tbuckley/cabot-search huggingface dataset:
Tracing the Diploid Ancestry of the Cultivated Octoploid Strawberry
Authors: Chao Feng, Jing Wang, A J Harris, Kevin M Folta, Mizhen Zhao, Ming Kang
Journal: Molecular Biology and Evolution (2020)

Abstract The commercial strawberry, Fragaria × ananassa, is a recent allo-octoploid that is cultivated worldwide. However, other than Fragaria vesca, which is universally accepted one of its diploid ancestors, its other early diploid progenitors remain unclear. Here, we performed comparative analyses of the genomes of five diploid strawberries, F. iinumae, F. vesca, F. nilgerrensis, F. nubicola, and F. viridis, of which the latter three are newly sequenced. We found that the genomes of these species share highly conserved gene content and gene order. Using an alignment-based approach, we show that F. iinumae and F. vesca are the diploid progenitors to the octoploid F. × ananassa, whereas the other three diploids that we analyzed in this study are not parental species. We generated a fully resolved, dated phylogeny of Fragaria, and determined that the genus arose ∼6.37 Ma. Our results effectively resolve conflicting hypotheses regarding the putative diploid progenitors of the cultivated strawberry, establish a reliable backbone phylogeny for the genus, and provide genetic resources for molecular breeding.
KRAS<sup>G12C</sup> Inhibition with Sotorasib in Advanced Solid Tumors
Authors: David S. Hong, Marwan G. Fakih, John H. Strickler, Jayesh Desai, Gregory A. Durm, Geoffrey I. Shapiro, Gerald S. Falchook, Timothy J. Price, Adrian Sacher, Crystal S. Denlinger, Yung-Jue Bang, Grace K. Dy, John C. Krauss, Yasutoshi Kuboki, James C. Kuo, Andrew L. Coveler, Keunchil Park, Tae Won Kim, Fabrice Barlesi, Pamela N. Munster, Suresh S. Ramalingam, Timothy F. Burns, Funda Meric-Bernstam, Haby Henary, Jude Ngang, Gataree Ngarmchamnanrith, June Kim, Brett E. Houk, Jude Canon, J. Russell Lipford, Gregory Friberg, Piro Lito, Ramaswamy Govindan, Bob T. Li
Journal: New England Journal of Medicine (2020)

No therapies for targeting
Physicians and Social Determinants of Health
Authors: Kevin Hinchey, Sarah Perez McAdoo, Rebecca D. Blanchard
Journal: JAMA (2020)

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 Publications 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 2023 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
Assessment of High School Students’ Participation in Blood Donation and Registration as an Organ Donor
Authors: John Tat, Barton Hays, Martin Teachworth, Alexander Kuo, Renate B. Pilz, Beatrice A. Golomb, Gerry R. Boss
Journal: JAMA Network Open (2020)

This cross-sectional study assesses the association between blood donation and willingness to register as an organ donor among California high school students.
European Registry on <i>Helicobacter pylori</i> management shows that gastroenterology has largely failed in its efforts to guide practitioners
Authors: David Y Graham, Hashem B El-Serag
Journal: Gut (2020)

The authors report the results of a 5-year (2013–2018) audit of the effectiveness of Helicobacter pylori therapy in clinical practice in several regions of Europe.1 The study provides a contemporary prospective regarding empirical H. pylori treatment. Importantly, there was little centralised influence on choice of therapy apart from sending periodic updates, presenting updates at the meeting of the European H. pylori study group and including local feedback in the form of post-treatment testing for cure. The strengths of the report include the large sample size, representative population, and high level of complete data on treatment type, duration and follow-up. Overall, 30 394 patients from 27 European countries provided data on 21 533 first-line empirical H. pylori treatments using more than 100 different schemes. Antibiotic susceptibility data were obtained from 11% (2.7% to 16.7% in different regions). In that small sample, the prevalence of H. pylori resistance to clarithromycin and metronidazole was high (ie, 23% and 32%, respectively). Clarithromycin triple therapy was most commonly used but use declined over time from >50% in 2013–2015 to 32% in 2017–2018. The use of bismuth quadruple therapy was uncommon and varied markedly between regions but also tended to increase over time. They concluded that the management of H. pylori infection by European gastroenterologists was heterogeneous, suboptimal and discrepant with current recommendations.

There seems to be an ongoing slow paradigm shift from therapies identified by trial and …
Prevalence of Human Papillomavirus and Estimation of Human Papillomavirus Vaccine Effectiveness in Thimphu, Bhutan, in 2011–2012 and 2018
Authors: Iacopo Baussano, Ugyen Tshomo, Vanessa Tenet, Daniëlle A.M. Heideman, Tshering Wangden, Silvia Franceschi, Gary M. Clifford
Journal: Annals of Internal Medicine (2020)

Background: Bhutan implemented a national program for human papillomavirus (HPV) vaccination in 2010 involving girls aged 12 to 18 years and achieving nearly 90% coverage. Objective: To estimate HPV vaccine effectiveness in a city in Bhutan. Design: 2 cross-sectional surveys, 2011–2012 and 2018. Setting: 2 hospitals in Thimphu, capital of Bhutan. Participants: Sexually active women aged 17 to 29 years: 1445 participants from the baseline survey and 1595 from the repeated survey. Intervention: National HPV vaccination program. Measurements: HPV was assessed in cervical cell samples by using general primer GP5+/GP6+–mediated polymerase chain reaction. Human papillomavirus types were stratified as vaccine types (HPV6/11/16/18) and nonvaccine types. Age- and sexual behavior–adjusted overall, total, and indirect (herd immunity) vaccine effectiveness (VE) was computed as (1 − HPV prevalence ratio) for HPV among all women and among unvaccinated women. Results: Between the 2 surveys, the prevalence of HPV vaccine types decreased from 8.3% to 1.4%, whereas the prevalence of nonvaccine types increased from 25.8% to 31.4%. The overall and indirect adjusted VE against vaccine-targeted HPV types was 88% (95% CI, 80% to 92%) and 78% (CI, 61% to 88%), respectively. Among women younger than 27 years, who were targeted by the vaccination program, the overall and indirect adjusted VE was 93% (CI, 87% to 97%) and 88% (CI, 69% to 95%), respectively. No impact on nonvaccine HPV types was detectable. Limitation: Hospital-based recruitment; self-reported vaccination status. Conclusion: In Bhutan, the prevalence of vaccine-targeted HPV types has decreased sharply, providing the first evidence of the effectiveness of a high-coverage national HPV vaccination program in a lower-middle-income country. Primary Funding Source: Bill & Melinda Gates Foundation.
Analysis of the Global Burden of Disease study highlights the trends in death and disability‐adjusted life years of leukemia from 1990 to 2017
Authors: Zejin Ou, Danfeng Yu, Yuanhao Liang, Wenqiao He, Yongzhi Li, Minyi Zhang, Fangfei You, Huan He, Qing Chen
Journal: Cancer Communications (2020)

Abstract Background The patterns of leukemia burden have dramatically changed in recent years. This study aimed to estimate the global trends of leukemia‐related death and disability‐adjusted life‐years (DALYs) from 1990 to 2017. Methods The data was acquired from the latest version of the Global Burden of Disease (GBD) study. Estimated annual percentage changes (EAPCs) were calculated to estimate the trend of age‐standardized rate (ASR) of death and DALYs due to leukemia and its main subtypes from 1990 to 2017. Results Globally, the numbers of death and DALYs due to leukemia were 347.58 × 10 3 (95% uncertainty interval [UI] = 317.26 × 10 3 ‐364.88 × 10 3 ) and 11975.35 × 10 3 (95% UI = 10749.15 × 10 3 ‐12793.58 × 10 3 ) in 2017, with a 31.22% and 0.03% increase in absolute numbers from 1990 to 2017, respectively. Both of their ASR showed decreasing trends from 1990 to 2017 with the EAPCs being −1.04 (95% confidence interval [CI] = (−1.10‐−0.99) and −1.52 (95% CI = −1.59‐−1.44), respectively. Globally, the most pronounced decreasing trend of death and DALYs occurred in chronic myeloid leukemia with EAPCs of −2.76 (95% CI = −2.88‐−2.64) and −2.84 (95% CI = −2.97‐−2.70), respectively, while the trend increased in acute myeloid leukemia. The death and DALYs of leukemia decreased in most areas and countries with high socio‐demographic index (SDI) including Bahrain, Finland, and Australia. Conclusions The disease burden of death and DALYs due to leukemia decreased globally, and for most regions and countries from 1990 to 2017. However, the leukemia burden is still a substantial challenge globally and required adequate and affordable medical resources to improve the survival and quality of life of leukemia patients.
IN-VIVO GENE-THERAPY OF ANTI-THY-1 NEPHRITIS USING E2F DECOY OLIGONUCLEOTIDE
Authors: Tomita N, Kim J, Gibbons Gh, Baran D, Ogborn M, Stahl Rak, Tomita S, Zhang L, Kaneda Y, Dzau Vj
Journal: Journal of the American Society of Nephrology (1995)
Surufatinib in advanced pancreatic neuroendocrine tumours (SANET-p): a randomised, double-blind, placebo-controlled, phase 3 study
Authors: Jianming Xu, Lin Shen, Chunmei Bai, Wei Wang, Jie Li, Xianjun Yu, Zhiping Li, Enxiao Li, Xianglin Yuan, Yihebali Chi, Yongmei Yin, Wenhui Lou, Nong Xu, Yuxian Bai, Tao Zhang, Dianrong Xiu, Xiuwen Wang, Ying Yuan, Jia Chen, Shukui Qin, Ru Jia, Ming Lu, Yuejuan Cheng, Zhiwei Zhou, Jing Li, James He, Weiguo Su
Journal: The Lancet Oncology (2020)
Wise Use of Surveillance Data: Evolving HIV Policy and Emerging Considerations Regarding COVID-19
Authors: Naomi Seiler, Katie Horton, Anya Vanecek, Claire Heyison
Journal: The American Journal of Bioethics (2020)

Click to increase image sizeClick to decrease image sizeThis article refers to:Reassessing the Ethics of Molecular HIV Surveillance in the Era of Cluster Detection and Response: Toward HIV Data Justice
Potential Pathogenicity Determinants Identified from Structural Proteomics of SARS-CoV and SARS-CoV-2
Authors: Erica T Prates, Michael R Garvin, Mirko Pavicic, Piet Jones, Manesh Shah, Omar Demerdash, B Kirtley Amos, Armin Geiger, Daniel Jacobson
Journal: Molecular Biology and Evolution (2020)

Abstract Despite SARS-CoV and SARS-CoV-2 being equipped with highly similar protein arsenals, the corresponding zoonoses have spread among humans at extremely different rates. The specific characteristics of these viruses that led to such distinct outcomes remain unclear. Here, we apply proteome-wide comparative structural analysis aiming to identify the unique molecular elements in the SARS-CoV-2 proteome that may explain the differing consequences. By combining protein modeling and molecular dynamics simulations, we suggest nonconservative substitutions in functional regions of the spike glycoprotein (S), nsp1, and nsp3 that are contributing to differences in virulence. Particularly, we explain why the substitutions at the receptor-binding domain of S affect the structure–dynamics behavior in complexes with putative host receptors. Conservation of functional protein regions within the two taxa is also noteworthy. We suggest that the highly conserved main protease, nsp5, of SARS-CoV and SARS-CoV-2 is part of their mechanism of circumventing the host interferon antiviral response. Overall, most substitutions occur on the protein surfaces and may be modulating their antigenic properties and interactions with other macromolecules. Our results imply that the striking difference in the pervasiveness of SARS-CoV-2 and SARS-CoV among humans seems to significantly derive from molecular features that modulate the efficiency of viral particles in entering the host cells and blocking the host immune response.
Incidence of Hospitalization for Heart Failure Relative to Major Atherosclerotic Events in Type 2 Diabetes: A Meta-analysis of Cardiovascular Outcomes Trials
Authors: Julian W. Sacre, Dianna J. Magliano, Jonathan E. Shaw
Journal: Diabetes Care (2020)

BACKGROUND Emerging evidence points to heart failure as being a common first presentation of cardiovascular (CV) disease in type 2 diabetes. PURPOSE The purpose of this study was to determine whether hospitalization for heart failure (HHF) occurs more or less frequently than major adverse CV events (MACE) in people with type 2 diabetes. DATA SOURCES Placebo arms of CV outcomes trials in type 2 diabetes were included. STUDY SELECTION Sixteen CV outcomes trials were selected, including five dipeptidyl peptidase 4 inhibitor trials, seven glucagon-like peptide 1 receptor agonist trials, and four sodium–glucose cotransporter 2 inhibitor trials. DATA EXTRACTION We extracted incidence rates of HHF, myocardial infarction (MI), stroke, and the composite outcomes of CV death or HHF and MACE (CV death, nonfatal MI, or nonfatal stroke). DATA SYNTHESIS In two trials enriched with people with chronic kidney disease, HHF was more common than both MI and stroke. Among the remaining 14 trials, HHF was less frequent than MI in 13 (93%), with this difference being significant in 8 (57%); however, HHF surpassed stroke in all but 1 study (93%; significant in 7 studies [50%]). Heterogeneity among trials was moderate/high (I2 &amp;gt;50%) and partly explained by HHF/MI correlating with age and previous MI history (P &amp;lt; 0.05). In seven trials that reported events stratified by presence/absence of preexisting CV disease, ratios of HHF/MI and HHF/stroke were similar between groups. LIMITATIONS Enrichment of trial populations with those at high risk of CV events limits generalizability. CONCLUSIONS Although less frequent than MI, HHF is a common event in type 2 diabetes, both in those with and those without prior CV disease.
Two Remedies for Inappropriate Percutaneous Coronary Intervention—Closing the Gap Between Evidence and Practice
Authors: James W. Salazar, Rita F. Redberg
Journal: JAMA Internal Medicine (2020)

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 Internal Medicine HomeNew OnlineCurrent IssueFor Authors Podcast Publications 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 2023 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 Internal Medicine journal
Transcriptomic and clonal characterization of T cells in the human central nervous system
Authors: Jenna L. Pappalardo, Le Zhang, Maggie K. Pecsok, Kelly Perlman, Chrysoula Zografou, Khadir Raddassi, Ahmad Abulaban, Smita Krishnaswamy, Jack Antel, David van Dijk, David A. Hafler
Journal: Science Immunology (2020)

We have profiled cerebrospinal fluid T cells in healthy individuals and patients with MS using single-cell RNA and TCR sequencing.
Siglec-15 as an Emerging Target for Next-generation Cancer Immunotherapy
Authors: Jingwei Sun, Qiao Lu, Miguel F. Sanmamed, Jun Wang
Journal: Clinical Cancer Research (2020)

Immunomodulatory agents blocking the PD-1/PD-L1 pathway have shown a new way to treat cancer. The explanation underlying the success of these agents may be the selective expression of PD-L1 with dominant immune-suppressive activities in the tumor microenvironment (TME), supporting a more favorable tumor response-to-toxicity ratio. However, despite the big success of these drugs, most patients with cancer show primary or acquired resistance, calling for the identification of new immune modulators in the TME. Using a genome-scale T-cell activity array in combination with bioinformatic analysis of human cancer databases, we identified Siglec-15 as a critical immune suppressor with broad upregulation on various cancer types and a potential target for cancer immunotherapy. Siglec-15 has unique molecular features compared with many other known checkpoint inhibitory ligands. It shows prominent expression on macrophages and cancer cells and a mutually exclusive expression with PD-L1, suggesting that it may be a critical immune evasion mechanism in PD-L1-negative patients. Interestingly, Siglec-15 has also been identified as a key regulator for osteoclast differentiation and may have potential implications in bone disorders not limited to osteoporosis. Here, we provide an overview of Siglec-15 biology, its role in cancer immune regulation, the preliminary and encouraging clinical data related to the first-in-class Siglec-15 targeting mAb, as well as many unsolved questions in this pathway. As a new player in the cancer immunotherapeutic arena, Siglec-15 may represent a novel class of immune inhibitors with tumor-associated expression and divergent mechanisms of action to PD-L1, with potential implications in anti-PD-1/PD-L1-resistant patients.
Management of Cancer Cachexia: ASCO Guideline—Time to Address the Elephant in the Room
Authors: Olivier Huillard, Romain Seban, Francois Goldwasser
Journal: Journal of Clinical Oncology (2020)

Roeland et al 1 have provided an important review of the treatment of cancer cachexia aimed at developing clinical practice guideline recommendations.In their recommendations, they developed three axes: nutritional interventions, pharmacologic intervention, and other interventions (eg, exercise).Cachexia is one of the life-threatening consequences of cancer that depends on various factors, one of them being anticancer therapies.Many of these therapies have been shown to induce cachexia or sarcopenia, 2-4 possibly by a mechanism of action different from that of cancer. 2 For example, we retrospectively assessed the lean body mass of patients with radioactive iodine-resistant thyroid cancers included in the phase III DECISION (ClinicalTrials.govidentifier: NCT00984282) trial that compared sorafenib to placebo. 4 A total of 365 patients were eligible for this analysis.After 6 months of treatment, the mean weight, body mass index, and lean body mass of patients receiving sorafenib were all lower than at baseline, and they were significantly lower than those for patients receiving placebo (for all, P , .0001).Importantly, this trial demonstrated that sorafenib had significant anticancer action because it significantly improved progression-free survival compared with placebo.
Comparative outcomes of cefazolin versus antistaphylococcal penicillins in methicillin-susceptible Staphylococcus aureus infective endocarditis: a post hoc analysis of a prospective multicentre French cohort study
Authors: Raphaël Lecomte, Alexis Bourreau, Colin Deschanvres, Nahéma Issa, Paul Le Turnier, Benjamin Gaborit, Marie Chauveau, Anne-Gaëlle Leroy, Thierry Le Tourneau, Jocelyne Caillon, Fabrice Camou, David Boutoille
Journal: Clinical Microbiology and Infection (2020)
Intravenous Ibuprofen Reduces Opioids After Orthopedic Trauma
Authors: Anita Slomski
Journal: JAMA (2020)

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 Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More Publications 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 2023 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
Adrenal Castleman Disease on 99mTc-HYNIC-TOC Scan and FDG PET/CT
Authors: Jie Ding, Xin Cheng, Guozhu Hou, Hongli Jing, Li Huo
Journal: Clinical Nuclear Medicine (2020)

Adrenal Castleman disease is very rare. We reported image findings of a right adrenal mass in a 75-year-old man on Tc-HYNIC-TOC scan and FDG PET/CT. There was obviously elevated Tc-HYNIC-TOC activity, but the intensity of FDG activity was remarkable. Pheochromocytoma was initially suspected. However, pathology from resected specimen showed adrenal Castleman disease.
Signatures of Introgression across the Allele Frequency Spectrum
Authors: Simon H Martin, William Amos
Journal: Molecular Biology and Evolution (2020)

The detection of introgression from genomic data is transforming our view of species and the origins of adaptive variation. Among the most widely used approaches to detect introgression is the so-called ABBA-BABA test or D-statistic, which identifies excess allele sharing between nonsister taxa. Part of the appeal of D is its simplicity, but this also limits its informativeness, particularly about the timing and direction of introgression. Here we present a simple extension, D frequency spectrum or DFS, in which D is partitioned according to the frequencies of derived alleles. We use simulations over a large parameter space to show how DFS carries information about various factors. In particular, recent introgression reliably leads to a peak in DFS among low-frequency derived alleles, whereas violation of model assumptions can lead to a lack of signal at low frequencies. We also reanalyze published empirical data from six different animal and plant taxa, and interpret the results in the light of our simulations, showing how DFS provides novel insights. We currently see DFS as a descriptive tool that will augment both simple and sophisticated tests for introgression, but in the future it may be usefully incorporated into probabilistic inference frameworks.
Abstract 11330: High and Low Pacing Burden Associations for Pacemakers Implanted Post Tavr
Authors: Ethan Fry, Jerry Fan, Arthur Davis, Clinton Thurber, Roxanne Bautista, Bryce Rhodehouse, Jordan Potter, Lily Shirazi, Javier E Banchs
Journal: Circulation (2019)

Introduction: Transcatheter Aortic Valve Replacement (TAVR) is associated with increased risk of developing complete heart block (CHB) which could develop days after the procedure. Intermittent com...