bluuebunny/crossref_metadata_2025_split huggingface dataset:
LONP1 regulation of mitochondrial protein folding provides insight into beta cell failure in type 2 diabetes
Authors: Li Jin , Zhu Jie , Deng Yamei , Reck Emma C. , Walker Emily M. , Sidarala Vaibhav , Hubers Dre L. , Pasmooij Mabelle B. , Shin Chun-Shik , Bandesh Khushdeep , Motakis Eftyhmios , Nargund Siddhi , Kursawe Romy , Basrur Venkatesha , Nesvizhskii Alexey I. , Stitzel Michael L. , Chan David C. , Soleimanpour Scott A. 
Published: June 2024

ABSTRACTProteotoxicity is a contributor to the development of type 2 diabetes (T2D), but it is unknown whether protein misfolding in T2D is generalized or has special features. Here, we report a robust accumulation of misfolded proteins within the mitochondria of human pancreatic islets in T2D and elucidate its impact on β cell viability. Surprisingly, quantitative proteomics studies of protein aggregates reveal that human islets from donors with T2D have a signature more closely resembling mitochondrial rather than ER protein misfolding. The matrix protease LonP1 and its chaperone partner mtHSP70 were among the proteins enriched in protein aggregates. Deletion of LONP1 in mice yields mitochondrial protein misfolding and reduced respiratory function, ultimately leading to β cell apoptosis and hyperglycemia. Intriguingly, LONP1 gain of function ameliorates mitochondrial protein misfolding and restores human β cell survival following glucolipotoxicity via a protease-independent effect requiring LONP1-mtHSP70 chaperone activity. Thus, LONP1 promotes β cell survival and prevents hyperglycemia by facilitating mitochondrial protein folding. These observations may open novel insights into the nature of impaired proteostasis on β cell loss in the pathogenesis of T2D that could be considered as future therapeutic targets.
Do Deep Learning Models for Co-Folding Learn the Physics of Protein-Ligand Interactions?
Authors: Masters Matthew R. , Mahmoud Amr H. , Lill Markus A. 
Published: June 2024

ABSTRACTCo-folding models are the newest innovation in deep-learning-based protein-ligand structure prediction. The recent publications of RoseTTAFold All-Atom and AlphaFold 3 have shown high-quality results on predicting the structures of proteins interacting with small-molecules, other proteins and nucleic-acids. Despite these advanced capabilities and broad potential, the current study presents critical findings that question these models’ adherence to fundamental physical principles and its susceptibility to overfitting specific protein families. Through adversarial examples based on established physical, chemical, and biological principles, we demonstrate notable discrepancies in protein-ligand structural predictions when subjected to biologically plausible perturbations. These discrepancies reveal a significant divergence from expected physical behaviors, indicating potential overfitting to particular data subsets within its training corpus. Our findings underscore the models’ limitations in generalizing effectively across diverse biological structures and highlight the necessity of integrating robust physical and chemical priors in the development of such predictive tools. The results advocate a measured reliance on deep-learning-based models for critical applications in drug discovery and protein engineering, where a deep understanding of the underlying physical and chemical properties is crucial.
Group identification drives brain integration for collective performance
Authors: Xie Enhui , Zha Shuyi , Xu Yiyang , Li Xianchun 
Published: June 2024

AbstractGroup identification may influence collective behaviors and result in variations in collective performance. However, the evidence for this hypothesis and the neural mechanisms involved remain elusive. To this end, we conducted a study using both single-brain activation and multi-brain synchronization analyses to investigate how group identification influences collective problem-solving in a murder mystery case. Our results showed that groups with high levels of identification performed better individually compared to those with low identification, as supported by single-brain activation in the dorsolateral prefrontal cortex (DLPFC). Furthermore, high-identification groups also showed enhanced collective performance, supported by within-group neural synchronization (GNS) in the orbitofrontal cortex (OFC). The DLPFC-OFC connectivity played a crucial role in linking individual and collective performance. Overall, our study provides a two-in-one neural model to explain how group identification affects collective decision-making processes, offering valuable insights into the dynamics of group interactions.
Prominin-1 null Xenopus laevis develop subretinal drusenoid-like deposits, cone-rod dystrophy, and RPE atrophy
Authors: Carr Brittany J. , Skitsko Dominic , Song Jun , Li Zixuan , Ju Myeong Jin , Moritz Orson L. 
Published: June 2024

ABSTRACTMutations in thePROMININ-1(PROM1)gene are associated with inherited, non-syndromic vision loss. Here, we used CRISPR/Cas9 to induce truncatingprom1-null mutations inXenopus laevisto create a disease model. We then tracked progression of retinal degeneration in these animals from the ages of 6 weeks to 3 years old. We found that retinal degeneration caused byprom1-null is age-dependent and likely involves death or damage to the retinal pigment epithelium (RPE) that precedes photoreceptor degeneration. Asprom1-null frogs age, they develop large cellular debris deposits in the subretinal space and outer segment layer which resemble subretinal drusenoid deposits (SDD) in their location, histology, and representation in color fundus photography and optical coherence tomography (OCT). In older frogs, these SDD-like deposits accumulate in size and number, and they are present before retinal degeneration occurs. Evidence for an RPE origin of these deposits includes infiltration of pigment granules into the deposits, thinning of RPE as measured by OCT, and RPE disorganization as measured by histology and OCT. The appearance and accumulation of SDD-like deposits and RPE thinning and disorganization in our animal model suggests an underlying disease mechanism forprom1-null mediated blindness of death and dysfunction of the RPE preceding photoreceptor degeneration, instead of direct effects upon photoreceptor outer segment morphogenesis, as was previously hypothesized.
Transcriptomic Analysis of the Spatiotemporal Axis of Oogenesis and Fertilization inC. elegans
Authors: Su Yangqi , Shea Jonathan , DeStephanis Darla , Su Zhengchang 
Published: June 2024

AbstractThe oocyte germline of theC. eleganshermaphrodite presents a unique model to study the formation of oocytes. However, the size of the model animal and difficulties in retrieval of specific stages of the germline have obviated closer systematic studies of this process throughout the years. Here, we present a transcriptomic level analysis into the oogenesis ofC. eleganshermaphrodites. We dissected a hermaphrodite gonad into seven sections corresponding to the mitotic distal region, the pachytene, the diplotene, the early diakinesis region and the 3 most proximal oocytes, and deeply sequenced the transcriptome of each of them along with that of the fertilized egg using a single-cell RNA-seq protocol. We identified specific gene expression events as well as gene splicing events in finer detail along the oocyte germline and provided novel insights into underlying mechanisms of the oogenesis process. Furthermore, through careful review of relevant research literature coupled with patterns observed in our analysis, we attempt to delineate transcripts that may serve functions in the interaction between the germline and cells of the somatic gonad. These results expand our knowledge of the transcriptomic space of theC. elegansgermline and lay a foundation on which future studies of the germline can be based upon.
Comparative Analysis of Human-Chimpanzee Divergence in Brain Connectivity and its Genetic Correlates
Authors: Wang Yufan , Cheng Luqi , Li Deying , Lu Yuheng , Wang Changshuo , Wang Yaping , Gao Chaohong , Wang Haiyan , Vanduffel Wim , Hopkins William D. , Sherwood Chet C. , Jiang Tianzi , Chu Congying , Fan Lingzhong 
Published: June 2024

AbstractChimpanzees (Pan troglodytes) are humans’ closest living relatives, making them the most directly relevant comparison point for understanding human brain evolution. Zeroing in on the differences in brain connectivity between humans and chimpanzees can provide key insights into the specific evolutionary changes that might have occured along the human lineage. However, conducting comparisons of brain connectivity between humans and chimpanzees remains challenging, as cross-species brain atlases established within the same framework are currently lacking. Without the availability of cross-species brain atlases, the region-wise connectivity patterns between humans and chimpanzees cannot be directly compared. To address this gap, we built the first Chimpanzee Brainnetome Atlas (ChimpBNA) by following a well-established connectivity-based parcellation framework. Leveraging this new resource, we found substantial divergence in connectivity patterns across most association cortices, notably in the lateral temporal and dorsolateral prefrontal cortex between the two species. Intriguingly, these patterns significantly deviate from the patterns of cortical expansion observed in humans compared to chimpanzees. Additionally, we identified regions displaying connectional asymmetries that differed between species, likely resulting from evolutionary divergence. Genes associated with these divergent connectivities were found to be enriched in cell types crucial for cortical projection circuits and synapse formation. These genes exhibited more pronounced differences in expression patterns in regions with higher connectivity divergence, suggesting a potential foundation for brain connectivity evolution. Therefore, our study not only provides a fine-scale brain atlas of chimpanzees but also highlights the connectivity divergence between humans and chimpanzees in a more rigorous and comparative manner and suggests potential genetic correlates for the observed divergence in brain connectivity patterns between the two species. This can help us better understand the origins and development of uniquely human cognitive capabilities.
GCRTcall: a Transformer based basecaller for nanopore RNA sequencing enhanced by gated convolution and relative position embedding via joint loss training
Authors: Li Qingwen , Sun Chen , Wang Daqian , Lou Jizhong 
Published: June 2024

AbstractNanopore sequencing, renowned for its ability to sequence DNA and RNA directly with read lengths extending to several hundred kilobases or even megabases, holds significant promise in fields like transcriptomics and other omics studies. Despite its potential, the technology’s limited accuracy in base identification has restricted its widespread application. Although many algorithms have been developed to improve DNA decoding, advancements in RNA sequencing remain limited. Addressing this challenge, we introduce GCRTcall, a novel approach integrating Transformer architecture with gated convolutional networks and relative positional encoding for RNA sequencing signal decoding. Our evaluation demonstrates that GCRTcall achieves state-of-the-art performance in RNA basecalling.
Development and validation of a food safety survey for older adults
Authors: Kavanaugh Melissa , Shewokis Patricia A. , Quinlan Jennifer J. 
Published: June 2024

PurposeThe purpose of this study was to create and validate a food safety survey for older adults.Design/methodology/approachThe survey was designed to measure food handling and consumption behaviors related to high-risk foods. Survey questions were also designed to capture behavioral constructs from the health belief model (HBM). The first administration of the survey was completed by 349 participants, 55 years of age and older. Exploratory factor analysis was used to assess construct validity, and Cronbach’s alpha was used to assess the internal consistency of the subscales generated through factor analysis. Two weeks after the first administration, the survey was completed a second time by 149 participants from the original sample. The intraclass correlation coefficient was used to evaluate test-retest reliability.FindingsExploratory factor analysis yielded four factors related to the HBM (perceived susceptibility, perceived severity, perceived barriers and cues to action) and three factors related to food handling practices (handling of processed meats, food thermometer use with poultry and washing or rinsing poultry). Inclusion in a factor meant that the related questions measured the same underlying construct. Cronbach’s alpha for these factors ranged from 0.63 to 0.77. Modification of the survey following validation resulted in the development of a 44-question instrument that can be used with older adults.Practical implicationsThis survey will next be administered to a representative sample of older adults to assess relationships between HBM constructs and food handling behaviors and is available for use by other researchers.Originality/valueThere are few validated tools that can be used with older adults to evaluate food safety risks.
Influence of welding-induced mechanical stress on the electromagnetic properties of magnetic lamination
Authors: Ukwungwu David , Emadmostoufi Sobhan , Reisgen Uwe , Hameyer Kay 
Published: June 2024

Purpose
This paper aims to analyze the influence of welding-induced mechanical stress of a magnetic core material on the performance behavior of a permanent magnet excited synchronous machine (PMSM). Welding, interlocking, clinching and the use of adhesives are state-of-the-art packaging technologies used in the manufacturing of electrical machines. However, the packaging processes degrade the electromagnetic properties of the electric steel sheets, thereby decreasing the performance and achievable range of the electric vehicle.

Design/methodology/approach
In this paper, an approach that maps the local changes in magnetic properties due to welding induced stress with the stress values is developed. The welding process induces internal stress inside the steel sheet due to the diffusion of thermal energy into the sheets. Other effects are the changes in the micro structures of the steel sheets (grain sizes). These induced mechanical stresses lead to significant deterioration of the electromagnetic properties. They also lead to an increase in iron loss attributed to steel lamination.

Findings
A low speed (city), a high-speed (highway) and WLTC-c3 driving cycle will be used to analyze the effects of the induced stresses on the machine efficiency at the different operating conditions. A high-speed PMSM with a maximum speed of 26,000 min−1 and maximum torque of 130 Nm is designed for this study.

Originality/value
The value of this study is in the development of a local varying modeling approach that analyses the influence of weld-induced stress on the performance of electrical machines. Its originality is evident in the mapping methodology. This will enable an application dependent improvement possibilities due to the understanding of the impact of weld-induced stress on the electromagnetic properties of weld-packaged core.
Decoding the networking strategies of Asian and Black workers in the London Insurance Market
Authors: Pillai Mani 
Published: June 2024

PurposeThis study utilizes Bourdieu’s concepts of field, capital and habitus to investigate the networking strategies of Asian and Black knowledge workers in the London Insurance Market. It also examines the factors contributing to the success or failure of these strategies. The trading activities of the London Insurance Market are underpinned by interdependent relations among its participants. It provides an appropriate context for examining the networking strategies adopted by Asian and Black workers to accelerate their careers.Design/methodology/approachThis research employed a qualitative methodology, gathering data from 24 participants through semi-structured interviews. Participants were selected using purposive, convenience, and snowball sampling methods. Thematic analysis was used to analyze data and develop aggregated concepts from the identified themes and subthemes.FindingsThe London Insurance Market accords great importance to networking. Interpersonal connections significantly influenced career progression, often overshadowing educational attainments. Asian and Black workers faced systemic nepotism and limited access to influential networks in this field. Participants strategically used their interactions to overcome these challenges and advance their careers. Many believed that their careers had a better chance of progressing through informal networks than through formal channels such as Human Resources. Some participants declined to engage in the commonly accepted networking practices, choosing alternative ways to further their careers.Practical implicationsFindings underscore the need for implementing specific organizational policies to address systemic biases and nepotism, particularly in front-office recruitment. Such policies could include prioritizing merit-based hiring practices and developing targeted initiatives to reduce the underrepresentation of minority ethnic workers in front-office positions. By adopting these measures, organizations can create more equitable career advancement opportunities and leverage the full potential of their diverse workforce.Originality/valueThis study contributes to the existing literature on minority ethnic workers' careers, networking theory and workplace diversity. It provides insights into the networking strategies of Asian and Black workers within the London Insurance Market, revealing that these strategies are dependent on contextual factors. The study also highlights the pervasive practice of nepotism deeply ingrained in the habitus of the London Insurance Market and which acts as a barrier for gaining access to influential networks.
The L3 Assessment Framework: what we do and do not know about the characterisation of activity component for primary school
Authors: Mealings Kiri , Buchholz Joerg M. 
Published: June 2024

Purpose
The Listen to Learn for Life (L3) Assessment Framework is a framework that outlines how to systematically assess the links between the classroom environment, listening, learning and well-being. The purpose of this paper is to review the published literature to understand what is known about the characterisation of activity component of the L3 Assessment Framework and determine what is not known and needs to be investigated in future research.

Design/methodology/approach
Literature reviews (Web searches for systematic, scoping or general reviews; scoping reviews following the preferred reporting items for systematic reviews and meta-analyses extension for scoping reviews protocol; and extended Web searches) were conducted to characterise lecture, group work and independent work activities in terms of the perceptual setting, source degradation and transmission degradation.

Findings
Most research that has been conducted is for classrooms in general and does not specify results specifically for lecture, group work and independent work, which is important for understanding how the learning environment changes with the different activities. What is known about the lecture, group work and independent work activities are discussed; however, it is noted that this often comes from only a few studies. Future research areas to contribute to this literature as well as fill current research gaps are proposed.

Originality/value
To the best of the authors’ knowledge, this paper is the first review paper to synthesize previous research characterising the classroom environment for different activities using the L3 Assessment Framework. It provides an analysis of the limitations of existing literature and proposes future research to help fill in these gaps.
Climate change adaptation in Malta: assessment of skills in the built environment
Authors: Borg Axisa Glorianne , Borg Ruben Paul 
Published: June 2024

Purpose
The construction industry is one of the major contributors of greenhouse gas emissions (UNEP, 2022), but it provides numerous valuable opportunities to contribute to the reduction of greenhouse gas emissions (IPPC, 2023). Innovation within the industry and the adoption of sustainable practices are key to achieve this. This is possible with the contribution of highly knowledgeable professionals and skilled workers. However, different countries, including Malta are facing skill gaps and resource shortages. The purpose of this paper is to define the existing skill gaps and mismatches in climate change adaptation in the built environment in Malta. The research focuses on the positionality of the professionals working in the sector as they operate within a legal framework guided through various policies, and through their role and responsibility, they are in contact with the other stakeholders in the sector.

Design/methodology/approach
The data generation strategy used in this study involved a pragmatic approach through a mixed method research methodology, namely, interviews, a questionnaire and a focus group discussion. The three tier scaffolding approach in the data generation strategy allowed for a progressive validation of the data generated.

Findings
The research indicates that the professionals in the sector are aware of their roles and responsibilities to address climate change in their practices, and they have the disposition to acknowledge the need of continuous professional training. Moreover, this study points out that the professionals in the built environment sector are concerned about other gaps within the industry and not solely by skill gaps. Their responsibility to address climate change through greener solutions is often hindered by fragmentation in the system including bureaucratic procedures, clients’ demands, lack of enforcement and general education of the need to address and adapt climate change among the general public. The professionals appeal for an overhaul in the “culture” of the construction industry through a comprehensive rather than a piecemeal approach. This research puts in the limelight the need of a comprehensive strategy to address skill gaps and mismatches in accordance with the need for climate change adaptation as the ultimate challenge rather than addressing different issues separately within the sector.

Originality/value
The paper is to define the existing skill gaps and mismatches in climate change adaptation in the built environment in Malta. By identifying these skill gaps and mismatches, it would be possible to devise an action plan to iron-out such hindrances as part of a broader climate action adaptation strategy.