tbuckley/cabot-search huggingface dataset:
GLIOMAS GENETIC MARKERS AND PREFERENTIAL SUPRATENTORIAL BRAIN LOCATIONS
Authors: Isaac Phang, Anna Craig-Mcquaide, Adamantios Mavrakis, Athanasios Grivas
Journal: Neuro-Oncology (2018)

Gliomas are associated with preferential locations in secondary functional areas. We examine our data to see if there is a genetic difference between the gliomas in different supratentorial locations using IDH-1, MGMT methylation and 1p19q co-deletion status. Methods WHO Grade II and III glioma patients with histology were included retrospectively from the MDT database from 2013 – 2017. Glioma location was determined by the MRI report. In cases where the glioma expanded beyond one lobe, consensus was obtained between the authors to determine where the majority of the tumour bulk was located. IDH-1, MGMT methylation and 1p19q co-deletion status were obtained from the histopathology report. χ2test with Bonferroni correction was used to compare the actual and expected numbers observed. Results191 gliomas were included. There were 55 astrocytomas Grade II, 81 astrocytomas Grade III, 24 oligodendrogliomas Grade II, 29 oligodendrogliomas Grade III and 2 anaplastic pleomorphic xanthoastrocytomas. There were 74 frontal, 25 insular, 64 temporal, 20 parietal and 8 basal ganglia tumours. 64.1% of the gliomas were IDH-1 mutated. However, 82.4% in the frontal lobe, 70.8% in the insula, 46.2% in the temporal lobe, 60.0% in the parietal lobe and 14.3% in the basal ganglia regions were IDH-1 mutated (p< 0.001). 57.3% of the gliomas were MGMT methylated. However, 64.9% in the frontal lobe, 62.5% in the insula, 50.8% in the temporal lobe, 60.0% in the parietal lobe and 42.9% in the basal ganglia regions were MGMT methylated (p<0.001). 31.3% of the gliomas were 1p19q co-deleted. However, 43.2% in the frontal lobe, 29.2% in the insula, 23.1% in the temporal lobe, 25% in the parietal lobe and none in the basal ganglia were 1p19q co-deleted (p<0.001). Our data suggest gliomas in different supratentorial locations have genetic differences based on the three genetic markers.
Abstract 17334: Mediterranean Diet But Not DASH Diet and AHEI Score is Associated With Lower Risk of Heart Failure in the Physicians’ Health Study
Authors: Yash Patel, Hyun Shin, John M Gaziano, Luc Djousse
Journal: Circulation (2016)

Introduction: Dietary patterns including Mediterranean (MED), Dietary Approach to Stop Hypertension (DASH), and Alternative Healthy Eating Index (AHEI) have shown to be associated with lower risk o...
Factors Associated With Variation in Outcomes in Bariatric Surgery Centers of Excellence—Reply
Authors: Tapan Mehta, David B. Allison
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
The cystic fibrosis airway milieu enhances rescue of F508del in a pre-clinical model
Authors: Martina Gentzsch, Deborah M. Cholon, Nancy L. Quinney, Susan E. Boyles, Mary E.B. Martino, Carla M.P. Ribeiro
Journal: European Respiratory Journal (2018)

<b>The CF airway inflammatory milieu has a major impact on the efficacy of CFTR modulators, indicating that pre-clinical evaluation under conditions that mimic native inflamed CF airways is critical for optimising therapies.</b>http://ow.ly/VrD130m770X
A nomogram-based immunoprofile predicts overall survival for previously untreated patients with esophageal squamous cell carcinoma after esophagectomy
Authors: Jingjing Duan, Yongwei Xie, Lijuan Qu, Lingxiong Wang, Shunkai Zhou, Yu Wang, Zhongyi Fan, Shengsheng Yang, Shunchang Jiao
Journal: Journal for ImmunoTherapy of Cancer (2018)

<h3>Background</h3> Immunoscore, as a prognostic tool defined to quantify in situ immune cell infiltrates, appears to be superior to the TNM staging system. In esophageal squamous cell carcinoma (ESCC), no immunoscore has been established; however, in situ tumor immunology is recognized as highly important. Our study aimed to construct a comprehensive immunoprofile for ESCC. <h3>Methods</h3> The infiltration of four immune cell types (CD8+/CD4+/Foxp3+/CD33+ cells), the expression of both inhibitory (PD-1/PD-L1/Tim-3/LAG-3) and stimulatory checkpoints (OX-40/ICOS), and IDO1 were evaluated by IHC staining and multi-color immunofluorescence in two independent cohorts (95 patients in the primary cohort and 55 patients in the validation cohort). The association with patients' overall survival was analyzed by the Kaplan-Meier method and the Cox model. Nomogram-based immunoprofile was established using the independent prognostic variables. To determine its predictive accuracy and discriminatory capacity, the C-index and calibration curve were calculated. <h3>Results</h3> Significant correlation of PD-L1 expression in tumor cells with PD-1+ T cell infiltration was found (<i>P</i> = 0.035), indicating the activation of the inhibitory PD-1/PD-L1 pathway in ESCC cases. More PD-L1+ ICs, Tim-3+ ICs and LAG-3+ ICs were found in the CD8-rich tumor microenvironment, which is in accordance with the feedback nature of immune system. After adjustment by TNM stage, four immune variables including the infiltration of CD8+/Foxp3+/CD33+ cells and the PD-L1 expression by tumor cells were selected to construct a prognostic nomogram. The calibration curves showed good accuracy of the nomogram for survival prediction. To overcome the complexity of applying a nomogram in a clinical setting, a simple immunoprofile was then established according to the points of each factor from the nomogram. Our immunoprofile model could separate same-stage patients into different risk subgroups, and showed superior accuracy for survival prediction than the TNM staging system based on the C-index calculation and ROC analysis. <h3>Conclusions</h3> Our nomogram-based immunoprofile can provide more accurate prognosis prediction and is an important complement to the TNM staging system for operable ESCC patients.
Abstract 19841: Gut Microbiome Influences Immune Modulating Therapy for Inflammatory Vasculitis in a Lethal Herpesviral Infection
Authors: Sriram Ambadapadi, Ryan Thomas, Christian Jobin, Sufi Morshed, Katrina Grau, Stephanie Karst, Scott Tibbetts, Grant McFadden, Alexandra Lucas
Journal: Circulation (2016)

Introduction: The role of the microbiome on vascular disease, viral infections, and immune modulating therapy is not well defined. Changes in bacterial signatures are seen in inflammatory vasculiti...
Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.
Authors: Jisen Zhang, Xingtan Zhang, Haibao Tang, Qing Zhang, Xiuting Hua, Xiaokai Ma, Fan Zhu, Tyler Jones, Xinguang Zhu, John Bowers, Ching Man Wai, Chunfang Zheng, Yan Shi, Shuai Chen, Xiuming Xu, Jingjing Yue, David R. Nelson, Lixian Huang, Zhen Li, Huimin Xu, Dong Zhou, Yongjun Wang, Weichang Hu, Jishan Lin, Youjin Deng, Neha Pandey, Melina Mancini, Dessireé Zerpa, Julie K. Nguyen, Liming Wang, Liang Yu, Yinghui Xin, Liangfa Ge, Jie Arro, Jennifer O. Han, Setu Chakrabarty, Marija Pushko, Wenping Zhang, Yanhong Ma, Panpan Ma, Mingju Lv, Faming Chen, Guangyong Zheng, Jingsheng Xu, Zhenhui Yang, Fang Deng, Xuequn Chen, Zhenyang Liao, Xunxiao Zhang, Zhicong Lin, Hai Lin, Hansong Yan, Zheng Kuang, Weimin Zhong, Pingping Liang, Guofeng Wang, Yuan Yuan, Jiaxian Shi, Jinxiang Hou, Jingxian Lin, Jingjing Jin, Peijian Cao, Qiaochu Shen, Qing Jiang, Ping Zhou, Yaying Ma, Xiaodan Zhang, Rongrong Xu, Juan Liu, Yongmei Zhou, Haifeng Jia, Qing Ma, Rui Qi, Zhiliang Zhang, Jingping Fang, Hongkun Fang, Jinjin Song, Mengjuan Wang, Guangrui Dong, Gang Wang, Zheng Chen, Teng Ma, Hong Liu, Singha R. Dhungana, Sarah E. Huss, Xiping Yang, Anupma Sharma, Jhon H. Trujillo, Maria C. Martinez, Matthew Hudson, John J. Riascos, Mary Schuler, Li-Qing Chen, David M. Braun, Lei Li, Qingyi Yu, Jianping Wang, Kai Wang, Michael C. Schatz, David Heckerman, Marie-Anne Van Sluys, Glaucia Mendes Souza, Paul H. Moore, David Sankoff, Robert VanBuren, Andrew H. Paterson, Chifumi Nagai, Ray Ming
Journal: Nature Genetics (2018)

Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum spontaneum. Sequencing of a haploid S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined. The reduction of basic chromosome number from 10 to 8 in S. spontaneum was caused by fissions of 2 ancestral chromosomes followed by translocations to 4 chromosomes. Surprisingly, 80% of nucleotide binding site-encoding genes associated with disease resistance are located in 4 rearranged chromosomes and 51% of those in rearranged regions. Resequencing of 64 S. spontaneum genomes identified balancing selection in rearranged regions, maintaining their diversity. Introgressed S. spontaneum chromosomes in modern sugarcanes are randomly distributed in AP85-441 genome, indicating random recombination among homologs in different S. spontaneum accessions. The allele-defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement. Sequencing of haploid sugarcane, Saccharum spontaneum, allows assembly of a prototypical version of the sugarcane chromosome set. This new reference genome will serve as a resource to accelerate sugarcane improvement.
Abstract 14437: Protein Kinase D1 Signaling is the Key to Arterial Differentiation of Vascular Endothelial Cells
Authors: Cynthia Opansky, Brad Best, Rong Yuan, Qi Cao, Bin Ren
Journal: Circulation (2016)

Endothelial cell (EC) differentiation through transcriptional reprogramming plays a fundamental role in functional angiogenesis that is important in recovering blood supply in ischemic cardiovascul...
Dickkopf-3 (DKK3) in Urine Identifies Patients with Short-Term Risk of eGFR Loss
Authors: Stephen Zewinger, Thomas Rauen, Michael Rudnicki, Giuseppina Federico, Martina Wagner, Sarah Triem, Stefan J. Schunk, Ioannis Petrakis, David Schmit, Stefan Wagenpfeil, Gunnar H. Heine, Gert Mayer, Jürgen Floege, Danilo Fliser, Hermann-Josef Gröne, Thimoteus Speer
Journal: Journal of the American Society of Nephrology (2018)

Background The individual course of CKD may vary, and improved methods for identifying which patients will experience short-term eGFR loss are needed. Assessing urinary Dickkopf-3 (DKK3), a stress-induced tubular epithelia–derived profibrotic glycoprotein, may provide information about ongoing tubulointerstitial fibrosis and short-term eGFR loss. Methods To investigate urinary DKK3’s potential as a biomarker of short-term eGFR loss (over 12 months), we prospectively assessed eGFR and urinary DKK3 levels in patients with CKD of various etiologies at baseline and annual follow-ups. We also measured urinary DKK3 in a general population sample and patients with diagnostic kidney biopsies or IgA nephropathy under treatment. Results Median urinary DKK3-to-creatinine concentration at baseline was significantly higher in patients with CKD than the general population sample (431 versus 33 pg/mg). In the CKD cohort, having a urinary DKK3-to-creatinine level &gt;4000 pg/mg was independently and significantly associated after multiple adjustments with mean annual decline in eGFR of 7.6% over 12 months. Urinary DKK3 significantly improved prediction of kidney function decline compared with eGFR or albuminuria alone. Urinary DKK3-to-creatinine levels were related to the extent of tubulointerstitial fibrosis in kidney biopsies. In patients with IgA nephropathy, a rise in urinary DKK3 was associated with significant eGFR decline within 6 months, whereas stable or decreasing urinary DKK3 indicated a more favorable course. Conclusions Urinary DKK3 levels identify patients at high risk for eGFR decline over the next 12 months regardless of the cause of kidney injury and beyond established biomarkers, potentially providing a tool to monitor CKD progression and assess effects of interventions.
Obstructive sleep apnoea as a risk factor for incident metabolic syndrome: a joined Episono and HypnoLaus prospective cohorts study
Authors: Camila Hirotsu, Jose Haba-Rubio, Sonia M. Togeiro, Pedro Marques-Vidal, Luciano F. Drager, Peter Vollenweider, Gérard Waeber, Lia Bittencourt, Sergio Tufik, Raphael Heinzer
Journal: European Respiratory Journal (2018)

Cross-sectional studies have demonstrated that obstructive sleep apnoea (OSA) and metabolic syndrome (MetS) are often associated, but whether a temporal relationship exists is unknown. We aimed to investigate the effect of OSA on the risk of developing MetS in the general population. A prospective study was conducted combining two population-based samples: Episono (Brazil) and HypnoLaus (Switzerland). MetS was assessed according to unified criteria. Polysomnography (PSG) was performed at baseline and follow-up in Episono, and at baseline in HypnoLaus. OSA was defined according to the apnoea–hypopnoea index as mild (≥5– &lt;15 events h −1 ) and moderate-to-severe (≥15 events·h −1 ). We included 1853 participants (mean± sd age 52±13 years, 56% female) without MetS at baseline. After mean± sd 6±1 years, 318 (17.2%) participants developed MetS. Moderate-to-severe OSA was independently associated with incident MetS (OR 2.58, 95% CI 1.61–4.11) and increased the number of MetS components from baseline to follow-up through mediation of the percentage of time with arterial oxygen saturation &lt;90%. Subset analysis in Episono confirmed that the increase in this parameter between baseline and follow-up PSGs represented a risk factor for incident MetS (OR 1.42, 95% CI 1.04–1.95, for each 10% increase). OSA is independently associated with an increased risk of developing MetS through mediation of nocturnal hypoxaemia in the general population.
Abstract P157: Examining Differences in Interest in Clinical Trial Participation Between Those With and Without a Previous Diagnosis of Hypertension or Heart Disease
Authors: Danielle Haney, Richard Moser, Bradford Hesse, Alexandra Greenberg-Worisek
Journal: Circulation (2018)

Purpose: Despite the large impact heart disease has on morbidity and mortality, many are unaware of the risk factors and the steps they can take to reduce their own risk. Participation in clinical trials for discovering new approaches for the prevention and treatment of heart disease is important. This study sought to determine interest in participation in clinical trials of those diagnosed with heart disease and hypertension as compared to those without such diagnoses, and to assess associated sociodemographic characteristics of interest in participation Methods: Analyses were conducted using data from the 2014 administration of the National Cancer Institute's Health Information National Trends Survey . HINTS is a nationally-representative survey of the US adult (18+) population. The primary outcome of interest was whether respondents expressed interest in participating in research. Bivariate analyses were conducted initially to explore potential associations between sociodemographic factors and having had a diagnosis of hypertension or heart disease. Multivariate logistic regression was used to assess relationships between sociodemographic factors and outcomes, controlling for relevant sociodemographic characteristics and prior diagnosis of hypertension or heart attack. Weighted analyses were done to obtain population-level estimates. Findings: Of the 3,498 respondents, 1,569 (33.3%,) reported having a prior diagnosis of hypertension; 362 of 3,493 (7.0%,) respondents indicated that they had a previously diagnosed heart condition. Logistic regression showed that younger hypertensive participants had higher odds of being interested in participating in clinical trials as compared to those aged 75 years and older (OR = 3.62, 95% CI = 1.94-6.78). Those with regular care providers had higher odds of being interested in clinical trial participation compared to those without regular providers (OR = 1.51, 95% CI = 1.07-2.11). Likewise, younger participants aged 18-34 reporting heart conditions (OR = 3.58, 95% CI = 1.79-7.16) had higher odds of being interested in clinical trial participation compared to those aged 75 and older. No statistical differences were seen in clinical trial awareness, participation, or interest across race or gender. Conclusions: Participants who have a diagnosis of heart disease or hypertension and report being interested in engaging in clinical trial research are generally younger and have a regular health care provider. Therefore, behavioral intervention efforts should focus on translating clinical trial participation interest to participation in younger adults. Clinical trial recruitment efforts should also focus on unique methods to increase interest and subsequent trial enrollment in older adults and those without regularly provided care.
Late growth of infantile hemangiomas in children &gt;3 years of age: A retrospective study
Authors: Kathleen F. O'Brien, Sonal D. Shah, Elena Pope, Roderic J. Phillips, Francine Blei, Eulalia Baselga, Maria C. Garzon, Catherine McCuaig, Anita N. Haggstrom, Peter H. Hoeger, James R. Treat, Marissa J. Perman, Jane S. Bellet, Xavier Cubiró, Jeffrey Poole, Ilona J. Frieden
Journal: Journal of the American Academy of Dermatology (2018)
Optimizing the Detection of Left Ventricular Thrombus Following Acute Myocardial Infarction in the Current Era—Reply
Authors: Cian P. McCarthy, Muthiah Vaduganathan, John W. McEvoy
Journal: JAMA Cardiology (2018)

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Bronchiolitis needs a revisit: Distinguishing between virus entities and their treatments
Authors: Tuomas Jartti, Hermelijn H. Smits, Klaus Bønnelykke, Ozlem Bircan, Varpu Elenius, Jon R. Konradsen, Paraskevi Maggina, Heidi Makrinioti, Jakob Stokholm, Gunilla Hedlin, Nikolaos Papadopoulos, Marek Ruszczynski, Klaudia Ryczaj, Bianca Schaub, Jürgen Schwarze, Chrysanthi Skevaki, Katarina Stenberg‐Hammar, Wojciech Feleszko
Journal: Allergy (2018)

Current data indicate that the "bronchiolitis" diagnosis comprises more than one condition. Clinically, pathophysiologically, and even genetically three main clusters of patients can be identified among children suffering from severe bronchiolitis (or first wheezing episode): (a) respiratory syncytial virus (RSV)-induced bronchiolitis, characterized by young age of the patient, mechanical obstruction of the airways due to mucus and cell debris, and increased risk of recurrent wheezing. For this illness, an effective prophylactic RSV-specific monoclonal antibody is available; (b) rhinovirus-induced wheezing, associated with atopic predisposition of the patient and high risk of subsequent asthma development, which may, however, be reversed with systemic corticosteroids in those with severe illness; and (c) wheeze due to other viruses, characteristically likely to be less frequent and severe. Clinically, it is important to distinguish between these partially overlapping patient groups as they are likely to respond to different treatments. It appears that the first episode of severe bronchiolitis in under 2-year-old children is a critical event and an important opportunity for designing secondary prevention strategies for asthma. As data have shown bronchiolitis cannot simply be diagnosed using a certain cutoff age, but instead, as we suggest, using the viral etiology as the differentiating factor.
DNA methylation spread within HLTF CpG island in colorectal cancer
Authors: Alfa H. Bai, Michael W. Chan, Jun Yu, Ellen P. Man, Joseph J. Sung, Wai K. Leung
Journal: Cancer Research (2004)

Proc Amer Assoc Cancer Res, Volume 45, 2004

4176 

Background: Promoter hypermethylation causes transcriptional silencing and subsequent loss of protein expression of tumor suppressor genes which is commonly found in neoplasia. Helicase-like transcription factor (HLTF), a SWI/SNF family gene, is frequently methylated in colorectal cancer. Recent studies have demonstrated the spread of methylated CpG islands from exon to promoter region during tumor progression. However the mechanism governing this phenomenon is not fully understood. This study elucidated the distribution of methylation patterns within HLTF CpG islands and try to correlate with its methylation profile in colorectal cancer. Methods: We examined 10 sporadic colorectal carcinomas and 5 colonic biopsies from patients without cancer and the colorectal cancer cell line HT29. DNA was extracted from microdissected paraffin embedded sections and chemically modified by sodium bisulfite. Randomly selected PCR amplified clones were used for further bisulfite sequence analysis. Results: We analyzed a total of 57 CpG sites within HLTF gene, 42 were located in the promoter region and 15 were located in exon 1 region. Dense methylation of the promoter region (>85%) and exon region (>66%) was found in the HT29 cell line. In primary colorectal cancer samples, high methylation density was also observed in both promoter region (>87%) and exon region (>92%), except for one sample which showed high methylation density in promoter region (>88%) but rare in exon region (<8%). In contrast, CpG site methylation was not found in both promoter and exon region of normal colonic tissue.Conclusion: Our study demonstrated the densely methylated CpG islands of the HLTF gene in colorectal carcinoma. Although there is no methylated CpG site in the exon region of normal colonic samples, there is a distinct methylation pattern in various carcinoma samples suggesting that methylation spread within HLTF may occur during tumor progression in colorectal cancer.



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Left Ventricular Diastolic Dysfunction Predicts Mortality in Patients With Systemic Sclerosis
Authors: Anders H. Tennøe, Klaus Murbræch, Johanna C. Andreassen, Håvard Fretheim, Torhild Garen, Einar Gude, Arne Andreassen, Svend Aakhus, Øyvind Molberg, Anna-Maria Hoffmann-Vold
Journal: Journal of the American College of Cardiology (2018)