tbuckley/cabot-search huggingface dataset:
Berberine and its structural analogs have differing effects on functional profiles of individual gut microbiomes
Authors: Leyuan Li, Lu Chang, Xu Zhang, Zhibin Ning, Janice Mayne, Yang Ye, Alain Stintzi, Jia Liu, Daniel Figeys
Journal: Gut Microbes (2020)

The understanding of the effects of compounds on the gut microbiome is limited. In particular, it is unclear whether structurally similar compounds would have similar or distinct effects on the gut microbiome. Here, we selected berberine (BBR), an isoquinoline quaternary alkaloid, and 16 structural analogs and evaluated their effects on seven individual gut microbiomes cultured in vitro. The responses of the individual microbiomes were evaluated by metaproteomic profiles and by assessing butyrate production. We show that both interindividual differences and compound treatments significantly contributed to the variance of metaproteomic profiles. BBR and eight analogs led to changes in proteins involved in microbial defense and stress responses and enrichment of proteins from Verrucomicrobia, Proteobacteria, and Bacteroidetes phyla. It also led to a decrease in proteins from the Firmicutes phylum and its Clostridiales order which correlated to decrease proteins involved in the butyrate production pathway and butyrate concentration. Three of the compounds, sanguinarine, chelerythrine, and ethoxysanguinarine, activated bacterial protective mechanisms, enriched Proteobacteria, increased opacity proteins, and markedly reduced butyrate production. Dihydroberberine had a similar function to BBR in enriching the Akkermansia genus. In addition, it showed less overall adverse impacts on the functionality of the gut microbiome, including a better maintenance of the butyrate level. Our study shows that ex vivo microbiome assay can assess differential regulating effects of compounds with subtle differences and reveals that compound analogs can have distinct effects on the microbiome.
Joint prediction and time estimation of COVID-19 developing severe symptoms using chest CT scan
Authors: Xiaofeng Zhu, Bin Song, Feng Shi, Yanbo Chen, Rongyao Hu, Jiangzhang Gan, Wenhai Zhang, Man Li, Liye Wang, Yaozong Gao, Fei Shan, Dinggang Shen
Journal: Medical Image Analysis (2020)
mHealth Technologies Towards Parkinson's Disease Detection and Monitoring in Daily Life: A Comprehensive Review
Authors: Hanbin Zhang, Chen Song, Aditya Singh Rathore, Ming-Chun Huang, Yuan Zhang, Wenyao Xu
Journal: IEEE Reviews in Biomedical Engineering (2020)

Parkinson's disease (PD) can gradually affect people's lives thus attracting tremendous attention. Early PD detection and treatment can help control the disease progress, relief from the symptoms and improve the patients' life quality. However, the current practice of PD diagnosis is conducted in a clinical setup and administrated by a PD specialist due to the early signs of PD are not noticeable in daily life. According to the report of CDC/NIH, the diagnosed time of PD ranges from 2-10 years after onset. Therefore, a more accessible PD diagnosis approach is urgently demanded. In recent years, mobile health (for short mHealth) technology has been intensively investigated for preventive medicine, particularly in chronic disease management. Notably, many types of research have explored the possibility of using mobile and wearable personal devices to detect the symptom of PD and shown promising results. It provides opportunities for transforming early PD detection from clinical to daily life. This survey paper attempts to conduct a comprehensive review of mHealth technologies for PD detection from 2000 to 2019, and compares their pros and cons in practical applications and provides insights to close the performance gap between state-of-the-art clinical approaches and mHealth technologies.
Obligations to whom, obligations to what? A philosophical perspective on the objects of our obligations
Authors: Kati Kish Bar-On
Journal: Behavioral and Brain Sciences (2020)

Abstract Tomasello strives to understand the underlying psychology behind the human sense of obligation, but he only addresses a specific kind of obligation: to other human beings. We argue that in order to account for the psychological underpinning of human behavior, one should also consider people's sense of commitment to non-human entities, such as ideals, values, and moral principles.
Serum bactericidal titres for monitoring antimicrobial therapy: current status and potential role in the management of multidrug-resistant Gram-negative infections
Authors: I. Zaghi, P. Gaibani, C. Campoli, M. Bartoletti, M. Giannella, S. Ambretti, P. Viale, R.E. Lewis
Journal: Clinical Microbiology and Infection (2020)
2020 American College of Rheumatology Guideline for the Management of Gout
Authors: John D. FitzGerald, Nicola Dalbeth, Ted Mikuls, Romina Brignardello‐Petersen, Gordon Guyatt, Aryeh M. Abeles, Allan C. Gelber, Leslie R. Harrold, Dinesh Khanna, Charles King, Gerald Levy, Caryn Libbey, David Mount, Michael H. Pillinger, Ann Rosenthal, Jasvinder A. Singh, James Edward Sims, Benjamin J. Smith, Neil S. Wenger, Sangmee Sharon Bae, Abhijeet Danve, Puja P. Khanna, Seoyoung C. Kim, Aleksander Lenert, Samuel Poon, Anila Qasim, Shiv T. Sehra, Tarun Sudhir Kumar Sharma, Michael Toprover, Marat Turgunbaev, Linan Zeng, Mary Ann Zhang, Amy S. Turner, Tuhina Neogi
Journal: Arthritis & Rheumatology (2020)

Objective To provide guidance for the management of gout, including indications for and optimal use of urate‐lowering therapy ( ULT ), treatment of gout flares, and lifestyle and other medication recommendations. Methods Fifty‐seven population, intervention, comparator, and outcomes questions were developed, followed by a systematic literature review, including network meta‐analyses with ratings of the available evidence according to the Grading of Recommendations Assessment, Development and Evaluation ( GRADE ) methodology, and patient input. A group consensus process was used to compose the final recommendations and grade their strength as strong or conditional. Results Forty‐two recommendations (including 16 strong recommendations) were generated. Strong recommendations included initiation of ULT for all patients with tophaceous gout, radiographic damage due to gout, or frequent gout flares; allopurinol as the preferred first‐line ULT , including for those with moderate‐to‐severe chronic kidney disease ( CKD ; stage &gt; 3); using a low starting dose of allopurinol (≤100 mg/day, and lower in CKD ) or febuxostat ( &lt; 40 mg/day); and a treat‐to‐target management strategy with ULT dose titration guided by serial serum urate ( SU ) measurements, with an SU target of &lt;6 mg/dl. When initiating ULT , concomitant antiinflammatory prophylaxis therapy for a duration of at least 3–6 months was strongly recommended. For management of gout flares, colchicine, nonsteroidal antiinflammatory drugs, or glucocorticoids (oral, intraarticular, or intramuscular) were strongly recommended. Conclusion Using GRADE methodology and informed by a consensus process based on evidence from the current literature and patient preferences, this guideline provides direction for clinicians and patients making decisions on the management of gout.
Improving Detection and Response to Respiratory Events — Kenya, April 2016–April 2020
Authors: Osatohamwen I. Idubor, Miwako Kobayashi, Linus Ndegwa, Mary Okeyo, Tura Galgalo, Rosalia Kalani, Susan Githii, Elizabeth Hunsperger, Arunmozhi Balajee, Jennifer R. Verani, Maria da Gloria Carvalho, Jonas Winchell, Chris A. Van Beneden, Marc-Alain Widdowson, Lyndah Makayotto, Sandra S. Chaves
Journal: MMWR Morbidity and Mortality Weekly Report (2020)

Piloted in Kenya, the Detection and Response to Respiratory Events (DaRRE) strategy could serve as a model for other countries in the region to build capacity for prevention, detection, and response to respiratory disease outbreaks.
Ovomucoid epitope‐specific repertoire of IgE, IgG<sub>4</sub>, IgG<sub>1</sub>, IgA<sub>1</sub>, and IgD antibodies in egg‐allergic children
Authors: Maria Suprun, Robert Getts, Galina Grishina, Angela Tsuang, Mayte Suárez‐Fariñas, Hugh A. Sampson
Journal: Allergy (2020)

Abstract Background Egg‐white ovomucoid, that is, Gal d 1, is associated with IgE‐mediated allergic reactions in most egg‐allergic children. Epitope‐specific IgE levels have been correlated with the severity of egg allergy, while emerging evidence suggests that other antibody isotypes (IgG 1 , IgG 4 , IgA, and IgD) may have a protective function; yet, their epitope‐specific repertoires and associations with atopic comorbidities have not been studied. Methods Bead‐based epitope assay (BBEA) was used to quantitate the levels of epitope‐specific ( es )IgA, es IgE, es IgD, es IgG 1 , and es IgG 4 antibodies directed at 58 (15‐mer) overlapping peptides, covering the entire sequence of ovomucoid, in plasma of 38 egg‐allergic and 6 atopic children. Intraclass correlation (ICC) and coefficient of variation (CV) were used for the reliability assessment. The relationships across es Igs were evaluated using network analysis; linear and logistic regressions were used to compare groups based on egg allergy status and comorbidities. Results BBEA had high reliability (ICC &gt;0.75) and low variability (CV &lt;20%) and could detect known IgE‐binding epitopes. Egg‐allergic children had lower es IgA 1 ( P = .010) and es IgG 1 ( P = .016) and higher es IgE ( P &lt; .001) and es IgD ( P = .015) levels compared to the atopic controls. Interestingly, within the allergic group, children with higher es IgD had decreased odds of anaphylactic reactions (OR =0.48, P = .038). Network analysis identified most associations between es IgE with either es IgG 4 or es IgD; indicating that IgE‐secreting plasma cells could originate from either sequential isotype switch from antigen‐experienced intermediate isotypes or directly from the IgD + B cells. Conclusions Collectively, these data point toward a contribution of epitope‐specific antibody repertoires to the pathogenesis of egg allergy.
Genomic characterization of meningiomas.
Authors: Priscilla Kaliopi Brastianos, Peleg Horowitz, Sandro Santagata, Robert T. Jones, Aaron McKenna, Keith Ligon, Emanuele Palescandolo, Paul Van Hummelen, Gad Getz, William C Hahn, Ian F. Dunn, Rameen Beroukhim
Journal: Journal of Clinical Oncology (2012)

2020 Background: Understanding the genetic alterations in cancer has lead to groundbreaking discoveries in targeted therapies. Meningiomas are among the most common primary brain tumors, with approximately 18,000 new cases diagnosed annually. Though certain genes have been associated with the development of meningiomas, most notably the tumor suppressor gene neurofibromatosis 2 (NF2), the genetic changes that drive meningiomas remain poorly understood. Our objective was to comprehensively characterize the somatic genetic alterations of meningiomas to gain insight into the molecular pathways that drive this disease. Methods: Fresh frozen specimens and paired blood were collected from 16 consented patients. DNA was extracted from regions of high tumor purity determined by evaluation of H&amp;E slides. Whole-genome sequencing from 10 tumor-normal pairs and whole-exome sequencing from 6 tumor-normal pairs was carried out. We performed an unbiased screen for point mutations, insertions-deletions, rearrangements and copy-number changes across the exomes and genomes. Recurrent (potential driver) events were then analyzed with additional algorithms for statistical significance. Results: Alterations in the NF2 gene were present in 9 of 16 patients. Multiple novel rearrangements and recurrent non-NF2 mutations were also identified in the cohort. Massive genomic rearrangement termed chromothripsis was observed in chromosome 1 in one sample, which has never previously been described in meningiomas, and represents a potentially new mechanism of malignant transformation in this tumor type. Conclusions: While NF2 mutations appear to drive a majority of these tumors, our analysis has uncovered additional potential driver genes in meningiomas, particularly in those tumors negative for NF2 alterations. To our knowledge, this is the first study to comprehensively characterize the totality of somatic genetic alterations in meningiomas, and brings us closer to the development of new therapeutic targets for this disease.
Between two absolutes: public opinion and the politics of abortion.
Authors: Cook Ea, Jelen Tg, Wilcox C, Horan Dj, Arie S, Belton S, Whittaker A, Fonseca Z, Wells-Brown T, Pais P, Madrazo A, Faundes A, Rao K, Briozzo L, Moloney A, Bianco M, Belizán Jm, Althabe F, Shepard Bl, Becerra Lc, Talia J
Journal: BMJ (1992)

The authors examine changes in public attitudes toward abortion in the United States.  They suggest that control of abortion is being removed from the federal courts and put into the hands of elected officials at both federal and state levels and that public opinion on abortion will therefore come to play an increasing role in the molding of abortion policy.  They examine the factors that influence peoples abortion attitudes the role of religion in shaping those attitudes and the consequences of abortion attitudes for electoral politics.  (ANNOTATION)
Treatment of Asthma
Authors: D. J. Salberg
Journal: JAMA (1980)

<h3>To the Editor.—</h3> In view of the recent interest in theophylline pharmacokinetics and β<sub>2</sub>-adrenergic agents, the article by Josephson et al (242:639, 1979) was a refreshing reminder of the efficacy of epinephrine in the treatment of acute asthma. Apparently, all subjects experienced improvement in the peak expiratory flow rates (PEF), although only group mean values and SDs were presented. Presumably, the clinical response was directly related to the PEF. Ultimately, 75% of subjects were discharged after 90 minutes; 22% were discharged within 12 hours; and only 3% required admission. Unfortunately, the authors did not relate the criteria used in determining the discharge or admission of subjects. The data provided indicate that only 2.5% of subjects showed greater than 70% of their predicted PEFs during the study. Most subjects failed to improve their PEFs to 60% of predicted values. Thus, the majority of subjects seem to have been discharged
BiTEing the Tumor
Authors: Shaji Kumar, S. Vincent Rajkumar
Journal: Journal of Clinical Oncology (2020)

Article Tools UNDERSTANDING THE PATHWAY Article Tools OPTIONS & TOOLS Export Citation Track Citation Add To Favorites Rights & Permissions COMPANION ARTICLES Anti–B-Cell Maturation Antigen BiTE Molecule AMG 420 Induces Responses in Multiple Myeloma. January 02, 2020 ARTICLE CITATION DOI: 10.1200/JCO.20.00223 Journal of Clinical Oncology - published online before print May 6, 2020 PMID: 32374643 BiTEing the Tumor Shaji Kumar, MDxShaji KumarSearch for articles by this author, and S. Vincent Rajkumar, MDxS. Vincent RajkumarSearch for articles by this author Show More Division of Hematology, Mayo Clinic, Rochester, MN https://doi.org/10.1200/JCO.20.00223 First Page Full Text PDF Figures and Tables © 2020 by American Society of Clinical Oncology Companion Anti–B-Cell Maturation Antigen BiTE Molecule AMG 420 Induces Responses in Multiple Myeloma
Abstract 13794: Automated Disease Detection Using Document Classification Outperforms Encounter-Level Diagnostic Codes for Cardiovascular Diseases
Authors: Max Homilius, Alexander J Blood, Brian H Park, Daniel Yazdi, Jason N Veytsman, Calum A MacRae, Rahul C Deo
Journal: Circulation (2019)

Introduction: Researchers increasingly turn to electronic health records (EHR) to develop predictive models of disease. Such models can suffer from inaccurate patient diagnoses captured in EHR code...
Pomalidomide, dexamethasone, and daratumumab in relapsed refractory multiple myeloma after lenalidomide treatment
Authors: David S. Siegel, Gary J. Schiller, Christy Samaras, Michael Sebag, Jesus Berdeja, Siddhartha Ganguly, Jeffrey Matous, Kevin Song, Christopher S. Seet, Giampaolo Talamo, Mirelis Acosta-Rivera, Michael Bar, Donald Quick, Bertrand Anz, Gustavo Fonseca, Donna Reece, William E. Pierceall, Weiyuan Chung, Faiza Zafar, Amit Agarwal, Nizar J. Bahlis
Journal: Leukemia (2020)

Abstract Patients with multiple myeloma who have relapsed after or become refractory to lenalidomide in early treatment lines represent a clinically important population in need of effective therapies. The safety and efficacy of pomalidomide, low-dose dexamethasone, and daratumumab was evaluated in lenalidomide-pretreated patients with relapsed or refractory multiple myeloma (RRMM) after one to two prior treatment lines in the phase 2 MM-014 study. Patients received pomalidomide 4 mg daily from days 1–21 and dexamethasone 40 mg weekly (28-day cycles). Daratumumab 16 mg/kg was administered per label. Primary endpoint was overall response rate (ORR); secondary endpoints included progression-free survival (PFS) and safety. Per protocol, all patients ( N = 112) had received lenalidomide in their most recent prior regimen (75.0% lenalidomide refractory). ORR was 77.7% (76.2% in lenalidomide-refractory patients); median follow-up was 17.2 months. Median PFS was not reached (1-year PFS rate 75.1%). The most common hematologic grade 3/4 treatment-emergent adverse event was neutropenia (62.5%). Grade 3/4 infections were reported in 31.3% of patients, including 13.4% with grade 3/4 pneumonia. These results demonstrate the safety and efficacy of pomalidomide-based therapy as early as second line in patients with RRMM, even immediately after lenalidomide failure, indicating that switching from the immunomodulatory agent class is not necessary.
Multicenter cohort study demonstrates more consolidation in upper lungs on initial CT increases the risk of adverse clinical outcome in COVID-19 patients
Authors: Qian Yu, Yuancheng Wang, Shan Huang, Songqiao Liu, Zhen Zhou, Shijun Zhang, Zhen Zhao, Yizhou Yu, Yi Yang, Shenghong Ju
Journal: Theranostics (2020)

Rationale: Chest computed tomography (CT) has been used for the coronavirus disease 2019 (COVID-19) monitoring. However, the imaging risk factors for poor clinical outcomes remain unclear. In this study, we aimed to assess the imaging characteristics and risk factors associated with adverse composite endpoints in patients with COVID-19 pneumonia. Methods: This retrospective cohort study enrolled patients with laboratory-confirmed COVID-19 from 24 designated hospitals in Jiangsu province, China, between 10 January and 18 February 2020. Clinical and initial CT findings at admission were extracted from medical records. Patients aged < 18 years or without available clinical or CT records were excluded. The composite endpoints were admission to ICU, acute respiratory failure occurrence, or shock during hospitalization. The volume, density, and location of lesions, including ground-glass opacity (GGO) and consolidation, were quantitatively analyzed in each patient. Multivariable logistic regression models were used to identify the risk factors among age and CT parameters associated with the composite endpoints. Results: In this study, 625 laboratory-confirmed COVID-19 patients were enrolled; among them, 179 patients without an initial CT at admission and 25 patients aged < 18 years old were excluded and 421 patients were included in analysis. The median age was 48.0 years and the male proportion was 53% (224/421). During the follow-up period, 64 (15%) patients had a composite endpoint. There was an association of older age (odds ratio [OR], 1.04; 95% confidence interval [CI]: 1.01-1.06; P = 0.003), larger consolidation lesions in the upper lung (Right: OR, 1.13; 95%CI: 1.03-1.25, P =0.01; Left: OR,1.15; 95%CI: 1.01-1.32; P = 0.04) with increased odds of adverse endpoints. Conclusion: There was an association of older age and larger consolidation in upper lungs on admission with higher odds of poor outcomes in patients with COVID-19.
Surfing the Waves of the COVID-19 Pandemic as a Cardiovascular Clinician
Authors: Payal Kohli, Salim S. Virani
Journal: Circulation (2020)

he way we practice medicine during the coronavirus disease 2019 (CO-VID-19) pandemic is unprecedented.The healing power of the face-to-face visit and the human touch are no longer privileges afforded to us.Clinical decisions previously made on the basis of appropriate diagnostic testing and careful contemplation are now made on the basis of intuition because of a lack of testing resources.Therapies administered on the basis of data from rigorously conducted clinical trials have been replaced with therapies that are based on anecdotal evidence.The novel coronavirus has, in a few months, collapsed the global economy, changed the landscape of healthcare delivery, and left many types of casualtieshuman and nonhuman-in its wake.Our only defense is to flatten the curve of destruction by practicing social distancing.It is a paradox that as we flatten the curve of infection, we may inadvertently steepen the curve of non-guideline-based healthcare delivery.
Tuberculous autonephrectomy
Authors: S.-Y. Li, K.-L. Wang, J.-Y. Chen, T.-W. Chen
Journal: Kidney International (2006)

A 55-year-old woman presented with fever, turbid urine, and right-flank pain. She had a past history of renal tuberculosis at age 17. Plain films of her abdomen showed five ovoid rings of calcification over the left-flank region (Figure 1). An abdominal computed tomography scan demonstrated marked dilatation of the left renal pelvicaliceal system with thinning and calcification of the parenchyma (Figure 2). Right-sided hydronephrosis was due to the stricture of the ureter. Urine culture grew out Escherichia coli. Acid-fast stain, tuberculous culture, and tuberculosis polymerase chain reaction were all negative. The patient was treated by right percutaneous nephrostomy and intravenous antibiotic administration. Her symptoms and pyuria resolved in 1 week. Renal tuberculosis can be associated with autonephrectomy of the kidney and ureteral strictures.Figure 2A non-contrast computed tomography scan demonstrated autonephrectomy of the left kidney and hydronephrosis of the right kidney.View Large Image Figure ViewerDownload (PPT)
Reply to Donald Lamm, Andreas Böhle, Joan Palou, et al.’s Letter to the Editor re: Per-Uno Malmström, Richard J. Sylvester, David E. Crawford, et al. An Individual Patient Data Meta-Analysis of the Long-Term Outcome of Randomised Studies Comparing Intravesical Mitomycin C versus Bacillus Calmette-Guérin for Non–Muscle-Invasive Bladder Cancer. Eur Urol 2009;56:247–56
Authors: Per-Uno Malmström, Richard J. Sylvester
Journal: European Urology (2009)
Diastolic Wall Strain can Noninvasively Predict Hemodynamic Deterioration Unassociated with Systolic Dysfunction in Hypertensive Hearts | Article Information | J-GLOBAL
Authors: Omori Yosuke, Sakata Yasushi, Mano Toshiaki, Ohtani Tomohito, Takeda Yasuharu, Tamaki Shunsuke, Kamimura Daisuke, Higashimori Mitsuru, Kaneko Makoto, Yamamoto Kazuhiro
Journal: Circulation (2009)
Cross-sectional study of blood biomarkers of patients with moderate to severe alopecia areata reveals systemic immune and cardiovascular biomarker dysregulation
Authors: Jacob W. Glickman, Celina Dubin, Yael Renert-Yuval, Dante Dahabreh, Grace W. Kimmel, Kelsey Auyeung, Yeriel D. Estrada, Giselle Singer, James G. Krueger, Ana B. Pavel, Emma Guttman-Yassky
Journal: Journal of the American Academy of Dermatology (2020)
Surgical Pathology of Non-Neoplastic Lung Disease.
Authors: A A Katzenstein, F B Askin
Journal: Annals of Internal Medicine (1983)

Handling and interpretation acute lung injury patterns - DAD, AIP, BOOP idiopathic interstitial pneumonia/pulmonary fibrosis drug-induced lung disease pneumoconiosis immunologic lung disease systemic diseases involving the lung angiitis and granulomatosis lymphoid lung lesions infection I infection II the lung in AIDS pulmonary hypertension and other vascular disorders paediatric disorders I paediatric disorders II miscellaneous I miscellaneous II transbronchial lung biopsy.