bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating the Early Transmission Inhibition of New Treatment Regimens for Drug-Resistant Tuberculosis
Authors: Stoltz A , Nathavitharana R R , de Kock E , Ueckermann V , Jensen P , Mendel C M , Spigelman M , Nardell E A 
Published: January 2025

Abstract

Background
Most drug-resistant tuberculosis occurs due to transmission of unsuspected or ineffectively treated drug-resistant tuberculosis. The duration of treatment to stop person-to-person spread of drug-resistant tuberculosis is uncertain. We evaluated the impact of novel regimens, including BPaL (bedaquiline, 1200-mg linezolid, and pretomanid), on drug-resistant tuberculosis transmission, using the human–guinea pig (H-GP) transmission model.

Methods
In experiment 1, patients initiated an optimized drug-resistant tuberculosis regimen including bedaquiline and linezolid. In experiment 2, patients initiated the BPaL regimen. We measured baseline infectivity for each cohort by exhausting ward air to one of two guinea pig exposure rooms (control group), each containing 90 guinea pigs, for 8 patient-days. Then, after 72 hours of treatment, ward air was exhausted to the second guinea pig exposure room for 8 patient-days (intervention group). The infectiousness of each cohort was compared by performing tuberculin skin tests in guinea pigs at baseline (before treatment) and 6 weeks after the exposure period.

Results
In experiment 1, before treatment, 5 patients with drug-resistant tuberculosis infected 24 of 90 guinea pigs (26.7%) (control group). After treatment (72 hours after drug initiation), the same patients infected 25 of 90 guinea pigs (27.8%) (intervention group) (P &gt; .99). In experiment 2, before treatment, 9 patients with drug-resistant tuberculosis infected 40 of 90 guinea pigs (44.4%) (control group). After treatment (beginning 72 hours after drug initiation), the same patients infected 0 of 90 guinea pigs (0%) (intervention group) (P &lt; .0001).

Conclusions
In this study, drug-resistant tuberculosis drug regimens, including bedaquiline and standard-dose linezolid for 72 hours, did not decrease drug-resistant tuberculosis transmission. In contrast, transmission was rapidly and completely inhibited in patients treated with BPaL for 72 hours, suggesting an early and profound impact on transmission.
Uncertainty estimation in diagnosis generation from large language models: next-word probability is not pre-test probability
Authors: Gao Yanjun , Myers Skatje , Chen Shan , Dligach Dmitriy , Miller Timothy , Bitterman Danielle S , Chen Guanhua , Mayampurath Anoop , Churpek Matthew M , Afshar Majid 
Published: January 2025

Abstract

Objective
To evaluate large language models (LLMs) for pre-test diagnostic probability estimation and compare their uncertainty estimation performance with a traditional machine learning classifier.

Materials and Methods
We assessed 2 instruction-tuned LLMs, Mistral-7B-Instruct and Llama3-70B-chat-hf, on predicting binary outcomes for Sepsis, Arrhythmia, and Congestive Heart Failure (CHF) using electronic health record (EHR) data from 660 patients. Three uncertainty estimation methods—Verbalized Confidence, Token Logits, and LLM Embedding+XGB—were compared against an eXtreme Gradient Boosting (XGB) classifier trained on raw EHR data. Performance metrics included AUROC and Pearson correlation between predicted probabilities.

Results
The XGB classifier outperformed the LLM-based methods across all tasks. LLM Embedding+XGB showed the closest performance to the XGB baseline, while Verbalized Confidence and Token Logits underperformed.

Discussion
These findings, consistent across multiple models and demographic groups, highlight the limitations of current LLMs in providing reliable pre-test probability estimations and underscore the need for improved calibration and bias mitigation strategies. Future work should explore hybrid approaches that integrate LLMs with numerical reasoning modules and calibrated embeddings to enhance diagnostic accuracy and ensure fairer predictions across diverse populations.

Conclusions
LLMs demonstrate potential but currently fall short in estimating diagnostic probabilities compared to traditional machine learning classifiers trained on structured EHR data. Further improvements are needed for reliable clinical use.
Bone turnover markers predict changes in bone mineral density in men treated with abaloparatide: results from the abaloparatide for the treatment of men with osteoporosis (ATOM) study
Authors: Eastell Richard , Brown Jacques P , Adler Robert A , Lewiecki E Michael , Binkley Neil , Orwoll Eric S , Kendler David , Mitlak Bruce H , Wang Yamei 
Published: January 2025

Abstract
Early increases in bone turnover markers (BTMs) in response to anabolic therapy correlate with 18-mo BMD increases in postmenopausal women with osteoporosis; however, this relationship has not been assessed in men. In this analysis, the correlation between changes from baseline in fasting intact serum procollagen type I N propeptide (PINP) and serum CTX at 1, 3, 6, and 12 mo and percent increase from baseline in BMD at 12 mo in men from the randomized phase 3 ATOM study (NCT03512262) were evaluated using Pearson’s correlation coefficients. The uncoupling index (UI), a measure of the balance between markers of bone formation (PINP) and bone resorption (CTX), with positive UI favoring bone formation, was calculated. Results in men were compared to 12-mo results for women from the ACTIVE study using the z score test after Fisher’s Z transformation. In abaloparatide-treated men, PINP increases at 1 mo (r = 0.485), 3 mo (r = 0.614), 6 mo (r = 0.632), and 12 mo (r = 0.521) were highly correlated (p &lt; .0001) with 12-mo LS BMD increases. The mean UI for abaloparatide-treated men was greater than placebo as early as 1 mo (2.26 vs −0.25). At month 3, the mean UI for men was greater (1.32) than for women (0.88) (p &lt; .001). There was a significant correlation between 3-mo UI and LS BMD at 12 mo in both men (r = 0.453; p &lt; .001) and women (r = 0.252; p &lt; .01). UI at months 6 and 12 were also significantly correlated with 12-mo LS BMD in men and women, but the correlation was stronger in men than women. These data support that early changes in BTMs in men treated with abaloparatide are associated with subsequent changes in BMD similar to what has been reported in women.
Ethanol release patterns and captures of Xylosandrus spp. (Coleoptera: Curculionidae) in ornamental nursery
Authors: Govindaraju Ramkumar , Joseph Shimat V 
Published: January 2025

Abstract
Xylosandrus crassiusculus Motschulsky and Xylosandrus germanus Blandford are serious ambrosia beetle pests in ornamental nurseries. Three ethanol baits, AgBio low release (LR), AgBio high release (HR), and Trécé are commercially available for use in bottle traps to determine flight activity of adult Xylosandrus spp. However, release patterns of ethanol from these baits under varying temperatures and captures of Xylosandrus spp. are poorly understood. Thus, the objectives of this study were (i) to determine ethanol release rates from these baits under constant and variable temperatures and (ii) to compare relative adult Xylosandrus spp. captures using these baits in ornamental nurseries. When 3-d difference (3-d difference) bait weights were recorded under constant 15.6, 21.1, 26.7, and 32.2 °C, an increase in release rates was recorded with an increase in temperature from 15.6 to 32.2 °C for LR bait. At 32.2 °C, no increase or reduction in the 3-d-difference weights was found for the HR and Trécé baits, respectively, compared to LR bait. The 3-d-difference weights were steady with all 3 baits when temperatures gradually increased and decreased in variable sequence for 30 d. In 2022, 2023, and 2024, although all 3 baits captured adult X. crassiusculus and X. germanus, LR bait captured significantly more numbers of X. crassiusculus than the other 2 baits in 2022 and 2023, and in 2024, X. crassiusculus captures were greater in traps with the Trécé bait than the other 2 baits. Thus, ethanol baits can effectively detect the early flight activity of Xylosandrus spp. adults in ornamental nurseries.
The Book of Malachi: Its Place in the Twelve Minor Prophets, in Jewish and in Christian Canon
Authors: Kalimi Isaac 
Published: January 2025

ABSTRACT
This study discusses the establishment of the corpus of the Twelve Minor Prophets into which the book of Malachi is integrated. The grouping of the Twelve in one body was known prior to the second century bce, and the Baraita explains the necessity of putting them together. After exploring the place, literary status, and standing of Malachi within the Twelve and the Prophets more generally, the study examines whether or not the canonicity of the book was disputed among Jews and Christians. Malachi plays a significant role in the Jewish canon: It connects Nebe’im with Torah, serves as a transition from Prophets to Writings, and is the transition point from the Written to the Oral Torah. In the Christian canon, Malachi is located at the end of the Old Testament, just before Matthew that opens the New Testament and recounts the birth of Jesus. That Elijah is forerunner of the Messiah is common to Jewish and Christian tradition. However, while in Judaism he will appear again, in Christianity, he has already appeared and was identified with John the Baptist who announced Jesus as Christ.
Breaking vaccination barriers among migrants? Human rights and crisis preparedness
Authors: Litins’ka Yana 
Published: January 2025

Abstract
Vaccination hesitancy is one of the critical threats to public health. The coronavirus disease pandemic reconfirmed that certain groups of populations are more reluctant to vaccinate than others, particularly migrants. This article examines legal obligations related to protecting the right to health in addressing vaccination barriers among newly arrived adult migrants, taking Ukrainians granted temporary protection as an example. From human rights law requirements delineated by the United Nations and Council of Europe, it maps out a framework of vaccination-related obligations. Furthermore, the article tests the framework created in one national legal system—Sweden—to show where the gaps in transposing obligations into national law still exist. To deepen the analysis, the interview study with Ukrainian refugees in Sweden is presented, which allows reflection on what obligations have not reached their recipients and resulted in vaccination barriers. The article advocates for further specification of obligations related to vaccinations in both national and international laws for better crisis preparedness.
The onset of bar formation in a massive galaxy at z ∼ 3.8
Authors: Amvrosiadis A , Lange S , Nightingale J W , He Q , Frenk C S , Oman K A , Smail I , Swinbank A M , Fragkoudi F , Gadotti D A , Cole S , Borsato E , Robertson A , Massey R , Cao X , Li R 
Published: January 2025

ABSTRACT
We examine the morphological and kinematical properties of SPT-2147, a strongly lensed, massive, dusty, star-forming galaxy at $z = 3.762$. Combining data from JWST, Hubble Space Telescope, and ALMA, we study the galaxy’s stellar emission, dust continuum, and gas properties. The imaging reveals a central bar structure in the stars and gas embedded within an extended disc with a spiral arm-like feature. The kinematics confirm the presence of the bar and of the regularly rotating disc. Dynamical modelling yields a dynamical mass, ${M}_{\rm dyn} = (9.7 \pm 2.0) \times 10^{10}$${\rm M}_{\odot }$, and a maximum rotational velocity to velocity dispersion ratio, $V / \sigma = 9.8 \pm 1.2$. From multiband imaging we infer, via spectral energy distribution fitting, a stellar mass, ${M}_{\star } = (6.3 \pm 0.9) \times 10^{10}$$\rm {M}_{\odot }$, and a star formation rate, ${\rm SFR} = 781 \pm 99$${\rm {\rm M}_{\odot } yr^{-1}}$, after correcting for magnification. Combining these measurements with the molecular gas mass, we derive a baryonic-to-total mass ratio of ${M}_{\rm bar} / {M}_{\rm dyn} = 1.1 \pm 0.3$ within 4.0 kpc. This finding suggests that the formation of bars in galaxies begins earlier in the history of the Universe than previously thought and can also occur in galaxies with elevated gas fractions.
Establishing a living biobank of pediatric high-grade glioma and ependymoma suitable for cancer pharmacology
Authors: Deligne Clémence , Tourbez Arthur , Bénard Flavie , Meyer Swann , Curt Alexis , Gianesello Matteo , Hamadou Maud , Clavier Léna , Coquet Claire , Bocquet Charlotte , Tomine Julia , Diot Thomas , Paraqindes Hermes , Marcel Virginie , Berthelot Clément , Engel Justine , Rochet Isabelle , Barritault Marc , Savary Clara , Gadot Nicolas , Attignon Valéry , Carrere Marjorie , Billaud Marc , Dutour Aurélie , Cordier-Bussat Martine , Beuriat Pierre-Aurélien , Szathmari Alexandru , Di Rocco Federico , Blay Jean-Yves , Tiberi Luca , Vasiljevic Alexandre , Meyronet David , Castets Marie , Leblond Pierre , Broutier Laura 
Published: January 2025

Abstract

Background
Brain tumors are the deadliest solid tumors in children and adolescents. Most of these tumors are glial in origin and exhibit strong heterogeneity, hampering the development of effective therapeutic strategies. In the past decades, patient-derived tumor organoids (PDT-O) have emerged as powerful tools for modeling tumoral cell diversity and dynamics, and they could then help define new therapeutic options for pediatric brain tumors.

Methods
Through an integrative approach based on our expertise and a careful review of the literature about glioblastoma 3D primary cultures, we set up a standardized methodological pipeline for the establishment, characterization, and biobanking of PDT-O through direct 3D in vitro culture of the deadliest pediatric glial brain tumors. To assess PDT-O fidelity and validate their preclinical relevance, we performed comprehensive histological, molecular, and drug-response analyses.

Results
Our methodological pipeline allowed the rapid and efficient generation of PDT-O recapitulating their parental tumor features, including intratumoral heterogeneity, even after several passages and cryopreservation/revival as 3D cultures. Moreover, we successfully performed preclinical test responses on these PDT-O to standard-of-care therapies and new therapeutic options. Finally, we identified ONC201 as a selective drug for pediatric glial tumor types not restricted to H3K27-altered glial tumors, as well as combination strategies to increase the therapeutic response to ONC201.

Conclusions
Hence, we describe a fast and robust process to biobank PDT-O for pediatric glial brain tumors. These PDT-O models have the potential for patient-specific modeling even after long-term expansion in vitro, and we established the proof-of-concept of their usefulness to support powerful preclinical studies.
Global elevation of algal bloom frequency in large lakes over the past two decades
Authors: Wang Ying , Zhao Dan , Woolway R Iestyn , Yan Haoran , Paerl Hans W , Zheng Yi , Zheng Chunmiao , Feng Lian 
Published: January 2025

ABSTRACT
The recent increase in algal blooms in lakes, potentially exacerbated by climate warming, is of global concern. However, a spatially and temporally detailed characterization of algal bloom trends at a global scale has been lacking, posing challenges to definitively attribute the increase trend to warming as a primary driver. Here, we used daily MODIS satellite observations from 2003 to 2022 to analyze algal bloom trends in 1956 large freshwater lakes worldwide. Among these lakes, 620 have experienced algal bloom events in over half of the years during the past two decades, with an upward trend in bloom frequency observed in 504 lakes. This trend is particularly prominent in subtropical regions and has become most pronounced after 2015. The global median annual bloom frequency has significantly increased at a rate of +1.8%/yr over the past two decades, showing a significant correlation with air temperatures (r2 = 0.43, P &lt; 0.05). Furthermore, in 44.8% of the bloom-affected lakes, we observed a strong correlation between air temperature and bloom frequency. Our study helps clarify the factors contributing to the global expansion of algal blooms and emphasizes the urgent need to recognize and address this growing environmental challenge within the context of climate warming.
Cotinine-Measured Secondhand Smoke Exposure Among Federal Housing Assistance Recipients Without Active Tobacco or Nicotine Use in the United States: NHANES, 2007–2018
Authors: Stierman Bryan , Helms Garrison Veronica , Brody Debra J , Bachand Jacqueline V 
Published: January 2025

Abstract

Introduction
The prevalence of cigarette smoking is high among U.S. Department of Housing and Urban Development (HUD) assistance recipients, putting others at risk for secondhand smoke (SHS) exposure. We evaluated the burden of SHS exposure among HUD-assisted children, adolescents, and adults.

Aims and Methods
Using 2007–2018 National Health and Nutrition Examination Survey (NHANES) data linked with HUD administrative data, we assessed SHS exposure prevalence, defined using serum cotinine, among non-tobacco, non-nicotine-using, HUD-assisted children and adolescents (ages 3–17 years, n = 955) and adults (ages ≥ 18 years, n = 878) and among low-income, HUD-unassisted children and adolescents (n = 5788) and adults (n = 8027). Time trends were evaluated. Unadjusted and adjusted multivariable logistic regression models were created to assess SHS exposure by HUD assistance status.

Results
The prevalence of SHS exposure during 2015–2018 was 73.2% (95% CI = 63.2% to 81.7%) among HUD-assisted children and adolescents and 50.1% (95% CI = 40.1% to 60.1%) among HUD-assisted adults. Decreases in SHS exposure among HUD-assisted individuals from 2007–2010 through 2015–2018 were significant only for ages 12–17 years (78.6% [95% CI = 68.0% to 87.0%] to 64.3% [95% CI = 52.5% to 74.9%]; p = .04). Among low-income individuals, SHS exposure was higher during 2007–2018 among HUD-assisted than HUD-unassisted children and adolescents (OR = 3.39 [95% CI = 2.58 to 4.47]) and adults (2.11 [95% CI = 1.66 to 2.68]). Results remained significant after adjusting for social, demographic, and housing characteristics.

Conclusions
HUD-assisted children, adolescents, and adults had higher exposure to SHS than those not receiving HUD assistance. SHS exposure among HUD-assisted individuals was high for all years studied, compared to published estimates for the general US population, but did decrease among children and adolescents aged 12–17 years.

Implications
This study is the first to provide biomarker-derived prevalence estimates of SHS exposure among recipients of HUD assistance within a nationally representative sample of the United States. The findings suggest that HUD-assisted children, adolescents, and adults are an at-risk population for SHS exposure, independent of known confounding social and demographic factors.
Genome-Wide Association Study of Varenicline-Aided Smoking Cessation
Authors: Coley Kayesha , Wang Qingning , Packer Richard , John Catherine , Abner Erik , Reis Kadri ,   Estonian Biobank Research Team, Bedair Khaled F , Srinivasan Sundararajan , Paciga Sara , Hyde Craig , Free Robert C , Reeve Nicola F , Shepherd David J , Esko Tõnu , Palmer Colin , Pearson Ewan , Malarstig Anders , Tobin Martin D , Batini Chiara 
Published: January 2025

Abstract

Introduction
Varenicline is an α4β2 nicotinic acetylcholine receptor partial agonist with the highest therapeutic efficacy of any pharmacological smoking cessation aid and a 12-month cessation rate of 26%. Genetic variation may be associated with varenicline response, but to date, no genome-wide association studies of varenicline response have been published.

Methods
In this study, we investigated the genetic contribution to varenicline effectiveness using two electronic health record-derived phenotypes. We defined short-term varenicline effectiveness (SVE) and long-term varenicline effectiveness (LVE) by assessing smoking status at 3 and 12 months, respectively, after initiating varenicline treatment. In Stage 1, comprising five European cohort studies, we tested genome-wide associations with SVE (1405 cases, 2074 controls) and LVE (1576 cases, 2555 controls), defining sentinel variants (the most strongly associated variant within 1 Mb) with p-value &lt; 5 × 10−6 to follow up in Stage 2. In Stage 2, we tested association between sentinel variants and comparable smoking cessation endpoints in varenicline randomized controlled trials. We subsequently meta-analyzed Stages 1 and 2.

Results
No variants reached genome-wide significance in the meta-analysis. In Stage 1, 10 sentinel variants were associated with SVE and five with LVE at a suggestive significance threshold (p-value &lt; 5 × 10−6); none of these sentinels were previously implicated in varenicline-aided smoking cessation or in genetic studies of smoking behavior.

Conclusions
We provide initial insights into the biological underpinnings of varenicline-aided smoking cessation, through implicating genes involved in various processes, including gene expression, cilium assembly, and early-stage development.

Implications
Leveraging electronic health records, we undertook the largest genetic study of varenicline-aided smoking cessation to date, and the only such study to test genome-wide associations. We showed distinct genetic variants associated (p-value &lt; 5 × 10−6) with varenicline-aided smoking cessation which implicate diverse cellular functions, including transcriptional regulation, RNA modification, and cilium assembly. These provide insights which, if independently corroborated, will improve understanding of varenicline response. The growing availability of biobank resources with genetic and varenicline response data will provide future opportunities for larger studies using the approach we developed.
Spanish Pistolerismo and Labour Violence in Post-War Europe, 1917–1923
Authors: Zoffmann Rodriguez Arturo 
Published: January 2025

Abstract
Political violence in Europe in 1917–23 has typically been associated with the destabilizing impact of the First World War. However, some forms of violence displayed continuities with the pre-1914 period and were not directly related to the war, as was the case with trade union violence. This article engages with debates about the character and causality of the convulsions that shook the continent in 1917–23 through the case study of labour violence in Spain. This country remained neutral throughout the conflagration but experienced episodes of intense social warfare connected to strikes that came to be known as pistolerismo (the rule of the gunman). Pistolerismo had a complex prehistory, but it crystallized in 1917–19 due to the economic fallout of the war and the radicalizing influence of the Russian Revolution. This study traces the evolution of labour violence in these years, exploring how neutrality shaped pistolerismo, the retaliatory logic of aggressions, the formation and professionalization of trade union armed detachments, and the entanglements between social and political violence. It does so by interweaving social and cultural approaches. Viewed through this prism, trade union violence stands out as an important driver of instability and polarization in post-war Europe.