tbuckley/cabot-search huggingface dataset:
Increased prevalence of pathogenic bacteria in the gut microbiota of infants at risk of developing celiac disease: The PROFICEL study
Authors: Marta Olivares, Alfonso Benítez-Páez, Giada de Palma, Amalia Capilla, Esther Nova, Gemma Castillejo, Vicente Varea, Ascensión Marcos, José Antonio Garrote, Isabel Polanco, Ester Donat, Carmen Ribes-Koninckx, Carmen Calvo, Luis Ortigosa, Francesc Palau, Yolanda Sanz
Journal: Gut Microbes (2018)

Celiac disease (CD) is an immune-mediated enteropathy involving genetic and environmental factors, whose interaction influences disease risk. The intestinal microbiota, including viruses and bacteria, could play a role in the pathological process leading to gluten intolerance. In this study, we investigated the prevalence of pathogens in the intestinal microbiota of infants at familial risk of developing CD. We included 127 full-term newborns with at least one first-degree relative with CD. Infants were classified according to milk-feeding practice (breastfeeding or formula feeding) and HLA-DQ genotype (low, intermediate or high genetic risk). The prevalence of pathogenic bacteria and viruses was assessed in the faeces of the infants at 7 days, 1 month and 4 months of age. The prevalence of Clostridium perfringens was higher in formula-fed infants than in breast-fed over the study period, and that of C. difficile at 4 months. Among breastfed infants, a higher prevalence of enterotoxigenic E. coli (ETEC) was found in infants with the highest genetic risk compared either to those with a low or intermediate risk. Among formula-fed infants, a higher prevalence of ETEC was also found in infants with a high genetic risk compared to those of intermediate risk. Our results show that specific factors, such as formula feeding and the HLA-DQ2 genotype, previously linked to a higher risk of developing CD, influence the presence of pathogenic bacteria differently in the intestinal microbiota in early life. Further studies are warranted to establish whether these associations are related to CD onset later in life.
TCTAP A-118 Comparison of Traditional Two Catheters Versus Single Radial Specific Catheter for Transradial Coronary Angiography: A Prospective Randomized Control Study
Authors: Lalita Nemani, Malleswara Rao Dangeti, V.S.R. Bhupal, Indrani Garre, Janaswamy Vibhav Sri Narayana, Maddury Jyotsna
Journal: Journal of the American College of Cardiology (2018)
Clustered Regularly Interspaced Short Palindromic Repeats-Based Genome Surgery for the Treatment of Autosomal Dominant Retinitis Pigmentosa
Authors: Yi-Ting Tsai, Wen-Hsuan Wu, Ting-Ting Lee, Wei-Pu Wu, Christine L. Xu, Karen S. Park, Xuan Cui, Sally Justus, Chyuan-Sheng Lin, Ruben Jauregui, Pei-Yin Su, Stephen H. Tsang
Journal: Ophthalmology (2018)
CEA as a pharmacodynamic biomarker for metastatic anal cancer.
Authors: Robert Harrison Hester, Cullen M. Taniguchi, Emma Brey Holliday, Eugene Jon Koay, Prajnan Das, Bruce D. Minsky, Asif Rashid, Amir Mehdizadeh, Aki Ohinata, Craig Messick, Y. Nancy You, George J. Chang, Brian Bednarski, Miguel A. Rodriguez-Bigas, John Michael Skibber, Robert A. Wolff, Cathy Eng, Van Karlyle Morris
Journal: Journal of Clinical Oncology (2018)

684 Background: While carcinoembryonic antigen (CEA) as a tumor marker is frequently used in the management of colorectal adenocarcinoma, its clinical utility in squamous cell carcinoma of the anus (SCCA) has never been reported. Indeed, no tumor markers have been validated for monitoring tumor burden in the course of any HPV-associated malignancy like SCCA. We hypothesized that CEA levels might be preferentially elevated in patients with metastatic SCCA. Methods: Charts from 212 patients with SCCA were reviewed under an IRB-approved protocol for correlations between CEA levels and corresponding oncologic status. Clinical status was categorized as newly diagnosed non-metastatic (D), after chemoradiation with no evident remnant disease (N), recurrent/resectable SCCA (R), locally advanced/unresectable SCCA (U), metastatic SCCA to lymph nodes only (M-LN), or metastatic SCCA to visceral organs (M-V). Mean CEA levels were compared between subgroups via student t-tests, and frequencies of elevated CEA were compared via Chi-squared analyses. Results: 118 SCCA patients had metastatic disease (98 M-V, 19 M-LN). Mean CEA levels by clinical status were 5.4 (D), 2.0 (N), 2.3 (R), 4.6 (U), 6.0 (M-LN), and 22.2 (M-V), with a higher (statistically insignificant) mean CEA level in the M-V relative to other populations. However, patients with visceral metastases were more likely to have an elevated CEA at presentation (40.4%) relative to patients with newly diagnosed, non-metastatic SCCA (17.6%, p = .07) or recurrent SCCA (11.1%, p = .02). For patients with metastatic SCCA, a significant association existed between change in CEA and corresponding change in radiographic tumor dimensions (OR 24, p &lt; 0.0001). Conclusions: Trends in CEA correlate with dynamic changes in tumor burden for patients with metastatic SCCA, and patients with metastatic SCCA were more likely to have an elevated CEA. Given that immune checkpoint blockade agents like nivolumab have proven benefit for metastatic SCCA, these data provide rationale for use of newer generation immunotherapeutic approaches like CEA-T cell bispecific antibodies, which target CEA-expressing tumors, in clinical trials for patients with metastatic SCCA.
Proliferative glomerulonephritis with monoclonal immunoglobulin G deposits is associated with high rate of early recurrence in the allograft
Authors: Samar M. Said, Fernando G. Cosio, Anthony M. Valeri, Nelson Leung, Sanjeev Sethi, Hassan Salameh, Lynn D. Cornell, Mary E. Fidler, Mariam P. Alexander, Fernando C. Fervenza, Maria Eleni Drosou, Da Zhang, Vivette D. D’Agati, Samih H. Nasr
Journal: Kidney International (2018)
Mass Bat Exposure at National Park
Authors: Bridget Kuehn
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 Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More 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) 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
Identifying epigenetic markers for characterization of host response to hepatitis B virus infection during the development of hepatocellular carcinoma
Authors: W.-J. Wu, S.-H. Yang, W.-J. Liu, W.-Y. Kao, Y.-C. Kuo, C.-L. Lin, C.-J. Liu, Y.-W. Huang, C.-F. Wu, M.-W. Yu
Journal: Journal of Hepatology (2018)
P111Retention of mesenchymal stem cells in the heart is lower after retrograde coronary venous infusion compared to intracoronary infusion in a porcine model of chronic myocardial infarction
Authors: W A Gathier, M Van Der Naald, B R Van Klarenbosch, A E Tuinenburg, JLM Bemelmans, JPG Sluijter, F J Van Slochteren, P A Doevendans, SAJ Chamuleau
Journal: Cardiovascular Research (2018)
Forecasting liver disease burden based on a real life cohort of the linked to care patients in Italy. Does the ‘underwater portion of the iceberg’ matter to reach the WHO HCV eliminating goals in the high HCV prevalent countries?
Authors: S. Robbins, L. Kondili, S. Blach, I. Gamkrelidze, A. Zignego, M. Brunetto, G. Raimondo, G. Taliani, A. Iannone, F.P. Russo, T.A. Santantonio, M.G. Zuin, L. Chessa, P. Blanc, M. Puoti, M. Vinci, E.M. Erne, M. Strazzabosco, M. Massari, P. Lampertico, M.G. Rumi, A. Federico, C. Ferrari, A. Ciancio, G. Borgia, P. Andreone, N. Caporaso, M. Persico, D. Ieluzzi, A. Gori, A. Gasbarrini, C. Coppola, G.B. Gaeta, A. Andriulli, S. Montilla, H. Razavi, M. Melazzini, S. Vella, A. Craxi
Journal: Journal of Hepatology (2018)
Non-alcoholic fatty liver disease is omega-6 fatty acids diet dipendent in a group of obese children
Authors: A. Dalbeni, A. Mantovani, A. Tagetti, S. Bonafini, V. Paon, R. Gaudino, M. Montagnana, E. Danese, A. Donato, P. Minuz, C. Maffeis, F. Antoniazzi, F. Capra, C. Fava
Journal: Journal of Hepatology (2018)
Association of Dasatinib With Progression-Free Survival Among Patients With Advanced Gastrointestinal Stromal Tumors Resistant to Imatinib
Authors: Scott M. Schuetze, Vanessa Bolejack, Dafydd G. Thomas, Margaret von Mehren, Shreyaskumar Patel, Brian Samuels, Edwin Choy, Gina D’Amato, Arthur P. Staddon, Kristen N. Ganjoo, Warren A. Chow, Daniel A. Rushing, Charles A. Forscher, Dennis A. Priebat, David M. Loeb, Rashmi Chugh, Scott Okuno, Denise K. Reinke, Laurence H. Baker
Journal: JAMA Oncology (2018)

<h3>Importance</h3> Gastrointestinal stromal tumors (GISTs) are life-threatening when metastatic or not amenable to surgical removal. In a few patients with advanced GISTs refractory to imatinib mesylate, treatment with sunitinib malate followed by regorafenib provides tumor control; however, additional active treatments are needed for most patients. <h3>Objective</h3> To evaluate the 6-month progression-free survival (PFS), tumor objective response, and overall survival rates in patients with GISTs treated with dasatinib. <h3>Design, Setting, and Participants</h3> This single-arm clinical trial used a Bayesian design to enroll patients 13 years or older with measurable imatinib-refractory metastatic GISTs treated at 14 sarcoma referral centers from June 1, 2008, through December 31, 2009. A control group was not included. Patients were followed up for survival for a minimum of 5 years from date of enrollment. Tumor imaging using computed tomography or magnetic resonance imaging was performed every 8 weeks for the first 24 weeks and every 12 weeks thereafter. Tumor response was assessed by local site using the Choi criteria. Treatment was continued until tumor progression, unacceptable toxic effects after reduction in drug dose, or patient or physician decision. Archival tumor tissue was evaluated for expression of the proto-oncogene tyrosine-protein kinase Src (SRC), phosphorylated SRC (pSRC), and succinate dehydrogenase complex iron sulfur subunit B (SDHB) proteins and for mutation in the V-Kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (<i>KIT</i>) and platelet-derived growth factor receptor α (<i>PDGFRA</i>) genes. Data analysis was performed from May 19, 2017, through December 20, 2017. <h3>Interventions</h3> Dasatinib, 70 mg orally twice daily. <h3>Main Outcomes and Measures</h3> The primary end point was the 6-month PFS estimate using greater than 30% as evidence of an active drug and less than 10% as evidence of inactive treatment. <h3>Results</h3> In this study, 50 patients were enrolled (median age, 60 years; age range, 19-78 years; 31 [62%] male and 19 [38%] female; 41 [82%] white), and 48 were evaluable for response. The estimated 6-month PFS rate was 29% in the overall population and 50% in a subset of 14 patients with pSRC in GISTs. Objective tumor response was observed in 25%, including 1 patient with an imatinib-resistant mutation in<i>PDGFRA</i>exon 18. <h3>Conclusions and Relevance</h3> Dasatinib may have activity in a subset of patients with imatinib-resistant GISTs. Further study is needed to determine whether pSRC is a prognostic biomarker.
Predictive biomarkers to ramucirumab in Asian metastatic gastric cancer patients: Circulating angiogenic factors of VEGFR2 and neurophilin as predictive to ramucirumab efficacy in Asain recurrent/metatatic gastric cancer patients.
Authors: Seungtaek Lim, Sun Young Rha, Tae Soo Kim, Hyo Song Kim, Seung Hoon Beom, Hyun Cheol Chung, Minkyu Jung, Hyeong Ju Kwon, Jee Hung Kim, Su Jin Heo
Journal: Journal of Clinical Oncology (2016)

e15536 Background: We conducted an exploratory study to identify potential biomarkers to predict therapeutic effect of ramucirumab in combination with paclitaxel as a second line treatment for recurrent/metastatic Korean gastric cancer (GC) patients. Methods: We retrospectively reviewed clinical efficacay and toxicity in 70 GC patients who received ramucirumab with weekly paclitaxel in an open-label expanded access program after failure to first line chemotherapy. To find potential biomarker of ramucirumab, we investigated the association between efficacy of ramucirumab and tissue molecular characteristics (EBV, MMR, HER2, EGFR, C-MET etc.). Also, we measured circulating biomarkers (VEGF, sVEGFR2, HGF, neuropillin-1, IL-8, and PIGF,) by ELISA method before and after treatment in a subset of patients (n = 44 vs. n = 14, respectively). Results: With the median follow up of 3.1 months (range 0.5~7.6 months), the median progression free survival (PFS) was 3.9 months (95% CI, 3.3~4.6months), and median overall survival (OS) was not reached. Of the 55 evaluable patients, the overall response rate (ORR) was 14.5% (8 partial responses), and disease control rate was 74.5%. Although there was no difference in PFS, OS or ORR according to receptor status, higher DCR was found in patients with EGFR high expression tumors (2+~3+) compared with low expression tumors (0~1+) (87.5% vs. 50%, p = 0.02). Regarding circulating biomarkers related to angiogenesis, longer PFS was seen in patients with higher level of pretreatment serum VEGFR2 (4.1 vs. 2.3 months; p = 0.01) and lower level of pretreatment serum neuropillin-1 (4.1 vs. 2.4 months; p = 0.02). The circulatory biomarkers were not related to toxicity. Currently, test of tissue based biomarkers are also under way. Conclusions: Current study suggested that circulating biomarkers related to angiogenesis quantified by ELISA method may predict prolonged response to ramucirumab in the treatment of gastric cancer patient.
Analysis of the influence of alcohol abstinence on the risk of developing hepatocellular carcinoma (HCC) in patients with alcoholic liver cirrhosis (ALC)
Authors: A. Castano-Garcia, C. Álvarez-Navascués, A. Gomez, M. Varela, M. Fraile, V. Cadahía-Rodrigo, M. Torner, M.L.G. Dieguez, M. Rodríguez
Journal: Journal of Hepatology (2018)
Ancestral Function and Diversification of a Horizontally Acquired Oomycete Carboxylic Acid Transporter
Authors: Fiona R Savory, David S Milner, Daniel C Miles, Thomas A Richards
Journal: Molecular Biology and Evolution (2018)

Horizontal gene transfer (HGT) can equip organisms with novel genes, expanding the repertoire of genetic material available for evolutionary innovation and allowing recipient lineages to colonize new environments. However, few studies have characterized the functions of HGT genes experimentally or examined postacquisition functional divergence. Here, we report the use of ancestral sequence reconstruction and heterologous expression in Saccharomyces cerevisiae to examine the evolutionary history of an oomycete transporter gene family that was horizontally acquired from fungi. We demonstrate that the inferred ancestral oomycete HGT transporter proteins and their extant descendants transport dicarboxylic acids which are intermediates of the tricarboxylic acid cycle. The substrate specificity profile of the most ancestral protein has largely been retained throughout the radiation of oomycetes, including in both plant and animal pathogens and in a free-living saprotroph, indicating that the ancestral HGT transporter function has been maintained by selection across a range of different lifestyles. No evidence of neofunctionalization in terms of substrate specificity was detected for different HGT transporter paralogues which have different patterns of temporal expression. However, a striking expansion of substrate range was observed for one plant pathogenic oomycete, with a HGT derived paralogue from Pythium aphanidermatum encoding a protein that enables tricarboxylic acid uptake in addition to dicarboxylic acid uptake. This demonstrates that HGT acquisitions can provide functional additions to the recipient proteome as well as the foundation material for the evolution of expanded protein functions.
B-Type Natriuretic Peptide Levels and Mortality in Patients With and Without Heart Failure
Authors: Michelle K. York, Deepak K. Gupta, Cassandra F. Reynolds, Eric Farber-Eger, Quinn S. Wells, Katherine N. Bachmann, Meng Xu, Frank E. Harrell, Thomas J. Wang
Journal: Journal of the American College of Cardiology (2018)
Detection and description of <i>ERBB2</i> amplification using circulating cell free tumor DNA (ctDNA) genomic analysis in metastatic colorectal cancer (mCRC).
Authors: Kanwal Pratap Singh Raghav, Jonathan M. Loree, Jeffrey Morris, Shanequa Manuel, Shadarra Crosby, Funda Meric-Bernstam, David Menter, Victoria Raymond, Richard B. Lanman, AmirAli Talasaz, Scott Kopetz
Journal: Journal of Clinical Oncology (2018)

661 Background: ERBB2 amplification (HER2amp) is evolving as a distinct subset of mCRC with therapeutic implications. Although seen in 3-4% of mCRC in tumor tissue, little is known about occurrence of HER2amp in ctDNA. The purpose of this study was to assess the value of ctDNA in detection of HER2amp in blood and to delineate its landscape in mCRC. Methods: We performed a retrospective analysis of mCRC patients (pts) who underwent plasma-derived NGS of ctDNA in a CLIA-certified lab (Guardant Health, Inc.) using a high sensitivity assay that reports copy-number variations using pre-specified algorithms. Pts with no detectable alterations were excluded. The cohort was divided into 2 groups: HER2amp and ERBB2 non-amplified (HER2NA). Descriptive statistics and Fisher’s exact test were used. Results: Between 5/2014 and 5/2016, 1625 mCRC pts had a ctDNA NGS assay and of these 1387 met our inclusion criteria. Among these, HER2amp was seen in 69 pts (4.9%, 95%CI: 3.9 – 6.3). HER2amp were found to be enriched in RAS wild-type (WT) (6.4% v 2.9%, OR 2.3, P = 0.002) and RAS/BRAFV600E WT (6.9% v 2.7%; OR 2.7, P &lt; 0.001). When co-existing with RAS mutations, HER2amps were seen more with sub-clonal ( &lt; 50% relative mutation allele frequency) RAS mutations than clonal RAS mutations (6.6% v 2.1%, OR 3.1, P = 0.03). The most common co-occurring mutations were TP53 (77%), APC (59%), EGFR (25%), PIK3CA (25%) and KRAS (23%). HER2 (13% v 5%, OR 2.6, P = 0.017) and TP53 (77% v 62%, OR 2.1, P = 0.011) mutations co-occurred more frequently with HER2amp than with HER2NA cases. No significant association was seen with PIK3CA, EGFR and APC mutation status. Conclusions: In one of the largest series of CRC pts with ctDNA NGS, ERBB2 amplification were confirmed to be enriched in RAS/BRAF WT mCRC. In these pts, co-existing clonal RAS mutations are uncommon, but concurrent PIK3CA and ERBB2 mutations are present in a sizable minority of cases. These findings may have implications for anticipated innate/acquired resistance mechanisms to HER2-targeting therapies under evaluation for CRC.
P542Human monocyte subsets differentially express tissue factor in vivo and in vitro
Authors: B Thaler, K A Krychtiuk, P J Hohensinner, M Lenz, K Huber, G Heinz, J Wojta, W Speidl
Journal: Cardiovascular Research (2018)

Results: Figure 1 shows the relative fold changes of miRNA-1, miRNA-133 and miRNA-208 during AMI and after reperfusion.All 3 types of miRNAs could be detected in the plasma exosomes.However, ultimately no significant change in the levels of miRNA-1, miRNA-133 and miRNA-208 could be shown at the different time points.Conclusion: Even though all investigated miRNAs could be detected in plasma exosomes, no significant relative changes in miR-1, miR-133 and miR-208 levels could be shown in this study.The reason for this could potentially be that 90 minutes of ischemia are too short to significantly change levels of miRNA expression and miRNA levels in circulating plasma-exosomes.
CeO2NPs are similarly effective as sorafenib in increasing survival in rats with HCC
Authors: G.F. Varo, D. Oró, S.C. Restoy, L. Boix, E. Casals, M.P. Corominas, L. Oller, G. Casals, M. Morales-Ruiz, J. Bruix, V. Puntes, W. Jiménez
Journal: Journal of Hepatology (2018)
Transfer of Cell-Surface Antigens by Scavenger Receptor CD36 Promotes Thymic Regulatory T Cell Receptor Repertoire Development and Allo-tolerance
Authors: Justin S.A. Perry, Emilie V. Russler-Germain, You W. Zhou, Whitney Purtha, Matthew L. Cooper, Jaebok Choi, Mark A. Schroeder, Vanessa Salazar, Takeshi Egawa, Byeong-Chel Lee, Nada A. Abumrad, Brian S. Kim, Mark S. Anderson, John F. DiPersio, Chyi-Song Hsieh
Journal: Immunity (2018)
The percentage of patients with HCV infection in need of a liver transplant is rapidly declining while their survival after transplantation is improving: A study based on European liver transplant registry
Authors: G. Perricone, C. Mazzarelli, R. Viganò, C. Duvoux, P. Cortesi, R. Facchetti, M. Vangeli, V. Karam, R. Adam, M. Strazzabosco, L.S. Belli
Journal: Journal of Hepatology (2018)
Magnetic Resonance Elastography versus Transient Elastography in detection of fibrosis in nonalcoholic fatty liver disease: A systematic review and meta-analysis of individual participant date
Authors: C. Hsu, C. Caussy, K. Imajo, J. Chen, S. Singh, K. Kaulback, M. Le, J. Hooker, R. Bettencourt, M. Yin, C. Sirlin, R.L. Ehman, A. Nakajima, R. Loomba
Journal: Journal of Hepatology (2018)
The incidence of ulcer bleeding post endoscopic band ligation of esophageal varices
Authors: S. Machlab, J. Da Costa, D. Horta, P. Ruiz, J. Profitós, M.V. Gómez, M. Miquel, M. Casas, B. Dalmau, R. Campo, E. Brullet, F. Junquera, V. Puig-Diví, E. Martínez-Bauer, P. García-Iglesias, A. Villoria, M. Gallach, L. Melcarne, X. Calvet, J. Sánchez-Delgado
Journal: Journal of Hepatology (2018)
PD-1 blocks lytic granule polarization with concomitant impairment of integrin outside-in signaling in the natural killer cell immunological synapse
Authors: Yu Huang, Zhiying Chen, Joon Hee Jang, Mirza S. Baig, Grant Bertolet, Casey Schroeder, Shengjian Huang, Qian Hu, Yong Zhao, Dorothy E. Lewis, Lidong Qin, Michael Xi Zhu, Dongfang Liu
Journal: Journal of Allergy and Clinical Immunology (2018)