bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of kinship‐identification methods for robust stock assessment using close‐kin mark–recapture data for Pacific bluefin tuna
Authors: Tsukahara Yohei , Nakamichi Reiichiro , Matsuura Aiko , Akita Tetsuya , Fujiwara Atushi , Suzuki Nobuaki 
Published: January 2025

AbstractSeveral attempts have been made to understand the population dynamics of fishery resources, such as tuna species using an integrated analysis model with multiple data sources. However, estimating absolute abundance levels in practical stock assessments remains a challenge. Close‐kin mark–recapture (CKMR) methods provide information about the number of adults in a population using close‐kinship pairs identified by genetic markers and statistical methods. In this study, we compared three methods for kinship identification using different algorithms in samples of wild Pacific bluefin tuna genotyped across 5029 genome‐wide single nucleotide polymorphisms in 4108 samples. The flexible relationship analyzer by random forest method we developed employs pairwise identity‐by‐descent values as inputs for random forest classification. The other two methods were CKMRsim and COLONY, which have been published and applied in several studies. These three methods were applied to the actual genotyping data with moderate missing genotypes, in addition to the pseudo‐generated genotyping data for the simulation test. The simulation test mimicked genotyping data with physical linkages as well as genetic characteristics similar to those of actual samples. The three methods resulted in different numbers of inferred kinship pairs for both generated and actual data. Particularly for the half‐sibling pairs, a considerable number of false‐positives and false‐negatives existed in the identification results. The differences in kinship identification results were interpreted based on a simulation test. This study may enhance the understanding of how each software performs when applied to single‐nucleotide polymorphism data with moderate missing genotypes, as demonstrated in this study.
Lived Employment Experiences of Young Adults With Childhood‐ and Adult‐Onset Systemic Lupus Erythematosus: A Multicenter Canadian Qualitative Study
Authors: Golding Michael A. , Nishat Fareha , Merrill Kaitlyn A. , Lacaille Diane , Oğuzoğlu Umut , Protudjer Jennifer L. P. , Woodgate Roberta L. , Stinson Jennifer N. , Peschken Christine , Touma Zahi , Lim Lily Siok Hoon 
Published: January 2025

ObjectiveThis study examined the lived employment experiences of young adults with childhood‐ and adult‐onset systemic lupus erythematosus (SLE).MethodsParticipants were recruited from three Canadian lupus clinics and asked to complete semistructured, qualitative video/phone interviews. Interviews were transcribed verbatim and analyzed using thematic analysis. Participants were recruited until consolidated thematic saturation.ResultsTwenty‐one participants (median age: 27 years)—14 woman, 5 men, and 2 gender‐nonconforming individuals—were included. Thirty‐eight percent had childhood‐onset SLE. Seventy‐one percent of the participants were employed, 19% were looking for work, and 10% were not working and not looking for work. Qualitative analysis revealed two themes. 1) “Maintaining control internally and externally”: Participants described how the ability to exercise control over their symptoms (internally) and their job (externally) allowed them to gain and maintain employment. 2) “Tough choices: Health, then work and everything else”: Participants described challenges in maintaining a balance among their health, other social responsibilities, and work because of their SLE‐related limitations. Within this theme, participants also offered advice on how others could best manage the conflicting demands on their time and energy, which was summarized in a subtheme called “Recommendations for others—‘take care of yourself first.’”ConclusionWhen faced with the competing demands of their health (managing their SLE) and work, many young adults with SLE choose to prioritize their health, sacrificing their work or social responsibilities. Efforts aimed at promoting the employment success of young adults with SLE should inform individuals of these challenges and offer potential coping strategies.
Comprehensive Insight Into Electronic Modulation of Rare‐Earth Elements for Enhancing Electrocatalytic Performance of Atomically Dispersed Materials
Authors: Cao Yanhui , Zheng Xuerong , Deng Yida , Hu Wenbin 
Published: January 2025

AbstractAtomically dispersed materials have been a thriving research field due to their maximum atomic utilization and remarkable performance in energy conversion and storage systems. Owing to the large atomic radius, strong oxophilicity, and unique electronic properties, rare‐earth (RE) elements have been widely investigated as oxide carriers and promoters in atomically dispersed materials to manipulate and regulate the electronic structure of active species. Single‐atom state with an adjustable coordination environment on the N‐doped carbon endows RE metals with special electronic states and outstanding catalytic performances. A thorough comprehension of the electronic modulation mechanism of RE elements paves the way for the construction of advanced RE‐based electrocatalysts with high activity, stability, and selectivity. This review provides a widespread insight into the roles of RE elements in modulating the electronic properties of atomically dispersed materials combined with the structure–performance relationship in electrocatalysis processes. The characteristic physical and chemical properties of RE elements are highlighted, and the synthetic strategy of RE‐based atomically dispersed materials is discussed. Finally, a summary and perspectives for rational design and development of highly efficient RE‐based catalysts are proposed. This review aims to provide a guideline for promoting the rational and effective utilization of RE elements in advanced functional materials.
Microbial DNA Profiles of Bacterial Extracellular Vesicles from 3D Salivary Polymicrobial Biofilms – A Pilot Study
Authors: Liu Chun , Udawatte Nadeeka S. , Liaw Andrew , Staples Reuben , Salomon Carlos , Seneviratne Chaminda Jayampath , Ivanovski Sašo , Han Pingping 
Published: January 2025

AbstractWith the advent of multi‐layered and 3D scaffolds, the understanding of microbiome composition and pathogenic mechanisms within polymicrobial biofilms is continuously evolving. A fundamental component in mediating the microenvironment and bacterial‐host communication within the biofilm are bilayered nanoparticles secreted by bacteria, known as bacterial extracellular vesicles (BEVs), which transport key biomolecules including proteins, nucleic acids, and metabolites. Their characteristics and microbiome profiles are yet to be explored in the context of in vitro salivary polymicrobial biofilm. This pilot study aimed to compare the profiles of BEVs from salivary biofilm cultured on a 2D tissue culture plate and 3D melt electrowritten medical‐grade polycaprolactone (MEW mPCL) scaffold. BEVs derived from MEW mPCL biofilm exhibited enhanced purity and yield without altered EV morphology and lipopolysaccharide (LPS) content, with enriched BEVs‐associated DNA from Capnocytophaga, porphyromonas, and veillonella genus. Moreover, compared to saliva controls, MEW mPCL BEVs showed comparable DNA expression of Tannerella forsythia, and Treponema denticola and significantly higher expression in Porphyromonas gingivalis, Eikenella corrodens and Lactobacillus acidophilus. Together, these findings highlight a more detailed microbial profile with BEVs derived from salivary biofilms cultured on 3D MEW PCL scaffolds, which facilitates an effective in vitro model with a greater resemblance to naturally occurring biofilms.
Generalizability of Graph Neural Network Force Fields for Predicting Solid‐State Properties
Authors: Mohanty Shaswat , Wang Yifan , Cai Wei 
Published: January 2025

AbstractMachine‐learned force fields (MLFFs) promise to offer a computationally efficient alternative to ab initio simulations for complex molecular systems. However, ensuring their generalizability beyond training data is crucial for their wide application in studying solid materials. This work investigates the ability of a graph neural network (GNN)‐based MLFF, trained on Lennard–Jones Argon, to describe solid‐state phenomena not explicitly included during training. The MLFF's performance is assessed in predicting phonon density of states (PDOS) for a perfect face‐centered cubic (FCC) crystal structure at both zero and finite temperatures. Additionally, vacancy migration rates and energy barriers are evaluated in an imperfect crystal using direct molecular dynamics (MD) simulations and the string method. Notably, vacancy configurations are absent from the training data. These results demonstrate the MLFF's capability to capture essential solid‐state properties with good agreement to reference data, even for unseen configurations. Data engineering strategies are further discussed to enhance the generalizability of MLFFs. The proposed set of benchmark tests and workflow for evaluating MLFF performance in describing perfect and imperfect crystals pave the way for reliable application of MLFFs in studying complex solid‐state materials.
A Multi‐Colored, Structure‐Tolerant Vanadate Cathode for High‐Performance Aqueous Zinc‐Ion Batteries
Authors: Zhang Qian , Ju Shidi , Zhang Shaohua , Xu Shilong , Zhang Zhipan 
Published: January 2025

AbstractVanadium‐based cathode materials for aqueous zinc‐ion batteries (AZIBs) have attracted much attention in large‐scale energy storage devices yet their unsatisfactory cyclic stability and slow diffusion rate of Zn2+ ions during insertion and extraction hinder further commercial applications. Therefore, the development of vanadium‐based cathode materials with stable crystal structures and fast Zn2+ storage remains challenging. Herein, Na2CaV4O12 (NCVO) nanowires are reported as a promising cathode of excellent electrochemical performance in AZIBs, simultaneously rendering high specific capacity (443.2 mAh g−1 at 0.1 A g−1) and high average voltage plateau (0.91 V) with impressive energy density (403.3 Wh kg−1) and power density (1533 W kg−1). As NCVO features a unique open crystal structure with alternately arranged inactive layers ([NaO6] and [CaO8] polyhedra) and active layers ([VO4] tetrahedra), the expansion of the [VO4] tetrahedra during Zn2+ insertion is well balanced by the contraction of the inactive layer, thus enabling remarkable long‐term cycling stability (91.9% and 80% capacity retention after 5000 and 10 000 cycles at 10 A g−1, respectively). With the electrochromic property of the NCVO cathode, the AZIB can further be used for adaptive camouflage under a range of scenarios, shedding light on the future development of high‐performance cathodes for AZIBs.
Health shock and indebtedness: Does having access to health insurance reduce the reliance on borrowing as a shock coping strategy?
Authors: Nguyen Linh D. , Nguyen Thanh T. , Nguyen Tung T. , Grote Ulrike 
Published: January 2025

AbstractHouseholds in developing countries are often impaired in their economic opportunities by major health shocks. In this article, we first investigate the impact of a health shock on rural household consumption and explore the mechanisms how the health shock brings a household into indebtedness. We then examine the role of health insurance in reducing the reliance on borrowing as a shock coping strategy. Our estimations show that while rural households are able to insure non‐health‐related consumption, a health shock pushes them into severe indebtedness by increasing informal borrowing to smooth consumption. Promotion of health insurance is recommended as it helps to protect households from falling into severe indebtedness when a health shock strikes.
Diagnosis of TET3‐Related Beck–Fahrner Syndrome in an Individual With Chorioretinal and Iris Colobomata Using a DNA Methylation Signature
Authors: Man Alice , Di Scipio Matteo , McConkey Haley , Hough Rebecca , Stein Nina , Diehl Eric , Marshall Christian R. , Sadikovic Bekim , Ejaz Resham 
Published: January 2025

ABSTRACTDisorders of developmental delay can occur from pathogenic variants in genes responsible for epigenetic regulation. Heterozygous and biallelic pathogenic variants in TET3 have recently been described in TET3‐related Beck–Fahrner syndrome (TET3‐BEFAHRS), representing an autosomal dominant disorder with variable expressivity. Typical features include intellectual disability and developmental delay. Patients can also present with facial dysmorphism, seizure disorder, ophthalmic findings, and other neurobehavioral features. As the condition has recently been described and few patients have been reported in literature, the full scope of the phenotypic spectrum and approaches to identify them are still emerging. We report an individual meeting the criteria for TET3‐BEFAHRS confirmed through clinical, genetic, and DNA methylation episignature analysis, who uniquely presents with bilateral chorioretinal and unilateral right iris colobomata. This case suggests a broader ophthalmic phenotype to TET3‐BEFAHRS and demonstrates the utility of episignatures for the diagnosis of Mendelian disorders of epigenetic machinery.
Hajdu–Cheney Syndrome, a Rare Cause of Acro‐Osteolysis and Osteoporosis With Zoledronic Acid Experience
Authors: Buyukyilmaz Gonul , Adiguzel Mehmet , Gurbuz Fatih , Kılıc Esra 
Published: January 2025

ABSTRACTHajdu–Cheney syndrome (HCS), caused by a heterozygous gain of function variant of the NOTCH2 gene, is a rare skeletal dysplasia. Although the main presentation is acro‐osteolysis, osteoporosis, and facial dysmorphism, having a wide range of clinical manifestations creates diagnostic difficulties. Here, a 15‐year‐old male patient with HCS who had no complaints until this age except for two short bone fractures and one vertebral collapse fracture due to a fall was reported. The patient presented with acro‐osteolysis, facial anomalies, skull deformity, and osteoporosis. The clinical diagnosis of HCS was supported by a positive genetic test of a novel de novo heterozygous pathogenic variant in exon 34 of NOTCH2 c.6614dupAfs*. Zoledronic acid treatment was applied for 2 years, and the patient responded well to the treatment, showing signs of improved bone density and improvement in vertebral height. We identified a novel NOTCH2 gene variant related to HCS. Our findings could extend phenotypic spectrum and genotype–phenotype correlations. The results of this case report support that antiresorptive treatment with zoledronic acid increased bone mineral density. Nevertheless, because of the low prevalence of the syndrome and the small number of reported cases, further studies are required to understand the syndrome better and establish treatment guidelines.
Exerkines and brain rejuvenation
Authors: Leiter Odette , Lowe Joshua , Brici David , Walker Tara L 
Published: January 2025

AbstractAgeing changes the adult brain at the molecular, cellular and functional levels, driving regenerative decline, inflammation, cognitive impairments and susceptibility to dementia‐related neurodegenerative disorders, such as Alzheimer’s disease (AD). There is overwhelming evidence that regular physical exercise can counteract cognitive decline in both healthy ageing and in neurodegenerative conditions such as AD, with exerkines, the circulating humoral factors that are secreted into the blood stream in response to exercise, emerging as likely mediators of this response. However, the source and identity of these exerkines remain unclear. We have recently found that platelets, the small immune cells that primarily regulate haemostasis, are activated after acute periods of running and release factors, including the chemokine platelet factor 4 (PF4), that promote neurogenesis and cognitive rejuvenation.This presentation will highlight the key role that platelet‐derived exerkines play in mediating cognitive rejuvenation and suggest that platelets represent a unique and underexplored therapeutic approach to counteract age‐related cognitive decline.
Faster DunedinPACE, an epigenetic clock for pace of biological aging, is associated with accelerated cognitive aging among older adults in the Framingham Heart Study
Authors: Savin Micah J. 
Published: January 2025

AbstractBackgroundBiomarkers that predict the heterogenous nature and late onset of cognitive decline are needed to evaluate geroscience interventions designed to delay or prevent the progression of Alzheimer’s Disease and related dementias (ADRD). The DunedinPACE epigenetic clock is designed to measure pace of biological aging, and is therefore a promising candidate biomarker. Here we (1) investigate if DunedinPACE is associated with cognitive aging, and (2) the extent to which these associations are independent of education.MethodWe analyzed data from the Framingham Heart Study Offspring Cohort. Our analysis sample included participants with neuropsychological testing data and blood DNA methylation data collected within 14 months of their baseline cognitive assessment (n = 2,296 non‐Hispanic White adults, 46% male; M age = 61.6 ± 9.0 [25‐101y]). A series of growth curve models tested the interactive effects of DundeinPACE and education upon baseline and longitudinal changes in global unadjusted T scores. All models included covariates to adjust for cellular composition of blood samples, smoking status, sex, age at baseline (specified as a quadratic term), and date of blood draw.ResultA faster DunedinPACE was associated with worse global cognition, and steeper decline in cognition over time (Bs = ‐.37 ‐ ‐.45; ps< .001). After adjusting for education, DunedinPACE remained robustly associated with global cognition and steeper decline in cognition over time (Bs = ‐.33 ‐ ‐38; ps<.01). In effect modification analyses, higher education buffered the effect of faster DunedinPACE upon global cognition at baseline (B = ‐.21; p<.01), but did not significantly modify the effect of DunedinPACE upon cognitive decline over time (p = .95).ConclusionThe presented findings support prior work that highlight the role of systemic biological aging in cognitive decline, and further validates the utility of the epigenetic clock, DunedinPACE, as a potential biomarker for decline in cognitive aging. Further validation of DunedinPACE and its clinical utility as a biomarker for geroscience interventions targeting ADRD is warranted. Greater years of education appears to mitigate some of the deleterious effect of biological aging upon cognition. Future studies should critically examine these relationships among nationally representative samples and diverse samples disproportionately impacted by ADRD.
Neuroimmune regulation of Alzheimer’s pathology by age‐related blood‐borne factors
Authors: Hemmer Brittany M. , Grau‐Perales Alejandro B. , Ferreira Ana Catarina , Pallikunnath Ralphyn , Rosenstadt Jacob L. , Castellano Joseph M. 
Published: January 2025

AbstractBackgroundAlzheimer’s disease (AD) is a complex neurodegenerative disorder characterized by hallmark pathologies that affect many brain regions, including the cellular microenvironment with the hippocampus, ultimately leading to profound deficits in cognition. Surprising recent work has shown that factors in the systemic environment regulate the hippocampal cellular niche; age‐associated blood‐borne factors exacerbate brain aging phenotypes, whereas youth‐associated blood‐borne factors, including tissue inhibitor of metalloproteinases 2 (TIMP2), reverse or ameliorate features of brain aging. As aging serves as the major risk factor for AD, and recent work shows that systemic factors can regulate AD pathology, we sought to characterize mechanisms by which the systemic environment regulates CNS phenotypes relevant to AD pathology through changes in neuroinflammation.MethodWe used both global and conditional deletion approaches in wildtype and APP‐knockin (NL‐F) or 5XFAD mice to target sources of TIMP2, a youth‐associated systemic factor previously shown to rejuvenate the aged hippocampus. We applied conventional and super‐resolution confocal microscopy approaches to characterize the impact on amyloid pathology and neuroinflammation. Changes in microglial morphology and state in the setting of TIMP2 modulation were characterized using a variety of approaches, including in vivo microdialysis and snRNA‐sequencing. We also restored levels of TIMP2 in aged APP‐KI mice to examine the impact on cognitive deficits. Conversely, we systemically injected APP‐KI mice with proteins associated with advanced age to examine the impact of age‐accumulating blood‐borne factors on amyloid accumulation and microglial state.ResultDeletion of TIMP2 from specific sources is associated with significant changes in microglial state. Its loss is associated with dysfunctional activation state, senescence, and perturbed morphology. We also find that TIMP2 deletion exacerbates accumulation of amyloid in various brain regions associated with accumulated extracellular matrix and its rescue in aged APP‐KI mice improves memory. Conversely, injecting specific factors present in aged blood significantly exacerbates amyloid pathology and alters microglial state while impairing adult neurogenesis in the hippocampus.ConclusionTogether our results highlight mechanisms by which both youth‐associated and age‐associated blood‐borne factors regulate AD pathology. Factors in the systemic environment appear to interact with microglia, cells that are intimately involved in modulation of canonical AD pathology.