tbuckley/cabot-search huggingface dataset:
Perturbations of the Gut Microbiome and Metabolome in Children with Calcium Oxalate Kidney Stone Disease
Authors: Michelle R. Denburg, Kristen Koepsell, Jung-Jin Lee, Jeffrey Gerber, Kyle Bittinger, Gregory E. Tasian
Journal: Journal of the American Society of Nephrology (2020)

Significance Statement Although antibiotics have been associated with an increased risk of kidney stones, particularly early in life, perturbations of the gut microbiome and metabolome in early-onset nephrolithiasis have not been investigated. Using shotgun metagenomic sequencing and untargeted metabolomics of stool samples in a study of 44 children with kidney stones and 44 controls matched for age, sex, and race, the authors found that 31 bacterial taxa—including seven butyrate-producing taxa and three that degrade oxalate—were less abundant among children with calcium oxalate stones. Levels of 18 metabolites differed between cases and controls and correlated with the fecal bacteria that were less abundant among children with nephrolithiasis. Such disruptions in the gut microbiome and metabolome may thus be determinants of early-onset disease and may explain the association between antibiotics and nephrolithiasis. Background The relationship between the composition and function of gut microbial communities and early-onset calcium oxalate kidney stone disease is unknown. Methods We conducted a case-control study of 88 individuals aged 4–18 years, which included 44 individuals with kidney stones containing ≥50% calcium oxalate and 44 controls matched for age, sex, and race. Shotgun metagenomic sequencing and untargeted metabolomics were performed on stool samples. Results Participants who were kidney stone formers had a significantly less diverse gut microbiome compared with controls. Among bacterial taxa with a prevalence &gt;0.1%, 31 taxa were less abundant among individuals with nephrolithiasis. These included seven taxa that produce butyrate and three taxa that degrade oxalate. The lower abundance of these bacteria was reflected in decreased abundance of the gene encoding butyryl-coA dehydrogenase ( P =0.02). The relative abundance of these bacteria was correlated with the levels of 18 fecal metabolites, and levels of these metabolites differed in individuals with kidney stones compared with controls. The oxalate-degrading bacterial taxa identified as decreased in those who were kidney stone formers were components of a larger abundance correlation network that included Eggerthella lenta and several Lactobacillus species. The microbial ( α ) diversity was associated with age of stone onset, first decreasing and then increasing with age. For the individuals who were stone formers, we found the lowest α diversity among individuals who first formed stones at age 9–14 years, whereas controls displayed no age-related differences in diversity. Conclusions Loss of gut bacteria, particularly loss of those that produce butyrate and degrade oxalate, associates with perturbations of the metabolome that may be upstream determinants of early-onset calcium oxalate kidney stone disease.
A meta-analysis on interparental conflict, parenting, and child adjustment in divorced families: Examining mediation using meta-analytic structural equation models
Authors: Rianne van Dijk, Inge E. van der Valk, Maja Deković, Susan Branje
Journal: Clinical Psychology Review (2020)

Every year, parental divorce becomes the reality of many families. The aim of this meta-analysis was to identify post-divorce family processes to explain child functioning. Both direct and indirect associations between interparental conflict, parenting, and child adjustment were examined. After a systematic search for articles published before October 2019, we coded 2257 correlations in 115 samples of N = 24,854 divorced families. Analyses consisted of: (1) Performing multiple three-level meta-analyses to calculate the bivariate correlations between interparental conflict, parenting (i.e., support, hostility, structuring, intrusiveness, parent-child relationship quality, parent-child conflict, and role diffusion) and child psychosocial adjustment. (2) Testing four meta-analytic structural equation models in which parenting dimensions were examined as potential mediators. First, results showed that correlations between interparental conflict, parenting, and child adjustment were mostly significant, in the expected direction, and of small effect size. Second, parental support, hostility, structuring, intrusiveness, and role diffusion indeed served as mediating mechanisms underlying the persistent link between interparental conflict and children's internalizing and externalizing problems. This was not true for dyadic parent-child processes. Third, our findings hinted towards a stronger impact of negative versus positive parenting behaviors, and parental role diffusion was considered a particular risk in the context of post-divorce interparental conflict.
AB1391 Obstacles facing evidence based medicine in physical medicine and rehabilitation: from opinion and knowledge to practice
Authors: M. Babaee, S.A. Raeissadat, S.M. Rayegani, M.H. Bahrami
Journal: Annals of the Rheumatic Diseases (2018)

<h3>Background</h3> Evidence-based medicine (EBM) is a new approach to medicine. Up to now, there have been fewavailable articles about specialists' EBM status, specifically the status of physiatrists in the area of EBM. <h3>Objectives</h3> To determine the present status of physiatrists' attitudes, knowledge and skill in the area of EBM andthe existing obstacles <h3>Methods</h3> The cross-sectional study was performed among physiatrists in Iran. The valid and reliablequestionnaire contained 25 questions in 8 fields including demographic and professional information, point ofview regarding EBM, familiarity with databases, educational history and information about EBM, use ofscientific resources, scientific evidence usage, and the amount of access to resources. <h3>Results</h3> One hundred twenty-eight questionnaires were completed (response percentage 52.2%). In total, 48.4%specialists had attended EBM workshops and 89.6% of people were familiar with medical search engines. Theamount of familiarity with databases was mostly with MEDLINE/PubMed (52.3%). Respondents mainly had apositive point of view towards EBM. Those who had access to databases at work or somewhere out of home hada more positive attitude (p=0.002). Those who had attended EBM workshops and members of faculty also hadmore positive attitudes (p=0.003 and p=0.01, respectively). Around 70% of responders had adequate knowledgeregarding EBM. Physicians, members of faculty and participants who had spent more time on research, reviewedarticles and attended workshops had more knowledge (p=0.001). <h3>Conclusions</h3> Results from our study revealed that although there is a significant number of physiatrists who are familiar with the practicality of EBM, they are still not familiar enough with its concepts and applications. <h3>References</h3> [1] Raeissadat SA, Samadi B, Rayegani SM, Bahrami MH, Mahmoudi H. Survey of Medical Residents' Attitude Toward Physical Medicine and Rehabilitation. American Journal of Physical Medicine &amp; Rehabilitation. 2014; 93(6): 540–7. doi: 10.1097/PHM.0000000000000057. PMID: 24508929. [2] Raeissadat SA, Bahrami MH, Rayegani SM, Babaee M, Roshan Pajoh R. Attitude, beliefs and knowledge of iranian physiatrists towards Evidence Based Medicine and its barriers. A cross-sectional study. Eur J Phys Rehabil Med. 2016; 52(5): 755–7. PMID: 27164540. [3] Raeissadat SA, Bahrami MH, Rayegani SM, Hassanabadi H, Babaee M, Najafi S, et al. Obstacles facing evidence based medicine in physical medicine and rehabilitation: from opinion and knowledge to practice. Electronic Physician. 2017;9(11). <h3>Disclosure of Interest</h3> None declared
Confusion over CPR in patients with covid-19
Authors: Francesco P Cappuccio
Journal: BMJ (2020)

Summary: Solitary fibrous tumors are submesothelial mesenchymal fibroblastic tumors that typically occur in relation to parietal or visceral pleura. However, the tumor also occurs in extrapleural sites, including the peritoneum, mediastinum, orbit, and oral cavity. With the advent of immunohistochemical testing, certain tumors may be more readily identifiable; however, the diagnosis often must be reached by histomorphology and imaging studies alone. We describe a case of a solitary fibrous tumor of the buccal space, including clinical presentation, imaging characteristics, gross pathology, and histopathologic description.
Coronary Artery Disease
Authors: Sharon Parmet
Journal: JAMA (2004)

Coronary Artery DiseaseC oronary artery disease means narrowing of the coronary arteries (arteries that supply blood to the heart).This narrowing is due to a buildup in the walls of the arteries of plaque (deposits made up of cholesterol, other fats, and calcium)-a process called atherosclerosis (hardening of the arteries).If a plaque becomes delicate and breaks, a blood clot will quickly form that can block blood flow in the artery and may lead to a myocardial infarction (death of the heart muscle area supplied by the blocked artery), often referred to as a heart attack.The November 24, 2004, issue of JAMA includes an article about coronary artery disease.
Re: Adjuvant Chemotherapy in Upper Tract Urothelial Carcinoma (the POUT Trial): A Phase 3, Open-label, Randomised Controlled Trial
Authors: Luca Afferi, Marco Moschini, Agostino Mattei, Francesco Montorsi, Alberto Briganti, Xavier Cathelineau, Rafael Sanchez-Salas
Journal: European Urology (2020)
Publisher Correction: A mountable toilet system for personalized health monitoring via the analysis of excreta
Authors: Seung-min Park, Daeyoun D. Won, Brian J. Lee, Diego Escobedo, Andre Esteva, Amin Aalipour, T. Jessie Ge, Jung Ha Kim, Susie Suh, Elliot H. Choi, Alexander X. Lozano, Chengyang Yao, Sunil Bodapati, Friso B. Achterberg, Jeesu Kim, Hwan Park, Youngjae Choi, Woo Jin Kim, Jung Ho Yu, Alexander M. Bhatt, Jong Kyun Lee, Ryan Spitler, Shan X. Wang, Sanjiv S. Gambhir
Journal: Nature Biomedical Engineering (2020)
Abstract #4711: Amplification of EGFR T790M causes resistance to the irreversible EGFR inhibitor PF00299804
Authors: Dalia Ercan, Kreshnik Zejnullahu, Yun Xiao, Marzia Capelletti, Andrew Rogers, Charles Lee, James Christensen, Pasi Janne
Journal: Cancer Research (2009)

Background: The EGFR acquired resistance mutation EGFR T790M causes resistance to the EGFR kinase inhibitor gefitinib in non-small cell lung cancer. Irreversible EGFR inhibitors, such as PF00299804, are effective in NSCLC models harboring EGFR T790M (Engelman et al., Cancer Res 2007). The mechanism(s) of resistance to irreversible EGFR inhibitors is not well defined Methods and Results: We exposed the gefitinib resistant PC9 GR cells (EGFR E746_A740/T790M; IC50 to PF00299804: ~100nM) to increasing concentrations of PF00299804 to generate PC9 DR (double resistant) cells (IC50 to PF00299804 ~3µM). The PC9 DR cells harbored a focal amplification on chromosome 7 encompassing the EGFR locus as detected by a single nucleotide polymorphism (SNP) array. We detected a significantly higher fraction of EGFR T790M alleles in the PC9 DR cells by both direct DNA sequencing and by RT-PCR followed by cloning in the PC9 DR cells (56.8% of clones with EGFR E746_A750/T790M) compared to the PC9 GR cells (6.4% of clones with EGFR E746_A750/T790M) suggesting a preferential amplification of the T790M containing allele. The PC9 DR cells also demonstrated an increase in basal EGFR phosphorylation (pY 1068) compared to the PC9 GR cells. Both the PC9 DR and GR cells were similarly growth inhibited by both EGFR and ERBB3 specific short hairpin (sh) RNAs suggesting that the PC9 DR cells were still EGFR/ERBB3 dependent for their growth. Interestingly, using fluorescence in situ hybridization (FISH) for EGFR/CEP7 we were able to detect 2 populations in the PC9 DR cells. In PC9 DR1, EGFR amplification was predominately (82%) in extra-chromosomal (double minute (DM)) regions while in a smaller population (18%) EGFR was amplified in an intra-chromosomal region. In PC9 DR2, EGFR amplification occurred exclusively in DMs. As DMs may be chromosomally unstable, we cultured both PC9 DR1 and DR2 without PF00299804. After 18 passages, the PC9 DR2 cells lost their resistance to PF00299804 with a concomitant loss of DMs while the PC9 DR1 cells remained resistant to PF00299804. Conclusions: EGFR T790M causes resistance to gefitinib and when amplified also to PF00299804. EGFR T790M amplified cancers remain dependent on EGFR for their growth suggesting a continued need to develop therapeutic agents targeting EGFR signaling.  Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 4711.
Public Health Response to the Initiation and Spread of Pandemic COVID-19 in the United States, February 24–April 21, 2020
Authors: Anne Schuchat
Journal: MMWR Morbidity and Mortality Weekly Report (2020)

From January 21 through February 23, 2020, a total of 14 cases of coronavirus disease 2019 (COVID-19) were diagnosed in six U.S. states, including 12 cases in travelers arriving from China and two in household contacts of persons with confirmed infections. An additional 39 cases were identified in persons repatriated from affected areas outside the United States (1). Starting in late February, reports of cases with no recent travel to affected areas or links to known cases signaled the initiation of pandemic spread in the United States (2). By mid-March, transmission of SARS-CoV-2, the virus that causes COVID-19, had accelerated, with rapidly increasing case counts indicating established transmission in the United States. Ongoing traveler importation of SARS-CoV-2, attendance at professional and social events, introduction into facilities or settings prone to amplification, and challenges in virus detection all contributed to rapid acceleration of transmission during March. Public health responses included intensive efforts to detect cases and trace contacts, and implementation of multiple community mitigation strategies. Because most of the population remains susceptible to infection, recognition of factors associated with amplified spread during the early acceleration period will help inform future decisions as locations in the United States scale back some components of mitigation and strengthen systems to detect a potential transmission resurgence. U.S. circulation of SARS-CoV-2 continues, and sustained efforts will be needed to prevent future spread within the United States.
Application of Lymphatic Mapping and Sentinel Node Biopsy in Surgical Oncology
Authors: Ramin Sadeghi, Leili Zarifmahmoudi
Journal: Clinical Nuclear Medicine (2020)

The concept of sentinel node (SN) is an important aspect of surgical oncology that has revolutionized the treatment of solid tumors. The concept of sentinel node mapping suggests that lymphatic basin involvement starts from the sentinel nodes, and if sentinel nodes are pathologically clear from tumor cells, the other lymph nodes of the basin are clear either.In the current chapter, general aspects of sentinel node mapping have been discussed, including various mapping materials and radiopharmaceuticals; injection site, time, dose, and volume; imaging (lymphoscintigraphy); and gamma-probe-related issues.Special considerations for sentinel node mapping in breast cancer, melanoma, and uterine cervix, endometrial, vulvar, penile, colorectal, and head and neck cancers were also discussed.
Persistent exercise intolerance after pulmonary endarterectomy for chronic thromboembolic pulmonary hypertension
Authors: Dieuwertje Ruigrok, Lilian J. Meijboom, Esther J. Nossent, Anco Boonstra, Natalia J. Braams, Jessie van Wezenbeek, Frances S. de Man, J. Tim Marcus, Anton Vonk Noordegraaf, Petr Symersky, Harm-Jan Bogaard
Journal: European Respiratory Journal (2020)

Aim Haemodynamic normalisation is the ultimate goal of pulmonary endarterectomy (PEA) for chronic thromboembolic pulmonary hypertension (CTEPH). However, whether normalisation of haemodynamics translates into normalisation of exercise capacity is unknown. The incidence, determinants and clinical implications of exercise intolerance after PEA are unknown. We performed a prospective analysis to determine the incidence of exercise intolerance after PEA, assess the relationship between exercise capacity and (resting) haemodynamics and search for preoperative predictors of exercise intolerance after PEA. Methods According to clinical protocol all patients underwent cardiopulmonary exercise testing (CPET), right heart catheterisation and cardiac magnetic resonance (CMR) imaging before and 6 months after PEA. Exercise intolerance was defined as a peak oxygen consumption ( V ′ O 2 ) &lt;80% predicted. CPET parameters were judged to determine the cause of exercise limitation. Relationships were analysed between exercise intolerance and resting haemodynamics and CMR-derived right ventricular function. Potential preoperative predictors of exercise intolerance were analysed using logistic regression analysis. Results 68 patients were included in the final analysis. 45 (66%) patients had exercise intolerance 6 months after PEA; in 20 patients this was primarily caused by a cardiovascular limitation. The incidence of residual pulmonary hypertension was significantly higher in patients with persistent exercise intolerance (p=0.001). However, 27 out of 45 patients with persistent exercise intolerance had no residual pulmonary hypertension. In the multivariate analysis, preoperative transfer factor of the lung for carbon monoxide ( T LCO ) was the only predictor of exercise intolerance after PEA. Conclusions The majority of CTEPH patients have exercise intolerance after PEA, often despite normalisation of resting haemodynamics. Not all exercise intolerance after PEA is explained by the presence of residual pulmonary hypertension, and lower preoperative T LCO was a strong predictor of exercise intolerance 6 months after PEA.
Distinct features of SARS-CoV-2-specific IgA response in COVID-19 patients
Authors: Hai-qiong Yu, Bao-qing Sun, Zhang-fu Fang, Jin-cun Zhao, Xiao-yu Liu, Yi-min Li, Xi-zhuo Sun, Hong-feng Liang, Bei Zhong, Zhi-feng Huang, Pei-yan Zheng, Li-feng Tian, Hui-Qi Qu, De-chen Liu, Er-yi Wang, Xiao-jun Xiao, Shi-yue Li, Feng Ye, Li Guan, Dong-sheng Hu, Hakon Hakonarson, Zhi-gang Liu, Nan-shan Zhong
Journal: European Respiratory Journal (2020)

<b>Humoral immune response to SARS-CoV-2 showed an early response of IgA, instead of IgM, in COVID-19 patients. As highlighted by this study, enhanced IgA responses observed in severe COVID-19 might confer damaging effects in severe COVID-19.</b>https://bit.ly/3fA7c1I
THE DIAGNOSTIC YIELD OF ILEAL INTUBATION DURING COLONOSCOPY AMONG PATIENTS WITH GASTROINTESTINAL COMPLAINTS
Authors: K Manukyan, A Khalatyan, S Khachatryan
Journal: Endoscopy (2020)

Aims Ileal intubation and biopsy are considered as a main method for diagnosis of IBD, enteropathy and etc, nevertheless there is no definite recommendation for routinely ileal intubation during colonoscopy in patients without IBD suspicion. The aim of this study was to evaluate necessity of terminal ileum intubation during endoscopy among patients with GI complaints but without IBD suspicion.
Predicting conversion to wet age-related macular degeneration using deep learning
Authors: Jason Yim, Reena Chopra, Terry Spitz, Jim Winkens, Annette Obika, Christopher Kelly, Harry Askham, Marko Lukic, Josef Huemer, Katrin Fasler, Gabriella Moraes, Clemens Meyer, Marc Wilson, Jonathan Dixon, Cian Hughes, Geraint Rees, Peng T. Khaw, Alan Karthikesalingam, Dominic King, Demis Hassabis, Mustafa Suleyman, Trevor Back, Joseph R. Ledsam, Pearse A. Keane, Jeffrey De Fauw
Journal: Nature Medicine (2020)
AIDS: Politics and Science
Authors: J E Osborn
Journal: New England Journal of Medicine (1988)

Ethicists sometimes embark on an approach to thorny issues with the assertion that "good data make good ethics"; the same could be said of good politics. The burgeoning problems posed by the acquired immunodeficiency syndrome (AIDS) epidemic will put social systems and political skills to a severe test, but in the six years since the first cases of AIDS were diagnosed, biomedical and epidemiologic scientists have established a firm foundation of data on which to construct focused public health programs responsive to the precise contours of the epidemic. Meanwhile, the hazards of overreaction are becoming very clear. The good news . . .
SIRT3 Is a Novel Metabolic Driver of and Therapeutic Target for Chemotherapy Resistant Dlbcls
Authors: Meng Li, Ying-Ling Chiang, Costas Lyssiotis, Matthew Teater, Hao Shen, Ling Wang, Jun Young Hong, Hui Jin, Cihangir Duy, Sucharita Mistry, Leandro Cerchietti, Justin Cross, Lewis Cantley, Hening Lin, Ari Melnick
Journal: Blood (2017)
Use of all cause mortality to quantify the consequences of covid-19 in Nembro, Lombardy: descriptive study
Authors: Marco Piccininni, Jessica L Rohmann, Luca Foresti, Caterina Lurani, Tobias Kurth
Journal: BMJ (2020)

Abstract Objective To quantify the impact of coronavirus disease 2019 (covid-19) on all cause mortality in Nembro, an Italian city severely affected by the covid-19 pandemic. Design Descriptive study. Setting Nembro, in the Bergamo province of Lombardy, northern Italy. Population Residents of Nembro. Main outcome measures Monthly all cause mortality between January 2012 and April 2020 (data to 11 April), number of confirmed deaths from covid-19 to 11 April 2020, and weekly absolute number of deaths between 1 January and 4 April across recent years by age group and sex. Results Nembro had 11 505 residents as of 1 January 2020. Monthly all cause mortality between January 2012 and February 2020 fluctuated around 10 per 1000 person years, with a maximum of 21.5 per 1000 person years. In March 2020, monthly all cause mortality reached a peak of 154.4 per 1000 person years. For the first 11 days in April, this rate decreased to 23.0 per 1000 person years. The observed increase in mortality was driven by the number of deaths among older people (≥65 years), especially men. From the outbreak onset until 11 April 2020, only 85 confirmed deaths from covid-19 in Nembro were recorded, corresponding to about half of the 166 deaths from all causes observed in that period. Conclusions The study findings show how covid-19 can have a considerable impact on the health of a small community. Furthermore, the results suggest that the full implications of the covid-19 pandemic can only be completely understood if, in addition to confirmed deaths related to covid-19, consideration is also given to all cause mortality in a given region and time frame.
EFFICACY OF PURASTAT AS A RESCUE THERAPY FOR REFRACTORY ACUTE GASTROINTESTINAL BLEEDINGS: A THREE CENTRE EXPERIENCE IN ITALY
Authors: G de Nucci, R Reati, E Mandelli, C Bezzio, B Omazzi, D Redaelli, D Morganti, C della Corte, S Saibeni, I Arena, G Manes, M Devani
Journal: Endoscopy (2020)

Aims Acute gastrointestinal bleeding (AGIB) results in significant mortality and morbidity. Topical haemostatic products have been developed for endoscopic use to help in the management of difficult bleeding. Our aim is to demonstrate the feasibility, efficacy and safety of PuraStat, a novel haemostat, to control acute gastrointestinal bleedings
Peripartum cardiomyopathy: can the link between prolactin and PAI-1 provide a clue?
Authors: Diana A Gorog, Gemma Vilahur
Journal: Cardiovascular Research (2020)

© 2020 Oxford University Press. This is a pre-copyedited, author-produced PDF of an article accepted for publication in Cardiovascular Research following peer review. The version of record, Diana A Gorog, Gemma Vilahur, Peripartum cardiomyopathy: can the link between prolactin and PAI-1 provide a clue?, Cardiovascular Research, cvaa109, is available online at: https://doi.org/10.1093/cvr/cvaa109.