tbuckley/cabot-search huggingface dataset:
Efficiencies of Fast Algorithms of Phylogenetic Inference Under the Criteria of Maximum Parsimony, Minimum Evolution, and Maximum Likelihood When a Large Number of Sequences Are Used
Authors: Kei Takahashi, Masatoshi Nei
Journal: Molecular Biology and Evolution (2000)

In phylogenetic inference by maximum-parsimony (MP), minimum-evolution (ME), and maximum-likelihood (ML) methods, it is customary to conduct extensive heuristic searches of MP, ME, and ML trees, examining a large number of different topologies. However, these extensive searches tend to give incorrect tree topologies. Here we show by extensive computer simulation that when the number of nucleotide sequences (m) is large and the number of nucleotides used (n) is relatively small, the simple MP or ML tree search algorithms such as the stepwise addition (SA) plus nearest neighbor interchange (NNI) search and the SA plus subtree pruning regrafting (SPR) search are as efficient as the extensive search algorithms such as the SA plus tree bisection-reconnection (TBR) search in inferring the true tree. In the case of ME methods, the simple neighbor-joining (NJ) algorithm is as efficient as or more efficient than the extensive NJ+TBR search. We show that when ME methods are used, the simple p distance generally gives better results in phylogenetic inference than more complicated distance measures such as the Hasegawa-Kishino-Yano (HKY) distance, even when nucleotide substitution follows the HKY model. When ML methods are used, the simple Jukes-Cantor (JC) model of phylogenetic inference generally shows a better performance than the HKY model even if the likelihood value for the HKY model is much higher than that for the JC model. This indicates that at least in the present case, selecting of a substitution model by using the likelihood ratio test or the AIC index is not appropriate. When n is small relative to m and the extent of sequence divergence is high, the NJ method with p distance often shows a better performance than ML methods with the JC model. However, when the level of sequence divergence is low, this is not the case.
Intravenous Cocaine and HIV Infection-Reply
Authors: Peter Bacchetti
Journal: JAMA (1989)

<h3>In Reply.—</h3> Mr French suggests that we fail to establish that IV cocaine use is associated with human immunodeficiency virus (HIV) infection. We strongly disagree. The association of HIV infection with cocaine injection was strong in our data and persisted in numerous analyses. We examined literally hundreds of multivariate models to establish that the effect of cocaine injection could not somehow be "explained away." We presented the model in Table 1 of our original article because it was simple and showed all subgroups who had elevated HIV seroprevalence. Each of the variables in the model defines a subgroup with higher-than-expected HIV seroprevalence after controlling for other variables in the model. The fact that some of the subgroups are defined as possessing two characteristics (eg, being nonwhite and injecting cocaine daily) does not seem to us to lead to any ambiguity. As noted in the article, models that include other variables
Involvement of the bcl-2 Gene in Hodgkin's Disease
Authors: M. Stetler-Stevenson, S. Crush-Stanton, J. Cossman
Journal: JNCI Journal of the National Cancer Institute (1990)

Journal Article Involvement of the bcl-2 Gene in Hodgkin's Disease Get access Maryalice Stetler-Stevenson, Maryalice Stetler-Stevenson Hematopathology Section, Laboratory of Pathology, National Cancer InstituteBethesda, MD Search for other works by this author on: Oxford Academic PubMed Google Scholar Sylvia Crush-Stanton, Sylvia Crush-Stanton Molecular Oncology, Inc.Gaithersburg, MD Search for other works by this author on: Oxford Academic PubMed Google Scholar Jeffrey Cossman Jeffrey Cossman * Hematopathology Section, Laboratory of Pathology, National Cancer InstituteBethesda, MD *Correspondence to : Jeffrey Cossman, M.D., Department of Pathology, Georgetown University, 3900 Reservoir Rd., N.W., Washington, DC 20007. Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 82, Issue 10, 16 May 1990, Pages 855–858, https://doi.org/10.1093/jnci/82.10.855 Published: 16 May 1990 Article history Received: 16 January 1990 Accepted: 24 January 1990 Published: 16 May 1990
Primary Prevention With Metoprolol in Patients With Hypertension-Reply
Authors: John Wikstrand
Journal: JAMA (1988)

In Reply.—  The protocol for the trial of β-blockers vs diuretics in hypertension was defined in 1975. All centers randomized patients either to metoprolol or a diuretic counterpart, with the exception of one center with 46 patients taking propranolol (atenolol was not included as an option in the original study). More than two years after the first patient was randomized, a separate part randomizing patients to atenolol or diuretics was started (Fig 2). Many patients were followed up for only one year in this part, partially explaining a low mortality rate, probably about six deaths per 1000 patient-years in the diuretic-treated group. That tendencies in one or the other direction may occur when mortality rates are low, as in the part comparing atenolol with diuretics, might be expected by chance. This does not change the interpretation of the results of the MAPHY Study since, as pointed out by the chairman
158. Real-Time Visualization of Neuronal Differentiation and Neurite Projection Using an Indicator HSV Amplicon Vector
Authors: Shigeru Tanaka, Kazue Kasai, E. Antonio Chiocca, Yoshinaga Saeki
Journal: Molecular Therapy (2006)

Stem cell-based replacement therapy has great potential in treating neurological disorders, including brain and spinal cord injuries. Although several studies have demonstrated neuronal and glial differentiation of transplanted neural stem cells (NSCs) in vivo, the efficacy of the transplanted NSCs to generate neurons and of the newly generated neurons to form new synaptic connections with the remaining host neurons still needs clarification. To address these issues, we have constructed an HSV amplicon-based indicator vector that allows visualization of neuronal differentiation and neurite projection. Synapsin I (SYN) is a well characterized gene that expresses selectively in neurons. Thiel and colleagues found that a 400-bp 5′ untranslated promoter region of SYN directed prominent expression of a reporter gene in various neuronal cell lines, but that no expression was detected in cell lines derived from non-neuronal tissue (Thiel G et al., PNAS 1991). On the other hand, microtubule- associated protein tau-reporter fusion protein has been used as a genetic reporter to visualize neuronal processes in vivo (Callahan CA et al., PNAS 1994). We, therefore, combined the two genetic elements in the context of HSV amplicon vectors, producing an indicator herpes simplex virus (HSV) amplicon vector, HSV-SYN-tauR, that carries tau fused with a monomeric red fluorescent protein (mRFP, Campbell et al., PNAS 2002) under the control of the 400- bp SYN promoter. When a mixed culture of mouse cortical neurons and glia was transduced with the HSV-SYN-tauR amplicon vector, RFP reporter was expressed only in neurons along their neurites, allowing visualization of every axon, dendrite, and spine. Time- lapse imaging of mixed cortical cultures transduced with the HSV- SYN-tauR amplicon vector allowed noninvasive real-time monitoring of extension and retraction of the neurites of live neurons. This indicator HSV amplicon vector could prove useful in studying neuronal differentiation, neurite projections, and regeneration of neuronal networks in vitro and in vivo.
Nuclear War: The Medical and Biological Consequences—Soviet Physicians' Viewpoint
Authors: Gordon K. MacLeod
Journal: JAMA (1985)

Yevgeni I. Chazov, MD, has been a spokesman conjointly with US physicians for an international effort by physicians to prevent nuclear war<sup>1</sup>. This book, however, is already out of date as a scientific treatise on the consequences of nuclear war. While Dr Chazov and his coauthors concur with the generally accepted conclusion that nuclear warfare results in biologic devastation, they make only a passing reference to the view that nuclear warfare will probably result in nuclear winter—a catastrophe far worse than the authors' description of the consequences of nuclear war. On page 97, they say, "nuclear explosions would cloak the atmosphere in a dark veil which would hinder sunlight for many weeks." If nuclear winter follows in the wake of nuclear warfare, the authors' efforts to distinguish between the effects of nuclear weapons and those of nuclear war is a distinction without a difference.
Abstract 2383: Translesion DNA synthesis by DNA polymerase kappa somatic variants found in prostate cancer
Authors: Santosh Yadav, Sudurika Mukhopadhyay, Nick Makridakis
Journal: Cancer Research (2014)

Abstract Prostate cancer is one of the most prevalent malignancies affecting men worldwide, and is the most frequent cancer among men in the USA, with an estimated 238,590 new cases and 29720 deaths in 2013 (NCI). DNA damage found in prostate cancer promotes tumor progression. Repair of DNA lesions that occur endogenously or in response to diverse genotoxic stresses is indispensable for genome integrity. DNA lesions activate checkpoint pathways that regulate specific DNA-repair mechanisms. During replication, DNA polymerases frequently encounter unrepaired DNA lesions and posses 3′→5′ exonuclease proofreading activities. Such polymerases tend to stall at sites of damage, which can lead to replication fork collapse and which, unless rescued, can eventually cause large-scale genomic rearrangements and cell death. As a preventative measure, most organisms have alternative polymerases that are capable of ‘damage tolerance’ and can synthesize past DNA lesions by a mechanism called translesion synthesis (TLS). Polymerase kappa (Polκ) a Y-family polymerase participates in the process of TLS. Current study was designed to investigate the TLS of somatic missense mutations of Polκ such as p.F155S, p.L442F, p.G154E, p.E29K, p.E449K and p.E430G found after sequence analysis of prostate tumor DNA from 30 prostate cancer patients. We studied these variants to identify the nucleotide incorporated opposite to the apurinic (AP) site template, in vitro using site-specific tetrahydrofuran (AP site analog). We report that missense somatic mutations of Polκ at p.F155S, p.L442F, p.G154E, p.E29K, p.E449K mutants significantly decreases catalytic efficiency (k(cat)/Km). The biological consequence of an unrepaired DNA lesion is determined by whether it is bypassed or not, bypassed error prone. Our results provide evidence that mutations in the polymerase kappa gene can causes interference in Translesion DNA synthesis, this interference in pol κ function may play a role in prostate tumor progression. We acknowledge to Prof. Dr. Guengerich, for providing Polκ construct. This work was supported by DOD grant PC094628, and NIH grant 8 P20 GM103518. Citation Format: Santosh Yadav, Sudurika Mukhopadhyay, Nick Makridakis. Translesion DNA synthesis by DNA polymerase kappa somatic variants found in prostate cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2383. doi:10.1158/1538-7445.AM2014-2383
Mass Antibiotic Administration for Eradication of Ocular &lt;emph type="ital"&gt;Chlamydia trachomatis&lt;/emph&gt;
Authors: David Mabey
Journal: JAMA (2008)

triiodothyronine combination therapy versus thyroxine monotherapy for clinical hypothyroidism: meta-analysis of randomized controlled trials. J Clin Endocrinol Metab. 2006;91(7):2592-2599. 14. Appelhof BC, Brouwer JP, van Dyck R, et al. Triiodothyronine addition to paroxetine in the treatment of major depressive disorder. J Clin Endocrinol Metab. 2004;89(12):6271-6276. 15. Joffe RT, Brimacombe M, Levitt AJ, Stagnaro-Green A. Treatment of clinical hypothyroidism with thyroxine and triiodothyronine: a literature review and metaanalysis. Psychosomatics. 2007;48(5):379-384. 16. Bunevicius R, Prange AJ. Mental improvement after replacement therapy with thyroxine plus triiodothyronine: relationship to cause of hypothyroidism. Int J Neuropsychopharmacol. 2000;3(2):167-174. 17. Hennemann G, Docter R, Visser TJ, Postema PT, Krenning EP. Thyroxine plus low-dose, slow-release triiodothyronine replacement in hypothyroidism: proof of principle. Thyroid. 2004;14(4):271-275. 18. Pharmacy Compounding Facts and Information. http://www.ppsinc.org /phcom/02news.htm. Accessed January 18, 2008. 19. Jonklaas J, Davidson B, Bhagat S, Soldin SJ. Triiodothyronine levels in athyreotic individuals during levothyroxine therapy. JAMA. 2008;299(7):769-777. 20. Jonklaas J, Sarlis NJ, Litofsky D, et al. Outcomes of patients with differentiated thyroid carcinoma following initial therapy. Thyroid. 2006;16(12):12291242. 21. Petersen K, Bengtsson C, Lapidus L, Lindstedt G, Nystrom E. Morbidity, mortality, and quality of life for patients treated with levothyroxine. Arch Intern Med. 1990;150(10):2077-2081. 22. Saravanan P, Chau WF, Roberts N, Vedhara K, Greenwood R, Dayan CM. Psychological well-being in patients on “adequate” doses of L-thyroxine: results of a large, controlled community-based questionnaire study. Clin Endocrinol (Oxf ). 2002;57(5):577-585. 23. Wekking EM, Appelhof BC, Fliers E, et al. Cognitive functioning and wellbeing in euthyroid patients on thyroxine replacement therapy for primary hypothyroidism. Eur J Endocrinol. 2005;153(6):747-753. 24. Samuels MH, Schuff KG, Carlson NE, Carello P, Janowsky JS. Health status, psychological symptoms, mood, and cognition in L-thyroxine-treated hypothyroid subjects. Thyroid. 2007;17(3):249-258. 25. Pop VJ, Maartens LH, Leusink G, et al. Are autoimmune thyroid dysfunction and depression related? J Clin Endocrinol Metab. 1998;83(9):3194-3197. 26. Nationwide Inpatient Sample (NIS). Healthcare Cost and Utilization Project (HCUP). Rockville, MD: Agency for Healthcare Research and Quality; 2005. http://www.hcup-us.ahrq.gov/nisoverview.jsp. Accessed January 18, 2008.
A friend in need: why friendship matters in medicine
Authors: D. Loxterkamp
Journal: BMJ (2008)

Something caught my eye in the news report of David Demuth’s untimely death—something more than the tragedy of his dying at age 58, just a week after receiving the “American Family Physician of the Year” award for 2008.

Some would say small wonder—he provided check-ups for every age group, delivered babies (by caesarean section when necessary), helped out in the emergency department, attended hospital patients, and consulted for subspecialists when they needed a generalist. He made home visits to families in crisis and stood in for an elderly physician in a neighbouring town on weekends “to give him a break.” He was the team physician for York (Nebraska) area athletics, volunteered for the York County Drug Task Force and Habitat for Humanity, and raised beef cattle in his spare time.

But the busy doctor left us with more than the example of his self sacrifice. He coached us to “listen to your patients. Most of the time, they’ll tell you what’s wrong with them.”1 He set his own priorities: “I pride myself in giving that individual person his time. After all, they’re interrupting their day to see us. I believe in the saying that patients don’t care what certifications you have on your wall; they know when you care.”1 And his admission that “we become friends and family with our patients”1 is something we all know is more than cliche.

I grew up in a medical family. My mother was a “stay at home” nurse who returned to her profession after my father died. He was a general practitioner who poured small town values into my veins before his early death. His role as a solo practitioner in a small town—with all of its mixed blessings—cast a long shadow over my career. By his example, he prepared …
Metastatic Thyroid Carcinoma Causing Superior Vena Caval Obstruction Diagnosed on I-131 Scan
Authors: Kshama Wechalekar, Masud Haq, Clive Harmer, Gary Cook
Journal: Clinical Nuclear Medicine (2005)

An 80-year-old woman was referred for a painless mass arising in right side of her neck of 4 months' duration. Ultrasound revealed a multinodular goiter, but cytology confirmed a follicular carcinoma. Thyroid function was normal. Total thyroidectomy was performed with evidence of tumor infiltration into the strap muscles extending up to the right submandibular gland and right internal jugular vein, which was completely occluded. Radioiodine was considered as the treatment of choice postoperatively. This is an unusual case of SVC obstruction caused by tumor embolus diagnosed on I-131 scan.
Can audit improve patient care? Effects of studying use of digoxin in general practice.
Authors: C. M. Anderson, S. Chambers, M. Clamp, I. A. Dunn, M. F. McGhee, K. R. Sumner, A. M. Wood
Journal: BMJ (1988)

A survey of monitoring of digoxin treatment in five practices examined the indications for prescribing digoxin, its long term use, and how its use could be monitored. These data were used to generate a protocol for monitoring treatment with digoxin in general practice. The findings of the survey and the protocol were distributed to and discussed with all the partners in the practices participating in the study. One year later similar analysis showed that record keeping (recording of pulse rate and rhythm) had improved significantly in the group of principals carrying out the audit but not in other principals in these practices. Audit may change only the auditors.
Streptokinase in acute aortic dissection.
Authors: G Hartnell
Journal: BMJ (1990)

been developing such systems for the management of a varietv of medical conditions, of which a system for the diagnosis, physical examination, and treatment of hvpercholesterolaemia is cur- rentlv undergoing field trials with general practi- tioners in the west midlands.The system is supplied for the use of a Psion Organiser and incorporates regional knowledge in a particular subject as appropriate for use in primary care or by junior hospital medical staff.The medical know-
Improvement in Surgical Drains-Reply
Authors: Ernest A. Gould
Journal: JAMA (1961)

<h3>To the Editor:—</h3> Will Dr. Touroff please accept my heartfelt apology for not having reviewed the literature sufficiently to have come upon his recommendation in 1931 in the<i>Annals of Surgery?</i>I assure you that I am most embarrassed and I know that Dr. Flax undoubtedly feels the same embarrassment that I do. It would seem only natural, having come upon Dr. Beneventi's article in 1953, that we should assume his priority, but obviously we were in error.
Coughs cause systemic blood flow.
Authors: J M Cary, R Krugmeier, B Newman, B Ross, J Butler
Journal: Thorax (1984)

Although it is known that rhythmic coughing can preserve consciousness during ventricular fibrillation, the arterial pressure transients which result have not yet been shown to reflect forward blood flow in man. The effectiveness of cough in causing forward flow in eight normal volunteers with bradycardia was studied. They coughed between cardiac cycles, using an audio and visual display of the electrocardiogram. The force of the cough was varied and measured with an oesophageal balloon. Blood flow was recorded with a Döppler velocity probe over the radial artery and a finger or ear photoplethysmograph. Motion artefact on the Döppler record due to coughing was excluded by transiently obstructing the brachial artery. We compared the areas under 5-10 consecutive Döppler and photoplethysmograph pulse flow tracings due to the cough and heart beat with those due to the immediately preceding heart beat alone. They were significantly increased. This augmentation was greater in those flow pulses accompanied by a more vigorous cough. It is concluded that coughing is associated with an effort dependent forward flow pulse in the arterial circulation.
Colin Michael Dent
Authors: C. Wilson
Journal: BMJ (2009)

Having lost his father as a teenager, Colin Michael Dent left his local comprehensive school in Gloucestershire and worked in a laboratory. He was later successful in his application to study medicine at University College London, going up to UCL in 1979.

His great intelligence and his unique sense of humour were already apparent as a medical student, and these helped him through demanding posts in old style preregistration house surgeon jobs at UCH and in Darlington. He entered basic surgical training in Bristol and London and in August 1988 entered orthopaedic higher surgical training in Cardiff, becoming a senior registrar in 1991.

During his senior registrar years he held several prestigious fellowships, including a research fellowship in the upper limb surgery unit working for John Stanley in Wrightington Hospital and a British Orthopaedic Association Honorary Research Fellowship during a spell of basic science research in Cardiff in 1993.

He became senior lecturer in the Trauma/Orthopaedic Unit in Cardiff, in what was then the University of Wales College of Medicine, in July 1994. From April 1995 onwards he spent six months in upper limb fellowship in Boston, USA, and on his return continued to develop his interest in upper limb surgery, particularly rheumatoid disease, and in his other main research interest, the basic science of degenerative joint disease, collaborating extensively with Professor Bruce Caterson. …
The In-Training Examination in Internal Medicine: An Analysis of Resident Performance over Time
Authors: Richard A. Garibaldi, Raja Subhiyah, Mary E. Moore, Herbert Waxman
Journal: Annals of Internal Medicine (2002)

Background: The In-Training Examination in Internal Medicine (IM-ITE) has been offered annually to all trainees in U.S. medical residency programs since 1988. Its purpose is to provide residents and program directors with an objective assessment of each resident's personal performance on a written, multiple-choice examination and the performance of the residency program compared with that of its peers. Objective: To analyze trends in the demographic characteristics and scores of examinees during the first 12 years of administration of this examination. Design: Descriptive analysis over time. Setting: U.S. residency programs in internal medicine, 1988–2000. Participants: Residents at all levels of training in categorical, primary care, and medicine–pediatrics programs in the United States and Canada. The number of examinees increased from 7500 in 1988 to almost 18 000 in 2000. Measurements: After calibration of the scores for each examination, test results were compared and analyzed for selected cohorts of residents over 12 years. Results: More than 80% of residents in medicine training programs participate in the IM-ITE, most on an annual basis throughout their period of training. Test performance improves at a predictable rate with each year of training. Since 1995, international medical school graduates have persistently outperformed graduates of U.S. medical schools. Test results were affected by the timing of the examination, the time that was available to complete the examination, and the actual time that residents spent in internal medicine training before each examination. Conclusions: The IM-ITE scores generally improve with year of training time spent in internal medicine training before the examination and time permitted to complete the examination. These observations provide evidence that the IM-ITE is a valid measure of knowledge acquired during internal medicine training.
Towards functional movement: Implications for research and therapy
Authors: C. J. Worringham, G. K. Kerr, C. O'Brien
Journal: Behavioral and Brain Sciences (1996)

Abstract Researchers and clinicians have different goals and constraints in trying to understand and treat movement disorders. Research on primary and secondary aspects of disorders may lead to effective treatment aimed at restoring functional movements even if the primary disorder cannot be cured. Similarly, movement patterns may be maladaptive and hence need therapeutic intervention to restore functional movement skills.