tbuckley/cabot-search huggingface dataset:
Global, cancer-specific microRNA cluster hypomethylation was functionally associated with the development of non-B non-C hepatocellular carcinoma
Authors: Masanori Nojima, Takeshi Matsui, Akihiro Tamori, Shoji Kubo, Ken Shirabe, Koichi Kimura, Mitsuo Shimada, Tohru Utsunomiya, Yasuteru Kondo, Etsuko Iio, Yutaka Naito, Takahiro Ochiya, Yasuhito Tanaka
Journal: Molecular Cancer (2016)

While hepatitis B and C viral infection have been suppressed, non-B non-C hepatocellular carcinoma (NBNC-HCC) is considered to be rising in incidence terms in some developed countries where prevalence of those viral infections among HCC patients had been very high (such as Japan, Korea, and Italy). To elucidate critical molecular changes in NBNC-HCC, we integrated three large datasets relating to comprehensive array-based analysis of genome-wide DNA methylation (N = 43 pairs) and mRNA/miRNA expression (N = 15, and 24 pairs, respectively) via statistical modeling. Hierarchical clustering of DNA methylation in miRNA coding regions clearly distinguished NBNC-HCC tissue samples from relevant background tissues, revealing a remarkable tumor-specific hypomethylation cluster. In addition, miRNA clusters were extremely hypomethylated in tumor samples (median methylation change for non-clustered miRNAs: -2.3%, clustered miRNAs: -24.6%). The proportion of CpGs hypomethylated in more than 90% of the samples was 55.9% of all CpGs within miRNA clusters, and the peak methylation level was drastically shifted from 84% to 39%. Following statistical adjustment, the difference in methylation levels within miRNA coding regions was positively associated with their expression change. Receiver operating characteristic (ROC) analysis revealed a great discriminatory ability in respect to cluster-miRNA methylation. Moreover, miRNA methylation change was negatively correlated with corresponding target gene expression amongst conserved and highly matched miRNA sites. We observed a drastic negative shift of methylation levels in miRNA cluster regions. Changes in methylation status of miRNAs were more indicative of target gene expression and pathological diagnosis than respective miRNA expression changes, suggesting the importance of genome-wide miRNA methylation for tumor development. Our study dynamically summarized global miRNA hypomethylation and its genome-wide scale consequence in NBNC-HCC.
Soundings: Spin doctor
Authors: James Owen Drife
Journal: BMJ (1999)

I used to enjoy firing off letters to newspapers. If they were published they produced no discernible results apart from occasional postcards from long lost relatives. Nevertheless, I felt that the papers were trying to help.

Now, recently installed as press officer to a royal college, how do I feel about the media? Uncomfortable when they focus on medicine’s shortcomings. Stimulated when journalists ask incisive questions. Paranoid? No, surprisingly. The media rarely seem to be out to get us for no reason.

In a era of government by focus group, even the most altruistic college needs to work on public opinion if it wants to improve care. But it is hard to influence the media’s agenda. They are today’s control freaks.

Should we become a pressure group? Last week, when launching recommendations for safer labour ward care, should we have suggested that at present things are really dangerous? Or wheeled out a couple who have lost a baby? Certainly not, I thought, but part of me mourned the lost opportunity.

Next day, it was easy to persuade myself that I could do more for womankind by broadcasting on national radio than by attending my antenatal clinic. When I reached our local studios an apologetic receptionist told me that my interview had been cancelled because America’s leading femme fatale—Monica Lewinsky—had turned up at the BBC.

Such setbacks are understandable, but occasionally I get the feeling that the media are being devious. Take this month’s number one obstetrical issue—the millennium baby. The first questions were factual. When should a couple make love to schedule delivery on 1 January 2000? The reporters did not want to hear about odds or biological variation. They wanted understandable physiology.

The next questions were on the advisability of elective caesarean section at 00 01 on a public holiday. That would be unwise, said I, because of possible staff shortages, unpredictable emergencies, and the millennium bug.

The third wave was trickier. Would the college regard such an operation as unethical? Say the woman had enough money to pay privately for all the staff that she could possibly need? I began to suspect that my questioner’s ethical stance would depend on whether it is his paper or a rival which is financing the stunt. I think that I am losing my innocence.
Interim results: influenza A (H1N1) 2009 monovalent vaccination coverage - United States, October-December 2009.
Authors: J. A. Singleton, T. A. Santibanez, P. J. Lu, H. Ding, G. L. Euler, G. L. Armstrong, B. P. Bell, M. Town, L. Balluz
Journal: MMWR Morbidity and Mortality Weekly Report (2010)
Liver Cancer Death Rate Increases as Overall Cancer Deaths Decline
Authors: Julie A. Jacob
Journal: JAMA (2016)

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
A retrospective review of wide excision alone for ductal carcinoma in situ (DCIS) of the breast
Authors: S. S. Mitra, A. Salman, D. Bloomfield, A. Johri
Journal: Journal of Clinical Oncology (2004)

785 Background: The standard treatment for ductal carcinoma in situ (DCIS) of the breast today is wide excision (WE) followed by radiotherapy.This is due to the results of 3 randomised trials .The major benefit is a 50–60% reduction in the risks of recurrence.The recurrence rates vary from centre to centre .Historically, some centres have had low local recurrence rates while treating DCIS with a policy of WE and selective mastectomy.They have questioned whether radiotherapy should be routinely done.We reviewed the DCIS patients at Worthing general hospital where the recurrence rates were thought to be low. Methods: We retrospectively reviewed 190 patients with DCIS treated by surgery alone from January 1989 to December 1998.These patients had 5–14 years follow up with a median follow up of 90 months.145 (75%) patients were given Tamoxifen for a minimum of 5 years. Results:83 (42.5%) patients underwent a mastectomy .8(4%) patients developed DCIS recurrence while 8(4%) went on to have an invasive recurrence.2(1%) patients died of bony secondaries with normal breasts and must have had occult invasive disease.9 patients died from causes unrelated to their disease.Overall mortality was 5.6% with disease specific mortality being 1%. Conclusions: The local recurrence rate for DCIS was 8% over a median follow up of about 71/2 years.The recurrence rate of 1% per patient-year is lower than that reported in major trials.However, a large number of patients had mastectomy and Tamoxifen .If the mastectomy patients are not included in the analysis, then the recurrence rate is 15% at 71/2 years(16/107) or 2% per patient-year.This is similar to that reported in the literature.Therefore, centres with low recurrence rates for DCIS are likely to have higher rates for mastectomy .The literature stresses the reduction of recurrences as the main benefit of radiotherapy in DCIS.Radiotherapy much more importantly reduces the mastectomy rate.However, 15 (107/16) patients need to be treated to prevent 1 local recurrence.Since the long term side effects of radiotherapy in DCIS are unknown and it has an excellent prognosis, we need a reliable prognostic system to use radiotherapy selectively after WE. No significant financial relationships to disclose.
Five-Year Outcomes with Anti–Vascular Endothelial Growth Factor Treatment of Neovascular Age-Related Macular Degeneration
Authors: Maureen G. Maguire, Daniel F. Martin, Gui-shuang Ying, Glenn J. Jaffe, Ebenezer Daniel, Juan E. Grunwald, Cynthia A. Toth, Frederick L. Ferris, Stuart L. Fine
Journal: Ophthalmology (2016)
How Can We Protect Susceptible Individuals from the Adverse Cardiovascular Effects of Air Pollution?
Authors: Nicholas L. Mills, Mark R. Miller
Journal: American Journal of Respiratory and Critical Care Medicine (2016)

treatment in the drinking water would also deplete the GI microbiota.The GI microbiome can have profound effects on systemic inflammatory processes and may influence lung disease (14,15), so examination of its effect in this model would be informative.Yadava and colleagues present a tantalizing possibility that the lung bacterial microbiome plays a causal role in chronic lung inflammation and COPD (10).If these results hold up to the validation in other animal models of COPD and in humans, the microbiota could be a tangible goal for therapeutic interventions.Indeed, antibiotics have a beneficial effect on exacerbations of COPD ( 16) and might be able to be used in a more targeted approach based on the lung bacterial microbiome.Alternatively, manipulation of specific aspects of the immune response to the microbiome could improve outcomes in COPD.With this study, we truly are launching out into the deep, and whether the investigation of lung bacterial microbiome causality in COPD sinks or swims will depend on the ability to meet the substantial challenges posed by these investigations.
Fish oil supplementation during pregnancy and allergic respiratory disease in the adult offspring
Authors: Susanne Hansen, Marin Strøm, Ekaterina Maslova, Ronald Dahl, Hans Jürgen Hoffmann, Dorte Rytter, Bodil Hammer Bech, Tine Brink Henriksen, Charlotta Granström, Thorhallur I. Halldorsson, Jorge E. Chavarro, Allan Linneberg, Sjurdur F. Olsen
Journal: Journal of Allergy and Clinical Immunology (2016)
HHS Awards $94 Million to Treat Opioid Use Disorders
Authors: Julie A. Jacob
Journal: JAMA (2016)

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
Phenotypic Identification Of Subclones In Multiple Myeloma With Different Genomic Profile, Clonogenic Potential and Drug Sensitivity
Authors: Teresa Paíno, Bruno Paiva, José M Sayagués, Ines Mota, Tiago Carvalheiro, Luis A Corchete, Norma C Gutiérrez, Irene Aires-Mejia, Maria Luz Sanchez, Paloma Barcena, Enrique M. Ocio, Albert Oriol, Miguel T Hernandez, Maria Asunción Echeveste, Artur Paiva, Joan Blade, Alberto Orfao, Maria Victoria Mateos, Jesus F San Miguel
Journal: Blood (2013)
US drug regulator warns manufacturers that it will not accept data from Indian research center
Authors: Owen Dyer
Journal: BMJ (2016)

The US Food and Drug Administration has warned an unspecified number of drug makers that marketing applications containing clinical trial data prepared by an Indian contract research organization will not be accepted because of concerns about the integrity of the data.

An FDA inspection last October at Semler Research Center, based in Bengaluru (Bangalore), found “significant instances of misconduct and violations of federal regulations, including the substitution and manipulation of study subject samples.”1

The agency warned, “FDA is notifying sponsors …
Abstract 277: Insights Into The Transcriptional Reprogramming Induced By Beta-3 Adrenergic Cardioprotection
Authors: Jaime Garcia-Prieto, David Sanz-Rosa, Fatima Sanchez-Cabo, Ana Dopazo, Valentin Fuster, Borja Ibanez
Journal: Circulation Research (2014)

Background: Beta-3 adrenergic receptor (β3AR) stimulation reduces myocardial ischemia/reperfusion injury (IRI) in vivo. The molecular mechanisms that regulate this cardioprotective therapy are a matter of intense research. The aim of this study was to assess the transcriptional reprogramming underpinning cardioprotection. Methods and Results: HL-1 cardiomyocytes were subjected to 6 hours of hypoxia followed by 18h of reoxygenation (H/R) in the presence or absence of the beta-3 adrenergic receptor agonist BRL37344 (5μM). As expected, H/R caused cardiomyocyte death, which was significantly supressed by beta-3 agonist treatment. In order to uncover the molecular basis of cytoprotection we analysed gene expression profiles in HL-1 cells subjected to hypoxia (6h) and reoxygenation (1h, 6h). Immediate reoxygentation proufoundly altered the hypoxia gene expression signature at 1h but this effect was lost upon extended reoxygenation. BRL treatment was able to reverse transcriptomic alterations associated with increased cell death, by supressing the dysregulation of cell survival pathways (possibly implicating mTORC, EGF, eNOS, JAK/Stat, and IL-10 signalling.) Conclusion: Beta-3-adrenergic stimulation induces an adaptive transcriptional reprogramming that preserves cell viability by converging a variety of cytoprotective pathways.
LP16 : Mutations in DCDC2, encoding doublecortin domain-containing protein 2, cause neonatal sclerosing cholangitis
Authors: T. Grammatikopoulos, S. Strautnieks, M. Sambrotta, A.S. Knisely, G. Mieli-Vergani, J. Smith, L Bull, R.J. Thompson
Journal: Journal of Hepatology (2015)
TCTAP C-079 Antegrade Approach to Stumpless Chronic Total Occlusion of Ostial Left Anterior Descending Artery
Authors: Chun-Yuan Chu, Wen-Hsien Lee, Po-Chao Hsu, Cheng-An Chiu, Ho-Ming Su, Tsung-Hsien Lin
Journal: Journal of the American College of Cardiology (2016)
IL-25 Receptor Expression on Airway Dendritic Cells after Allergen Challenge in Subjects with Asthma
Authors: Damian Tworek, Steven G. Smith, Brittany M. Salter, Adrian J. Baatjes, Tara Scime, Rick Watson, Caitlin Obminski, Gail M. Gauvreau, Paul M. O’Byrne
Journal: American Journal of Respiratory and Critical Care Medicine (2015)

IL-25 is an epithelial-derived cytokine, whose effects are mediated by the IL-25 receptor (IL-17RB), and that has been implicated in the pathogenesis of allergic disease and airway viral responses. Airway myeloid dendritic cells (mDCs) and plasmacytoid dendritic cells (pDCs) are professional antigen-presenting cells. pDCs may play a protective role in asthma and are key players in the innate immune response through recognition of microbial products via Toll-like receptors (TLRs). The effects of inhaled allergens on the expression of IL-17RB by mDCs and pDCs, and the effects of IL-25 on pDCs, are unknown.To evaluate allergen-induced changes in IL-17RB expression by mDCs and pDCs and to investigate the effects of IL-25 on pDCs.Patients with mild atopic asthma (n = 13) were challenged with inhaled allergen. Blood and sputum DCs were enumerated and IL-17RB expression was determined by flow cytometry before and 7 and 24 hours after allergen challenge. The effects of IL-25 on pDCs in vitro were also assessed.Inhaled allergen significantly increased mDC and pDC numbers in sputum but not in blood. The percentage of IL-17RB(+) mDCs and pDCs was significantly increased in blood and sputum 24 hours after challenge. IL-25 up-regulated TLR9 expression by pDCs and orchestrated the responses to TLR9 ligation.IL-17RB is up-regulated on blood and sputum mDCs and pDCs after allergen inhalation. IL-25 modulates pDC function through an effect on TLR9 expression.
TCTAP A-080 First and Second Generation Drug Eluting Stents Versus Bare Metal Stents in All Comer Population of Patients Undergoing PCI of Saphenous Vein Graft in 1-Year Follow-up
Authors: Wojciech Wanha, Tomasz Roleder, Szymon Ladzinski, Sylwia Gladysz, Grzegorz Smolka, Andrzej Ochala, Michal Tendera, Wojciech Wojakowski
Journal: Journal of the American College of Cardiology (2016)
The risk of distant metastases in patients with non-small cell lung cancer (NSCLC) with cytologically proven malignant pleural effusion, stage IIIB: A retrospective analysis
Authors: O. Altundag, D. J. Stewart, C. Stevens, D. C. Rice, G. D. Ayers, G. R. Blumenschein, D. D. Karp, W. K. Hong, F. V. Fossella, R. G. Zinner
Journal: Journal of Clinical Oncology (2005)

9568 Background: NSCLC patients (pts) with stage IIIB disease on the basis of malignant pleural effusion (“wet IIIB”) are considered incurable because they are deemed inappropriate candidates for definitive local therapy; they are therefore treated as stage IV with systemic therapy. The risk of distant disease in such pts is not clear from the literature, so we performed a retrospective analysis of wet IIIB pts to determine their propensity for distant metastases. Methods: We did a chart review of all pts with advanced NSCLC treated on 15 first-line protocols at M. D. Anderson Cancer Center 1997 - 2003. Results: Of 575 pts, 37 had cytologically confirmed wet IIIB disease at study entry; all were evaluable for survival. Key demographics included 24 male, median age of 56 (35–77), 31 with adenoca, and 6 with large cell undifferentiated ca. Nodal status (based on CT scans) were N0 (9 pts), N1 (7), N2 (17), and N3 (4). Median time to progression was 5.5 months (mos) (1.5–26.5) and median overall survival was 12.5 mos (2.5–47.5). With minimum follow-up of 13 mos, 12/37 (32%) pts have not had any distant mets despite documented local recurrence (primary, lymph node or pleural effusion); 9 of these 12 pts died without ever developing distant disease. Of these 12 pts, 6/37 (16%) > 8.5 mos (8.5–17) were without distant metastases after local recurrence. Three of these 6 pts (8% of the 37) were greater than 1yr. Conclusions: We present data describing the risk of distant metastasis in cytologically-proven wet IIIB NSCLC. Though almost all these patients will die of their disease, there was an absence of distant metastases in 12/37 (32%) pts. In addition, 6 of these 12 pts, or 16% of the 37, had > 8.5 mos without evidence of distant metastases after documented local progression. This suggests that in some cases these wet IIIB cancers may have a different biology than stage IV NSCLC. Therefore, selected pts with wet IIIB malignant effusion may benefit from aggressive local treatment strategies. Updated data and analyses from matched stage IV controls from each of these trials will be presented at the poster. No significant financial relationships to disclose.
Neural correlates of consciousness in patients who have emerged from a minimally conscious state: a cross-sectional multimodal imaging study
Authors: Carol Di Perri, Mohamed Ali Bahri, Enrico Amico, Aurore Thibaut, Lizette Heine, Georgios Antonopoulos, Vanessa Charland-Verville, Sarah Wannez, Francisco Gomez, Roland Hustinx, Luaba Tshibanda, Athena Demertzi, Andrea Soddu, Steven Laureys
Journal: The Lancet Neurology (2016)
FRI0206 Prevalence of Irritable Bowel Syndrome in Patients with Ankylosing Spondylitis
Authors: D. Solmaz, O. Avci, O. Yildirim, R. Mete
Journal: Annals of the Rheumatic Diseases (2015)

<h3>Background</h3> Irritable bowel syndrome (IBS) is a functional bowel disease that cannot be explained with an organic pathology, characterized by change in bowel habits and abdominal pain that relaxes with defecation. It is well known that IBS has an increased association with psychosomatic illnesses such as depression, anxiety, chronic fatigue syndrome and fibromyalgia. Similarly, publications are available in the literature that IBS has also an increased association with chronic, painful inflammatory pathologies such as rheumatoid arthritis and systemic lupus erythematosus. And also ankylosing spondylitis (AS) is a chronic inflammatory disease of the axial skeleton, that is characterized by new bone formation can eventually cause ankylosis and limitation of motion and disability. Accordingly, we aimed to assess the prevalence of IBS in patients with AS. <h3>Methods</h3> The study was conducted at a university hospital rheumatology clinic and 113 consecutive patients with AS according to the modified New York criteria were included. Patients demographics, clinic and laboratory data were recorded. Functional status was evaluated with BASFI (Bath Ankylosing Spondylitis Functional Index), health quality with ASQOL (Ankylosing Spondylitis Health Quality) and disease activity with BASDAI (Bath Ankylosing Spondylitis Activity Index). Then all patients were questioned with diagnosis of IBS and type according to ROME III criteria. The mean and standard deviation values for continuous variables were given. Categorical variables were expressed as percentage. While Mann-Whitney U test was used for comparison of continuous variables between two groups, chi-square test was used for categorical variables. P&lt;0.05 was considered statistically significant. <h3>Results</h3> Clinical and demographic characteristics of the patients are given in the table. Prevalence of IBS in patients with AS was found to be 30.1%. The distribution of types of IBS is following; 38% alternating diarrhea and constipation type, 23% constipation dominant type, 21% diarrhea dominant type and 18% mixed type. Frequency of IBS was found to be significantly higher in higher disease activity group (BASDAI&gt;4) and in patients treated with biologic agents. (p values &lt;0.001, 0.017, respectively). Prevalence of IBS between the sexes was found to be significantly higher in female patients (p: 0.031). <h3>Conclusions</h3> IBS; when compared to the normal population was found to be higher (%30) in patients with AS. In a similar manner to the community, frequency of IBS is significantly higher in female patients, although AS is more frequent in male patients. As a result, in patients with AS, especially with high disease activity, gastroenterological complaints should be questioned; and the diagnosis of IBS should not be ignored in the treatment process. <h3>Disclosure of Interest</h3> None declared
Sustained Remissions Following Chimeric Antigen Receptor Modified T Cells Directed Against CD19 (CTL019) in Patients with Relapsed or Refractory CD19+ Lymphomas
Authors: Stephen J. Schuster, Jakub Svoboda, Sunita Dwivedy Nasta, David L. Porter, Elise A. Chong, Daniel J. Landsburg, Anthony R. Mato, Simon F. Lacey, Jan J. Melenhorst, Anne Chew, Jens Hasskarl, Gaurav D. Shah, Mariusz A. Wasik, Katherine T. Marcucci, Zhaohui Zheng, Bruce L. Levine, Carl H. June
Journal: Blood (2015)