tbuckley/cabot-search huggingface dataset:
FUSE: Improving the estimation and imputation of variant impacts in functional screening
Authors: Tian Yu, James D Fife, Vineel Bhat, Ivan Adzhubey, Richard Sherwood, Christopher A Cassa
Journal: Cell Genomics (2024)

Deep mutational scanning enables high-throughput functional assessment of genetic variants. While phenotypic measurements from screening assays generally align with clinical outcomes, experimental noise may affect the accuracy of individual variant estimates. We developed the FUSE (functional substitution estimation) pipeline, which leverages measurements collectively within screening assays to improve the estimation of variant impacts. Drawing data from 115 published functional assays, FUSE assesses the mean functional effect per amino acid position and makes estimates for individual allelic variants. It enhances the correlation of variant functional effects from different assay platforms and increases the classification accuracy of missense variants in ClinVar across 29 genes (area under the receiver operating characteristic [ROC] curve [AUC] from 0.83 to 0.90). In UK Biobank patients with rare missense variants in BRCA1, LDLR, or TP53, FUSE improves the classification accuracy of associated phenotypes. FUSE can also impute variant effects for substitutions not experimentally screened. This approach improves accuracy and broadens the utility of data from functional screening.
Genome-wide association study of maternal plasma metabolites during pregnancy
Authors: Siyang Liu, Jilong Yao, Liang Lin, Xianmei Lan, Linlin Wu, Xuelian He, Nannan Kong, Yan Li, Yuqing Deng, Jiansheng Xie, Huanhuan Zhu, Xiaoxia Wu, Zilong Li, Likuan Xiong, Yuan Wang, Jinghui Ren, Xuemei Qiu, Weihua Zhao, Ya Gao, Yuanqing Chen, Fengxia Su, Yun Zhou, Weiqiao Rao, Jing Zhang, Guixue Hou, Liping Huang, Linxuan Li, Xinhong Liu, Chao Nie, Liqiong Luo, Mei Zhao, Zengyou Liu, Fang Chen, Shengmou Lin, Lijian Zhao, Qingmei Fu, Dan Jiang, Ye Yin, Xun Xu, Jian Wang, Huanming Yang, Rong Wang, Jianmin Niu, Fengxiang Wei, Xin Jin, Siqi Liu
Journal: Cell Genomics (2024)

Metabolites are key indicators of health and therapeutic targets, but their genetic underpinnings during pregnancy-a critical period for human reproduction-are largely unexplored. Using genetic data from non-invasive prenatal testing, we performed a genome-wide association study on 84 metabolites, including 37 amino acids, 24 elements, 13 hormones, and 10 vitamins, involving 34,394 pregnant Chinese women, with sample sizes ranging from 6,394 to 13,392 for specific metabolites. We identified 53 metabolite-gene associations, 23 of which are novel. Significant differences in genetic effects between pregnant and non-pregnant women were observed for 16.7%-100% of these associations, indicating gene-environment interactions. Additionally, 50.94% of genetic associations exhibited pleiotropy among metabolites and between six metabolites and eight pregnancy phenotypes. Mendelian randomization revealed potential causal relationships between seven maternal metabolites and 15 human traits and diseases. These findings provide new insights into the genetic basis of maternal plasma metabolites during pregnancy.
Medication Changes Among Older Drivers Involved in Motor Vehicle Crashes
Authors: Andrew R. Zullo, Melissa R. Riester, Adam M. D’Amico, Monika Reddy Bhuma, Marzan A. Khan, Allison E. Curry, Melissa R. Pfeiffer, Seth A. Margolis, Brian R. Ott, Thomas Bayer, Nina R. Joyce
Journal: JAMA Network Open (2024)

Although older adults may use potentially driver-impairing (PDI) medications that can produce psychomotor impairment, little is known about changes to PDI medication use among older adults from the time before to the time after a motor vehicle crash (MVC). To quantify use of and changes in PDI medications among older adults before and after an MVC. This cohort study used linked Medicare claims and police-reported MVC data on 154 096 person-crashes among 121 846 older drivers. Eligible persons were drivers aged 66 years or older, involved in a police-reported MVC in New Jersey from May 1, 2007, through December 31, 2017, and with continuous enrollment in Medicare fee-for-service Parts A and B for at least 12 months and Part D for at least 120 days prior to the MVC. Data were analyzed from January 2022 to May 2024. Use of benzodiazepines, nonbenzodiazepine hypnotics, opioid analgesics, and other PDI medications in the 120 days before and 120 days after the MVC. Because each person could contribute multiple MVCs during the study period if they met eligibility criteria, the unit of analysis was the number of person-crashes. The proportion of person-crashes after which PDI medications were started, discontinued, or continued was quantified as well. Among 154 096 eligible person-crashes, the mean (SD) age of the drivers was 75.2 (6.7) years at the time of the MVC. Of 121 846 unique persons, 51.6% were women. In 80.0% of the person-crashes, drivers used 1 or more PDI medications before the crash, and in 81.0% of the person-crashes, drivers used 1 or more PDI medications after the crash. Use of benzodiazepines (8.1% before the crash and 8.8% after the crash), nonbenzodiazepine hypnotics (5.9% before the crash and 6.0% after the crash), and opioid analgesics (15.4% before the crash and 17.5% after the crash) was slightly higher after the MVC. After the MVC, drivers in 2.1% of person-crashes started benzodiazepines and 1.4% stopped benzodiazepines, drivers in 1.2% of person-crashes started nonbenzodiazepine hypnotics and 1.2% stopped nonbenzodiazepine hypnotics, and drivers in 8.4% of person-crashes started opioid analgesics and 6.3% stopped opioid analgesics. This cohort study suggests that most older drivers involved in MVCs did not use fewer PDI medications after crashes than before crashes. Qualitative research of perceived risks vs benefits of PDI medications is necessary to understand the reasons why MVCs do not appear to motivate clinicians to deprescribe PDI medications as a strategy to avert potential harms, including additional MVCs.
Advances in using non-invasive prenatal testing to study genomics related to maternity
Authors: Xin Jin, Xun Xu, Aifen Zhou, Huanhuan Zhu, Qiyuan Li, Siyang Liu, Siqi Liu, Shujia Huang, Jianguo Zhang, Ting Wang, Hankui Liu
Journal: Cell Genomics (2024)

In Chinese, we have a saying, "Women hold up half the sky," and across almost every culture, motherhood is revered for its role in the continuation of humanity. However, the significance of pregnancy and its effects on women and their children have not been reflected in current genetic research. There is a bias in the GWAS Catalog, which compiles publications and summary statistics of genome-wide association studies (GWAS), toward diseases such as diabetes, cancer, and cardiovascular disease. Furthermore, most of these studies have been conducted in European populations.
Unemployment and Personal Income Loss After Traumatic Brain Injury
Authors: Armaan K. Malhotra, Rachael H. Jaffe, Husain Shakil, Francois Mathieu, Avery B. Nathens, Abhaya V. Kulkarni, Calvin Diep, Eva Y. Yuan, Karim S. Ladha, Peter C. Coyte, Jefferson R. Wilson, Walter P. Wodchis, Christopher D. Witiw
Journal: JAMA Surgery (2024)

Employment and personal income loss after traumatic brain injury is a major source of postinjury stress and a barrier to societal reintegration. The magnitude of labor market ramifications following traumatic brain injury remains largely unknown.
Ventricular Septal Rupture After ST-Segment Elevation Myocardial Infarction
Authors: Alex Melot, Pierre Groussin, Raphaël P. Martins
Journal: JAMA Cardiology (2024)

This case report describes a diagnosis of ventricular septal rupture in a patient in his 70s after ST-segment elevation myocardial infarction (STEMI) due to right coronary artery occlusion.
Extended Follow-Up in Patients With Gastric Cancer—Applicable to Western Patients?—Reply
Authors: Ju-Hee Lee, Jiyeong Kim, Ji Yoon Choi
Journal: JAMA Surgery (2024)

In Reply We write in response to the comments made by van Hootegem and colleagues concerning our article titled "Feasibility of Extended Postoperative Follow-Up in Patients With Gastric Cancer."1 We appreciate the thoughtful feedback and the opportunity to further discuss and clarify our findings.
Lifestyle Interventions for Obesity—Reply
Authors: Jamy D. Ard, Kristina H. Lewis, Justin B. Moore
Journal: JAMA (2024)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors JAMA+ AI Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Suicidal Thoughts and Behaviors Among Autistic Transgender or Gender-Nonconforming US College Students
Authors: Annabelle M. Mournet, John K. Kellerman, Roscoe C. Garner, Evan M. Kleiman
Journal: JAMA Network Open (2024)

Suicide risk is a global public health crisis, with suicide ranking as a consistent leading cause of death among adults in the US. Autistic individuals and transgender or gender-nonconforming (TGNC) individuals represent populations with notably elevated rates of suicidal thoughts and behaviors (STBs).
Combined Methylphenidate and Selective Serotonin Reuptake Inhibitors in Adults With Attention-Deficit/Hyperactivity Disorder
Authors: Dong Yun Lee, Chungsoo Kim, Yunmi Shin, Rae Woong Park
Journal: JAMA Network Open (2024)

Importance Depression is a common comorbidity of adult attention-deficit/hyperactivity disorder (ADHD), and the combination of methylphenidate and selective serotonin reuptake inhibitors (SSRIs) is a frequently prescribed treatment. However, there is limited clinical evidence on the safety of this medication combination in adults with ADHD. Objective To evaluate the safety of administering a combination of SSRI and methylphenidate in adults with ADHD and comorbid depression. Design, Setting, and Participants This cohort study obtained data from a nationwide claims database in South Korea from January 2016 to February 2021. Participants were adults aged 18 years or older with a diagnosis of ADHD and depressive disorder who were prescribed methylphenidate. Comparisons of 4 groups who received prescriptions were conducted: (1) SSRI plus methylphenidate (hereafter, SSRI) group vs methylphenidate-only group and (2) methylphenidate plus fluoxetine (hereafter, fluoxetine) group vs methylphenidate plus escitalopram (hereafter, escitalopram) group (compared to find a preferable treatment option). Data analysis was conducted between July and December 2023. Exposures New users of the methylphenidate and SSRI combination among adults with both ADHD and depressive disorder. Main Outcomes and Measures A total of 17 primary and secondary outcomes, including neuropsychiatric and other events, were assessed, with respiratory tract infection used as a control outcome. Groups were matched at a 1:1 ratio using a propensity score to balance confounders. A Cox proportional hazards regression model was used to calculate hazard ratio (HRs) and 95% CIs. Subgroup analysis by sex and sensitivity analyses in varying epidemiologic settings were conducted. Results The study included 17 234 adults with ADHD (mean [SD] age at study entry, 29.4 [10.8] years; 9079 females [52.7%]). There was no difference in the risk of outcomes between the methylphenidate-only and SSRI groups, except for a lower risk of headache in the SSRI group (HR, 0.50; 95% CI, 0.24-0.99). In sensitivity analyses of fluoxetine vs escitalopram, the risk of hypertension (HR: 1:n matching, 0.26; 95% CI, 0.08-0.67) and hyperlipidemia (HR: 1:n matching, 0.23; 95% CI, 0.04-0.81) was lower in the fluoxetine group than in the escitalopram group. Conclusions and Relevance Results of this study revealed no significant increase in adverse event risk associated with use of SSRI plus methylphenidate vs methylphenidate alone in adults with ADHD and comorbid depression. Instead, the combination was associated with a lower risk of headache.
Lifestyle Interventions for Obesity
Authors: Catherine L. Davis, Kate Lorig
Journal: JAMA (2024)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors JAMA+ AI Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
A small population of stress-responsive neurons in the hypothalamus-habenula circuit mediates development of depression-like behavior in mice
Authors: Zhiwei Zheng, Yiqin Liu, Ruiqi Mu, Xiaonan Guo, Yirong Feng, Chen Guo, Liang Yang, Wenxi Qiu, Qi Zhang, Wei Yang, Zhaoqi Dong, Shuang Qiu, Yiyan Dong, Yihui Cui
Journal: Neuron (2024)
Mindfulness Meditation vs Escitalopram for Treatment of Anxiety Disorders
Authors: Hiroe Hu, Mihriye Mete, Neil K. Rustgi, Charisma I. Washington, Kavya Sanghavi, Mary Ann Dutton, Naomi M. Simon, Amanda W. Baker, Eric Bui, Elizabeth A. Hoge
Journal: JAMA Network Open (2024)

This secondary analysis of a randomized clinical trial assesses patient-reported anxiety, depression, and quality of life among patients receiving mindfulness-based stress reduction vs escitalopram for the treatment of anxiety disorders.
Unlocking the genetic influence on milk variation and its potential implication for infant health
Authors: Claudia Nussbaum, Sarah Kim-Hellmuth
Journal: Cell Genomics (2024)

Human milk has long been recognized for its critical role in infant and maternal health. In this issue of Cell Genomics, Johnson et al.1 apply a human genetics and genomics approach to shed light on the complex relationship between maternal genetics, milk variation, and the infant gut microbiome.
Novel insights into the genetic architecture of pregnancy glycemic traits from 14,744 Chinese maternities
Authors: Huanhuan Zhu, Han Xiao, Linxuan Li, Meng Yang, Ying Lin, Jieqiong Zhou, Xinyi Zhang, Yan Zhou, Xianmei Lan, Jiuying Liu, Jingyu Zeng, Lin Wang, Yuanyuan Zhong, Xiaobo Qian, Zhongqiang Cao, Panhong Liu, Hong Mei, Mingzhi Cai, Xiaonan Cai, Zhuangyuan Tang, Liqin Hu, Rui Zhou, Xun Xu, Huanming Yang, Jian Wang, Xin Jin, Aifen Zhou
Journal: Cell Genomics (2024)

Glycemic traits are critical indicators of maternal and fetal health during pregnancy. We performed genetic analysis for five glycemic traits in 14,744 Chinese pregnant women. Our genome-wide association study identified 25 locus-trait associations, including established links between gestational diabetes mellitus (GDM) and the genes CDKAL1 and MTNR1B. Notably, we discovered a novel association between fasting glucose during pregnancy and the ESR1 gene (estrogen receptor), which was validated by an independent study in pregnant women. The ESR1-GDM link was recently reported by the FinnGen project. Our work enhances the findings in East Asian populations and highlights the need for independent studies. Further analyses, including genetic correlation, Mendelian randomization, and transcriptome-wide association studies, provided genetic insights into the relationship between pregnancy glycemic traits and hypertension. Overall, our findings advance the understanding of genetic architecture of pregnancy glycemic traits, especially in East Asian populations.
Antiosteoporosis Medication Prescriptions After Fragility Fractures
Authors: William K. Silverstein, Sping Wang, Mahnaz Alavinejad, Ania Sarnocinska, Nathan M. Stall, Kamil Malikov, Michael P. Hillmer, Jonathan S. Zipursky
Journal: JAMA Network Open (2024)

This cohort study assesses prescribing rates for antiosteoporosis medication following a fragility fracture and factors associated with filling a prescription after a fracture among patients in Ontario, Canada.
Comparative Effectiveness of Antipsychotics in Patients With Schizophrenia Spectrum Disorder
Authors: Aleksi Hamina, Heidi Taipale, Johannes Lieslehto, Markku Lähteenvuo, Antti Tanskanen, Ellenor Mittendorfer-Rutz, Jari Tiihonen
Journal: JAMA Network Open (2024)

Antipsychotics are the cornerstone of maintenance treatment in schizophrenia spectrum disorders, but it is unclear which agents should be prioritized by prescribers.
Sensing steroid hormone 17α-hydroxypregnenolone by GPR56 enables protection from ferroptosis-induced liver injury
Authors: Hui Lin, Chuanshun Ma, Xiao Zhuang, Shuo Liu, Dong Liu, Mingxiang Zhang, Yan Lu, Guangjian Zhou, Chao Zhang, Tengwei Wang, Zihao Zhang, Lin Lv, Daolai Zhang, Xiong-Zhong Ruan, Yunfei Xu, Renjie Chai, Xiao Yu, Jin-Peng Sun, Bo Chu
Journal: Cell Metabolism (2024)
Glorified
Authors: Donna Pucciani
Journal: JAMA (2024)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors JAMA+ AI Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Genetic analyses of 104 phenotypes in 20,900 Chinese pregnant women reveal pregnancy-specific discoveries
Authors: Han Xiao, Linxuan Li, Meng Yang, Xinyi Zhang, Jieqiong Zhou, Jingyu Zeng, Yan Zhou, Xianmei Lan, Jiuying Liu, Ying Lin, Yuanyuan Zhong, Xiaoqian Zhang, Lin Wang, Zhongqiang Cao, Panhong Liu, Hong Mei, Mingzhi Cai, Xiaonan Cai, Ye Tao, Yunqing Zhu, Canqing Yu, Liqin Hu, Yu Wang, Yushan Huang, Fengxia Su, Ya Gao, Rui Zhou, Xun Xu, Huanming Yang, Jian Wang, Huanhuan Zhu, Aifen Zhou, Xin Jin
Journal: Cell Genomics (2024)
Deconstructing Cognitive Impairment in Psychosis With a Machine Learning Approach
Authors: Robert A. McCutcheon, Richard S. E. Keefe, Philip M. McGuire, Andre Marquand
Journal: JAMA Psychiatry (2024)

Cognitive functioning is associated with various factors, such as age, sex, education, and childhood adversity, and is impaired in people with psychosis. In addition to specific effects of the disorder, cognitive impairments may reflect a greater exposure to general risk factors for poor cognition.
Extended Follow-Up in Patients With Gastric Cancer—Applicable to Western Patients?
Authors: Sander J. M. van Hootegem, Matteo Pittacolo, Sjoerd M. Lagarde
Journal: JAMA Surgery (2024)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Surgery HomeNew OnlineCurrent IssueFor Authors Podcast JAMA+ AI Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Surgery journal
Defining the Role of Machine Learning in Optimizing Surgical Outcomes
Authors: Thomas H. Shin, Stanley W. Ashley, Thomas C. Tsai
Journal: JAMA Surgery (2024)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Surgery HomeNew OnlineCurrent IssueFor Authors Podcast JAMA+ AI Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Surgery journal