tbuckley/cabot-search huggingface dataset:
Analysis of Codon Usage Patterns of Bacterial Genomes Using the Self-Organizing Map
Authors: Huai-Chun Wang, Jonathan Badger, Paul Kearney, Ming Li
Journal: Molecular Biology and Evolution (2001)

Codon usage varies both between organisms and between different genes in the same organism. This observation has been used as a basis for earlier work in identifying highly expressed and horizontally transferred genes in Escherichia coli. In this work, we applied Kohonen's self-organizing map to analysis of the codon usage pattern of the Escherichia coli, Aquifex aeolicus, Archaeoglobus fulgidus, Haemophilus influenzae Rd., Methanococcus jannaschii, Methanobacterium thermoautotrophicum, and Pyrococcus horikoshii genomes for evidence of highly expressed genes and horizontally transferred genes. All of the analyzed genomes had a clear category of horizontally transferred genes, and their apparent percentages ranged from 7.7% to 21.4%. The apparent percentage of highly expressed genes ranges from 0% to 11.8%. A clustering of average codon usage of main gene categories of the seven genomes showed an interesting mixing of gene classes in four thermophilic/hyperthermophilic organisms, A. aeolicus, A. fulgidus, M. thermoautotrophicum, and P. horikoshii, which suggests possible origins of their horizontally transferred genes as well as the need for adaptation to a specific environment. Further classification of the three gene categories in E. coli and H. influenzae according to gene function revealed that genes involved in communication (such as regulation and cell process) and structure (cell structure and structural proteins) are more likely to be horizontally transferred than are genes involved in information (transcription, translation, and related processes) and in some groups of energy (such as energy metabolism and carbon compound catabolism).
Lung liquid clearance and Na,K-ATPase during acute hyperoxia and recovery in rats.
Authors: W G Olivera, K M Ridge, J I Sznajder
Journal: American Journal of Respiratory and Critical Care Medicine (1995)

Lung liquid clearance, epithelial permeability for Na+, mannitol and albumin, as well as Na,K-ATPase activity in alveolar type 2 (AT2) cells were studied during the acute and the recovery phase of hyperoxic lung injury. Rats exposed to 100% oxygen for 64 h were studied at 0, 7 and 14 d after removal from the hyperoxic chamber and compared with control rats breathing room air. In the isolated-perfused, liquid-filled rat lung, the albumin flux from the perfusate into the air spaces increased immediately after the oxygen exposure (220 +/- 56 mg/h) and returned to control values (28 +/- 7 mg/h) after 7 and 14 d of recovery. The small solutes (Na+ and mannitol) flux across the alveolar epithelium normalized only after 14 d of recovery in room air. Active Na+ transport and lung liquid clearance were reduced by approximately 45% immediately after oxygen exposure when compared with control values, increased by approximately 56% above control values after 7 d of recovery, and returned to control values after 14 d of recovery. Paralleling these changes the Na,K-ATPase activity decreased by approximately 41% in AT2 cells isolated from rats after 64 h of breathing 100% O2 and increased by approximately 25% after the rats recovered in room air for 7 d. These results suggest that alveolar epithelial Na,K-ATPase may contribute in the recovery from the hyperoxic lung injury by participating in the clearance of lung edema.
Telemedical Interventional Monitoring in Heart Failure (TIM‐HF), a randomized, controlled intervention trial investigating the impact of telemedicine on mortality in ambulatory patients with heart failure: study design
Authors: Friedrich Koehler, Sebastian Winkler, Michael Schieber, Udo Sechtem, Karl Stangl, Michael Böhm, Herbert Boll, Simone S. Kim, Kerstin Koehler, Stephanie Lücke, Marcus Honold, Peter Heinze, Thomas Schweizer, Martin Braecklein, Bridget‐Anne Kirwan, Goetz Gelbrich, Stefan D. Anker
Journal: European Journal of Heart Failure (2010)
Gene Expression Profiles of Endocrine Resistant Breast Tumours.
Authors: A. Larionov, D. Faratian, H. Caldwell, A. Sims, A. Fawkes, L. Murphy, L. Renshaw, J. Dixon, J. Dixon
Journal: Cancer Research (2009)

Abstract AimTo identify molecular sub-classes of endocrine-resistant breast tumours.MethodsWhole genome expression profiles of 55 endocrine-resistant tumours were obtained using Illumina HT-12 BeadChip arrays. Endocrine resistance was defined as either (i) tumour increased in size during hormonal treatment or (ii) appearance of local recurrence or (iii) contra-lateral breast lesion (metastases or new cancers) during hormonal treatment. Most of the treated patients were post-menopausal. Hormonal treatment included either aromatase inhibitors (letrozole, anastrazole, arimidex) or tamoxifen.ResultsUnsupervised hierarchical clustering using 500 most variable genes split tumours into three major clusters of approximately equal size. The genes discriminating between these clusters included oestrogen receptor- and proliferation- associated set of genes (ESR1, TFF1, TFF3, FOXA1, AGR2, AGR3, XBP1, GATA3, PRAD6B, MYB, CCND1), and stroma-related genes (DCN, COL1A1, COL1A2, COL3A1, COL5A2). Initial analysis of the studied tumours was unable to identify genes associated with clinical features. Sub-division of the dataset may be required to identify these genes more clearly. Genes that tended to separate between tumours resistant to AI and Tamoxifen included MYB, GPR137B, RNF19A, FRMD6, ZNF217 and RPS12. More detailed analysis of the data is underway.DiscussionUnderstanding and overcoming of endocrine resistance will improve treatment results for the majority of breast cancer patients. This abstract reports a new gene expression dataset to compare molecular features of biopsies collected from tumours growing while on endocrine treatment. The initial analysis demonstrates diversity of the resistance mechanisms, enhancing development of individual approaches to endocrine-resistant tumours. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5132.
Basic life support
Authors: J A Mclean
Journal: British Journal of Sports Medicine (2000)

The term basic life support (BLS) means maintaining an airway and supporting breathing and circulation without the use of equipment (except for a protective shield). It consists of: ( a ) initial assessment; ( b ) airway maintenance; ( c ) expired air ventilation; ( d ) chest compression. Three quarters of all cardiac arrests occur out of hospital, and, when witnessed, up to 30% of patients who suffer out of hospital ventricular fibrillation arrests survive to leave hospital. Bystander initiated life support can double the number of people who survive the period before hospital admission. BLS skills once learned must be maintained. The European guidelines describe a "sequence of actions"
Treatment of Osteoporotic Vertebral Fractures
Authors: Avram Allan Edidin, Steven M. Kurtz, Kevin L. Ong
Journal: JAMA Internal Medicine (2014)

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 Internal Medicine HomeNew OnlineCurrent IssueFor Authors Podcast 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 Internal Medicine journal
LONG-TERM EFFECT OF EZETIMIBE-STATIN COMBINATION THERAPY ON LOW-DENSITY LIPOPROTEIN CHOLESTEROL LOWERING IN PATIENTS WITH CORONARY ARTERY DISEASE; FOCUS ON CHOLESTEROL ABSORPTION AND SYNTHESIS
Authors: Kozo Okada, Kazuki Fukui, Hideo Himeno, Tutomu Endo, Makoto Shimizu, Shunichi Kobayashi, Tomohiko Shigemasa, Yukiko Morita, Atsushi Wada, Tomoaki Shimizu, Yasuyuki Mochida, Reimin Sawada, Tomoaki Ishigami, Kazuaki Uchino, Noriaki Iwahashi, Kazuo Kimura, Satoshi Umemura
Journal: Journal of the American College of Cardiology (2011)
Color Doppler flow mapping in patients with coarctation of the aorta: new observations and improved evaluation with color flow diameter and proximal acceleration as predictors of severity.
Authors: I A Simpson, D J Sahn, L M Valdes-Cruz, K J Chung, F S Sherman, R E Swensson
Journal: Circulation (1988)

We performed color Doppler flow mapping in 15 patients, 1 week to 17 years old (mean 42 months), with coarctation of the aorta that was confirmed subsequently by angiography and/or surgery. Twelve patients had native coarctation and three had mild recoarctation after surgical repair. Color Doppler flow maps were analyzed with a digital analysis package and a Sony computer system. The diameter in the region of coarctation from the color Doppler flow map (mean = 2.0 +/- 0.8 mm [SD]) correlated well with the coarctation diameter measured at angiography (mean = 1.8 +/- 0.8 mm; r = .83, SEE 0.43 mm) in the 10 patients with native coarctation undergoing angiography, but the coarctation diameter measured by two-dimensional echocardiography (3.9 +/- 1.5 mm) was poorly predictive of the angiographic severity (r = .23). Additionally, spatial acceleration was seen in all patients proximal to the coarctation site, with an aliased and accelerating stream narrowing progressively as it proceeded toward the coarctation site, a pattern that is not seen in healthy subjects. Computer analysis of the color Doppler images provided pseudo three-dimensional and digital velocity maps for blue, red, and green (turbulent) flow velocities to allow an enhanced appreciation of the accelerating stream, easily separating this from normal descending aortic aliasing patterns. The narrowing of the acceleration area in the proximal descending aorta (distal/proximal acceleration zone ratio) was also predictive of the angiographic severity of coarctation (r = .83). The distribution of low-level turbulence seen proximally paralleled the distribution of the proximal accelerating stream.(ABSTRACT TRUNCATED AT 250 WORDS)
A SATISFACTORY OPERATION FOR CERTAIN CASES OF RETROVERSION OF THE UTERUS.
Authors: J. CLARENCE WEBSTER
Journal: JAMA (1901)

During the past year I have carried out the following procedure in a number of cases where operative interference has been deemed advisable for retroversion of the uterus. The patient being in the Trendelenburg position, the abdomen is opened, adhesions are separated and other pathologic conditions, which may be present, attended to. The fundus of the uterus is elevated and pushed forward. A small hole is then made through the broad ligament on one side under the utero-ovarian ligament near the uterus. Through it a pair of forceps is passed from behind in order to grasp the round ligament about an inch from its uterine end. The latter is then pulled through the broad ligament in a double fold. It is carried across the back of the uterus a short distance above the utero-sacral ligaments and is then stitched in this position with chromic catgut. A similar procedure is carried
Papilloedema and respiratory failure.
Authors: P Reeve, G Harvey, D Seaton
Journal: BMJ (1985)

<h3>Abstract</h3> Up to 70% of SARS-CoV-2 infections in working- and school-age people are asymptomatic (Poletti et al., 2020), creating anxiety over reopening workplaces and schools around the world. In the absence of effective treatments or a vaccine, peace of mind will come only with community-based SARS-CoV-2 screening, where many people are tested on a regular basis. However, recent models show that short sample-to-answer turnaround time will be a critical property of effective screening strategies (Larremore et al., 2020). Here, we describe an RT-LAMP test for SARS-CoV-2 in raw saliva that takes about 45 minutes from sample to answer and requires only simple equipment (pipettes and a heating source). The assay has a limit of detection of 100 virions per microliter, and targets two separate regions of the SARS-CoV-2 genome. By combining rapid sample-to-answer turnaround time with the use of saliva, our RT-LAMP assay provides a low-complexity, portable, and robust system for real-time community screening.
Alterations of systemic and muscle iron metabolism in human subjects treated with low-dose recombinant erythropoietin
Authors: Paul Robach, Stefania Recalcati, Domenico Girelli, Cecilia Gelfi, Niels J. Aachmann-Andersen, Jonas J. Thomsen, Anne M. Norgaard, Alessandra Alberghini, Natascia Campostrini, Annalisa Castagna, Agnese Viganò, Paolo Santambrogio, Tibor Kempf, Kai C. Wollert, Stéphane Moutereau, Carsten Lundby, Gaetano Cairo
Journal: Blood (2009)
Letter: Prazosin in hypertension.
Authors: J M Hayes, R M Graham, B P O'Connell
Journal: BMJ (1974)

<h3>Background</h3> Inflammatory bowel disease (IBD) is a group of inflammatory conditions of the colon and small intestine. The major types of IBD are ulcerative colitis and Chron’s disease. Symptoms can occur at any time and exacerbations can be followed by periods of remission. The objective of IBD treatment is induction, maintenance of remission or both. An increasing number of biologics have been approved for the treatment of refractory moderate to severe IBD in patients who have not responded to traditional therapy, but due to the absence of direct comparison data and the introduction of biosimilars, treatment choice is still controversial. <h3>Purpose</h3> The aim of this study is to analyse prescribing trends of biologics used at the centre for the treatment of patients with moderate to severe IBD refractory to traditional therapy. <h3>Material and methods</h3> Data were extracted from the management software used at the centre and collected in an Excel spreadsheet. Included data were: dispensing data of biologics prescribed for every refractory moderate to severe patient with IBD treated at the centre between January 2014 and November 2017. For each patient dispensed treatments, switches and reason for switches were analysed. <h3>Results</h3> Eight-hundred and fourteen patients with IBD treated with biologics were included: Adalimumab (42.7%), Infliximab (27.4% originator; 14.4% biosimilar), Golimumab (6.8%) and Vedolizumab (8.7%). Five per cent of overall in-treatment patients changed treatment. Switch rates were: 8.5% from Infliximab originator to Vedolizumab, 3.6% from Golimumab to Adalimumab, 1.8% from Golimumab to Infliximab biosimilar, 12.8% from Infliximab biosimilar to Vedolizumab, 2.8% from Vedolizumab to Infliximab biosimilar, 4.5% from Infliximab originator to Infliximab biosimilar and 1.7% from Infliximab biosimilar to originator. Reasons for switching were inefficacy (61%) or treatment cost reduction (39%). <h3>Conclusion</h3> Analysis showed a high variability in biological therapy prescription trends at the centre, which could be related to patients’ characteristics. Even in the absence of clear comparison data between different treatments, clinical choices included all biological treatments approved in Italy, which were almost always effective and were associated with a low overall switch rate. <h3>References and/or acknowledgements</h3> No conflict of interest.
TCT- 309 Influence of subtended myocardial mass on intracoronary physiology indices of stenosis severity and microcirculatory function.
Authors: Mauro Echavarria-Pinto, Tim P. van de Hoef, Sukhjinder S. Nijjer, Enrico Cerrato, Borja Ibañez, Nieves Gonzalo, Ricardo Petraco, Luis Nombela-Franco, Alicia Quirós, Sayan Sen, Ivan Nuñez-Gil, Pilar Jimenez-Quevedo, Carlos Macaya, Justin E. Davies, Patrick W. Serruys, Jan Piek, Javier Escaned
Journal: Journal of the American College of Cardiology (2014)
Meningitis outbreak prompts review
Authors: R. Dobson
Journal: BMJ (1997)

A new review of guidelines on the handling of meningococcal infections in colleges and universities has been urged after an outbreak of meningitis at the University of Wales, Cardiff, in which two women students died.

In the outbreak at the end of last year seven cases of infection were established, more than 80 students were admitted to hospital, and more than 1000 people were immunised with meningococcal AC vaccine. The outbreak …
Acute Myocardial Infarction in a Pregnant Woman at Term
Authors: Wayne R. Cohen
Journal: JAMA (1983)

MANIFESTATIONS of arteriosclerotic cardiovascular disease are rare in pregnant women. We describe a case of acute myocardial infarction in a woman at 39 weeks' gestation. General guidelines for management of pregnancy associated with this complication are suggested. <h3>Report of a Case</h3> A 42-year-old woman (gravida 7, para 6) had a massive anterior-wall myocardial infarction within the 39th week of an otherwise normal pregnancy. Shortly after the onset of her first episode of chest pain, she sustained ventricular fibrillation and was resuscitated successfully. Twenty-four hours later, after severe postarrest congestive heart failure was treated, she was transferred to Beth Israel Hospital, Boston. The patient's first pregnancy had been complicated by preeclampsia, but her others had been uneventful. She had a 20-year history of mild hypertension (treated intermittently with diuretics and propranolol hydrochloride), a five-pack-year smoking history, and a family history of arteriosclerotic cardiovascular disease. Results of her serum lipid profile were
Cyclin D1 Splice Variants: Polymorphism, Risk, and Isoform-Specific Regulation in Prostate Cancer
Authors: Clay E.S. Comstock, Michael A. Augello, Ruth Pe Benito, Jason Karch, Thai H. Tran, Fransiscus E. Utama, Elizabeth A. Tindall, Ying Wang, Craig J. Burd, Eric M. Groh, Hoa N. Hoang, Graham G. Giles, Gianluca Severi, Vanessa M. Hayes, Brian E. Henderson, Loic Le Marchand, Laurence N. Kolonel, Christopher A. Haiman, Raffaele Baffa, Leonard G. Gomella, Erik S. Knudsen, Hallgeir Rui, Susan M. Henshall, Robert L. Sutherland, Karen E. Knudsen
Journal: Clinical Cancer Research (2009)

Alternative CCND1 splicing results in cyclin D1b, which has specialized, protumorigenic functions in prostate not shared by the cyclin D1a (full length) isoform. Here, the frequency, tumor relevance, and mechanisms controlling cyclin D1b were challenged.
Numerators without denominators. There is no FDA for the surgeon
Authors: D. H. Spodick
Journal: JAMA (1975)

EACH day, physicians face complex decisions in choosing accurate diagnoses and optimum treatments. We have become quite adept at marshaling objective data for diagnostic choices. Therapeutic decisions must often depend on less substantial evidence. In consequence, elaborate methods are required for clinical trials to test the effectiveness and safety of new drugs, but, somehow, the same type of rigorous criteria are not demanded for trials of new operations. Much thought and huge sums of money have been directed toward ensuring the outcome when the physician writes a prescription, but there is not this type of concern generated when he flourishes a scalpel. If this division of requirements were really proportionate, it might be justified as a backhanded acknowledgment that the pen is indeed mightier than the sword. Unfortunately, this is nottrue; there is no evidence that we need less demanding criteria for making surgical than medical choices. <h3>Comparing Treatments: The</h3>
The composition and signaling of the IL-35 receptor are unconventional
Authors: Lauren W Collison, Greg M Delgoffe, Clifford S Guy, Kate M Vignali, Vandana Chaturvedi, DeLisa Fairweather, Abhay R Satoskar, K Christopher Garcia, Christopher A Hunter, Charles G Drake, Peter J Murray, Dario A A Vignali
Journal: Nature Immunology (2012)
INTEGRATING NATIONAL CARDIOVASCULAR DATA REGISTRY (NCDR®) INFORMATION INTO THE CARE OF PERCUTANEOUS CORONARY INTERVENTION PATIENTS: A QUALITATIVE PERSPECTIVE
Authors: Karl E. Minges, Peggy G. Chen, Emily Cherlin, John Rumsfeld, John Messenger, Tony Hermann, Mary Anne Elma, Jeptha Curtis
Journal: Journal of the American College of Cardiology (2014)
Epidemiology of IDDM in Southern Chinese Children in Hong Kong
Authors: Gary W Wong, Sophie S Leung, Stephen J Oppenheimer
Journal: Diabetes Care (1993)

To provide reliable data on the incidence of IDDM in southern Chinese children in Hong Kong.A registry was established in 1991 to collect childhood IDDM cases retrospectively and prospectively from four districts in Hong Kong. The study included all newly diagnosed cases of IDDM with onset < 15 yr of age from 1 January 1986 to 31 December 1990. Primary ascertainment was based on review of medical records at a regional hospital serving the four districts. An independent school survey validated registry data.The completeness of ascertainment was 93.8%. The age-standardized incidence of IDDM was 2.0/100,000/yr with the 95% confidence interval of 1.2-3.0/100,000/yr for children < 15 yr of age during the study period. The incidence rates/100,000/yr for the three age-groups were: < or = 4 yr, 0.8; 5-9 yr, 2.2; 10-14 yr, 2.8. The incidence for males was 1.5/100,000/yr (95% confidence interval 0.7-2.9/100,000/yr) and for females, 2.4/100,000/yr (95% confidence interval 1.3-4.0/100,000/yr).This study documents a very low incidence rate of childhood IDDM in southern Chinese in Hong Kong.
How to drain without lymphatics? Dendritic cells migrate from the cerebrospinal fluid to the B-cell follicles of cervical lymph nodes
Authors: Eric Hatterer, Nathalie Davoust, Marianne Didier-Bazes, Carine Vuaillat, Christophe Malcus, Marie-Françoise Belin, Serge Nataf
Journal: Blood (2005)
Managing patients with multimorbidity in primary care
Authors: E. Wallace, C. Salisbury, B. Guthrie, C. Lewis, T. Fahey, S. M. Smith
Journal: BMJ (2015)

8][9] Patients with multimorbidity have a high treatment burden in terms of understanding and self managing the conditions, attending multiple appointments, and managing complex drug regimens. 10ualitative research highlights the "endless struggle" patients experience in trying to manage their conditions well. 11Psychological distress is common: in an Australian survey of 7620 patients in primary care, 23% of those with one chronic condition reported depression compared with 40% of those with five or more conditions. 12Multimorbidity presents many challenges, which may at times seem overwhelming.This review provides evidence based practice points that are feasible to implement in general practice and offers guidance for general practitioners in organising care delivery.