tbuckley/cabot-search huggingface dataset:
Antibody-Coated Bacteria
Authors: Larry W. Rumans
Journal: JAMA (1977)

<h3>To the Editor.—</h3> The article entitled "Lessons Learned From a Patient: Changing Concepts Rather Than Facts" by Dr. Beccia et al (236:1268, 1976) is correct in its statement that many concepts relating to urinary tract infections which are considered to be established may, in fact, be incorrect. The authors describe a patient with a community-acquired urinary tract infection in whom a diagnosis of acute pyelonephritis was suspected on the basis of clinical presentation; however, the authors suggest that the infection was limited to the lower urinary tract. This supposition appears to rest primarily on the efficacy of the immunofluorescent method for the detection of antibody-coated bacteria (ACB) in urine. We have recently completed an evaluation of the immunofluorescent method for the detection of ACB in an unselected population by the study of consecutive urine specimens submitted to the diagnostic laboratory with colony counts of 10<sup>5</sup>/ml or more. The
Uncoupling histone H3K4 trimethylation from developmental gene expression via an equilibrium of COMPASS, Polycomb and DNA methylation
Authors: Delphine Douillet, Christie C. Sze, Caila Ryan, Andrea Piunti, Avani P. Shah, Michal Ugarenko, Stacy A. Marshall, Emily J. Rendleman, Didi Zha, Kathryn A. Helmin, Zibo Zhao, Kaixiang Cao, Marc A. Morgan, Benjamin D. Singer, Elizabeth T. Bartom, Edwin R. Smith, Ali Shilatifard
Journal: Nature Genetics (2020)
Optimizing use of theranostic nanoparticles as a life-saving strategy for treating COVID-19 patients
Authors: Rasha Itani, Mansour Tobaiqy, Achraf Al Faraj
Journal: Theranostics (2020)

On the 30 th of January 2020, the World Health Organization fired up the sirens against a fast spreading infectious disease caused by a newly discovered Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and gave this disease the name COVID-19.While there is currently no specific treatment for COVID-19, several off label drugs approved for other indications are being investigated in clinical trials across the globe.In the last decade, theranostic nanoparticles were reported as promising tool for efficiently and selectively deliver therapeutic moieties (i.e.drugs, vaccines, siRNA, peptide) to target sites of infection.In addition, they allow monitoring infectious sides and treatment responses using noninvasive imaging modalities.While intranasal delivery was proposed as the preferred administration route for therapeutic agents against viral pulmonary diseases, NP-based delivery systems offer numerous benefits to overcome challenges associated with mucosal administration, and ensure that these agents achieve a concentration that is many times higher than expected in the targeted sites of infection while limiting side effects on normal cells.In this article, we have shed light on the promising role of nanoparticles as effective carriers for therapeutics or immune modulators to help in fighting against COVID-19.
Successful Treatment of Mature T-Cell Lymphoma with Allogeneic Stem Cell Transplantation: The Largest Multicenter Retrospective Analysis
Authors: Neha Mehta-Shah, Stephanie Teja, Yu Tao, Amanda F. Cashen, Anne Beaven, Onder Alpdogan, Pierluigi Porcu, Mackenzie Wiggin, Kevin W Song, Musa Alzahrani, Parastoo B. Dahi, Alison J. Moskowitz, Steven M. Horwitz, Eric D. Jacobsen
Journal: Blood (2020)
Very late relapses in glioblastoma long-term survivors
Authors: O. Baehr, U. Herrlinger, M. Weller, J. P. Steinbach
Journal: Journal of Clinical Oncology (2009)

e13017 Background: Long-term survival of patients with histologically confirmed glioblastoma is a rare event with figures in the range of 2–3% for 5-year survival. Prognosis and further clinical course of these patients beyond 5 years after diagnosis are in essence unknown with only anecdotal reports of patients surviving for 10 years or more. Methods: We here report on the extended follow-up (mean, 139.4 months) of a cohort of 10 glioblastoma long-term survivors. Retrospective central histology, clinical monitoring, and regular magnetic resonance imaging were done. Results: A total of 5 patients of the 9 patients alive at a previous analysis have died during the extended follow-up. Four of these patients died from recurrent tumor. One patient died from leukoencephalopathy-associated complications without evidence of tumor progression. Details concerning the occurrence of relapses and their treatment are displayed in table 1. Notably, very late relapses occurred in three patients after 118, 124, and 126 months of progression-free survival. Thus, from the original cohort of 10 patients only 3 remain free from recurrence after the extended follow up of more than 10 years. Conclusions: Very late relapses pose a serious threat for glioblastoma long-term survivors and call for continuous vigilance. The maintenance of a tight control schedule even in patients surviving for more than 10 years should be considered. [Table: see text] No significant financial relationships to disclose.
Гендерные и возрастные особенности морфологического состояния слизистой оболочки толстой кишки больных хроническими воспалительными заболеваниями кишечника
Authors: Yu.A. Gaydar, M.V. Stoykevich, O.V. Sіmonova, D.F. Milostiva, M.V. Tіtova, N.V. Nedzvetska
Journal: GASTROENTEROLOGY (2020)

Актуальность. Важность проблемы хронических заболеваний кишечника на сегодняшний день не подлежит сомнению. Это подтверждается этиологией неизвестного генеза, отсутствием специфического лечения, развитием ­угрожающих жизни осложнений, необходимостью проведения длительной, часто пожизненной, дорогой терапии и неблагоприятным прогнозом. Большую часть больных составляют лица молодого трудоспособного возраста, средний возраст которых — 20–35 лет. Но в 30–50 % случаев заболевание может проявиться в любом возрасте. Цель: оценить особенности морфологического состояния слизистой оболочки толстой кишки больных при хронических воспалительных заболеваниях кишечника в зависимости от возраста и пола. Материалы и методы. Для исследования были использованы биоптаты слизистой оболочки толстой кишки больных, находившихся на лечении в отделении заболеваний кишечника ГУ «Институт гастроэнтерологии НАМН Украины» и распределенных по полу и возрасту. Результаты. При анализе морфофункционального состояния слизистой оболочки больных были выявлены признаки хронического неспецифического воспаления умеренной и четко выраженной степени выраженности при неспецифическом язвенном колите. При болезни Крона как у мужчин, так и у женщин отмечались признаки хронического неспецифического воспаления первой степени. Аллергический компонент воспаления, представленный эозинофилами, был отмечен во всех случаях. Также отмечались нарушение архитектоники крипт, истощение муцинового слоя и нарушение целостности эпителия. Выводы. Пациенты молодого возраста имели более четко выраженную морфологическую картину хронического воспаления слизистой оболочки толстой кишки при неспецифическом язвенном колите. Мужчины, больные неспецифическим язвенным колитом, имеют большее истощение слоя муцина и нарушение архитектоники крипт в молодом и среднем возрасте, а при болезни Крона такие признаки чаще встречаются у женщин.
Next Generation Sequencing Identifies Smoldering Multiple Myeloma Patients with a High Risk of Disease Progression
Authors: Mark Bustoros, Jihye Park, Karma Ziad Salem, Chia-Jen Liu, Marzia Capelletti, Daisy Huynh, Yu-Tzu Tai, Tarek H Mouhieddine, Samuel Freeman, Gavin Ha, Justin Rhoades, Sarah Reed, Gregory Gydush, Denisse Rotem, Adriana Perilla Glen, Patrick Henrick, Aaron Caola, Bradley Rivotto, Alexandra Savell, Kimberly Noonan, Kaitlen Reyes, Antonio Sacco, Cody J Boehner, Houry Leblebjian, David Liu, Elizabeth A Morgan, Aldo M. Roccaro, Claudia Paba-Prada, Eliezer Van Allen, Christopher Love, Viktor Adalsteinsson, Jacob Laubach, Robert Schlossman, Nikhil Munshi, Paul G Richardson, Kenneth C Anderson, Shaji K Kumar, Gad Getz, Irene M Ghobrial, Salomon Manier
Journal: Blood (2017)
Comparison Between Rituximab Treatment for New-Onset Generalized Myasthenia Gravis and Refractory Generalized Myasthenia Gravis
Authors: Susanna Brauner, Ann Eriksson-Dufva, Max Albert Hietala, Thomas Frisell, Rayomand Press, Fredrik Piehl
Journal: JAMA Neurology (2020)

Use of biologic agents in generalized myasthenia gravis is generally limited to therapy-refractory cases; benefit in new-onset disease is unknown.To assess rituximab in refractory and new-onset generalized myasthenia gravis and rituximab vs conventional immunotherapy in new-onset disease.A retrospective cohort study with prospectively collected data was conducted on a county-based community sample at Karolinska University Hospital, Stockholm, Sweden. Participants included 72 patients with myasthenia gravis, excluding those displaying muscle-specific tyrosine kinase antibodies, initiating rituximab treatment from January 1, 2010, to December 31, 2018, and patients with new-onset disease initiating conventional immunotherapy from January 1, 2003, to December 31, 2012, with 12 months or more of observation time. The present study was conducted from March 1, 2019, to January 31, 2020.Treatment with low-dose rituximab (most often 500 mg every 6 months) or conventional immunosuppressants.Time to remission (main outcome) as well as use of rescue therapies or additional immunotherapies and time in remission (secondary outcomes).Of the 72 patients included, 31 patients (43%) were women; mean (SD) age at treatment start was 60 (18) years. Twenty-four patients had received rituximab within 12 months of disease onset and 48 received rituximab at a later time, 34 of whom had therapy-refractory disease. A total of 26 patients (3 [12%] women; mean [SD] age, 68 [11] years at treatment start) received conventional immunosuppressant therapy. Median time to remission was shorter for new-onset vs refractory disease (7 vs 16 months: hazard ratio [HR], 2.53; 95% CI, 1.26-5.07; P = .009 after adjustment for age, sex, and disease severity) and for rituximab vs conventional immunosuppressant therapies (7 vs 11 months: HR, 2.97; 95% CI, 1.43-6.18; P = .004 after adjustment). In addition, fewer rescue therapy episodes during the first 24 months were required (mean [SD], 0.38 [1.10] vs 1.31 [1.59] times; mean difference, -1.26; 95% CI, -1.97 to -0.56; P < .001 after adjustment), and a larger proportion of patients had minimal or no need of additional immunotherapies (70% vs 35%; OR, 5.47; 95% CI, 1.40-21.43; P = .02 after adjustment). Rates of treatment discontinuation due to adverse events were lower with rituximab compared with conventional therapies (3% vs 46%; P < .001 after adjustment).Clinical outcomes with rituximab appeared to be more favorable in new-onset generalized myasthenia gravis, and rituximab also appeared to perform better than conventional immunosuppressant therapy. These findings suggest a relatively greater benefit of rituximab earlier in the disease course. A placebo-controlled randomized trial to corroborate these findings is warranted.
Longitudinal hematologic and immunologic variations associated with the progression of COVID-19 patients in China
Authors: Ruchong Chen, Ling Sang, Mei Jiang, Zhaowei Yang, Nan Jia, Wanyi Fu, Jiaxing Xie, Weijie Guan, Wenhua Liang, Zhengyi Ni, Yu Hu, Lei Liu, Hong Shan, Chunliang Lei, Yixiang Peng, Li Wei, Yong Liu, Yahua Hu, Peng Peng, Jianming Wang, Jiyang Liu, Zhong Chen, Gang Li, Zhijian Zheng, Shaoqin Qiu, Jie Luo, Changjiang Ye, Shaoyong Zhu, Jinping Zheng, Nuofu Zhang, Yimin Li, Jianxing He, Jing Li, Shiyue Li, Nanshan Zhong
Journal: Journal of Allergy and Clinical Immunology (2020)

Crucial roles of hematologic and immunologic responses in progression of coronavirus disease 2019 (COVID-19) remain largely unclear.We sought to address the dynamic changes in hematologic and immunologic biomarkers and their associations with severity and outcomes of COVID-19.A retrospective study including 548 patients with COVID-19 with clarified outcome (discharged or deceased) from a national cohort in China was performed. Cross-sectional and longitudinal variations were compared and the associations with different severity and outcomes were analyzed.On admission, the counts of lymphocytes, T-cell subsets, eosinophils, and platelets decreased markedly, especially in severe/critical and fatal patients. Increased neutrophil count and neutrophils-to-lymphocytes ratio were predominant in severe/critical cases or nonsurvivors. During hospitalization, eosinophils, lymphocytes, and platelets showed an increasing trend in survivors, but maintained lower levels or dropped significantly afterwards in nonsurvivors. Nonsurvivors kept a high level or showed an upward trend for neutrophils, IL-6, procalcitonin, D-dimer, amyloid A protein, and C-reactive protein, which were kept stable or showed a downward trend in survivors. Positive correlation between CD8+ T-cell and lymphocytes count was found in survivors but not in nonsurvivors. A multivariate Cox regression model suggested that restored levels of lymphocytes, eosinophils, and platelets could serve as predictors for recovery, whereas progressive increases in neutrophils, basophils, and IL-6 were associated with fatal outcome.Hematologic and immunologic impairment showed a significantly different profile between survivors and nonsurvivors in patients with COVID-19 with different severity. The longitudinal variations in these biomarkers could serve to predict recovery or fatal outcome.
A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors
Authors: Michal Slyper, Caroline B. M. Porter, Orr Ashenberg, Julia Waldman, Eugene Drokhlyansky, Isaac Wakiro, Christopher Smillie, Gabriela Smith-Rosario, Jingyi Wu, Danielle Dionne, Sébastien Vigneau, Judit Jané-Valbuena, Timothy L. Tickle, Sara Napolitano, Mei-Ju Su, Anand G. Patel, Asa Karlstrom, Simon Gritsch, Masashi Nomura, Avinash Waghray, Satyen H. Gohil, Alexander M. Tsankov, Livnat Jerby-Arnon, Ofir Cohen, Johanna Klughammer, Yanay Rosen, Joshua Gould, Lan Nguyen, Matan Hofree, Peter J. Tramontozzi, Bo Li, Catherine J. Wu, Benjamin Izar, Rizwan Haq, F. Stephen Hodi, Charles H. Yoon, Aaron N. Hata, Suzanne J. Baker, Mario L. Suvà, Raphael Bueno, Elizabeth H. Stover, Michael R. Clay, Michael A. Dyer, Natalie B. Collins, Ursula A. Matulonis, Nikhil Wagle, Bruce E. Johnson, Asaf Rotem, Orit Rozenblatt-Rosen, Aviv Regev
Journal: Nature Medicine (2020)

Abstract Single-cell genomics is essential to chart tumor ecosystems. Although single-cell RNA-Seq (scRNA-Seq) profiles RNA from cells dissociated from fresh tumors, single-nucleus RNA-Seq (snRNA-Seq) is needed to profile frozen or hard-to-dissociate tumors. Each requires customization to different tissue and tumor types, posing a barrier to adoption. Here, we have developed a systematic toolbox for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Seq, respectively. We analyzed 216,490 cells and nuclei from 40 samples across 23 specimens spanning eight tumor types of varying tissue and sample characteristics. We evaluated protocols by cell and nucleus quality, recovery rate and cellular composition. scRNA-Seq and snRNA-Seq from matched samples recovered the same cell types, but at different proportions. Our work provides guidance for studies in a broad range of tumors, including criteria for testing and selecting methods from the toolbox for other tumors, thus paving the way for charting tumor atlases.
Ethnic differences in viral dominance patterns in patients with hepatitis B virus and hepatitis C virus dual infection
Authors: Gabriele Rockenbach, Alexandre JosÉ De Melo Neto, Nêmora Tregnago Barcellos, Fernando Herz Wolff
Journal: Hepatology (2011)

We read with great interest the article entitled "Ethnic Differences in Viral Dominance Patterns in Patients with Hepatitis B Virus and Hepatitis C Virus Dual Infection," recently published by Nguyen et al. in this journal. 1 The study was designed to evaluate and compare the demographic, clinical, and viral characteristics of multiethnic patients infected by hepatitis virus admitted at two large liver centers in the United States. The investigators defined the study design as a matched case-control study, in which the case group included patients with hepatitis B virus (HBV) and hepatitis C virus (HCV) dual infection, and the control group comprised patients with HBV monoinfection. However, in our opinion, there is an important methodological issue in the reported data: The main conclusion of the article was not about the comparison between cases and controls, but rather it underscored a secondary analysis with cases only in which ethnic differences were examined in terms of viral dominance patterns among HBV and HCV dual-infected patients. It is our opinion that the investigators deviated from the scope of the case-control study originally proposed, because it is clear that the investigation was not delineated to test the hypothesis that ended up becoming the core conclusion, including the title of the article. Therefore, the investigators' conclusions regarding viral dominance were not consistent with the a priori study aims proposed. Gabriele Rockenbach M.Sc.*, Alexandre JosÉ De Melo Neto M.D.*, Nêmora Tregnago Barcellos M.D., Ph.D.*, Fernando Herz Wolff M.D., Ph.D.*, * Postgraduate Studies in Epidemiology, School of Medicine, Universidade Federal do Rio Grande do Sul, Ramiro Barcelos, Brazil.
Randomized Trial of Text Messaging to Reduce Early Discontinuation of Adjuvant Aromatase Inhibitor Therapy in Women With Early-Stage Breast Cancer: SWOG S1105
Authors: Dawn L. Hershman, Joseph M. Unger, Grace Clarke Hillyer, Anna Moseley, Kathryn B. Arnold, Shaker R. Dakhil, Benjamin T. Esparaz, Ming C. Kuan, Mark L. Graham, Douglas M. Lackowski, William J. Edenfield, Zoneddy R. Dayao, N. Lynn Henry, Julie R. Gralow, Scott D. Ramsey, Alfred I. Neugut
Journal: Journal of Clinical Oncology (2020)

Nonadherence to aromatase inhibitors (AIs) for breast cancer is common and increases the risk of recurrence. Text messaging increases adherence to medications for chronic conditions.
Association between rosacea and cardiometabolic disease: A systematic review and meta-analysis
Authors: Qi Chen, Xiao Shi, Yan Tang, Ben Wang, Hong-fu Xie, Wei Shi, Ji Li
Journal: Journal of the American Academy of Dermatology (2020)

BackgroundRosacea is recognized as a chronic inflammatory cutaneous disorder associated with multiple systemic illnesses. However, the association between rosacea and cardiometabolic disease (CMD) remains controversial.ObjectiveTo evaluate the association between rosacea and CMD by a systematic review and meta-analysis.MethodsA comprehensive search of studies published before October 16, 2019, was performed in databases of PubMed, Embase, Cochrane Library, and Web of Science. The pooled risk ratios or standardized mean differences were calculated.ResultsThirteen studies were included, representing 50,442 patients with rosacea. Patients with rosacea had higher prevalence of dyslipidemia, higher prevalence of hypertension, higher total cholesterol, higher low-density lipoprotein, higher triglycerides, higher systolic blood pressure, higher diastolic blood pressure, and higher fasting blood glucose. Rosacea was not associated with ischemic heart disease, stroke, diabetes, and high-density lipoprotein.LimitationsNo subgroup analysis could be performed according to the subtypes and severity of rosacea.ConclusionsRosacea showed a correlation with hypertension and dyslipidemia but not with ischemic heart disease, stroke, or diabetes. We advocate screening for CMD indicators among patients with rosacea, which may be helpful for diagnosis and appropriate treatment at an early stage of disease. Rosacea is recognized as a chronic inflammatory cutaneous disorder associated with multiple systemic illnesses. However, the association between rosacea and cardiometabolic disease (CMD) remains controversial. To evaluate the association between rosacea and CMD by a systematic review and meta-analysis. A comprehensive search of studies published before October 16, 2019, was performed in databases of PubMed, Embase, Cochrane Library, and Web of Science. The pooled risk ratios or standardized mean differences were calculated. Thirteen studies were included, representing 50,442 patients with rosacea. Patients with rosacea had higher prevalence of dyslipidemia, higher prevalence of hypertension, higher total cholesterol, higher low-density lipoprotein, higher triglycerides, higher systolic blood pressure, higher diastolic blood pressure, and higher fasting blood glucose. Rosacea was not associated with ischemic heart disease, stroke, diabetes, and high-density lipoprotein. No subgroup analysis could be performed according to the subtypes and severity of rosacea. Rosacea showed a correlation with hypertension and dyslipidemia but not with ischemic heart disease, stroke, or diabetes. We advocate screening for CMD indicators among patients with rosacea, which may be helpful for diagnosis and appropriate treatment at an early stage of disease.
Abstract 15371: Prevalence and Electronic Health Record-Based Phenotype of Loss-Of-Function Genetic Variants in Arrhythmogenic Cardiomyopathy-Associated Genes in 61,000 Individuals
Authors: Christopher M Haggerty, Wilson Young, Cynthia A James, Hugh Calkins, Linyuan Jing, Dustin N Hartzel, Joseph B Leader, Brandon K Fornwalt
Journal: Circulation (2018)

Introduction: Arrhythmogenic cardiomyopathy (ACM) is associated with genetic variants in desmosome genes. Incidental findings of pathogenic/likely pathogenic (P/LP) variants in these genes, primari...
Adjunct Immunotherapies for the Management of Severely Ill COVID-19 Patients
Authors: Srinivasa Reddy Bonam, Srini V. Kaveri, Anavaj Sakuntabhai, Laurent Gilardin, Jagadeesh Bayry
Journal: Cell Reports Medicine (2020)

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has infected millions, with more than 275,000 fatal cases as of May 8, 2020. Currently, there are no specific COVID-19 therapies. Most patients depend on mechanical ventilation. Current COVID-19 data clearly highlight that cytokine storm and activated immune cell migration to the lungs characterize the early immune response to COVID-19 that causes severe lung damage and development of acute respiratory distress syndrome. In view of uncertainty associated with immunosuppressive treatments, such as corticosteroids and their possible secondary effects, including risks of secondary infections, we suggest immunotherapies as an adjunct therapy in severe COVID-19 cases. Such immunotherapies based on inflammatory cytokine neutralization, immunomodulation, and passive viral neutralization not only reduce inflammation, inflammation-associated lung damage, or viral load but could also prevent intensive care unit hospitalization and dependency on mechanical ventilation, both of which are limited resources.Graphical abstract