tbuckley/cabot-search huggingface dataset:
Bertram Maurice Mandelbrote
Authors: J. R. Robinson
Journal: BMJ (2011)

<h3>Abstract</h3> Although each cell within an organism contains a nearly identical genome sequence, the three-dimensional (3D) packing of the genome varies among individual cells, influencing cell-type-specific gene expression. Genome Architecture Mapping (GAM) is the first genome-wide experimental method for capturing 3D proximities between any number of genomic loci without ligation. GAM overcomes several limitations of 3C-based methods by sequencing DNA from a large collection of thin sections sliced from individual nuclei. The GAM technique measures locus co-segregation, extracts radial positions, infers chromatin compaction, requires small numbers of cells, does not depend on ligation, and provides rich single-cell information. However, previous analyses of GAM data focused exclusively on population averages, neglecting the variation in 3D topology among individual cells. We present the first single-cell analysis of GAM data, demonstrating that the slices from individual cells reveal intercellular heterogeneity in chromosome conformation. By simultaneously clustering both slices and genomic loci, we identify topological variation among single cells, including differential compaction of cell cycle genes. We also develop a geometric model of the nucleus, allowing prediction of the 3D positions of each slice. Using GAM data from mouse embryonic stem cells, we make new discoveries about the structure of the major mammalian histone gene locus, which is incorporated into the Histone Locus Body (HLB), including structural fluctuations and putative causal molecular mechanisms. Our methods are packaged as <i>SluiceBox</i>, a toolkit for mining GAM data. Our approach represents a new method of investigating variation in 3D genome topology among individual cells across space and time.
Destruction of data prompts calls for Swedish agency to investigate research misconduct
Authors: Caroline White
Journal: BMJ (2004)

Leading academics are pressing the Swedish government to set up an independent agency to investigate issues relating to scientific research misconduct after a long running dispute resulted in the destruction of years of patient data.

The man at the centre of the dispute is Christopher Gillberg, professor of child and adolescent psychiatry at the University of Gothenburg, Sweden, and St George's Hospital, London, and a world expert on attention-deficit/hyperactivity disorder (ADHD) and autism.

In May, years of data relating to Professor Gillberg's research were destroyed by two of his collaborators, associate professors Carina Gillberg and Peder Rasmussen, and university administrator Kerstin Lamberg, in a bid to protect patient confidentiality.

Vice …
OC-101 Predictive factors for postoperative mortality after resection of junctional and gastric adenocarcinomas
Authors: W B Robb, M Messager, G Piessen, C Gronnier, N Briez, C Mariette
Journal: Gut (2012)

<h3>Introduction</h3> Postoperative mortality (POM) within 30 days of oesophago-gastric resection remains significant and should be minimised to provide maximal chance of long-term survival. This study identifies factors predictive of 30-day POM in a large national multicentre cohort. <h3>Methods</h3> A retrospective analysis was performed of 2670 patients (mean age 64±13 years) who underwent resection of junctional or gastric adenocarcinomas from 1997 to 2010 in 19 French centres. Ordinal data were compared using either the χ<sup>2</sup> test or Mann–Whitney U test, as appropriate. A stepwise logistic regression model was built to identify by multivariate analysis variables independently predictive of 30-day POM. <h3>Results</h3> This study included 1893 men and 777 females, with a mean patient age of 64.2±13 years. 774 patients (29.0%) had a junctional, Siewert I or Siewert II type tumour and 1896 patients (71.0%) had either a Siewert type III or gastric adenocarcinoma. The majority of patients (2045, 76.6%) underwent gastrectomy, 625 (23.4%) oesophagectomy and proximal gastrectomy and 209 (7.8%) total oesophagogastrectomy. Resection was R0 in 2224 patients (83.3%). Neoadjuvant treatment was given to 665 patients (24.5%). A total of 114 patients died within 30 days of surgery (4.3%). POM rates increased during three study periods (1997–2000, 3.3%; 2001–2005, 3.6%; 2006–2010, 5.6%; p=0.021). The POM rate was significantly higher in patients who experienced grade III and IV toxicity during neoadjuvant chemotherapy when compared to those who did not (8.7% vs 2.6% respectively, p=0.007). Patients ≥60 years old and American Society of Anaesthesiology grade III or IV correlated with POM (p=0.002 and p=0.000, respectively). Variables indicating advanced disease consistently predicted POM (metastases at diagnosis, p=0.005; disease requiring extended resection, p=0.005; surgery with palliative intent, p 8 resections/annum (OR 0.389, 95% CI 0.157 to 0.965, p=0.042) and no grade III or IV toxicity during neoadjuvant treatment (OR 0.286, 95% CI 0.107 to 0.762, p=0.012) were protective factors. <h3>Conclusion</h3> This large national cohort study confirms patients with advanced disease are at higher risk of POM and centralisation of oesophago-gastric cancer resection is warranted. The novel finding that poor tolerance of neoadjuvant therapy increases the POM rate has significant implications for decision making in this subgroup of patients (Clinical Trial.gov identifier NCT01249859). <h3>Competing interests</h3> None declared.
Long-term ursodeoxycholic acid therapy is associated with reduced risk of biliary pain and acute cholecystitis in patients with gallbladder stones: A cohort analysis
Authors: Shinji Tomida, Masato Abei, Takashi Yamaguchi, Yasushi Matsuzaki, Junichi Shoda, Naomi Tanaka, Toshiaki Osuga
Journal: Hepatology (1999)

Whether ursodeoxycholic acid (UDCA) therapy alters the long-term clinical course of gallstones (GS) without stone dissolution remains unknown. We aimed to clarify the relationship between long-term UDCA therapy and risks of biliary pain or acute cholecystitis in GS patients. We also aimed to identify factors affecting the natural course, and to explore a simple patient selection criteria for UDCA therapy. A cohort of 527 uncomplicated GS patients with or without UDCA (600 mg/d) followed for up to 18 years was analyzed. Patients who had frequent attacks or were complicated with cholecystitis were converted to cholecystectomy. History and UDCA therapy were identified on Cox analysis as 2 factors affecting the long-term clinical course. In patients without therapy, history was the only predictor of biliary pain among various patient or stone characteristics; biliary pain was rare in asymptomatic patients, while frequent in symptomatic patients ( P &lt; .001). UDCA therapy was associated with reduced risk for biliary pain in both symptomatic (62% vs. 92% in untreated patients at 10 years; P &lt; .001; relative risk, 0.19; 95% CI, 0.10-0.34) and asymptomatic patients (6% vs. 12% in untreated patients at 10 years; P = .037; relative risk, 0.19; 95% CI, 0.04-0.91). Risk for the conversion was also reduced in UDCA-treated symptomatic patients (26% vs. 88% in untreated patients at 10 years, P &lt; .001; relative risk, 0.08; 95% CI, 0.03-0.22). These effects were independent of stone dissolution. Three factors were identified on Cox analysis as affecting GS dissolution: radiolucency, small size (&lt;10 mm) of stones, and visualized gallbladder (GB) on cholecystogram. A selection criteria based on these appears to exhibit high sensitivity (74%) and specificity (95%) for dissolution. UDCA therapy might be considered in symptomatic patients fulfilling these criteria, and also in patients who have significant surgical risk, because the longterm therapy is clearly associated with reduced risk of biliary pain and acute cholecystitis
Lower Urinary Tract Symptoms and Male Sexual Dysfunction: The Multinational Survey of the Aging Male (MSAM-7)
Authors: Raymond Rosen, Jens Altwein, Peter Boyle, Roger S Kirby, B Lukacs, Eric Meuleman, Michael P O’Leary, Paolo Puppo, Chris Robertson, Francois Giuliano
Journal: European Urology (2003)
Carbenicillin: A Clinical and Laboratory Evaluation
Authors: MELVIN I. MARKS
Journal: Annals of Internal Medicine (1970)

Carbenicillin therapy was given for Gram-negative infections, especially those due to Pseudomonas aeruginosa. In vitro studies demonstrated antibacterial activity against P. aeruginosa only at high drug concentrations. Forty-five patients with Gram-negative infections, including 38 due to Pseudomonas, were treated with carbenicillin. Therapy was successful in 10 patients, resulted in improvement in 19, and was considered a failure or indeterminate in 16 patients. Nine additional patients with Gram-negative infections were treated with carbenicillin and gentamicin; three were successfully treated; two improved; and four were failures or indeterminate. Carbenicillin was most effective in treating pseudomonas urinary-tract infections, although the relapse rate was high. Results of therapy for bacteremia, pneumonia, and other foci of infection were far less satisfactory, partly because of the serious nature of underlying disease. Carbenicillin-resistant Pseudomonas strains emerged during therapy in four patients. No serious drug toxicity was encountered, but superinfection was frequent.
WHY DOES APICAL HYPERTROPHIC CARDIOMYOPATHY HAVE A FAVORABLE OUTCOME THAN NON-APICAL TYPES? CARDIAC MAGNETIC RESONANCE AND ECHOCARDIOGRAPHIC FINDINGS FROM 350 PATIENTS WITH HYPERTROPHIC CARDIOMYOPATHY
Authors: Eun Kyoung Kim, Sang-Chol Lee, Hye Bin Gwag, Ji Won Hwang, Sung-A Chang, Sung-Ji Park, Seung Woo Park, Sung Mok Kim, Yeon Hyeon Choe, Jae K Oh
Journal: Journal of the American College of Cardiology (2014)
Hypoxia-induced adrenomedullin production in the kidney
Authors: Daisuke Nagata, Yasunobu Hirata, Etsu Suzuki, Masao Kakoki, Hiroshi Hayakawa, Atsuo Goto, Toshihiko Ishimitsu, Naoto Minamino, Yukari Ono, Kenji Kangawa, Hisayuki Matsuo, Masao Omata
Journal: Kidney International (1999)
Dose dependent response of symptoms, pituitary, and bone to transdermal oestrogen in postmenopausal women.
Authors: M Peacock, P Selby
Journal: BMJ (1987)

depth.The well informed patient and relative will probably be happier and less likely to call on NHS facilities unnecessarily.While acute illness is usually dealt with effectively and promptly, the doubts and bewilderment accompanying the diagnosis of a prolonged or lifelong illness deserve and demand our response.Money may be needed.for rooms, an information person, and an administrator/welcomer.The teaching sessions would mostly be run by people not needing pay.Diabetologists have already set an example on education: why should we not follow?
Investigation of recurrent miscarriages
Authors: Fred Kavalier
Journal: BMJ (2005)

The coronavirus causing the COVID-19 pandemic, SARS-CoV-2, uses −1 programmed ribosomal frameshifting (−1 PRF) to control the relative expression of viral proteins. As modulating −1 PRF can inhibit viral replication, the RNA pseudoknot stimulating −1 PRF may be a fruitful target for therapeutics treating COVID-19. We modeled the unusual 3-stem structure of the stimulatory pseudoknot of SARS-CoV-2 computationally, using multiple blind structural prediction tools followed by μs-long molecular dynamics simulations. The results were compared for consistency with nuclease-protection assays and single-molecule force spectroscopy measurements of the SARS-CoV-1 pseudoknot, to determine the most likely conformations. We found several possible conformations for the SARS-CoV-2 pseudoknot, all having an extended stem 3 but with different packing of stems 1 and 2. Several conformations featured rarely-seen threading of a single strand through the junction formed between two helices. These structural models may help interpret future experiments and support efforts to discover ligands inhibiting −1 PRF in SARS-CoV-2.
Bromocriptine-induced psychosis in acromegaly.
Authors: C M Le Feuvre, A J Isaacs, O S Frank
Journal: BMJ (1982)

Bromocriptine-induced psychosis in acromegalyDopaminergic mechanisms have been implicated in the pathogenesis of schizophrenia.' Psychosis induced by the dopamine-receptor agonist bromocriptine has been described mainly with high-dose regimens in Parkinsonism and less frequently with the lower doses used in hormonal disorders.24The following case is of interest because of the insidious onset of psychosis and the family history of paranoid schizophrenia. CommentThis psychotic episode appears to have been precipitated by bromocriptine.There is evidence of a liability to levodopa-induced affective disorder in those with a family history of affective illness.5This case suggests an analogous genetic vulnerability to bromocriptine- induced psychosis.A family history of schizophrenia in addition to a personal history may be relevant in considering the use of bromo- criptine.
His Bundle Ectopic Beats
Authors: Zainul Abedin
Journal: JAMA (1974)

Atrial pacing, and His bundle electrograms were recorded in a 62-year-old man with sinus bradycardia and a complex junctional arrhythmia. The arrhythmia was shown to be due to His bundle extrasystoles. The recognition of main-stem extrasystoles, based on analysis of surface electrocardiogram may not be possible, and His bundle electrocardiographic studies are necessary for the precise diagnosis of His bundle extrasystoles.
Expression and Regulation of Adhesion Molecules in Cardiac Cells by Cytokines
Authors: Rachid Kacimi, Joel S. Karliner, Farid Koudssi, Carlin S. Long
Journal: Circulation Research (1998)

Abstract —Adhesion molecules mediate inflammatory myocardial injury after ischemia/reperfusion. Cytokine release and hypoxia are features of acute ischemia that may influence expression of these molecules. Accordingly, we studied intercellular adhesion molecule (ICAM) and vascular cell adhesion molecule (VCAM) responses to cytokines and acute hypoxia in cultured myocardial cells. Northern blot analysis and immunoassay showed that the proinflammatory cytokines interleukin-1β (IL-1β) and tumor necrosis factor-α stimulated concentration-dependent increases in ICAM and VCAM mRNA and protein. In both cardiac myocytes and fibroblasts, pretreatment with a specific inhibitor of nuclear transcription factor-κB (NF-κB) prevented cytokine induction of both molecules. We also found that inhibition of tyrosine kinase and p38/RK (stress-activated protein kinase) pathways prevented IL-1β–induced ICAM and VCAM protein synthesis, whereas extracellular signal–regulated protein kinase (ERK1/ERK2) inhibition did not. Neither hypoxia (0% O 2 for 6 hours) alone nor hypoxia/reoxygenation had any significant effect on ICAM and VCAM mRNA. However, hypoxia did enhance IL-1β–induced ICAM mRNA expression in myocytes. As a possible mechanism of this synergistic action on CAM expression, hypoxia induced a time-dependent increase in the DNA binding activity of both NF-κB and activator protein-1 (AP-1), two transcription factors important for cell adhesion molecule expression. In contrast to the enhanced ICAM mRNA induced by IL-1β during hypoxia, however, protein levels for this adhesion molecule were unchanged beyond IL-1β–stimulated levels, suggesting posttranscriptional and/or posttranslational control mechanisms. We conclude that cytokines regulate ICAM and VCAM mRNA and protein in both cardiac myocytes and fibroblasts. Furthermore, adhesion molecule induction requires translocation of at least two transcription factors, NF-κB and AP-1.
Effects of elevated extracellular potassium concentrations on the Class III antiarrhythmic action of sotalol
Authors: Cobbe Sm, Manley Bs
Journal: Cardiovascular Research (1985)

Journal Article Effects of elevated extracellular potassium concentrations on the Class III antiarrhythmic action of sotalol Get access STUART M COBBE, STUART M COBBE * From the Department of Cardiovascular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX39DU *Correspondence to Dr S M Cobbe, Cardiac Department, John Radcliffe Hospital, Oxford OX3 9DU. Search for other works by this author on: Oxford Academic PubMed Google Scholar B STEWART MANLEY B STEWART MANLEY From the Department of Cardiovascular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX39DU Search for other works by this author on: Oxford Academic PubMed Google Scholar Cardiovascular Research, Volume 19, Issue 2, February 1985, Pages 69–75, https://doi.org/10.1093/cvr/19.2.69 Published: 01 February 1985
SUBCLINICAL THYROID DISEASE AND RISK OF NEW-ONSET ATRIAL FIBRILLATION
Authors: Christian Selmer, Jonas Olesen, jesper lindhardsen, Anne-Marie Schjerning Olsen, Jesper Clausager Madsen, Peter Riis Hansen, Ulla Schmidt, Jens Faber, Ole Dyg Pedersen, Morten Hansen, Christian Torp-Pedersen, Gunnar Gislason
Journal: Journal of the American College of Cardiology (2012)
Intensifying Platelet Inhibition — Navigating between Scylla and Charybdis
Authors: Deepak L. Bhatt
Journal: New England Journal of Medicine (2007)

In Greek mythology, Scylla was a ferocious beast and Charybdis was a monstrous whirlpool. The wily Odysseus successfully navigated between these two dangers by steering closer to Scylla, though he did lose a few crew members to her. In a similar manner, the astute clinician managing myocardial ischemia by using antiplatelet therapy attempts to balance coronary thrombosis, the basic cause of myocardial ischemia, against hemorrhage, the most-feared complication of antiplatelet therapy. There are many pathways by which antiplatelet drugs may antagonize platelet activation or aggregation, all of which increase the risk of bleeding, and many of which decrease the risk . . .
The Community's Responsibility for Rheumatic-Fever Prevention
Authors: Gene H. Stollerman
Journal: New England Journal of Medicine (1970)

These are times when public pressure to translate modern medical knowledge into practical healthcare services weighs heavily upon the medical and allied health professions. Often, the scientific facts do not lend themselves to simple, clear-cut clinical solutions, and the socioeconomic ills of the community conspire to frustrate attempts at implementation even of seemingly straightforward medical recommendations. The opportunities for the control of rheumatic fever and the prevention of rheumatic heart disease serve as a case in point. Despite the fact that streptococcal sore throat can be readily diagnosed and simply treated, acute rheumatic fever still occurs with unacceptable frequency. Acute . . .
Possibilities and Problems of Immunologic Intervention in Cancer
Authors: Richard T. Smith
Journal: New England Journal of Medicine (1972)

Background for InterventionTHE possibility of altering the course of cancer by manipulation of host-defense mechanisms has for years been an attractive lure for physicians. A base of knowledge to guide rational intervention, however, has simply not existed. Much ignorance still separates us from thoughtful and effective application, but some growth in understanding of the tumor-host relation has occurred during the past few years.1 2 3 4 5 6 7 From this recent yield several principles governing this relation appear firm enough to justify adoption as a foundation for this speculative discussion of both the promise and problems of intervention.In the first place, with certain . . .
Physicians and the Investment Industry
Authors: Eric J. Topol
Journal: JAMA (2005)

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
Sequence‐Specific Crosslinking of Electrospun, Elastin‐Like Protein Preserves Bioactivity and Native‐Like Mechanics
Authors: Patrick L. Benitez, Jeffrey A. Sweet, Helen Fink, Krishna P. Chennazhi, Shantikumar V. Nair, Annika Enejder, Sarah C. Heilshorn
Journal: Advanced Healthcare Materials (2012)

A nanoscale mimic of the extracellular matrix is electrospun from a highly tunable family of elastin-like proteins. A sequence-specific, two-step crosslinking procedure is developed to preserve the nanofiber morphology, elastin-like mechanics, and specific bioactivity. Rodent marrow stromal cells show sequence-specific adhesion on the matrices, which are imaged using label-free coherent anti-Stokes Raman scattering (CARS) microscopy.
Molecular analysis of RAS-RAF tyrosine-kinase signaling pathway alterations in patients with plasma cell myeloma
Authors: V Grossmann, U Bacher, V Artusi, A Kohlmann, N Nadarajah, W Kern, S Schnittger, T Haferlach, C Haferlach
Journal: Blood Cancer Journal (2012)

In patients with plasma cell myeloma (PCM), interphase fluorescence in situ hybridization (FISH) detects prognostically relevant genetic alterations, for example, the prognostically adverse t(4;14)(p16;q32) or 17p deletions. Furthermore, mutations of the RAS protooncogene were suggested to be associated to myeloma pathogenesis.1 The RAS pathway inhibitor lonafarnib combined with the proteasome inhibitor bortezomib demonstrated synergistic cell death in human myeloma cells in association with downregulation of p-AKT in an in vitro setting.2 By whole-genome and whole-exome sequencing, Chapman et al.3 found frequent involvement of genes associated to the nuclear factor-kappaB pathway. Rare PCM cases were positive for BRAF mutations,3 which had previously been detected in solid tumors (for example, melanoma) and hematological neoplasms, for example, hairy cell leukemia.4
THE INFLUENCE OF X-RAYS IN THE TREATMENT OF LEUKEMIA AND HODGKIN'S DISEASE, WITH A REPORT OF TWO CASES.
Authors: AUGUSTUS H. ROTH
Journal: JAMA (1906)

Since the therapeutic value of<i>x</i>-rays in Hodgkin's disease and leukemia is still in the experimental stage, and requires the report of more cases which have been under careful observation and treatment for longer periods of time, in order to arrive at definite conclusions, the two following cases are submitted with their detailed histories, and results of treatment; together with an account of some experimental observations concerning the action of<i>x</i>-rays on the blood and urine in leukemia. <h3>HODGKIN'S DISEASE: REPORT OF A CASE WITH A SYMTOMATIC CURE.</h3><h3>Patient.</h3> —Mrs. R. came to the medical clinic of Dr. Dock, May 13, 1904, because of nodules in the sides of the neck and pain in the neck and thorax. <h3>History.</h3> —The patient's family history is negative. She has had measles, scarlet fever and three attacks of "la grippe." Five years ago she noticed a mass on the left side