bluuebunny/crossref_metadata_2025 huggingface dataset:
Nurses' Perceptions of the Role of Nursing Organizations in Promoting Engagement with the Sustainable Development Goals: A Global Study
Authors: Hawkins Janice Evans , Chiu Patrick , Mumba Mercy Ngosa , Gray Sarah E. , Hawkins Robert Joseph
Published: January 2025

Background:

RNs are integral to achieving the United Nations' 17 Sustainable Development Goals (SDGs). Professional nursing organizations can play a significant role in educating and preparing nurses to work more effectively toward achieving the SDGs. While there is much literature that speaks to the importance of nurses engaging in these goals, there is a lack of research that has explored nurses' perceptions of the role of professional nursing organizations in promoting SDG-related knowledge and engagement. Since 2012, Sigma Theta Tau International Honor Society of Nursing (Sigma) has been formally accredited as a nongovernmental organization with special consultative status to the United Nations Economic and Social Council. As such, Sigma is committed to educating RNs about the SDGs and engaging them in working to advance the goals.

Purpose:

This study examined RNs' learning preferences regarding the SDGs, and their perceptions of their professional nursing organization's engagement in advancing these goals, its recognition of nursing's contributions to these goals, and its impact on increasing nurses' knowledge of these goals.

Methods:

This descriptive cross-sectional study used convenience and snowball sampling methods to recruit participants from multiple countries. Data were collected via an anonymous online survey. Descriptive and nonparametric statistics were used for data analysis.

Results:

The majority (84%) of Sigma members enrolled in this study believed Sigma should be actively engaged in advancing the SDGs. Forty-eight percent were aware of Sigma's engagement and 44% reported that Sigma had increased their knowledge of the SDGs. When comparing participants who were Sigma members to those who were not, Sigma members had significantly higher levels of perceived knowledge of the SDGs and higher levels of belief that nurses are integral to SDG advancement. There were no significant between-group differences regarding nurses' desire to know more about the goals, what nurses are doing to advance them, and how to take action themselves. Participants' top 3 preferred means of learning about the SDGs were emailed and online newsletters (28.8%), webinars and online presentations (24.3%), and internet websites (14.9%).

Conclusions:

The results of this study underscore the importance of professional nursing organizations' efforts to increase nurses' engagement with the SDGs and can be used in developing multilevel strategies to further educate nurses about the SDGs.
The Challenge of Convenient Care
Authors: Freyer Felice J.
Published: January 2025

NP-run retail clinics seek footing in a shifting health care landscape.
Prescribing rate, healthcare utilization, and expenditure of older adults using potentially inappropriate medications in China: A nationwide cross-sectional study
Authors: Zhao Zinan , Fu Mengyuan , Li Can , Gong Zhiwen , Li Ting , Ling Kexin , Li Huangqianyu , Li Jianchun , Cao Weihang , Hong Dongzhe , Hu Xin , Shi Luwen , Guan Xiaodong , Jin Pengfei
Published: January 2025

Background:

The use of potentially inappropriate medications (PIMs) is a major concern for medication safety as it may entail more harm than potential benefits for older adults. This study aimed to explore the prescribing rate, healthcare utilization, and expenditure of older adults using PIMs in China.

Methods:

A cross-sectional analysis was conducted using a national representative database of all medical insurance beneficiaries across China, extracting ambulatory visit records of adults aged 65 years and above between 2015 and 2017. Descriptive analysis was conducted to measure the rate of patients exposed to PIM, prescribing rate of each PIM, average annual outpatient visits per patient, average total medication costs for each visit, average annual cost of PIMs for each patient, and average annual medication costs for each patient. Generalized linear model with logit link function and binomial distribution was used to examine the adjusted associations between PIMs and independent variables.

Results:

In total, 845,278 (33.2%) participants were identified to be exposed to at least one PIM. Patients aged 75–84 years (38.1%) and ≥85 years (37.9%) were more likely to be prescribed with PIMs. Beneficiaries of the Urban Employee Basic Medical Insurance (UEBMI) and living in eastern and southern regions were more frequently prescribed with PIMs. Compared with patients without PIM exposure (7.5 visits, drug cost of RMB 1545.0 Yuan), patients with PIM exposure showed higher adjusted average annual number of outpatient visits (10.7 visits, β = 3.228, 95% confidence interval [CI] = 3.196–3.261) and higher annual drug costs (RMB 2461.8 Yuan, Coef. = 916.864, 95% CI = RMB 906.292–927.436 Yuan).

Conclusions:

The results showed that the use of PIM among older adults was common in China. This study suggests that it represents a clear target, pending multidimensional efforts, to promote rational prescribing for older adults.
The Cutaneous Pathology of Erythromelalgia and Its Role in Establishing Critical Clues Regarding Pathogenesis
Authors: Magro Cynthia , Kalomeris Taylor , Guo Lily
Published: January 2025

Erythromelalgia, a rare cutaneous pain syndrome, is characterized by acral burning pain and flushing, often alleviated by cold and rest. Primary erythromelalgia is caused by gain-of-function mutations of genes encoding for sodium channels, resulting in hyperexcitability of pain signaling neurons. Autoimmunity and hematologic dyscrasias such as thrombocythemia have been implicated in secondary erythromelalgia. The pathology of this rare disease remains poorly defined. The Weill Cornell dermatopathology database was analyzed for acral biopsies procured from patients here there was a clinical concern for erythromelalgia. We identified 9 patients with clinical diagnoses of erythromelalgia who had a skin biopsy from an affected area. The female-to-male ratio was 2:1. Three of 9 individuals had concurrent diagnoses of autoimmune disease including vitiligo, lupus erythematosus, and psoriatic arthritis. Biopsies showed superficial vascular ectasia in association with microvascular C5b-9 and variable upregulation of type I interferon expression in endothelial cells. CD56 stain revealed diminished autonomic innervation of the eccrine coil and arteries, mirroring similar autonomic denervation seen in small fiber neuropathy. This study suggests that erythromelalgia is a dysautonomia syndrome with reproducible findings on biopsy, hallmarked by vascular ectasia and denervation of the eccrine coil and arteries. In addition, there is a potential link to immune and nonimmune-based microvascular compromise.
Reverse Fragility Index in Plastic Surgery Randomized Controlled Trials
Authors: Ahdoot Rodney , Benítez Trista M. , Wang Chien-Wei , Chung Kevin C.
Published: January 2025

Background:

The reverse fragility index (RFI) is a measure used to evaluate the neutrality of statistically nonsignificant findings in randomized controlled trials (RCTs). The RFI represents the minimum number of events needed to reverse a statistically nonsignificant result into a significant one. This study applied the RFI to examine the robustness of statistically nonsignificant RCTs in plastic surgery.

Methods:

A systematic literature search of the 10 highest impact journals covering plastic and reconstructive surgery topics was conducted to identify RCTs published between January 2000 and March 2023. The Fisher exact test was used to calculate the RFI for each primary outcome. Bivariate analysis was performed to investigate the association of trial characteristics with the RFI.

Results:

Forty RCTs that yielded 65 primary outcomes were included in the analysis with a median sample size of 76 participants (interquartile range [IQR], 49–129) and a median of 10 events (IQR, 3–22). The median RFI was 4 (IQR, 3–5), indicating that statistical significance would have been achieved if 4 participants had a change in event status. The median RFQ was 0.053 (IQR, 0.038–0.08). Most studies (21 of 40) did not perform statistical power analysis. Twelve of 40 RCTs did not report or clearly indicate loss to follow-up.

Conclusions:

The findings of RCTs in the plastic surgery literature demonstrate fragility as the preservation of nonsignificant results rested on a small number of events. The RFI is a useful measure to complement the P value and examine the neutrality of null clinical trials.
Distribution of opioid analgesics by community racial/ethnic and socioeconomic profiles, 2011-2021
Authors: Hu Ju-Chen , Chakraborty Promi , Zhang Hao , Portenoy Russell , Rosa William E. , Zhang Yiye , Reid M. Carrington , Tamimi Rulla M. , Zhang Fang , Bruera Eduardo , Paice Judith A. , Bao Yuhua
Published: January 2025

Rapid declines in opioid analgesics dispensed in American communities since 2011 raise concerns about inadequate access to effective pain management among patients for whom opioid therapies are appropriate, especially for those living in racial/ethnic minority and socioeconomically deprived communities. Using 2011 to 2021 national data from the Automated Reports and Consolidated Ordering System and generalized linear models, this study examined quarterly per capita distribution of oxycodone, hydrocodone, and morphine (in oral morphine milligram equivalents [MMEs]) by communities' racial/ethnic and socioeconomic profiles. Communities (defined by 3-digit-zip codes areas) were classified as “majority White” (≥50% self-reported non-Hispanic White population) vs “majority non-White.” Community socioeconomic deprivation was measured by quartiles of population-weighted Social Deprivation Index. Overall, majority non-White communities had at least 40% lower mean adjusted per capita distribution than majority White communities across all levels of socioeconomic deprivation. Among the least deprived communities, the adjusted mean per capita distribution was 46.0 (95% confidence interval [CI], 40.0-52.0) for majority non-White vs 82.8 (95% CI, 78.5-87.1) MMEs for majority White communities. Among the most deprived communities, the distribution was 78.0 (95% CI, 70.8-85.1) for majority non-White vs 134.4 (95% CI, 125.4-143.4) MMEs for majority White communities. The lower distribution in majority non-White communities was statistically significant across all socioeconomic deprivation levels and over all study years. Availability of commonly prescribed opioid analgesics was substantially lower in majority non-White communities than in majority White communities across all levels of socioeconomic deprivation. Policies governing opioid analgesic availability warrant careful consideration and potential adjustments.
Patients, parents and professional perspectives on molecular radiotherapy for neuroblastoma and paediatric neuroendocrine cancers
Authors: Whittaker Lisa , Knox Leona , Aitchison Zara , Peet Connie , O’Donovan Aine , Gray Juliet , Wan Simon , Flux Glenn D. , Gaze Mark N.
Published: January 2025

Treatment with radioactive drugs (molecular radiotherapy, MRT) is an option for selected children with neuroblastoma and neuroendocrine cancers. As few hospitals are appropriately equipped and staffed to provide paediatric MRT, many families have to travel long distances from home for prolonged periods. To improve professional understanding of the challenges faced by children receiving these treatments and their parents, and to help them appreciate the difficulties faced by professionals in delivering complex treatments, a meeting bringing together parents, patients and professionals was held. Ten people (five parents of children with neuroblastoma, two parents of children with neuroendocrine cancers, two adults who had received treatment for neuroendocrine cancers in childhood and one adult treated for neuroblastoma) gave personal perspectives of treatment with MRT. Three professionals from different disciplines involved with this treatment and research to improve its results gave their views on the administration of MRT, and how treatment outcomes might be improved. Fifteen people, including parents and professionals, contributed to the general discussion. Following the meeting, a questionnaire was circulated to those attending to capture their overall views, and any reflections they may have had after the meeting. Whilst many positive comments and compliments were received, this report focuses on the reported challenges and difficulties. The event is an example of meaningful Patient and Public Involvement and Engagement and has resulted in development of better information resources, strategies to mitigate inconveniences experienced and a standing group of advocates to advise on research design and acceptability.
Hidden Trauma
Authors: Du Lydia R. , Waters David M. , Reynolds Meredith A. , Gitto Lorenzo
Published: January 2025

While abrasions and lacerations are typically easily identified, darker pigmentation of the skin may obscure contusions. Forensic pathology literature shows a disproportionate number of illustrations of contusions on lighter skin tones compared to darker ones. Skin and soft tissue dissection is the most reliable method to confirm contusions.

The authors seek to establish a correlation between skin tone and the visual identification of contusions, confirmed by soft tissue dissection. Additionally, they aim to determine the utility of specialized dissections for identifying contusions on different skin tones to identify cases that may benefit from such procedures.

A review of cases from the Cook County Medical Examiner's Office from 2014 to 2024 was conducted. The office database was searched for deaths in custody, causes including “assault,” and “child abuse.” Autopsy photos were compiled into predissection and postdissection sets, reviewed for skin tone, visual identification of contusions, and final confirmation of soft tissue hemorrhage.

Results found a negative association between skin color and accurate visual identification of contusions and determined that decedents with a skin tone of 7 or higher on the Massey-Martin scale may benefit from specialized dissections.
Intrauterine and Neonatal Deaths
Authors: Wilkinson Zachary A. , Weaver Kaitlin , Gilson Thomas , Krywanczyk Alison
Published: January 2025

Forensic investigation of intrauterine and perinatal deaths can be challenging, given their relative infrequency and the possible involvement of maternal substance use, trauma, and socioeconomic factors. Intrauterine and perinatal deaths investigated by the Cuyahoga County Medical Examiner's Officer between 2013–2023 were reviewed. One hundred twenty-eight cases were identified (83 stillborn and 45 live births). The predominant indications for referral were concern for maternal substance use (57.8%) or trauma (35.2%). Gestational ages ranged from 11.5 to 42.5 weeks; 36.7% were <22 weeks, and only 10.2% were full term (>37 weeks). The maternal age range was 16–41 years, with most (65.2%) between 20–34 years. Not all case files included obstetric history or home address; of those which did, 53.0% received no prenatal care and 81.7% came from zip codes in the bottom quartile of household incomes. Causes of death included acute and/or chronic maternal substance use (28.9%), chorioamnionitis (21.9%), and abruption (19.5%). Manners of death (when applicable) included natural (53.3%), accident (26.7%), homicide (8.9%), and undetermined/unassigned (11.1%). Potentially confounding socioeconomic factors were identified in most cases. This demonstrates the importance of considering these factors and exercising caution when assigning specific causes and manners to intrauterine and perinatal deaths.
A Death From Necrotizing Wound Infection After Cesarean Section
Authors: Ogburn Timothy , Knight Laura D.
Published: January 2025

Necrotizing wound infections are potentially lethal complications of surgeries, including cesarean deliveries. A 32-year-old female with obesity and hidradenitis suppurativa (HS) underwent uncomplicated cesarean section. Four days later, she developed abdominal pain and imaging showed ascites; she was treated with antibiotics. She progressed to septic shock and expired the following day from cardiopulmonary arrest. Hospital blood cultures grew no microorganisms. Autopsy revealed soft tissue purulence around the incision and copious purulent ascites without evidence of tubo-ovarian abscess, retained products of conception, or emboli. Microscopic examination of the tissues demonstrated inflammatory debris with neutrophils and gram-positive cocciform bacteria. Postmortem bacterial cultures had no growth. Paraffin blocks submitted to the Centers for Disease Control Infectious Disease Pathology Branch revealed Streptococcus pyogenes. Historically, group A streptococcus (GAS) was a major cause of peripartum mortality, and the prevalence of puerperal sepsis-associated deaths declined with antibiotic usage. Although the rates of mortality have remained stable in the United States, GAS has made a resurgence over recent decades. Additionally, there is some evidence in the literature of cutaneous bacterial biofilms associated with HS. Theoretically, this could have increased the risk of perioperative infection due to colonization or secondary infection of HS lesions.
Improving Evidenced-based Outpatient Order Set Utilization in the Gastrointestinal Division of a Large Pediatric Health System
Authors: Watson Kevin L. , Love April M. , Lemerman Hanna , Gustaevel Cathy , Rajbhandari Prabi
Published: January 2025

Introduction:

Standardization is crucial in improving healthcare outcomes, equity and quality. Clinical decision support tools are key to achieving this goal. At our organization, Epic serves as our electronic health record, and SmartSets are Epic’s version of outpatient standardized order sets with embedded clinical decision support tools. In 2022, the utilization of SmartSets in our hospital’s gastrointestinal division was only 1.9%, far below our organizational target of 50%.

Methods:

Our group formed a quality improvement (QI) team and chose the model for improvement methodology. The interventions focused on education, buy-in, feedback performance monitoring, and the enhancement and development of new SmartSets. Our primary aim was to increase the utilization rate of SmartSets by gastrointestinal providers from 1.9% to 20%, and our secondary aim was to reduce the time spent by providers on orders by 10% from 3.3 to 2.8 minutes per encounter. Our balancing measure was monitoring safety reports during the study period.

Results:

SmartSet utilization improved to greater than 20% within 7 months of the project initiation. Three months after implementing SmartSet updates and introducing new SmartSets into production, time spent on orders during clinical encounters decreased from a median of 3.3 to 2.4 minutes per encounter. We appreciated that there was no change in safety reporting during the project timeline.

Conclusions:

We achieved our goal of improving utilization rates of standardized SmartSets and reducing time spent on orders using a QI methodology. Our achievements underscore the effectiveness of QI methods in enhancing SmartSet utilization and streamlining order processes.
Schizophrenia and retention in HIV care among adults insured through Medicaid in the United States: a population-based retrospective cohort study.
Authors: Bazazi Alexander R. , Thomas Marilyn , Vittinghoff Eric , Walkup James , Hermida Richard , Arnold Emily A. , Cournos Francine , Crystal Stephen , Dawson Lindsey , Dahiya Priya , Alonso-Fraire Paola , Dilley James , Olfson Mark , Mangurian Christina
Published: January 2025

Background:

People with schizophrenia spectrum disorders are at elevated risk of HIV, and people with both HIV and schizophrenia are at elevated risk of death compared to individuals with either diagnosis alone. Limited research has assessed the HIV care cascade, and in particular retention in care, among people with HIV (PWH) and schizophrenia in the U.S.

Methods:

This population-based retrospective cohort used Medicaid claims data to compare retention in HIV care between PWH with schizophrenia (n=38,217) and matched controls without schizophrenia (n=29,455) from 2001-2012. The primary outcome of annual retention in HIV care was at least 2 tests for CD4+ T-cell count or HIV viral load at least 90 days apart per year. Unadjusted and covariate-adjusted differences in period prevalence of retention among cases and controls were estimated.

Findings:

Annual retention in HIV care was 29·9% (95% CI: 29·4-30·4%) among people with schizophrenia and 38·5% (95% CI: 37·9-39·1%) among controls, representing 8·5% (95% CI 9·3-7·7) lower retention in unadjusted and 9·0% (95% CI 9·9-8·2) lower retention in adjusted estimates for people with HIV and schizophrenia. This disparity varied across states. Over time, retention increased and the disparity between people with and without schizophrenia diminished.

Interpretation:

PWH in the U.S. insured through Medicaid and diagnosed with schizophrenia experience lower retention in HIV care than controls. Suboptimal retention likely drives disparities in HIV-related morbidity and mortality for PWH with schizophrenia, and targeted individual and structural interventions are merited to improve the health of this population.
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

In 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

Human 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

Frailty 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

Plasmid 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.

IMPORTANCE

Plasmid 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

Inflammasomes 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

ABSTRACT

Fertilization 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.
Spinning fields on
Sd
and
dSd
, unitary irreducible representations, and ladder operators
Authors: Letsios Vasileios A. , Sempé Matías N. , Silva Guillermo A.
Published: January 2025

We construct, for spin 0,1,2 tensor fields on Sd, a set of ladder operators that connect the distinct unitary irreducible representations (UIRs) of SO(d+1). This is achieved by relying on the conformal Killing vectors of Sd. For the case of spinning fields, the ladder operators generalize previous expressions with a compensating transformation necessary to preserve the transversality condition. We then extend the results to the exceptional/discrete UIRs of SO(d,1), again relying on the conformal Killing vectors of de Sitter space. Our construction recovers the conventional conformal primary transformations for the scalar fields when the mass term leads to conformal coupling. A similar approach for the spin-2 field leads to the conformal-like operators found recently.

Published by the American Physical Society
2025
Motion of a point dipole in a strip
Authors: Bulycheva A. I. , Kulik K. M. , Yanovsky V. V.
Published: January 2025

A Hamiltonian system of equations to describe the evolution of a dipole-type point vortex in an infinite strip of an ideal incompressible fluid bounded by impermeable solid boundaries was obtained. The existence of two conservation laws in involution was demonstrated. Exact solutions of this system of equations in quadratures were found in the general case. It has been demonstrared that the vortex executes periodic motions in the transverse direction while moving in the longitudinal direction. The properties and characteristics of the vortex motion in the strip were studied. Two limiting cases were identified. The first case is the vortex motion only in transverse direction with vortex annihilation at reaching the boundary. The second case is only the longitudinal motion of the vortex at a constant velocity.

Published by the American Physical Society
2025
Pellet Rocket Effect in Magnetic Confinement Fusion Plasmas
Authors: Guth Nico J. , Vallhagen Oskar , Helander Per , Pusztai Istvan , Newton Sarah L. , Fülöp Tünde
Published: January 2025

Pellets of frozen material traveling into a magnetically confined fusion plasma are accelerated by the so-called pellet rocket effect. The nonuniform plasma heats the pellet ablation cloud asymmetrically, producing pressure-driven, rocketlike propulsion of the pellet. We present a semianalytical model of this process by perturbing a spherically symmetric ablation model. Predicted pellet accelerations match experimental estimates in current tokamaks (∼105  m/s2). Projections for ITER high-confinement scenarios (∼106   m/s2) indicate significantly shorter pellet penetration than expected without this effect, which could limit the effectiveness of disruption mitigation.

Published by the American Physical Society
2025
Examining equity and graduation rates at two institutions using a course deficit model and the collaborative learning through active sense-making in physics curriculum
Authors: Paul Cassandra A. , Webb David J.
Published: January 2025

We have previously described the reformed introductory physics course, collaborative learning through active sense-making in physics (CLASP), for bioscience students at a large public research one university (Original University) and presented evidence that the course was more successful and more equitable than the course it replaced by several measures. Now we compare the original success of CLASP with an implementation at a second institution. We find that the original results hold at another institution despite some changes to the original curriculum and a somewhat different student population. We find that students who take CLASP are (1) less likely to drop, (2) less likely to fail, and (3) do as well in later coursework when compared to students who took the courses that CLASP replaced, even if that coursework is not similarly reformed. We find the above items to be independently true for historically marginalized students and remarkably, also find that (4) marginalized students who take CLASP are more likely to graduate from a science, technology, engineering, and mathematics field. We use a course deficit model perspective to examine these results and discuss some of the factors that may have contributed to this success. We argue that higher education has the tools needed to significantly increase equity and improve student success and retention.

Published by the American Physical Society
2025
Variational Quantum Simulation: A Case Study for Understanding Warm Starts
Authors: Puig Ricard , Drudis Marc , Thanasilp Supanut , Holmes Zoë
Published: January 2025

The barren plateau phenomenon, characterized by loss gradients that vanish exponentially with system size, poses a challenge to scaling variational quantum algorithms. Here we explore the potential of warm starts, whereby one initializes closer to a solution in the hope of enjoying larger loss variances. Focusing on an iterative variational method for learning shorter-depth circuits for quantum we conduct a case study to elucidate the potential and limitations of warm starts. We start by proving that the iterative variational algorithm will exhibit substantial (at worst vanishing polynomially in system size) gradients in a small region around the initializations at each time step. Convexity guarantees for these regions are then established, suggesting trainability for polynomial-size time steps. However, our study highlights scenarios where a good minimum shifts outside the region with trainability guarantees. Our analysis leaves open the question whether such minima jumps necessitate optimization across barren plateau landscapes or whether there exist gradient flows, i.e., fertile valleys away from the plateau with substantial gradients, that allow for training. While our main focus is on this case study of variational quantum simulation, we end by discussing how our results work in other iterative settings.

Published by the American Physical Society
2025
High-pressure and low-temperature behaviour of organic ferroelectric (R)-3-quinuclidinol
Authors: Sharaya Svetlana S. , Bogdanov Nikita E. , Zakharov Boris A. , Boldyreva Elena V.
Published: January 2025

High-pressure and low-temperature structural changes in the ferroelectric phase of (R)-3-quinuclidinol are analysed. The changes in unit-cell volume and parameters are continuous both on cooling and under increasing pressure. The anisotropy of the structural strain, however, is found to be different. At high pressures, the shortest possible distances for H...H contacts are achieved. Since the deformation along the polarization axis can be related to spontaneous polarization, different piezoelectric responses may be expected on cooling and under hydrostatic compression.
Family involvement in board of directors and market valuation: evidence from Egyptian listed firms
Authors: Moussa Amr Ahmed
Published: January 2025

Purpose

This 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/approach

Tobin’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.

Findings

The 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/value

This 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.