tbuckley/cabot-search huggingface dataset:
Publisher Correction: PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape
Authors: Noah Gamble, Alexandra Bradu, Jason A Caldwell, Joshua McKeever, Olubusayo Bolonduro, Ebru Ermis, Caroline Kaiser, YeEun Kim, Benjamin Parks, Sandy Klemm, William J Greenleaf, Gerald R Crabtree, Andrew S Koh
Journal: Nature Immunology (2024)
Clotrimazole-Betamethasone Dipropionate Prescribing for Nonfungal Skin Conditions
Authors: Jeremy A. W. Gold, Avrom S. Caplan, Kaitlin Benedict, Shari R. Lipner, Dallas J. Smith
Journal: JAMA Network Open (2024)

This cross-sectional study identifies the common diagnoses and physician encounter types associated with clotrimazole-betamethasone dipropionate prescriptions among Medicare enrollees in 2021.
Real-Time Use of a Dynamic Model To Measure the Impact of Public Health Interventions on Measles Outbreak Size and Duration — Chicago, Illinois, 2024
Authors: Nina B. Masters, Inga Holmdahl, Paige B. Miller, Chirag K. Kumar, Catherine M. Herzog, Peter M. DeJonge, Stephanie Gretsch, Sara E. Oliver, Manisha Patel, David E. Sugerman, Beau B. Bruce, Brian F. Borah, Scott W. Olesen
Journal: MMWR Morbidity and Mortality Weekly Report (2024)

Measles is a highly infectious, vaccine-preventable disease that can cause severe illness, hospitalization, and death. A measles outbreak associated with a migrant shelter in Chicago occurred during February-April 2024, in which a total of 57 confirmed cases were identified, including 52 among shelter residents, three among staff members, and two among community members with a known link to the shelter. CDC simulated a measles outbreak among shelter residents using a dynamic disease model, updated in real time as additional cases were identified, to produce outbreak forecasts and assess the impact of public health interventions. As of April 8, the model forecasted a median final outbreak size of 58 cases (IQR = 56-60 cases); model fit and prediction range improved as more case data became available. Counterfactual analysis of different intervention scenarios demonstrated the importance of early deployment of public health interventions in Chicago, with a 69% chance of an outbreak of 100 or more cases had there been no mass vaccination or active case-finding compared with only a 1% chance when those interventions were deployed. This analysis highlights the value of using real-time, dynamic models to aid public health response, set expectations about outbreak size and duration, and quantify the impact of interventions. The model shows that prompt mass vaccination and active case-finding likely substantially reduced the chance of a large (100 or more cases) outbreak in Chicago.
Electronically delivered rehabilitation after acute pulmonary embolism is safe and improves quality of life
Authors: Daniel Lachant, Deborah Haight, Dominick Roto, Alyssa Williams, Kyle Norton, R. James White
Journal: European Respiratory Journal (2024)

Survivors of acute pulmonary embolism (PE) often have residual dyspnea (post-PE impairment) and consume substantial health care resources despite effective anti-coagulation (17% [1]-50% [2]). Cardiopulmonary exercise testing has demonstrated deconditioning as a common finding [3, 4], and anxiety may fuel sedentary behavior which prevents recovery. Rehabilitation programs >3 months after PE are beneficial [5, 6]; however, an influx of acute PE patients would soon overwhelm facilities, even if the system only focused on higher-risk patients. With the goals of improving access (by eliminating transportation), reducing costs, and enabling early recovery, we developed a home exercise program for patients discharged after intermediate- or high-risk PE [7]. Our primary goal was to assess safety, but we also measured 6-minute walk distance (6MWD), actigraphy, and quality of life. Footnotes This manuscript has recently been accepted for publication in the European Respiratory Journal . It is published here in its accepted form prior to copyediting and typesetting by our production team. After these production processes are complete and the authors have approved the resulting proofs, the article will move to the latest issue of the ERJ online. Please open or download the PDF to view this article. Conflict of interest: All authors report support for the present manuscript from Chest Foundation Grant and URMC KL2 Scholar Award. Conflict of interest: In addition, outside the submitted work, Daniel Lachant reports consulting fees and lecture honoraria from United Therapeutics, Liquidia. Conflict of interest: All other authors have nothing further to disclose.
<i>QuickStats:</i> Percentage Distribution of Deaths Involving Injuries from Recreational and Nonrecreational Use of Watercraft,* by Month — United States, 2020–2022
Journal: MMWR Morbidity and Mortality Weekly Report (2024)

Deaths were identified using International Classification of Diseases, Tenth Revision underlying cause of death codes V90-V94 (water transport).Water transport includes both recreational and nonrecreational use of motorized (e.g., merchant ship, ferry, passenger ship, fishing boat, and jet ski) and nonmotorized (e
Variability in cell division among anatomical sites shapes Escherichia coli antibiotic survival in a urinary tract infection mouse model
Authors: Ariane Amoura, Claire Pistien, Camille Chaligné, Sara Dion, Mélanie Magnan, Antoine Bridier-Nahmias, Alexandra Baron, Françoise Chau, Emmanuel Bourgogne, Minh Le, Erick Denamur, Molly A. Ingersoll, Bruno Fantin, Agnès Lefort, Imane El Meouche
Journal: Cell Host & Microbe (2024)

Urinary tract infection (UTI), mainly caused by Escherichia coli, are frequent and have a recurrent nature even after antibiotic treatment. Potential bacterial escape mechanisms include growth defects, but probing bacterial division in vivo and establishing its relation to the antibiotic response remain challenging. Using a synthetic reporter of cell division, we follow the temporal dynamics of cell division for different E. coli clinical strains in a UTI mouse model with and without antibiotics. We show that more bacteria are actively dividing in the kidneys and urine compared with the bladder. Bacteria that survive antibiotic treatment are consistently non-dividing in three sites of infection. Additionally, we demonstrate how both the strain in vitro persistence profile and the microenvironment impact infection and treatment dynamics. Understanding the relative contribution of the host environment, growth heterogeneity, non-dividing bacteria, and antibiotic persistence is crucial to improve therapies for recurrent infections.
Data-Driven Characterization of Genetic Variability in Disease Pathways and Pesticide-Induced Nervous System Disease in the United States Population
Authors: Marissa B. Kosnik, Philipp Antczak, Peter Fantke
Journal: Environmental Health Perspectives (2024)

BACKGROUND: Genetic susceptibility to chemicals is incompletely characterized.However, nervous system disease development following pesticide exposure can vary in a population, implying some individuals may have higher genetic susceptibility to pesticide-induced nervous system disease.OBJECTIVES: We aimed to build a computational approach to characterize single-nucleotide polymorphisms (SNPs) implicated in chemically induced adverse outcomes and used this framework to assess the link between differential population susceptibility to pesticides and human nervous system disease.METHODS: We integrated publicly available datasets of Chemical-Gene, Gene-Pathway, and SNP-Disease associations to build Chemical-Pathway-Gene-SNP-Disease linkages for humans.As a case study, we integrated these linkages with spatialized pesticide application data for the US from 1992 to 2018 and spatialized nervous system disease rates for 2018.Through this, we characterized SNPs that may be important in states with high disease occurrence based on the pesticides used there.RESULTS: We found that the number of SNP hits per pesticide in US states positively correlated with disease incidence and prevalence for Alzheimer's disease, Parkinson disease, and multiple sclerosis.We performed frequent itemset mining to differentiate pesticides used over time in states with high and low disease occurrence and found that only 19% of pesticide sets overlapped between 10 states with high disease occurrence and 10 states with low disease occurrence rates, and more SNPs were implicated in pathways in high disease occurrence states.Through a crossvalidation of subsets of five high and low disease occurrence states, we characterized SNPs, genes, pathways, and pesticides more frequently implicated in high disease occurrence states.DISCUSSION: Our findings support that pesticides contribute to nervous system disease, and we developed priority lists of SNPs, pesticides, and pathways for further study.This data-driven approach can be adapted to other chemicals, diseases, and locations to characterize differential population susceptibility to chemical exposures.
Chromatic visual evoked potentials: a review of physiology, methods and clinical applications
Authors: Oliver R. Marmoy, Manca Tekavčič Pompe, Jan Kremers
Journal: Progress in Retinal and Eye Research (2024)

Objective assessment of the visual system can be performed electrophysiologically using the visual evoked potential (VEP). In many clinical circumstances, this is performed using high contrast achromatic patterns or diffuse flash stimuli. These methods are clinically valuable but they may only assess a subset of possible physiological circuitries within the visual system, particularly those involved in achromatic (luminance) processing. The use of chromatic VEPs (cVEPs) in addition to standard VEPs can inform us of the function or dysfunction of chromatic pathways. The chromatic VEP has been well studied in human health and disease. Yet, to date our knowledge of their underlying mechanisms and applications remains limited. This likely reflects a heterogeneity in the methodology, analysis and conclusions of different works, which leads to ambiguity in their clinical use. This review sought to identify the primary methodologies employed for recording cVEPs. Furthermore cVEP maturation and application in understanding the function of the chromatic system under healthy and diseased conditions are reviewed. We first briefly describe the physiology of normal colour vision, before describing the methodologies and historical developments which have led to our understanding of cVEPs. We thereafter describe the expected maturation of the cVEP, followed by reviewing their application in several disorders: congenital colour vision deficiencies, retinal disease, glaucoma, optic nerve and neurological disorders, diabetes, amblyopia and dyslexia. We finalise the review with recommendations for testing and future directions.
Emerging treatments in HER2-positive advanced breast cancer: Keep raising the bar
Authors: Elisa Agostinetto, Giuseppe Curigliano, Martine Piccart
Journal: Cell Reports Medicine (2024)

Patients with human epidermal receptor 2 (HER2)-positive breast cancer are experiencing a consistent shift toward better survival across the years, thanks to tremendous advancements in treatment strategies. The consistent improvements of outcomes set a high bar for new drug development and the need to explore new ways to overcome resistance mechanisms. Emerging treatments in HER2-positive breast cancer aim to tackle the disease by acting on different targets, including not only HER2 (both at the extra- and intracellular level), but also HER3, PD-(L)1, CTLA4, NKG2A, AKT, PI3K, and, in triple-positive tumors, the estrogen receptors and the cyclin-dependent kinases 4/6. This review describes the evolving treatment landscape of HER2-positive breast cancer, from the current approved therapies to the future perspectives, with a focus on the new agents which are likely to get approved in the next future.
Water Fluoridation and Birth Outcomes in California
Authors: Dana E. Goin, Amy M. Padula, Tracey J. Woodruff, Allison Sherris, Kiley Charbonneau, Rachel Morello-Frosch
Journal: Environmental Health Perspectives (2024)

BACKGROUND: There is a lack of research on the relationship between water fluoridation and pregnancy outcomes.OBJECTIVES: We assessed whether hypothetical interventions to reduce fluoride levels would improve birth outcomes in California.METHODS: We linked California birth records from 2000 to 2018 to annual average fluoride levels by community water system.Fluoride levels were collected from consumer confidence reports using publicly available data and public record requests.We estimated the effects of a hypothetical intervention reducing water fluoride levels to 0:7 ppm (the current level recommended by the US Department of Health and Human Services) and 0:5 ppm (below the current recommendation) on birth weight, birth-weight-for-gestational age z-scores, gestational age, preterm birth, small-for-gestational age, large-forgestational age, and macrosomia using linear regression with natural cubic splines and G-computation.Inference was calculated using a clustered bootstrap with Wald-type confidence intervals.We evaluated race/ethnicity, health insurance type, fetal sex, and arsenic levels as potential effect modifiers.RESULTS: Fluoride levels ranged from 0 to 2:5 ppm, with a median of 0:51 ppm.There was a small negative association on birth weight with the hypothetical intervention to reduce fluoride levels to 0:7 ppm [-2:2 g; 95% confidence interval (CI): -4:4, 0.0] and to 0:5 ppm (-5:8 g; 95% CI: -10:0, -1:6).There were small negative associations with birth-weight-for-gestational-age z-scores for both hypothetical interventions (0:7 ppm: -0:004; 95% CI: -0:007, 0.000 and 0:5 ppm: -0:006; 95% CI: -0:013, 0.000).We also observed small negative associations for risk of large-for-gestational age for both the hypothetical interventions to 0:7 ppm [risk difference ðRDÞ = -0:001; 95% CI: -0:002, 0.000 and 0:5 ppm (-0:001; 95% CI: -0:003, 0.000)].We did not observe any associations with preterm birth or with being small for gestational age for either hypothetical intervention.We did not observe any associations with risk of preterm birth or small-for-gestational age for either hypothetical intervention.CONCLUSION: We estimated that a reduction in water fluoride levels would modestly decrease birth weight and birth-weight-for-gestational-age z-scores in California.
Hospice Readmission, Hospitalization, and Hospital Death Among Patients Discharged Alive from Hospice
Authors: Elizabeth A. Luth, Caitlin Brennan, Susan L. Hurley, Veerawat Phongtankuel, Holly G. Prigerson, Miriam Ryvicker, Hui Shao, Yongkang Zhang
Journal: JAMA Network Open (2024)

Transitions in care settings following live discharge from hospice care are burdensome for patients and families. Factors contributing to risk of burdensome transitions following hospice discharge are understudied.
Primary spontaneous pneumothorax: does size matter?
Authors: Gerben Keijzers, Michaela Donaghy, Mark Weatherall, Richard Beasley, Emma L. Ball, Graham Simpson, Diana Egerton-Warburton, Y.C. Gary Lee, Simon G.A. Brown
Journal: European Respiratory Journal (2024)

There is increasing evidence supporting conservative management for patients with primary spontaneous pneumothorax (PSP) regardless of size [1, 2] which is reflected in the recent British Thoracic Society Guideline [3]. However, the size of the pneumothorax on radiograph likely still has an important influence on management decisions, as illustrated by a recent interactive clinical decision debate [4]. The studies showing non-inferiority in terms of re-expansion and more favorable patient-centered and safety outcomes for the conservative approach included a range of PSP sizes from medium to complete. Clinicians will benefit from understanding if efficacy and safety outcomes of conservative management are dependent on pneumothorax size. Footnotes This manuscript has recently been accepted for publication in the European Respiratory Journal . It is published here in its accepted form prior to copyediting and typesetting by our production team. After these production processes are complete and the authors have approved the resulting proofs, the article will move to the latest issue of the ERJ online. Please open or download the PDF to view this article. Conflict of Interest: All authors have nothing to disclose.
Quantification of the Heat-Related Risk and Burden of Hospitalizations for Cause-Specific Injuries and Contribution of Human-Induced Climate Change: A Time-Stratified Case-Crossover Study in China
Authors: Lu Zhou, Cong Liu, Cheng He, Jian Lei, Yixiang Zhu, Ya Gao, Jianwei Xuan, Haidong Kan, Renjie Chen
Journal: Environmental Health Perspectives (2024)

Although ambient temperature has been linked with injury incidence, there have been few nationwide studies to quantify the temperature-related risk and burden of cause-specific injury hospitalizations. Additionally, the impact of human-induced climate change to injury burden remains unknown.
The Effect of City-Level Sugar-Sweetened Beverage Taxes on Longitudinal HbA1c and Incident Diabetes in Adults With Prediabetes
Authors: Catherine Lee, Margo A. Sidell, Deborah Rohm Young, Monique M. Hedderson, Deborah A. Cohen, Emily F. Liu, Lee J. Barton, Jennifer Falbe, Galina Inzhakova, Sneha Sridhar, Allison C. Voorhees, Bing Han
Journal: Diabetes Care (2024)

OBJECTIVE Prediabetes, which is a condition characterized by higher-than-normal blood glucose levels that are under the threshold for diabetes, impacts over one-third of U.S. adults. Excise taxes on sugar-sweetened beverages (SSBs) are a proposed policy intervention to lower population consumption of SSBs and generate revenue to support health-related programs, thus potentially delaying or preventing the development of diabetes in individuals with prediabetes. We leveraged data from Kaiser Permanente in California to examine the impact of SSB taxes in California on individual-level mean HbA1c levels and rates of incident diabetes. RESEARCH DESIGN AND METHODS We compared two outcomes, mean HbA1c levels and rates of incident diabetes, among a matched cohort of adults with prediabetes who lived and did not live in SSB excise tax cities, using outcomes collected in the 6 years prior and 4 years following SSB tax implementation. We used multivariable linear mixed effects models to analyze longitudinal mean HbA1c and discrete-time survival models for incident diabetes. RESULTS We included 68,658 adults in the analysis. In adjusted models, longitudinal mean HbA1c was 0.007% (95% CI 0.002, 0.011) higher in the tax cities compared with control individuals; while the estimated difference was statistically significant, it was not clinically significant (HbA1c &amp;lt;0.5%). There was no significant difference in the risk of incident diabetes between individuals living in tax and control cities. CONCLUSIONS We found no clinically significant association between SSB taxes and either longitudinal mean HbA1c or incident diabetes among adults with prediabetes in the 4 years following SSB tax implementation.
Artificial Intelligence Based Quantitative Myocardial Blood Flow Assessment Facilitates the Detection of Multi-Vessel Coronary Artery Disease Following Vasodilator Stress Perfusion Cardiovascular MR Imaging
Authors: Georgios Moutzoukis, Benedikt Wagner, Marie K Lorenz, Heiko Mahrholdt, Andreas Seitz
Journal:  (2024)

AI based quantitative perfusion analysis detects ischemia missed by visual approach.
Dual Checkpoint Inhibition in Melanoma With ≥1% PD-L1—Time to Reassess the Evidence
Authors: Marco Donia, Vinay Prasad
Journal: JAMA Oncology (2024)

This Viewpoint discusses use of anti–PD-1 monotherapy as the primary treatment option for patients with treatment-naive metastatic melanoma staining positive for PD-L1 over dual checkpoint inhibition therapy.
Axillary Surgery for Chemoresidual (ypN-Positive) Nodal Disease
Authors: Eric D. Brooks, Adeline M. Deladisma, Christopher G. Morris, Erin M. Mobley, Leigh A. Neumayer, Julie A. Bradley, Raymond B. Mailhot Vega
Journal: JAMA Oncology (2024)

This cohort study using pooled data from 2 randomized clinical trials examines whether removing more lymph nodes with axillary lymph node dissection improved outcomes over sentinel lymph node biopsy when most patients received adjuvant radiation therapy or regional nodal irradiation.
Bidirectional regulation of levodopa-induced dyskinesia by a specific neural ensemble in globus pallidus external segment
Authors: Cong Shen, Bo Shen, Dechen Liu, Linlin Han, Kexin Zou, Linhua Gan, Jingyu Ren, Bin Wu, Yilin Tang, Jue Zhao, Yimin Sun, Fengtao Liu, Wenbo Yu, Haishan Yao, Jianjun Wu, Jian Wang
Journal: Cell Reports Medicine (2024)

Levodopa-induced dyskinesia (LID) is an intractable motor complication arising in Parkinson's disease with the progression of disease and chronic treatment of levodopa. However, the specific cell assemblies mediating dyskinesia have not been fully elucidated. Here, we utilize the activity-dependent tool to identify three brain regions (globus pallidus external segment [GPe], parafascicular thalamic nucleus, and subthalamic nucleus) that specifically contain dyskinesia-activated ensembles. An intensity-dependent hyperactivity in the dyskinesia-activated subpopulation in GPe (GPeTRAPed in LID) is observed during dyskinesia. Optogenetic inhibition of GPeTRAPed in LID significantly ameliorates LID, whereas reactivation of GPeTRAPed in LID evokes dyskinetic behavior in the levodopa-off state. Simultaneous chemogenetic reactivation of GPeTRAPed in LID and another previously reported ensemble in striatum fully reproduces the dyskinesia induced by high-dose levodopa. Finally, we characterize GPeTRAPed in LID as a subset of prototypic neurons in GPe. These findings provide theoretical foundations for precision medication and modulation of LID in the future.
Distinct feedforward and feedback pathways for cell-type specific attention effects
Authors: Georgios Spyropoulos, Marius Schneider, Jochem van Kempen, Marc Alwin Gieselmann, Alexander Thiele, Martin Vinck
Journal: Neuron (2024)

Selective attention is thought to depend on enhanced firing activity in extrastriate areas. Theories suggest that this enhancement depends on selective inter-areal communication via gamma (30-80 Hz) phase-locking. To test this, we simultaneously recorded from different cell types and cortical layers of macaque V1 and V4. We find that while V1-V4 gamma phase-locking between local field potentials increases with attention, the V1 gamma rhythm does not engage V4 excitatory-neurons, but only fast-spiking interneurons in L4 of V4. By contrast, attention enhances V4 spike-rates in both excitatory and inhibitory cells, most strongly in L2/3. The rate increase in L2/3 of V4 precedes V1 in time. These findings suggest enhanced signal transmission with attention does not depend on inter-areal gamma phase-locking and show that the endogenous gamma rhythm has cell-type- and layer-specific effects on downstream target areas. Similar findings were made in the mouse visual system, based on opto-tagging of identified interneurons.
Integrative molecular and spatial analysis reveals evolutionary dynamics and tumor-immune interplay of in situ and invasive acral melanoma
Authors: Hengkang Liu, Jiawen Gao, Mei Feng, Jinghui Cheng, Yuchen Tang, Qi Cao, Ziji Zhao, Ziqiao Meng, Jiarui Zhang, Guohong Zhang, Chong Zhang, Mingming Zhao, Yicen Yan, Yang Wang, Ruidong Xue, Ning Zhang, Hang Li
Journal: Cancer Cell (2024)

In acral melanoma (AM), progression from in situ (AMis) to invasive AM (iAM) leads to significantly reduced survival. However, evolutionary dynamics during this process remain elusive. Here, we report integrative molecular and spatial characterization of 147 AMs using genomics, bulk and single-cell transcriptomics, and spatial transcriptomics and proteomics. Vertical invasion from AMis to iAM displays an early and monoclonal seeding pattern. The subsequent regional expansion of iAM exhibits two distinct patterns, clonal expansion and subclonal diversification. Notably, molecular subtyping reveals an aggressive iAM subset featured with subclonal diversification, increased epithelial-mesenchymal transition (EMT), and spatial enrichment of APOE