bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic and Phenotypic Intra-Clade Variation in Candida auris Isolated from Critically Ill Patients in a New York City Tertiary Care Center
Authors: Smithgall Marie C , Kilic Abdullah , Weidmann Maxwell , Ofori Kenneth , Gu Yue , Koganti Lahari , Mi Shijun , Xia Hongai , Shi Jun , Pang Jiuhong , Mansukhani Mahesh , Hsiao Susan , Wu Fann 
Published: January 2025

Abstract

Background
Candida auris is an emerging multidrug-resistant pathogen. Interpretation of susceptibility testing can be difficult since minimum inhibitory concentration (MIC) breakpoints have not been fully established.

Methods
All C. auris isolates from unique patients identified at a large urban hospital between 2020 and 2024 (n = 66) underwent whole-genome sequencing (WGS). Genomic DNA was extracted from pure culture isolates and underwent PCR-free library preparation. WGS was performed on an Illumina platform (NextSeq2000) with an average coverage of 50×. Genomic analysis was conducted via an adapted GATK-based pipeline using the B11205 strain as the reference genome based on the CDC (MycoSNP) protocol. All isolates underwent FKS1 gene Sanger sequencing for confirmation of WGS results. Genotypic results were correlated with antifungal susceptibility testing.

Results
All clinical isolates were part of Clade I and carried azole resistance mutations in ERG11, TAC1b, and CDR1, consistent with 100% phenotypic fluconazole resistance. Across all isolates, 5 distinct missense variants in FKS1 were identified: one case with p.Ser639Tyr, one case with both a p.Arg1354Ser and a p.Asp642His, 7 cases with p.Met690Ile, and 9 cases with p.Val1818Ile. Isolates with known echinocandin resistance conferring mutations p.Ser639Tyr and p.Arg1354Ser were resistant to micafungin and anidulafungin. Two isolates with Met690Ile were resistant to caspofungin alone.

Conclusions
With potential resistance to all 3 major antifungal classes of drugs, C. auris is an emerging public health threat. Early detection of echinocandin resistance by molecular methods could impact treatment course to include novel antifungal agents. Further study of the FKS1 Met690Ile variant is warranted.
Polygenic Risk Scores in Human Disease
Authors: Maamari Dimitri J , Abou-Karam Roukoz , Fahed Akl C 
Published: January 2025

Abstract

Background
Polygenic risk scores (PRS) are measures of genetic susceptibility to human health traits. With the advent of large data repositories combining genetic data and phenotypic information, PRS are providing valuable insights into the genetic architecture of complex diseases and are transforming the landscape of precision medicine.

Content
PRS have emerged as tools with clinical utility in human disease. Herein, details on how to develop PRS are provided, followed by 5 areas in which they can be used to improve human health: (a) augmenting risk prediction, (b) refining diagnosis, (c) guiding treatment choices, (d) making clinical trials more efficient, and (e) improving public health. Finally, some of the ongoing challenges to the clinical implementation of PRS are noted.

Summary
PRS can offer valuable information for providers and patients, including identifying risk of disease earlier in life and before the onset of clinical risk factors, guiding treatment decisions, improving public health outcomes, and making clinical trials more efficient. The future of genomic-informed risk assessments of disease is through integrated risk models that combine genetic factors including PRS, monogenic, and somatic DNA information with nongenetic risk factors such as clinical risk estimators and multiomic data. However, adopting PRS in a clinical setting at scale faces some challenges, including cross-ancestry performance, standardization and calibration of risk models, downstream clinical decision-making from risk information, and seamless integration into existing health systems.
SARS-CoV-2 Diversity and Transmission on a University Campus across Two Academic Years during the Pandemic
Authors: Casto Amanda M , Paredes Miguel I , Bennett Julia C , Luiten Kyle G , Han Peter D , Gamboa Luis S , McDermot Evan , Gottlieb Geoffrey S , Acker Zachary , Lo Natalie K , McDonald Devon , McCaffrey Kathryn M , Figgins Marlin D , Lockwood Christina M , Shendure Jay , Uyeki Timothy M , Starita Lea M , Bedford Trevor , Chu Helen Y , Weil Ana A 
Published: January 2025

Abstract

Background
Institutions of higher education (IHE) have been a focus of SARS-CoV-2 transmission studies but there is limited information on how viral diversity and transmission at IHE changed as the pandemic progressed.

Methods
Here we analyze 3606 viral genomes from unique COVID-19 episodes collected at a public university in Seattle, Washington from September 2020 to September 2022.

Results
Across the study period, we found evidence of frequent viral transmission among university affiliates with 60% (n = 2153) of viral genomes from campus specimens genetically identical to at least one other campus specimen. Moreover, viruses from students were observed in transmission clusters at a higher frequency than in the overall dataset while viruses from symptomatic infections were observed in transmission clusters at a lower frequency. Although only a small percentage of community viruses were identified as possible descendants of viruses isolated in university study specimens, phylodynamic modeling suggested a high rate of transmission events from campus into the local community, particularly during the 2021–2022 academic year.

Conclusions
We conclude that viral transmission was common within the university population throughout the study period but that not all university affiliates were equally likely to be involved. In addition, the transmission rate from campus into the surrounding community may have increased during the second year of the study, possibly due to return to in-person instruction.
Hypertrophic cardiomyopathy management: a systematic review of the clinical practice guidelines and recommendations
Authors: Sanghvi Mihir M , Dhall Eamon , Anwar A. Chahal C , O'Mahony Constantinos , Mohiddin Saidi A , Savvatis Konstantinos , Ricci Fabrizio , Munroe Patricia B , Petersen Steffen E , Aung Nay , Khanji Mohammed Y 
Published: January 2025

Abstract

Aims
In light of recent advances in imaging techniques, molecular understanding and therapeutic options in hypertrophic cardiomyopathy (HCM), we performed a systematic review of current guidelines for the diagnosis and management of HCM in order to identify consensus and discrepant areas in the clinical practice guidelines.

Methods and results
We systematically reviewed the English language guidelines and recommendations for the management of HCM in adults. MEDLINE and EMBASE databases were searched for guidelines published in the last 10 years. Following a systematic search, three guidelines on the diagnosis and management of HCM were identified, all of which were robustly developed (AGREE rigour of development score ≥50%). These guidelines were authored by the major European (European Society of Cardiology; 2023), American (American Heart Association /American College of Cardiology/American Medical Society for Sports Medicine /Heart Rhythm Society/Pediatric and Congenital Electrophysiology Society/Society for Cardiovascular Magnetic Resonance; 2024), and Japanese [Japanese Circulation Society (JCS)/Japanese Heart Failure Society (JHFS); 2018] cardiovascular societies. There was broad consensus on echocardiographic recommendations, the medical and invasive management of HCM, the application of genetic testing and family screening, and exercise and reproductive recommendations in HCM. There were areas of variability in the definition and diagnostic criteria for HCM, cardiovascular magnetic resonance imaging recommendations, and assessment of sudden cardiac death (SCD) risk and prevention strategies. Due to the JCS/JHFS guidelines being older, there are no recommendations on the use of cardiac myosin ATPase inhibitors.

Conclusion
Contemporary guidelines for HCM achieve consensus across a broad range of criteria and recommendations concerning diagnosis and management. However, variations in the approach towards risk assessment for SCD exist between the guidelines. There are also more subtle differences concerning diagnostic criteria and the utility of late gadolinium enhancement for risk stratification, which will likely evolve as the evidence-base broadens.
Atrial fibrillation ablation timing: where is the sweet spot?
Authors: Kalman Jonathan M , Kistler Peter M , Hindricks Gerhard , Sanders Prashanthan 
Published: January 2025

Abstract
Convincing evidence for the efficacy of ablation as first-line therapy in paroxysmal AF (PAF) and its clear superiority to medical therapy for rhythm control in both PAF and persistent AF (PsAF) has generated considerable interest in the optimal timing of ablation. Based on this data, there is a widespread view that the principle of ‘the earlier the better’ should be generally applied. However, the natural history of AF is highly variable and non-linear, and for this reason, it is difficult to be emphatic that all patients are best served by ablation early after their initial AF episodes. Sufficient evidence exists to indicate a conservative approach is reasonable in patients with infrequent and non-progressive episodes (i.e. absence of progressive increase in burden culminating in PsAF) in whom symptoms remain mild and well-controlled. A conservative management phase should be marked by assiduous attention to risk factor modification, changes in frequency and duration of AF episodes, and patient preferences. If and when AF does begin to progress, accumulating evidence indicates that early ablation accompanied by ongoing attention to risk factors provides the best outcomes.
The Cumulative Burden of Social Risk Factors and 10-Year Change in Quality of Life
Authors: Reid Ro-Jay , Safford Monika , Lambert W Marcus , Bryan Joanna , Pinheiro Laura C , Sterling Madeline R , Bowling C Barrett , Levitan Emily B , Banerjee Samprit , Durant Raegan , Kim Michael , Lau Jennifer D , Goyal Parag 
Published: January 2025

Abstract

Background
Social risk factors are linked to adverse health outcomes, but their total impact on long-term quality of life is obscure. We hypothesized that a higher burden of social risk factors is associated with greater decline in quality of life over 10 years.

Methods
We examined associations between social risk factors count and decline &gt;5 points in (i) physical component summary, and (ii) mental component summary scores from the Short Form-12 among Black and White participants in the Reasons for Geographic and Racial Differences in Stroke study (n = 14 401).

Results
For physical component summary, White participants with 1 social risk factor had relative risk (RR) for decline of 1.14 [95% confidence intervals (CI): 1.07–1.12]. Those with ≥2 social risk factors had RR of 1.26 [95% CI: 1.17–1.35], after adjusting for baseline demographics, health behaviors, medical conditions, medications, and physiological variables. Black participants with 1 social risk factor had RR of 1.03 [95% CI: 0.93–1.15]. Those with ≥2 social risk factors had RR of 1.24 [95% CI: 1.13–1.36]. For mental component summary, White participants with 1 social risk factor had RR for decline of 1.19 [95% CI: 1.04–1.37]. Those with ≥2 social risk factors had RR of 1.47 [95% CI: 1.28–1.68]. Black participants with 1 social risk factor had RR of 1.18 [95% CI: 0.96–1.45]. Those with ≥2 social risk factors had RR of 1.38 [95% CI: 1.14–1.66].

Conclusions
More social risk factors increased the risk of decline of quality of life for Black and White individuals, especially impacting mental health.
The Antimilitarist Feminist Network: Addressing Mexico’s Security Failures
Authors: García Daniela Philipson 
Published: January 2025

Abstract
Despite adopting progressive policies and making significant progress in gender parity, Mexico faces important security challenges that undermine gender equality. Mexico's security policies, especially its military-based solutions, risk undoing the country's ambitious gender equality agenda. In response to increasing security failures and militarization, Mexican antimilitarist feminist activists have pushed back against the government with some success despite setbacks. But what are the underlying preconditions for the rise of antimilitarist feminists? And how are they organizing in response to increasing militarization? This paper begins by describing the context and recent history of militarization and antimilitarism in Mexico. Then it explores the underlying preconditions that enable the emergence of antimilitarist feminist mobilizations: feminist peace and security theorizing and political democratization and human rights frameworks. Drawing on semistructured interviews with feminist activists, it finds that the Antimilitarist Feminist Network has been pivotal in exposing Mexico's contradictions and failures regarding its policies on security and gender equality. The Antimilitarist Feminist Network (re)defines security and (re)imagines alternatives to militarization by promoting and demanding women's meaningful participation and feminist perspectives in security policymaking.
Can States Be Interviewed?
Authors: Markiewicz Tadek 
Published: January 2025

Abstracts
While states are not human beings, they are institutionalized social groups. It is humans who constitute and run them. Consequently, it is argued that countries can be interviewed. This claim is based on in-depth interviews with seventy Israeli and British officials, which “captured” states’ anxiety. In ontological security studies, countries’ anxieties are typically inferred from historical and narrative analysis. The article lays another path to establish that states are anxious. Despite the increasing acknowledgement of the “emotional turn” in international relations, there is a notable lack of methodological focus on how emotions impact statecraft. This study bridges the gap by showing how interviewing can investigate the internal lives of states. The research also addresses critiques of ontological security studies, namely the challenge of applying an individual-level concept to state behavior and empirically validating its relevance in statecraft. It traced how officials’ anxiety about their country’s policies “scales up” to the state level. The rich evidence—coming from country officials themselves—affirmed ontological security’s capacity to explain state behavior and underscored the importance of integrating political psychology into international relations research. Moreover, it is the first study to use elite interviews to investigate whether countries experience ontological insecurity.
Supporting wild bee development with a bacterial symbiont
Authors: Nguyen Phuong N , Rehan Sandra M 
Published: January 2025

Abstract

Aims
Wild bees foster diverse microbiota that may determine survival success of developing larvae. Here, we compare survivorship and microbial communities of Ceratina calcarata small carpenter bees reared from eggs across three treatments: maternally collected control provisions with diverse microbiota, sterile provisions, and probiotic provisions supplemented with a beneficial symbiont, Apilactobacillus kunkeei.

Methods and results
Survival probability and adult masses differed across treatments, with the probiotic treatment resulting in highest survivorship and masses. By comparing the bacterial (16S rRNA), fungal (ITS), and plant (rbcL) communities of adults reared across treatments, we characterized distinct microbial communities across each that suggest the microbiome may be sensitive to microbial succession and competition.

Conclusions
We describe positive implications for the usage of probiotics on wild bees. Furthermore, the sensitivity of bee microbiota’s relationships to their host, floral resources, and the environment suggests that holistic approaches best encapsulate the complex network of interactions between bees and their microbes.
Accelerating biosimilar market access: the case for allowing earlier standing
Authors: Tu S Sean , Goode Rachel , Turner Matthew , Van de Wiele Victor 
Published: January 2025

Abstract
Biosimilars, which are affordable alternatives to biologic medicines, face delays in market entry due to the current patent litigation framework under the Biologic Price Competition and Innovation Act. Currently, biosimilar manufacturers can only initiate patent litigation to attempt to clear weak and invalid patents after submitting their Biologic License Application to the Food and Drug Administration (FDA), which happens after completing extensive, and costly clinical trials. By contrast, generic drug manufacturers can start litigation earlier due to shorter development times and less stringent clinical requirements, allowing them to launch immediately after the primary patent expires. We propose allowing biosimilars to begin patent litigation at the start of phase 3 clinical trials, the final stage of biosimilar development, where the product and manufacturing process and product profile are largely finalized. This change would enable biosimilar firms to resolve patent issues well before the brand biologic’s primary patent expiration date, potentially reducing market entry delays by about 1.8 years. This article examines the issues surrounding initiation of biosimilar litigation and suggests litigation reforms to expedite biosimilar market availability.
Investigation of the safety of Radium-223 chloride in combination with external beam radiotherapy for bone metastases of prostate cancer
Authors: Makino Soichi , Miyazawa Kazunari , Katsuoka Yoji , Ooe Takeru , Aikawa Ken , Segawa Akira , Kobayashi Hiroshi 
Published: January 2025

Abstract
This study aimed to investigate the safety of combining radium-223 chloride (Ra-223) therapy with external beam radiation therapy (EBRT) for patients with multiple bone metastases from castration-resistant prostate cancer (CRPC), including lesions requiring urgent treatment such as those causing neurological symptoms due to spinal cord compression. We retrospectively analyzed data from patients with CRPC and bone metastases treated with Ra-223 therapy at our hospital between September 1, 2018, and December 31, 2023. Adverse events were evaluated using the Common Terminology Criteria for Adverse Events version 4.0. Of the 23 patients referred, data from 17 were included; 8 received concurrent Ra-223 therapy and EBRT, whereas others received only Ra-223 therapy. The median follow-up period was 20 months. Grade (G) 2 or higher adverse events occurred in seven patients (41.2%), and G 3 or higher in 2 (11.7%). None of the patients who received EBRT with fields involving the gastrointestinal tract experienced diarrhea, constipation, bleeding, perforation, or obstruction. Ra-223 therapy with EBRT did not increase adverse events compared with studies of Ra-223 therapy without EBRT. One case of G 5 Pneumocystis carinii pneumonia, likely because of steroid use for neurological symptoms and the patient’s underlying diabetes mellitus, was noted. The effects of EBRT cannot be entirely excluded, so minimizing field size and dose is recommended when combining Ra-223 therapy and EBRT. Our findings indicate that concurrent Ra-223 therapy and EBRT could be safe for managing patients with symptomatic bone metastases and castration-resistant prostate cancer who require specialized treatment, provided sufficient attention is given to the field and the prescribed dose.
Combustion-related isoprene contributes substantially to the formation of wintertime secondary organic aerosols
Authors: Zhang Yanli , Men Yatai , Guo Hao , Shen Guofeng , Gao Yang , Xiong Rui , Tao Shu , Wang Xinming 
Published: January 2025

ABSTRACT
Isoprene is a key reactive organic gas involved in organic aerosol formation. While biogenic isoprene from terrestrial plants has been extensively studied and is recognized as a major contributor to secondary organic aerosol (SOA), high levels of observed SOA, especially in winter, cannot be fully explained by biogenic isoprene alone. In this study, we developed a comprehensive bottom-up emission inventory for isoprene, incorporating both biogenic and combustion sources and modeling their contributions to SOA in China from 2000 to 2016. Combustion-related isoprene emissions from open biomass burning and residential fuel combustion were estimated at 52.0 (39.1–65.7) Gg in 2000, declining to 14.8 (10.6–19.0) Gg by 2016. Open biomass burning contributes ∼40% of combustion-related isoprene emissions. Though, annually, combustion-related isoprene emissions were much smaller than the biogenic emissions, they did account for 32%–80% of total isoprene emissions in many north and west provinces in the colder months in 2016, and were even higher during the early 2000s owing to more biofuel-burning emissions. Model simulation results indicated that combustion-related isoprene could contribute 25%–40% of winter SOA in northern regions. Wintertime isoprene-derived SOA levels declined since 2000, corresponding with decreased combustion-related isoprene emissions; however, the extent of this decline varied regionally due to the influence of other precursors like nitrogen oxides (NOx). In the northeast region with high NOx levels, while combustion-related isoprene emissions decreased by &gt;80% from 2000 to 2016, isoprene-derived SOA declined by only ∼20%. These findings highlight the previously underappreciated contributions of combustion-related isoprene to observed high wintertime isoprene-derived SOA levels.
Effects of Dietary Interventions in Patients With Migraine: A Systematic Review
Authors: Roldán-Ruiz Alberto , Bertotti Gabriele , López-Moreno Miguel 
Published: January 2025

Abstract

Context
Migraine is a disabling neurological disorder. Diet may be a factor to consider because measures of diet quality have been linked to both frequency and severity of attacks.

Objectives
To investigate the effects of dietary interventions on the clinical symptoms of migraine, quality of life, and body composition of patients with migraine.

Data Sources
The MEDLINE, Embase, and Web of Sciences databases were searched since database inception to February 13, 2024. We included articles on randomized clinical trials that assessed the effect dietary interventions on clinical symptoms of migraines and the quality of life and body composition of individuals with migraine.

Data Extraction
Data from the included articles were independently extracted by 2 researchers; another independent reviewer further verified the extractions. The Cochrane risk-of-bias tool was used to evaluate the risk of bias of selected studies, and the Physiotherapy Evidence Database scale was used to assess the methodological quality.

Results
Eight articles were included in this review. Of these, 3 reported on studies that assessed the ketogenic diet (KD), 2 reported on the Dietary Approaches to Stop Hypertension (DASH), and 3 reported on studies of other dietary strategies. Strong evidence exists regarding the effectiveness of the KD and DASH in reducing the frequency of migraine attacks, whereas their efficacy in improving patients’ quality of life was supported only by limited evidence. There also is strong evidence regarding the effectiveness of DASH in reducing migraine’s severity and patients’ body weight. Insufficient evidence was found regarding the effectiveness of the other dietary interventions on all variables.

Conclusions
The DASH and KD may help reduce migraine frequency and severity. However, more high-quality studies are needed to confirm their effectiveness.

Systematic Review Registration
PROSPERO No. CRD42024516161.