tbuckley/cabot-search huggingface dataset:
Variation in US Hospital Mortality Rates for Patients Admitted With COVID-19 During the First 6 Months of the Pandemic
Authors: David A. Asch, Natalie E. Sheils, Md Nazmul Islam, Yong Chen, Rachel M. Werner, John Buresh, Jalpa A. Doshi
Journal: JAMA Internal Medicine (2020)

It is unknown how much the mortality of patients with coronavirus disease 2019 (COVID-19) depends on the hospital that cares for them, and whether COVID-19 hospital mortality rates are improving.
Hexokinase-2 is a key therapeutic target in brain metastasis derived from breast cancer.
Authors: S. Shreeve, Diane Palmieri, Emily Hua, Matthew Johnson, Kenneth Aldape, Gary Davis, Christina Hoffmann, Seth Steinberg, Patricia Steeg
Journal: Cancer Research (2008)

4354  The prevalence of brain metastasis from breast cancer is increasing. Current treatment options are limited and have no impact on survival. We are evaluating several potential therapeutic targets identified from cDNA microarray analysis of surgically resected human brain metastases. One of these, hexokinase II (HK-2), was validated using quantitative RT-PCR, and showed an approximately 2-fold up-regulation (p=0.01) in brain metastases (n=8) compared to unmatched primary invasive ductal breast carcinomas (n=8). Since HK-2 is not normally found in brain, this suggests that this isoenzyme may be a selective target for metastatic disease in this organ. HK-2 is up-regulated in many tumors, and belongs to a family of four hexokinases which play a vital role in the generation of ATP as they catalyze the first step of the glycolytic pathway converting glucose to glucose-6-phosphate. Production of this substrate also drives the pentose phosphate pathway providing many components required for cell growth. In addition, through mitochondrial binding, HK-2 inhibits apoptosis. We therefore hypothesized that HK-2 would play a key role in cell growth and survival in brain metastasis derived from breast cancer, and that its level of expression would affect overall survival. To test this hypothesis we examined survival curves in patients that were divided into one of two groups based on the degree of HK-2 expression in brain metastases, as determined by immunohistochemistry. Median survival for patients (n=94) with a high level of HK-2 was 9.6 months post-surgery as compared to a median survival of 17.5 months in patients (n=19) with a low level of HK-2 (p=0.0275 by two-tailed log rank test). To further validate HK-2 as a therapeutic target and evaluate the functional role of HK-2 in brain metastases, we are using a human breast cancer cell subline that is selectively metastatic to the brain (MDA-MB-231BR). These cells were transduced using VSV-g pseudotyped lentiviral particles carrying a shRNA targeting either HK-2 or a non-target control (Sigma-Aldrich). Knockdown of HK-2 was verified by Western blotting and QT-PCR. Cell growth is measured using 5-bromo-29-deoxy-uridine labeling. Knockdown of HK-2 expression by 95 % inhibited tumor cell proliferation by 40 % (p=0.0012 by two-tailed t test) under normal growth conditions at five days. These data suggest that over-expression of HK-2 is associated with poorer overall patient survival because it plays a key role in the proliferation and long-term survival of metastatic cells in brain. Thus, HK-2 is likely an important therapeutic targetin brain metastasis derived from breast cancer.
Longitudinal course of clinical lung clearance index in children with cystic fibrosis
Authors: Bettina S. Frauchiger, Severin Binggeli, Sophie Yammine, Ben Spycher, Linn Krüger, Kathryn A. Ramsey, Philipp Latzin
Journal: European Respiratory Journal (2020)

Background Although the lung clearance index (LCI) is a sensitive marker of small airway disease in individuals with cystic fibrosis (CF), less is known about longitudinal changes in LCI during routine clinical surveillance. Here, our objectives were to describe the longitudinal course of LCI in children with CF during routine clinical surveillance and assess influencing factors. Methods Children with CF aged 3–18 years performed LCI measurements every 3 months as part of routine clinical care between 2011 and 2018. We recorded clinical data at every visit. We used a multilevel mixed effect model to determine changes in LCI over time and identify clinical factors that influence LCI course. Results We collected LCI measurements from 1204 visits (3603 trials) in 78 participants, of which 907 visits had acceptable LCI data. The average unadjusted increase in LCI for the entire population was 0.29 (95% CI 0.20–0.38) LCI units·year −1 . The increase in LCI was more pronounced in adolescence (0.41 (95% CI 0.27–0.54) LCI units·year −1 ). Colonisation with either Pseudomonas aeruginosa or Aspergillus fumigatus , pulmonary exacerbations, CF-related diabetes and bronchopulmonary aspergillosis were associated with a higher increase in LCI over time. Adjusting for clinical risk factors reduced the increase in LCI over time to 0.24 (95% CI 0.16–0.33) LCI units·year −1 . Conclusions LCI measured during routine clinical surveillance is associated with underlying disease progression in children with CF. An increased change in LCI over time should prompt further diagnostic intervention.
Терапевтические возможности Холопланта в лечении дисфункции сфинктера Одди после холецистэктомии
Authors: T.D. Zviahintseva, Ya.K. Hamanenko
Journal: GASTROENTEROLOGY (2014)

Статья посвящена вопросам диагностики и лечения недостаточности сфинктера Одди у пациентов, перенесших холецистэктомию. Делается акцент на применении препаратов с комбинированным действием, например Холопланта. В проведенном исследовании показано, что Холоплант позволяет эффективно восстановить дренажную функцию желчевыводящих путей, улучшить отток желчи, снизить литогенные свойства желчи, что способствует предупреждению образования конкрементов, нормализации моторной функции желчевыводящих путей, восстановлению тонуса сфинктера Одди, повышению антиоксидантной защиты организма.
Race Differences in Blood Pressure Trajectory After Delivery—A Window Into Opportunities to Decrease Racial Disparities in Maternal Morbidity and Mortality
Authors: Adi Hirshberg
Journal: JAMA Network Open (2020)

Alisse Hauspurg, MD; Lara Lemon, PhD, PharmD; Camila Cabrera, MD; Amal Javaid, BS; Anna Binstock, MD; Beth Quinn, RN; Jacob Larkin, MD; Andrew R. Watson, MD; Richard H. Beigi, MD; Hyagriv Simhan, MD
Maternal consumption of artificially sweetened beverages during pregnancy is associated with infant gut microbiota and metabolic modifications and increased infant body mass index
Authors: Isabelle Laforest-Lapointe, Allan B. Becker, Piushkumar J. Mandhane, Stuart E. Turvey, Theo J. Moraes, Malcolm R. Sears, Padmaja Subbarao, Laura K. Sycuro, Meghan B. Azad, Marie-Claire Arrieta
Journal: Gut Microbes (2020)

Artificial sweetener consumption by pregnant women has been associated with an increased risk of infant obesity, but the underlying mechanisms are unknown. We aimed to determine if maternal consumption of artificially sweetened beverages (ASB) during pregnancy is associated with modifications of infant gut bacterial community composition and function during the first year of life, and whether these alterations are linked with infant body mass index (BMI) at one year of age. We studied 100 infants from the prospective Canadian CHILD Cohort Study, selected based on maternal ASB consumption during pregnancy (50 non-consumers and 50 daily consumers). BMI was higher among ASB-exposed infants. Infant stool (16S rRNA gene sequencing) and urine (untargeted metabolomics) were acquired in early (3-4 months) and late (12 months) infancy. We identified four microbiome clusters, of which two recapitulated the maturation trajectory of the infant gut bacterial communities from immature (Cluster 1) to mature (Cluster 4) and two deviated from this trajectory (Clusters 2 and 3). Maternal ASB consumption did not differ between clusters, but was associated with community-level shifts in infant gut bacterial taxonomy structure and depletion of several Bacteroides sp. in Cluster 2. In the complete dataset, urine succinate and spermidine levels at 3 months were higher in ASB-exposed infants, and urine succinate was positively associated with BMI at one-year-old. Overall, gestational exposure to ASB was associated with gut microbiota structure in infants from Cluster 2, and gut microbiota structure was associated with infant BMI. Gestational exposure to ASB was positively associated with infant urine succinate and spermidine. Succinate was found to mediate 29% of the effect of ASB exposure on BMI at one-year-old, revealing a potential role of this metabolite in increased infant weight linked to gestational ASB consumption. As we face an unprecedented rise in childhood obesity, future studies should evaluate the causal relationships between maternal ASB consumption (a modifiable exposure), gut microbiota and metabolites, infant metabolism, and body composition.
Efficacy and safety of fecal microbiota transplantation for the treatment of diseases other than <i>Clostridium difficile</i> infection: a systematic review and meta-analysis
Authors: Jessica Emily Green, Jessica A. Davis, Michael Berk, Christopher Hair, Amy Loughman, David Castle, Eugene Athan, Andrew A. Nierenberg, John F. Cryan, Felice Jacka, Wolfgang Marx
Journal: Gut Microbes (2020)

The intestinal microbiome has been identified as a key modifier for a variety of health conditions. Fecal Microbiota Transplantation (FMT) has emerged as a fast, safe, and effective means by which to modify the intestinal microbiome and potentially treat a variety of health conditions. Despite extensive research of FMT for CDI, there is a lack of clarity informed by systematic synthesis of data regarding the safety and efficacy of FMT for other health conditions. This systematic review used PRISMA guidelines and was prospectively registered with PROSPERO (CRD42018104243). In March 2020, a search of MEDLINE, EMBASE, and PsycINFO was conducted. We identified 26 eligible studies. A meta-analysis of FMT for active Ulcerative Colitis (UC) showed that FMT significantly improved rates of clinical remission (OR = 3.634, 95% CI = 1.940 to 6.808, I2 = 0%, p < .001), clinical response (OR = 2.634, 95% CI = 1.441 to 4.815, I2 = 33%, p = .002) and endoscopic remission (OR = 4.431, 95% CI = 1.901 to 10.324, I2 = 0%, p = .001). With respect to Irritable Bowel Syndrome, a meta-analysis showed no significant change in symptoms following FMT (p = .739). Hepatic disorders, metabolic syndrome, and antibiotic-resistant organisms were conditions with emerging data on FMT. Serious adverse events (AE) were more often reported in control group participants (n = 43) compared with FMT group participants (n = 26). There were similar rates of mild to moderate AE in both groups. Preliminary data suggest that FMT is a potentially safe, well-tolerated and efficacious treatment for certain conditions other than CDI, with evidence for active UC being the most compelling.
From waste of marine culture to natural patch in cardiac tissue engineering
Authors: Yutong He, Honghao Hou, Shuqi Wang, Rurong Lin, Leyu Wang, Lei Yu, Xiaozhong Qiu
Journal: Bioactive Materials (2020)

Sea squirt, as a highly invasive species and main biofouling source in marine aquaculture, has seriously threatened the biodiversity and aquaculture economy. On the other hand, a conductive biomaterial with excellent biocompatibility, and appropriate mechanical property from renewable resources is urgently required for tissue engineering patches. To meet these targets, we presented a novel and robust strategy for sustainable development aiming at the marine pollution via recycling and upgrading the waste biomass-sea squirts and serving as a renewable resource for functional bio-scaffold patch in tissue engineering. We firstly demonstrated that the tunic cellulose derived natural self-conductive scaffolds successfully served as functional cardiac patches, which significantly promote the maturation and spontaneous contraction of cardiomyocytes both in vitro and enhance cardiac function of MI rats in vivo. We believe this novel, feasible and "Trash to Treasure" strategy to gain cardiac patches via recycling the waste biomass must be promising and beneficial for marine environmental bio-pollution issue and sustainable development considering the large-scale consumption potential for tissue engineering and other applications.
Racial Disparities in Epigenetic Aging of the Right vs Left Colon
Authors: Matthew Devall, Xiangqing Sun, Fangcheng Yuan, Gregory S Cooper, Joseph Willis, Daniel J Weisenberger, Graham Casey, Li Li
Journal: JNCI Journal of the National Cancer Institute (2020)

Abstract There are well-documented racial differences in age-of-onset and laterality of colorectal cancer. Epigenetic age acceleration is postulated to be an underlying factor. However, comparative studies of side-specific colonic tissue epigenetic aging are lacking. Here, we performed DNA methylation analysis of matched right and left biopsies of normal colon from 128 individuals. Among African Americans (n = 88), the right colon showed accelerated epigenetic aging as compared with individual-matched left colon (1.51 years; 95% confidence interval [CI] = 0.62 to 2.40 years; 2-sided P = .001). In contrast, among European Americans (n = 40), the right colon shows remarkable age deceleration (1.93 years; 95% CI = 0.65 to 3.21 years; 2-sided P = .004). Further, epigenome-wide analysis of DNA methylation identifies a unique pattern of hypermethylation in African American right colon. Our study is the first to report such race and side-specific differences in epigenetic aging of normal colon, providing novel insight into the observed younger age-of-onset and relative preponderance of right-side colon neoplasia in African Americans.
Plasticity of Epididymal Adipose Tissue in Response to Diet-Induced Obesity at Single-Nucleus Resolution
Authors: Anitta Kinga Sárvári, Elvira Laila Van Hauwaert, Lasse Kruse Markussen, Ellen Gammelmark, Ann-Britt Marcher, Morten Frendø Ebbesen, Ronni Nielsen, Jonathan Richard Brewer, Jesper Grud Skat Madsen, Susanne Mandrup
Journal: Cell Metabolism (2020)
HAPHPIPE: Haplotype Reconstruction and Phylodynamics for Deep Sequencing of Intrahost Viral Populations
Authors: Matthew L Bendall, Keylie M Gibson, Margaret C Steiner, Uzma Rentia, Marcos Pérez-Losada, Keith A Crandall
Journal: Molecular Biology and Evolution (2020)

Deep sequencing of viral populations using next-generation sequencing (NGS) offers opportunities to understand and investigate evolution, transmission dynamics, and population genetics. Currently, the standard practice for processing NGS data to study viral populations is to summarize all the observed sequences from a sample as a single consensus sequence, thus discarding valuable information about the intrahost viral molecular epidemiology. Furthermore, existing analytical pipelines may only analyze genomic regions involved in drug resistance, thus are not suited for full viral genome analysis. Here, we present HAPHPIPE, a HAplotype and PHylodynamics PIPEline for genome-wide assembly of viral consensus sequences and haplotypes. The HAPHPIPE protocol includes modules for quality trimming, error correction, de novo assembly, alignment, and haplotype reconstruction. The resulting consensus sequences, haplotypes, and alignments can be further analyzed using a variety of phylogenetic and population genetic software. HAPHPIPE is designed to provide users with a single pipeline to rapidly analyze sequences from viral populations generated from NGS platforms and provide quality output properly formatted for downstream evolutionary analyses.
Association of Improved Periconception Hemoglobin A<sub>1c</sub> With Pregnancy Outcomes in Women With Diabetes
Authors: Alexander J. F. Davidson, Alison L. Park, Howard Berger, Kazuyoshi Aoyama, Ziv Harel, Eyal Cohen, Jocelynn L. Cook, Joel G. Ray
Journal: JAMA Network Open (2020)

<h3>Importance</h3> Prepregnancy diabetes is associated with higher perinatal and maternal morbidity, especially if periconception glycemic control is suboptimal. It is not known whether improved glycemic control from preconception to early pregnancy and midpregnancy periods can reduce the risk of adverse perinatal and maternal outcomes. <h3>Objective</h3> To determine whether a net decline in glycated hemoglobin A<sub>1c</sub>(HbA<sub>1c</sub>) from preconception to the first half of pregnancy is associated with a lower risk of adverse outcomes for mother and child. <h3>Design, Setting, and Participants</h3> This population-based cohort study was completed in all of Ontario, Canada, from 2007 to 2018. Included were births among women with prepregnancy diabetes whose HbA<sub>1c</sub>was measured within 90 days preconception and again from conception through 21 weeks completed gestation (early pregnancy to midpregnancy). Statistical analysis was performed from July to September 2020. <h3>Exposures</h3> Net decrease in HbA<sub>1c</sub>from preconception to early pregnancy and midpregnancy. <h3>Main Outcomes and Measures</h3> The main outcome was a congenital anomaly from birth to age 1 year. Other outcomes included preterm birth or perinatal mortality among offspring as well as severe maternal morbidity (SMM) or death among mothers. Adjusted relative risks (aRRs) were calculated per 0.5% absolute net decline in HbA<sub>1c</sub>from preconception up to early pregnancy and midpregnancy, adjusting for maternal age at conception, preconception HbA<sub>1c</sub>and hemoglobin concentration, and gestational age at HbA<sub>1c</sub>measurement. <h3>Results</h3> A total of 3459 births were included, with a mean (SD) maternal age of 32.6 (5.0) years at conception. Overall, the mean (SD) HbA<sub>1c</sub>decreased from 7.2% (1.6%) preconception to 6.4% (1.1%) in early pregnancy to midpregnancy. There were 497 pregnancies (14.4%) with a congenital anomaly, with an aRR of 0.94 (95% CI, 0.89-0.98) per 0.5% net decrease in HbA<sub>1c</sub>, including for cardiac anomalies (237 infants; aRR, 0.89; 95% CI, 0.84-0.95). The risk was also reduced for preterm birth (847 events; aRR, 0.89; 95% CI, 0.86-0.91). SMM or death occurred among 191 women (5.5%), with an aRR of 0.90 (95% CI, 0.84-0.96) per 0.5% net decrease in HbA<sub>1c</sub>. <h3>Conclusions and Relevance</h3> These findings suggest that women with prepregnancy diabetes who achieve a reduction in HbA<sub>1c</sub>may have improved perinatal and maternal outcomes. Further study is recommended to determine the best combination of factors, such as lifestyle changes and/or glucose-lowering medications, that can influence periconception HbA<sub>1c</sub>reduction.
A Study of Physicians' Handwriting as a Time Waster
Authors: None Anonymous
Journal: JAMA (1979)

WRITTEN communication is the legal basis for the hospital practice of medicine. Two major methods of communication are (1) telephone orders that require written confirmation and (2) written orders and progress notes. The legal requirements for written orders and progress notes are that they be legible and that there be a printed signature if the written signature is not legible. These are the documents of medical care. In the present day 250- to 500-bed setting, there are many persons who may legally write on the patient's order sheet and also in the patient's record. Therefore, a complete study would include physicians, nurses, pharmacists, nurse specialists, interns, residents, and medical students. What effect does the clarity of handwriting have on the effectiveness of communications within the hospital community? The purpose of this study is to indicate that physicians' handwriting causes a considerable waste of hospital employees' time. <h3>Scope and Method of</h3>
A cross-sectional study of olfactory and taste disorders among COVID-19 patients in China
Authors: Jian-Hui Li, Yi Sun, Mei-Rong Li, Hu Yuan, Chang-Liang Yang, Cheng-Cheng Huang, Feng-Jie Zhou, Rui-Yao Chen, Lei-Bo Zhang, Ning Yu, Qiong Liu, Jing-Jing He, Xue-Jun Zhou, Xiao-Bing Fu, Shi-Ming Yang
Journal: Military Medical Research (2021)

Abstract To determine the prevalence and clinical features of olfactory and taste disorders among coronavirus disease 2019 (COVID-19) patients in China. A cross-sectional study was performed in Wuhan from April 3, 2020 to April 15, 2020. A total of 187 patients with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) completed face-to-face interviews or telephone follow-ups. We found that the prevalence of olfactory and taste disorders was significantly lower in the Chinese cohort than in foreign COVID-19 cohorts. Females were more prone to olfactory and taste disorders. In some patients, olfactory and taste disorders precede other symptoms and can be used as early screening and warning signs.
Detection of Vulnerable Coronary Artery Plaques: Lesion Level Risk Assessment Within the Coronary Arterial Tree?⁎⁎Editorials published in JACC: Cardiovascular Imaging reflect the views of the authors and do not necessarily represent the views of JACC: Cardiovascular Imaging or the American College of Cardiology.
Authors: John J. Young
Journal: JACC. Cardiovascular imaging (2008)
Abstract 10694: Depletion of Gut Microbiota Attenuates Cardiac Hypertrophy Induced by Isoproterenol in Mice
Authors: Takako Yao, Takehiro Kamo
Journal: Circulation (2018)

Introduction: Gut microbiota play an essential role in the maintenance of host homeostasis. There is growing evidence that an imbalance in the composition of gut microbiota, known as dysbiosis, is ...
The prebiotic effects of omega-3 fatty acid supplementation: A six-week randomised intervention trial
Authors: Amrita Vijay, Stuart Astbury, Caroline Le Roy, Tim D Spector, Ana M Valdes
Journal: Gut Microbes (2020)

Prebiotics are compounds in food that benefit health via affecting the gut microbiome. Omega-3 fatty acids have been associated with differences in gut microbiome composition and are widely accepted to have health benefits, although recent large trials have been inconclusive. We carried out a 6-week dietary intervention comparing the effects of daily supplementation with 500 mg of omega-3 versus 20 g of a well-characterized prebiotic, inulin. Inulin supplementation resulted in large increases in Bifidobacterium and Lachnospiraceae. In contrast, omega-3 supplementation resulted in significant increases in Coprococcus spp. and Bacteroides spp, and significant decreases in the fatty-liver associated Collinsella spp. On the other hand, similar to the results with inulin supplementation which resulted in significant increases in butyrate, iso-valerate, and iso-butyrate (p < .004), omega-3 supplementation resulted in significant increases in iso-butyrate and isovalerate (p < .002) and nearly significant increases in butyrate (p < .053). Coprococcus, which was significantly increased post-supplementation with omega-3, was found to be positively associated with iso-butyric acid (Beta (SE) = 0.69 (0.02), P = 1.4 x 10-3) and negatively associated with triglyceride-rich lipoproteins such as VLDL (Beta (SE) = -0.381 (0.01), P = .001) and VLDL-TG (Beta (SE) = -0.372 (0.04), P = .001) after adjusting for confounders. Dietary omega-3 alters gut microbiome composition and some of its cardiovascular effects appear to be potentially mediated by its effect on gut microbial fermentation products indicating that it may be a prebiotic nutrient.
Endoscopic approach to complex gastric tube stricture after laparoscopic sleeve gastroplasty: a case report
Authors: Mateus Pereira Funari, Antônio Afonso Miranda Neto, Vitor Massaro Takamatsu Sagae, Thiago Ferreira de Souza, Maurício Kazuyoshi Minata, Spencer Cheng, Eduardo Guimarães Hourneaux de Moura
Journal: Endoscopy (2020)

As bariatric surgery becomes more prevalent, endoscopists commonly face adverse events now that this minimally invasive treatment has little morbidity and great efficacy [1]. Gastric tube stricture is one of the most common adverse events, occurring in 0.1 to 3.9 % of patients [2] [3]. Mechanical stricture (gastric sleeve) and axis deviation are the entities that can cause obstruction [2].