bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpersonal Brain Synchronization in Social Pain Contexts: An fNIRS-Based Exploration of Empathy
Authors: Lian Tao , Jiao Zhibin , Song Juan , Zhang Peng 
Published: January 2025

Abstract
Social pain is a common occurrence in interpersonal interactions, yet limited research has explored the neural mechanisms underlying both social pain and social pain empathy. Existing studies often focus on the neural processes of individuals experiencing pain, referred to as “subjects,” or those empathizing with them, known as “observers.” This study examines the neural mechanisms involved in the process of social pain empathy from the perspective of interpersonal brain synchronization (IBS). To do so, we employed functional near-infrared spectroscopy (fNIRS) to simultaneously scan the brains of both subjects and observers in social pain scenarios created using the Cyberball paradigm. The study’s findings indicate that in social pain contexts, the IBS among dyads composed of subjects and observers was significantly enhanced in the dorsolateral prefrontal cortex (dlPFC) compared to non-social pain contexts. This brain region is associated with emotion regulation. Furthermore, we found that this enhancement depended on the observers’ levels of rejection sensitivity. This study provides the inaugural exploration into the neural mechanisms underlying social pain empathy through the lens of IBS.
Gendered wealth and the challenges of child support in India
Authors: Garnaik Upasana 
Published: January 2025

Abstract
In this paper, I examine the challenges in the legal processes of securing child support in India. Drawing from a qualitative study of family disputes—including ethnographic observations in courts, mediation centers, and legal offices, as well as in-depth interviews and archival research, I reveal how gendered institutional practices shape child support negotiations, often to the detriment of women. I make three significant contributions. First, while much research has focused on judicial decision making in family law disputes, I turn my attention to mediation, a growing method of dispute resolution, to show how this private ordering of family law often places women in financially precarious positions. Second, building on the concept of relational work, I show how mediators perform institutional gendered relational work and persuasive relational work in their roles as facilitators and reinforce inequality by reproducing gendered expectations and constructing notions of parenthood. Third, I demonstrate how women’s privileged class status does not necessarily guarantee favorable outcomes. Instead, gendered institutional dynamics intersect with systemic failure to perpetuate the gendered wealth gap, pushing women into debt, economic dependence, and financial insecurity. By analyzing these processes, this paper underscores how legal processes create persistent barriers to economic equality contributing to the gendered wealth gap and provides critical insights into the economic conditions of separated and divorced women.
The intergenerational reproduction of self-direction at work: Revisiting Class and Conformity
Authors: Burger Kaspar , Mele Francesca , Johnson Monica Kirkpatrick , Mortimer Jeylan , Han Xiaowen 
Published: January 2025

Abstract
In his path-breaking monograph, Class and Conformity, Melvin Kohn reasoned that parents prepare their children for the same conditions of work that they themselves experience. Kohn and his colleagues’ research focused on the influence of parental self-direction at work on parental child-rearing values and practices, as well as the self-directed values of children. The intergenerational transmission of occupational self-direction from parents to the succeeding generation of adult children, strongly implied by Kohn’s analysis, has not been empirically tested. Using two-generation longitudinal data from the Youth Development Study (N = 1139), we estimate a structural equation model to assess the intergenerational continuity of occupational self-direction. We find evidence supporting a key inference of Kohn’s analysis: that self-direction at work, a primary feature of jobs of higher social class standing, is transmitted across generations via self-directed psychological orientations, operationalized here as intrinsic work values. Intrinsic values also significantly predicted second-generation educational attainment, contributing further to the reproduction of socioeconomic inequality. The findings enhance understanding of the intergenerational transmission of advantage.
Adult Human Heart ECM Improves Human iPSC-CM Function via Mitochondrial and Metabolic Maturation
Authors: Gulberk Ozcebe S , Tristan Mateo , Zorlutuna Pinar 
Published: January 2025

Abstract
Myocardial infarction can lead to the loss of billions of cardiomyocytes, and while cell-based therapies are an option, immature nature of in vitro-generated human induced pluripotent stem cell (iPSC)-derived cardiomyocytes (iCMs) is a roadblock to their development. Existing iPSC differentiation protocols don’t go beyond producing fetal iCMs.
Recently, adult extracellular matrix (ECM) was shown to retain tissue memory and have some success driving tissue-specific differentiation in unspecified cells in various organ systems. Therefore, we focused on investigating the effect of adult human heart-derived ECM on iPSC cardiac differentiation and subsequent maturation. By preconditioning iPSCs with ECM, we tested whether creating cardiac environments around iPSCs would drive iPSCs toward cardiac fate and which ECM components might be involved.
We report novel high- and low- abundance proteomes of young, adult, and aged human hearts, with relative abundances to total proteins and each other. We found that adult ECM had extracellular galactin-1, fibronectin, fibrillins, and perlecan (HSPG2) which are implicated in normal heart development. We also showed preconditioning iPSCs with adult cardiac ECM resulted in enhanced cardiac differentiation, yielding iCMs with higher functional maturity, more developed mitochondrial network and coverage, enhanced metabolic maturity, and shift towards more energetic profile.
These findings demonstrate the potential use of cardiac ECM in iCM maturation and as a promising strategy for developing iCM-based therapies, disease modeling, and drug screening studies. Upon manipulating ECM, we concluded that the beneficial effects observed were not solely due to the ECM proteins, which might be related to the decorative units attached.
Policy in practice: Cystic Fibrosis Australia and Phage Australia surveys: understanding clinical needs and attitudes towards phage therapy in the cystic fibrosis community
Authors: Lynch Stephanie , Sinclair Holly , Khatami Ameneh , Mileham Nicki , Sacher Jessica C , Zheng Jan , Lin Ruby C Y , Iredell Jonathan 
Published: January 2025

Abstract
Cystic fibrosis (CF) is the most prevalent serious inherited disease in Australia, imposing significant health risks. CF is characterized by chronic lung inflammation and recurrent pulmonary infections that increase morbidity and premature mortality rates. The emergence of antimicrobial resistance (AMR) places further challenges on the treatment and management of CF, necessitating research into alternative strategies for treatment of bacterial infections. Bacteriophage therapy, involving bacterial-specific viruses, is a potential avenue for AMR infections in patients with CF. Existing literature supports the feasibility of phage therapy in CF but there has been a gap in investigating attitudes of the CF community including affected individuals and their caregivers, regarding phage therapy. Understanding perspectives and needs of the CF community is essential for successful implementation and acceptance of novel therapies including phage therapy. We conducted a survey that encompasses responses from 112 consumers from across Australia, comprising people living with CF (38.4%), parents of affected children (49.6%), carers (6.4%), and family members (3%). The findings showed a significant reliance on antibiotics with 51.4% requiring oral, 43.4% nebulized, and 11.4% intravenous antibiotics within the preceding 2 weeks. Respondents highlighted the availability of new treatments, duration of hospitalizations and costs associated with treatment as important priorities to address. Despite an awareness of phage therapy among 62.4% of respondents, 86.4% expressed interest in obtaining more information, primarily from medical staff (66.7%). Notably, 96.0% of respondents expressed willingness to participate in phage therapy trials. The results of this survey highlighted the CF community’s strong interest in advanced therapeutic approaches, specifically phage therapy. The findings reveal a notable recognition and acceptance of phage therapy as a viable treatment option for pulmonary infections associated with CF. This study addresses UN Sustainable Development Goal 3: Good Health and Wellbeing by advancing knowledge on alternative therapeutic strategies for managing AMR in CF. By exploring community attitudes towards bacteriophage therapy, the research promotes informed development and implementation of innovative, targeted treatments for CF-associated infections. These findings support the sustainable management of AMR, fostering better health outcomes and reducing reliance on traditional antibiotics, thereby contributing to long-term health resilience.
An arginine switch drives the stepwise activation of β-arrestin
Authors: Ji Jeong Seok , Yun Yaejin , Stepniewski Tomasz Maciej , Yoon Hye-Jin , Min Kyungjin , Park Ji Young , Chung Chiwoon , Chung Ka Young , Selent Jana , Lee Hyung Ho 
Published: January 2025

Abstract
β-arrestins (βarrs) play a crucial role in regulating G protein-coupled
receptor (GPCR) signaling and trafficking. Canonically, interactions of βarr
with the phosphorylated intracellular GPCR-tail induce a multi-step
conformational transition that results in the activation of βarr. Depending on
the specific interaction pattern with the receptor, βarrs adopt multiple
conformational states, each tightly linked to a specific functional outcome of
βarr recruitment. Despite its physiological relevance, the structural
determinants of βarr activation remain poorly understood. Using a combination of
molecular dynamics simulations, biochemical and cell-based experiments, we
reveal how specific interactions with a prototypical GPCR promote the unbinding
of the βarr2 C-tail—a crucial step in arrestin activation. Importantly, we
observe that the expulsion of the C-tail is promoted by the displacement of a
conserved arginine residue (Arg394) within the βarr polar core, which we dub
“the arginine switch.” Our study uncovers a previously unknown molecular switch
that, upon engagement, destabilizes the polar core as a crucial step in the
GPCR-induced βarr activation.
Melchior: A Hybrid Mamba-Transformer RNA Basecaller
Authors: Litman Elon 
Published: January 2025

AbstractSequence transduction from raw nanopore signals is notoriously difficult because the signal level does not naturally correspond to a single base, but rather many adjacent nucleotides. Thus, we introduce Melchior, an RNA basecaller that uses a hybrid Mamba-Transformer backbone to achieve global visual context at a lower computational complexity. This is in contrast to temporal convolutions, which collate features by fusing both spatial and channel features in the local receptive field. Melchior is also able to exploit the full complementarity between local and global features, unlike Vision Transformers, which have empirically been observed to ignore local features. Augmenting a selective structured state-space sequence model with self-attention unlocks unprecedented performance gains, particularly in homopolymer regions, by modeling fine-grained details in both short and long-range spatial dependencies.
A Fine-tuned ProtGPT2 (transformer model) for Predicting more Virulent
SARS-CoV-2 variants and understanding its virulence by biophysical
methods
Authors: Dhamodharan Sam Paul , Jeyaraj Abraham Rebairo , Siddalingappa Rashmi , Venkatachalam Rajakannan , Kothandan Gugan 
Published: January 2025

Abstract
The emergence of Variants of Concern (VOCs) of SARS-COV2 with increased
virulence and transmissibility has been linked to multiple mutations in the RBD
region, altering their antigenic properties. In this study, we used a
specialized ProtGPT2 model trained on the SARS-COV2 spike protein to forecast
probable mutations on the spike protein that have not yet emerged. Upon
prediction, we systematically studied the stability of single-site and multisite
mutations using unbiased molecular dynamics simulations. Binding free energies
were used to study the physicochemical significance of the mutations and their
affinity to human ACE2 receptor. Our results show that there are specific
hot-spots that mutate in the spike protein that enhance binding affinity through
electrostatic and improved non-bonded interactions and highlight the role of
specific energetic contributions in viral adaptation and infectivity. Our
analysis revealed that the reduction of a disulphide bridge within sites 480-488
lowered the binding free energy and increased the flexibility of the loop
region, enhancing its interface interaction with ACE, leading to a more virulent
variant than Omicron.
Three annotated chromosome-levelde novogenome assemblies ofLomentospora prolificansprovide evidence for a chromosomal translocation event
Authors: Grossman Nina T , Fan Yunfan , Zimin Aleksey V. , Wear Maggie P. , Jedlicka Anne , Dziedzic Amanda , Liporagi-Lopes Livia , Timp Winston , Casadevall Arturo 
Published: January 2025

AbstractLomentospora prolificansis a fungal pathogen responsible for serious, often fatal, illness in patients with compromised immune systems. Treatment is rarely successful becauseL. prolificansis inherently resistant to all major classes of antifungal drugs. In this study we publish three chromosome-levelde novogenome assemblies, including the first complete-level assembly ofL. prolificans, along with genome annotations. The L. prolificans genome is packaged in 11 nuclear chromosomes and one mitochondrial chromosome, has 36.7-37.1 Mb, and encodes for a putative 7357-7640 genes. The length and composition of contigs in one stain varied from those of the other two strains, supporting the hypothesis that a chromosomal translocation took place. These assemblies were confirmed with pulsed-field gel electrophoresis. The availability of more complete genomes will hopefully help the search for new antifungal drugs and provides insights into the evolutionary history of this pathogenic fungus.
Hybrid zone analysis using coalescent-based estimates of introgression and migration
Authors: Leaché Adam D. , Davis Hayden R. , Singhal Sonal 
Published: January 2025

AbstractHybrid zones can serve as natural experiments allowing us to investigate the evolutionary consequences of introgression between distinct populations with divergent genomic backgrounds. Modeling hybrid zones using a coalescent framework can provide critical insights into the historical demography of populations, including population divergence times, population sizes, introgression proportions, migration rates, and the timing of hybrid zone formation. We used coalescent analyses to test whether a hybrid zone between Plateau Fence Lizard (Sceloporus tristichus) populations in Arizona formed recently because of human-induced landscape alterations or originated during Pleistocene climatic shifts. Introgression analysis places the divergence time between the parental populations at approximately 140 kya and their secondary contact and hybridization at approximately 10 kya at the end of the Pleistocene. Introgression proportions for hybrid populations are correlated with their geographic distance from the parental populations, a pattern that is repeated with admixture proportions and hybrid index values. The multispecies coalescent with migration model supports asymmetric migration rates with a bias for gene flow moving towards the northern end of the hybrid zone. The direction of this asymmetry is consistent with spatial cline analyses that suggest a slow but steady northward shift of the center of the hybrid zone. When analyzing hybrid populations sampled along a linear transect, coalescent methods can provide novel insights into the evolutionary history of hybrid zone formation that complement existing spatial and genomic methods.
SqueezeCall: Nanopore basecalling using a Squeezeformer network
Authors: Zhu Zhongxu 
Published: January 2025

ABSTRACTNanopore sequencing, a novel third-generation sequencing technique, offers significant advantages over other sequencing approaches, owing especially to its capabilities for direct RNA sequencing, real-time analysis, and long-read length. During nanopore sequencing, the sequencer measures changes in electrical current that occur as each nucleotide passes through the nanopores. A basecaller identifies the base sequences according to the raw current measurements. However, due to variations in DNA and RNA molecules, noise from the sequencing process, and limitations in existing methodology, accurate basecalling remains a challenge. In this paper, we introduce SqueezeCall, a novel approach that uses an end-to-end Squeezeformer-based model for accurate nanopore basecalling. In SqueezeCall, convolution layers are used to down sample raw signals and to model local dependencies. A Squeezeformer network is employed to capture the global context. Finally, a connectionist temporal classification (CTC) decoder generates the DNA sequence by a beam search algorithm. Inspired by the Wav2vec2.0 model, we masked a proportion of the time steps of the convolution outputs before feeding them to the Squeezeformer network and replaced them with a trained feature vector shared between all masked time steps. Experimental results demonstrate that this method enhances our model’s ability to resist noise and allows for improved basecalling accuracy. We trained SqueezeCall using a combination of three types of loss: CTC-CRF loss, intermediate CTC-CRF loss, and KL loss. Ablation experiments show that all three types of loss contribute to basecalling accuracy. Experiments on multiple species further demonstrate the potential of the Squeezeformer-based model to improve basecalling accuracy and its superiority over a recurrent neural network (RNN)-based model and Transformer-based models.
End-to-end prediction of clinical outcomes in head and neck squamous cell carcinoma with foundation model-based multiple instance learning
Authors: Rabasco Meneghetti Asier , Ligero Hernández Marta , Kuehn Jens-Peter , Löck Steffen , Itzel Carrero Zunamys , Perez-Lopez Raquel , Bressem Keno , Brinker Titus K. , Pearson Alexander T. , Truhn Daniel , Nebelung Sven , Kather Jakob Nikolas 
Published: January 2025

AbstractBackgroundFoundation models (FMs) show promise in medical AI by learning flexible features from large datasets, potentially surpassing handcrafted radiomics. Outcome prediction of head and neck squamous cell carcinomas (HNSCC) with FMs using routine imaging remains unexplored.PurposeTo evaluate end-to-end FM-based multiple instance learning (MIL) for 2-year overall survival (OS), locoregional control (LRC), and freedom from distant metastasis (FFDM) prediction and risk group stratification using pretreatment CT scans in HNSCC.Materials and MethodsWe analyzed data of 2485 patients from three retrospective HNSCC cohorts (RADCURE, HN1, HN-PET-CT), treated between 2004 and 2017 with available pre-treatment CTs and primary gross tumor volume (GTVp) segmentations. The RADCURE cohort was split into training (n=1464) and test (N=606), with HN1 (n=131) and HN-PET-CT (n=284) as additional test cohorts. FM-based MIL models (2D, multiview and 3D) for 2-year endpoint prediction and risk stratification wre evaluated based on area under the receiver operator curve (AUROC) and Kaplan-Meier (KM) with hazard ratios (HR), compared with radiomics and assessed for multimodal enhancement with clinical baselines.Results2D MIL models achieved 2-year test AUROCs of 0.75-0.84 (OS), 0.66-0.75 (LRC) and 0.71-0.78 (FFDM), outperforming multiview and 3D MIL (AUROCs: 0.50-0.77, p≥0.15) and comparable or superior to radiomics (AUROCs: 0.64-0.74, p≥0.012). Significant stratification was observed (HRs: 2.14-4.77, p≤0.039). Multimodal enhancement of 2-year OS/FFDM (AUROCs: 0.82-0.87, p≤0.018) was observed for patients without human papilloma virus positive (HPV+) tumors.ConclusionFM-based MIL demonstrates promise in HNSCC risk prediction, showing similar or superior performance to radiomics and enhancing clinical baselines in non-HPV+ patients.Key ResultsFirst end-to-end study using both foundation models and multiple instance learning for outcome prediction in head and neck squamous cell carcinoma.Multiple instance learning approaches predict clinically-relevant 2-year endpoints and stratify patients across external cohorts with similar or better performance than handcrafted radiomics.Multimodal inclusion of clinical and multiple instance learning information improve clinical baseline models in patients without human papillomavirus positive tumors.
Factors influencing the prescription of first-line treatment for type 2 diabetes mellitus: a systematic review
Authors: Moreira Helena , Moreira Fernando , Jesus Ângelo , Monteiro-Soares Matilde , Santos Paulo 
Published: January 2025

AbstractIntroductionUnderstanding and predicting prescription preferences for type 2 diabetes mellitus, a heterogeneous and complex condition that affects over 10% of the global adult population, can improve prescribing practices, guide policymakers in promoting evidence-based medicine, and help tailor first-line treatments to individual characteristics or specific subgroups, improving patient outcomes. This study aimed to identify factors influencing metformin prescription, the first-line therapy recommended in Western guidelines, and to assess factors leading to its avoidance and their alignment with evidence-based medicine. It also explores factors associated with initial combination therapy, a newer and controversial approach compared to stepwise therapy.MethodsWe performed a systematic search in PubMed, Scopus and Web of Science for observational analytical studies evaluating factors associated with metformin or combination therapy initiation. Quality assessment was done using the Joanna Briggs Institute critical appraisal checklists. (PROSPERO registry numberCRD42023438313).ResultsThirty studies were included, evaluating 105 variables, mostly (62%) assessed in one study. The 25 variables using combination therapy as outcome were mostly (72%) evaluated also in one study. Initial metformin prescription was strongly associated with the age of individuals with diabetes, glycated haemoglobin levels, body mass index, and renal complications, while combination therapy was mainly linked with glycated haemoglobin levels and comorbidities. Findings also highlighted a discrepancy between clinical practice and evidence-based recommendations. However, concerns were raised regarding both the internal and external validity of the included studies.ConclusionOur systematic review, that offers insights into real-world clinical practices, indicated that there is a misalignment between clinical practices and evidence-based recommendations supporting the need for interventions of this field.