido Juan J. , Montoya María 
Published: March 2023

SummarySARS-CoV-2, the cause of the COVID19 pandemic, possesses eleven accessory proteins encoded in its genome. Their roles during infection are still not completely understood. Transcriptomic analysis revealed that bothWNT5AandIL11were significantly up-regulated in A549 cells expressing individual accessory proteins ORF6, ORF8, ORF9b or ORF9c from SARS-CoV-2 (Wuhan-Hu-1 isolate). IL11 signaling-related genes were also differentially expressed. Bioinformatics analysis disclosed that bothWNT5AandIL11were involved in pulmonary fibrosis idiopathic disease. Functional assays confirmed their association with profibrotic cell responses. Subsequently, data comparison with lung cell lines infected with SARS-CoV-2 or lung biopsies from patients with COVID19 evidenced altered gene expression that matched those obtained in this study. Our results show ORF6, ORF8, ORF9b and ORF9c involvement in inflammatory and profibrotic responses. Thus, these accessory proteins could be targeted by new therapies against COVID19 disease.Research topic(s)Viral diseases, COVID19 insights
Dynamics of the DYNLL1/MRE11 complex regulates DNA end resection and recruitment of the Shieldin complex to DSBs
Authors: Zhou Rui , Swift Michelle L. , Syed Aleem , Huang Kaimeng , Moreau Lisa , Tainer John A. , Konstantinopoulos Panagiotis A. , D’Andrea Alan D. , He Yizhou Joseph , Chowdhury Dipanjan 
Published: March 2023

ABSTRACTExtent and efficacy of DNA end resection at DNA double strand break (DSB)s determines the choice of repair pathway. Here we describe how the 53BP1 associated protein DYNLL1 works in tandem with Shieldin and the CST complex to protect DNA ends. DYNLL1 is recruited to DSBs by 53BP1 where it limits end resection by binding and disrupting the MRE11 dimer. The Shieldin complex is recruited to a fraction of 53BP1-positive DSBs hours after DYNLL1 predominantly in the G1 cells. Shieldin localization to DSBs is dependent on MRE11 activity and is regulated by the interaction of DYNLL1 with MRE11. BRCA1-deficient cells rendered resistant to PARP inhibitors by the loss of Shieldin proteins can be re-sensitized by the constitutive association of DYNLL1 with MRE11. These results define the temporal and functional dynamics of the 53BP1-centric DNA end resection factors in cells.
Intrinsic protein disorder is insufficient to drive subnuclear clustering in embryonic transcription factors
Authors: Hannon Colleen E. , Eisen Michael B. 
Published: March 2023

AbstractModern microscopy has revealed that core nuclear functions, including transcription, replication, and heterochromatin formation occur in spatially restricted clusters. Previous work from our lab has shown that subnuclear high-concentration clusters of transcription factors may play a role in regulating RNA synthesis in the earlyDrosophilaembryo. A nearly ubiquitous feature of eukaryotic transcription factors is that they contain intrinsically disordered regions (IDRs) that often arise from low complexity amino acid sequences within the protein. It has been proposed that IDRs within transcription factors drive co-localization of transcriptional machinery and target genes into high concentration clusters within nuclei. Here we test that hypothesis directly, by conducting a broad survey of the subnuclear localization of IDRs derived from transcription factors. Using a novel algorithm to identify IDRs in theDrosophilaproteome, we generated a library of IDRs from transcription factors expressed in the earlyDrosophilaembryo. We used this library to perform a high throughput imaging screen inDrosophilaS2 cells. We found that while subnuclear clustering does not occur when the majority of IDRs are expressed alone, it is frequently seen in full length transcription factors. These results are consistent in liveDrosophilaembryos, suggesting that IDRs are insufficient to drive the subnuclear clustering behavior of transcription factors. Furthermore, the clustering of transcription factors in living embryos was unaffected by the deletion of IDR sequences. Our results demonstrate that IDRs are unlikely to be the primary molecular drivers of the clustering observed during transcription, suggesting a more complex and nuanced role for these disordered protein sequences.
Deep learning for SDN-enabled campus networks: proposed solutions, challenges and future directions
Authors: Chanhemo Wilson Charles , Mohsini Mustafa H. , Mjahidi Mohamedi M. , Rashidi Florence U. 
Published: March 2023

PurposeThis study explores challenges facing the applicability of deep learning (DL) in software-defined networks (SDN) based campus networks. The study intensively explains the automation problem that exists in traditional campus networks and how SDN and DL can provide mitigating solutions. It further highlights some challenges which need to be addressed in order to successfully implement SDN and DL in campus networks to make them better than traditional networks.Design/methodology/approachThe study uses a systematic literature review. Studies on DL relevant to campus networks have been presented for different use cases. Their limitations are given out for further research.FindingsFollowing the analysis of the selected studies, it showed that the availability of specific training datasets for campus networks, SDN and DL interfacing and integration in production networks are key issues that must be addressed to successfully deploy DL in SDN-enabled campus networks.Originality/valueThis study reports on challenges associated with implementation of SDN and DL models in campus networks. It contributes towards further thinking and architecting of proposed SDN-based DL solutions for campus networks. It highlights that single problem-based solutions are harder to implement and unlikely to be adopted in production networks.
The gender dimension of outsiderness in Western Europe: a comparative cross-model analysis
Authors: Giuliani Giovanni Amerigo 
Published: March 2023

PurposeThe article investigates whether and to what extent outsiderness is gendered in Western Europe, both in terms of its spread and degree. It thus explores which male and female post-Fordist social classes are more exposed to the risk of this phenomenon. It also scrutinizes whether such a gendered characterization has varied over time and across clusters of Western European countries.Design/methodology/approachRelying on a comparative analysis of the data provided by the European Social Survey (ESS) dataset and comparing two points in time – the early/mid-2000s and the late 2010s – the work provides both a dichotomous and continuous variable of outsiderness, which measure its spread and degree in the female and male workforces of a pooled set of growth models.FindingsThe empirical analysis shows that outsiderness is profoundly gendered in Western Europe and thus a feminized social phenomenon. However, the comparative investigation highlights that outsiderness has been genderized in diverse ways across the four growth models. Different patterns of gendered outsiderness can be identified.Originality/valueThe article provides a comparative and diachronic analysis of outsiderness from a gender lens, putting into a mutual dialogue different literature on labour market, and shows that outsiderness represents a key analytical dimension for assessing gender inequalities.
Developing organizational resilience from business process management maturity
Authors: Sincorá Larissa Alves , Oliveira Marcos Paulo Valadares de , Zanquetto-Filho Hélio , Alvarenga Murilo Zamboni 
Published: March 2023

PurposeIn the current business context, there is a current need to adopt contemporary practices of process management as a competitive advantage to leverage organizational results. This study aims to explore such relationships, considering the performance results in the organizational resilience (OR) dimension.Design/methodology/approachThe authors collected 82 valid responses from a survey targeted at professionals occupying positions or functions in the operations area. For data analysis, the authors used the technique of structural equation modeling (SEM) using the partial least squares (PLS) algorithm.FindingsThe results show that maturity in the management of business processes positively influences the behavior of OR, with the highest level of maturity primarily being responsible for this impact. This result reveals that resilience naturally depends on mature and well-established processes in the organizational structure. The proposed model explained 78.5% of OR.Practical implicationsCompanies that maintain mature management of their business processes will be better able to positively influence OR since process management can make organizations less fragile supply chains and more adaptable to changes.Originality/valueThe findings helped clarify the extent to which process management influences the results of OR. Although the literature indicates that maturity in business processes is formed by five first-order constructs, only the “innovated” dimension proved to be significant in the present study.
Gamified virtual labs: shifting from physical environments for low-risk interactive learning
Authors: Sanzana Mirza Rayana , Abdulrazic Mostafa Osama Mostafa , Wong Jing Ying , Karunagharan Jaya Kumar , Chia Jason 
Published: March 2023

PurposeThis paper presents two educational gamified virtual labs and investigates different methods of including gamified elements in virtual labs used for teaching. The purpose of this study is to investigate if immersive gamified virtual labs can be used as effective pedagogical tools by properly incorporating them into higher education curricula to assist low-risk active learning and student engagement.Design/methodology/approachThis research design comprises two gamified virtual labs including nine essential experiments of biology and chemistry integrated into the higher education curriculum of the Foundation of Science at an international University. Students filled in a survey after participating in the lab to shed light on appropriate ways of using gamification approaches in virtual labs.FindingsFrom the predominant findings of the study, gamified virtual labs increase student involvement thereby enhancing knowledge development with active learning and may be a potentially suitable pedagogical tool for low-risk interactive learning.Research limitations/implicationsLimitations of the study include findings based on gamified virtual labs but not comparing the gamified virtual labs to simple virtual simulations to further investigate the pedagogical approach and understand the student perceptions in a simple virtual simulation and a gamified virtual lab.Practical implicationsThe findings of this study will provide evidence that gamified virtual labs integrated into higher education curricula as supplementary tools for laboratory experimentation improve the educational delivery process.Originality/valueThis research highlights an appropriate way of integrating 3D virtual labs into practical curricula while discussing the benefits.
Design and input saturation control with full-state constraints of lightweight tendon-driven musculoskeletal arm
Authors: Yuan Jianbo , Fan Yerui , Wu Yaxiong 
Published: March 2023

Purpose
This study aims to propose a novel lightweight tendon-driven musculoskeletal arm (LTDM-arm) robot with a flexible series–parallel mixed skeletal joint structure and modularized artificial muscle system (MAMS). The proposed LTDM-arm exhibits human-like flexibility, safety and operational accuracy. In addition, to improve the safety and stability of the LTDM-arm, a control method is proposed to solve local artificial muscle overload accidents.

Design/methodology/approach
The proposed LTDM-arm comprises seven degrees of freedom skeletons, 15 MAMSs and various sensor systems (joint sensing, muscle tension sensing, visual sensing, etc.). It retains the morphology of a human skeleton (humerus, ulna and radius) and a simplified muscle configuration. This study proposes an input saturation control with full-state constraints to reduce local artificial muscle overload accidents caused by redundant muscle tension calculations.

Findings
3D circular trajectory experiments were conducted to verify the stability of the control method and the flexibility of the LTDM-arm. The results showed that the average error of the muscle length was approximately 0.35 mm (0.38%), which indicates that the proposed control scheme can make the output follow the target trajectory while ensuring constraint satisfaction.

Originality/value
The human arm is capable of performing compliant operations rapidly, flexibly and robustly in unstructured environments. Existing musculoskeletal arm robots lack simulations of the full morphology of the human arm and are insufficient in dexterity. However, the flexibility and safety features of the proposed LTDM-arm were consistent with that of the human arm. Therefore, this study offers a new approach for investigating the advantages of the musculoskeletal system and the concepts of muscle control.
Appropriation, migration, and unemployment
Authors: Pi Jiancai , Duan Shuxi 
Published: March 2023

AbstractThis article builds general equilibrium models to explore the relationship among appropriation, rural–urban migration, the minimum wage and unemployment. We find that the proportion of appropriated capital plays a key role in the effects of appropriation on unemployment and rural–urban migration. When the proportion of appropriated capital is large, a stronger control on appropriation by the government results in a lower unemployment rate and more rural–urban migrants, and vice versa. In the extended models, the conclusion may be different when the plundered factor changes from capital to land. In the situation with the agricultural sector employing unskilled labour and capital, appropriation has no impact on unemployment, and the effect on migration remains the same. We also discuss the implications of the minimum wage, and find that under plausible conditions, the rise of the minimum wage can alleviate appropriation and reduce unemployment. The situation of migration is ambiguous due to the impacts of two opposite factors.
MOVEMENT 3. NAVIGATING URBAN ARRANGEMENTS
Authors:   The Re‐Arrangements Collective, Cante Fabien , Hussain Ajmal , Makori Timo , Mohamed Surer Qassim , Osbourne Alana , Pilo' Francesca , Ramakrishnan Kavita , Simone AbdouMaliq , Sitas Rike , Suhail Adeem 
Published: March 2023

AbstractThe third movement explores how (re)arrangements are made and re‐worked as people navigate fractured, ever‐shifting landscapes of urban opportunity, conflict and uncertainty. Drawing on fieldwork in Paris, Mogadishu and Abidjan, we point to the fragile, collective and anticipatory knowledges accumulated during navigations, and to how these knowledges become contained within and (re)constitute embodied archives.
MOVEMENT 4. BREATH SIGH TEMPEST: On the Temporal Dimensions of Re‐arrangements
Authors:   The Re‐Arrangements Collective, Cante Fabien , Hussain Ajmal , Makori Timo , Mohamed Surer Qassim , Osbourne Alana , Pilo' Francesca , Ramakrishnan Kavita , Simone AbdouMaliq , Sitas Rike , Suhail Adeem 
Published: March 2023

AbstractThe fourth movement explores the temporal relationship between arrangements and re‐arrangements, addressing the question of how an obdurate and ‘sticky’ temporal order may give way to palpable re‐arrangement of the ways in which subjects experience time. Eschewing a concern with linear homogenous time, it addresses the processes of re‐arrangement by understanding the dynamics of grave events, hauntings of the past, subtly changing rhythms of everyday life, and the force of potential futures in synchrony.
MOVEMENT 5. SENSING THE AFFECTIVE LIVES OF ARRANGEMENTS
Authors:   The Re‐Arrangements Collective, Cante Fabien , Hussain Ajmal , Makori Timo , Mohamed Surer Qassim , Osbourne Alana , Pilo' Francesca , Ramakrishnan Kavita , Simone AbdouMaliq , Sitas Rike , Suhail Adeem 
Published: March 2023

AbstractThis final movement explores whether thinking with re‐arrangements can help us account for that which is hidden, unseen or nested in the recesses and folds of urban practices. And if so, how we might then talk about and account for elusive parts of an arrangement that both exert an influence and are influenced. This essay uses sensibilities as an entry point into the intangible interactions between subjects and (re)arrangements.
Goal commitment and goal confidence mediate the path between desire to get drunk and binge drinking among young adults receiving text message goal‐related feedback
Authors: Suffoletto Brian , Chung Tammy 
Published: March 2023

AbstractBackgroundCounteracting desires to drink are cognitive processes that exert self‐control to mitigate impulses or strengthen other, perhaps more distal, goals to limit consumption. Young adults are particularly challenged by mismatches between self‐regulation and desires to drink that make them susceptible to hazardous alcohol use.MethodsWe assessed whether drinking limit goal commitment and goal confidence mediate the association between desire to get drunk and binge drinking (4+ drinks for females and 5+ drinks for males on a given occasion) among young adults exposed to text message goal‐related feedback. We randomized 297 young adults to one of two text message interventions that incorporated drinking limit goal‐related assessments and feedback over 12 weeks of intervention exposure. On the 2 days per week that they typically drank alcohol, participants were asked to report plans to drink (yes/no). If a drinking plan was endorsed, participants reported their desire to get drunk (0 [not at all] to 8 [completely]), willingness to commit to a drinking limit goal (yes/no), and (contingent on goal commitment) goal confidence (0 [not at all] to 8 [completely]). The next day, participants reported their drinking quantity, coded as a binge drinking day (yes/no). Mediation was tested using path models of simultaneous between‐ and within‐person effects using maximum likelihood.ResultsAt both within‐ and between‐person levels, we found significant indirect path effects of goal commitment and goal confidence between desire to get drunk and binge drinking. Greater than usual desire to get drunk was associated with lower drinking limit goal commitment and confidence, whereas greater than usual goal commitment and confidence were associated with lower likelihood of same‐day binge drinking.DiscussionFindings support a mechanistic model where contextual variations in same‐day drinking limit goal commitment and confidence mitigate the path between desire to get drunk and binge drinking among young adults. Employing just‐in‐time strategies to reinforce drinking limit goal commitment and goal confidence could reduce hazardous drinking and related harms.