bluuebunny/crossref_metadata_2025_split huggingface dataset:
Updates to HIV transmission rate estimates along the HIV care continuum in the United States, 2019
Authors: Baxter Arden , Gopalappa Chaitra , Islam Md Hafizul , Viguerie Alex , Lyles Cynthia , Johnson Anna Satcher , Khurana Nidhi , Farnham Paul G. 
Published: January 2025

Background:
In 2019, there were an estimated 1.2 million persons with HIV (PWH) and 35,100 new infections in the United States. The HIV care continuum has a large influence on transmission dynamics.

Methods:
We updated Progression and Transmission of HIV 3.0, an agent-based simulation model, to estimate 2019 HIV transmission rates and distribution of transmissions by the HIV care continuum, race/ethnicity, transmission group, and age group.

Results:
In 2019, the estimated transmission rate in the United States was 2.94 new infections per 100 person-years (inf /100

p-y)
. Transmission rates decreased along the HIV care continuum; the highest transmission rate was associated with persons with acute HIV infection and unaware of their HIV status at 16.35 inf /100

p-y
, followed by persons with HIV (non-acute) and unaware of their HIV status (9.52), persons aware of their HIV status and not in care (5.96), persons receiving HIV care (on antiretroviral therapy) but not virally suppressed (4.53), and persons virally suppressed (0). The highest transmission rate by transmission group was among men who have sex with men at 3.68 inf /100

p-y
. Transmission rates decreased as age increased and are similar by race/ethnicity, after accounting for the HIV care continuum.

Conclusion:
Our results support a continued emphasis on helping PWH move along the care continuum through early diagnosis, linkage to care, and adherence to ART, resulting in viral suppression to reduce HIV transmissions. Further, efforts should focus on reducing disparities in the provision of HIV prevention and care services, particularly for populations disproportionally affected by HIV.
Reliability and Validity of the Turkish Version of the Tinetti Falls Efficacy Scale in Older Adults and Comparison With Other Fall Scales
Authors: Durmuş Melahat Selin , SERTEL Meral , Aydoğan Arslan Saniye 
Published: January 2025

Objective:
This study aims to determine the validity and reliability of the Turkish version of the Tinetti Falls Efficacy Scale (TFES) in older adults. In addition, TFES was compared with other scales such as the Timed Up and Go Test (TUG), Fall Risk Self-Questionnaire Scale (FRQS), Activity-Specific Balance Confidence Scale (ABC), and Tinetti Balance and Gait Test (TBT&TGT) in the study.

Method:
The study included 100 older adults living in the community. The participants’ sociodemographic information was recorded. Their cognitive status was evaluated with the Mini-Mental State Examination. The validity of TFES was evaluated with TUG, FRQS, ABC, and TBT&TGT. For test-retest reliability, 51 individuals were re-evaluated 5 to 7 days later by the same physiotherapist under the same conditions.

Result:
Test-retest reliability was calculated with the intraclass correlation coefficient. The internal consistency of the items of the TFES was calculated by Cronbach’s alpha analysis. Explanatory and confirmatory factor analyses were used to determine the validity. In reliability tests, the Cronbach alpha value was .888, and the intraclass correlation coefficient was 0.983. In addition, when the relationship between TFES and other scales is examined, it is found that it is statistically significant with TUG and FRQS and has positive and moderate correlations (in order of P = .000; r = 0.470; P = .000; r = 0.584); it is statistically significant with ABC and TBT&TGT and has negative and moderate correlations (in order of P = .000; r = −0.540; P = .000; r = −0.420).

Conclusion:
This study demonstrated that the Turkish version of the TFES is a valid and reliable scale for older adults. This study will be a guide for health professionals working in this field to be used in future studies.
Comparing Diagnostic Performance Properties of Fear of Falling Scales in Older Adults
Authors: Hiteh Masoud , Sharif-Nia Hamid , Assarroudi Abdolghader 
Published: January 2025

Objectives:
This study aimed to compare the psychometric properties of Falls Efficacy Scale-International, Activities-Specific Balance Confidence Scale, short version of Activities-Specific Balance Confidence Scale, and Geriatric Fear of Falling Measure in older adults.

Material and Methods:
The translation and back translation, qualitative and quantitative of face and content validity and construct validity were performed using exploratory factor analysis and convergent validity. The reliability of the scales was assessed by internal consistency (Cronbach’s α) and test-retest (intra-class correlation).

Results:
The results showed that the ABC-6 scale has the best diagnostic performance properties among older adults.
When We Make Errors and Do Harm: A Narrative Review of Second Victim Syndrome and Implications for Neuro-Ophthalmologists
Authors: Rabinovitch David , De Lott Lindsey B. , Margolin Edward 
Published: January 2025

Background:
In the aftermath of an adverse event, the first priority is to provide care for the patient, known as the first victim. However, the experiences of healthcare professionals (HCPs) involved in these events, known as “second victims”, have been largely overlooked. This review aims to consolidate existing knowledge on second victim syndrome (SVS), explore its unique implications for neuro-ophthalmologists, and suggest support strategies to increase awareness and meet the needs of affected colleagues.

Evidence Acquisition:
A comprehensive review of the literature was conducted using PubMed, analyzing peer-reviewed articles and reports on SVS across medical specialties. The review focused on the prevalence, risk factors, outcomes, and strategies for addressing SVS at both the individual and system-wide levels.

Results:
SVS is alarmingly prevalent among HCPs, with estimates ranging from 10% to 43%, and nearly half of all HCPs are expected to experience SVS at least once in their careers. Although direct evidence is lacking, neuro-ophthalmologists may be particularly vulnerable due to the complexity of their patients, frequent diagnostic challenges, and the risk of poor outcomes. Effective coping strategies include peer support at the institutional level, with an urgent need for healthcare systems to transition toward a “Just Culture” that fosters openness and collective learning.

Conclusions:
Neuro-ophthalmologists are likely among several specialty fields suffering in silence following medical errors. To reduce these errors and optimize patient care, we must focus on enhancing support for the physicians involved. Sustainable improvements in healthcare require both targeted clinician support and comprehensive system-level changes to foster resilience and improve quality of care. Key efforts should include formal peer support programs, targeted educational initiatives, and a deliberate shift toward a “Just Culture.” These initiatives are essential for fostering clinician resilience, promoting effective recovery, and ultimately improving the broader healthcare system and quality of care.
Meta-analysis of RNA-seq gene fusion detection tools: performance and variability across benchmarks
Authors: Ostrowska Iga , Gambin Tomasz 
Published: January 2025

ABSTRACTIn this study, we conducted a comprehensive meta-analysis of ten publicly available benchmark tests evaluating the performance of gene fusion detection tools using RNA-seq data. Our analysis focused on key performance metrics, including sensitivity, precision and F1 scores. We evaluated how the tools perform in different data sets. We examined the impact of data set characteristics such as sample type (real or simulated) and read length, as well as additional sample and sequencing parameters on the results. In addition to evaluating performance, we analyzed the organization and design of the benchmark tests, highlighting good practices such as clear descriptions of the datasets, detailed instrument parameters and transparent methodologies. However, we also identified common pitfalls, including insufficient reproducibility information, limited diversity of datasets, and the lack of widely accepted gold standard datasets. These limitations make it difficult to consistently evaluate tools and compare across benchmarks. By synthesizing these findings, we make recommendations for future benchmark projects, emphasizing the need for standardization, increased transparency and the development of robust truth sets. This study aims to help the community create more reliable and reproducible benchmark tests, ultimately accelerating the development and evaluation of gene fusion detection tools for clinical and research applications.
Transposon invasion of primate genomes shaped human inflammatory enhancers and susceptibility to inflammatory diseases
Authors: Ye Mengliang , Rotival Maxime , Amigorena Sebastian , Zueva Elina 
Published: January 2025

AbstractHuman immune inflammatory response reflects the evolutionary adaptation of immune-cell regulatory elements1, where recent mutations can control both pathogen defence and susceptibility to chronic inflammatory and autoimmune diseases2–4. The impact of the deeper evolutionary history of these elements within primate genomes on human inflammatory responses remains poorly understood. Evolutionary young transposons have uniquely reshaped primate genomes5and spread novelcis-regulatory sequences6. To understand how these events influenced human inflammation, we traced sequence changes in annotated human immune-cell enhancers back to macaque. We show that Alu elements and endogenous retroviruses dispersed motifs for the inflammation-related NF-κB and IRF1, redefining their binding patterns and contributing most prominently to great ape-specific binding sites. After the human-macaque split, many of these motifs shifted toward higher predicted binding affinity. In humans, population genetics analyses reveal that positive selection favors alleles, often Alu-derived, that increase enhancer affinity toward NF-κB. Enhancers containing Alu elements are more likely to undergo positive selection at the locus level, particularly when associated with chronic inflammatory diseases. As the most mutable enhancer sequences, Alus harbor disproportionately high numbers of single nucleotide polymorphisms and significantly contribute to selected alleles, some associated with chronic inflammatory diseases. We propose that the invasion of primate-specific transposons has created unique opportunities to adapt inflammatory responses in rapidly evolving great apes, with ancestral Alus continuing to influence evolutionary potential in humans.
Metabolomics biomarkers of frailty: a longitudinal study of aging female and male mice
Authors: Zhu Dantong , Wu Judy Z. , Griffin Patrick , Samuelson Brady A. , Sinclair David A. , Kane Alice E. 
Published: January 2025

AbstractFrailty is an age-related geriatric syndrome, for which the mechanisms remain largely unknown. We performed a longitudinal study of aging female (n = 40) and male (n = 47) C57BL/6NIA mice, measured frailty index and derived metabolomics data from plasma samples. We identify differentially abundant metabolites related to aging, determine frailty related metabolites via a machine learning approach, and generate a union set of frailty features, both in the whole cohort and in sex-stratified subgroups. Using the features, we perform an association study and build a metabolomics-based frailty clock. We find that frailty related metabolites are enriched for amino acid metabolism and metabolism of cofactors and vitamins, include ergothioneine, tryptophan, and alpha-ketoglutarate, and present sex dimorphism. We identify B vitamin metabolism related flavin adenine dinucleotide and pyridoxate as female-specific frailty biomarkers, and lipid metabolism related sphingomyelins, glycerophosphoethanolamine and glycerophosphocholine as male-specific frailty biomarkers. These associations are confirmed in a validation cohort, with ergothioneine and perfluorooctanesulfonate identified as robust frailty biomarkers. In summary, our results identify sex-specific metabolite biomarkers of frailty in aging, and shed light on potential mechanisms involved in frailty.
Type I partition-related proteins enhance conjugative transfer through transcriptional activation andoriTregion binding
Authors: Kishida Kouhei , Kudo Koji , Kumagai Ren , Deng Wenhao , Stari Leonardo , Ogawa-Kishida Natsumi , Ohtsubo Yoshiyuki , Nagata Yuji , Tsuda Masataka 
Published: January 2025

ABSTRACTPlasmid partitioning and bacterial conjugation are critical processes ensuring plasmid maintenance and dissemination, respectively, within bacterial populations. Although traditionally regarded as distinct phenomena, these two processes are increasingly recognized as interconnected. While partitioning ensures plasmid inheritance during cell division, its potential influence on conjugative transfer remains poorly understood. A major impediment to understanding their interplay is that partition systems are often essential for plasmid stability, making it difficult to distinguish their direct effects on conjugation. In this study, we addressed this challenge using a mini-conjugative plasmid derived from thePseudomonas putidaNAH7 plasmid. This engineered plasmid, containing all conjugation-related genes, was cloned into anE. coli-compatible vector. Additionally, thepargenes from NAH7 were expressed from a separate plasmid to investigate their roles in conjugative transfer. Our results revealed that thepargene cluster plays a significant role in enhancing the conjugative transfer of the mini-conjugative plasmid. Specifically, ParB, a centromere-binding protein, functions as a transcriptional activator of conjugation-related genes with bindingparSNAHsite. In contrast, ParR, a KorA homolog, was not found to enhance transcription directly but binds extensively to theoriTregion. This binding probably facilitates the recruitment or stabilization of the relaxosome, thereby enhancing conjugation efficiency. Together, these findings unveil a previously unappreciated role for partition proteins in stimulating bacterial conjugation, providing new insights into how plasmids coordinate vertical and horizontal dissemination, highlighting that these processes can occur simultaneously within bacterial communities.IMPORTANCEPlasmid partition systems are classified into three types. While some systems have been reported to influence conjugative transfer, this study uncovers a novel mechanism utilized by a Type I system to enhance DNA transfer. Strikingly, repeat sequences perfectly matching theparSNAHsite—bound by ParB to activate downstream conjugative transfer genes—were identified on both plasmids and chromosomes across diverse proteobacterial taxa. Furthermore, many of these repeat sequences were localized near genes involved in conjugative transfer and partitioning, suggesting the presence of a conserved regulatory mechanism mediated by these repeats. This study provides important insights into how plasmid partition systems coordinate both vertical and horizontal dissemination. Such knowledge is essential for understanding and mitigating the spread of antibiotic resistance and other plasmid-encoded traits, and it offers a foundation for developing strategies to manage plasmid-associated genetic exchange.
Macrophage Inflammasome Activation Drives Anti-inflammatory Responses via Neutrophil-Derived ASC Speck Transfer and Gasdermin-Dependent Caspase-1 Inhibition
Authors: Pedoto Annamaria , Lozano-Gil Juan M. , Nguyen-Chi Mai E. , Lutfalla Georges , García-Moreno Diana , Mulero Victoriano , Tyrkalska Sylwia D. 
Published: January 2025

ABSTRACTInflammasomes are critical components of the innate immune system, traditionally associated with pro-inflammatory responses. While the inflammasome in macrophages has been extensively studied and linked to pyroptosis and cytokine release, the neutrophil inflammasome remains poorly understood. Neutrophil inflammasome activation drives unique outcomes such as NETosis and robust IL-1β production without inducing pyroptosis. In contrast, macrophage inflammasome activation promotes pyroptosis and the release of cytokines like IL-1α, IL-1β and IL-18. Here, using zebrafish models ofSalmonella entericaserovar Typhimurium infection and COVID-19-associated cytokine storm syndrome (CSS), we reveal opposing roles of neutrophil and macrophage inflammasomes: neutrophil inflammasomes are pro-inflammatory, whereas macrophage inflammasomes mediate anti-inflammatory responses. We show that Gasdermin E (Gsdme)- and Ninjurin-1-mediated cell death in neutrophils releases ASC specks, which are taken up by macrophages. This transfer negatively regulates caspase-1 activity via the Gsdme, promoting the resolution of inflammation. To our knowledge, this is the first study to reveal the anti-inflammatory role of the macrophage inflammasome, document the in vivo transfer of ASC specks between neutrophils and macrophages, and uncover the negative feedback regulation of the inflammasome by the Gsdme. These results offer novel insights into potential therapeutic approaches for hyperinflammatory diseases like bacterial infections and COVID-19-associated CSS.
A sperm–oocyte protein partnership required for egg activation inCaenorhabditiselegans
Authors: Tsukamoto Tatsuya , Kwah Ji Kent , Zweifel Mark E. , Courtemanche Naomi , Gearhart Micah D. , Walstrom Katherine M. , Jaramillo-Lambert Aimee , Greenstein David 
Published: January 2025

ABSTRACTFertilization triggers the completion of female meiosis and launches the oocyte-to-embryo transition.C. elegans spe-11is one of the few known paternal-effect embryonic lethal genes. We report that the sperm protein, SPE-11, forms a complex with an oocyte protein, OOPS-1 (OocytePartner ofSPE-11), and that the protein complex is required for the completion of meiosis, the block to polyspermy, and eggshell formation. Consistent with the molecular interaction of their encoded proteins,oops-1andspe-11exhibit identical null phenotypes, displaying defects in meiotic progression and cytokinesis. We show that the complex binds F-actin in the absence of other proteins and inhibits the nucleation of actin filamentsin vitro. Thus, the OOPS-1–SPE-11 complex may function to promote F-actin-mediated meiotic cytokinesis. Both OOPS-1 and SPE-11 are intrinsically disordered proteins that are highly phosphorylated. Biochemical and genetic experiments define interactions with the protein phosphatase 1 homologs GSP-3/4, which appear to promote OOPS-1–SPE-11 function. Genetic results support a model in which the OOPS-1–SPE-11 complex interacts with the cortical EGG complex to promote meiotic cytokinesis and to activate synthesis of the eggshell.
Family involvement in board of directors and market valuation: evidence from Egyptian listed firms
Authors: Moussa Amr Ahmed 
Published: January 2025

PurposeThis study aimed to investigate how family involvement in management (FIM) affects market valuation and whether this effect is influenced by the presence of founder chief executive officers (CEOs) and the dual role of their CEO positions.Design/methodology/approachTobin’s Q ratio measured market valuation, while FIM was measured by the ratio of family managers to the total number of board of directors (BOD) seats. Additionally, the appointment of founders to CEO positions and the dual role of their CEO positions were used as moderators. As a panel data technique, the dynamic generalized method of moments (GMM) estimator was employed for a sample of 85 Egyptian-listed firms from 2011 to 2018.FindingsThe findings revealed that FIM negatively affects market valuation; hence, the more family managers serving on the BOD, the lower the firm’s market value. Moreover, the findings showed that the impact of FIM on market valuation is mitigated by the presence of founder CEOs and the dual role of their CEO positions.Originality/valueThis study highlights the negative repercussions of FIM on firm value and the urgency of professionalizing the family business through an independent BOD and ensuring more effective monitoring systems.
A wavelet analysis of monetary policy transmission channels in Morocco
Authors: Ouchchikh Rachid , Belghouat Khalil , Ait Bari Ahmed 
Published: January 2025

PurposeThis paper examines the effects of monetary policy and the interdependencies between the real economy, the financial sector and monetary variables.Design/methodology/approachThe authors employ the continuous wavelet transform to examine how the relationship between the variables in question evolves over time and across various frequencies.FindingsThe results underscore the ineffectiveness of the exchange rate channel. Despite monetary policy consistently leading long-term interest rates, its limited impact on investment suggests the interest rate channel may be less operational. Conversely, the study presents evidence supporting the credit channel’s effectiveness, not only in low market volatility but also during economic downturns. Finally, the examination of the asset prices channel uncovers that the stock market was influenced by monetary policy during its brisk ascent, while real estate led monetary policy.Practical implicationsThe study yields several practical implications. It emphasizes employing advanced mathematical methods to capture the dynamic relationships between monetary policy and economic variables. It highlights the importance of a resilient banking sector given its significant role in the economic advancement of the country. It underscores the need to develop a more inclusive and dynamic financial system and diversify funding alternatives for the private sector to make asset prices a pivotal channel for achieving monetary policy objectives. And with Morocco’s transition to an inflation targeting framework and a flexible exchange rate regime, assessing the effectiveness of the interest rate and exchange rate channels becomes crucial. While the innovative use of wavelet coherence methodology sets a precedent for evaluating monetary policy transmission channels in developing countries, urging researchers and policymakers to explore novel quantitative approaches.Originality/valueThis article stands out as one of the few to employ the wavelet coherence methodology to investigate monetary policy transmission across multiple channels, specifically within the context of a developing country.
Risk assessment of mountain tunnel entrance collapse based on PSO-LSTM surface settlement prediction
Authors: Sun Yazhen , Lin Kun , Wang Jinchang , Zhu Fengbin , Wang Longyan , Lu Linhan 
Published: January 2025

PurposePredicting surface settlement at mountain tunnel entrances during construction is increasingly crucial for risk analysis, as the accuracy of these predictions directly impacts collapse risk assessments and personnel safety.Design/methodology/approachThis study introduces a novel approach using a particle swarm optimization (PSO)-optimized long short-term memory (LSTM) neural network for surface settlement prediction. The PSO algorithm optimizes key hyperparameters of the LSTM model, including the number of hidden layer neurons, the learning rate and L2 regularization, while the Adam optimizer refines LSTM iterations. Dropout is used in combination with adaptive L2 regularization parameters to avoid overfitting situations, and sensitivity analysis of the remaining variables ensures the identification of the optimal solution.FindingsThe model, based on monitoring data from the Aketepu No. 1 Tunnel’s left tunnel, establishes evaluation criteria incorporating error margins and root mean square error (RMSE). By examining the range of maximum (minimum) settlement rates for the cumulative settlement values, the study determined that the section is exposed to an average risk of collapse with slow deformation, which is consistent with actual observations.Originality/valueThis suggests that construction can proceed normally, with appropriate monitoring to mitigate the risk of collapse. The PSO-LSTM forecast model presents a promising approach for predicting collapse risks at mountain tunnel entrances.