tbuckley/cabot-search huggingface dataset:
The Complete Mitochondrial Genome of the Nudibranch Roboastra europaea (Mollusca: Gastropoda) Supports the Monophyly of Opisthobranchs
Authors: Cristina Grande, José Templado, J. Lucas Cervera, Rafael Zardoya
Journal: Molecular Biology and Evolution (2002)

The complete nucleotide sequence (14,472 bp) of the mitochondrial genome of the nudibranch Roboastra europaea (Gastropoda: Opisthobranchia) was determined. This highly compact mitochondrial genome is nearly identical in gene organization to that found in opisthobranchs and pulmonates (Euthyneura) but not to that in prosobranchs (a paraphyletic group including the most basal lineages of gastropods). The newly determined mitochondrial genome differs only in the relative position of the trnC gene when compared with the mitochondrial genome of Pupa strigosa, the only opisthobranch mitochondrial genome sequenced so far. Pupa and Roboastra represent the most basal and derived lineages of opisthobranchs, respectively, and their mitochondrial genomes are more similar in sequence when compared with those of pulmonates. All phylogenetic analyses (maximum parsimony, minimum evolution, maximum likelihood, and Bayesian) based on the deduced amino acid sequences of all mitochondrial protein-coding genes supported the monophyly of opisthobranchs. These results are in agreement with the classical view that recognizes Opisthobranchia as a natural group and contradict recent phylogenetic studies of the group based on shorter sequence data sets. The monophyly of opisthobranchs was further confirmed when a fragment of 2,500 nucleotides including the mitochondrial cox1,rrnL,nad6, and nad5 genes was analyzed in several species representing five different orders of opisthobranchs with all common methods of phylogenetic inference. Within opisthobranchs, the polyphyly of cephalaspideans and the monophyly of nudibranchs were recovered. The evolution of mitochondrial tRNA rearrangements was analyzed using the cox1+rrnL+nad6+nad5 gene phylogeny. The relative position of the trnP gene between the trnA and nad6 genes was found to be a synapomorphy of opisthobranchs that supports their monophyly.
Molecular Mimicry between <i>Helicobacter pylori</i> Antigens and H+,K+–Adenosine Triphosphatase in Human Gastric Autoimmunity
Authors: Amedeo Amedei, Mathijs P. Bergman, Ben J. Appelmelk, Annalisa Azzurri, Marisa Benagiano, Carlo Tamburini, Ruurd van der Zee, John L. Telford, Christina M.J.E. Vandenbroucke-Grauls, Mario M. D'Elios, Gianfranco Del Prete
Journal: The Journal of Experimental Medicine (2003)

Autoimmune gastritis and Helicobacter pylori–associated gastric atrophy develop through similar mechanisms involving the proton pump H+,K+–adenosine triphosphatase as autoantigen. Here, we report that H. pylori–infected patients with gastric autoimmunity harbor in vivo–activated gastric CD4+ T cells that recognize both H+,K+–adenosine triphosphatase and H. pylori antigens. We characterized the submolecular specificity of such gastric T cells and identified cross-reactive epitopes from nine H. pylori proteins. Cross-reactive H. pylori peptides induced T cell proliferation and expression of T helper type 1 functions. We suggest that in genetically susceptible individuals, H. pylori infection can activate cross-reactive gastric T cells leading to gastric autoimmunity via molecular mimicry.
Prediction of volumetric change in the “triple ring” caused by glioma I-125 brachytherapy
Authors: Jenő Julow, Zsuzsa Kolumbán, Árpád Viola, Tibor Major, Géza Kolumbán
Journal: Neuro-Oncology (2008)

The aim of this study was to reveal the volumetric changes in tumor necrosis, reactive zone, and edema referred to as the "triple ring" appearing after low-dose-rate iodine-125 (I-125) interstitial irradiation of 20 inoperable low-grade gliomas. To enable prediction of these volumetric changes, we provide mathematical expressions that describe the dynamics of the triple ring. Volumes of the three regions on image-fused control CT/MR images were measured for a 24-month period. The delivered dose on the tumor surface was 50-60 Gy. Dose planning and image fusion were performed with Brain-Lab Target 1.19 software; mathematical and statistical computations were carried out with Matlab numeric computation and visualization software. To determine the volumes, control images with the triple rings were fused with the planning images. Relative volumes normalized with respect to the volume of reference dose were calculated and plotted in the time domain. First, the mean values of volumes were determined from the patients' measured data; then, polynomials were fitted to the mean values using the polynomial curve-fitting method. The accuracy of our results was verified by correlating the predicted data with the measured ones. The polynomial prediction approach proposed here reveals the dynamics of the triple ring. These polynomials will assist with (1) designing the best treatment, (2) following the patient's condition, and (3) planning reirradiation if necessary.
Hepatitis B reactivation after withdrawal of pre-emptive lamivudine in patients with haematological malignancy on completion of cytotoxic chemotherapy
Authors: C-K Hui
Journal: Gut (2005)

The hepatic outcome of hepatitis B surface antigen (HBsAg) positive patients undergoing chemotherapy after withdrawal of pre-emptive lamivudine is unknown.To examine the occurrence of hepatitis B virus (HBV) reactivation after withdrawal of pre-emptive lamivudine.Pre-emptive lamivudine was started one week before initiation of chemotherapy in 46 consecutive HBsAg positive patients and continued for the entire duration of chemotherapy. Pre-emptive lamivudine was stopped at a median 3.1 (range 3.0-3.4) months after completion of chemotherapy. Patients were longitudinally followed up after withdrawal of pre-emptive lamivudine.Median time of follow up after withdrawal of lamivudine was 25.7 (range 5.7-75.7) months. Eleven of the 46 patients (23.9%) developed HBV reactivation after withdrawal of pre-emptive lamivudine. Eight of the 16 patients with high pre-chemotherapy HBV DNA (> or =10(4) copies/ml) compared with three of the 30 patients with low pre-chemotherapy HBV DNA (<10(4) copies/ml) developed HBV reactivation (50.0% v 10.0%, respectively; p<0.001). Hepatitis B e antigen positive patients were also more likely to develop HBV reactivation (5/11 (45.5%) v 6/35 (17.1%), respectively; p = 0.041). A high pre-chemotherapy HBV DNA (> or =10(4) copies/ml) was the most important risk factor for HBV reactivation after withdrawal of pre-emptive lamivudine on Cox proportional hazards analysis (relative risk 16.13, (95% confidence interval 2.99-87.01; p = 0.001).HBV reactivation is more likely to occur in patients with high pre-chemotherapy HBV DNA after withdrawal of pre-emptive lamivudine. A more prolonged course of antiviral therapy may be necessary in these patients after completion of chemotherapy in order to reduce post-chemotherapy HBV reactivation.
Bronchiolitis obliterans organizing pneumonia in three children with acute leukaemias treated with cytosine arabinoside and anthracyclines
Authors: E Battistini, G Dini, C Savioli, A Morando, A Gandolfo, Z Kotitsa, A Garaventa, GA Rossi
Journal: European Respiratory Journal (1997)

Bronchiolitis obliterans organizing pneumonia (BOOP) is a clinicopathological entity with well-defined diagnostic criteria, which can be idiopathic or produced by a variety of biological processes. We describe the occurrence of BOOP in three children, one with acute lymphoblastic leukaemia and two with acute promyelocytic leukaemia. In the three patients, BOOP developed 10-20 days after a course of therapy with cytosine arabinoside and anthracyclines. The possible relationships between the small conducting airway lesions, lung toxic reaction to the drugs and/or nonidentified infectious agents are discussed.
Does effectiveness of exercise therapy and mobilisation techniques offer guidance for the treatment of lateral and medial epicondylitis? A systematic review
Authors: Peter Hoogvliet, Manon S Randsdorp, Rudi Dingemanse, Bart W Koes, Bionka M A Huisstede
Journal: British Journal of Sports Medicine (2013)

Owing to the change in paradigm of the histological nature of epicondylitis, therapeutic modalities as exercises such as stretching and eccentric loading and mobilisation are considered for its treatment.To assess the evidence for effectiveness of exercise therapy and mobilisation techniques for both medial and lateral epicondylitis.Searches in PubMed, Embase, Cinahl and Pedro were performed to identify relevant randomised clinical trials (RCTs) and systematic reviews. Two reviewers independently extracted data and assessed the methodological quality.One review and 12 RCTs, all studying lateral epicondylitis, were included. Different therapeutic regimes were evaluated: stretching, strengthening, concentric/eccentric exercises and manipulation of the cervical or thoracic spine, elbow or wrist. No statistical pooling of the results could be performed owing to heterogeneity of the included studies. Therefore, a best-evidence synthesis was used to summarise the results. Moderate evidence for the short-term effectiveness was found in favour of stretching plus strengthening exercises versus ultrasound plus friction massage. Moderate evidence for short-term and mid-term effectiveness was found for the manipulation of the cervical and thoracic spine as add-on therapy to concentric and eccentric stretching plus mobilisation of wrist and forearm. For all other interventions only limited, conflicting or no evidence was found.Although not yet conclusive, these results support the belief that strength training decreases symptoms in tendinosis. The short-term analgesic effect of manipulation techniques may allow more vigorous stretching and strengthening exercises resulting in a better and faster recovery process of the affected tendon in lateral epicondylitis.
No holds barred sport fighting: a 10 year review of mixed martial arts competition
Authors: G J Buse
Journal: British Journal of Sports Medicine (2006)

To identify the most salient medical issues that may be associated with mixed martial arts competition by determining the types and proportions of match stoppages.Publicly available video footage of 1284 men competing in 642 consecutive televised matches from November 1993 to November 2003 was reviewed to determine the reasons for which matches were stopped. Matches were sanctioned by either a United States or Japan based mixed martial arts organisation.Of the 642 matches, 182 (28.3+/-3.4%) were stopped because of head impact, 106 (16.5+/-2.9%) because of musculoskeletal stress, 91 (14.1+/-2.7%) because of neck choke, 83 (12.9+/-2.6%) because of miscellaneous trauma, 173 (27.0+/-3.4%) because of expiration of match time, and seven (1.0+/-0.8%) because of disqualification, where the values in parentheses are percentages+/-95% confidence interval.Blunt force to the head resulted in the highest proportion of match stoppages. Further research is warranted to delineate the morbidity associated with participation in mixed martial arts.
Flt3 Ligand Regulates Dendritic Cell Development from Flt3+ Lymphoid and Myeloid-committed Progenitors to Flt3+ Dendritic Cells In Vivo
Authors: Holger Karsunky, Miriam Merad, Antonio Cozzio, Irving L. Weissman, Markus G. Manz
Journal: The Journal of Experimental Medicine (2003)

Stimulation of Flt3 receptor tyrosine kinase through its cognate ligand expands early hematopoietic progenitor and dendritic cells (DCs) in humans and mice. The exact developmental stages at which hematopoietic progenitors express Flt3, are responsive to its ligand, and subsequently develop to DCs, are not known. Here we show that common lymphoid and common myeloid progenitors, as well as steady state DCs in thymus, spleen, and epidermis, express Flt3. The receptor is down-regulated once definitive B cell, T cell, and megakaryocyte/erythrocyte commitment occurs, and Flt3 is not detectable on other steady state hematopoietic cell populations. Upon in vivo Flt3 ligand (Flt3L) administration, Flt3+ progenitor cells and their progeny DCs are expanded, whereas Flt3- downstream progenitors are not, or are only slightly increased. Transplantation of common lymphoid and common myeloid progenitors and subsequent Flt3L injection increases progeny DCs of both precursor populations. These findings provide a definitive map of Flt3 expression in the hematopoietic hierarchy and directly demonstrate that Flt3L can drive DC development along both the lymphoid and myeloid developmental pathways from Flt3+ progenitors to Flt3+ DCs.
Revision of Grant Program
Authors: Lester M. Crawford, Jr
Journal: JAMA (2002)

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Gemtuzumab Ozogamicin: One Size Does Not Fit All—The Case for Personalized Therapy
Authors: Farhad Ravandi
Journal: Journal of Clinical Oncology (2010)

communication of prognosis in the metastatic setting. J Clin Oncol 22:17211730, 2004 7. Butow PN, Dowsett S, Hagerty R, et al: Communicating prognosis to patients with metastatic disease: What do they really want to know? Support Care Cancer 10:161-168, 2002 8. Helft PR, Petronio S: Communication pitfalls with cancer patients: “Hitand-run” deliveries of bad news. J Am Coll Surg 205:807-811, 2007 9. Wright AA, Zhang B, Ray A, et al: Associations between end-of-life discussions, patient mental health, medical care near death, and caregiver bereavement adjustment. JAMA 300:1665-1673, 2008 10. Bradley JG, Zia MJ, Hamilton N: Patient preferences for control in medical decision making: A scenario-based approach. Fam Med 28:496-501, 1996 11. Mack JW, Wolfe J, Cook EF, et al: Hope and prognostic disclosure. J Clin Oncol 25:5636-5642, 2007 12. Clayton JM, Hancock KM, Butow PN, et al: Clinical practice guidelines for communicating prognosis and end-of-life issues with adults in the advanced stages of a life-limiting illness, and their caregivers. Med J Aust 186 (12 Suppl):S 77, S79, S83-S108, 2007 13. Kiely BE, Soon YY, Tattersall MHN, et al: How long have I got? Estimating typical, best-case, and worst-case scenarios for patients starting first-line chemotherapy for metastatic breast cancer—A systematic review of recent randomized trials. J Clin Oncol 29:456-463, 2011
Safety and efficacy of neratinib (HKI-272) plus vinorelbine in the treatment of patients with ErbB2-positive metastatic breast cancer pretreated with anti-HER2 therapy
Authors: A. Awada, L. Dirix, L. Manso Sanchez, B. Xu, T. Luu, V. Diéras, D.L. Hershman, V. Agrapart, R. Ananthakrishnan, E. Staroslawska
Journal: Annals of Oncology (2012)
Signals from dying hepatocytes trigger growth of liver progenitors
Authors: Y. Jung, R. P. Witek, W. K. Syn, S. S. Choi, A. Omenetti, R. Premont, C. D. Guy, A. M. Diehl
Journal: Gut (2010)

The death rate of mature hepatocytes is chronically increased in various liver diseases, triggering responses that prevent liver atrophy, but often cause fibrosis. Mice with targeted disruption of inhibitor kappa B kinase (Ikk) in hepatocytes (HEP mice) provide a model to investigate this process because inhibiting Ikk-nuclear factor-kappaB (NF-kappaB) signalling in hepatocytes increases their apoptosis.Cell proliferation, apoptosis, progenitors, fibrosis and production of Hedgehog (Hh) ligands (progenitor and myofibroblast growth factors) were compared in HEP and control mice before and after feeding methionine choline-deficient ethionine-supplemented (MCDE) diets. Ikkbeta was deleted from primary hepatocytes to determine the effects on Hh ligand production; Hh signalling was inhibited directly in progenitors to determine the effects on viability. Liver sections from patients were examined to assess relationships between hepatocyte production of Hh ligands, accumulation of myofibroblastic cells and liver fibrosis.Disrupting the Ikk-NF-kappaB pathway in hepatocytes inhibited their proliferation but induced their production of Hh ligands. The latter provided viability signals for progenitors and myofibroblasts, enhancing accumulation of these cell types and causing fibrogenesis. Findings in the mouse models were recapitulated in diseased human livers.Dying mature hepatocytes produce Hh ligands which promote the compensatory outgrowth of progenitors and myofibroblasts. These results help to explain why diseases that chronically increase hepatocyte death promote cirrhosis.
Testing “Species Pair” Hypotheses: Evolutionary Processes in the Lichen-Forming Species Complex Porpidia flavocoerulescens and Porpidia melinodes
Authors: Jutta Buschbom, Gregory M. Mueller
Journal: Molecular Biology and Evolution (2005)

Pairs of taxa are commonly found in lichen-forming ascomycetes that differ primarily in their reproductive modes: one taxon reproduces sexually, the other vegetatively. The evolutionary processes underlying such "species pairs" are unknown. The species pair formed by Porpidia flavocoerulescens (sexual) and Porpidia melinodes (vegetative) was chosen to investigate four previously proposed hypotheses. These hypotheses posit that species pairs are either two monophyletic, independently evolving species with contrasting reproductive mode; a single outcrossing species polymorphic with regard to its reproductive modes; a sexual mother lineage frequently giving rise to asexual spin-offs; or a complex of cryptic species. The phylogenetic patterns observed within the species pair in the present study were analyzed using stringent hypothesis testing and visualizations of relationships and conflict based on tree and network reconstructions. DNA sequences at the three analyzed loci revealed the same four to five deeply divergent lineages. A detailed analysis of DNA-sequence variability revealed closely linked gene loci, but high levels of conflict within each of the gene fragments, as well as between observed genetic lineages. The observed patterns of phylogenetic relationships, linkage, and conflict are not congruent with any of the previously proposed species pair hypotheses. Rather, it is proposed that the observed results can be explained by conflicting reproductive and nutritional requirements imposed by an obligate symbiotic lifestyle. These interacting constraints produce recurring selective sweeps within predominantly vegetatively reproducing lineages and are the main forces that shape the evolution within the investigated species pair.
Verapamil induced ventricular hypertrophy in conscious dogs
Authors: W. J FRENCH, D. GARNER, G. E ADOMIAN, W. AVERILL, M. M LAKS
Journal: Cardiovascular Research (1989)

Verapamil is used clinically in the treatment of various cardiac diseases including hypertrophic cardiomyopathy. Its long term effects on ventricular mass are not well known. In 11 conscious dogs heart rate, aortic and left ventricular pressures, cardiac output, a methoxamine induced stress ventricular function test and left ventriculography were performed. These variables were measured prior to and following a mean 7.2 month infusion of verapamil at 0.005 or 0.01 mg·kg−1·min−1 using a subcutaneously implanted pump. Resting haemodynamic variables and left ventricular ejection fraction [60(SD 6) v 55(6)%] were unchanged between baseline and chronic verapamil studies, but the slope of the methoxamine induced stress ventricular function test decreased from 3.9(0.8) to 2.1(1.3). After verapamil was discontinued the mean slope of the stress ventricular function test returned to the baseline 4.0(1.7). Total ventricular weight increased 22% from 176.1(17.5) g·m−2 in controls to 215.6(29.5) g·m−2 (p<0.01) in the verapamil animals. The right ventricular weight increased 25% from 46(5.9) to 57.6(9.1) g·m−2 (p<0.01); the septum weight increased 26% from 42.5(4.1) to 53.7(7.2) g·m−2 (p<0.001); and the left ventricular free wall weight increased 19% from 87.4(9.8) to 103.9(15.7) g·m−2 (p<0.01). The increase in ventricular weights was not due to fibrosis or oedema since hydroxyproline contents and wet/dry ratios were not increased. In conclusion, a chronic infusion of verapamil in conscious dogs caused no change in resting haemodynamic variables but produced reversible depression of stress ventricular function and biventricular and septal hypertrophy.
<i>Staphylococcus aureus</i>colonization in atopic dermatitis and its therapeutic implications
Authors: None Abeck, None Mempel
Journal: British Journal of Dermatology (1998)

Skin colonization with Staphylococcus aureus is a characteristic feature of atopic dermatitis with more than 90% of patients being colonized. Extracellular matrix proteins are important for the adherence of S. aureus to human keratinocytes. The bacterium interferes in the inflammatory process of atopic dermatitis in various ways, among which the ability to release superantigens in a high percentage of clinical isolates is of great importance. As the colonization correlates significantly with the severity of eczema, anti-staphylococcal treatment measurements are widely used. In cases of atopic dermatitis exacerbation with wide-spread weeping lesions, a systemic antibiotic treatment is warranted, with erythromycin no longer being recommended due to an increased resistance rate. In localized superinfected lesions the topical application of an antibiotic-glucocorticoid preparation may offer advantages to the mere steroid application. Based on efficacy and resistance data, fusidic acid is the antibiotic of choice. There is evidence that phototherapy in atopic dermatitis may be even more effective when combined with anti-staphylococcal measurements. In the future new therapeutical options may be available.
Estrogen Receptor α Gene Variation Is Associated With Risk of Myocardial Infarction in More Than Seven Thousand Men From Five Cohorts
Authors: Amanda M. Shearman, Jackie A. Cooper, Paul J. Kotwinski, George J. Miller, Steve E. Humphries, Kristin G. Ardlie, Barbara Jordan, Kathryn Irenze, Kathryn L. Lunetta, Stephanie C. E. Schuit, André G. Uitterlinden, Huibert A. P. Pols, Serkalem Demissie, L. Adrienne Cupples, Michael E. Mendelsohn, Daniel Levy, David E. Housman
Journal: Circulation Research (2006)

Understanding the mechanisms by which estrogens affect cardiovascular disease risk, including the role of variation in the gene for estrogen receptor alpha (ESR1), may be key to new treatment strategies. We investigated whether the CC genotype at ESR1 c.454-397T>C is associated with increased risk among men. Study of more than 7000 whites in 5 cohorts from 4 countries provided evidence that genotype CC, present in roughly 20% of individuals, is a risk factor for nonfatal acute myocardial infarction (odds ratio=1.44; P<0.0001), after adjustment for established cardiovascular risk factors. After exclusion of younger subjects from 2 cohorts, because of age interaction, the odds ratio increased (to 1.63).