tbuckley/cabot-search huggingface dataset:
COVID-19 Vaccination in the First Trimester and Major Structural Birth Defects Among Live Births
Authors: Elyse O. Kharbanda, Malini B. DeSilva, Heather S. Lipkind, Paul A. Romitti, Jingyi Zhu, Kimberly K. Vesco, Thomas G. Boyce, Matthew F. Daley, Candace C. Fuller, Darios Getahun, Lisa A. Jackson, Joshua T. B. Williams, Ousseny Zerbo, Eric S. Weintraub, Gabriela Vazquez-Benitez
Journal: JAMA Pediatrics (2024)

Importance COVID-19 vaccination is recommended throughout pregnancy to prevent pregnancy complications and adverse birth outcomes associated with COVID-19 disease. To date, data on birth defects after first-trimester vaccination are limited. Objective To evaluate the associated risks for selected major structural birth defects among live-born infants after first-trimester receipt of a messenger RNA (mRNA) COVID-19 vaccine. Design, Setting, and Participants This was a retrospective cohort study of singleton pregnancies with estimated last menstrual period (LMP) between September 13, 2020, and April 3, 2021, and ending in live birth from March 5, 2021, to January 25, 2022. Included were data from 8 health systems in California, Oregon, Washington, Colorado, Minnesota, and Wisconsin in the Vaccine Safety Datalink. Exposures Receipt of 1 or 2 mRNA COVID-19 vaccine doses in the first trimester, as part of the primary series. Main Outcomes and Measures Selected major structural birth defects among live-born infants, identified from electronic health data using validated algorithms, with neural tube defects confirmed via medical record review. Results Among 42 156 eligible pregnancies (mean [SD] maternal age, 30.9 [5.0] years) 7632 (18.1%) received an mRNA COVID-19 vaccine in the first trimester. Of 34 524 pregnancies without a first-trimester COVID-19 vaccination, 2045 (5.9%) were vaccinated before pregnancy, 13 494 (39.1%) during the second or third trimester, and 18 985 (55.0%) were unvaccinated before or during pregnancy. Compared with pregnant people unvaccinated in the first trimester, those vaccinated in the first trimester were older (mean [SD] age, 32.3 [4.5] years vs 30.6 [5.1] years) and differed by LMP date. After applying stabilized inverse probability weighting, differences in baseline characteristics between vaccinated and unvaccinated pregnant persons in the first trimester were negligible (standardized mean difference &amp;amp;lt;0.20). Selected major structural birth defects occurred in 113 infants (1.48%) after first-trimester mRNA COVID-19 vaccination and in 488 infants (1.41%) without first-trimester vaccine exposure; the adjusted prevalence ratio was 1.02 (95% CI, 0.78-1.33). In secondary analyses, with major structural birth defect outcomes grouped by organ system, no significant differences between infants vaccinated or unvaccinated in the first trimester were identified. Conclusions and Relevance In this multisite cohort study, among live-born infants, first-trimester mRNA COVID-19 vaccine exposure was not associated with an increased risk for selected major structural birth defects.
Māori Medical Student and Physician Exposure to Racism, Discrimination, Harassment, and Bullying
Authors: Donna Cormack, Claire Gooder, Rhiannon Jones, Cameron Lacey, James Stanley, Sarah-Jane Paine, Elana Curtis, Ricci Harris
Journal: JAMA Network Open (2024)

Discrimination, bullying, and harassment in medicine have been reported internationally, but exposures for Indigenous medical students and physicians, and for racism specifically, remain less examined.
Preventive Effect of Neuromuscular Training on Chemotherapy-Induced Neuropathy
Authors: Fiona Streckmann, Thomas Elter, Helmar C. Lehmann, Hansjörg Baurecht, Tatjana Nazarenus, Vanessa Oschwald, Christina Koliamitra, Sarah Otten, Andreas Draube, Petra Heinen, Tilman Steinmetz, Michael Hallek, Michael Leitzmann, Wilhelm Bloch, Maryam Balke
Journal: JAMA Internal Medicine (2024)

Chemotherapy-induced peripheral neuropathy (CIPN) is a highly prevalent and clinically relevant adverse effect of chemotherapy, negatively impacting patient quality of life. The lack of effective preventive or therapeutic options regarding CIPN often requires changes in cancer therapy, potentially resulting in reduced survival.
Routine Electrocardiogram Screening and Cardiovascular Disease Events in Adults
Authors: Ryuichiro Yagi, Yuichiro Mori, Shinichi Goto, Taku Iwami, Kosuke Inoue
Journal: JAMA Internal Medicine (2024)

The resting electrocardiogram (ECG) is commonly performed for cardiovascular disease (CVD) screening purposes in Japan. However, evidence is limited regarding the prognostic significance of ECG in clinical practice settings.
Derivation and Validation of <i>ICD-10</i> Codes for Identifying Incident Stroke
Authors: Jesse A. Columbo, Natalie Daya, Lisandro D. Colantonio, Zhixin Wang, Kathryn Foti, Hyacinth I. Hyacinth, Michelle C. Johansen, Rebecca Gottesman, Phillip P. Goodney, Virginia J. Howard, Paul Muntner, Andrea L. C. Schneider, Elizabeth Selvin, Caitlin W. Hicks
Journal: JAMA Neurology (2024)

Claims data with International Statistical Classification of Diseases, Tenth Revision (ICD-10) codes are routinely used in clinical research. However, the use of ICD-10 codes to define incident stroke has not been validated against expert-adjudicated outcomes in the US population.
The canonical antiviral protein oligoadenylate synthetase 1 elicits antibacterial functions by enhancing IRF1 translation
Authors: Munesh K. Harioudh, Joseph Perez, Lomon So, Mayank Maheshwari, Thomas S. Ebert, Veit Hornung, Ram Savan, A. Rouf Banday, Michael S. Diamond, Vijay A. Rathinam, Saumendra N. Sarkar
Journal: Immunity (2024)
Dynamic assemblies of parvalbumin interneurons in brain oscillations
Authors: Yi-Chieh Huang, Hui-Ching Chen, Yu-Ting Lin, Szu-Ting Lin, Qinsi Zheng, Ahmed S. Abdelfattah, Luke D. Lavis, Eric R. Schreiter, Bei-Jung Lin, Tsai-Wen Chen
Journal: Neuron (2024)
Maternal gestational diabetes mellitus associates with altered gut microbiome composition and head circumference abnormalities in male offspring
Authors: Shilan Wang, Yingzhi Liu, Wing Hung Tam, Jessica Y.L. Ching, Wenye Xu, Shuai Yan, Biyan Qin, Ling Lin, Ye Peng, Jie Zhu, Chun Pan Cheung, Ka Long Ip, Yuen Man Wong, Pui Kuan Cheong, Yuk Ling Yeung, Wing Him Betty Kan, Ting Fan Leung, Tak Yeung Leung, Eugene B. Chang, David T. Rubin, Erika C. Claud, William K.K. Wu, Hein M. Tun, Francis K.L. Chan, Siew C. Ng, Lin Zhang
Journal: Cell Host & Microbe (2024)

The impact of gestational diabetes mellitus (GDM) on maternal or infant microbiome trajectory remains poorly understood. Utilizing large-scale longitudinal fecal samples from 264 mother-baby dyads, we present the gut microbiome trajectory of the mothers throughout pregnancy and infants during the first year of life. GDM mothers had a distinct microbiome diversity and composition during the gestation period. GDM leaves fingerprints on the infant's gut microbiome, which are confounded by delivery mode. Further, Clostridium species positively correlate with a larger head circumference at month 12 in male offspring but not females. The gut microbiome of GDM mothers with male fetuses displays depleted gut-brain modules, including acetate synthesis I and degradation and glutamate synthesis II. The gut microbiome of female infants of GDM mothers has higher histamine degradation and dopamine degradation. Together, our integrative analysis indicates that GDM affects maternal and infant gut composition, which is associated with sexually dimorphic infant head growth.
The antagonistic role of an E3 ligase pair in regulating plant NLR-mediated autoimmunity and fungal pathogen resistance
Authors: Jun Liu, Yong Yang, Fausto Andres Ortiz-Morea, Yulu Zhou, Derui Liu, Yanyan Huang, Jiarui Zheng, Yan Chen, Liang Kong, Zunyong Liu, Dongdong Ge, Mingli Yong, Wenwei Lin, Eugenia Russinova, Libo Shan, Ping He
Journal: Cell Host & Microbe (2024)
Excess US Deaths Attributable to High All-Cause Mortality Rates Among Youths Aged 0 to 19 Years
Authors: Steven H. Woolf, Derek A. Chapman
Journal: JAMA Pediatrics (2024)

This cross-sectional study compares US mortality rates among youths aged 0 to 19 years with rates in 16 high-income countries, calculates excess deaths from 1999 to 2019, and examines temporal trends through 2021.
Prediction-Augmented Shared Decision-Making and Lung Cancer Screening Uptake
Authors: Tanner J. Caverly, Renda S. Wiener, Kyle Kumbier, Julie Lowery, Angela Fagerlin
Journal: JAMA Network Open (2024)

Importance Addressing poor uptake of low-dose computed tomography lung cancer screening (LCS) is critical, especially for those having the most to gain—high-benefit persons with high lung cancer risk and life expectancy more than 10 years. Objective To assess the association between LCS uptake and implementing a prediction-augmented shared decision-making (SDM) tool, which enables clinicians to identify persons predicted to be at high benefit and encourage LCS more strongly for these persons. Design, Setting, and Participants Quality improvement interrupted time series study at 6 Veterans Affairs sites that used a standard set of clinical reminders to prompt primary care clinicians and screening coordinators to engage in SDM for LCS-eligible persons. Participants were persons without a history of LCS who met LCS eligibility criteria at the time (aged 55-80 years, smoked ≥30 pack-years, and current smoking or quit &amp;amp;lt;15 years ago) and were not documented to be an inappropriate candidate for LCS by a clinician during October 2017 through September 2019. Data were analyzed from September to November 2023. Exposure Decision support tool augmented by a prediction model that helps clinicians personalize SDM for LCS, tailoring the strength of screening encouragement according to predicted benefit. Main outcome and measure LCS uptake. Results In a cohort of 9904 individuals, the median (IQR) age was 64 (57-69) years; 9277 (94%) were male, 1537 (16%) were Black, 8159 (82%) were White, 5153 (52%) were predicted to be at intermediate (preference-sensitive) benefit and 4751 (48%) at high benefit, and 1084 (11%) received screening during the study period. Following implementation of the tool, higher rates of LCS uptake were observed overall along with an increase in benefit-based LCS uptake (higher screening uptake among persons anticipated to be at high benefit compared with those at intermediate benefit; primary analysis). Mean (SD) predicted probability of getting screened for a high-benefit person was 24.8% (15.5%) vs 15.8% (11.8%) for a person at intermediate benefit (mean absolute difference 9.0 percentage points; 95% CI, 1.6%-16.5%). Conclusions and Relevance Implementing a robust approach to personalized LCS, which integrates SDM, and a decision support tool augmented by a prediction model, are associated with improved uptake of LCS and may be particularly important for those most likely to benefit. These findings are timely given the ongoing poor rates of LCS uptake.
Why Evidence Generation Should Matter to Payers and How They Can Help
Authors: Ali B. Abbasi, Lesley H. Curtis, Lee A. Fleisher, Robert M. Califf
Journal: JAMA (2024)

The US leads the world in bringing new medical products to market, but the ability to generate evidence to inform clinical practice in postmarket settings needs improvement. Although a diverse group of stakeholders is working to improve postmarket evidence generation, the role of private payers has been underappreciated.
Two-Year Outcomes of Umbilical Cord Milking in Nonvigorous Infants
Authors: Anup C. Katheria, Laure El Ghormli, Erin Clark, Bradley Yoder, Georg M. Schmölzer, Brenda H. Y. Law, Walid El-Naggar, David Rittenberg, Sheetal Sheth, Courtney Martin, Farha Vora, Satyan Lakshminrusimha, Mark Underwood, Jan Mazela, Joseph Kaempf, Mark Tomlinson, Yvonne Gollin, Wade Rich, Ana Morales, Michael Varner, Debra Poeltler, Yvonne Vaucher, Judith Mercer, Neil Finer, Madeline Murguia Rice
Journal: JAMA Network Open (2024)

Compared with early cord clamping (ECC), umbilical cord milking (UCM) reduces delivery room cardiorespiratory support, hypoxic-ischemic encephalopathy, and therapeutic hypothermia in nonvigorous near-term and full-term infants. However, UCM postdischarge outcomes are not known.
A multicenter, phase 1, Adult Brain Tumor Consortium trial of oral terameprocol for patients with recurrent high-grade glioma (GATOR)
Authors: Manmeet S. Ahluwalia, Ahmad Ozair, Michelle Rudek, Xiaobu Ye, Matthias Holdhoff, Frank S. Lieberman, Anna F. Piotrowski, Burt Nabors, Arati Desai, Glenn Lesser, Ru Chih Huang, Steve Glenn, Atulya A. Khosla, David M. Peereboom, Patrick Y. Wen, Stuart A. Grossman
Journal: Cell Reports Medicine (2024)

Recurrent high-grade gliomas (rHGGs) have a dismal prognosis, where the maximum tolerated dose (MTD) of IV terameprocol (5 days/month), a transcriptional inhibitor of specificity protein 1 (Sp1)-regulated proteins, is 1,700 mg/day with median area under the plasma concentration-time curve (AUC) of 31.3 μg∗h/mL. Given potentially increased efficacy with sustained systemic exposure and challenging logistics of daily IV therapy, here we investigate oral terameprocol for rHGGs in a multicenter, phase 1 trial (GATOR). Using a 3 + 3 dose-escalation design, we enroll 20 patients, with median age 60 years (range 31–80), 70% male, and median one relapse (range 1–3). Fasting patients tolerate 1,200 mg/day (n = 3), 2,400 mg/day (n = 6), 3,600 mg/day (n = 3), and 6,000 mg/day (n = 2) oral doses without major toxicities. However, increased dosage does not lead to increased systemic exposure, including in fed state (6,000 mg/day, n = 4), with maximal AUC <5 μg∗h/mL. These findings warrant trials investigating approaches that provide sustained systemic levels of transcription inhibitors to exploit their therapeutic potential. This study was registered at ClinicalTrials.gov (NCT02575794).
Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data
Authors: Hsuanlin Her, Katherine L. Rothamel, Grady G. Nguyen, Evan A. Boyle, Gene W. Yeo
Journal: Cell Genomics (2024)

The uncovering of protein-RNA interactions enables a deeper understanding of RNA processing. Recent multiplexed crosslinking and immunoprecipitation (CLIP) technologies such as antibody-barcoded eCLIP (ABC) dramatically increase the throughput of mapping RNA binding protein (RBP) binding sites. However, multiplex CLIP datasets are multivariate, and each RBP suffers non-uniform signal-to-noise ratio. To address this, we developed Mudskipper, a versatile computational suite comprising two components: a Dirichlet multinomial mixture model to account for the multivariate nature of ABC datasets and a softmasking approach that identifies and removes non-specific protein-RNA interactions in RBPs with low signal-to-noise ratio. Mudskipper demonstrates superior precision and recall over existing tools on multiplex datasets and supports analysis of repetitive elements and small non-coding RNAs. Our findings unravel splicing outcomes and variant-associated disruptions, enabling higher-throughput investigations into diseases and regulation mediated by RBPs.
Recommendations to advance digital health equity: a systematic review of qualitative studies
Authors: Sarah Wilson, Clare Tolley, Ríona Mc Ardle, Lauren Lawson, Emily Beswick, Nehal Hassan, Robert Slight, Sarah Slight
Journal: npj Digital Medicine (2024)

Abstract The World Health Organisation advocates Digital Health Technologies (DHTs) for advancing population health, yet concerns about inequitable outcomes persist. Differences in access and use of DHTs across different demographic groups can contribute to inequities. Academics and policy makers have acknowledged this issue and called for inclusive digital health strategies. This systematic review synthesizes literature on these strategies and assesses facilitators and barriers to their implementation. We searched four large databases for qualitative studies using terms relevant to digital technology, health inequities, and socio-demographic factors associated with digital exclusion summarised by the CLEARS framework (Culture, Limiting conditions, Education, Age, Residence, Socioeconomic status). Following the PRISMA guidelines, 10,401 articles were screened independently by two reviewers, with ten articles meeting our inclusion criteria. Strategies were grouped into either outreach programmes or co-design approaches. Narrative synthesis of these strategies highlighted three key themes: firstly, using user-friendly designs, which included software and website interfaces that were easy to navigate and compatible with existing devices, culturally appropriate content, and engaging features. Secondly, providing supportive infrastructure to users, which included devices, free connectivity, and non-digital options to help access healthcare. Thirdly, providing educational support from family, friends, or professionals to help individuals develop their digital literacy skills to support the use of DHTs. Recommendations for advancing digital health equity include adopting a collaborative working approach to meet users’ needs, and using effective advertising to raise awareness of the available support. Further research is needed to assess the feasibility and impact of these recommendations in practice.
Do engagement and behavioural mechanisms underpin the effectiveness of the Drink Less app?
Authors: Claire Garnett, Larisa-Maria Dinu, Melissa Oldham, Olga Perski, Gemma Loebenberg, Emma Beard, Colin Angus, Robyn Burton, Matt Field, Felix Greaves, Matthew Hickman, Eileen Kaner, Susan Michie, Marcus Munafò, Elena Pizzo, Jamie Brown
Journal: npj Digital Medicine (2024)

Abstract This is a process evaluation of a large UK-based randomised controlled trial (RCT) ( n = 5602) evaluating the effectiveness of recommending an alcohol reduction app, Drink Less, compared with usual digital care in reducing alcohol consumption in increasing and higher risk drinkers. The aim was to understand whether participants’ engagement (‘self-reported adherence’) and behavioural characteristics were mechanisms of action underpinning the effectiveness of Drink Less. Self-reported adherence with both digital tools was over 70% (Drink Less: 78.0%, 95% CI = 77.6–78.4; usual digital care: 71.5%, 95% CI = 71.0–71.9). Self-reported adherence to the intervention (average causal mediation effect [ACME] = −0.250, 95% CI = −0.42, −0.11) and self-monitoring behaviour (ACME = −0.235, 95% CI = −0.44, −0.03) both partially mediated the effect of the intervention (versus comparator) on alcohol reduction. Following the recommendation (self-reported adherence) and the tracking (self-monitoring behaviour) feature of the Drink Less app appear to be important mechanisms of action for alcohol reduction among increasing and higher risk drinkers.
Kids’ noses resist COVID-19
Authors: Ivan Zanoni
Journal: The Journal of Experimental Medicine (2024)

Children resist COVID-19, and previous studies reported increased innate immunity in their upper airways. A new paper by Watkins et al. (https://doi.org/10.1084/jem.20230911) shows that the nasal mucosa of children is characterized by often asymptomatic viral and/or bacterial infections that dynamically regulate distinct innate immune programs.
High burden of viruses and bacterial pathobionts drives heightened nasal innate immunity in children
Authors: Timothy A. Watkins, Alex B. Green, Julien A.R. Amat, Nagarjuna R. Cheemarla, Katrin Hänsel, Richard Lozano, Sarah N. Dudgeon, Gregory Germain, Marie L. Landry, Wade L. Schulz, Ellen F. Foxman
Journal: The Journal of Experimental Medicine (2024)

Studies during the COVID-19 pandemic showed that children had heightened nasal innate immune responses compared with adults. To evaluate the role of nasal viruses and bacteria in driving these responses, we performed cytokine profiling and comprehensive, symptom-agnostic testing for respiratory viruses and bacterial pathobionts in nasopharyngeal samples from children tested for SARS-CoV-2 in 2021-22 (n = 467). Respiratory viruses and/or pathobionts were highly prevalent (82% of symptomatic and 30% asymptomatic children; 90 and 49% for children <5 years). Virus detection and load correlated with the nasal interferon response biomarker CXCL10, and the previously reported discrepancy between SARS-CoV-2 viral load and nasal interferon response was explained by viral coinfections. Bacterial pathobionts correlated with a distinct proinflammatory response with elevated IL-1β and TNF but not CXCL10. Furthermore, paired samples from healthy 1-year-olds collected 1-2 wk apart revealed frequent respiratory virus acquisition or clearance, with mucosal immunophenotype changing in parallel. These findings reveal that frequent, dynamic host-pathogen interactions drive nasal innate immune activation in children.
FOXP3 snatches transcription factors depending on the context
Authors: Lisa Schmidleithner, Philipp Stüve, Markus Feuerer
Journal: The Journal of Experimental Medicine (2024)

FOXP3 hijacks DNA-binding proteins to regulate gene expression. In this issue of JEM, He et al. (https://doi.org/10.1084/jem.20232068) propose a dynamic model in which FOXP3 associates with DNA-binding proteins to regulate Treg cell function in response to environmental cues.
STAT3 gain of function: Too much of a good thing in the skin!
Authors: Cindy S. Ma, Stuart G. Tangye
Journal: The Journal of Experimental Medicine (2024)

Germline activating mutations in STAT3 cause a multi-systemic autoimmune and autoinflammatory condition. By studying a mouse model, Toth et al. (https://doi.org/10.1084/jem.20232091) propose a role for dysregulated IL-22 production by Th17 cells in causing some aspects of immune-mediated skin inflammation in human STAT3 GOF syndrome.
Female alternative reproductive tactics: diversity and drivers
Authors: Daiping Wang, Jessica Abbott, Franziska A. Brenninger, Kora Klein, Angela Nava-Bolaños, Lengxob Yong, Xiang-Yi Li Richter
Journal: Trends in Ecology & Evolution (2024)

It is often argued that anisogamy causes alternative reproductive tactics (ARTs) to be more common in males than females. We challenge this view by pointing out logical flaws in the argument. We then review recent work on the diversity of female ARTs, listing several understudied types such as solitary versus communal breeding and facultative parthenogenesis. We highlight an important difference between male and female ARTs that caused female ARTs to be overlooked: male ARTs tend to focus on successful fertilization, whereas female ARTs occur at many stages of reproduction and often form complex networks of decision points. We propose to study correlated female ARTs as a whole to better understand their drivers and eco-evolutionary dynamics.
Quality of life in patients with statin intolerance: a multicentre prospective registry study
Authors: Paulina E Stürzebecher, Ioanna Gouni-Berthold, Christina Mateev, Ole Frenzel, Stephan Erbe, Jes-Niels Boeckel, Markus Scholz, Ulrike Schatz, Oliver Weingärtner, Ursula Kassner, Ulrich Laufs
Journal: The Lancet Regional Health - Europe (2024)
Trends in incidence of pneumothorax in England before, during and after the COVID-19 pandemic (2017–2023): a population-based observational study
Authors: Xiaomin Zhong, Raph Goldacre, Eva J A Morris, Rob J Hallifax
Journal: The Lancet Regional Health - Europe (2024)

COVID-19 is a risk factor for pneumothorax. The pandemic may have influenced healthcare-seeking behaviour for pneumothorax. This study aimed to investigate recent trends in the incidence of pneumothorax in England.
Time of sample collection is critical for the replicability of microbiome analyses
Authors: Celeste Allaband, Amulya Lingaraju, Stephany Flores Ramos, Tanya Kumar, Haniyeh Javaheri, Maria D. Tiu, Ana Carolina Dantas Machado, R. Alexander Richter, Emmanuel Elijah, Gabriel G. Haddad, Vanessa A. Leone, Pieter C. Dorrestein, Rob Knight, Amir Zarrinpar
Journal: Nature Metabolism (2024)