tbuckley/cabot-search huggingface dataset:
Variation in gene duplicates with low synonymous divergence in Saccharomyces cerevisiae relative to Caenorhabditis elegans
Authors: Vaishali Katju, James C Farslow, Ulfar Bergthorsson
Journal: Genome biology (2009)

The direct examination of large, unbiased samples of young gene duplicates in their early stages of evolution is crucial to understanding the origin, divergence and preservation of new genes. Furthermore, comparative analysis of multiple genomes is necessary to determine whether patterns of gene duplication can be generalized across diverse lineages or are species-specific. Here we present results from an analysis comprising 68 duplication events in the Saccharomyces cerevisiae genome. We partition the yeast duplicates into ohnologs (generated by a whole-genome duplication) and non-ohnologs (from small-scale duplication events) to determine whether their disparate origins commit them to divergent evolutionary trajectories and genomic attributes. We conclude that, for the most part, ohnologs tend to appear remarkably similar to non-ohnologs in their structural attributes (specifically the relative composition frequencies of complete, partial and chimeric duplicates), the discernible length of the duplicated region (duplication span) as well as genomic location. Furthermore, we find notable differences in the features of S. cerevisiae gene duplicates relative to those of another eukaryote, Caenorhabditis elegans, with respect to chromosomal location, extent of duplication and the relative frequencies of complete, partial and chimeric duplications. We conclude that the variation between yeast and worm duplicates can be attributed to differing mechanisms of duplication in conjunction with the varying efficacy of natural selection in these two genomes as dictated by their disparate effective population sizes.
Biodegradation of poly(anhydride-esters) into non-steroidal anti-inflammatory drugs and their effect on Pseudomonas aeruginosa biofilms in vitro and on the foreign-body response in vivo
Authors: James D. Bryers, Rebecca A. Jarvis, Jason Lebo, Almudena Prudencio, Themis R. Kyriakides, Kathryn Uhrich
Journal: Biomaterials (2006)
Coagulopathy of peritoneovenous shunts: studies on the pathogenic role of ascitic fluid collagen and value of antiplatelet therapy.
Authors: H H Salem, F J Dudley, A Merrett, J Perkin, B G Firkin
Journal: Gut (1983)

The effect of moderate exercise on jejunal absorption was examined in seven healthy subjects using a triple lumen perfusion technique. Moderate exercise on a bicycle ergometer significantly reduced net absorption of water from 32.0 (4.0) to 16.2 (6.1) ml/30 cm/50 min (p less than 0.02), sodium from 2.4 (0.4) to 0.5 (0.9) mmol/30 cm/50 cm (p less than 0.05), chloride from 2.0 (0.4) to 0.3 (0.7) mmol/30 cm/50 min (p less than 0.05), and potassium from 0.20 (0.02) to 0.01 (0.04) mmol/30 cm/50 min (p less than 0.01). After exercise, water, sodium, and chloride absorption returned towards basal values, but potassium absorption remained significantly decreased. These results suggest that moderate exercise can influence jejunal absorption of salt and water in man. They support the possibility that the autonomic nervous system has a physiological role in the control of intestinal transport, although other mechanisms may be involved.
Paralimbic Cortical Thickness in First-Episode Depression: Evidence for Trait-Related Differences in Mood Regulation
Authors: Philip van Eijndhoven, Guido van Wingen, Maartje Katzenbauer, Wouter Groen, Ralf Tepest, Guillen Fernández, Jan Buitelaar, Indira Tendolkar
Journal: American Journal of Psychiatry (2013)

Impaired mood regulation is a key deficit of major depressive disorder that is primarily mediated by an interaction between the paralimbic cortex (i.e., orbitofrontal, cingulate, insular, parahippocampal, and temporopolar cortices) and limbic regions. The authors investigated whether depressed patients and healthy comparison subjects have differences in cortical thickness in the paralimbic cortex and whether potential differences are evident only during a depressive state or are trait related.Forty patients with a first episode of major depressive disorder participated: 20 medication-naive currently depressed patients and 20 medication-free recovered patients. The patients and 31 matched healthy comparison subjects underwent structural magnetic resonance imaging. Group differences in mean cortical thickness of the paralimbic cortex were measured by using FreeSurfer software, with adjustment for age, sex, and intracranial volume, and subgroup analyses were performed to assess state and trait effects.The medial orbitofrontal cortex was thinner in the depressed patients than in the comparison subjects. Greater thickness was present in the temporal pole and the caudal anterior and posterior cingulate cortex. All changes were trait related.The data provide evidence that even early in the course of depression brain regions involved in mood regulation show trait-related differences in cortical thickness.
A Multicenter Randomized Trial of Computer-driven Protocolized Weaning from Mechanical Ventilation
Authors: Francçois Lellouche, Jordi Mancebo, Philippe Jolliet, Jean Roeseler, Fréderique Schortgen, Michel Dojat, Belen Cabello, Lila Bouadma, Pablo Rodriguez, Salvatore Maggiore, Marc Reynaert, Stefan Mersmann, Laurent Brochard
Journal: American Journal of Respiratory and Critical Care Medicine (2006)

Rationale and Objectives: Duration of weaning from mechanical ventilation may be reduced by the use of a systematic approach. We assessed whether a closed-loop knowledge-based algorithm introduced in a ventilator to act as a computer-driven weaning protocol can improve patient outcomes as compared with usual care.Methods and Measurements: We conducted a multicenter randomized controlled study with concealed allocation to compare usual care for weaning with computer-driven weaning. The computerized protocol included an automatic gradual reduction in pressure support, automatic performance of spontaneous breathing trials (SBT), and generation of an incentive message when an SBT was successfully passed. One hundred forty-four patients were enrolled before weaning initiation. They were randomly allocated to computer-driven weaning or to physician-controlled weaning according to local guidelines. Weaning duration until successful extubation and total duration of ventilation were the primary endpoints.Main Results: Weaning duration was reduced in the computer-driven group from a median of 5 to 3 d (p = 0.01) and total duration of mechanical ventilation from 12 to 7.5 d (p = 0.003). Reintubation rate did not differ (23 vs. 16%, p = 0.40). Computer-driven weaning also decreased median intensive care unit (ICU) stay duration from 15.5 to 12 d (p = 0.02) and caused no adverse events. The amount of sedation did not differ between groups. In the usual care group, compliance to recommended modes and to SBT was estimated, respectively, at 96 and 51%.Conclusions: The specific computer-driven system used in this study can reduce mechanical ventilation duration and ICU length of stay, as compared with a physician-controlled weaning process.
Relation of interlobar collaterals to radiological heterogeneity in severe emphysema
Authors: T Higuchi
Journal: Thorax (2006)

A study was undertaken to assess the prevalence of interlobar collateral ventilation in patients with severe emphysema to identify factors that may help to predict patients with significant collateral ventilation.Between April 2002 and August 2003, ex vivo assessment of the lungs 17 consecutive patients with smoking related severe emphysema was performed. To assess collateral flow, all lobes of explanted specimens were selectively intubated using a wedged cuffed microlaryngeal intubation tube and then manually ventilated using a bagging circuit. Interlobar collateral ventilation was defined as the ability to easily inflate a non-intubated lobe at physiological pressures. Pre-transplant demographic characteristics, physiological data, radiological results, and explant histology were assessed for retrospective relationships with the degree of interlobar collateral ventilation in the explanted lung.A total of 23 lungs were evaluated, 15 of which (66%) had significant collateral interlobar airflow. There were no significant differences in any demographic, physiological, or pathological variables between patients with collateral ventilation and those with no collateral ventilation. However, there was a significant relationship between the presence of interlobar collateral ventilation and radiological scores (p<0.05).Interlobar collateral ventilation occurs to a much greater extent in patients with radiologically homogeneous emphysema than in those with heterogeneous emphysema. Heterogeneity of emphysema may predict patients with a significantly reduced risk of interlobar collateral ventilation.
Micrometastatic bone marrow cells at diagnosis have no impact on survival of primary breast cancer patients with extensive axillary lymph node involvement treated with stem cell-supported high-dose chemotherapy
Authors: A. Schneeweiss, I. Diel, M. Hensel, S. Kaul, H.-P. Sinn, K. Unnebrink, C. Rudlowski, I. Lauschner, F. Schuetz, G. Egerer, R. Haas, A.D. Ho, G. Bastert
Journal: Annals of Oncology (2004)
Improvement of Survival in Patients With Primary Cutaneous Diffuse Large B-Cell Lymphoma, Leg Type, in France
Authors: Florent Grange, Pascal Joly, Coralie Barbe, Martine Bagot, Stéphane Dalle, Saskia Ingen-Housz-Oro, Eve Maubec, Michel D’Incan, Caroline Ram-Wolff, Sophie Dalac, Isabelle Templier, Eric Esteve, Gaëlle Quereux, Laurent Machet, Marion Leduc, Olivier Dereure, Liliane Laroche, Philippe Saiag, Béatrice Vergier, Marie Beylot-Barry
Journal: JAMA Dermatology (2014)

<h3>Importance</h3> Primary cutaneous diffuse large B-cell lymphoma, leg type (PCDLBCL-LT), occurs in elderly patients and has been considered as a lymphoma with a poor prognosis, with estimated 5-year specific survival rates of approximately 50%. The hypothesis of an improvement in prognosis over time has not been studied. <h3>Objectives</h3> To evaluate this hypothesis in a large series of patients and investigate factors associated with prognosis as well as improvement in the prognosis. <h3>Design, Setting, and Participants</h3> A retrospective multicenter study was conducted including dermatology departments belonging to the French Study Group on Cutaneous Lymphoma. Participants were 115 patients with PCDLBCL-LT diagnosed between 1988 and 2003 (period 1) or between 2004 and 2010 (period 2). <h3>Main Outcomes and Measures</h3> Age, sex, period of diagnosis, number of skin lesions, tumor stage, tumor location (leg vs nonleg), lactate dehydrogenase level, type of therapy (with or without a combination of rituximab and polychemotherapy [PCT]), and outcome were recorded. Baseline characteristics and outcome were compared according to period of diagnosis and type of therapy. Prognosis factors were identified by univariate and multivariate survival analyses. <h3>Results</h3> The mean age of the patients was 76.9 years, and 47% of the patients were older than 80 years. The 3- and 5-year specific survival rates improved between period 1 and period 2, from 55% to 74% and from 46% to 66%, respectively (<i>P</i> = .01). Patients had similar baseline characteristics during both periods, but rituximab-PCT regimens were administered to 88.5% of the patients in period 2 vs 16.7% in period 1 (<i>P</i> &lt; .001). The 3- and 5-year specific survival rates were 80% and 74%, respectively, in patients who received a rituximab-PCT regimen compared with 48% and 38% in those who received less-intensive therapies. No significant difference was observed between both groups in age and baseline prognostic factors. In multivariate analysis, treatment without rituximab-PCT was the only adverse prognostic factor (odds ratio, 4.6 [95% CI, 2.4-9.1];<i>P</i> &lt; .001), whereas the number of skin lesions (<i>P</i> = .06) and location on the leg (<i>P</i> = .07) had only borderline significance. <h3>Conclusions and Relevance</h3> A major improvement in the survival of patients with PCDLBCL-LT has occurred over time in France, mainly as a result of the use of intensive rituximab-PCT regimens in most patients, including very elderly ones. Until further prospective clinical trials are conducted, such regimens should be considered as the standard of care in these patients.
THE NATURE OF THE IMMUNOLOGIC INADEQUACY OF NEONATAL RABBITS
Authors: Frank J. Dixon, William O. Weigle
Journal: The Journal of Experimental Medicine (1959)

It has been shown that cells from neonatal rabbits are capable of producing considerable amounts of antibody after exposure to antigen in vitro and transfer to x-radiated adult recipients. This suggests that the immunological inadequacy of these neonates is not dependent primarily upon the lack of cells capable of antibody formation. Both in vitro sensitized neonatal lymphoid cells and in vivo sensitized adult lymphoid cells made much more antibody after transfer to x-rayed adult recipients than to neonatal recipients. Possible reasons for and significance of these observations are pointed out in the discussion.
Regeneration of chronic myocardial infarction by injectable hydrogels containing stem cell homing factor SDF-1 and angiogenic peptide Ac-SDKP
Authors: Myeongjin Song, Hwanseok Jang, Jaeyeon Lee, Ji Hyun Kim, Soo Hyun Kim, Kyung Sun, Yongdoo Park
Journal: Biomaterials (2014)
Obsessive-Compulsive Disorder: Prevalence, Comorbidity, Impact, and Help-Seeking in the British National Psychiatric Morbidity Survey of 2000
Authors: Albina R. Torres, Martin J. Prince, Paul E. Bebbington, Dinesh Bhugra, Traolach S. Brugha, Michael Farrell, Rachel Jenkins, Glyn Lewis, Howard Meltzer, Nicola Singleton
Journal: American Journal of Psychiatry (2006)

There is little information about obsessive-compulsive disorder in large representative community samples. The authors aimed to establish obsessive-compulsive disorder prevalence and its clinical typology among adults in private households in Great Britain and to obtain generalizable estimates of impairment and help-seeking.Data from the British National Psychiatric Morbidity Survey of 2000, comprising 8,580 individuals, were analyzed using appropriate measurements. The study compared individuals with obsessive-compulsive disorder, individuals with other neurotic disorders, and a non-neurotic comparison group. ICD-10 diagnoses were derived from the Clinical Interview Schedule-Revised.The authors identified 114 individuals (74 women, 40 men) with obsessive-compulsive disorder, with a weighted 1-month prevalence of 1.1%. Most individuals (55%) in the obsessive-compulsive group had obsessions only. Comorbidity occurred in 62% of these individuals, which was significantly greater than the group with other neuroses (10%). Co-occurring neuroses were depressive episode (37%), generalized anxiety disorder (31%), agoraphobia or panic disorder (22%), social phobia (17%), and specific phobia (15%). Alcohol dependence was present in 20% of participants, mainly men, and drug dependence was present in 13%. Obsessive-compulsive disorder, compared with other neurotic disorders, was associated with more marked social and occupational impairment. One-quarter of obsessive-compulsive disorder participants had previously attempted suicide. Individuals with pure and comorbid obsessive-compulsive disorder did not differ according to most indices of impairment, including suicidal behavior, but pure individuals were significantly less likely to have sought help (14% versus 56%).A rare yet severe mental disorder, obsessive-compulsive disorder is an atypical neurosis, of which the public health significance has been underestimated. Unmet need among individuals with pure obsessive-compulsive disorder is a cause for concern, requiring further investigation of barriers to care and interventions to encourage help-seeking.
Variable effects of heart rate on phasic and regional left ventricular muscle blood flow in anaesthetized dogs
Authors: G. D. BUCKBERG, D. E. FIXLER, J. P. ARCHIE, R. P. HENNEY, J. I. E. HOFFMAN
Journal: Cardiovascular Research (1975)

Journal Article Variable effects of heart rate on phasic and regional left ventricular muscle blood flow in anaesthetized dogs Get access GERALD D. BUCKBERG, GERALD D. BUCKBERG From the Division of Thoracic Surgery, University of California, Center for the Health Sciences, Los Angeles, California 90024, and the Cardiovascular Research Institute and Department of Pediatrics, University of California, San Francisco, California 94143, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar DAVID E. FIXLER, DAVID E. FIXLER 2 From the Division of Thoracic Surgery, University of California, Center for the Health Sciences, Los Angeles, California 90024, and the Cardiovascular Research Institute and Department of Pediatrics, University of California, San Francisco, California 94143, USA 2Department of Pediatrics, Texas Southwestern Medical School, Dallas, Texas, USA. Search for other works by this author on: Oxford Academic PubMed Google Scholar JOSEPH P. ARCHIE, JOSEPH P. ARCHIE From the Division of Thoracic Surgery, University of California, Center for the Health Sciences, Los Angeles, California 90024, and the Cardiovascular Research Institute and Department of Pediatrics, University of California, San Francisco, California 94143, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar R. PETER HENNEY, R. PETER HENNEY From the Division of Thoracic Surgery, University of California, Center for the Health Sciences, Los Angeles, California 90024, and the Cardiovascular Research Institute and Department of Pediatrics, University of California, San Francisco, California 94143, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar JULIEN I. E. HOFFMAN JULIEN I. E. HOFFMAN From the Division of Thoracic Surgery, University of California, Center for the Health Sciences, Los Angeles, California 90024, and the Cardiovascular Research Institute and Department of Pediatrics, University of California, San Francisco, California 94143, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Cardiovascular Research, Volume 9, Issue 1, January 1975, Pages 1–11, https://doi.org/10.1093/cvr/9.1.1 Published: 01 January 1975
Chondrocyte apoptosis induced in vitro is caspase-3-mediated, but is not demonstrated in cartilage from patients with rheumatoid arthritis or osteoarthritis
Authors: J.F. Van Offel, I.C. Koster, G.J. Van Elsen, A.J. Schuerwegh, C.H. Bridts, M.M. Kockx, W.J. Stevens, L.S. De Clerck
Journal: Journal of Allergy and Clinical Immunology (2003)
Major-histocompatibility-complex DRB genes of a New-World monkey, the cottontop tamarin (Saguinus oedipus).
Authors: B Grahovac, W E Mayer, V Vincek, F Figueroa, C O'hUigin, H Tichy, J Klein
Journal: Molecular Biology and Evolution (1992)

The DRB region of the human and great-ape major histocompatibility complex displays not only gene but also haplotype polymorphism. The number of genes in the human DRB region can vary from one to four, and even greater variability exists among the DRB haplotypes of chimpanzees, gorillas, and orangutans. Accumulating evidence indicates that, like gene polymorphism, part of the haplotype polymorphism predates speciation. In an effort to determine when the gene haplotype polymorphisms emerged in the primate lineage, we sequenced three cDNA clones of the New-World monkey, the cottontop tamarin (Saguinus oedipus). We could identify two DRB loci in this species, one (Saoe-DRB1) occupied by apparently functional alleles (*0101 and *0102) which differ by only two nucleotide substitutions and the other (Saoe-DRB2) occupied by an apparent pseudogene. The Saoe-DRB2 gene contains an extra sequence derived from the 3' portion of exon 2 and placed 5' to this exon. This sequence contains a stop codon which makes the translation of the bulk of the Saoe-DRB2 gene unlikely. Preliminary Southern blot hybridization analysis with probes derived from these two genes suggests that both the DRB gene polymorphism and the haplotype polymorphism in the cottontop tamarin may be low. In most individuals the DRB region of this species probably consists of three genes. Comparisons of the Saoe-DRB sequences with those of other primates suggest that probably all of the DRB genes found until now in the Catarrhini were derived from a common ancestor after the separation of the Catarrhini and Platyrrhini lineages. The extant DRB gene and haplotype polymorphism may therefore have been founded in the mid-Oligocene some 33 Mya.
Dynamic contrast-enhanced magnetic resonance imaging biomarkers predict survival and response in hepatocellular carcinoma patients treated with sorafenib and metronomic tegafur/uracil
Authors: Chao-Yu Hsu, Ying-Chun Shen, Chih-Wei Yu, Chiun Hsu, Fu-Chang Hu, Chih-Hung Hsu, Bang-Bin Chen, Shwu-Yuan Wei, Ann-Lii Cheng, Tiffany Ting-Fang Shih
Journal: Journal of Hepatology (2011)
Enoxaparin versus Unfractionated Heparin with Fibrinolysis for ST-Elevation Myocardial Infarction
Authors: Elliott M. Antman, David A. Morrow, Carolyn H. McCabe, Sabina A. Murphy, Mikhail Ruda, Zygmunt Sadowski, Andrzej Budaj, Jose L. López-Sendón, Sema Guneri, Frank Jiang, Harvey D. White, Keith A.A. Fox, Eugene Braunwald
Journal: New England Journal of Medicine (2006)

Unfractionated heparin is often used as adjunctive therapy with fibrinolysis in patients with ST-elevation myocardial infarction. We compared a low-molecular-weight heparin, enoxaparin, with unfractionated heparin for this purpose.
Diagnosis of chronic brucellar meningitis and meningoencephalitis: the results of the Istanbul-2 study
Authors: H. Erdem, S. Kilic, B. Sener, C. Acikel, E. Alp, M. Karahocagil, F. Yetkin, A. Inan, V. Kecik-Bosnak, H.C. Gul, S. Tekin-Koruk, N. Ceran, T. Demirdal, G. Yilmaz, A. Ulu-Kilic, B. Ceylan, A. Dogan-Celik, S. Nayman-Alpat, R. Tekin, A. Yalci, V. Turban, I. Karaoglan, H. Yilmaz, B. Mete, A. Batirel, A. Ulcay, S. Dayan, A. Seza Inal, S.S. Ahmed, Z.K. Tufan, A. Karakas, B. Teker, M. Namiduru, U. Savasci, G. Pappas
Journal: Clinical Microbiology and Infection (2012)
Coloured filters may reduce symptoms of dyslexia in those with visual stress
Authors: B. J. W. Evans, P. M. Allen
Journal: BMJ (2014)

Henderson and colleagues did not consider one obvious explanation for the endorsement of coloured filters by dyslexia charities: these charities are in close contact with their members, some of whom provide feedback on benefits from coloured filters.1 Coloured filters are not a treatment for dyslexia but reduce symptoms in individuals with visual stress,2 which affects only about one third of people with dyslexia.3 4 Consequently, studies that ask whether coloured …
Chemoradiotherapy for locally advanced head and neck cancer: 10-year follow-up of the UK Head and Neck (UKHAN1) trial
Authors: Jeffrey S Tobias, Kathryn Monson, Nirmal Gupta, Hugh MacDougall, John Glaholm, Iain Hutchison, Latha Kadalayil, Allan Hackshaw
Journal: The Lancet Oncology (2009)