tbuckley/cabot-search huggingface dataset:
ORCHESTRA Delphi Consensus: Diagnostic and Therapeutic Management of SARS-CoV-2 Infection in Solid Organ Transplant Recipients
Authors: Beatrice Tazza, Natascia Caroccia, Alice Toschi, Renato Pascale, Effrosyni Gkrania-Klotsas, Paula Olivares Navarro, Lorenzo Maria Canziani, Alessandro Tavelli, Andrea Antinori, Paolo Antonio Grossi, Maddalena Peghin, Evelina Tacconelli, Zaira Raquel Palacios-Baena, Pierluigi Viale, Maddalena Giannella
Journal: Clinical Microbiology and Infection (2025)
Mapping Neuroimaging Findings of Creativity and Brain Disease Onto a Common Brain Circuit
Authors: Julian Kutsche, Joseph J. Taylor, Michael G. Erkkinen, Haya Akkad, Sanaz Khosravani, William Drew, Anna Abraham, Derek V. M. Ott, Juliana Wall, Alexander Li Cohen, Andreas Horn, Wolf-Julian Neumann, Isaiah Kletenik, Michael D. Fox
Journal: JAMA Network Open (2025)

Importance Creativity is important for problem solving, adaptation to a changing environment, and innovation. Neuroimaging studies seeking to map creativity have yielded conflicting results, and studies of patients with brain disease have reported both decreases and paradoxical increases in creativity, leaving the neural basis of creativity unclear. Objective To investigate the brain circuit underlying creativity and assess its association with brain injury and neurodegenerative disease. Design, Setting, and Participants This study examined neuroimaging coordinates from a meta-analysis of 36 studies published between 2004 and 2019 associated with increased activity during creative tasks in healthy participants. A validated method termed coordinate network mapping and a database of resting-state functional connectivity from 1000 healthy individuals were used to test whether these coordinates mapped to a common brain circuit. Specificity was assessed through comparison to random coordinates and coordinates from working memory tasks in healthy participants. Reproducibility was assessed using an independent dataset of coordinates from additional studies of creativity in healthy participants. Finally, alignment with effects of focal brain damage on creativity was tested using data from patients with brain lesions and coordinates of brain atrophy from 7 different neurodegenerative disorders. Main Outcomes and Measures The primary outcomes were creativity or no creativity and alignment with a creativity circuit or no alignment. Results Creativity tasks activated heterogenous locations, with coordinates scattered across many different brain regions (415 coordinates derived from 857 healthy participants; pooled mean [SD] age, 24.1 [6.91] years; 461 [54%] female). However, these activation coordinates were part of a common brain circuit, defined by negative connectivity to the right frontal pole. This result was consistent across creative domains, reproducible in an independent dataset (383 coordinates derived from 691 participants) and specific to creativity when compared with random gray matter coordinates (n = 415) or coordinates activated by working memory tasks (3072 coordinates derived from 2900 healthy participants). Damage to this creativity circuit by lesions (n = 56 patients) or neurodegenerative disease (2262 coordinates derived from 4804 patients) aligned with both decreases and increases in creativity observed in these disorders. Conclusions and Relevance Findings from this study suggest that brain regions activated by creativity tasks map to a brain circuit defined by negative functional connectivity to the right frontal pole. Damage to this circuit aligned with changes in creativity observed in individuals with certain brain diseases, including paradoxical creativity increases.
Intraoperative Esketamine and Postpartum Depression Among Women With Cesarean Delivery
Authors: Li Ren, Ting Zhang, Bingyu Zou, Xin Su, Yi Tao, Jie Yang, Feng Lv, Ping Li, Fangliang Peng, Gangming Wu
Journal: JAMA Network Open (2025)

Importance Esketamine has been found to reduce the incidence of postpartum depression (PPD) in randomized clinical trials. However, current evidence from randomized clinical trials does not reflect esketamine’s efficacy in clinical settings. Objective To assess the clinical efficacy of intraoperative esketamine administration for preventing PPD among women who underwent cesarean delivery. Design, Setting, and Participants This randomized clinical trial was conducted at The First Affiliated Hospital of Chongqing Medical University in Chongqing, China, from March 2023 to February 2024. Pregnant patients admitted for cesarean delivery were included, while those with intellectual dysfunction or contraindications to esketamine were excluded. All participants were assigned randomly to either the esketamine group or control group in a 1:1 ratio. Data analysis was based on the intention-to-treat principle. Interventions Patients in the esketamine group received an infusion of 0.25 mg/kg esketamine in 20 mL of saline over 20 minutes, whereas patients in the control group received 20 mL saline over 20 minutes. Main Outcomes and Measures The primary outcome was the incidence of PPD at 6 weeks post partum. PPD was assessed using the Edinburgh Postnatal Depression Scale. Results A total of 308 pregnant women were randomly assigned to 1 of 2 groups: esketamine (n = 154; mean [SD] patient age, 31.57 [4.26] years) and control (n = 154; mean [SD] patient age, 32.53 [7.74] years). Incidence of PPD was significantly lower in the esketamine group compared with the control group at 6 weeks post partum (10.4% [16] vs 19.5% [30]; relative risk, 0.53; 95% CI, 0.30-0.93; P = .02). Conclusions and Relevance This randomized clinical trial demonstrated esketamine’s advantage in reducing the incidence of PPD at 6 weeks post partum in patients who underwent cesarean delivery. The efficacy and safety of esketamine in preventing PPD warrant further investigation in clinical practice. Trial Registration Chinese Clinical Trial Registry Identifier: ChiCTR2200065494
Mental Health of Residents of Ukraine Exposed to the Russia-Ukraine Conflict
Authors: Jiafu An, Tenghui Wang, Bin Chen, Anatoly Oleksiyenko, Chen Lin
Journal: JAMA Network Open (2025)

Quantifying the association between the ongoing Russia-Ukraine war and Ukrainians' mental health is crucial for guiding reconstruction and rebuilding efforts in the postwar period. To examine the association between war exposure and civilians' mental health in both the short and medium term and the potential channels through which these associations occur. This cohort study used data from 7 nationally representative surveys conducted by the Kyiv International Institute of Sociology between December 4, 2015, and July 18, 2022. Six surveys were conducted before the war and one during the ongoing conflict in July 2022. Each survey included approximately 2000 respondents aged 18 to 95 years in 110 localities. The magnitude of war damage exposure was represented by an indicator variable set to 1 if an oblast (province) experienced severe war damage and 0 if the damage was moderate at the time of the survey. The classification of severe or moderate damage was based on the economic losses incurred. The main outcomes were respondents' self-reported thoughts of suicide and feelings of helplessness, both represented as dummy variables. The sample included 14 140 respondents, with 3933 (27.8%) exposed to severe war damage and 10 207 (72.2%) to moderate war damage. These included 8174 female respondents (57.8%), with an overall mean (SD) age of 48.9 (16.8) years. The differences in the likelihood of reporting suicidal thoughts and feelings of helplessness between areas with severe vs moderate war damage increased by 2.2 percentage points (β estimate, 0.022 [SE, 0.006]; 95% CI, 0.009-0.036) and 4.9 percentage points (β estimate, 0.049 [SE, 0.019]; 95% CI, 0.009-0.088), respectively. Subsample analyses revealed that male respondents were more vulnerable to suicidal thoughts (β estimate, 0.030 [SE, 0.013]; 95% CI, 0.004-0.056), while female respondents were more at risk of feelings of helplessness (β estimate, 0.063 [SE, 0.024]; 95% CI, 0.013-0.113). In this survey study of war exposure, bombing was associated with increased mental health concerns among civilians, including a higher likelihood of suicidal thoughts and feelings of helplessness, which may hinder postwar recovery. These findings suggest that policymakers should prioritize creating job opportunities and ensuring a safe living environment to support citizens' recovery in the aftermath of conflict.
US Abortion Bans and Infant Mortality
Authors: Alison Gemmill, Alexander M. Franks, Selena Anjur-Dietrich, Amy Ozinsky, David Arbour, Elizabeth A. Stuart, Eli Ben-Michael, Avi Feller, Suzanne O. Bell
Journal: JAMA (2025)

Importance The impact of recent abortion bans on infant mortality is not fully understood. There is also limited evidence on how these bans may interact with long-standing racial and ethnic disparities in infant health. Objective To examine the association of abortion bans with changes in infant mortality and to compare this association in racial and ethnic groups based on analyses within and across states. Design, Setting, and Participants This population-based, serial, cross-sectional study used a bayesian panel model to examine infant mortality rates in 14 states that implemented complete or 6-week abortion bans and compared them with predictions of infant mortality rates based on pre-ban mortality rates and states without bans. Data included all live births and infant deaths from all 50 US states and the District of Columbia for 2012 through 2023. Models accounted for temporal trends and state-specific factors, with analyses stratified by race and ethnicity, timing of death, and cause of death. Exposure Complete or 6-week abortion bans. Main Outcome and Measures Infant mortality rate, analyzed overall and by subgroups. Results The analysis found higher than expected infant mortality in states after adoption of abortion bans (observed vs expected, 6.26 vs 5.93 per 1000 live births; absolute increase, 0.33 [95% credible interval (CrI), 0.14-0.51]; relative increase, 5.60% [95% CrI, 2.43%-8.73%]). This resulted in an estimated 478 excess infant deaths in the 14 states with bans during the months affected by bans. The estimated increases were higher among non-Hispanic Black infants compared with other racial and ethnic groups, with 11.81 observed vs 10.66 expected infant deaths per 1000 live births, an absolute increase of 1.15 (95% CrI, 0.53-1.81) and relative increase of 10.98% (95% CrI, 4.87%-17.89%). The observed infant mortality rate due to congenital anomalies was 1.37 vs 1.24 expected (absolute increase, 0.13 [95% CrI, 0.04-0.21]; relative increase, 10.87% [95% CrI, 3.39%-18.08%]), while the rate not due to congenital anomalies was 4.89 observed vs 4.69 expected (absolute increase, 0.20 [95% CrI, 0.02-0.38]; relative increase, 4.23% [95% CrI, 0.49%-8.23%]). Texas had a dominant influence on the overall results and there were larger increases in southern vs nonsouthern states. Conclusions US states that adopted abortion bans had higher than expected infant mortality after the bans took effect. The estimated relative increases in infant mortality were larger for deaths with congenital causes and among groups that had higher than average infant mortality rates at baseline, including Black infants and those in southern states.
US Abortion Bans and Fertility
Authors: Suzanne O. Bell, Alexander M. Franks, David Arbour, Selena Anjur-Dietrich, Elizabeth A. Stuart, Eli Ben-Michael, Avi Feller, Alison Gemmill
Journal: JAMA (2025)

Importance Abortion bans may lead to births among those who are unable to overcome barriers to abortion. The population-level effects of these policies, particularly their unequal impacts across subpopulations in the US, remain unclear. Objective To assess heterogeneity in the association of abortion bans with changes in fertility in the US, within and across states. Design, Setting, and Participants Drawing from birth certificate and US Census Bureau data from 2012 through 2023 for all 50 states and the District of Columbia, this study used a bayesian panel data model to evaluate state-by-subgroup-specific changes in fertility associated with complete or 6-week abortion bans in 14 US states. The average percent and absolute change in the fertility rate among females aged 15 through 44 years was estimated overall and by state, and within and across states by age, race and ethnicity, marital status, education, and insurance payer. Exposure Complete or 6-week abortion ban. Main outcome and Measures Fertility rate (births per 1000 reproductive-aged females) overall and by subgroups. Results There were an estimated 1.01 (95% credible interval [CrI], 0.45-1.64) additional births above expectation per 1000 females aged 15 through 44 years (reproductive age) in states following adoption of abortion bans (60.55 observed vs 59.54 expected; 1.70% increase; 95% CrI, 0.75%-2.78%), equivalent to 22 180 excess births, with evidence of variation by state and subgroup. Estimated differences above expectation were largest for racially minoritized individuals (≈2.0%), unmarried individuals (1.79%), individuals younger than 35 years (≈2.0%), Medicaid beneficiaries (2.41%), and those without college degrees (high school diploma, 2.36%; some college, 1.58%), particularly in southern states. Differences in race and ethnicity and education across states explain most of the variability in the state-level association between abortion bans and fertility rates. Conclusion and Relevance These findings provide evidence that fertility rates in states with abortion bans were higher than would have been expected in the absence of these policies, with the largest estimated differences among subpopulations experiencing the greatest structural disadvantages and in states with among the worst maternal and child health and well-being outcomes.
Workplace Injury and Mental Health Outcomes
Authors: Anthony Wightman, Justin P. Gawaziuk, Rae Spiwak, Lauren Burton, Brenda Comaskey, Dan Chateau, Jordan Nantais, Thomas Turgeon, Jitender Sareen, James Bolton, Allen Kraut, Sarvesh Logsetty
Journal: JAMA Network Open (2025)

Importance Workplace injury is a widespread problem that impacts mental health and quality of life and places a substantial burden on employers and the health care system. Objective To determine whether mental disorder rates differ following workplace injury compared with injuries outside the workplace. Design, Setting, and Participants This retrospective cohort study assessed individuals hospitalized for an injury requiring surgery between January 1, 2002, and December 31, 2018, with a 2-year follow-up period using population-based administrative data in Manitoba, Canada. Analyses were completed June to July 2021. This study compared 2 cohorts: individuals with a workplace injury matched 1:5 on sex, age, geographical region, and surgical procedure code with individuals with a nonworkplace injury in the general population. Exposure Traumatic physical injury that required surgery with anesthetic. Main Outcomes and Measures The outcome of interest was a diagnosis of mental disorder (anxiety, depression, substance abuse, suicide attempt, and any mental disorder), measured 2 years prior to and following injury. Results In this cohort study, 7556 individuals (mean [SD] age, 44.8 [13.3] years; 5721 [75.7%] male; 4624 individuals [61.2%] with urban residence; 4545 individuals [60.1%] with low income) with a workplace injury were compared with 28 901 matches from the general population. The workplace cohort had lower rates of all mental disorders (anxiety: adjusted rate ratio [ARR], 0.82; 95% CI, 0.77-0.87; depression: ARR, 0.78; 95% CI, 0.72-0.84; substance abuse: ARR, 0.63; 95% CI, 0.55-0.72; suicide attempt: ARR, 0.28; 95% CI, 0.11-0.70; and any mental disorder: ARR, 0.82; 95% CI, 0.78-0.86; all P &amp;amp;lt; .0006) before their injury and for depression (ARR, 0.89; 95% CI, 0.82-0.95) and substance abuse (ARR, 0.83; 95% CI, 0.73-0.94) after their injury. The group × care period interaction term was significant for anxiety ( P &amp;amp;lt; .0001) and any mental disorder ( P &amp;amp;lt; .0001), suggesting that individuals with workplace injuries had worse mental disorder outcomes over time than individuals with nonworkplace injuries. Conclusions and Relevance This cohort study found that the mental health trajectory from the preinjury to postinjury period was worse for individuals with a workplace injury compared with those injured outside the workplace. These findings suggest that there may be features unique to the workplace and/or injury claims and compensation processes that contribute to this pattern, which warrant further examination.
Resolving Leukemia Heterogeneity and Lineage Aberrations with HematoMap
Authors: Yuting Dai, Wen Ouyang, Wen Jin, Fan Zhang, Wenyan Cheng, Jianfeng Li, Shuo He, Junqi Zong, Shijia Cao, Chenxin Zhou, Junchen Luo, Gang Lu, Jinyan Huang, Hai Fang, Xiaojian Sun, Kankan Wang, Saijuan Chen
Journal: Genomics Proteomics & Bioinformatics (2025)

Abstract Precise mapping of leukemic cells onto the known hematopoietic hierarchy is important for understanding the cell-of-origin and mechanisms underlying disease initiation and development. However, this task remains challenging because of the high interpatient and intrapatient heterogeneity of leukemia cell clones as well as the differences existed between leukemic and normal hematopoietic cells. Using single-cell RNA sequencing (scRNA-seq) data with a curated clustering approach, we constructed a comprehensive reference hierarchy of normal hematopoiesis. This reference hierarchy was accomplished through multistep clustering and annotating over 100,000 bone marrow mononuclear cells derived from 25 healthy donors. We further employed the cosine distance algorithm to develop a likelihood score, determining the similarities of leukemic cells to their putative normal counterparts. Using our scoring strategies, we mapped the cells of acute myeloid leukemia (AML) and B cell precursor acute lymphoblastic leukemia (BCP-ALL) samples to their corresponding counterparts. The reference hierarchy also facilitated bulk RNA sequencing (RNA-seq) analysis, enabling the development of a least absolute shrinkage and selection operator (LASSO) score model to reveal subtle differences in lineage aberrancy within AML or BCP-ALL patients. To facilitate interpretation and application, we have established an R-based package (HematoMap) that offers a fast, convenient, and user-friendly tool for identifying and visualizing lineage aberrations in leukemia from scRNA-seq and bulk RNA-seq data. Our tool provides curated resources and data analytics for understanding leukemogenesis, with the potential to enhance leukemia risk stratification and personalized treatments. The HematoMap is available at https://github.com/NRCTM-bioinfo/HematoMap.
Advanced Adenoma and Long-Term Risk of Colorectal Cancer, Cancer-Related Mortality, and Mortality
Authors: Aasma Shaukat, Paolo Goffredo, Jack M. Wolf, Kyle Rudser, Timothy R. Church
Journal: JAMA Network Open (2025)

This cohort study investigates the association of adenomas and advanced adenomas with colorectal cancer (CRC) incidence and mortality and all-cause mortality.
Trends in Obesity-Related Measures Among US Children, Adolescents, and Adults
Authors: Samuel D. Emmerich, Cheryl D. Fryar, Bryan Stierman, Qiuping Gu, Joseph Afful, Cynthia L. Ogden
Journal: JAMA (2025)

This study examines trends in the prevalence of obesity-related measures in the US overall and by sex and age group, including weight-for-length, body mass index, and waist circumference.
Endocrine Therapy Interruption, Resumption, and Outcomes Associated With Pregnancy After Breast Cancer
Authors: Julia D. Ransohoff, Rebecca M. Lewinsohn, James Dickerson, Ingrid Luo, Mina Satoyoshi, Victor Ritter, Rachael Chavez, Amanda J. Wheeler, Su-Ying Liang, Pragati Kenkare, Scarlett L. Gomez, Lidia Schapira, Esther M. John, Summer S. Han, Allison W. Kurian
Journal: JAMA Oncology (2025)

This cohort study examines interruption and resumption of endocrine therapy among women with breast cancer who became pregnant.
Regulation of Controlled Substances and Reproductive Health
Authors: Julia Tasset, Kimberly K. Scarsi, Alison Edelman
Journal: JAMA (2025)

This Viewpoint reviews the US legal landscape for regulation of drugs with the potential for addiction, the pharmacology of mifepristone and misoprostol, evidence demonstrating their lack of dependency, and the consequences of 2024 policy changes in Louisiana state law.
The Germline and Somatic Origins of Prostate Cancer Heterogeneity
Authors: Takafumi N. Yamaguchi, Kathleen E. Houlahan, Helen Zhu, Natalie Kurganovs, Julie Livingstone, Natalie S. Fox, Jiapei Yuan, Jocelyn Sietsma Penington, Chol-Hee Jung, Tommer Schwarz, Weerachai Jaratlerdsiri, Job van Riet, Peter Georgeson, Stefano Mangiola, Kodi Taraszka, Robert Lesurf, Jue Jiang, Ken Chow, Lawrence E. Heisler, Yu-Jia Shiah, Susmita G. Ramanand, Michael J. Clarkson, Anne Nguyen, Shadrielle Melijah G. Espiritu, Ryan Stuchbery, Richard Jovelin, Vincent Huang, Connor Bell, Edward O'Connor, Patrick J. McCoy, Christopher M. Lalansingh, Marek Cmero, Adriana Salcedo, Eva K.F. Chan, Lydia Y. Liu, Phillip D. Stricker, Vinayak Bhandari, Riana M.S. Bornman, Dorota HS. Sendorek, Andrew Lonie, Stephenie D. Prokopec, Michael Fraser, Justin S. Peters, Adrien Foucal, Shingai B A. Mutambirwa, Lachlan Mcintosh, Michèle Orain, Matthew Wakefield, Valérie Picard, Daniel J. Park, Hélène Hovington, Michael Kerger, Alain Bergeron, Veronica Sabelnykova, Ji-Heui Seo, Mark M. Pomerantz, Noah Zaitlen, Sebastian M. Waszak, Alexander Gusev, Louis Lacombe, Yves Fradet, Andrew Ryan, Amar U. Kishan, Martijn P. Lolkema, Joachim Weischenfeldt, Bernard Têtu, Anthony J. Costello, Vanessa M. Hayes, Rayjean J. Hung, Housheng H. He, John D. McPherson, Bogdan Pasaniuc, Theodorus van der Kwast, Anthony T. Papenfuss, Matthew L. Freedman, Bernard J. Pope, Robert G. Bristow, Ram S. Mani, Niall M. Corcoran, Jüri Reimand, Christopher M. Hovens, Paul C. Boutros
Journal: Cancer Discovery (2025)

Abstract Newly diagnosed prostate cancers differ dramatically in mutational composition and lethality. The most accurate clinical predictor of lethality is tumor tissue architecture, quantified as tumor grade. To interrogate the evolutionary origins of prostate cancer heterogeneity, we analyzed 666 prostate tumor whole genomes. We identified a compendium of 223 recurrently mutated driver regions, most influencing downstream mutational processes and gene expression. We identified and validated individual germline variants that predispose tumors to acquire specific somatic driver mutations: these explain heterogeneity in disease presentation and ancestry differences. High-grade tumors have a superset of the drivers in lower-grade tumors, including increased frequency of BRCA2 and MYC mutations. Grade-associated driver mutations occur early in tumor evolution, and their earlier occurrence strongly predicts cancer relapse and metastasis. Our data suggest high- and low-grade prostate tumors both emerge from a common pre-malignant field, influenced by germline genomic context and stochastic mutation-timing.
Targeting Protein Kinase D in oral squamous cell carcinoma: a promising therapeutic approach
Authors: Swaminadhan D, Vishnu Priya Veeraraghavan, Krishna Mohan Surapaneni, Lavina Prashar, Ullas Mony
Journal: International Journal of Surgery (2025)

D, Swaminadhan; Veeraraghavan, Vishnu Priya; Surapaneni, Krishna Mohan; Prashar, Lavina MBChB., MD; Mony, Ullas Author Information