bluuebunny/crossref_metadata_2025_split huggingface dataset:
CryoVIA - An image analysis toolkit for the quantification of membrane structures from cryo-EM micrographs
Authors: Schönnenbeck Philipp , Junglas Benedikt , Sachse Carsten 
Published: January 2025

SummaryImaging of lipid structures and associated protein complexes using electron cryo-microscopy (cryo-EM) is a common visualization and structure determination technique. The quantitative analysis of the membrane structures, however, is not routine and time consuming in particular when large amounts of data are involved. Here, we introduce the automated image-processing softwarecryo-vesicle image analyzer(CryoVIA) that parametrizes lipid structures of large data sets from cryo-EM images. This toolkit combines segmentation, structure identification with methods to automatically perform a large-scale data analysis of local and global membrane properties such as bilayer thickness, size, and curvature including membrane shape classifications. We included analyses of exemplary data sets of different lipid compositions and protein-induced lipid changes through an ESCRT-III membrane remodeling protein. The toolkit opens new possibilities to systematically study structural properties of membrane structures and their modifications from cryo-EM images.
Longitudinal Stability of Mood-Related Resting-State Networks in Youth with Symptomatic Bipolar-I/II Disorder
Authors: Hafeman Danella M. , Feldman Jamie , Mak Jessica , Merranko John , Goldstein Tina R. , Gratton Caterina , Phillips Mary L. , Birmaher Boris 
Published: January 2025

ABSTRACTBipolar disorder (BD) is characterized by temporal instability of mood and energy, but the neural correlates of this instability are poorly understood. In previous cross-sectional studies, mood state in BD has been associated with differential functional connectivity (FC) amongst several subcortical regions and ventromedial prefrontal cortex. Here, we assess whether BD is associated with longitudinal instability within this mood-related network of interest (NOI). Young people with BD-I/II were scanned 4-6 times and healthy controls (HC) were scanned 4 times over 9 months. Following preprocessing of 20-minute resting-state scans, we assessed across-scan correlation of FC, focusing on FC between regions previously associated with BD mood state. Utilizing Bayesian models, we assessed the relationship between diagnostic group and within-person, across-scan correlation, adjusting for motion, time-of-day, and inter-scan interval; prediction intervals (PI) are reported. In a sample of 16 youth (11 BD, 5 HC; 16.3-23.3 years old) with 70 scans (50 BD, 20 HC), across-scan NOI stability was higher within-than between-person (0.70 vs. 0.54; p<.0001). BD (vs. HC) within-person scan-pairs showed lower NOI stability (mean -0.109; 95% PI -0.181, -0.038), distinguishing BD vs. HC with excellent accuracy (AUC=0.95). NOI instability was more pronounced with manic symptoms (mean -0.012; 95% PI -0.023, -0.0002) and in BD-II (vs. BD-I; mean -0.071; 90% PI -0.136, -0.007). Results persisted after accounting for medications, comorbidity, and sleep/arousal measures. Within this pilot sample, BD is characterized by less within-person stability of a mood-related NOI. While preliminary, these results highlight a possible role for precision imaging approaches to elucidate neural mechanisms underlying BD.
Rhythmicity of photoreceptor outer segment phagocytosis differs between the cone subtypes in the larval zebrafish
Authors: Partinen Jenni , Nevala Noora , Erämies Sanni , Ihalainen Teemu , Nymark Soile 
Published: January 2025

AbstractPhagocytosis of retinal rod and cone outer segment (OS) tips by the retinal pigment epithelium (RPE) occurs daily to prevent accumulation of harmful compounds in the photoreceptors. Rhythmic bursts of phagocytosis, seen as increased levels of phagocytosed OS particles in the RPE, are known to appear once or twice a day depending on the animal species. However, differences in the rhythmicity of phagocytosis between distinct photoreceptor types are not well understood. Here, we show that phagocytosis of cone subtype OSs does not have identical rhythmic profiles in young zebrafish larvae. We investigated this by immunolabelling histological sections from the eyes of larvae that were collected at seven different time points throughout a 24 h circadian cycle. Internalized OS particles were then quantified from confocal images. The results revealed that OSs of all cone subtypes are phagocytosed continuously at some levels in young zebrafish. Interestingly, we observed a significant increase in the OS phagosome numbers from UV and blue cones at two time points, whereas green and red cones were phagocytosed more evenly throughout the day. We also investigated whether this rhythmicity is regulated by the external light by keeping the larvae in constant darkness before sample preparation. We found that complete darkness condition dampened the peaks in OS phagosome numbers from UV and blue cones indicating that the rhythmicity is primarily driven by the external light rather than the intrinsic circadian clocks in young larval zebrafish. Our findings provide new understanding on the rhythmicity of cone OS phagocytosis and its regulation.
Immunogenomic profiling of circulating T cells in pediatric cancer patients during standard-of-care
Authors: Nabbi Arash , Jiang Yiyue , Espin Garcia Osvaldo , Mohanraj Suluxan , Pedersen Stephanie , Regala Johanna , Vernau Lauren , Perazzelli Jessica , Barrett David M. , Pugh Trevor J. 
Published: January 2025

AbstractWhile pediatric cancer patients receive intensive chemotherapy, its impact on peripheral T cells and subsequently to disease outcomes are not fully characterized. Here, we assessed T-cell dynamics during treatment, identifying associations with outcomes through immune phenotyping and T-cell Receptor (TCR) sequencing in pediatric solid and hematologic malignancies. We show that while levels of immune checkpoint proteins (PD-1, LAG3, and TIM3) at baseline were highest in lymphomas compared to other cancer groups, they increased significantly in response to therapy in all cancers. Levels of Central Memory (CM) T cells increased in leukemias and solid tumors, while naïve T cells and cell-free TCR diversity decreased in lymphomas. By combining immune cell and TCR repertoire features across all timepoints, we proposed the Dynamic Immunogenomic Score (DIS) to measure patient-specific effects of therapy on the peripheral T-cell population. Higher DIS was associated with high-risk cancer types and logistic regression analysis revealed it may predict incidence of relapse in leukemia patients. TCR specificity analysis revealed patient-specific clonal dynamics and differential detection of virally-associated TCRs in cancer patients compared to healthy individuals. Our results highlight the potential of early upfront immunogenomic profiling in identifying high-risk patients that may be predictive in light of emerging cellular immunotherapies.
A study of pelvic organs’ sizes and findings in transvaginal sonography
Authors: Adrita Farzana Rahman , Sarker Azmal Kabir , Akter Sanjida , Paul Sabuz 
Published: January 2025

ABSTRACTPurposeThis retrospective cross-sectional study evaluated the correlation among pelvic organs’ size, correlation of sizes with age, the change of uterine and cervical sizes in presence and absence of pathologies, and the pattern of ovarian volume asymmetry in the absence of pathology.Patients and methodsMeasurement of pelvic organs from all consecutive premenopausal, non-pregnant patients who underwent TVS for gynecologic workup were included in the analysis. The correlation of the sizes, and variation of sizes among a finding-based category was checked.ResultsData from 43 women with mean (±SD) age of 33.4±8.7 years were included. Among the finding-based categories, bulky uteri in comparison to normal uteri were more likely to harbor myoma or adenomyosis (Risk ratio 2.07, p < 0.01). Positive correlations were found between, antero-posterior (AP) diameter of uterus and age (R 0.4, p < 0.01), AP diameter of uterus and its length (R 0.7, p < 0.01), AP diameter of uterus and cervix (R 0.44, p < 0.01), length of uterus and that of cervix (R 0.37, p < 0.05), AP diameter of cervix and it length (R 0.47, p < 0.01) and pair of otherwise healthy ovaries (R 0.53, p < 0.01). This dataset suggests that the presence of pathologies may not always be associated with uterine enlargement (p > 0.05), but the presence of a pathology is associated with enlargement of uterine cervical AP diameter (p < 0.01) as well as its length (p < 0.05). Among the healthy pairs of ovaries, the right one was larger than the left with a significant difference between the mean volumes (p < 0.05), in 70.4% pairs.ConclusionsOverall, the findings from this small series are expected to add factual evidence to our existing concepts and help to shape some future research questions.
Correlates and Consequences of Clonal Hematopoiesis Expansion Rate: A 15-Year Longitudinal Study of 6,986 Women
Authors: Pershad Yash , Uddin Md Mesbah , Xue Liying , Haessler Jeffrey , Collins Jason M. , Mack Taralynn M. , Glick Elena , Glaser Veronica , Zhao Kun , Jaiswal Siddhartha , Manson JoAnn E. , Pandey Urvashi , Desai Pinkal , Natarajan Pradeep , Honigberg Michael C. , Kooperberg Charles , Whitsel Eric A. , Kitzman Jacob O. , Bick Alexander G. , Reiner Alexander P. 
Published: January 2025

AbstractClonal hematopoiesis of indeterminate potential (CHIP) is associated with increased mortality and malignancy risk, yet the determinants of clonal expansion remain poorly understood. We performed sequencing at >4,000x depth of coverage for CHIP mutations in 6,986 postmenopausal women from the Women’s Health Initiative at two timepoints approximately 15 years apart. Among 3,685 mutations detected at baseline (VAF ≥ 0.5%), 50% progressed to CHIP (VAF ≥ 2%) at follow-up. We confirmed that clonal expansion is highly dependent on initial clone size and CHIP driver gene, withSF3B1andJAK2mutations exhibiting the fastest growth rate. We identified germline variants inTERT,IL6R,TCL1A, andMSI2that modulate clonal expansion rate. Measured baseline leukocyte telomere length showed differential effects on incident CHIP risk, with shorter baseline leukocyte telomere length predisposing to incidentPPM1Dmutations and longer baseline leukocyte telomere length favoring incidentDNMT3Amutations. We discovered that theIL6Rmissense variant p.Asp358Ala specifically impairsTET2clonal expansion, supported by direct measurements of soluble interleukin-6 receptor and interleukin-6. Faster clonal growth rate was associated with increased risk of cytopenia, leukemia, and all-cause mortality. Notably, CHIP clonal expansion rate mediated 34.4% and 43.7% of the Clonal Hematopoiesis Risk Score’s predictive value for leukemia and all-cause mortality, respectively. These findings reveal key biological determinants of CHIP progression and suggest that incorporating growth rate measurements could enhance risk stratification.
Systematic Identification of Microtubule Inner Proteins Reveals JPT2 as a Key Regulator of Lumen Microenvironment and Drug Sensitivity
Authors: Shao Jinhui , Zhang Rui , Wu Peiyuan , Xu Honglin , Zhou Zhengrong , Gu Lusheng , Wang Lei , Ren Jinqi , Huang Xiahe , Xie Qi , Wang Yingchun , Ji Wei , Feng Wei , Liang Xin , Meng Wenxiang 
Published: January 2025

AbstractMicrotubules are primarily studied for the interactions of proteins that bind to their outer surfaces and ends, while the regulatory mechanisms within the microtubule lumen, particularly in singlet microtubules critical for essential cellular processes, remain largely unexplored. Our study provides the first systematic identification of key regulatory proteins within the single microtubule lumen. Using proximity-dependent biotin identification (Bio-ID) coupled with mass spectrometry, we identified candidate microtubule inner proteins (MIPs), including Jupiter microtubule-associated homolog 2 (JPT2). JPT2 binds directly to microtubules and specifically localizes within the lumen, where it modulates the luminal environment by inhibiting acetylase MEC17 and independently affects the binding and efficacy of Paclitaxel. Furthermore, our screening identified additional MIPs that influence cellular sensitivity to Paclitaxel, indicating a link between luminal regulation and drug responsiveness. These discoveries reveal JPT2’s critical role in singlet microtubule regulation and suggest new therapeutic targets for enhancing cancer drug sensitivity.
Specialized Molecular Pathways Drive the Formation of Light-Scattering Assemblies in Leucophores
Authors: Barzilay Y. , Eyal Z. , Noy Y. , Varsano N. , Olender T. , Bera S. , Lerer-Goldshtein T. , Kedmi M. , Porat Z. , Pinkas I. , Levin-Zaidman S. , Dezorella N. , Gur D. 
Published: January 2025

AbstractPigmentation plays a vital role in the survival of organisms, supporting functions such as camouflage, communication, and mate attraction. In vertebrates, these functions are mediated by specialized pigment cells known as chromatophores of which, uric acid crystal-forming leucophores remain the least understood, with little known about their molecular mechanisms. A key question in pigment cell biology is whether different crystal chemistries require distinct molecular pathways, or whether similar cellular processes drive the formation of diverse crystals. This study was designed to unravel the uncharacterized process of uric acid crystallization in leucophores and compare them to guanine crystal formation in iridophores and pterin formation in xanthophores. The results of our transcriptomic, ultrastructural, and metabolomic analyses, demonstrate that leucophores share molecular pathways with iridophores, particularly those connected to organelle organization and purine metabolism, but express discrete genes involved in uric acid biosynthesis and storage. Additionally, leucophores share intracellular trafficking and pterin biosynthesis genes with xanthophores, suggesting universally conserved processes. Ultrastructural studies reveal star-like fibrous structures in leucosomes, which likely serve as scaffolds for unique one-dimensional uric acid assemblies that radiate from the core and act as efficient light scatterers. These findings provide new insights into leucophore cell biology and the specialized mechanisms driving molecular crystalline assembly, and reveal that while some cellular processes are conserved, the specific chemistry of each crystal type drives the evolution of distinct molecular pathways.
The biofilm matrix protectsBacillus subtilisagainst hydrogen peroxide
Authors: Muratov Erika , Keilholz Julian , Kovács Ákos , Moeller Ralf 
Published: January 2025

AbstractBiofilms formed byBacillus subtilisconfer protection against environmental stressors through extracellular polysaccharides (EPS) and sporulation. This study investigates the roles of these biofilm components in resistance to hydrogen peroxide, a common reactive oxygen species source and disinfectant. Using wild-type and mutant strains deficient in EPS or sporulation, biofilm colonies were cultivated at various maturation stages and exposed to hydrogen peroxide. EPS-deficient biofilms exhibited reduced resilience, particularly in early stages, highlighting the structural and protective importance of the matrix. Mature biofilms demonstrated additional protective mechanisms, potentially involving TasA protein fibers. In contrast, sporulation showed limited contribution to hydrogen peroxide resistance, as survival was primarily matrix-dependent. These findings underscore the necessity of targeting EPS and other matrix components in anti-biofilm strategies, suggesting that hydrogen peroxide-based disinfection could be enhanced by combining it with complementary sporicidal treatments. This study advances our understanding of biofilm resilience, contributing to the development of more effective sterilization protocols.
Investigator-initiated versus industry-sponsored trials – Visibility and relevance of randomized controlled trials in clinical practice guidelines (IMPACT)
Authors: Hecht Manuel , Blümle Anette , Binder Harald , Schumacher Martin , Binder Nadine 
Published: January 2025

AbstractBackgroundThe goal of evidence-based medicine is to make clinical decisions based on the best available, relevant evidence. For this to be possible, studies such as randomized controlled trials (RCTs), which are widely considered to provide the best evidence of all forms of primary research, must be visible and have an impact on clinical practice guidelines. We further investigated the impact of publicly and commercially sponsored RCTs on clinical practice guidelines by measuring direct and indirect impactful citations and the time to guideline impact.MethodsWe considered the sample from the IMPACT study, where a total of 691 RCTs (120 German investigator-initiated trials (IITs), 200 international IITs, 171 German industry-sponsored trials (ISTs) and 200 international ISTs) was sampled from registries and followed prospectively. Their publications in the form of original articles and systematic reviews (SRs) citing these articles had already been identified, as well as clinical practice guidelines (CPGs) which cited either the articles or the SRs. The methods and results of this effort were already published. In this investigation we aimed to better characterize the impact of RCTs in CPGs. Therefore, we identified all citations of the original articles and SRs in the citing CPGs and classified them into impactful and non-impactful. This allowed us to calculate an estimate for the guideline impact of a trial. In addition, we estimated the time-to-guideline-impact, defined as the time to a direct and indirect impactful citation in a CPG. Direct means that the publication of a trial was cited in the main text of a CPG. Indirect means that the publication was cited and included in the findings of a SR and the SR was cited in the main text of a CPG. We also investigated to what extent pre-defined study characteristics influenced the guideline impact using multivariable negative binomial regression as well as the time-to-guideline impact using multivariable Cox proportional hazards regression.ResultsOverall, 22% of RCTs impacted a CPG. For international ISTs, only 15% of trials had an impact in CPGs. Overall, of the 405 associated guidelines, 331 were impacted. Larger trials were associated with more impactful main text citations in CPGs and earlier time-to-guideline impact, while international industry-sponsored trials were associated with smaller impact on CPGs and longer time-to-guideline impact. IITs funded by governmental bodies in Germany reached an impact on CPGs that is on par with German ISTs or international IITs and ISTs.ConclusionThis study demonstrated that a considerable number of trials previously identi-fied as being linked to CPGs have had impact in those CPGs (85%). International ISTs seem to have a lower impact on CPGs, and fewer of them influence CPGs at all.
Chiral transition and meson melting within improved holographic soft wall models
Authors: Ballon-Bayona Alfonso , Bartz Sean , Mamani Luis A. H. , Rodrigues Diego M. 
Published: January 2025

We describe the chiral transition for the quark condensate and the melting of scalar and vector mesons in two-flavor holographic quantum chromodynamics (holographic QCD). This is done by extending the improved holographic soft wall models proposed in Ballon-Bayona [] to finite temperature, by means of introducing an asymptotically anti–de Sitter black brane. We find that the chiral transition is second order in the chiral limit and a crossover for physical quark masses, as expected in two-flavor QCD. We investigate the melting of vector and scalar mesons in the deconfined plasma through the calculation of hadronic spectral functions. Fixing the model parameters by the meson spectrum at zero temperature, we find that the mesons melt at temperatures between 90 and 110 MeV and the chiral transition occurs around 129 MeV. We also provide a prediction for the hydrodynamic diffusion constant associated with a flavor current in the deconfined plasma.

Published by the American Physical Society
2025
Unpacking transformation in community music discourse
Authors: Humphrey Ryan 
Published: January 2025

PurposeTransformation has become a commonly employed phrase in the field of community music. However, there has been little critical examination of its employment. This study aimed to explore how and why community musicians and project participants used this concept to describe their experiences of community music-making programmes.Design/methodology/approachA mixed methodological approach was utilised for this study. This included conducting an extensive literature review to establish a conceptual framework of transformations meaning within community music literature. Additionally, a historiography of the use of transformation in cultural policymaking and community music practice was developed to examine how this concept has gained prominence in the discourse. Alongside this, a case study was conducted on a music-making programme for adults with a mental health diagnosis to investigate the practical application of the concept of transformation.FindingsThe research reveals that musicians and participants often use “transformation” as a metaphor to articulate the personal impacts of community music programmes. These impacts include enhanced self-confidence, a greater sense of control and shifts in how individuals perceive themselves. The widespread use of this term is influenced by the messaging of funders and policymakers, who use the concept of personal transformation to rationalise funding for arts and cultural initiatives.Originality/valueThis research provides a new perspective on transformation and its meaning in community music practice. Additionally, it highlights the interconnection between community music activity and cultural policymaking, a relationship that has yet to receive much attention from scholars across both fields.
Exploring ESG and circular economy in Brazilian companies: the role of stakeholder engagement
Authors: Provensi Tais , Marcon Maiara Lais , Sehnem Simone , Campos Lucila M.S. , Queiroz Adriane Farias S.L. de 
Published: January 2025

PurposeThis study aims to analyze how the Environmental, Social and Governance (ESG) guidelines and the Circular Economy (CE) are being internalized in the companies that are part of the Corporate Sustainability Index – ISE B3, from the perspective of the stakeholder theory.Design/methodology/approachUsing a qualitative approach, the research was developed with data analysis collected from multiple sources: documentary research in sustainability reports and websites, application of a survey, and conducting in-depth interviews with managers of ISE organizations.FindingsESG practices are internalized in the companies surveyed, highlighting aspects of waste management, relationship with communities and anti-corruption. CE practices are still at an early or intermediate stage of adoption. It was identified that in the ESG and circular dynamics, suppliers, customers and employees are primary stakeholders, which have a direct influence on the sustainability context of organizations. Integrating ESG with CE principles provides a systemic view of sustainability, going beyond fragmented approaches that treat ESG and CE as isolated initiatives.Originality/valueThe contribution of the study is associated with managerial support for decision-making. The practical examples presented can be used as a benchmarking parameter, contributing to the planning of organizations that are in the process of transition to CE. The focus on the Brazilian Stock Exchange’s Corporate Sustainability Index (ISE B3) is an original contribution, given that most studies on CE and ESG focus on developed economies or specific sectors. The study offers valuable insights into how Brazilian companies – which operate in the context of regulatory challenges.