bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visceral Fat Predicts New-Onset Diabetes After Necrotizing Pancreatitis
Authors: Trikudanathan Guru , Abdallah Mohamed , Munigala Satish , Vantanasiri Kornpong , Jonason David , Faizi Nauroze , Schat Robben , Chauhan Anil , Freeman Martin L. , Bellin Melena D. 
Published: January 2024

Objectives
We aimed to estimate the incidence of new-onset diabetes (NOD) and identify risk factors for NOD in patients with necrotizing pancreatitis (NP).

Methods
Necrotizing pancreatitis patients were reviewed for NOD, diagnosed >90 days after acute pancreatitis. Baseline demographics, comorbidities, clinical outcomes, computed tomography (CT) characteristics of necrotic collections, and CT-derived abdominal fat measurements were analyzed to identify predictors for NOD.

Results
Among 390 eligible NP patients (66% men; median age, 51 years; interquartile range [IQR], 36–64) with a median follow-up of 400 days (IQR, 105–1074 days), NOD developed in 101 patients (26%) after a median of 216 days (IQR, 92–749 days) from NP. Of the NOD patients, 84% required insulin and 69% developed exocrine pancreatic insufficiency (EPI). Age (odds ratio [OR], 0.98), male sex (OR, 2.7), obesity (OR, 2.1), presence of EPI (OR, 2.7), and diffuse pancreatic necrosis (OR, 2.4) were independent predictors. In a separate multivariable model assessing abdominal fat on CT, visceral fat area (highest quartile) was an independent predictor for NOD (OR, 3.01).

Conclusions
New-onset diabetes was observed in 1 of 4 patients with NP, most within the first year and requiring insulin. Male sex, obesity, diffuse pancreatic necrosis, development of EPI, and high visceral adiposity identified those at highest risk.
Telemedicine and Cancer Clinical Research
Authors: von Itzstein Mitchell S. , Gwin Mary E. , Gupta Arjun , Gerber David E. 
Published: January 2024

Abstract
Telemedicine represents an established mode of patient care delivery that has and will continue to transform cancer clinical research. Through telemedicine, opportunities exist to improve patient care, enhance access to novel therapies, streamline data collection and monitoring, support communication, and increase trial efficiency. Potential challenges include disparities in technology access and literacy, physical examination performance, biospecimen collection, privacy and security concerns, coverage of services by insurance, and regulatory considerations. Coupled with artificial intelligence, telemedicine may offer ways to reach geographically dispersed candidates for narrowly focused cancer clinical trials, such as those targeting rare genomic subsets. Collaboration among clinical trial staff, clinicians, regulators, professional societies, patients, and their advocates is critical to optimize the benefits of telemedicine for clinical cancer research.
A Systematic Review of the Application of Simulation to Promote Empathy in Nursing Education
Authors: Juan Samantha , O'Connell Kathleen A. 
Published: January 2024

Summary Statement
This systematic review aimed to identify, appraise, and synthesize evidence for the effectiveness of simulation modalities in promoting nursing students' empathy. The Preferred Reporting Items for Systematic Reviews and Meta-Analysis was followed with 20 studies included. The Medical Education Research Study Quality Instrument (MERSQI) was used to evaluate the quality of the publications. The mean MERSQI score was 10.95 with an SD of 1.62, which was above the average in the literature.
Five simulation modalities were identified: standardized patient, simulated suit, manikin, virtual simulation, and virtual reality simulation. Most of the studies (n = 15) reported significant differences in the measured outcomes after their simulation activities, including all 5 simulation modalities, but the most effective modality was the simulation suit. The simulation suit replicates the lived experiences of others, which enhances perspective taking by “turning the student into the patient” through the physical and sensory effects of simulated suits. However, outcome measures were limited to self-report instruments in the studies.
How to Partner With Persons Living With Mental Health Conditions
Authors: Cavanagh Frances C. , Chevalier Natalie , Timmermans Katherine E. , Killam Laura A. 
Published: January 2024

Summary Statement
Screen-based simulation is an effective educational strategy that can enhance health care students' engagement with content and critical thinking across various topics, including mental health. To create relevant and realistic simulations, best-practice guidelines recommend the involvement of experts in the development process. We collaborated with persons with lived experience and community partners to cocreate a mental health-focused screen-based simulation. Cocreating meant establishing a nonhierarchical partnership, with shared decision-making from start to finish.
In this article, we present 8 principles developed to guide our cocreation with persons with lived experience: person-centeredness, trauma-informed approaches and ethical guidance, supportive environment, two-way partnership, mutual respect, choice and flexibility, open communication, and room to grow. These principles provide practical guidance for educators seeking to engage the expertise of persons who have been historically disadvantaged in society. By sharing these principles, we strive to contribute to a more equitable process in simulation development and promote meaningful, respectful, and safer collaborations.
Systematic discovery of directional regulatory motifs associated with human insulator sites
Authors: Osato Naoki , Hamada Michiaki 
Published: January 2024

AbstractInsulator proteins act as a barrier of enhancer–promoter interactions (EPIs). The main insulator protein in vertebrates is CTCF, a DNA-binding protein (DBP). However, other DBPs associated with insulators of EPIs are still unclear. Hence, we developed a systematic, comprehensive deep learning-based approach for identifying the DNA motifs of DBPs associated with insulators. We discovered 97 directional and minor nondirectional motifs in human fibroblast cells that corresponded to 23 DBPs related to insulator function, CTCF, and/or other types of chromosomal transcriptional regulation reported in previous studies. The estimated CTCF orientation bias was consistently proportional to CTCF orientation bias observed in chromatin interactions. The motifs were significantly more abundant at insulator sites separated by repressive and active regions, at boundary sites identified by chromatin interaction data, and at splice sites than other DBPs. Finally, the insulator-pairing model explains that homologous and heterologous insulator-insulator pairing interactions are orientation-dependent. These findings contribute to elucidate novel transcriptional regulations.
A novel and efficient Apple Latent Spherical Virus-based gene silencing method for functional genomic studies inChenopodium quinoa
Authors: Melgar Alejandra E. , Palacios María B. , Martínez Tosar Leandro J. , Zelada Alicia M. 
Published: January 2024

AbstractQuinoa (Chenopodium quinoaWilld.), with its resilience in harsh environments and excellent nutritional value, has become crucial for global food security. Despite recent progress in genomic research, the inability to perform functional studies in quinoa due to the absence of transformation techniques remains a significant obstacle. In this work, we present the development of a novelApple Latent Spherical Virus(ALSV)-mediated virus-induced gene silencing (VIGS) protocol that will allow to perform functional genomics studies in quinoa in a fast and simple way. The method was fine-tuned using ALSV plasmids that carry partial gene sequences of phytoene desaturase (PDS) fromNicotiana benthamianaand quinoa. The developed technique involves an initial inoculation inNicotianaplants through agroinfiltration withAgrobacterium tumefacienscultures carrying the different viral constructs. Viral extracts were prepared using local or systemic leaves, which were then used as inoculum to infect quinoa leaves through mechanical damage. The method was successfully tested in two contrasting quinoa varieties, although some differences were observed in infection phenotype and viral susceptibility. The effect of insertion sequence size in the viral vectors was also analyzed, resulting in differences in bleaching or chlorosis phenotype and impact on plant growth. The presence of the virus in infected plants was confirmed, and the reduction in PDS gene expression in silenced plants was verified. Because quinoa lacks stable transformation protocols, limiting heterologous expression assays, our ALSV-based VIGS protocol is very attractive for loss-of-function gene studies.
Bypassing PELO-mediated ATPase activation of NLR is a common pathogenic cause ofNLR-associated autoinflammatory diseases
Authors: Wu Xiurong , Yang Zhang-Hua , Zheng Yue , Wu Jianfeng , Han Jiahuai 
Published: January 2024

SUMMARYNucleotide-binding and oligomerization domain (NOD)-like receptors (NLRs) constitute the largest family of pattern recognition receptors. These receptors are master regulators of innate immunity. Recently, PELO-driven ATPase activation of NLRs was demonstrated as a critical step in NLR activation. Linkage studies in human with various inherited autoinflammatory conditions have revealed an extensive array of mutations and polymorphisms within NLRs. However, the precise mechanisms by which genetic variations in NLR genes contribute to disease onset remain largely elusive. Here we comprehensively analyze dozens of naturally occurring mutations across multiple human NLRs, and demonstrate thatNLRsharboring pathogenic mutations in their NACHT domain—not those with non-pathogenic variants—exhibit spontaneous PELO-independent ATPase activation. This aberrant activation triggers corresponding NLR to mediate inflammatory responses. Thus, bypassing the PELO-checkpoint for ATPase activation is a major disease-causing mechanism underlyingNLRmutations. Furthermore, quantifying this aberrant ATPase activation could serve as an assessment tool for classifying the pathogenesis ofNLR-associated diseases.
NeuralTE: an accurate approach for Transposable Element superfamily classification with multi-feature fusion
Authors: Hu Kang , Xu Minghua , Gao Xin , Wang Jianxin 
Published: January 2024

AbstractMotivationClassifying Transposable Elements (TEs) at the superfamily level offers deeper insights into species variation and evolution. Recent advancements in third-generation sequencing technologies have made a large number of genomes from non-model species becoming available. However, existing TE classification methods suffer from several limitations, including the necessity to train multiple hierarchical classification models, the incapacity to perform classification at the superfamily level, and deficiencies in both accuracy and robustness. Therefore, there is an urgent need for an accurate TE classification method to improve genome annotation.ResultsIn this study, we develop NeuralTE, a deep learning method designed to classify transposons at the superfamily level. To achieve accurate TE classification, we identify various structural features of transposons, and use different combinations of k-mers for terminal repeats and internal sequences to uncover distinct patterns. Evaluation on all transposons from Repbase shows that NeuralTE outperforms existing deep learning, machine learning, and homology-based methods in classifying TEs. Testing on the transposons from novel species highlights the superior performance of NeuralTE compared to existing methods. We also conduct TE annotation experiments on rice using different classification tools, and the results show that NeuralTE achieves annotations nearly identical to the gold standard, highlighting its robustness and accuracy in classifying transposons.AvailabilityNeuralTE is publicly available athttps://github.com/CSU-KangHu/NeuralTE.
Functionalising the electrical properties of Kombucha zoogleal mats for biosensing applications
Authors: Nikolaidou Anna , Chiolerio Alessandro , Dehshibi Mohammad Mahdi , Adamatzky Andrew 
Published: January 2024

AbstractKombucha is a type of tea that is fermented using yeast and bacteria. During this process, a film made of cellulose is produced. This film has unique properties such as biodegradability, flexibility, shape conformability, and ability to self-grow, as well as be produced across customised scales. In our previous studies, we demonstrated that Kombucha mats exhibit electrical activity represented by spikes of electrical potential. We propose using microbial fermentation as a method forin situfunctionalisation to modulate the electroactive nature of Kombucha cellulose mats, where graphene and zeolite were used for the functionalisation. We subjected the pure and functionalised Kombucha mats to mechanical stimulation by applying different weights and geometries. Our experiments demonstrated that Kombucha mats functionalised with graphene and zeolite exhibit memfractive properties and respond to load by producing distinctive spiking patterns. Our findings present incredible opportunities for thein situdevelopment of functionalised hybrid materials with sensing, computing, and memory capabilities. These materials can self-assemble and self-grow after fusing their living and synthetic components. This study contributes to an emergent area of research on bioelectronic sensing and hybrid living materials, opening up exciting opportunities for use in smart wearables, diagnostics, health monitoring and energy harvesting applications.
Nuclear reassembly defects after mitosis trigger apoptotic and p53-dependent safeguard mechanisms inDrosophila
Authors: Li Jingjing , Jordana Laia , Mehsen Haytham , Wang Xinyue , Archambault Vincent 
Published: January 2024

ABSTRACTIn animals, mitosis involves the breakdown of the nuclear envelope and the sorting of individualized, condensed chromosomes. During mitotic exit, emerging nuclei reassemble a nuclear envelope around a single mass of interconnecting chromosomes. The molecular mechanisms of nuclear reassembly are incompletely understood. Moreover, the cellular and physiological consequences of defects in this process are largely unexplored. Here, we have characterized a mechanism essential for nuclear reassembly inDrosophila. We show that Ankle2 promotes the PP2A-dependent recruitment of BAF and Lamin at reassembling nuclei, and that failures in this mechanism result in severe nuclear defects after mitosis. We then took advantage of perturbations in this mechanism to investigate the physiological responses to nuclear reassembly defects during tissue developmentin vivo. Partial depletion of Ankle2, BAF or Lamin in imaginal wing discs results in wing development defects accompanied by apoptosis. We found that blocking apoptosis strongly enhances developmental defects. Blocking p53 does not prevent apoptosis but enhances defects due to the loss of a cell cycle checkpoint. Our results suggest that apoptotic and p53-dependent responses play a crucial role in safeguarding tissue development in response to sporadic nuclear reassembly defects.
Depression is a more significant predictor for wellbeing in Inclusion Body Myositis than physical disability
Authors: Nunn G. , Glenister G. , Hird K. , Beer K. , Cooper I. , Needham M. , Brusch A. 
Published: January 2024

AbstractObjectives(1) determine if there is a correlation between disability, depression, and wellbeing in people with IBM, (2) determine if disability and depression can predict wellbeing in people with IBM, and (3) identify the prevalence of depression and impaired wellbeing in participants with IBM.MethodsIn this cross-sectional study, 101 participants with IBM completed the Neuromuscular Symptom Score (NSS), Personal Wellbeing Index (PWI), and Patient Health Questionnaire-9 (PHQ-9) surveys to serve as surrogate measures of physical disability, wellbeing, and depression respectively.ResultsLinear regression identified that PHQ-9 significantly predicts PWI, however NSS does not, with a negative predictive value of depression for wellbeing (−2.7513, p < 0.001) and a positive predictive value of disability for wellbeing (0.0575, p = 0.764). Moderate to severe depression was reported in 78.2% of participants, and all but one participant reported reduced wellbeing.ConclusionsDepression is a more significant predictor of wellbeing than disability in participants diagnosed with IBM. There was a high prevalence of depression and reduced wellbeing in participants, highlighting the importance of assessing these factors to optimise treatment in IBM.
Plasma Metabolic Profiling Analysis of Heart Failure with Preserved Ejection Fraction Patients Based on UHPLC-MS/MS
Authors: Abudurexiti Muyashaer , Naman Tuersunjiang , qin Duan dong , Aimaier Salamaiti , Mahemuti Ailiman 
Published: January 2024

AbstractBackgroundHeart failure with preserved ejection fraction (HFpEF) is a complex disease characterized by metabolic disturbances that can have various pathophysiological implications.MethodsData were collected from a prospective cohort consisting of 30 HFpEF participants and 30 healthy controls, matched by gender and age. untargeted metabolomic profiling UHPLC-MS/MS was performed on Venous blood. The analyses aimed to reveal the differences in plasma metabolic characteristics between HFpEF participants and healthy controls using untargeted metabolomics. Initial steps included Principal Components Analysis (PCA), Partial Least Squares-Discriminant Analysis (PLS-DA), and hierarchical clustering analysis to detect differing compounds groups. Subsequently, Receiver Operating Characteristic (ROC) curve analysis and pathway analysis of the different metabolites. Finally, we performed pathway enrichment analysis to identify significantly dysregulated processes.ResultsA total of 124 significantly different compounds were selected based on criteria of Variable Importance in Projection (VIP) > 1.0, Fold Change (FC) > 1.2 or FC < 0.833, and P-value < 0.05. Compared to healthy control group, the most altered metabolites in HFpEF were lipids and lipid-like molecules. KEGG enrichment and pathway impact analysis highlight the enrichment of these differentially expressed metabolites primarily in tryptophan metabolism. Hierarchical clustering results, showed varying compound levels between the two groups. ROC curve results, revealed Cytosine and 1,2-dihydroxyheptadec-16-yn-4-yl having higher AUC values.ConclusionsSignificant differences were observed in plasma metabolic profiles between HFpEF patients and healthy subjects using UHPLC-MS/MS. Cytosine appeared a potential biomarker. Tryptophan metabolism may be a novel metabolic pathway of HFpEF.
Curtailed CaSR expression in peripheral blood mononuclear cells is associated with hypertension
Authors: Bank Sarbashri , Sarkar Kunal , Chatterjee Arindam , Das Anwesha , Chakraborty Santanu , Chatterjee Srilagna , Malakar Subhajit , Pal Dilip Kumar , Karmakar Sanmoy , Mukherjee Sagar , De Subrata Kumar , Arumugam Somasundaram , Das Madhusudan 
Published: January 2024

AbstractThe calcium-sensing receptor (CaSR) is a GPCR family member. CaSR is abundantly expressed in the parathyroid gland and controls calcium homeostasis. There are no particular discoveries involving CaSR expression in hypertensive peripheral blood mononuclear cells. We investigated lower CaSR expression in hypertensive human and animal models. Nitric oxide (NO) has an important role in vascular function. Impaired NO production disrupts CaSR-mediated fine adjustment of the intra- and extracellular [Ca2+] gradients. According to the law Ca2+transportation through Ca channels maintains its connection from the circulatory micro-vascular bed to interstitial space, influenced by capillary and interstitial fluid hydrostatic pressure, as well as oncotic pressure. In that situation, the alterations in Ca2+microenvironment and dynamics remain unknown. CaSR on circulatory mononuclear cells may detect changes in the Ca2+microenvironment in the ISF of endothelial cells-VSMC and endothelium lining in hypertension. In this experiment, the decreased expression of CaSR revealed a molecular sensor in the presence of elevated blood pressure.
TDP43 aggregation at ER-exit sites impairs ER-to-Golgi transport
Authors: Wu Hongyi , Wang Loo Chien , Sow Belle M. , Leow Damien , Zhu Jin , Gallo Kathryn M. , Wilsbach Kathleen , Gupta Roshni , Ostrow Lyle W. , Yeo Crystal J. J. , Sobota Radoslaw M. , Li Rong 
Published: January 2024

AbstractProtein aggregation plays key roles in age-related degenerative diseases, but how different proteins coalesce to form inclusions that vary in composition, morphology, molecular dynamics and confer physiological consequences is poorly understood. Here we employed a general reporter based on mutant Hsp104 to identify proteins forming aggregates in human cells under common proteotoxic stress. Over 300 proteins were identified, forming different inclusions containing subsets of aggregating proteins. In particular, TDP43, implicated in Amyotrophic Lateral Sclerosis (ALS), partitions dynamically between two distinct types of aggregates: stress granule and a previously unknown solid inclusion at the ER exit sites (ERES). TDP43-ERES coaggregation is induced by diverse proteotoxic stresses and observed in the motor neurons of ALS patients. Such aggregation causes retention of secretory cargos at ERES and therefore delayed ER-to-Golgi transport, providing a link between TDP43 aggregation and compromised cellular function in ALS patients.
Cross-lingual speaker transfer for Cambodian based on feature disentangler and time-frequency attention adaptive normalization
Authors: Yang Yuanzhang , Wang Linqin , Gao Shengxiang , Yu Zhengtao , Dong Ling 
Published: January 2024

Purpose
This paper aims to disentangle Chinese-English-rich resources linguistic and speaker timbre features, achieving cross-lingual speaker transfer for Cambodian.

Design/methodology/approach
This study introduces a novel approach: the construction of a cross-lingual feature disentangler coupled with the integration of time-frequency attention adaptive normalization to proficiently convert Cambodian speaker timbre into Chinese-English without altering the underlying Cambodian speech content.

Findings
Considering the limited availability of multi-speaker corpora in Cambodia, conventional methods have demonstrated subpar performance in Cambodian speaker voice transfer.

Originality/value
The originality of this study lies in the effectiveness of the disentanglement process and precise control over speaker timbre feature transfer.