tbuckley/cabot-search huggingface dataset:
Passive Nocturnal Physiologic Monitoring Enables Early Detection of Exacerbations in Children with Asthma. A Proof-of-Concept Study
Authors: Michelle F. Huffaker, Michael Carchia, Bronwyn U. Harris, William C. Kethman, Todd E. Murphy, Charlotte C. D. Sakarovitch, FeiFei Qin, David N. Cornfield
Journal: American Journal of Respiratory and Critical Care Medicine (2018)

Rationale: Asthma management depends on prompt identification of symptoms, which challenges both patients and providers. In asthma, a misapprehension of health between exacerbations can compromise compliance. Thus, there is a need for a tool that permits objective longitudinal monitoring without increasing the burden of patient compliance.Objectives: We sought to determine whether changes in nocturnal physiology are associated with asthma symptoms in pediatric patients.Methods: Using a contactless bed sensor, nocturnal heart rate (HR), respiratory rate, relative stroke volume, and movement in children with asthma 5–18 years of age (n = 16) were recorded. Asthma symptoms and asthma control test (ACT) score were reported every 2 weeks. Random forest model was used to identify physiologic parameters associated with asthma symptoms. Elastic net regression was used to identify variables associated with ACT score.Measurements and Main Results: The model on the full cohort performed with sensitivity of 47.2%, specificity of 96.3%, and accuracy of 87.4%; HR and respiratory parameters were the most important variables in this model. The model predicted asthma symptoms 35% of the time on the day before perception of symptoms, and 100% of the time for a select subject for which the model performed with greater sensitivity. Multivariable and bivariable analyses demonstrated significant association between HR and respiratory rate parameters and ACT score.Conclusions: Nocturnal physiologic changes correlate with asthma symptoms, supporting the notion that nocturnal physiologic monitoring represents an objective diagnostic tool capable of longitudinally assessing disease control and predicting asthma exacerbations in children with asthma at home.
OCEAN-C: mapping hubs of open chromatin interactions across the genome reveals gene regulatory networks
Authors: Tingting Li, Lumeng Jia, Yong Cao, Qing Chen, Cheng Li
Journal: Genome biology (2018)

We develop a method called open chromatin enrichment and network Hi-C (OCEAN-C) for antibody-independent mapping of global open chromatin interactions. By integrating FAIRE-seq and Hi-C, OCEAN-C detects open chromatin interactions enriched by active cis-regulatory elements. We identify more than 10,000 hubs of open chromatin interactions (HOCIs) in human cells, which are mainly active promoters and enhancers bound by many DNA-binding proteins and form interaction networks crucial for gene transcription. In addition to identifying large-scale topological structures, including topologically associated domains and A/B compartments, OCEAN-C can detect HOCI-mediated chromatin interactions that are strongly associated with gene expression, super-enhancers, and broad H3K4me3 domains.
malERA: An updated research agenda for health systems and policy research in malaria elimination and eradication
Journal: PLoS Medicine (2017)

Health systems underpin disease elimination and eradication programmes. In an elimination and eradication context, innovative research approaches are needed across health systems to assess readiness for programme reorientation, mitigate any decreases in effectiveness of interventions (‘effectiveness decay’), and respond to dynamic and changing needs. The malaria eradication research agenda (malERA) Refresh consultative process for the Panel on Health Systems and Policy Research identifies opportunities to build health systems evidence and the tools needed to eliminate malaria from different zones, countries, and regions and to eradicate it globally. The research questions are organised as a portfolio that global health practitioners, researchers, and funders can identify with and support. This supports the promotion of an actionable and more cohesive approach to building the evidence base for scaled-up implementation of findings. Gaps and opportunities discussed in the paper include delivery strategies to meet the changing dynamics of needs of individuals, environments, and malaria programme successes; mechanisms and approaches to best support accelerated policy and financial responsiveness at national and global level to ensure timely response to evidence and needs, including in crisis situations; and systems’ readiness tools and decision-support systems.
Can sidedness predict for survival in primary locoregional colon cancers?
Authors: Weining Wang, Chin Jin Seo, Grace Hwei Ching Tan, Claramae Shulyn Chia, Khee Chee Soo, Melissa Ching Ching Teo
Journal: Journal of Clinical Oncology (2018)

584 Background: Right and left-sided colon cancers are embryonically distinct and present differently. Recently, there has been growing belief that sidedness could be independently associated with survival outcomes. This has important clinical implications regarding the prognostication, management and surveillance of colon cancer patients. Hence, we aim to investigate the impact of sidedness on survival in our patient population in this study. Methods: Patients who had primary treatment naïve colon cancer who underwent curative surgical resection in our institution from September 2002 to December 2010 were included in this study. Demographic and clinicopathological data was collected from electronic records and clinical charts. Tumours arising from the cecum, ascending colon, hepatic flexure and transverse colon were considered right-sided, while those arising from splenic flexure and descending colon were considered left-sided. Cancers of the rectosigmoid junction and rectum were excluded. Kaplan-Meier curves and log-rank test were used to compare overall, locoregional recurrence-free and distant recurrence-free survivals (OS, LRFS, DRFS respectively) between both groups. Multivariate analysis was performed using Cox regression proportional hazards. Results: 389 patients were included in this study. 238 had left-sided tumours while the remaining 151 had right-sided tumours. In our cohort, right-sided tumours were associated with older age and mucinous histology. Kaplan-Meier curves plotted showed improved LRFS in left-sided tumours (p = 0.04, median survival not reached) but no significant difference in OS and DRFS. On multivariate analysis, sidedness was also found to be an independent prognostic factor for LRFS but not OS and DRFS despite factoring in age, size of tumour, pT, pN and histology. Conclusions: Our study suggests that left-sided tumours in primary colon cancer are independently prognostic for improved locoregional survival as compared to the right-sided tumours, even after taking into account other known factors such as age, staging and histology.
A combined model based on spleen stiffness measurement and Baveno VI criteria to rule out high-risk varices in advanced chronic liver disease
Authors: Antonio Colecchia, Federico Ravaioli, Giovanni Marasco, Agostino Colli, Elton Dajti, Anna Rita Di Biase, Maria Letizia Bacchi Reggiani, Annalisa Berzigotti, Massimo Pinzani, Davide Festi
Journal: Journal of Hepatology (2018)
Acceleration of NASH in a mouse model provides novel insights on the mechanisms by which I148M PNPLA3 drives steatohepatitis
Authors: B. Banini, S. Cazanave, H.-K. Min, D. Kumar, P. Santhekadur, L. Wang, H.-P. Guan, M. Seneshaw, P. Bedossa, A. Oseini, F. Mirshahi, C. Alonso, S. Koduru, A. Sanyal
Journal: Journal of Hepatology (2018)
When You Hear Hoofbeats, Look for Horses, Not Zebras
Authors: Yuki Kataoka, Azusa Sakurai, Emiko Saito
Journal: JAMA Oncology (2018)

To the Editor We read the article by Hung et al1 with great interest. If anaplastic lymphoma kinase (ALK) rearrangements in peritoneal mesothelioma could be incorporated into the treatment, it would be a godsend for patients. However, we would like to address 1 concern about the diagnosis.
Statistical Analysis Plans for Clinical Trials
Authors: Bruno Mario Cesana
Journal: JAMA (2018)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Performance of a computer-aided digital dermoscopic image analyzer for melanoma detection in 1,076 pigmented skin lesion biopsies
Authors: Francis del Rosario, Jessica M. Farahi, Jesse Drendel, Talayesa Buntinx-Krieg, Joseph Caravaglio, Renee Domozych, Stephanie Chapman, Taylor Braunberger, Robert P. Dellavalle, David A. Norris, Ramin Fathi, Theodore Alkousakis
Journal: Journal of the American Academy of Dermatology (2018)
Treatment at high-volume facilities and academic centers in relation to overall survival in patients with locally advanced pancreatic cancer: A National Cancer Database analysis
Authors: John David, Sungjin Kim, Erik Anderson, Arman Torossian, Simon Lo, Nicholas N. Nissen, Andrew Eugene Hendifar, Richard Tuli
Journal: Journal of Clinical Oncology (2018)

392 Background: Numerous studies have shown that treatment at a high volume facility (HVF) for patients (pts) with pancreatic cancer is associated with improved outcomes, particularly with pancreatectomy. In fact, a recent study showed that pts undergoing a pancreatectomy at an academic center (AC) is independently associated with improved outcomes. However, the role of chemotherapy (CT) and radiation (RT) in the treatment of locally advanced pancreatic cancer (LAPC) at HVF and AC, to our knowledge, has not been studied. Herein, we investigate the benefit of treatment at HVF and AC compared to low volume facilities (LVF) and non-academic centers (NAC) with CT or chemoradiation (CRT) in pts with LAPC. Methods: The National Cancer Database (NCDB) was utilized to identify LAPC patients treated at all facility types. All patients were treated with CT or CRT. Univariate (UVA) and multivariate (MVA) Cox regression were performed to identify the impact of HVF and AC on overall survival (OS) when compared to LVF and NAC, respectively. HVF was defined as the top 5% of facilities by number of pts treated. Results: From 2004 – 2014, a total of 10139 pts were identified. The median age was 66 years (range 22-90) with median follow up of 48.8 months (46-52.1 months); 49.9% were male and 50.1% female. All pts had clinical stage 3/T4 disease irrespective of nodal metastases. Of these, 4779 pts were treated at an AC and 5260 were treated at a NAC and 588 were treated at HVF and 9551 were treated at LVF. On UVA, age, high median income, high education level, comorbidities, and recent year of diagnosis were associated with improved OS. ACs were associated with improved OS when compared to non-AC (HR 0.92 95% CI 0.88 – 0.96, p = 0.004), as were HVF when compared to LVH (HR 0.84 95% CI 0.76 – 0.92, p &lt; 0.001). Odds ratio for undergoing surgical resection at HVF and AC was 1.68 and 1.37 (p &lt; 0.001), respectively, when compared to LVF and NAC. Conclusions: The treatment of LAPC patients with CT or CRT at an AC led to significantly improved rate of surgical resection and OS. In the absence of prospective data, these results support the referral of pts with LAPC to HVF and/or AC for evaluation and treatment.
Is treatment of hepatitis C with controlled generic direct acting antiviral drugs effective? An Egyptian experience
Authors: G. Soliman, M.S. Negm, M. Elzalabany, A.A. Malik, A. Khattab, M. Elshair, M.G. Abdel-Hamid, M.Y. Soliman, D. Miller, T. Hassanein
Journal: Journal of Hepatology (2018)
[ 177 Lu]-PSMA-617 radionuclide treatment in patients with metastatic castration-resistant prostate cancer (LuPSMA trial): a single-centre, single-arm, phase 2 study
Authors: Michael S Hofman, John Violet, Rodney J Hicks, Justin Ferdinandus, Sue Ping Thang, Tim Akhurst, Amir Iravani, Grace Kong, Aravind Ravi Kumar, Declan G Murphy, Peter Eu, Price Jackson, Mark Scalzo, Scott G Williams, Shahneen Sandhu
Journal: The Lancet Oncology (2018)
Subcutaneous adipose tissue is a predictor of survival in patients with hepatocellular carcinoma
Authors: L. von Koeckritz, P. Kolly, M. Maurer, S.-E. Birgit, A. Berzigotti, A.D. Gottardi, N. Semmo, S. Casu, S. Guido, V. Banz, J. Bosch, J. -François Dufour
Journal: Journal of Hepatology (2018)
T cells isolated from patients with checkpoint inhibitor-resistant melanoma are functional and can mediate tumor regression
Authors: R. Andersen, T.H. Borch, A. Draghi, A. Gokuldass, M.A.H. Rana, M. Pedersen, M. Nielsen, P. Kongsted, J.W. Kjeldsen, M.C.W. Westergaard, H.D. Radic, C.A. Chamberlain, L.R. Hölmich, H.W. Hendel, M.S. Larsen, Ö Met, I.M. Svane, M. Donia
Journal: Annals of Oncology (2018)

Almost half of the patients with metastatic melanoma obtain only short-term or no benefit at all from checkpoint inhibitor (CPI) immunotherapy. In this study, we investigated whether the immune system of patients progressing following CPI treatment was able to generate functional tumor-specific immune responses.Tumor-infiltrating lymphocytes (TILs) were isolated and expanded from metastatic melanoma lesions which progressed during or after anti-programmed cell death protein 1 (PD)-1 and anti-Cytotoxic T-Lymphocyte Antigen 4 (CTLA-4) treatment. Tumor-specific immune responses were assessed with co-culture assays of TILs and autologous tumor cells.TILs from 23 metastases of individual patients could be assessed for T cells recognition of autologous tumor cells. All metastases were progressive on or following anti-PD-1 (23/23, 100%), and the majority also after anti-CTLA-4 (17/23, 74%). Functional antitumor immune responses were detected in 19/23 patients (83%). Both CD8+ (in 18/23 patients, 78%) and CD4+ (in 16/23 patients, 70%) TILs were able to recognize autologous tumors. A large fraction of CD8+ TILs (median 23%, range 1.0%-84%) recognized tumor cells. This is similar to the cohorts of unselected patient populations with metastatic melanoma presented in previous studies. The localization of intratumoral immune infiltrates was heterogeneous among samples. In a phase I/II clinical trial, TILs were administered with lymphodepleting chemotherapy, pegIFNα2b and interleukin-2 to 12 patients with CPI-resistant melanoma. Out of 12 patients who previously failed CPI therapy, treatment with TILs resulted in two partial responses, of which one is ongoing.Tumor-reactive T cells appear to heavily infiltrate the tumor microenvironment of patients who failed previous CPI treatment. These patients can still respond to an infusion of unselected autologous TILs. Our results warrant further testing of novel immune re-activation strategies in melanoma patients who failed multiple CPI therapy.
Outcomes of sequential treatment with sorafenib followed by regorafenib for HCC: Additional analyses from the phase III RESORCE trial
Authors: Richard S. Finn, Philippe Merle, Alessandro Granito, Yi-Hsiang Huang, György Bodoky, Marc Pracht, Osamu Yokosuka, Olivier Rosmorduc, René Gerolami, Chiara Caparello, Roniel Cabrera, Charissa Chang, Weijing Sun, Marie-Aude LeBerre, Annette Baumhauer, Gerold Meinhardt, Jordi Bruix
Journal: Journal of Hepatology (2018)
Clinical significance of Cystatin S in cancer diagnosis and treatment assessment.
Authors: Xiaojin Zhou, Yong Qin, Yaling Dou, Yulong Sun, Weichen Xu, Zhen Yang, Tao Wang
Journal: Journal of Clinical Oncology (2014)

e22226 Background: Cystatins are a family of cysteine protease inhibitor. The pathological significance of cystatins has recently been revealed. We systematically evaluated cystatin S as a biomarker for colorectal cancer (CRC) and gastric cancer (GC). Methods: We enrolled 170 CRC and 149 GC patients of all stages from 2011 to 2013. Meanwhile, we enrolled 130 healthy subjects (HS), 49 patients with other cancers (OC), 24 patients with benign colon or gastric tumors (BT) and 63 patients with non-cancer diseases such as enteritis (OD) as the control groups. Post-treatment blood samples of 48 CRC and 28 GC patients enrolled were acquired. Serum cystatin S level was quantified by ELISA assay. Results: The medians of serum cystatin S level for groups of CRC, GC, HS, OC, BT and OD groups were 116, 86.4, 46.7, 121, 51.7 and 70.3 μg/L respectively. Area-under-curve (AUC) values of ROC analysis were calculated to assess the performance of cystatin S. Cystatin S is a valid cancer marker to distinguish cancer patients from non-cancerous patients including those with benign tumors, with moderate-high sensitivity and specificity. (Table) Cystatin S is not capable to differentiate CRC or GC patients from other cancer patients. We noticed its better performance than CEA, with sensitivity of 30-40% and moderate specificity (i.e. 80%). It is noted that we were even able to detect 90.0% CRC (18/20) and 81.0% (17/21) GC patients of stage I using the optimal cutoff from the data above. We compared cystatin S levels of CRC or GC patients before and after treatments. Cystatin S level decrease was observed on 75% (36/48) CRC patients and 89% (25/28) GC patients, Among CRC and GC patients with decreased cystatin S levels, the stable disease rate (SD) is 66.7% (24/36) and 76% (19/25) respectively. Conclusions: Cystatin S is a promising tumor biomarker for early cancer diagnosis and treatment evaluation; it is not a specific marker for colorectal or gastric cancer. ROC analysis results for evaluation of Cystatin S as a biomarker for CRC and GC diagnosis and cancer diagnosis. Testing subgroups Control subgroups AUC CRC, GC OC, OD, HS, BT 0.677 CRC, GC, OC OD, HS, BT 0.741 CRC,GC OC 0.427
Comparison of the risks of hepatocellular carcinoma in patients with chronic hepatitis B virus infection: estimation of direct carcinogenic effect of hepatitis B virus
Authors: Y. Chang, J.-H. Lee, J.Y. Nam, H.Y. Lee, H. Cho, Y.Y. Cho, E.J. Cho, S. Yu, Y.J. Kim, J.-H. Yoon
Journal: Journal of Hepatology (2018)
The protein complex structural maintenance of chromosomes reappears after interferon alpha treatment in hepatitis B virus infected humanized mice but its presence does not hinder viral rebound
Authors: K. Giersch, T. Volz, L. Allweiss, A. Lohse, S. Urban, J. Petersen, M. Lütgehetmann, M. Dandri
Journal: Journal of Hepatology (2018)
Mechanosensitive Gene Regulation by Myocardin-Related Transcription Factors Is Required for Cardiomyocyte Integrity in Load-Induced Ventricular Hypertrophy
Authors: Michael A. Trembley, Pearl Quijada, Esperanza Agullo-Pascual, Kevin M. Tylock, Mert Colpan, Ronald A. Dirkx, Jason R. Myers, Deanne M. Mickelsen, Karen de Mesy Bentley, Eli Rothenberg, Christine S. Moravec, Jeffrey D. Alexis, Carol C. Gregorio, Robert T. Dirksen, Mario Delmar, Eric M. Small
Journal: Circulation (2018)

Background: Hypertrophic cardiomyocyte growth and dysfunction accompany various forms of heart disease. The mechanisms responsible for transcriptional changes that affect cardiac physiology and the transition to heart failure are not well understood. The intercalated disc (ID) is a specialized intercellular junction coupling cardiomyocyte force transmission and propagation of electrical activity. The ID is gaining attention as a mechanosensitive signaling hub and hotspot for causative mutations in cardiomyopathy. Methods: Transmission electron microscopy, confocal microscopy, and single-molecule localization microscopy were used to examine changes in ID structure and protein localization in the murine and human heart. We conducted detailed cardiac functional assessment and transcriptional profiling of mice lacking myocardin-related transcription factor (MRTF)-A and MRTF-B specifically in adult cardiomyocytes to evaluate the role of mechanosensitive regulation of gene expression in load-induced ventricular remodeling. Results: We found that MRTFs localize to IDs in the healthy human heart and accumulate in the nucleus in heart failure. Although mice lacking MRTFs in adult cardiomyocytes display normal cardiac physiology at baseline, pressure overload leads to rapid heart failure characterized by sarcomere disarray, ID disintegration, chamber dilation and wall thinning, cardiac functional decline, and partially penetrant acute lethality. Transcriptional profiling reveals a program of actin cytoskeleton and cardiomyocyte adhesion genes driven by MRTFs during pressure overload. Indeed, conspicuous remodeling of gap junctions at IDs identified by single-molecule localization microscopy may partially stem from a reduction in Mapre1 expression, which we show is a direct mechanosensitive MRTF target. Conclusions: Our study describes a novel paradigm in which MRTFs control an acute mechanosensitive signaling circuit that coordinates cross-talk between the actin and microtubule cytoskeleton and maintains ID integrity and cardiomyocyte homeostasis in heart disease.