bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-Perceived Decline in Memory and Concentration 9 and 12 months post COVID-19 infection
Authors: Ruivinho Carolina , Moniz Marta , Goes Ana Rita , Soares Patrícia , Leite Andreia ,   LOCUS group
Published: January 2025

AbstractIntroductionCOVID-19 infection caused by SARS-CoV-2 has led to significant long-term health challenges, including Long COVID or Post-COVID condition, that can include symptoms such as cognitive decline, memory loss, and concentration issues. This study investigates the prevalence and risk factors of post-COVID cognitive symptoms among individuals tested for COVID-19.MethodsA cross-sectional study was conducted in Lisbon and Tagus Valley, targeting individuals tested for COVID-19 in August 2022. Participants were selected from a random sample of 10,000 individuals. Data were collected via computer-assisted telephone interviews at 9 and 12 months post-test, covering sociodemographic details, health behaviors, pre-existing conditions, and COVID-19 symptoms. The primary outcome was the presence of at least one cognitive symptom (memory loss and/or concentration issues) at 9 and 12 months. Additionally, each symptom was assessed individually, along with a composite outcome of both symptoms concurrently.ResultsAt 9 months, memory loss was reported by 24.87% of COVID-19 positive cases versus 10.20% of negatives, and concentration issues by 15.45% of positives versus 7.45% of negatives. At 12 months, memory loss prevalence was 16.67% for positives and 9.45% for negatives, while concentration issues were 9.82% for positives and 2.99% for negatives. Additionally, the prevalence of at least one cognitive symptom was 28.24% in positive cases at 9 months compared to 12.16% in negatives, and 17.81% versus 9.95% at 12 months. Female sex was significantly associated with a higher prevalence of cognitive symptoms at both time points.DiscussionThese findings underscore the enduring cognitive impact of COVID-19, with significant disparities in cognitive symptoms between COVID-19 positive and negative individuals observed at both 9 and 12 months post-infection. The higher prevalence of memory loss and concentration issues among COVID-19 positives suggests potential neurological sequelae linked to SARS-CoV-2 infection. Notably, the association of female sex with increased cognitive symptom prevalence warrants further investigation into gender-specific vulnerabilities or biological mechanisms underlying these disparities. Addressing these persistent cognitive symptoms is crucial for long-term patient management and underscores the need for targeted interventions and comprehensive post-COVID care strategies to mitigate long-lasting health implications.
The structural basis forde novoDNA methylation in chromatin
Authors: Xie Xiaoyan , Liu Minmin , Zhou X. Edward , Dykstra Michelle L. , Jones Peter A. , Worden Evan J. 
Published: January 2025

AbstractDe novocytosine methylation is essential for mammalian development and is deposited by DNMT3A and DNMT3B. In cells, DNA methylation occurs in the context of chromatin, where nucleosomes are connected by DNA linkers. Here, we report Cryo-EM structures of DNMT3A2/3B3 bound to di-nucleosomes with different linker lengths. We show that DNMT3A2/3B3 preferentially binds di-nucleosomes separated by short DNA linkers by inducing large-scale changes to the di-nucleosome structure, enabling each DNMT3B3 subunit to bind each nucleosome. Linker length and the position of cytosines within the linker control DNA methylation, indicating that a significant fraction of linkers in chromatin are naturally resistant to DNMT3A2/3B3 activity. Finally, DNMT3A2/3B3 scans for H3K36me2-3 modifications, explaining how H3K36 methylation simulates DNMT3A2 activity. Our structure is the first example of a DNA methyltransferase interacting with higher-order nucleosome substrates and provides new insights on how DNA methylation takes place in chromatin.
Optimizing Family Self-Efficacy Through Self-Care Guidelines To Reduce Rehospitalization Rates In Stroke Patients: A Quasi-experimental study
Authors: Putra Komang Ardidhana Nugraha , Pandin Moses Glorino Rumambo , Dewi Ni Luh Putu Ayu Ratna , Shari Alfi 
Published: January 2025

ABSTRACTIntroductionSince 2007, there has been an alarming spike in stroke cases in Indonesia, leading to an increase in rehospitalization due to complications and recurrent stroke attacks. Self-care with family support has been proven effective in supporting stroke recovery.ObjectiveThis study aims to assess the effectiveness of self-care guidelines to prevent rehospitalization of stroke patients on family self- efficacy.MethodA quasi-experimental research design was used in this study. A total of 80 respondents were involved, consisting of 40 respondents in each group. Data collection was carried out using observation sheets and the General Self-Efficacy Scale (GSE).ResultsThere was an increase in self-efficacy in the intervention group before and after the implementation of self-care guidelines in families caring for stroke patients with a p value <0.001.ConclusionThe implementation of self-care guidelines is effective in increasing family self-efficacy in long-term care to prevent rehospitalization of stroke patients. Evaluation of the long-term impact of implementing guidelines on rehospitalization and quality of life of stroke patients is important to do.
KIF18A in HCC Metastasis: Dual Role in Anoikis Resistance and Chromosome Instability
Authors: Kan Changhao , Bai Weiyu , Yang Xinru , Hamdy Hayam , Yang Xianghui , Liu Xin , Lv Yan , Shen Junling , Sun Jianwei 
Published: January 2025

AbstractThe study explores the role of KIF18A, a gene linked to whole-genome doubling (WGD) and chromosomal instability (CIN), in the metastatic progression of hepatocellular carcinoma (HCC). We found that KIF18A is a critical link between CIN and anoikis resistance, key factors in HCC metastasis. Through the bulk-seq analysis, we identified the pressures of anoikis and CIN faced by tumor cells during HCC metastasis and identified hub genes central to this process. Our results reveal that E2F activation during HCC progression leads to the transcription of KIF18A, promoting the survival and metastasis of CIN tumors. Overexpression of KIF18A leads to longer tumor life, more micronuclei, and increased survival and metastasis through non-canonical NF-kB activation. Deletion of KIF18A stabilizes the nuclear membrane of the micronucleus, silences cGAS-STING and PI3K-AKT pathways, and inhibits classical NF-kB. The study’s limitations include the need for further animal studies to validate the findings and explore the transient activation of the cGAS-STING pathway. Additionally, future research could focus on the potential therapeutic implications of targeting KIF18A in cancer treatment.
Joint models reveal human subcortical underpinnings of choice and learning behaviour
Authors: Miletić Steven , Stevenson Niek , Bazin Pierre-Louis , Alkemade Anneke , Isherwood Scott J. S. , Trutti Anne C. , Tse Desmond H. Y. , Håberg Asta K. , Forstmann Birte U. 
Published: January 2025

AbstractDecision making and learning processes together enable adaptive goal-oriented behaviour. Animal studies demonstrated the importance of subcortical regions in these cognitive processes, but the human subcortical contributions remain poorly characterised. Here, we study choice and learning processes in the human subcor-tex, using a tailored ultra-high field 7 T fMRI imaging protocol combined with joint models. Joint models provide unbiased estimates of brain-behaviour rela-tions by simultaneously including behavioural and neural data at the participant and group level. Results demonstrate relations between subcortical regions and the adjustment of decision urgency. Value-related BOLD differences were found with opposite BOLD polarity in different parts of the striatum. Multiple sub-cortical regions showed BOLD signatures of reward prediction error processing, but contrary to expectations, these did not include the dopaminergic midbrain. Combined, this study characterises the human subcortical contributions to choice and learning, and demonstrates the feasibility and value of joint modelling in facilitating our understanding of brain-behaviour relationships.
Protein kinase G inhibition preserves photoreceptor viability and function in a new mouse model for autosomal dominant retinitis pigmentosa
Authors: Zhu Yu , Peiroten Lucia , Nanda Kumar Pranav , Hottin Catherine , Haq Wadood , Paquet-Durand François 
Published: January 2025

AbstractRetinitis Pigmentosa (RP) is the most common inherited retinal degeneration, characterized by an initial loss of rod photoreceptor cells. Photoreceptor cell death has been associated with high levels of cyclic guanosine-3′, 5′-monophosphate (cGMP) in animal models of autosomal recessive RP (ARRP) and autosomal dominant RP (ADRP). cGMP analogues inhibiting protein kinase G (PKG) have been found to prevent rod degeneration in ARRP disease models, but their effects on ADRP are unknown. Here, we used the recently generated rhodopsin-mutantRhoI255d/+ADRP mouse model to investigate cGMP-signaling and the effects of cGMP analogues targeting PKG.cGMP accumulation was investigated by retinal immunostaining in wild-type (WT),RhoI255d/+, andRhoI255d/I255dmice. The therapeutic efficacy of the cGMP analogues CN03 and CN238 was evaluated on organotypic retinal explant cultures derived from WT andRhoI255d/+mice. Readouts included the TUNEL assay and immunostaining for cone arrestin-3. Downstream effectors of cell death were visualized using calpain, poly-ADP-ribose polymerase (PARP), and histone deacetylase (HDAC)in situassays, as well as caspase-3 immunostaining. Photoreceptor function was assessed using micro-electroretinogram (µERG) recordings. When compared with WT,RhoI255dphotoreceptors displayed cGMP accumulation in outer segments. In theRhoI255d/+ADRP model, CN03 and CN238 significantly reduced the number of dying photoreceptors. However, the relatively small number of photoreceptors exhibiting caspase-3 activity was not changed by the treatment. Remarkably, CN238 effectively provided long-lasting neuroprotection of cone photoreceptors and preserved retinal light responsiveness ofRhoI255d/+retina.Overall, this study suggests caspase-independent but cGMP-dependent cell death as a dominant degenerative mechanism in theRhoI255d/+ADRP mouse model. PKG inhibition demonstrated robust neuroprotection of both rod and cone photoreceptors, while the marked preservation of retinal function, especially with the compound CN238, highlighted cGMP analogues for the treatment of ADRP.
Dynamics of efficient ensemble coding
Authors: Ni Long , Stocker Alan A. 
Published: January 2025

AbstractEnsemble coding creates compressed representations of a stimulus array. When discriminating the ensemble average against a reference, however, items in the ensemble with feature values closer to the reference are typically weighed stronger. We have recently shown that this “robust averaging” behavior can be explained as a form of efficient coding, where the sensory encoding precision is dynamically adapted to efficiently represent ensemble stimuli according to their overall distribution relative to a trial-by-trial varying reference. However, the specific mechanisms underlying such dynamic, efficient ensemble coding remain unknown. Here, we demonstrate that the relative timing between the presentation of the reference and the stimulus ensemble strongly affects efficient ensemble coding. We systematically probed participants’ decision behavior for varying time intervals between the presentation of the ensemble and the reference. We found that efficient ensemble coding was only clearly established when reference and ensemble were simultaneously presented. It was much weaker when the ensemble preceded the reference, and largely absent when the ensemble followed the reference. As captured by our model, reduced efficient ensemble coding thereby coincided with decreased decision accuracy in those asynchronous conditions. Our results indicate that any temporal offset between the ensemble and reference stimuli substantially disrupts the dynamic and efficient allocation of coding resource. This suggests that efficient ensemble coding is not the result of a preparatory attentional process nor due to evidence selection at the decision stage. Rather, it arises from a fast interaction between the simultaneously evoked, sensory representations of reference and ensemble stimuli.
Characterisation ofin vitroresistance selection against second-/last-line antibiotics in methicillin-resistantStaphylococcus aureus
Authors: Prasetyoputri Anggia , Pitt Miranda E. , Cao Minh Duc , Ramu Soumya , Kavanagh Angela , Elliott Alysha G. , Ganesamoorthy Devika , Monk Ian , Stinear Timothy P. , Cooper Matthew A. , Coin Lachlan J.M. , Blaskovich Mark A. T. 
Published: January 2025

SYNOPSISBackgroundThe increasing occurrence of MRSA clinical isolates harbouring reduced susceptibility to mainstay antibiotics has escalated the use of second and last line antibiotics. Hence, it is critical to evaluate the likelihood of MRSA developing clinical resistance to these antibiotics.ObjectivesOur study sought to identify the rate in which MRSA develop resistance to vancomycin, daptomycin and linezolidin vitroand further determine the mechanisms underpinning resistance.MethodsMRSA was exposed to increasing concentrations of vancomycin, daptomycin, and linezolid for 20 days, with eight replicates for each antibiotic conducted in parallel. The resulting day 20 (D20) isolates were subjected to antimicrobial susceptibility testing, whole genome sequencing, autolysis assays, and growth curves to determine bacterial fitness.ResultsExposure to vancomycin or linezolid for 20 days resulted in a subtle two-fold increase in the MIC, whereas daptomycin exposure yielded daptomycin-nonsusceptible isolates with up to 16-fold MIC increase. The MIC increase was accompanied by variable changes in relative fitness and reduced resistance to autolysis in some isolates. D20 isolates harboured mutations in genes commonly associated with resistance to the respective antibiotics (e.g.walKfor vancomycin,mprFandrpoBfor daptomycin,rplCfor linezolid), along with several previously unreported variants. Introduction of key mutations to these identified genes in the parental strain via allelic exchange confirmed their role in the development of resistance.ConclusionsIn vitroselection against vancomycin, daptomycin, or linezolid resulted in the acquisition of mutations similar to those correlated with clinical resistance, including the associated phenotypic alterations.
Chronic Complications of Type 2 Diabetes Patients in Southern Ethiopia
Authors: Demisse Andarge Biniyam , Hayelom Desta Haftu , Mehari Sayih , Esubalew Habtamu , Wondmagegn Habtamu , Habtegiorgis Yohannes , Bekele Muluken , Chisha Yilma 
Published: January 2025

AbstractBackgroundType 2 diabetes mellitus (T2DM) is a global health concern associated with complications that significantly impact patients’ quality of life and place significant burdens on healthcare systems. While the prevalence of T2DM is rising in Ethiopia, the scope and factors contributing to its complications remain understudied. Hence, this study aimed to assess the burden and identify associated factors of chronic complications among Type 2 diabetes mellitus patients attending Wolaita Sodo University Comprehensive Specialized Hospital in Southern Ethiopia.MethodsA facility-based cross-sectional quantitative study was conducted from July to August 2024, involving 404 systematically sampled T2DM patients. Data on sociodemographic characteristics, clinical profiles, self-care practices, and chronic complications were collected through structured interviews and medical record reviews. Descriptive statistics summarized patient characteristics, while General Poisson regression identified factors associated with chronic complications. Results were reported as Adjusted Prevalence Ratios (APRs) with 95% Confidence Intervals (CIs), and a p-value < 0.05 was considered statistically significant.ResultsOf the 404 participants, 45.54% (95% CI: 40.61 - 50.54) had at least one chronic complication. Among these, 20.05% experienced one complication, 14.60% had two, 8.42% had three, and 2.48% had four. Peripheral neuropathy (14.85%) and nephropathy (9.65%) were the most common microvascular complications, while congestive heart failure (14.11%) and cerebrovascular disorders (11.39%) were the leading macrovascular complications. Multivariable Poisson regression identified older age (APR = 2.30; 95% CI: 1.23–4.28), longer diabetes duration (APR = 1.87; 95% CI: 1.28–2.76), elevated blood pressure (APR = 2.02; 95% CI: 1.21–3.37), and higher Body Mass Index (APR = 2.63; 95% CI: 1.43–4.81) as significant factors associated with increased prevalence of chronic complications.ConclusionThe study reveals a substantial burden of chronic complications among T2DM patients, driven by modifiable and non-modifiable risk factors such as age, diabetes duration, blood pressure, and body mass index. These findings emphasize the urgent need for targeted interventions, including improved disease management, regular monitoring, and lifestyle modifications, to mitigate complications and enhance patient outcomes.
From Ice Cores to Dinosaurs: Physical Collections Managers’ Research Data Curation Perceptions and Behaviors
Authors: Bishop Bradley Wade , Fox Jaxx , Gavel Sidney Wanda Taylor , Chapin Emily Grace , Kansa Sarah 
Published: January 2025

AbstractPhysical collections provide the tangible objects that when analyzed become data informing all sciences. Physical collection managers aim to make physical objects discoverable, accessible, and reusable. The volume and variety of physical collections acquired, described, and stored across decades, and in some cases centuries, results from large public and private investments. The purpose of this study is to understand the curation perceptions and behaviors of physical collection managers across domains to inform cross-disciplinary research data management. Ten focus groups were conducted with thirty-two participants across several physical collection communities. Participants responded to open-ended questions about the data lifecycle of their physical objects. Results indicated that physical collections attempt to use universal metadata and data storage standards to increase discoverability, but interdisciplinary physical collections and derived data reuse require more investments to increase reusability of these invaluable items. This study concludes with a domain-agnostic discussion of the results to inform investment in cyberinfrastructure tools and services.Author summaryPhysical collections across the life and geosciences provide the tangible objects used to analyze and gain knowledge. There are collection managers in many museums and other information agencies working hard to curate these items in a way to keep them secure for long-term use. This study conducted focus groups with collection managers across several physical collection communities, including anthropology, archaeology, paleontology, ichthyology, herbaria, entomology, herpetology, and geology. Participants discussed their collection management approaches using the stages of the data lifecycle to frame how they make their items discoverable and reusable. Results indicated metadata and data storage standards help increase discoverability, but more work could be done to ensure better interdisciplinary reuse through increased investment and user-informed design of the cyberinfrastructure that preserves and makes available these invaluable items.
Identifying brain-penetrant small molecule modulators of human microglia using a cellular model of synaptic pruning
Authors: McCrea Liam T. , Batorsky Rebecca E. , Bowen Joshua J. , Yeh Hana , Thanos Jessica M. , Fu Ting , Perlis Roy H. , Sheridan Steven D. 
Published: January 2025

AbstractMicroglia dysregulation is implicated across a range of neurodevelopmental and neurodegenerative disorders, making their modulation a promising therapeutic target. Using PBMC-derived induced microglia-like cells (piMGLCs) in a scalable assay, we screened 489 CNS-penetrant compounds for modulation of microglial phagocytosis of human synaptosomes in a validated assay for microglia-mediated synaptic pruning. Compounds from the library that reduced phagocytosis by ≥2 standard deviations across the library without cytotoxicity were validated in secondary screens, with 28 of them further confirmed to reduce phagocytosis by 50% or more. Image-based morphological measurements were calculated to measure the degree of ramified vs. amoeboid morphotype as an indicator of activation state. Additionally, transcriptomic profiling indicated divergent effects on cell signaling, metabolism, activation, and actin dynamics across confirmed compounds. In particular, multiple CNS-penetrant small molecules with prior FDA approval or demonstration of safetyin vivodemonstrated modulatory effects on microglia. These potential disease-modifying agents represent high-priority candidates for repositioning studies in neurodevelopmental, neuroinflammatory, or neurodegenerative disorders.
A compendium of nonredundant short Polymerase III promoters for CRISPR applications
Authors: Deguchi Michihito , Sinclair Kayla M. , Patel Annie , Coile Mckenna , Ortega Maria A. , Bewg William P. , Tsai Chung-Jui 
Published: January 2025

AbstractMultiplex genome editing via CRISPR is a powerful tool for the simultaneous knockout, activation, and/or repression of distinct genes or noncoding sequences. However, current toolkits for multiplex editing lack diversity. Repeated use of the same promoter in multiple expression cassettes complicates construct assembly and has long been a concern for genetic stability in the host organism. Additionally, using unnecessarily long promoters may increase the genetic load and introduce uncertainties that impact CRISPR efficiency. To address these challenges, we present a collection of short Polymerase III (Pol III) promoters of diverse origins to support increasingly sophisticated genome editing applications in dicots.