tbuckley/cabot-search huggingface dataset:
Measuring the Fit of Sequence Data to Phylogenetic Model: Allowing for Missing Data
Authors: Peter J. Waddell
Journal: Molecular Biology and Evolution (2004)

It is fundamentally important to assess the fit of data to model in phylogenetic and evolutionary studies. Phylogenetic methods using molecular sequences typically start with a multiple alignment. It is possible to measure the fit of data to model expectations of data, for example, via the likelihood-ratio (G) test or the X(2) test, if all sites in all sequences have an unambiguous residue. However, nearly all alignments of interest contain sites (columns of the alignment) with missing data, that is, ambiguous nucleotides, gaps, or unsequenced regions, which must presently be removed before using the above tests. Unfortunately, this is often either undesirable or impractical, as it will discard much of the data. Here, we show how iterative ML estimators may directly estimate the site-pattern probabilities for columns with missing data, given only standard i.i.d. assumptions. The optimization may use an EM or Newton algorithm, or any other hill-climbing approach. The resulting optimal likelihood under the unconstrained or multinomial model may be compared directly with the likelihood of the data coming from the model (a G statistic). Alternatively the modified observed and the expected frequencies of site patterns may be compared using a X(2) test. The distribution of such statistics is best assessed using appropriate simulations. The new method is applicable to models using codons or paired sites. The methods are also useful with Hadamard conjugations (spectral analysis) and are illustrated with these and with ML evolutionary models that allow site-rate variability.
An expanded perspective on the role of effort phenomenology in motivation and performance
Authors: Daniel C. Molden
Journal: Behavioral and Brain Sciences (2013)

Abstract Kurzban and colleagues propose that experiences of effort alter motivations to persist during goal pursuit by highlighting costs of persistence. I expand this proposal by discussing how effort experiences (a) not only influence, but can be influenced by motivations to persist on a goal; and (b) not only highlight costs that undermine persistence, but can also signal progress and increase persistence.
Effect of biological therapy on work participation in patients with ankylosing spondylitis: a systematic review
Authors: Lennart R A van der Burg, Marieke M ter Wee, Annelies Boonen
Journal: Annals of the Rheumatic Diseases (2012)

<h3>Objectives</h3> To review systematically the effect of biological treatment in patients with ankylosing spondylitis (AS) on three work outcomes: work status, absence from paid work and at-work productivity. <h3>Methods</h3> A systematic literature search was performed (Pubmed, Embase, Cochrane Library) to identify relevant articles. Risk of bias of included studies was assessed using the Cochrane guidelines for cohorts and randomised controlled trials (RCTs). Data were extracted using a self-composed data extraction form. Owing to extensive interstudy heterogeneity, narrative summaries were used to present the data. <h3>Results</h3> Nine studies were included (six uncontrolled cohorts, one population-controlled cohort and two RCTs) that reported on 39 comparisons. Overall, 961 patients were treated with three different tumour necrosis factor α inhibitors (etanercept, infliximab, adalimumab). For presenteeism and absence from work, most comparisons showed improvement in favour of biological agents, but not all comparisons were statistically significant and they usually concerned before–after analyses. For work status, changes were less often positive, but studies dealt with patients with longstanding AS, lacked power and had a relatively short follow-up. <h3>Conclusions</h3> Although trends towards beneficial effects of biological agents in longstanding AS were seen on all work outcomes, the methodological limitations in the studies included hampers clear conclusions. Since the majority of studies were (extensions of) controlled trials, the generalisability of the effect of biological agents on work participation in real life should be further studied in larger (population-controlled) studies. The effect of biological agents in patients with early disease has not yet been examined.
Antiviral T cell responses
Authors: David N. Posnett, Manuel E. Engelhorn, Alan N. Houghton
Journal: The Journal of Experimental Medicine (2005)

Around 700 BCE, a new military formation called the phalanx was established in ancient Greece: a tight column of heavy infantry carrying long spears, or pikes, used in a single prong of attack. Later, in the battle of Marathon described by Herodotus, the Greeks learned the advantages of multipronged attacks, a strategy still used in modern warfare. Is the immune system similar in its approach to combatting pathogens or tumors?
THE ESSENTIAL DIFFERENCE BETWEEN THE TWO OPTIMUM PROPORTIONS FLOCCULATION RATIOS
Authors: William C. Boyd, Marjorie A. Purnell
Journal: The Journal of Experimental Medicine (1944)

The fact that the optimum proportion flocculation ratio is different when determined by the α (Dean and Webb) and ß (Ramon) procedures is pointed out. It is demonstrated that this difference is a consequence of the difference in the two methods, and that the two optima, though they may in certain cases lie near together, can never coincide. A new ratio (the ϵ ratio), intermediate between the α and ß ratios, and having theoretical advantages over both of them, is defined.
The Effects of Standard Anthracycline-Based Chemotherapy on Soluble ICAM-1 and Vascular Endothelial Growth Factor Levels in Breast Cancer
Authors: Paul J. Mills, Barbara Parker, Vicky Jones, Karen A. Adler, Christy J. Perez, Sherella Johnson, Mairav Cohen-Zion, Matthew Marler, Georgia R. Sadler, Joel E. Dimsdale, Sonia Ancoli-Israel
Journal: Clinical Cancer Research (2004)

Abstract Purpose: The circulating soluble form of intercellular adhesion molecule-1 (sICAM-1) and vascular endothelial growth factor (VEGF) are elevated in women with breast cancer and associated with tumor progression and poor prognosis. This study examined the effects of anthracycline-based chemotherapy on plasma sICAM-1 and VEGF, as well as soluble P-selectin, von Willebrand factor, and interleukin-6 levels. Experimental Design: Twenty-six women diagnosed with stage I–IIIA breast cancer (mean age, 48.4 ± 10.4 years; range, 34–79 years) were studied before (week 1) and at weeks 2 and 3 of cycles 1 and 4 of chemotherapy. Results: The initial effect of chemotherapy was to reduce sICAM-1 levels; compared with pretreatment, sICAM-1 levels were decreased at week 2 of both cycles (P values &amp;lt; 0.01). sICAM-1 levels were elevated, however, at the start of cycle 4 as compared with pretreatment (P &amp;lt; 0.01). Chemotherapy led to an increase in sICAM-1 levels in node-positive but not node-negative patients (P &amp;lt; 0.01). VEGF levels were decreased at week 2 of cycle 4 (P = 0.001) and remained so at week 3. Similar to sICAM-1, VEGF levels were elevated at the start of cycle 4 as compared with pretreatment (P &amp;lt; 0.006). Soluble P-selectin levels decreased during week 2 of cycle 4 (P = 0.026). Neither interleukin-6 or von Willebrand factor were significantly changed in response to chemotherapy. Conclusions: The findings support prior studies suggesting that sICAM-1 levels derive from sources other than endothelial cells. In addition, whereas the more immediate effect of chemotherapy is to reduce sICAM-1 and VEGF, continued treatment may lead to significant elevations.
The use of CpG-free plasmids to mediate persistent gene expression following repeated aerosol delivery of pDNA/PEI complexes
Authors: Lee A. Davies, Stephen C. Hyde, Graciela Nunez-Alonso, Reto P. Bazzani, Rebekka Harding-Smith, Ian A. Pringle, Anna E. Lawton, Syahril Abdullah, Thomas C. Roberts, Dominique McCormick, Stephanie G. Sumner-Jones, Deborah R. Gill
Journal: Biomaterials (2012)
Ventricular Tachycardia with Narrow QRS Complexes (Left Posterior Fascicular Tachycardia)
Authors: HOWARD C. COHEN, EDILBERTO G. GOZO, ALFRED PICK
Journal: Circulation (1972)

Ectopic atrial, A-V junctional, and ventricular tachycardias in man have been associated with digitalis medication. Recently it has become possible to distinguish various locations of pacemakers within the specialized conduction system of the ventricles on the basis of the form of the QRS complexes in the standard electrocardiogram. Tachycardias originating in the left bundle branch and documented by right, left, and His bundle recordings have been produced in animals given excessive digitalis. We have noted a similar tachycardia in a patient with ischemic heart disease receiving digitalis during hypokalemia. The QRS complexes were 0.10 sec in duration and by contour suggested an ectopic focus located in the posterior fascicle of the left bundle; His bundle recordings were consistent with this diagnosis. As the ectopic rhythm became synchronized with a slightly irregular sinus rhythm, bidirectional depolarization of the His bundle with fusion His potentials could be demonstrated.
Editorial. Constant prices in 1996 for multimedia Human Reproduction Update in its second year of print, disks and videos
Authors: R. Edwards
Journal: Human Reproduction Update (1996)

The journal has had a most successful, if technically fraught, first year in 1995. Many reviews and videos together with other articles were published. The new journal incorporated Oxford Reviews and Bibliography of Reproduction. With its multimedia format Human Reproduction Update has provided immense new opportunities for widening education in medicine and science, has removed previous space limitations and broadened the scope of publication to include videos, databases, a dictionary, monographs and libraries of illustration. Software difficulties encountered in supplying both PC and MAC users and in the presentation of graphics have largely been overcome. The software is under constant review. A direct support helpline has been established at Oxford University Press (OUP), Tel: (0)1865 267907; Fax: (0)1865 267485. Human Reproduction Update will continue to be published every 2 months. It will include articles, videos and other items in multimedia and print format, designed as a source of review and refresher material for practising clinicians and scientists. New opportunities have opened for our readers in 1996. Members of the European Society for Human Reproduction and Embryology (ESHRE) will be able to purchase Human Reproduction Update at last year’s prices, Human Reproduction and Molecular Human Reproduction combined for a reduced price and also Human Molecular Genetics from OUP at a discounted price (Table I). These four journals present a very broad base of information covering virtually every aspect of study on human reproduction. The prices to Institutional and Personal subscribers have risen only by the rate of inflation, despite planned increases in the size of the journal. All contents and abstracts of Human Reproduction Update, other ESHRE/OUP journals, and all supplements to Human Reproduction will become available on World Wide Web in 1996 (http://www.oup.co.uk/hru/). The whole contents of the ESHRE journals may also be published in this way at a future date, enabling subscribers to purchase either the printed journal or the electronic version. Details will be given in each particular journal, perhaps during 1996.
Cartilage repair using an in vitro generated scaffold-free tissue-engineered construct derived from porcine synovial mesenchymal stem cells
Authors: Wataru Ando, Kosuke Tateishi, David A. Hart, Daisuke Katakai, Yoshinari Tanaka, Ken Nakata, Jun Hashimoto, Hiromichi Fujie, Konsei Shino, Hideki Yoshikawa, Norimasa Nakamura
Journal: Biomaterials (2007)
Detection of Circulating Tumor Cells Harboring a Unique <i>ALK</i> Rearrangement in <i>ALK</i>-Positive Non–Small-Cell Lung Cancer
Authors: Emma Pailler, Julien Adam, Amélie Barthélémy, Marianne Oulhen, Nathalie Auger, Alexander Valent, Isabelle Borget, David Planchard, Melissa Taylor, Fabrice André, Jean Charles Soria, Philippe Vielh, Benjamin Besse, Françoise Farace
Journal: Journal of Clinical Oncology (2013)

Purpose The diagnostic test for ALK rearrangement in non–small-cell lung cancer (NSCLC) for crizotinib treatment is currently done on tumor biopsies or fine-needle aspirations. We evaluated whether ALK rearrangement diagnosis could be performed by using circulating tumor cells (CTCs). Patients and Methods The presence of an ALK rearrangement was examined in CTCs of 18 ALK-positive and 14 ALK-negative patients by using a filtration enrichment technique and filter-adapted fluorescent in situ hybridization (FA-FISH), a FISH method optimized for filters. ALK-rearrangement patterns were determined in CTCs and compared with those present in tumor biopsies. ALK-rearranged CTCs and tumor specimens were characterized for epithelial (cytokeratins, E-cadherin) and mesenchymal (vimentin, N-cadherin) marker expression. ALK-rearranged CTCs were monitored in five patients treated with crizotinib. Results All ALK-positive patients had four or more ALK-rearranged CTCs per 1 mL of blood (median, nine CTCs per 1 mL; range, four to 34 CTCs per 1 mL). No or only one ALK-rearranged CTC (median, one per 1 mL; range, zero to one per 1 mL) was detected in ALK-negative patients. ALK-rearranged CTCs harbored a unique (3′5′) split pattern, and heterogeneous patterns (3′5′, only 3′) of splits were present in tumors. ALK-rearranged CTCs expressed a mesenchymal phenotype contrasting with heterogeneous epithelial and mesenchymal marker expressions in tumors. Variations in ALK-rearranged CTC levels were detected in patients being treated with crizotinib. Conclusion ALK rearrangement can be detected in CTCs of patients with ALK-positive NSCLC by using a filtration technique and FA-FISH, enabling both diagnostic testing and monitoring of crizotinib treatment. Our results suggest that CTCs harboring a unique ALK rearrangement and mesenchymal phenotype may arise from clonal selection of tumor cells that have acquired the potential to drive metastatic progression of ALK-positive NSCLC.
A loss-of-function polymorphic mutation in the cytolytic P2X7 receptor gene and chronic lymphocytic leukaemia: a molecular study
Authors: James S Wiley, L Phuong Dao-Ung, Ben J Gu, Ronald Sluyter, Anne N Shemon, Changping Li, John Taper, John Gallo, Arumugam Manoharan
Journal: The Lancet (2002)
A Randomized Controlled Clinical Trial of Psychoanalytic Psychotherapy for Panic Disorder
Authors: Barbara Milrod, Andrew C. Leon, Fredric Busch, Marie Rudden, Michael Schwalberg, John Clarkin, Andrew Aronson, Meriamne Singer, Wendy Turchin, E. Toby Klass, Elizabeth Graf, Jed J. Teres, M. Katherine Shear
Journal: American Journal of Psychiatry (2007)

The purpose of this study was to determine the efficacy of panic-focused psychodynamic psychotherapy relative to applied relaxation training, a credible psychotherapy comparison condition. Despite the widespread clinical use of psychodynamic psychotherapies, randomized controlled clinical trials evaluating such psychotherapies for axis I disorders have lagged. To the authors' knowledge, this is the first efficacy randomized controlled clinical trial of panic-focused psychodynamic psychotherapy, a manualized psychoanalytical psychotherapy for patients with DSM-IV panic disorder.This was a randomized controlled clinical trial of subjects with primary DSM-IV panic disorder. Participants were recruited over 5 years in the New York City metropolitan area. Subjects were 49 adults ages 18-55 with primary DSM-IV panic disorder. All subjects received assigned treatment, panic-focused psychodynamic psychotherapy or applied relaxation training in twice-weekly sessions for 12 weeks. The Panic Disorder Severity Scale, rated by blinded independent evaluators, was the primary outcome measure.Subjects in panic-focused psychodynamic psychotherapy had significantly greater reduction in severity of panic symptoms. Furthermore, those receiving panic-focused psychodynamic psychotherapy were significantly more likely to respond at treatment termination (73% versus 39%), using the Multicenter Panic Disorder Study response criteria. The secondary outcome, change in psychosocial functioning, mirrored these results.Despite the small cohort size of this trial, it has demonstrated preliminary efficacy of panic-focused psychodynamic psychotherapy for panic disorder.
Pharmacology of the Endothelium in Ischemia-Reperfusion and Circulatory Shock
Authors: A M Lefer, D J Lefer
Journal: The Annual Review of Pharmacology and Toxicology (1993)

Due to the massive data sets available for drug candidates, modern drug discovery has advanced to the big data era. Central to this shift is the development of artificial intelligence approaches to implementing innovative modeling based on the dynamic, ...Read More
School-Based Interventions for Health Promotion and Weight Control: Not Just Waiting on the World to Change
Authors: D.L. Katz
Journal: Annual Review of Public Health (2009)

Controversy persists regarding the utility of school-based interventions for obesity prevention and control and for related health promotion. This article reviews the pertinent evidence, based partly on a recent systematic review and meta-analysis by the author and colleagues. Of 64 relevant papers, 21 papers representing 19 distinct studies met quality criteria; half of these were published since 2000. Despite marked variation in measures, methods, and populations that handicap interpretation of this literature, evidence clearly demonstrated that school-based interventions had significant effects on weight. Thus available research evidence does present a case for school-based interventions. Despite the fact that such evidence is limited to date, the urgency of the obesity and diabetes epidemics cries out for action. Intervention is warranted on the basis of both extant evidence and common sense, with methodologically robust evaluation concomitantly to test our assumptions and verify our intuition.
Terminal Complement Blockade With Pexelizumab During Coronary Artery Bypass Graft Surgery Requiring Cardiopulmonary Bypass
Authors: Edward D. Verrier, Stanton K. Shernan, Kenneth M. Taylor, Frans Van de Werf, Mark F. Newman, John C. Chen, Michel Carrier, Axel Haverich, Kevin J. Malloy, Peter X. Adams, Thomas G. Todaro, Christopher F. Mojcik, Scott A. Rollins, Jerrold H. Levy, None for the PRIMO-CABG Investigators
Journal: JAMA (2004)

Inflammation and ischemia-reperfusion injury during coronary artery bypass graft (CABG) surgery requiring cardiopulmonary bypass are associated with postoperative myocardial infarction (MI) and mortality.To determine the efficacy and safety of pexelizumab, a C5 complement inhibitor, in reducing perioperative MI and mortality in CABG surgery.A randomized, double-blind, placebo-controlled trial, including 3099 patients (> or = 18 years) undergoing CABG surgery with or without valve surgery at 205 hospitals in North America and Western Europe from January 2002 to February 2003.Patients were randomly assigned to receive intravenous pexelizumab (2.0 mg/kg bolus plus 0.05 mg/kg per hour for 24 hours; n = 1553) or placebo (n = 1546) 10 minutes before undergoing the procedure.The primary composite end point was the incidence of death or MI within 30 days of randomization in those undergoing CABG surgery only (n = 2746). Secondary analyses included the intent-to-treat analyses of death or MI composite at days 4 and 30 in all 3099 study patients.After 30 days, 134 (9.8%) of 1373 of patients receiving pexelizumab vs 161 (11.8%) of 1359 of patients receiving placebo (relative risk, 0.82; 95% confidence interval, 0.66-1.02; P =.07) died or experienced MI in the CABG surgery only population. In the intent-to-treat analyses, 178 (11.5%) of 1547 patients receiving pexelizumab vs 215 (14.0%) of 1535 receiving placebo died or experienced MI (relative risk, 0.82; 95% confidence interval, 0.68-0.99; P =.03). The trial was not powered to detect a reduction in mortality alone.Compared with placebo, pexelizumab was not associated with a significant reduction in the risk of the composite end point of death or MI in 2746 patients who had undergone CABG surgery only but was associated with a statistically significant risk reduction 30 days after the procedure among all 3099 patients undergoing CABG with or without valve surgery.
Genetic Structure of Natural Populations of the Plant RNA Virus Tobacco Mild Green Mosaic Virus
Authors: A Moya, E Rodriguez-Cerezo, F Garcia-Arenal
Journal: Molecular Biology and Evolution (1993)

The statistical analysis of population subdivision in five populations of tobacco mild green mosaic virus (TMGMV) naturally infecting Nicotiana glauca has shown that the populations can be considered as samples of an almost panmictic one.In spite of the high mutation rate of this RNA virus, the genetic divergence between pairs of haplotypes, both within and between subpopulations, is very small.The observed amount of variability cannot be exclusively explained in terms of the neutral theory of molecular evolution.Under such a model, an unrealistic estimate of the effective population size equal to 86 viral particles is obtained.Positive Darwinian selection can be invoked to account for the variability observed.No direct experimental evidence of selection is presented, but, by means of both (a) high selection coefficients for driver mutations and (b) reasonable neutral and driver mutation rates for RNA viruses, the amount of variability observed can be accounted for in terms of a model of periodic, positive, Darwinian selection.1.
Methylphenidate for gait hypokinesia and freezing in patients with Parkinson's disease undergoing subthalamic stimulation: a multicentre, parallel, randomised, placebo-controlled trial
Authors: Caroline Moreau, Arnaud Delval, Luc Defebvre, Kathy Dujardin, Alain Duhamel, Gregory Petyt, Isabelle Vuillaume, Jean-Christophe Corvol, Christine Brefel-Courbon, Fabienne Ory-Magne, Dominique Guehl, Alexandre Eusebio, Valérie Fraix, Pierre-Jean Saulnier, Ouhaid Lagha-Boukbiza, Frank Durif, Mirela Faighel, Caroline Giordana, Sophie Drapier, David Maltête, Christine Tranchant, Jean-Luc Houeto, Bettina Debû, Bernard Sablonniere, Jean-Philippe Azulay, François Tison, Olivier Rascol, Marie Vidailhet, Alain Destée, Bastiaan R Bloem, Régis Bordet, David Devos
Journal: The Lancet Neurology (2012)
The risk of infection and malignancy with tumor necrosis factor antagonists in adults with psoriatic disease: A systematic review and meta-analysis of randomized controlled trials
Authors: Erica D. Dommasch, Katrina Abuabara, Daniel B. Shin, Josephine Nguyen, Andrea B. Troxel, Joel M. Gelfand
Journal: Journal of the American Academy of Dermatology (2011)