tbuckley/cabot-search huggingface dataset:
Erratum: Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons
Authors: Ingo Braasch, Andrew R Gehrke, Jeramiah J Smith, Kazuhiko Kawasaki, Tereza Manousaki, Jeremy Pasquier, Angel Amores, Thomas Desvignes, Peter Batzel, Julian Catchen, Aaron M Berlin, Michael S Campbell, Daniel Barrell, Kyle J Martin, John F Mulley, Vydianathan Ravi, Alison P Lee, Tetsuya Nakamura, Domitille Chalopin, Shaohua Fan, Dustin Wcisel, Cristian Cañestro, Jason Sydes, Felix E G Beaudry, Yi Sun, Jana Hertel, Michael J Beam, Mario Fasold, Mikio Ishiyama, Jeremy Johnson, Steffi Kehr, Marcia Lara, John H Letaw, Gary W Litman, Ronda T Litman, Masato Mikami, Tatsuya Ota, Nil Ratan Saha, Louise Williams, Peter F Stadler, Han Wang, John S Taylor, Quenton Fontenot, Allyse Ferrara, Stephen M J Searle, Bronwen Aken, Mark Yandell, Igor Schneider, Jeffrey A Yoder, Jean-Nicolas Volff, Axel Meyer, Chris T Amemiya, Byrappa Venkatesh, Peter W H Holland, Yann Guiguen, Julien Bobe, Neil H Shubin, Federica Di Palma, Jessica Alfo¨ldi, Kerstin Lindblad-Toh, John H Postlethwait
Journal: Nature Genetics (2016)
Soundings: Dying we live
Authors: Colin Douglas
Journal: BMJ (2003)

On the stairs an evocative odour lingers. The anatomy department has gone but its lecture theatre remains: blackboard, dusty skylight, and tiered half-circle of fiercely uncomfortable benches exactly as they were. Even decades on there is a flicker of the bad-dream feeling of being trapped back in school, ignorant and accountable. The brachial plexus? The decussation of the pyramids? The foramen of Monro?

But someone has kindly removed the skeleton that stood sentinel on the hundreds of hours of anatomy teaching no one seems to need any more, and this afternoon a different audience climbs the wooden steps and settles down.

For years each new professor in our now quite ancient medical school has made a first impression here. Today's inaugural lecture brings together the mixture as before: undergraduates and postgraduates; friends and family; and a little platoon of gowned professors, on this occasion outnumbered by their retired forebears—the generation who taught us. After 20 minutes in the soothing half-light, a fair few of the latter have dozed off. Now they know. For the rest, discomfort takes its toll or memories distract. A minority pays attention and learns a lot.

Apoptosis—programmed cell death—was first thought of just 30 years ago and about 200 yards away: an observation and an idea that have gone on to deliver vast amounts of impressive, competitive, and seriously expensive international research.

Orderly cell death matters in growth and disease, and the emerging details are increasingly complex. Suddenly the sound system drowns our speaker in a random howl. People wake and listen, but have missed the intricacies, the elegance of recently determined apoptosis mechanisms, and—of course—their possible role in cancer.

A vote of thanks and we are free to go. A senior sample from three generations of Edinburgh medicine disperses: middle aged and older, some now very old and frail. Outside in the New Quad it is dark and cold.

Soon the New Quad, an elegant Italianate 1880s courtyard complex once the heart of the medical school, will be downgraded and abandoned to public health; 4 km to the south east, a boxy white building, contemporary in design and visibly temporary in comparison, is already in use. It sits within a PFI project and has a much shorter expected life. But it will do for now. Dying, we live.
A memorable patient: Fear
Authors: Lesley Jean Morrison
Journal: BMJ (2006)

I'm not sure how I managed it but, when I was arranging my preregistration year, I persuaded my medical school to let me satisfy my urge to experience New York and spend my year in hospitals in Brooklyn. The second six months were in Greenpoint, a hospital in a very poor Puerto Rican barrio made famous by the filming of the mob movie Serpico. The T-shaped emergency room had an unusual architectural feature, a portcullis arrangement at the juncture of the two corridors. When the going got tough with some of the local clientele, as it inevitably did on Saturday nights, the troublemakers were herded by the police officers on duty down to the intersection, where iron grid walls slid down from the ceiling and the offenders found themselves neatly confined in an iron cage. Such were the working conditions.

Three months into my time there, a junior doctors' strike was called for better pay and better conditions. They had a point: there were far too few of them, there was little attending (consultant) support, and the quality of care suffered badly. On the assigned day the wards emptied of junior staff as they took up position outside on the picket lines. I was in a dilemma. I wanted to support my colleagues, but I felt bad about leaving my patients. I felt especially worried about an elderly Puerto Rican woman at the end stages of chronic obstructive pulmonary disease. I didn't want to leave her, and it wasn't really my strike, but I was terrified of being the only doctor left in the hospital, exposed and expected to do things I did not feel competent to do.

I went to the picket line, and my elderly patient died. I don't remember the outcome of the strike, but I'll never forget her face.
Ronald Henry McClure
Authors: Elizabeth McClure
Journal: BMJ (2016)

Ronald Henry McClure (“Ron”) was born in Wroughton, Wiltshire, on 9 May 1927. His father, Sandy, from Castle Douglas, was the doctor for the railways. His mother, Muriel, was an only child from Frome, Somerset. He had one older sister, Jean. He was brought up in Wellington, Shropshire.

Growing up, he developed a great love of music, spending many hours with his father, calculating, with 7 figure logarithms, mean tone intervals for the design of what became the McClure organ, now in the Reid School of Music in Edinburgh. Madrigals were part of his childhood.

He went to Newport grammar school, then St Edward’s, …
Care of Older People: Community care: the independent sector
Authors: S Barodawala
Journal: BMJ (1996)

period before you purchase a handgun.Rifle and shotgun controls are barely on the agenda.There is a much lauded victory that saw military assault weapons banned.But let's read that again: newly manufactured assault weapons are banned, but not the hundreds of thousands of second-hand machine guns that can be openly traded with no gun register to track them, nor the tens of thousands that were stockpiled by gun dealers when they were given many months forewarning of the ban.Last week I went to a sporting goods store in Virginia, some 10 km from the heart of Washington DC.It was the size of an aircraft hangar.The place teemed with families buying joggers, rollerblades, and baseball gear.As natural as apple pie, an entire wall of the store was covered with rifles and shotguns, with a glass counter that ran about 20 metres filled with handguns.The American who took me there said with a straight face "Virginia has introduced very strict new gun laws-you can only buy one handgun a month."The National Rifle Association has a slogan "Guns don't kill people.People kill people" to which Handgun Control replies "Guns don't die.People do."American media parochialism shields most Americans from realising that the home-as-fortress mentality they live under is not normal.Thank heavens Australia's openness to the world allowed us enlightenment enough to read the sign "Go back-you're going the wrong way."1SC is a spokesperson for the Coalition for Gun Control.1 Centers for Disease Control.Deaths resulting from firearm-and motor-vehicle-related injuries -United States,
Exercise and Risk of Cardiovascular Events in Women With Nonmetastatic Breast Cancer
Authors: Lee W. Jones, Laurel A. Habel, Erin Weltzien, Adrienne Castillo, Dipti Gupta, Candyce H. Kroenke, Marilyn L. Kwan, Charles P. Quesenberry, Jessica Scott, Barbara Sternfeld, Anthony Yu, Lawrence H. Kushi, Bette J. Caan
Journal: Journal of Clinical Oncology (2016)

Purpose Cardiovascular disease (CVD) is a leading cause of death among women with nonmetastatic breast cancer. Whether exercise is associated with reductions in CVD risk in patients with breast cancer with an elevated CVD risk phenotype is not known. Methods Using a prospective design, women (n = 2,973; mean age, 57 years) diagnosed with nonmetastatic breast cancer participating in two registry-based, regional cohort studies, completed a questionnaire that assessed leisure-time recreational physical activity (metabolic equivalent task [MET]-h/wk). The primary end point was the first occurrence of any of the following: new diagnosis of coronary artery disease, heart failure, valve abnormality, arrhythmia, stroke, or CVD death, occurring after study enrollment. Results Median follow-up was 8.6 years (range, 0.2 to 14.8 years). In multivariable analysis, the incidence of cardiovascular events decreased across increasing total MET-h/wk categories (P trend &lt; .001). Compared with &lt; 2 MET-h/wk, the adjusted hazard ratio was 0.91 (95% CI, 0.76 to 1.09) for 2 to 10.9 MET-h/wk, 0.79 (95% CI, 0.66 to 0.96) for 11 to 24.5 MET-h/wk, and 0.65 (95% CI, 0.53 to 0.80) for ≥ 24.5 MET-h/wk. Similar trends were observed for the incidence of coronary artery disease and heart failure (P values &lt; .05). Adherence to national exercise guidelines for adult patients with cancer (ie, ≥ 9 MET-h/wk) was associated with an adjusted 23% reduction in the risk of cardiovascular events in comparison with not meeting the guidelines (&lt; 9 MET-h/wk; P &lt; .001). The association with exercise did not differ according to age, CVD risk factors, menopausal status, or anticancer treatment. Conclusion Exercise is associated with substantial, graded reductions in the incidence of cardiovascular events in women with nonmetastatic breast cancer.
Computerized Transaxial Tomographic and Neuropsychological Evaluations in Chronic Alcoholics and Heroin Abusers
Authors: Shirley Y. Hill, Michael A. Mikhael
Journal: American Journal of Psychiatry (1979)

Computerized transaxial tomographic (CTT) scans and the Halstead-Reitan Neuropsychological Battery were administered to 42 paid male volunteers (15 chronic alcoholics, 15 heroin abusers, and 12 matched control subjects). CTT scans revealed that only 1 of the chronic alcoholics had a ventricle/brain (V/B) index larger than normal. One unexpected finding was that the heroin abusers had significantly smaller sulci and V/B indices. Neuropsychological assessments of the alcoholics and heroin abusers revealed functional impairment in a majority of cases; the alcoholics were twice as likely as opiate abusers to show impairment.
Potential uses of computed tomography-SPECT and computed tomography-coincidence fusion images of the chest.
Authors: LOREN KETAI, MICHAEL HARTSHORNE
Journal: Clinical Nuclear Medicine (2001)

The ability to fuse (or merge) data sets from SPECT and coincidence nuclear medicine scans with computed tomographic images combines physiologic information from the former method with the superior anatomic resolution of the latter technique. In many cases, this allows more definitive diagnosis than can be obtained by simple visual comparison of nuclear medicine images and conventional cross-sectional imaging. The technique may be used in the staging and follow-up of lung carcinoma, pulmonary carcinoid, and lymphoma. It may also aid in the interpretation of perfusion defects in Tc-99m MAA lung scanning, aid in the interpretation of ground-glass opacity in selected cases of chest high-resolution computed tomography, and aid in the diagnosis of some mediastinal masses (e.g., intrathoracic goiters). In this nuclear medicine atlas, the method used to create fusion images in the chest is described, and examples of fusion imaging with radiopharmaceuticals are given that may be of clinical use in chest disease.
Mediastinitis Caused by EUS-FNA of a Bronchogenic Cyst
Authors: J. Annema, M. Veseliç, M. Versteegh, K. Rabe
Journal: Endoscopy (2003)

Endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) is a safe and minimally invasive diagnostic technique for the analysis of mediastinal lesions. This case report describes a patient who developed a life-threatening mediastinitis after EUS-FNA of a mediastinal lesion, which (based on computed tomography of the thorax) had been suspected to be a lymph-node metastasis, but proved to be a bronchogenic cyst.
News
Authors: Charles Marwick
Journal: BMJ (1989)

debateIn Britain the 21st anniversary of the implementation of the 1967 Abortion Act is on 27 April, and campaigners from both sides of the debate will be using the opportunity to put their cases.The debate on abortion is also raging strongly in the United States, where on 25 April the Supreme Court will hear arguments in a case concerning the consti- tutional position ofa law passed in the state of Missouri in 1986 restricting abortion.Although the court is unlikely to reach a decision until the summer, the hearing is attracting nationwide interest and observers are trying to divine the outcome from the way the judges are questioning both sides in the case.
Psychoanalytic group therapy in clinic and private practice
Authors: M Day
Journal: American Journal of Psychiatry (1981)

The author reviews the process of psychoanalytic group psychotherapy in private practice and in the clinic setting. He describes the patients who are most likely to be referred for such therapy, most of whom have "failed" in other types of therapy. The group therapist begins with an empathic diagnostic evaluation of the patient's difficulty. As the patient engages in the group, he or she can compensate his or her ego; at the same time the patient develops a transference that is the main source of future work. In time, ego analysis and analysis of the infantile neurosis can be done. Finally, all the analytic work is consolidated during the process of termination.
THERAPEUTICS VII
Authors: Heather Ashton, G. W. Beveridge, C. J. Stevenson
Journal: British Journal of Dermatology (1969)

Journal Article THERAPEUTICS VII Get access Heather Ashton, Heather Ashton Pharmacology Department, University of Newcastle upon Tyne Search for other works by this author on: Oxford Academic Google Scholar G. W. Beveridge, G. W. Beveridge Royal Infirmary, Edinburgh Search for other works by this author on: Oxford Academic Google Scholar C. J. Stevenson C. J. Stevenson Royal Victoria Infirmary, Newcastle upon Tyne Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 81, Issue 8, 1 August 1969, Pages 637–639, https://doi.org/10.1111/j.1365-2133.1969.tb16052.x Published: 01 August 1969
Predictors of alprazolam discontinuation with and without cognitive behavior therapy in panic disorder
Authors: T J Bruce, D A Spiegel, S F Gregg, A Nuzzarello
Journal: American Journal of Psychiatry (1995)

In a previous paper the authors reported survival data for 20 panic disorder patients whose therapeutic doses of alprazolam were tapered by one of two methods: slow, flexible drug taper with supportive medical management or the same taper procedure carried out concurrently with cognitive behavior therapy. This report is an analysis of predictors of drug discontinuation success in that study. In addition, between-group comparisons of clinical measures at follow-up are presented.The subjects in the previous study (10 in each group) were assessed blindly at baseline, 2 weeks after completion of drug taper, and at 3- and 6-month follow-up. Potential predictors of drug discontinuation success were tested by using logistic regression. Between-group differences in symptom severity at 3-month follow-up were examined by using analyses of covariance.Thirteen subjects (nine receiving alprazolam plus cognitive behavior therapy and four receiving alprazolam only) completed the drug taper on schedule and were still medication free at follow-up. A single variable--baseline-to-posttaper change in anxiety sensitivity--predicted drug status at follow-up in 85% of the cases. At follow-up, subjects in the combined-treatment group were significantly more improved on measures of anxiety, depression, catastrophic thinking related to anxiety, perception of emotional control, and disability than subjects in the drug-only group.Across groups, reduction in the fear of anxiety symptoms was the best predictor of patients' ability to achieve and maintain drug abstinence. Some implications of that finding for the pharmacotherapy of panic disorder are discussed.
Locus of state psychiatric hospitals in the United States, 1960-1980
Authors: A Checker
Journal: American Journal of Psychiatry (1983)

The community mental health movement of the mid-1960s included a novel belief that psychiatric hospitals should be located near population centers. The author studied the extent to which recent site configurations of state psychiatric hospitals have reflected that conceptual change. In the period 1960-1980, a large number of rural state hospitals closed; at the same time a smaller number of state hospitals were opened. Although one set of states moved in the direction of an urbanized setting concept, another set of states held firm in its devotion to the rural hospital tradition.
Proliferative pathways in CD1- CD3+ CD4+ CD8+ T-prolymphocytic leukemic cells: analysis with monoclonal antibodies and cytokines
Authors: MC Turco, M De Felice, F Alfinito, A Lamberti, F Costanzo, M Giordano, V Martinelli, B Rotoli, S Ferrone, S Venuta
Journal: Blood (1989)
Intracellular heme coordinately modulates globin chain synthesis, transferrin receptor number, and ferritin content in differentiating Friend erythroleukemia cells
Authors: A Battistini, EM Coccia, G Marziali, D Bulgarini, S Scalzo, G Fiorucci, G Romeo, E Affabris, U Testa, GB Rossi
Journal: Blood (1991)
Multilocus variable number of tandem repeats analysis (MLVA) - a reliable tool for rapid investigation of Salmonella Typhimurium outbreaks
Authors: M Heck
Journal: Eurosurveillance (2009)

Salmonella enterica subsp. enterica serovar Typhimurium is a frequently occurring foodborne pathogen which causes many sporadic cases worldwide and is frequently the responsible agent in outbreaks of gastroenteritis. In elucidating outbreaks involving consumption of contaminated food, source tracing in a timely manner is imperative. Furthermore, it is important for risk managers to be able to accurately attribute sporadic cases to specific animal host species and to understand transmission routes of S. Typhimurium. Epidemiological meaningful subdivision of this serotype is therefore indispensable.
Abstract IA15: “Next-gen” genomics-based clinical trials
Authors: Lillian L. Siu
Journal: Clinical Cancer Research (2016)

Abstract Next generation sequencing (NGS) technologies have gained increasing clinical applications as a strategy to screen and identify patients for genomic based clinical trials in oncology. Molecular characterization programs using NGS have been established in many cancer centers worldwide, including some that comprise part of nation-based efforts. With a growing number of patients whose tumors have undergone molecular profiling, there is an urgent need to justify these activities and translate genomic findings into clinically relevant outcome. Molecular profiling offers information beyond the histopathological classification of tumors, subdividing them into smaller genomic subsets ranging from those harboring common recurrent aberrations to others with rare variants of uncertain significance. The current era of genomic based clinical trials is populated by “umbrella” and “basket” trials which allocate patients with druggable genomic signatures to specific genotype-drug matched groups that remain histology-based (“umbrella” trials) or are histology-agnostic (“basket” trials). The pros and cons of these clinical trial designs, and their ability to bring the value of precision medicine to bear, will be discussed. Looking beyond the present clinical trials framework, it is unlikely that genomics is sufficient as a standalone strategy to fully characterize the complex molecular landscape of cancer. “Next-gen” clinical trials need to target the dynamic status of tumors and take into consideration intratumoral heterogeneity in their design. The extension of profiling algorithms to include transcriptomics and epigenetics is attractive to encompass other alterations that can lead to unchecked tumor growth. A systems biology approach should be considered to understand signaling pathway interactions and decipher mechanisms of oncogenic dependence, especially in tumors which lack readily actionable profiles. There are close interactions between the genome and the immunome such that NGS may inform the selection of patients most likely to benefit from immune-based therapies. “Next-gen” clinical trials must be capable of interrogating cancer in a multifaceted and dynamic manner in order to achieve substantial incremental benefits in therapeutic outcome. Citation Format: Lillian L. Siu. “Next-gen” genomics-based clinical trials. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr IA15.
Pulmonary hypertension begets pulmonary hypertension: mutually reinforcing roles for haemodynamics, inflammation, and cancer-like phenotypes
Authors: Danchen Wu, Stephen L Archer
Journal: Cardiovascular Research (2016)

This editorial refers to ‘Haemodynamic unloading reverses occlusive vascular lesions in severe pulmonary hypertension’ by K. Abe et al ., pp. 16–25. 

Pulmonary arterial hypertension (PAH) is a devastating disease of the pulmonary vasculature in which vasoconstriction, inflammation, and a cancer-like phenotype, defined as excessive cell proliferation, impaired apoptosis, and mitochondrial metabolic abnormalities, contribute to vascular obstruction. The resulting increase in right ventricular (RV) afterload ultimately leads to death from RV failure. The histology of PAH includes a variable mixture of lesions in small pulmonary arteries (PAs), including medial hypertrophy, intimal hyperplasia, adventitial fibrosis, and plexiform lesions, as well as fibrosis and reduced compliance of large PAs.

PAH is a heterogeneous syndrome; however, several phenotypes are recognized that offer mechanistic and therapeutic insights. PAH has a haemodynamic phenotype [increased vasoconstriction and mean pulmonary artery pressure (mPAP), due in part to endothelial dysfunction and changes in ion channel function and calcium homeostasis in pulmonary artery smooth muscle cells, PASMC], a cancer-like phenotype (increased PASMC proliferation and apoptosis resistance associated with a glycolytic metabolic shift, epigenetic silencing of key redox regulatory genes such as SOD2,1 and an increased mitochondrial fission/fusion ratio2), and an inflammatory phenotype [increased perivascular accumulation of proinflammatory macrophages and changes in the population of immunoregulatory T-cells (T-Reg)3 and natural killer cells].4

Current PAH therapies (prostanoids, phosphodiesterase-5 inhibitors, endothelin receptor antagonists, and soluble guanylate cyclase activators) are vasodilators and primarily address PAH's haemodynamic phenotype. They improve symptoms and reduce hospitalization but, on average, only decrease mPAP ∼5 mmHg.5 Their limited haemodynamic efficacy and lack of effects on PAH's inflammatory and cancer-like phenotypes suggest that they are unlikely to reverse the histological lesions of …