tbuckley/cabot-search huggingface dataset:
CDC Sexually Transmitted Infections Treatment Guidelines, 2021
Authors: Aniruddha Hazra, Maggie W. Collison, Andrew M. Davis
Journal: JAMA (2022)

This Clinical Guideline Synopsis discusses updated guidelines from the Centers for Disease Control and Prevention on the prevention, diagnosis, and management of sexually transmitted infections, specifically gonorrhea, chlamydia, Mycoplasma genitalium, and syphilis.
Masthead
Authors: Steven Echard, David Cohen, New York, Rohit Loomba, San Diego, Lewis Roberts, Hugo Rosen, Los Angeles, Jayant Talwalkar, Gianfranco Alpini, Carl Berg, Mark Durham, Atlanta Czaja, Nicholas Ga, Laurie Louis, Los Deleve, Juan Angeles, Marc Ghany, Wolfram Goessling, Richard Boston, Daryl T-Y Green, Hongliang Lau, Cara Mack, Laura Nagy, Irene Cleveland, Hong Ng, Tushar Kong, Michael Patel, Vienna Trauner, James Consulting Biostatistician, Hepatology Dziura, Harmeet Elsewhere -Basic Sciences, Kathleen Malhi, Irwin Corey, Steven Schenker, San Antonio, Paul Berk, Ny Montgomery Bissell, San Francisco, Andres Blei, Keith Lindor, Michael Nathanson, Anna Rutherford, Mary Rinella, Hepatology Highlights, Robert Brown, Robert Schwartz, Sonal Kumar, Ann Haran, Jennifer Hutchinson, James Macdiarmid, Erica Lowe, Bianca Hughes, Emili Malatesta, Stefan Ryter, Leon Adams, Estella Alonso, Frank Anania, Atlanta Ga, Jesper Andersen, Marco Arrese, Gavin Santiago, Sumeet Arteel, Matias Dallas, Jesus Banales, San Sebastian, Meena Spain, New Bansal, Thomas York, Simon Beaven, David Brenner, Naga Chalasani, Zhi-Nan Chen, Ann-Lii Cheng, John Chiang, Srinivasan Dasarathy, Paul Cleveland, Atlanta Dawson, Adrian Ga, St Bisceglie, Wen-Xing Louis, Daiming Ding, China Xi'an, Gen-Sheng Feng, Peter Ferenci, Peter Fickert, Robert Fontana, Ann Arbor, Mi Francis, Michael Fuchs, Michael Gale, Chandrashekhar Ghandi, Bin Gao, Shannon Bethesda, Lucy Glaser, Valerie Golden, New Gouon-Evans, Arash York, Atlanta Grakoui, Haitao Ga, Grace Guo, Sanjeev Guo, Theo Gupta, Anne Heller, Jay Hoofnagle, Phillip Bethesda, Pietro Richmond, Hartmuth Jaeschke, Cynthia Ju, Binita Denver, Canada Toronto, Los Kaplowitz, Saul Angeles, Atlanta Karpen, Andrew Keaveny, Rohit Kohli, Anna Kramvis, Jennifer Lai, Michelle Lai, Frank Lammert, Anne Larson, Konstantinos Lazaridis, Josh Levitsky, Simon Ling, Anna Lok, Kathy Mi, Shelly Loomes, Los Lu, Marco Marzioni, Alex Miethke, Tim Morgan, Cynthia Moylan, Michael Durham, Mindie Co, Stanford Nguyen, Guang Ning, Ran Oren, Israel Jerusalem, K Reddy, Barbara Rehermann, Shari Rogal, Kirsten Sadler, Shiv Sarin, Bernd Schnabl, Robert Schwabe, Vijay Shah, Morris Sherman, Canada Siddiqui, Siddarth Singh, Carlo Spirli, Ben Stanger, Todd Stravitz, Frank Richmond, Puneeta Tandon, Canada Tapper, Emmanuel Thomas, Natalie Torok, Tram Davis, Emmanuel Tsochatzis, Lisa Vanwagner, Hugo Vargas, Elizabeth Verna, Silvia Vilarinho, Michael Volk, Loma Linda, Li Wang, Hongyang Wang, Fusheng Wang, David Wang, Kymberly Louis, Rebecca Watt, Holger Wells, San Willenbring, Allan Francisco, Vincent Bronx, Hong Wong, Min Kong, Mengwei You, San Zhang, Lars Antonio, Yanqiao Zhang, Jiajun Zhao, Huiping Zhou, Ronald Sokol, Michael Aurora, Kimberly Fried, M Brown, Bruce Treasurer, Washington Luxon, M Councilors, Jorge Bezerra, Raymond Chung, Laurie Deleve, Julie Heimbach, John Lake, Lopa Mishra
Journal: Hepatology (2018)
Biological and technical factors in the assessment of blood-based tumor mutational burden (bTMB) in patients with NSCLC
Authors: Milou Schuurbiers, Zhongyun Huang, Senglor Saelee, Manana Javey, Leonie de Visser, Daan van den Broek, Michel van den Heuvel, Alexander F Lovejoy, Kim Monkhorst, Daniel Klass
Journal: Journal for ImmunoTherapy of Cancer (2022)

Patients treated with immunotherapy are at risk of considerable adverse events, and the ongoing struggle is to accurately identify the subset of patients who will benefit. Tumor mutational burden (TMB) has emerged as a promising predictive biomarker but requires tumor tissue which is not always available. Blood-based TMB (bTMB) may provide a minimally invasive assessment of mutational load. However, because of the required sequencing depth, bTMB analysis is costly and prone to false negative results. This study attempted to design a minimally sized bTMB panel, examined a counting-based method for bTMB in patients with stage I to IV non-small cell lung cancer (NSCLC) and evaluated both technical factors such as bTMB and tissue-based TMB (tTMB) cut-off, as well as sample-related factors such as cell-free DNA input mass which influence the correlation between bTMB and tTMB. Tissue, plasma, and whole blood samples collected as part of the LEMA trial (NCT02894853) were used in this study. Samples of 185 treatment naïve patients with stage I to IV NSCLC were sequenced at the Roche Sequencing Solutions with a custom panel designed for TMB, using reagents and workflows derived from the AVENIO Tumor Tissue and circulating tumor DNA Analysis Kits. A TMB panel of 1.1 Mb demonstrated highly accurate TMB high calls with a positive predictive value of 95% when using a tTMB cut-off of 16 mut/Mb, corresponding with 42 mut/Mb for bTMB. The positive per cent agreement (PPA) of bTMB was relatively low at 32%. In stage IV samples with at least 20 ng of cfDNA input, PPA of bTMB improved to 63% and minimizing the panel to a subset of 577 kb was possible while maintaining 63% PPA. Plasma samples with high bTMB values are highly correspondent with tTMB, whereas bTMB low results may also be the result of low tumor burden at earlier stages of disease as well as poorly shedding tumors. For advanced stages of disease, PPA (sensitivity) of bTMB is satisfactory in comparison to tTMB, even when using a panel of less than 600 kb, warranting consideration of bTMB as a predictive biomarker for patients with NSCLC eligible for immunotherapy in the future.
Generating 3D TOF-MRA volumes and segmentation labels using generative adversarial networks
Authors: Pooja Subramaniam, Tabea Kossen, Kerstin Ritter, Anja Hennemuth, Kristian Hildebrand, Adam Hilbert, Jan Sobesky, Michelle Livne, Ivana Galinovic, Ahmed A. Khalil, Jochen B. Fiebach, Dietmar Frey, Vince I. Madai
Journal: Medical Image Analysis (2022)

Deep learning requires large labeled datasets that are difficult to gather in medical imaging due to data privacy issues and time-consuming manual labeling. Generative Adversarial Networks (GANs) can alleviate these challenges enabling synthesis of shareable data. While 2D GANs have been used to generate 2D images with their corresponding labels, they cannot capture the volumetric information of 3D medical imaging. 3D GANs are more suitable for this and have been used to generate 3D volumes but not their corresponding labels. One reason might be that synthesizing 3D volumes is challenging owing to computational limitations. In this work, we present 3D GANs for the generation of 3D medical image volumes with corresponding labels applying mixed precision to alleviate computational constraints. We generated 3D Time-of-Flight Magnetic Resonance Angiography (TOF-MRA) patches with their corresponding brain blood vessel segmentation labels. We used four variants of 3D Wasserstein GAN (WGAN) with: 1) gradient penalty (GP), 2) GP with spectral normalization (SN), 3) SN with mixed precision (SN-MP), and 4) SN-MP with double filters per layer (c-SN-MP). The generated patches were quantitatively evaluated using the Fréchet Inception Distance (FID) and Precision and Recall of Distributions (PRD). Further, 3D U-Nets were trained with patch-label pairs from different WGAN models and their performance was compared to the performance of a benchmark U-Net trained on real data. The segmentation performance of all U-Net models was assessed using Dice Similarity Coefficient (DSC) and balanced Average Hausdorff Distance (bAVD) for a) all vessels, and b) intracranial vessels only. Our results show that patches generated with WGAN models using mixed precision (SN-MP and c-SN-MP) yielded the lowest FID scores and the best PRD curves. Among the 3D U-Nets trained with synthetic patch-label pairs, c-SN-MP pairs achieved the highest DSC (0.841) and lowest bAVD (0.508) compared to the benchmark U-Net trained on real data (DSC 0.901; bAVD 0.294) for intracranial vessels. In conclusion, our solution generates realistic 3D TOF-MRA patches and labels for brain vessel segmentation. We demonstrate the benefit of using mixed precision for computational efficiency resulting in the best-performing GAN-architecture. Our work paves the way towards sharing of labeled 3D medical data which would increase generalizability of deep learning models for clinical use.
Infectious diseases
Authors: M. Stoeckle
Journal: JAMA (1995)

Cryptosporidiosis is increasingly recognized to be a major cause of diarrheal disease in the United States. Cryptosporidiosis is a self-limited disease in immunocompetent persons, although symptoms may be prolonged, with an average duration of 2 weeks in patients who seek medical attention. In persons infected with the human immunodeficiency virus (HIV),<i>Cryptosporidium</i>causes a severe, unremitting diarrhea, often associated with biliary disease. The agent,<i>Cryptosporidium parvum</i>, is a protozoan parasite that is transmitted by fecally contaminated water and food and from person to person. The importance of cryptosporidiosis was dramatically highlighted in 1993 by a massive outbreak in Milwaukee, Wis, where an estimated 400 000 persons developed diarrheal disease due to contamination of the public water supply.<sup>1</sup>Cryptosporidial infection is endemic among domestic and wild animals, and the Milwaukee outbreak appeared to be due to spring runoff from livestock grazing areas into the municipal watershed. The cryptosporidial cysts are
Organellar homeostasis and innate immune sensing
Authors: Cassandra R. Harapas, Elina Idiiatullina, Mahmoud Al-Azab, Katja Hrovat-Schaale, Thomas Reygaerts, Annemarie Steiner, Pawat Laohamonthonkul, Sophia Davidson, Chien-Hsiung Yu, Lee Booty, Seth L. Masters
Journal: Nature reviews. Immunology (2022)
BONE METASTASES FROM HYPERNEPHROMA.
Journal: JAMA (1907)

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
Absence of familiarity triggers hallmarks of autism in mouse model through aberrant tail-of-striatum and prelimbic cortex signaling
Authors: Sebastian Krüttner, Antonio Falasconi, Sergio Valbuena, Ivan Galimberti, Tewis Bouwmeester, Silvia Arber, Pico Caroni
Journal: Neuron (2022)

Autism spectrum disorder (ASD) involves genetic and environmental components. The underlying circuit mechanisms are unclear, but behaviorally, aversion toward unfamiliarity, a hallmark of autism, might be involved. Here, we show that in Shank3ΔC/ΔC ASD model mice, exposure to novel environments lacking familiar features produces long-lasting failure to engage and repetitive behaviors upon re-exposure. Inclusion of familiar features at first context exposure prevented enhanced dopamine transients in tail of striatum (TS) and restored context-specific control of engagement to wild-type levels in Shank3ΔC/ΔC mice. Engagement upon context re-exposure depended on the activity in prelimbic cortex (PreL)-to-TS projection neurons in wild-type mice and was restored in Shank3ΔC/ΔC mice by the chemogenetic activation of PreL→TS projection neurons. Environmental enrichment prevented ASD-like phenotypes by obviating the dependence on PreL→TS activity. Therefore, novel context experience has a key role in triggering ASD-like phenotypes in genetically predisposed mice, and behavioral therapies involving familiarity and enrichment might prevent the emergence of ASD phenotypes.
Obinutuzumab Effective in Follicular Lymphoma, but at a Cost
Journal: Cancer Discovery (2017)

Abstract In a phase III trial involving more than 1,200 patients with follicular lymphoma, obinutuzumab plus chemotherapy reduced the risk of disease progression, relapse, or death by 34% compared with rituximab plus chemotherapy. However, patients receiving obinutuzumab experienced more serious side effects than those receiving rituximab.
Pathological Contributions to Medical Jurisprudence
Authors: W. B. Mushet
Journal: BMJ (1859)

as the parties are alive, I may confidently speak as to their present condition; arid I may say, that I know of no operation in surgery more successful, or capable of conferring greater benefit on society, than the great discovery of Stromeyer.CASE I. Talipes Equinuts: Foot resting on the Toe.(Re- ported in Lancet and llfedical Times, February 1844.)Mlrs.Mar-tin, of Newmarket, aged 46, about seven years since, after a severe attack of hysteria, or what was termed so, was left with rig,id contractions of the muscles at the back of the legs, whiclh had existed ever since.December 3rd, 1843.The heel was drawn up, the tarsal and metatarsal bones forming a straight line with the legs, the patienlt resting on the end of the great toe.Mechanical appa- ratus had from time to time been applied, without effecting the sliglhtest benefit; and she appeared to have abandoned all idea of ever walking.Having operated in several cases of this kind, I at once recommended it, to which she readily acceded.On the (lay above named, I divided both Achilles tendons, after the plan of Stromeyer, witlh but slight pain or loss of blood; they were found much enlarged and thickened; the feet were placedi in pasteboard splints; and on the third day, gentle extension was applied, so that on the seventh day, the feet were brouight to right angles with the legs, and the patient able to stanid.It is scarcely necessary to recapitulate the daily rapid pro- gress of this case.It is sufficient to state, that in six weeks sshe walked some distance to church, and was quite cured.In November 1857, I received a letter from her husband, in which lhe stated that the operation had continued up to that time most successful; that her feet were in perfect form; and that she could walk any distance, as well as she could before her deformity came on.There was no soreness left; nor did she ever feel any pain in the parts operated upon.CASE II.Talipes Varus: Feet resting on Outer Ankle.HenryWebb, of Dullingham, aged 8, was born with this deformity; he lhad never walked on the soles of the feet.An operation was perfornmed on February 26th, 1846. 1 divided both tendo Achillis, andcl treate(d the case in the usual way.He could walk wvell in six weeks.January 18359.This lad (now a fine man, a farm labourer, living at Dullingham) has a perfect cure.CASE III.James Hitchcock, aged 12, came under treatment on July :3rd, 1846.This wa-s a very severe case.
Breast Implants
Journal: JAMA (2000)

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
Medical Education and State Boards of Registration
Journal: JAMA (1918)

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
Periodic Paralysis
Authors: Hobart A. Reimann
Journal: JAMA (1964)

<h3>To the Editor:—</h3> The theory regarding the central neural origin of periodic paralysis (Editorial,<i>JAMA</i><b>186</b>:422 [Oct 26] 1963) is not new. Pudenz, McIntosh, and McEachern (1938) suspected that the defect responsible for paralysis lies in the central neural system. Disturbances in the hypophyseal-hypothalamic region are described in three other papers published by others, and cited in Gamstorp's essay.<sup>1</sup> It is uncertain if a primary neural disturbance influences the migration of potassium or if the reverse occurs. Anyhow, scant clinical attention has been given to sweating, fever, paresthesias, disturbed reflexes, ptosis, penile erections, mucosal congestion, thirst, polyuria, oliguria, anuria, hypotension, cardiac irregularities, and other autonomic responses incidental to episodes of periodic paralysis. A diencephalic disturbance may have a primary causal relation to periodic paralysis and to other periodic disorders.<sup>2</sup>
MEDICAL TEMPERANCE ASSOCIATION.
Journal: JAMA (1893)

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
Episodes of Diversification and Isolation in Island Southeast Asian and Near Oceanian Male Lineages
Authors: Monika Karmin, Rodrigo Flores, Lauri Saag, Georgi Hudjashov, Nicolas Brucato, Chelzie Crenna-Darusallam, Maximilian Larena, Phillip L Endicott, Mattias Jakobsson, J Stephen Lansing, Herawati Sudoyo, Matthew Leavesley, Mait Metspalu, François-Xavier Ricaut, Murray P Cox
Journal: Molecular Biology and Evolution (2022)

Island Southeast Asia (ISEA) and Oceania host one of the world's richest assemblages of human phenotypic, linguistic, and cultural diversity. Despite this, the region's male genetic lineages are globally among the last to remain unresolved. We compiled ∼9.7 Mb of Y chromosome (chrY) sequence from a diverse sample of over 380 men from this region, including 152 first reported here. The granularity of this data set allows us to fully resolve and date the regional chrY phylogeny. This new high-resolution tree confirms two main population bursts: multiple rapid diversifications following the region's initial settlement ∼50 kya, and extensive expansions <6 kya. Notably, ∼40-25 kya the deep rooting local lineages of C-M130, M-P256, and S-B254 show almost no further branching events in ISEA, New Guinea, and Australia, matching a similar pause in diversification seen in maternal mitochondrial DNA lineages. The main local lineages start diversifying ∼25 kya, at the time of the last glacial maximum. This improved chrY topology highlights localized events with important historical implications, including pre-Holocene contact between Mainland and ISEA, potential interactions between Australia and the Papuan world, and a sustained period of diversification following the flooding of the ancient Sunda and Sahul continents as the insular landscape observed today formed. The high-resolution phylogeny of the chrY presented here thus enables a detailed exploration of past isolation, interaction, and change in one of the world's least understood regions.
Single-cell eQTL analysis of activated T cell subsets reveals activation and cell type–dependent effects of disease-risk variants
Authors: Benjamin J. Schmiedel, Cristian Gonzalez-Colin, Vicente Fajardo, Job Rocha, Ariel Madrigal, Ciro Ramírez-Suástegui, Sourya Bhattacharyya, Hayley Simon, Jason A. Greenbaum, Bjoern Peters, Grégory Seumois, Ferhat Ay, Vivek Chandra, Pandurangan Vijayanand
Journal: Science Immunology (2022)

The impact of genetic variants on cells challenged in biologically relevant contexts has not been fully explored. Here, we activated CD4