tbuckley/cabot-search huggingface dataset:
Integrated proteogenomic analysis revealed the metabolic heterogeneity in noncancerous liver tissues of patients with hepatocellular carcinoma
Authors: Haotian Liao, Jinpeng Du, Haichuan Wang, Tian Lan, Jiajie Peng, Zhenru Wu, Kefei Yuan, Yong Zeng
Journal: Journal of Hematology & Oncology (2021)

Abstract Understanding the adjacent liver microenvironment of hepatocellular carcinoma (HCC) with possible metastasis tendency might provide a strategy for risk classification of patients and potential therapies by converting the unique metastasis-inclined microenvironment to a metastasis-averse one. In this study, we performed an integrated proteogenomic analysis to have a comprehensive view on the heterogeneity of hepatic microenvironment contributing to HCC metastasis. Pairing mRNA-protein analysis revealed consistent and discordant mRNA-protein expressions in metabolism regulations and cancer-related pathways, respectively. Proteomic profiling identified three subgroups associated with the recurrence-free survival of patients. These proteomic subgroups demonstrated distinct features in metabolic reprogramming, which was potentially modified by epigenetic alterations. This study raises the point of metabolic heterogeneity in HCC noncancerous tissues and may offer a new perspective on HCC treatment.
Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci
Authors: Feng-Hua Lv, Yin-Hong Cao, Guang-Jian Liu, Ling-Yun Luo, Ran Lu, Ming-Jun Liu, Wen-Rong Li, Ping Zhou, Xin-Hua Wang, Min Shen, Lei Gao, Jing-Quan Yang, Hua Yang, Yong-Lin Yang, Chang-Bin Liu, Peng-Cheng Wan, Yun-Sheng Zhang, Wen-Hui Pi, Yan-Ling Ren, Zhi-Qiang Shen, Feng Wang, Yu-Tao Wang, Jin-Quan Li, Hosein Salehian-Dehkordi, Eer Hehua, Yong-Gang Liu, Jian-Fei Chen, Jian-Kui Wang, Xue-Mei Deng, Ali Esmailizadeh, Mostafa Dehghani-Qanatqestani, Hadi Charati, Maryam Nosrati, Ondřej Štěpánek, Hossam E Rushdi, Ingrid Olsaker, Ino Curik, Neena A Gorkhali, Samuel R Paiva, Alexandre R Caetano, Elena Ciani, Marcel Amills, Christina Weimann, Georg Erhardt, Agraw Amane, Joram M Mwacharo, Jian-Lin Han, Olivier Hanotte, Kathiravan Periasamy, Anna M Johansson, Jón H Hallsson, Juha Kantanen, David W Coltman, Michael W Bruford, Johannes A Lenstra, Meng-Hua Li
Journal: Molecular Biology and Evolution (2021)

Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3'-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep.
173P Pseudotime dynamics in pancreatic ductal adenocarcinoma reveal different mechanisms of hindrance in immunity through bifurcation of regulatory and cytotoxic T-cell differentiation
Authors: A.K. Jainarayanan, N. Mouroug Anand, E.H. Arbe-Barnes, R. Bashford-Rogers, E. Abu-Shah, M.L. Dustin, S. Sivakumar
Journal: Annals of Oncology (2021)
A functional BCI model by the P2731 working group: control interface
Authors: Chuck Easttom, Luigi Bianchi, Davide Valeriani, Chang S. Nam, Ali Hossaini, Dariusz Zapała, Avid Roman-Gonzalez, Avinash K Singh, Alberto Antonietti, Guillermo Sahonero-Alvarez, Pradeep Balachandran
Journal: Brain-Computer Interfaces (2021)

In order to facilitate communication and collaboration between researchers, Brain–computer interfaces (BCI) require a generally applicable functional model as well as a common vocabulary. The IEEE P2731 working group is in the process of developing such a functional model and a lexicon of BCI terminology. Such a functional model has multiple aspects including the control interface, physiology, transducers, etc. This current paper focuses on the control interface aspects of that model. Having a generally applicable control interface model will facilitate interdisciplinar y research and communication. The control interface is a critical part of the functional model and is described in this current paper. The control interface presented intentionally is intentionally kept general in order to be widely applicable. Some details are specific to a particular application and are thus left to those applications. It does contain the encoder (which also contains a decoder), with a feedback submodule.
Research in brief
Authors: Sharmila Devi
Journal: The Lancet Infectious Diseases (2021)

Clinicians might have a new tool to predict which patients who test positive for SARS-CoV-2 will remain asymptomatic and who will develop symptoms. A study showed that low blood levels of a lipid, sphingosine, are linked with development of COVID-19 symptoms. High levels of the lipid and a protein used in its production, acid ceramidase (AC), were associated with asymptomatic infections, and some 75% of asymptomatic patients had high AC levels. Using blood levels of sphingosine has a 99% probability of correctly determining who will suffer from disease symptoms.
Effect of Mavacamten on Echocardiographic Features in Symptomatic Patients With Obstructive Hypertrophic Cardiomyopathy
Authors: Sheila M. Hegde, Steven J. Lester, Scott D. Solomon, Michelle Michels, Perry M. Elliott, Sherif F. Nagueh, Lubna Choudhury, David Zemanek, Donna R. Zwas, Daniel Jacoby, Andrew Wang, Carolyn Y. Ho, Wanying Li, Amy J. Sehnert, Iacopo Olivotto, Theodore P. Abraham
Journal: Journal of the American College of Cardiology (2021)
An Association between Positive Airway Pressure Device Manufacturer and Incident Cancer? A Secondary Data Analysis
Authors: Tetyana Kendzerska, Richard S. Leung, Mark I. Boulos, Daniel I. McIsaac, Brian J. Murray, Gregory L. Bryson, Robert Talarico, Atul Malhotra, Andrea S. Gershon, Constance Mackenzie, Marcus Povitz
Journal: American Journal of Respiratory and Critical Care Medicine (2021)

"An Association between Positive Airway Pressure Device Manufacturer and Incident Cancer? A Secondary Data Analysis." American Journal of Respiratory and Critical Care Medicine, 204(12), pp. 1484–1488
122MO Nivolumab (NIVO) + ipilimumab (IPI) as first-line (1L) treatment (tx) for patients (pts) with advanced NSCLC (aNSCLC) and baseline (BL) brain metastases (mets): Intracranial and systemic outcomes from CheckMate 227 Part 1
Authors: M. Reck, T.E. Ciuleanu, A. Pluzanski, J.S. Lee, R. Bernabe Caro, H. Linardou, J. Burgers, C. Gallardo, M. Nishio, S. Peters, L.G. Paz-Ares, M.D. Hellmann, H. Borghaei, S.S. Ramalingam, K. O’Byrne, N. Hu, J. Bushong, L. Eccles, D. Grootendorst, J.R. Brahmer
Journal: Annals of Oncology (2021)
Abstract 16848: The Effect Of Rhabdomyomas On Underlying Cardiomyopathy: A Case Report
Authors: Krista Young, Michelle Staron, Rabia S Khan
Journal: Circulation (2021)

Case Presentation: Term male infant born to SARS-CoV-2 positive mother with infant testing negative. ECG for perinatal bradycardia revealed ventricular pre-excitation. Echocardiogram showed asymmetric LV hypertrophy with prominent trabeculations, subaortic narrowing with no pressure gradient, and normal biventricular systolic function. Rapid increase in RV pressure estimates and NT-proBNP in first week if life concerning for diastolic dysfunction. Anti-arrhythmic therapy initiated for SVT with subsequent resolution. Later, developed progressive LV dilation and systolic dysfunction. Myocardium showed regions resembling non-compaction and others concerning for infiltrative process. Cardiac MRI showed no obvious tumors, but rhabdomyomas could not be ruled out given similar appearance to myocardium. Due to worsening heart failure, everolimus therapy initiated to target potential rhabdomyomas while awaiting genetic testing for tuberous sclerosis. Subaortic narrowing and LV hypertrophy improved within days, and LV appearance became more consistent with non-compaction. Genetic testing revealed a TSC2 gene variant consistent with tuberous sclerosis. Systolic function improved, and patient discharged on afterload reduction. Echocardiogram 6 months post-discharge shows continued LV dilation and mild systolic dysfunction. Discussion: Although outflow obstruction and arrhythmias are common with cardiac rhabdomyomas and can cause dysfunction, our patient developed progressive dysfunction in the absence of outflow tract gradient or prolonged arrhythmia. As rhabdomyomas subsided, it became clearer that he had an underlying cardiomyopathy. We suspect that rhabdomyomas in the setting of abnormal myocardium led to abnormalities in myocardial contractility and compliance causing combined systolic and diastolic dysfunction. After complete resolution of rhabdomyomas, cardiac function has improved. However, he continues to have ventricular dilation and mild dysfunction attributable to cardiomyopathy. It is unlikely that mother’s SARS-CoV-2 infection played a role as infant tested negative and clinical picture was not consistent with myocarditis.
Covid-19: Do vaccines work against omicron—and other questions answered
Authors: Elisabeth Mahase
Journal: BMJ (2021)

Covid-19: Do vaccines work against omicron-and other questions answeredThe SARS-CoV-2 omicron variant, first detected South Africa on 24 November, has now been found in 57 countries.Elisabeth Mahase looks at what we know about it so far, including how well treatments and vaccines work Elisabeth Mahase What mutations does omicron have?Omicron's spike protein has at least 30 amino acid substitutions, three small deletions, and one small insertion, says the US Centers for Disease Control and Prevention.The CDC has highlighted four key mutations that may aid transmission: N501Y, H655Y, N679K, and P681H, the last of which has also been found in the alpha variant, while a different mutation at this position (P681R) is found in delta.
Corrigendum to: PCSK9 regulates expression of scavenger receptors and ox-LDL uptake in macrophages
Authors: Zufeng Ding, Xianwei Wang, Shijie Liu, Jiwani Shahanawaz, Sue Theus, Yubo Fan, Xiaoyan Deng, Sichang Zhou, Jawahar L Mehta
Journal: Cardiovascular Research (2021)
Bhlhe40: Gatekeeper of the GC
Authors: Stephen L. Nutt, Julie Tellier
Journal: The Journal of Experimental Medicine (2021)

The generation of high-affinity antibodies in the germinal center (GC) requires interplay between GC B cells and T follicular helper cells. Rauschmeier et al. (2021. J. Exp. Med.https://doi.org/10.1084/jem.20211406) report that Bhlhe40 restrains GC output through distinct regulatory roles in both arms of the response.
Overweight in the Dutch National Cohort of Long-Term Survivors of Childhood Cancer
Authors: Vincent G. Pluimakers, Jenneke E. Van Atteveld, Demi T.C. de Winter, Marta Fiocco, Rutger A.J. Nievelstein, Dorine Bresters, Margriet Van der Heiden-Van der Loo, Andrica de Vries, Geert O Janssens, Marloes Louwerens, Helena J. Van der Pal, Cecile M. Ronckers, Hanneke M. Van Santen, Birgitta Versluys, Leontien Kremer, Jacqueline J. Loonen, Wim J.E. Tissing, Eline Van Dulmen-Den Broeder, Marry M. van den Heuvel-Eibrink, Sebastian J.C.M.M. Neggers
Journal: Blood (2021)
A Review of Chronic Pelvic Pain in Women
Authors: Tushar Garg, Apurva Shrigiriwar
Journal: JAMA (2021)

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
Highlights from this issue
Authors: The Triumvirate
Journal: Thorax (2021)

This will be the Last Christmas that this particular Trimuvirate contributes Airwaves.So to save you from tears, we will give you something special.The shops have Christmas items on display and the old familiar hits of previous decades are playing to get shoppers in a festive mood.Nothing old or familiar in December's Thorax though-quite the reverse.We bring you the new, the innovative and the frankly curious.
Technical Details of Redo Aortic Valve Replacement using St. Jude Medical Mechanical Prosthesis in a Patient with Thrombosed Aortic Mechanical Prosthesis: A Video Presentation
Authors: Ujjwal K. Chowdhury, Niwin George, Lakshmi Kumari Sankhyan, Shikha Goja, Sumanth Raghuprakash, Shradha Gupta, Shweta Sharma, Niraj Nirmal Pandey
Journal: Clinical Cardiology and Cardiovascular Interventions (2021)

Current consensus guidelines of the AHA and ESC, uniformly recommend either type of prosthetic valve for patients aged 60 to 70 years and mechanical prosthesis for patients aged less than 60 years
35P PD-1+ and TIM-3+ T-cells differ in the expression of common γ-chain cytokine receptors after AHSCT in multiple myeloma patients
Authors: E. Batorov, A. Ineshina, V. Sergeevicheva, T. Aristova, S. Sizikova, G. Ushakova, A. Fedorova, E. Shevela, A. Ostanin, E. Chernykh
Journal: Annals of Oncology (2021)
Skeletal Muscle Myosin Is Procoagulant By Binding Factor XI Via Its A3 Domain and Enhancing Factor XI Activation By Thrombin
Authors: Hiroshi Deguchi, Shravan Morla, Jevgenia Zilberman-Rudenko, Andras Gruber, Owen J T McCarty, Priyanka Srivastava, David Gailani, John H. Griffin
Journal: Blood (2021)
Abstract 17057: <i>Tropheryma Whipplei</i> Endocarditis: A Diagnosis In Hindsight
Authors: Liam Johnstone, Zia Mehmood, Jo Porter
Journal: Circulation (2021)

Description of case: We report a case of Tropheryma whipplei endocarditis, a rare cause of blood-culture-negative infective endocarditis (BCNIE). Due to its rarity and lack of availability of diagnostic tests in district hospitals, the diagnosis remains challenging. The objective of this case report is to increase physician awareness of this pathogen. A 61-year-old man presented to the Emergency Department with central chest pain at rest. A 12-lead ECG demonstrated ST- segment depression in V4-V6 leads, and his serial troponin levels were raised. He was commenced on treatment for acute coronary syndrome and transferred to the Coronary Care Unit. An echocardiogram showed a 15mm x 15mm vegetation in the aortic valve with mild aortic regurgitation. His initial microbiology workup, which included two sets of blood cultures (pre-antibiotics), MRSA screen &amp; COVID-19 PCR, was negative. He was transferred to a cardiothoracic centre four days later. Pre-operative CT coronary angiogram showed severe three vessel coronary artery disease. He underwent triple coronary artery by-pass grafts and tissue aortic valve replacement. During early post-op recovery, he had fever episodes and an elevated C-reactive protein of 280 mg/L but normal white cell counts. He was treated with intravenous Tazocin for hospital-acquired pneumonia and discharged on doxycycline. Two weeks post-discharge, he had a positive 16S/18S PCR for Tropheryma whipplei on molecular analysis of the aortic valve. He was treated for Whipples endocarditis with a 4-week course of IV Ceftriaxone, followed by a 12-month course of oral Cotrimoxazole. The patient has reported doing well since the surgery. Discussion: Molecular assay with PCR of the heart valve is the mainstay of diagnosing Whipple’s endocarditis. There have been 5 previously reported cases of Whipple’s endocarditis in the United Kingdom in our knowledge. It is likely under-reported because of a reliance on tissue diagnosis. Preceding intestinal manifestations and arthralgia should raise its clinical suspicion for timely workup. Physician awareness of Whipple’s Endocarditis is paramount in investigating for this pathogen.
10. Cardiovascular Disease and Risk Management: <i>Standards of Medical Care in Diabetes—2022</i>
Journal: Diabetes Care (2021)

The American Diabetes Association (ADA) “Standards of Medical Care in Diabetes” includes the ADA’s current clinical practice recommendations and is intended to provide the components of diabetes care, general treatment goals and guidelines, and tools to evaluate quality of care. Members of the ADA Professional Practice Committee, a multidisciplinary expert committee (https://doi.org/10.2337/dc22-SPPC), are responsible for updating the Standards of Care annually, or more frequently as warranted. For a detailed description of ADA standards, statements, and reports, as well as the evidence-grading system for ADA’s clinical practice recommendations, please refer to the Standards of Care Introduction (https://doi.org/10.2337/dc22-SINT). Readers who wish to comment on the Standards of Care are invited to do so at professional.diabetes.org/SOC.
first death
Authors: Jordynn Klein
Journal: JAMA (2021)

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
A Case for Palliative Care and Addiction Specialists Collaboration and Joint Research
Authors: Natalie Moryl, Vivek Tim Malhotra
Journal: JAMA Network Open (2021)

Jessica S. Merlin, MD, PhD; Dmitry Khodyakov, PhD; Robert Arnold, MD; Hailey W. Bulls, PhD; Emily Dao, MS; Jennifer Kapo, MD, MSCE; Caroline King, PhD; Diane Meier, MD; Judith Paice, PhD, RN; Christine Ritchie, MD, MSPH; Jane M. Liebschutz, MD, MPH
Treatment of Immune Thrombocytopenia (ITP) with Eltrombopag - Results of the 4 th Interim Analysis of the German Non-Interventional Trial RISA
Authors: Oliver Meyer, Rudolf Schlag, Thomas Stauch, Bastian Fleischmann, Marcel Reiser, Dietrich Kaempfe, Timo Behlendorf, Manfred Welslau, Claudia Willy, Martina Stauch
Journal: Blood (2021)
Factors Associated with Renal Impairment at Diagnosis in Multiple Myeloma with Survival Trends over Last Two Decades
Authors: Sagar Rakshit, Radhika Bansal, Prashant Kapoor, Angela Dispenzieri, Morie A. Gertz, Martha Q. Lacy, Suzanne R. Hayman, Francis K. Buadi, Yi L. Hwa, Amie Fonder, Miriam A. Hobbs, Wilson I Gonsalves, Eli Muchtar, David Dingli, Taxiarchis Kourelis, Rahma M Warsame, Robert A. Kyle, S. Vincent Rajkumar, Shaji Kumar, Nelson Leung
Journal: Blood (2021)
Consultative Medicine — An Emerging Specialty for Patients with Perplexing Conditions
Authors: Linda N. Geng, Abraham Verghese, Jon C. Tilburt
Journal: New England Journal of Medicine (2021)

The emerging specialty of consultative medicine is rooted in generalism and aims to integrate the best of the Oslerian diagnostic tradition with the multidisciplinary collaboration and modern technologies needed to tackle uncertain, difficult, or complex diagnoses.
Breast Cancer Diagnostics, Therapy, and Outcomes in Sub-Saharan Africa: A Population-Based Registry Study
Authors: Walburga Yvonne Joko-Fru, Mirko Griesel, Nikolaus Christian Simon Mezger, Lucia Hämmerl, Tobias Paul Seraphin, Jana Feuchtner, Henry Wabinga, Guy N’da, Assefa Mathewos, Bakarou Kamaté, Judith Nsonde Malanda, Freddy Houéhanou Rodrigue Gnangnon, Gladys Chebet Chesumbai, Anne Korir, Cesaltina Lorenzoni, Annelle Zietsman, Margaret Ziona Borok, Biying Liu, Christoph Thomssen, Paul McGale, Ahmedin Jemal, Donald Maxwell Parkin, Eva Johanna Kantelhardt
Journal: Journal of the National Comprehensive Cancer Network (2021)

Background: Breast cancer (BC) is the most common cancer in sub-Saharan Africa (SSA). However, little is known about the actual therapy received by women with BC and their survival outcome at the population level in SSA. This study aims to describe the cancer-directed therapy received by patients with BC at the population level in SSA, compare these results with the NCCN Harmonized Guidelines for SSA (NCCN Harmonized Guidelines), and evaluate the impact on survival. Methods: Random samples of patients with BC (≥40 patients per registry), diagnosed from 2009 through 2015, were drawn from 11 urban population–based cancer registries from 10 countries (Benin, Congo, Cote d’Ivoire, Ethiopia, Kenya, Mali, Mozambique, Namibia, Uganda, and Zimbabwe). Active methods were used to update the therapy and outcome data of diagnosed patients (“traced patients”). Excess hazards of death by therapy use were modeled in a relative survival context. Results: A total of 809 patients were included. Additional information was traced for 517 patients (63.8%), and this proportion varied by registry. One in 5 traced patients met the minimum diagnostic criteria (cancer stage and hormone receptor status known) for use of the NCCN Harmonized Guidelines. The hormone receptor status was unknown for 72.5% of patients. Of the traced patients with stage I–III BC (n=320), 50.9% received inadequate or no cancer-directed therapy. Access to therapy differed by registry area. Initiation of adequate therapy and early-stage diagnosis were the most important determinants of survival. Conclusions: Downstaging BC and improving access to diagnostics and care are necessary steps to increase guideline adherence and improve survival for women in SSA. It will also be important to strengthen health systems and facilities for data management in SSA to facilitate patient follow-up and disease surveillance.