tbuckley/cabot-search huggingface dataset:
Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations
Authors: Xiaoyang Chen, Keyi Li, Xiaoqing Wu, Zhen Li, Qun Jiang, Xuejian Cui, Zijing Gao, Yanhong Wu, Rui Jiang
Journal: Genome biology (2024)

Spatial epigenomic technologies enable simultaneous capture of spatial location and chromatin accessibility of cells within tissue slices. Identifying peaks that display spatial variation and cellular heterogeneity is the key analytic task for characterizing the spatial chromatin accessibility landscape of complex tissues. Here, we propose an efficient and iterative model, Descart, for spatially variable peaks identification based on the graph of inter-cellular correlations. Through the comprehensive benchmarking, we demonstrate the superiority of Descart in revealing cellular heterogeneity and capturing tissue structure. Utilizing the graph of inter-cellular correlations, Descart shows its potential to denoise data, identify peak modules, and detect gene-peak interactions.
vmrseq: probabilistic modeling of single-cell methylation heterogeneity
Authors: Ning Shen, Keegan Korthauer
Journal: Genome biology (2024)

Single-cell DNA methylation measurements reveal genome-scale inter-cellular epigenetic heterogeneity, but extreme sparsity and noise challenges rigorous analysis. Previous methods to detect variably methylated regions (VMRs) have relied on predefined regions or sliding windows and report regions insensitive to heterogeneity level present in input. We present vmrseq, a statistical method that overcomes these challenges to detect VMRs with increased accuracy in synthetic benchmarks and improved feature selection in case studies. vmrseq also highlights context-dependent correlations between methylation and gene expression, supporting previous findings and facilitating novel hypotheses on epigenetic regulation. vmrseq is available at https://github.com/nshen7/vmrseq .
Outbreak of Blastomycosis Among Paper Mill Workers — Michigan, November 2022–May 2023
Authors: R. Reid Harvey, Allyson W. O’Connor, Marcia L. Stanton, Ju-Hyeong Park, Dallas Shi, Perri C. Callaway, Xiaoming Liang, Ryan LeBouf, Rachel Bailey, Ethan Fechter-Leggett, Ian Hennessee, Mitsuru Toda, Rebecca Reik, Mary Grace Stobierski, Jevon McFadden, Sara Palmer, Melissa Millerick-May, Robert Yin, Michael Snyder, Jennifer Meece, Jeremy Olstadt, Alana K. Sterkel, Suzanne Dargle, Olivia Bree, David Weissman, Marie A. de Perio, Stella Hines, Jean Cox-Ganser
Journal: MMWR Morbidity and Mortality Weekly Report (2024)
Trajectories of breast density change over time and subsequent breast cancer risk: longitudinal study
Authors: Boyoung Park, Yoosoo Chang, Seungho Ryu, Thi Xuan Mai Tran
Journal: BMJ (2024)

Abstract Objective To identify clusters of women with similar trajectories of breast density change over four longitudinal assessments and to examine the association between these trajectories and the subsequent risk of breast cancer. Design Retrospective cohort study. Setting Data from the national breast cancer screening programme, which is embedded in the National Health Insurance Service database in Korea. Breast density was assessed using the four category Breast Imaging Reporting and Data System (BI-RADS) classification. Group based trajectory modelling was performed to identify the trajectories of breast density. Participants Women aged ≥40 years who underwent four biennial mammographic screenings between 2009 and 2016. Main outcome measures Breast cancer development was determined to 31 December 2021. Cox proportional hazard models were used to assess the associations between trajectories and breast cancer outcomes after adjusting for covariates. Results Among a cohort of 1 747 507 women (mean age 61.4 years), five breast density trajectory groups were identified. Group 1 included women with persistently fatty breast tissue, group 2 included women with fatty breast tissue at baseline but increased breast density over time, and groups 3-5 included women with denser breasts, with a slight decrease in density over time. Women in group 2 had a 1.60-fold (95% confidence interval 1.49 to 1.72) increased risk of breast cancer compared with those in group 1. Women in groups 3-5 had higher risks compared with those in group 1, with adjusted hazard ratios of 1.86 (1.74 to 1.98), 2.49 (2.33 to 2.65), and 3.07 (2.87 to 3.28), respectively. Similar results were observed across different age groups, regardless of changes in menopausal status or body mass index. Conclusions This study identified five distinct groups of women with similar trajectories of breast density change over time. Future risk of breast cancer was found to vary in these groups. Increasingly dense or persistently dense breasts were associated with a higher risk. Changes in breast density over time should be carefully considered during breast cancer risk stratification and incorporated into future risk models.
Updates on the Treatment of Drug-Susceptible and Drug-Resistant Tuberculosis: An Official ATS/CDC/ERS/IDSA Clinical Practice Guideline
Authors: Jussi J. Saukkonen, Raquel Duarte, Sonal S. Munsiff, Carla A. Winston, Manoj J. Mammen, Ibrahim Abubakar, Carlos Acuña-Villaorduña, Pennan M. Barry, Mayara L. Bastos, Wendy Carr, Hassan Chami, Lisa L. Chen, Terence Chorba, Charles L. Daley, Anthony J. Garcia-Prats, Kelly Holland, Ioannis Konstantinidis, Marc Lipman, Giovanni Battista Migliori, Farah M. Parvez, Adrienne E. Shapiro, Giovanni Sotgiu, Jeffrey R. Starke, Angela M. Starks, Sanket Thakore, Shu-Hua Wang, Jonathan M. Wortham, Payam Nahid
Journal: American Journal of Respiratory and Critical Care Medicine (2024)
Identification of a broad-inhibition influenza neuraminidase antibody from pre-existing memory B cells
Authors: Xin Wang, Huihui Kong, Bingxin Chu, Qian Yang, Chaohui Lin, Rui Liu, Changxu Chen, Yang Gao, Guojun Wang, Dayan Wang, Chen Qin, Xiaohua Ye, Lifei Yu, Xiangfei Xu, Jie Jin, Ren Sun, Hualan Chen, Xudong Wu, Zeli Zhang
Journal: Cell Host & Microbe (2024)
PPARα-ERRα crosstalk mitigates metabolic dysfunction-associated steatotic liver disease progression
Authors: Milton Boaheng Antwi, Sander Lefere, Dorien Clarisse, Lisa Koorneef, Anneleen Heldens, Louis Onghena, Kylian Decroix, Daria Fijalkowska, Jonathan Thommis, Madeleine Hellemans, Anne Hoorens, Anja Geerts, Lindsey Devisscher, Karolien De Bosscher
Journal: Metabolism (2024)
The role of gut microbiota in the pathogenesis of diverticular disease: where are we now?
Authors: Antonio Tursi, Alfredo Papa
Journal: Genome Medicine (2024)

Diverticular disease (DD) is widespread worldwide. The role of gut microbiota (GM) in DD is not entirely understood. Here we discuss the significance of the current knowledge on GM in the different stages of DD and how crucial these acquisitions are for designing diagnostic and therapeutic trials in this field.
The association between domestic water hardness and kidney stone disease: a prospective cohort study from the UK Biobank
Authors: Jiahao Zhang, Hongcheng Luo, Haoliang Wu, Yuxin Qian, Zhicheng Tang, Juan Wang, Zhibiao Li, Hanxiong Zheng, Fucai Tang, Zhaohui He
Journal: International Journal of Surgery (2024)
Syphilitic Lymphadenitis and Clavicle Pathological Fracture Mimicking Malignant Tumor on 18F-FDG PET/CT
Authors: Hongzheng Zhang, Youwen Dong, Sheng Dai
Journal: Clinical Nuclear Medicine (2024)

Abstract A 66-year-old woman presented with 9 days of left clavicle pain, with no history of recent trauma. CT images showed a left clavicle fracture with a surrounding soft tissue mass. An 18 F-FDG PET/CT scan revealed increased FDG uptake in the tonsils, multiple lymph nodes, and the pathologically fractured clavicle, initially suggesting malignancy. However, serologic tests and pathology confirmed syphilitic lymphadenitis and osteomyelitis. Given the inguinal and cervical lymphadenopathy with FDG uptake, potential bone destruction, or pathological fractures mimicking malignancy, syphilis should be considered in the differential diagnosis. Serologic testing and Treponema pallidum screening are essential.
Comparing robotic, laparoscopic, and laparotomy in endometrial cancer: a network meta-analysis
Authors: Wen-Rui Huang, Xing-Yan Ou, Xing-Zi Fang, Xiao-Xuan Tang, Lei Chen, Jing Ling, Wen-Cong Song, Xue-Lian Du
Journal: International Journal of Surgery (2024)
Single-cell and spatial transcriptomic analyses reveal heterogeneity characteristics and specific cell subtype regulators in growth hormone-secreting pituitary adenomas
Authors: Yu Zhang, Lifeng Wang, Xingcheng Yi, Xin Ma, Hongyu Wu, Mingzhao Zhang, Zhenqi Yang, Lizhen Ma, Zenghua Mi, Weijia Zhi, Cong Fu, Pinan Liu, Zhijun Yang
Journal: International Journal of Surgery (2024)
Current advance in comprehensive management of hilar cholangiocarcinoma and navigation in surgery: non-systematic reviews
Authors: Man Luo, Jiapeng Yang, Kai Zhang, Ji Sun, Zhiyu Lu, Wang Zhihao, Yaowei Hu, Jianxin Zhai, Peng Xie, Tana Siqin, Mengran Lang, Xuan Meng, Hongguang Wang
Journal: International Journal of Surgery (2024)
Hepatic Arterial Infusion Pump Complication With Multimodal Radiologic and Anatomic Review
Authors: Rihin Chavda, Amro Saad Aldine, Akhilesh Pillai, Jayesh Soni, Robert Carson Sibley
Journal: Clinical Nuclear Medicine (2024)

Abstract Hepatic arterial infusion therapy involves surgically implanting a subcutaneous hepatic arterial infusion pump with the catheter tip at the hepatic artery. This pump directly delivers chemotherapy to the liver, which may reduce systemic toxicity, improve resectability, and treat unresectable hepatic lesions. This therapy is used in primary or metastatic hepatic malignancies. We present a case that reviews a multimodal radiologic approach to a less common complication of hepatic arterial infusion pump. Using nuclear medicine, interventional radiology, and pictographic presentation, we provide an anatomic review, demonstrate radiologic intervention capability, and show posttreatment resolution of the complication.
Adult Embryonal Rhabdomyosarcoma of the Prostate Presented on 18F-FDG and Al18F-FAPI-74 PET/CT
Authors: Xin Cheng, Guozhu Hou, Rong Zheng, Xi Chen, Xuejuan Wang
Journal: Clinical Nuclear Medicine (2024)

Abstract A 21-year-old man with a 2-week history of abdominal pain and urinary hesitancy was admitted to our hospital. Sarcoma was suspected based on his PSA level, age, and MRI findings. He underwent 18 F-FDG and Al 18 F-FAPI-74 PET/CT scans. The scans revealed an irregularly dense prostate mass with indistinct borders to the rectum. The mass exhibited increased and heterogeneous FDG uptake and FAPI activity, with different distribution patterns between the 2 tracers. Histopathological analysis confirmed the diagnosis of embryonal rhabdomyosarcoma.
CXCR4—A Potential Novel Theranostic Target in Adrenocortical Carcinoma
Authors: Amir Nazar, Ashwini Kalshetty, Sandip Basu
Journal: Clinical Nuclear Medicine (2024)

Adrenocortical carcinoma (ACC) is a highly aggressive malignancy with high recurrence rates and poor prognosis. There are only limited treatment options with poor response rates. ACCs are documented to express chemokine receptor CXCR4, which can be visualized using 68Ga-pentixafor PET/CT. We herein present a case of ACC with local recurrence and peritoneal metastases, which was well visualized on FDG and pentixafor PET/CT. The high expression of CXCR4 offers the potential of theranostics and targeted endoradiotherapy in patients with metastatic ACC. We also observed thymic rebound to illustrate mild to moderate grade uptake of 68Ga-pentixafor in this patient.
Superiority of 18F-FAPI-42 PET/CT in Eosinophilic Gastrointestinal Disorders
Authors: Ye Dong, Wenlan Zhou
Journal: Clinical Nuclear Medicine (2024)

Abstract We report a rare case of eosinophilic gastrointestinal disorders in a 60-year-old woman, which extensively involved the digestive tract from the esophagus, gastric, duodenum to the small intestine, depicted well by 18 F-FAPI-42 PET/CT, superior to 18 F-FDG PET/CT. Under the guidance of 18 F-FAPI-42 PET/CT, the biopsy was successfully performed, and the diagnosis was established. This case highlights that 18 F-FAPI-42 PET/CT may serve as a novel noninvasive method for evaluating eosinophilic gastrointestinal disorders.
Central Nervous System Tumor-Embryonal Tumors Type With Neuroendocrine Differentiation
Authors: Yeshwanth Edamadaka, Rahul V Parghane, Sandip Basu
Journal: Clinical Nuclear Medicine (2024)

Abstract The central nervous system (CNS) tumor with embryonal tumors type is a rare type of CNS tumor with lack of unifying genetic alterations or diagnostic markers. The CNS tumor-embryonal tumors (CETs) have limited therapeutic options with high probability of adverse events associated with conventional treatment. Identification of somatostatin receptor expression and/or prostate-specific membrane antigen expression in CET patients by using PET/CT imaging may be helpful for deciding therapeutic approaches in these patients as theranostics. We present a 56-year-old woman who complained of headache, diminution of vision, and diagnosed CET and demonstrated high SSTR expression on PET/CT imaging, indicating peptide receptor radionuclide therapy could be effective therapeutic option in this case.
Second primary non-myeloid malignancies following intensive treatment for adult acute myeloid leukaemia: a Danish population-based cohort study
Authors: Nanna Nørtoft Nielsen, Jonas Faartoft Jensen, Joachim Baech, Trine Trab, Tarec Christoffer El-Galaly, Claudia Schöllkopf, Andreas Due Ørskov, Hans Beier Ommen, Lene Sofie Granfeldt, Daniel Tuyet Kristensen, Marianne Tang Severinsen
Journal: The Lancet Regional Health - Europe (2024)
Boosting with Omicron-specific mRNA vaccine or historical SARS-CoV-2 vaccines elicits discriminating immune responses against Omicron variants
Authors: Yi Wu, Xiaoying Jia, Namei Wu, Xinghai Zhang, Yan Wu, Yang Liu, Minmin Zhou, Yanqiong Shen, Entao Li, Wei Wang, Jiaming Lan, Yucai Wang, Sandra Chiu
Journal: Acta Pharmaceutica Sinica B (2024)

Booster vaccinations are highly recommended in combating the SARS-CoV-2 Omicron variant and its subvariants. However, the optimal booster vaccination strategies and related immune mechanisms with different prior vaccinations are under-revealed. In this study, we systematically evaluated the immune responses in mice and hamsters with different prime-boost regimens before their protective efficacies against Omicron were detected. We found that boosting with Ad5-nCoV, SWT-2P or SOmicron-6P induced significantly higher levels of neutralization activities against Omicron variants than CoronaVac and ZF2001 by eliciting stronger germinal center (GC) responses. Specifically, SOmicron-6P induced even stronger antibody responses against Omicron variants in CoronaVac and Ad5-nCoV-primed animals than non-Omicron-specific vaccines but with limited differences as compared to Ad5-nCoV and SWT-2P. In addition, boosting with a specific vaccine has the potential to remodel the existing immune profiles. These findings indicated that adenovirus-vectored vaccines and mRNA vaccines would be more effective than other types of vaccines as booster shots in combating Omicron infections. Moreover, the protective efficacies of the vaccines in booster vaccinations are highly related to GC reactions in secondary lymphatic organs. In summary, these findings provide timely important information on prime-boost regimens and future vaccine design.
Antibody Response to Respiratory Syncytial Virus Vaccination in Immunocompromised Persons
Authors: Andrew H. Karaba, Camille Hage, Isabella Sengsouk, Prasanthy Balasubramanian, Dorry L. Segev, Aaron A. A. R. Tobian, William A. Werbel
Journal: JAMA (2024)

This prospective study investigates antibody response following respiratory syncytial virus vaccination in immunocompromised individuals.
Adverse Childhood Experiences and Nonsuicidal Self-Injury and Suicidality in Chinese Adolescents
Authors: Yitong He, Weiqing Jiang, Wanxin Wang, Qianyu Liu, Shuyi Peng, Lan Guo
Journal: JAMA Network Open (2024)

Importance Studies investigating the role of supportive school environments in associations between adverse childhood experiences (ACEs) and nonsuicidal self-injury (NSSI) and suicidality among adolescents are lacking. Objective To assess associations of ACEs with NSSI and suicidality among adolescents and examine the modifying role of supportive school environments in such associations. Design, Setting, and Participants Using data from the 2021 School-Based Chinese Adolescents Health Survey, this cross-sectional study includes Chinese adolescents in grades 7 through 12 from 326 schools across 8 provinces in China. Statistical analysis was performed from March to October 2024. Exposure ACEs, including individual indicators and cumulative numbers by total and categorized as threat-related and deprivation-related ACEs, were assessed. Main Outcome and Measures NSSI, suicidal ideation, and suicide attempts were measured using validated questionnaires. Weighted Poisson regression models were used. The modifying interaction of supportive school environments was assessed using multiplicative interactions. Results Among 95 549 adolescents included in this study (mean [SD] age, 14.9 [1.8] years; 47 617 males [49.8%]), 45 236 individuals (47.3%) had experienced at least 1 ACE. Compared with adolescents with no ACEs, those who experienced 4 or more ACEs had an increased risk of NSSI (prevalence ratio [PR], 1.31; 95% CI, 1.30-1.33) and suicidality (ideation: PR, 1.41; 95% CI, 1.39-1.42; attempts: PR, 1.25; 95% CI, 1.24-1.27) after adjusting for covariates, including supportive school environments. A dose-response association was observed between the number of ACEs and the risk of NSSI and suicidality (eg, NSSI: PR, 1.06; 95% CI, 1.05-1.06 for exposure to 1 vs 0 ACEs; PR, 1.10; 95% CI, 1.10-1.11 for exposure to 2 vs 0 ACEs). The highest PRs were found for associations of threat-related ACEs (eg, physical abuse, emotional abuse, and bullying) with NSSI and suicidality (eg, exposure to ≥2 vs 0 threat-related ACEs: PR, 1.28; 95% CI, 1.27-1.29 for NSSI; PR, 1.33; 95% CI 1.32-1.34 for ideation; PR, 1.18; 95% CI, 1.17-1.19 for attempts). All individual ACE indicators were positively associated with NSSI and suicidality, with particularly high PRs for emotional abuse (eg, PR, 1.26; 95% CI, 1.24-1.27 for NSSI). Additionally, supportive school environments significantly modified associations of ACEs with NSSI and suicidality (eg, interaction ratio for NSSI, 0.81; 95% CI, 0.76-0.88). Conclusion and relevance In this study, exposure to ACEs was associated with an increased risk of NSSI and suicidality, with particularly high increases for threat-related ACEs, independent of the interaction of supportive school environments, but supportive school environments could modify such detrimental outcomes. These findings underscore the importance of enhancing school environments to prevent NSSI and suicidality among adolescents who have experienced ACEs.
Physician Engagement in Addressing Health-Related Social Needs and Burnout
Authors: Masami Tabata-Kelly, Xiaochu Hu, Michael J. Dill, Philip M. Alberti, Karen Bullock, William Crown, Malika Fair, Peter May, Pilar Ortega, Jennifer Perloff
Journal: JAMA Network Open (2024)

Importance Previous research suggests that a greater capacity of health care organizations to address patients’ health-related social needs (HRSNs) is associated with lower physician burnout. However, individual physician-level engagement in addressing HRSNs has not been fully characterized, and its association with physician burnout remains understudied. Objective To characterize physicians’ engagement in addressing HRSNs and examine its association with burnout. Design, Setting, and Participants This cross-sectional study used the 2022 Association of American Medical Colleges National Sample Survey of Physicians (NSSP), a nationally representative survey of active, practicing physicians in the US conducted from May to November 2022 that measured a diverse array of physician workforce characteristics. Main Outcome and Measures HRSN engagement was defined by physicians’ responses to the NSSP item, “During the past 12 months, how often did you spend work time helping your patients meet their social needs?” Engagement levels were categorized as no engagement, low to moderate engagement (monthly or &amp;amp;lt;1 time per month), or high engagement (weekly or daily). Burnout was measured using a single-item measure from the emotional exhaustion domain of the Maslach Burnout Inventory (high was defined as weekly or more). HRSN engagement was examined by physician characteristics, and multivariate logistic regression was conducted to explore associations between HRSN engagement and burnout. Data were weighted by age, gender, international medical graduate status, and specialty group. Results In the study cohort of 5447 physicians, the mean (SD) age was 50.9 (11.7) years, and 3735 (68.6%) identified as men or transgender men. Overall, 34.3% of physicians reported high HRSN engagement, with variability based on physician characteristics. Compared with no HRSN engagement, low to moderate HRSN engagement (adjusted odds ratio [AOR], 1.33; 95% CI, 1.03-1.72; P = .03) and high HRSN engagement (AOR, 1.72; 95% CI, 1.39-2.27; P &amp;amp;lt; .001) were significantly associated with high burnout. Conclusions and Relevance In this cross-sectional study of 5447 nationally representative physicians in the US, 34.3% regularly dedicated time to addressing HRSNs. The study identified variability in physicians’ engagement in addressing HRSNs and found that higher engagement was associated with a greater likelihood of burnout. The findings suggest the need for thorough assessment of the potential unintended consequences of physicians’ engagement in addressing HRSNs on their well-being.