tbuckley/cabot-search huggingface dataset:
Passive detection of COVID-19 with wearable sensors and explainable machine learning algorithms
Authors: Matteo Gadaleta, Jennifer M. Radin, Katie Baca-Motes, Edward Ramos, Vik Kheterpal, Eric J. Topol, Steven R. Steinhubl, Giorgio Quer
Journal: npj Digital Medicine (2021)

Abstract Individual smartwatch or fitness band sensor data in the setting of COVID-19 has shown promise to identify symptomatic and pre-symptomatic infection or the need for hospitalization, correlations between peripheral temperature and self-reported fever, and an association between changes in heart-rate-variability and infection. In our study, a total of 38,911 individuals (61% female, 15% over 65) have been enrolled between March 25, 2020 and April 3, 2021, with 1118 reported testing positive and 7032 negative for COVID-19 by nasopharyngeal PCR swab test. We propose an explainable gradient boosting prediction model based on decision trees for the detection of COVID-19 infection that can adapt to the absence of self-reported symptoms and to the available sensor data, and that can explain the importance of each feature and the post-test-behavior for the individuals. We tested it in a cohort of symptomatic individuals who exhibited an AUC of 0.83 [0.81–0.85], or AUC = 0.78 [0.75–0.80] when considering only data before the test date, outperforming state-of-the-art algorithm in these conditions. The analysis of all individuals (including asymptomatic and pre-symptomatic) when self-reported symptoms were excluded provided an AUC of 0.78 [0.76–0.79], or AUC of 0.70 [0.69–0.72] when considering only data before the test date. Extending the use of predictive algorithms for detection of COVID-19 infection based only on passively monitored data from any device, we showed that it is possible to scale up this platform and apply the algorithm in other settings where self-reported symptoms can not be collected.
JAMA Internal Medicine
Authors: Thomas Easley, Brian Shields, Karen Adams-Taylor, Paul Gee, Monica Smith, Jeff Ery, J Bonistalli, Kathy Russell, Mirna Monal, Stacey Mchugh, Tim Melroy, Marketing Thornbury, Tricia Castellano, Anna Frazier, Megan Thue, Sade Deramus-Townsend, Thalia Recruitment, Samantha Bauer, Hank Eurich, Marsha Fogler, Rachel Sisholtz, Saskia Bolore, Gretchen Linder, Brian Mccartney, Christine Hearne, Natasha Staff, Henry Aguillon, David Baum, Ron Marketing, Rick Bell, Elizabeth Solaro, Sara Zimmerman, Geoff Rey, Lindsay Dawson, Ellen Gibson, Craig Mccaff Rey, Michael Mcgraw, Daniel Pickhardt, Romando Rossini, Sarah Subramanian, Stacy Tucker, Walsh Business, Analyst Sirisha, Alluri Staff, Millette Jackson-Bates, Tom Miller, Jacob Mishkin, Morgan Business, Karl Elvin, Nancy Essex, Jaye Mize, Sean O'donnell, Sue Managers, David Antos, Anthony Bautista, Chris Borden, Debbie Camp, Jennifer Carney, Lydia Cruz, Scott Curl, Diane Darnell, Nanette Diaz, Jordynn Farrar, Allison Hughes, Colleen Kelly, John Lash, Chris Meyer, Annemarie Neff, J Neff, Sean Ohlson, Phil O'leary, Bill Pedone, Susan Price, Jaynam Shah, Erin Spencer, Denise Steinhauser, Joe Advertising, Production Services, Ahmed Avendano, Kim Boler, Rhonda Brown, Fin Carter, Michael Deegan, Euwanaha Joiner-Smith, Joshua Lane, Cindy Rendlen, Janis Trinchere, Annissa Zak, Circulation Services, Julie Burton, Ronna Hewitt, Mary Sieck, Geneine Someren, Jamaal Vargas, Content Systems, Mike Bujewski, Nathan Mitre, Digital Production, Regina Brownlee, Amanda Camino, Brenda Chandler-Grayer, Emily Dunn, Amy Evers, Maleeka Holden, Teri Hutchison, Dan Knowles, Joshua Lampinen, Natalie Marsh, Patricia Panek, Marla Seidell, La Son Diggs-Sledge, Julian Graphics, Joe Amft, Jonathan Chala, James Collver, Maria Duda, Fred Furtner, Carolyn Hall, Maria Kowalkowski, Proofreading Carol, Joy Farrell, Maria Giannini, Sasha Grossman, Kate Lander, Judith Literskis, Teresa Omiotek, Michael Ryder, James Madara, Terri Carter, Fellows Mithi, Del Rosario, Vinay Guduguntla, Anand Habib, Audrey Han, Natalie Richmond, Eric Ward, Zachary Goldberger, Nora Goldschlager, San Francisco, Elsayed Soliman, Winston-Salem North, Fiona Clement, Rita Redberg, Deborah Grady, Michael Incze, Salt City, Tanner Caverly, Ann Arbor, Brandon Combs, Sanket Dhruva
Journal: JAMA Internal Medicine (2022)

Mission Statement: To promote the art and science of medicine and the betterment of public health by publishing manuscripts of interest and relevance to internists practicing as generalists or as medical subspecialists.
Atlas of exercise metabolism reveals time-dependent signatures of metabolic homeostasis
Authors: Shogo Sato, Kenneth A. Dyar, Jonas T. Treebak, Sara L. Jepsen, Amy M. Ehrlich, Stephen P. Ashcroft, Kajetan Trost, Thomas Kunzke, Verena M. Prade, Lewin Small, Astrid Linde Basse, Milena Schönke, Siwei Chen, Muntaha Samad, Pierre Baldi, Romain Barrès, Axel Walch, Thomas Moritz, Jens J. Holst, Dominik Lutter, Juleen R. Zierath, Paolo Sassone-Corsi
Journal: Cell Metabolism (2022)

Tissue sensitivity and response to exercise vary according to the time of day and alignment of circadian clocks, but the optimal exercise time to elicit a desired metabolic outcome is not fully defined. To understand how tissues independently and collectively respond to timed exercise, we applied a systems biology approach. We mapped and compared global metabolite responses of seven different mouse tissues and serum after an acute exercise bout performed at different times of the day. Comparative analyses of intra- and inter-tissue metabolite dynamics, including temporal profiling and blood sampling across liver and hindlimb muscles, uncovered an unbiased view of local and systemic metabolic responses to exercise unique to time of day. This comprehensive atlas of exercise metabolism provides clarity and physiological context regarding the production and distribution of canonical and novel time-dependent exerkine metabolites, such as 2-hydroxybutyrate (2-HB), and reveals insight into the health-promoting benefits of exercise on metabolism.
Correction: Detection of <i>miR-34a</i> Promoter Methylation in Combination with Elevated Expression of c-Met and β-Catenin Predicts Distant Metastasis of Colon Cancer
Authors: Helge Siemens, Jens Neumann, Rene Jackstadt, Ulrich Mansmann, David Horst, Thomas Kirchner, Heiko Hermeking
Journal: Clinical Cancer Research (2022)

In the original version of this article (1), three errors exist in Fig. 1: splice lines were missing in both Fig. 1A and B, the same gel set was used to represent lanes M0-8 to M0-14 and M1-1 to M1-7 in Fig. 1B (lanes M1-1 to M1-7 are correct), and the figure legend referred to H2O instead of dH2O. The errors have been corrected in the latest online HTML and PDF versions of the article. The authors regret the errors.
Automated Network Assembly of Mechanistic Literature for Informed Evidence Identification to Support Cancer Risk Assessment
Authors: Bernice Scholten, Laura Guerrero Simón, Shaji Krishnan, Roel Vermeulen, Anjoeka Pronk, Benjamin M. Gyori, John A. Bachman, Jelle Vlaanderen, Rob Stierum
Journal: Environmental Health Perspectives (2022)

Background: Mechanistic data is increasingly used in hazard identification of chemicals. However, the volume of data is large, challenging the efficient identification and clustering of relevant data. Objectives: We investigated whether evidence identification for hazard assessment can become more efficient and informed through an automated approach that combines machine reading of publications with network visualization tools. Methods: We chose 13 chemicals that were evaluated by the International Agency for Research on Cancer (IARC) Monographs program incorporating the key characteristics of carcinogens (KCCs) approach. Using established literature search terms for KCCs, we retrieved and analyzed literature using Integrated Network and Dynamical Reasoning Assembler (INDRA). INDRA combines large-scale literature processing with pathway databases and extracts relationships between biomolecules, bioprocesses, and chemicals into statements (e.g., "benzene activates DNA damage"). These statements were subsequently assembled into networks and compared with the KCC evaluation by the IARC, to evaluate the informativeness of our approach. Results: We found, in general, larger networks for those chemicals which the IARC has evaluated the evidence to be strong for KCC induction. Larger networks were not directly linked to publication count, given that we retrieved small networks for several chemicals with little support for KCC activation according to the IARC, despite the significant volume of literature for these specific chemicals. In addition, interpreting networks for genotoxicity and DNA repair showed concordance with the IARC KCC evaluation. Discussion: Our method is an automated approach to condense mechanistic literature into searchable and interpretable networks based on an a priori ontology. The approach is no replacement of expert evaluation but, instead, provides an informed structure for experts to quickly identify which statements are made in which papers and how these could connect. We focused on the KCCs because these are supported by well-described search terms. The method needs to be tested in other frameworks as well to demonstrate its generalizability. https://doi.org/10.1289/EHP9112
Endothelial Yin Yang 1 Phosphorylation at S118 Induces Atherosclerosis Under Flow
Authors: Shu-Yi Wei, Yu-Tsung Shih, Hsin-Yi Wu, Wei-Li Wang, Pei-Ling Lee, Chih-I Lee, Chia-Yu Lin, Yu-Ju Chen, Shu Chien, Jeng-Jiann Chiu
Journal: Circulation Research (2021)

Rationale: Disturbed flow occurring in arterial branches and curvatures induces vascular endothelial cell (EC) dysfunction and atherosclerosis. We postulated that disturbed flow plays important role in modulating phosphoprotein expression profiles to regulate endothelial functions and atherogenesis. Objective: The goal of this study is to discover novel site-specific phosphorylation alterations induced by disturbed flow in ECs to contribute to atherosclerosis. Methods and Results: Quantitative phosphoproteomics analysis of ECs exposed to disturbed flow with low and oscillatory shear stress (0.5±4 dynes/cm 2 ) versus pulsatile shear stress (12±4 dynes/cm 2 ) revealed that oscillatory shear stress induces phospho-YY1 S118 (serine [S]118 phosphorylation of Yin Yang 1) in ECs. Elevated phospho-YY1 S118 level in ECs was further confirmed to be present in the disturbed flow regions in experimental animals and human atherosclerotic arteries. This disturbed flow-induced EC phospho-YY1 S118 is mediated by CK2α (casein kinase 2α) through its direct interaction with YY1. Yeast 2-hybrid library screening and in situ proximity ligation assays demonstrate that phospho-YY1 S118 directly binds ZKSCAN4 (zinc finger with KRAB [krüppel-associated box] and SCAN [SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA] domains 4) to induce promoter activity and gene expression of HDM2 (human double minute 2), which consequently induces EC proliferation through downregulation of p53 and p21 CIP1 . Administration of apoE-deficient ( ApoE −/− ) mice with CK2-specific inhibitor tetrabromocinnamic acid or atorvastatin inhibits atherosclerosis formation through downregulations of EC phospho-YY1 S118 and HDM2. Generation of novel transgenic mice bearing EC-specific overexpression of S118-nonphosphorylatable mutant of YY1 in ApoE −/− mice confirms the critical role of phospho-YY1 S118 in promoting atherosclerosis through EC HDM2. Conclusions: Our findings provide new insights into the mechanisms by which disturbed flow induces endothelial phospho-YY1 S118 to promote atherosclerosis, thus indicating phospho-YY1 S118 as a potential molecular target for atherosclerosis treatment.
Focal Xanthogranulomatous Pyelonephritis on FDG PET/CT
Authors: Yong Liu, Guansheng Tong, Zhe Wen
Journal: Clinical Nuclear Medicine (2022)

Abstract Xanthogranulomatous pyelonephritis is a rare disease that was often accompanied with urinary obstruction. The focal form of xanthogranulomatous pyelonephritis is frequently misdiagnosed as malignancy. Here we present FDG PET/CT findings of a case focal xanthogranulomatous pyelonephritis in a 66-year-old woman with polycystic liver and kidney disease. The image showed a polycystic mass in the inferior pole of right kidney with high FDG uptake in the cystic wall, which was suggestive of a cystic renal carcinoma. Right radical nephrectomy was subsequently performed. The postsurgical pathology revealed xanthogranulomatous pyelonephritis.
Melatonin attenuates radiation-induced cortical bone-derived stem cells injury and enhances bone repair in postradiation femoral defect model
Authors: Wei Hu, Jia-Wu Liang, Song Liao, Zhi-Dong Zhao, Yu-Xing Wang, Xiao-Fei Mao, Si-Wei Hao, Yi-Fan Wang, Heng Zhu, Bin Guo
Journal: Military Medical Research (2021)

Abstract Background The healing of bone defects can be challenging for clinicians to manage, especially after exposure to ionizing radiation. In this regard, radiation therapy and accidental exposure to gamma (γ)-ray radiation have been shown to inhibit bone formation and increase the risk of fractures. Cortical bone-derived stem cells (CBSCs) are reportedly essential for osteogenic lineages, bone maintenance and repair. This study aimed to investigate the effects of melatonin on postradiation CBSCs and bone defect healing. Methods CBSCs were extracted from C57BL/6 mice and were identified by flow cytometry. Then CBSCs were subjected to 6 Gy γ-ray radiation followed by treatment with various concentrations of melatonin. The effects of exogenous melatonin on the self-renewal and osteogenic capacity of postradiation CBSCs in vitro were analyzed. The underlying mechanisms involved in genomic stability, apoptosis and oxidative stress-related signaling were further analyzed by Western blotting, flow cytometry and immunofluorescence assays. Moreover, postradiation femoral defect models were established and treated with Matrigel and melatonin. The effects of melatonin on postradiation bone healing in vivo were evaluated by micro-CT and pathological analysis. Results The decrease in radiation-induced self-renewal and osteogenic capacity were partially reversed in postradiation CBSCs treated with melatonin ( P &lt; 0.05). Melatonin maintained genomic stability, reduced postradiation CBSC apoptosis and intracellular oxidative stress, and enhanced expression of antioxidant-related enzymes ( P &lt; 0.05). Western blotting validated the anti-inflammatory effects of melatonin by downregulating interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α) levels via the extracellular regulated kinase (ERK)/nuclear factor erythroid 2-related factor 2 (NRF2)/heme oxygenase-1 (HO-1) signaling pathway. Melatonin was also found to exhibit antioxidant effects via NRF2 signaling. In vivo experiments demonstrated that the newly formed bone in the melatonin plus Matrigel group had higher trabecular bone volume per tissue volume (BV/TV) and bone mineral density values with lower IL-6 and TNF-α levels than in the irradiation and the Matrigel groups ( P &lt; 0.05). Conclusion This study suggested that melatonin could protect CBSCs against γ-ray radiation and assist in the healing of postradiation bone defects.
Insecticide-Treated Nets and the Persistence of Childhood Survival Gains to Adulthood
Authors: Thomas P. Eisele, Laurence Slutsker
Journal: New England Journal of Medicine (2022)

Malaria is a mosquito-borne parasitic disease. In sub-Saharan Africa, the vast majority of cases are caused by Plasmodium falciparum infection in young children. In this region in 2020, there were an estimated 228 million cases and 602,000 deaths from malaria; 80% of the deaths occurred in children younger than 5 years of age.1 A series of community-based randomized, controlled trials that were conducted across a range of malaria transmission settings in sub-Saharan Africa in the 1990s showed that insecticide-treated mosquito nets substantially reduced the incidence of malaria and death from this disease among children.2 Since then, treated nets have become . . .
Abstract MP06: Impact Of Social Determinants Of Health On Optimal Cardiovascular Health Among Asian American Subgroups
Authors: Austin Le, Alicia Zhu, Yuemeng Li, Jaiveer Singh, Shozen Dan, Latha Palaniappan, Malathi Srinivasan, Tali Elfassy, Javier Valero Elizondo, Eugene Yang
Journal: Circulation (2022)

Background: Limited disaggregated Asian subgroup data exists on the impact of social determinants of health (SDOH) on optimal cardiovascular (CV) health. Hypothesis: Compared to non-Hispanic whites (NHW), Asian subgroups have a greater likelihood of optimal CV health, but this observation may be attenuated after controlling for SDOH. Methods: We analyzed results from the National Health Interview Survey (2013-2018), a nationally representative sample. Self-reported SDOH variables include demographics, food security, healthcare access, financial security, and neighborhood cohesion. We conducted stepwise, multivariable logistic regression, analyzing the association between race/ethnicity and CV risk profile score iteratively controlling for SDOH, based on the presence of CV risk factors (RF): diabetes mellitus, hypertension, obesity, smoking, insufficient physical activity, and high cholesterol. CV risk profile sum was categorized as optimal (0-1 RF) or sub-optimal (≥ 2 RF). Results: Our study sample included 112,380 individuals [mean age 49.1 (SD 18.6)]: 92.7% NHW, 1.6% Asian Indian, 1.5% Chinese, 1.6% Filipino, and 2.6% other Asian. The final model, adjusted for all domains of SDOH, showed that odds for optimal CV health for Filipinos compared to NHW were not significant (OR= 1.06, 95% CI: 0.90, 1.24, p = 0.47). After adjusting for all SDOH, Chinese had the highest odds of optimal CV health compared to NHWs (OR=2.47, 95% CI: 2.08, 2.94, p &lt; 0.001), while the greatest change was observed for Asian Indians [Model 1: OR 1.94 (95% CI 1.7, 2.22) versus Model 5: OR 1.7 (95% CI 1.47, 1.96)]. Conclusion: Asian Indian, Chinese, and other Asian subgroups had a higher likelihood of optimal CV health compared to NHWs after controlling for SDOH but no significant differences were observed for Filipinos. This association was modestly attenuated only for Asian Indians after controlling for all SDOH. Future research should focus on the modifying effects that race/ethnicity may have on the association between SDOH and optimal CV health.
Sexual dimorphism in COVID-19: potential clinical and public health implications
Authors: Nicole Bechmann, Andreas Barthel, Andreas Schedl, Stephan Herzig, Zsuzsanna Varga, Catherine Gebhard, Manuel Mayr, Constanze Hantel, Felix Beuschlein, Christian Wolfrum, Nikolaos Perakakis, Lucilla Poston, Cynthia L Andoniadou, Richard Siow, Raul R Gainetdinov, Arad Dotan, Yehuda Shoenfeld, Geltrude Mingrone, Stefan R Bornstein
Journal: The Lancet Diabetes & Endocrinology (2022)
Complete Resolution of Disease After Peptide Receptor Radionuclide Therapy in a Patient of Metastatic Insulinoma
Authors: Priyanka Verma, Gaurav Malhotra, Manjunath H. Dodamani, Anurag R. Lila, Ramesh V. Asopa, Tushar R. Bandgar
Journal: Clinical Nuclear Medicine (2021)

A 48-year-old man, a case of metastatic insulinoma, who failed transarterial chemoembolization of liver metastases underwent multiple cycles of peptide receptor radionuclide therapy with 177Lu-DOTATATE, following which a complete morphologic and metabolic response was demonstrated on 68Ga-DOTATATE PET/CT. Patient had a remarkable improvement in his quality of life as intractable hypoglycemic episodes resolved after treatment. Peptide receptor radionuclide therapy is a promising targeted radionuclide therapy in patients of metastatic insulinomas that can result in reduced tumor burden and improved quality of life, particularly those who fail the conventional treatment modalities as seen in the present case.
Abstract P147: Characterizing Self-reported Religious Affiliation Among Patients With Vascular Disease And Associations With Health Risk Behaviors
Authors: Chloe A Powell, Gloria Y Kim, John P O'Connor, Mary E Byrnes, Dawn M Coleman, Matthew A Corriere
Journal: Circulation (2022)

Introduction: Religion is an important aspect of personal identity, which is linked to education and wealth. Religion is changing in prevalence, notoriously difficult to obtain from surveys, and seldom accounted for in clinical research. We characterized religious affiliation among patients with common diagnoses treated by vascular surgeons and explored associations with patient-level factors and health risk behaviors. Hypothesis: We hypothesize health risk behaviors will be more common among vascular patients that are unaffiliated with a particular religion. Methods: Patients treated from 2019-2021 at a single center with vascular disease (abdominal aortic aneurysm; carotid, renal, or mesenteric stenosis; or peripheral artery disease) were identified. Self-reported religious affiliation was obtained from the medical record. Patients self-reporting any religion (regardless of religion name or denomination) were categorized as religion-affiliated (RA); self-reporting as atheist, agnostic, or no religion were categorized as unaffiliated (UA). Health risk behaviors were evaluated as individual outcomes and in aggregate based on heavy drinking (per CDC recommendations), tobacco, or illegal drug use. Statistical comparisons used chi-square and Wilcoxon scores. Results: Among 3,568 patients identified, 3,247 (91%) had self-reported religion and form the basis of analysis. 2198 (67.7%) reported RA, and over 40 denominations were identified. RA was more common among women [70.3% (1041 of 1480) vs. 65.5% (1157 of 1767); P=0.003] and married patients [71.1% (1162 of 1635) vs. 65.5% (598 of 913): P=0.003]. RA by race was most common among African American patients [70.9% (158 of 223)] and least common among Asians [48.2% (26 of 54)] (P=0.002). Self-reported health risk behaviors were more common among UA patients [33.2% (348 of 1049) versus 27.2% (598 of 2198); P&lt;0.001], who also had a higher median weekly alcohol consumption (1.2 [IQR 3.6] vs. 0.6 [IQR 2.4] ounces; P=0.024). Conclusions: Self-reported RA is associated with demographics and health risk behaviors among vascular patients. Interventions leveraging religious organizations and leaders may not reach nearly one third of patients who are UA. Future work will explore associations with socioeconomic factors and surgical outcomes.
Gender disparity regarding work-life balance satisfaction among German neuro-oncologists: a YoungNOA survey
Authors: Sied Kebir, Lazaros Lazaridis, Wolfgang Wick, Michael Platten, Ghazaleh Tabatabai, Stephanie E Combs, Teresa Schmidt, Sarina Agkatsev, Tobias Blau, Irina Mäurer, Ulf Kahlert, Andre Sagerer, Anne Berberich, Sina Heider, Michael Müther, Raphael Bodensohn, Felix Behling
Journal: Neuro-Oncology (2022)

Satisfaction with work-life balance (WLB) is an essential factor for persistent motivation of early career researchers. WLB satisfaction was strongly related to planned reduction in practice times among US medical oncologists.1 The neuro-oncological landscape, however, is sparsely characterized in this regard. We present the results of an interdisciplinary anonymous survey focusing on WLB among neuro-oncologists in Germany which are members of the Neuro-oncology Working Group “Neuroonkologische Arbeitsgemeinschaft” (NOA) of the German Cancer Society (Deutsche Krebsgesellschaft, DKG) (https://www.neuroonkologie.de/). The questionnaire sent to 351 physicians covered personal information and questions aimed to reveal individual motivations, scientific interests and activities as well as individual workload and job satisfaction. The survey was online from 18 March 2021 to 1 April 2021. Ninety-six physicians (36 female, 60 male, Figure 1a) participated in this survey. Most participants were neurosurgeons (42.7%) or neurologists (39.6%, Figure 1b). Furthermore, most participants were university hospital (80.0%, Figure 1c) attending (38.5%, Figure 1d) physicians.