tbuckley/cabot-search huggingface dataset:
Does human lymphocyte antigen matching improve the outcome in pediatric renal transplants?
Authors: P T McEnery, D M Stablein
Journal: Journal of the American Society of Nephrology (1992)

Adult studies have shown a high renal graft survival if the donor and recipient match for each antigen of the human lymphocyte antigen (HLA)-A, B and DR loci (six-antigen match). The 4 yr of data from the North American Pediatric Renal Transplant Cooperative Study Registry show a statistically beneficial effect of DR matching for cadaver graft outcome. No antigen matching clearly has a worse outcome, 72% at 1 yr versus those with one or more antigen matching at each loci with a 1-yr graft survival of 81% and 2-yr graft survival of 69%. The long-term improved outcome from better antigen matching suggests that cadaver donor allograft organ assignment should address both the need of the center-driven and patient-driven concepts of recipient selection to achieve the best use of this scarce resource and an improved quality of life.
An Address on STERILITY IN WOMAN
Authors: W. B. Bell
Journal: BMJ (1930)

Human T cell hybridomas, which constitutively secrete glycosylation inhibiting factor (GIF), were constructed from PBL of an allergic individual who was sensitive to honey bee venom. PBMC of the patient were stimulated with either denatured or cyanogen bromide-treated bee venom phospholipase A2 (PLA2), and Ag-activated cells were propagated by IL-2 in the presence of human recombinant lipocortin I. T cells obtained in the cultures were fused with a HAT-sensitive mutant of the human lymphoblastoid cell line CEM. Approximately one-third of hybridoma clones constitutively secreted GIF. The GIF-producing hybridomas were CD3+ and bore TCR-alpha beta. GIF formed by unstimulated hybridomas lacked affinity for bee venom PLA2. Upon cross-linking of CD3, however, a majority of the GIF-producing hybridomas formed IgE-binding factors and GIF, the latter of which had affinity for bee venom PLA2. Both nonspecific GIF and Ag-binding GIF from the hybridomas bound to an immunosorbent coupled with the anti-lipomodulin mAb 141-B9. Using an affinity-purified GIF as an immunogen, we established mouse B cell hybridomas that secreted monoclonal anti-human GIF. In order to characterize human nonspecific GIF, one of the GIF-producing hybridomas was adapted to a serum-free medium, and culture supernatant was fractionated by DEAE-Sepharose column chromatography and by gel filtration. The majority of nonspecific GIF in the culture supernatant was recovered from DEAE-Sepharose by elution of the column with 10 mM Tris-HCl buffer, pH 8.0, containing 50 mM NaCl. Affinity-purification of GIF in the DEAE Sepharose fraction by using anti-GIF-coupled Affigel, and analysis of the purified GIF by SDS-PAGE revealed that human GIF is a single polypeptide chain of 14 to 15 kDa. Gel filtration of both crude and affinity-purified GIF preparations confirmed the molecular size of the cytokine.
Visualization of the Renal Artery
Authors: YIHONG KONG, WILLIAM F. BARRY, ROBERT E. WHALEN, VICTOR A. POLITANO, HENRY D. MCINTOSH
Journal: Circulation (1963)

Renal arteriograms were performed by both percutaneous translumbar single film and percutaneous transfemoral catheter seriographic technics on each of 29 hypertensive patients with suspected renal arterial disease. Comparison of the renal arteriograms obtained by these two methods demonstrates [see figure in the PDF file] that the transfemoral catheter seriographic technic is a simpler and more reliable procedure and results in better visualization of the renal artery. Ninety-three per cent of the studies by this method resulted in excellent diagnostic renal arteriograms, whereas only 60 per cent of the studies utilizing the translumbar technic were of equal quality. Pathologic and congenital abnormalities were also better demonstrated with the transfemoral catheter seriographic technic. The advantages and pitfalls of both methods have been discussed.
An update of luteal phase support in stimulated IVF cycles
Authors: H.M. Fatemi, B. Popovic-Todorovic, E. Papanikolaou, P. Donoso, P. Devroey
Journal: Human Reproduction Update (2007)

Stimulated IVF cycles are associated with luteal phase defect. In order to overcome this, different doses, durations and types of luteal phase support (LPS) have been evaluated. There is still no agreement regarding the optimal supplementation scheme. The aim of this paper is to assess the past and the current clinical practices of luteal supplementation in IVF. The databases of Medline and PubMed were searched to identify relevant publications. LPS with human chorionic gonadotrophin (hCG) [n = 262, odds ratio (OR) 2.72 (95%), confidence interval (CI) 1.56–4.90, P < 0.05] or progesterone (n = 260, OR 1.57 CI 1.13, 2.17, P < 0.05) results in an increased pregnancy rate compared with placebo, however, hCG is associated with increased risk of ovarian hyperstimulation syndrome. Natural micronized progesterone is not efficient if taken orally. The data on oral dydrogesterone are still conflicting. Vaginal and intra muscular progesterone have comparable outcomes. The addition of estradiol (E2) seems to be beneficial in long GnRH agonist protocol (implantation rate 39.6% with E2 compared with no E2; P < 0.05) but not in the short GnRH agonist and GnRH antagonist protocol. Despite the early promising results, it is too early to recommend the use of GnRH agonist in LPS. LPS should cease on the day of positive HCG. Since the cause of luteal phase defect in IVF appears to be related to the supraphysiological levels of steroids, milder stimulation protocols should be advocated in order to eventually overcome the luteal phase defect.
Structural Basis for the Inhibition of Human 5,10-Methenyltetrahydrofolate Synthetase by N10-Substituted Folate Analogues
Authors: Dong Wu, Yang Li, Gaojie Song, Chongyun Cheng, Rongguang Zhang, Andrzej Joachimiak, Neil Shaw, Zhi-Jie Liu
Journal: Cancer Research (2009)

5,10-Methenyltetrahydrofolate synthetase (MTHFS) regulates the flow of carbon through the one-carbon metabolic network, which supplies essential components for the growth and proliferation of cells. Inhibition of MTHFS in human MCF-7 breast cancer cells has been shown to arrest the growth of cells. Absence of the three-dimensional structure of human MTHFS (hMTHFS) has hampered the rational design and optimization of drug candidates. Here, we report the structures of native hMTHFS, a binary complex of hMTHFS with ADP, hMTHFS bound with the N5-iminium phosphate reaction intermediate, and an enzyme-product complex of hMTHFS. The N5-iminium phosphate captured for the first time in our crystal structure unravels a unique strategy used by hMTHFS for recognition of the substrate and provides structural basis for the regulation of enzyme activity. Binding of N10-substituted folate analogues places Y152 in the middle of the channel connecting ATP binding site with the substrate binding pocket, precluding the positioning of gamma-phosphate for a nucleophilic attack. Using the structures of hMTHFS as a guide, we have probed the role of residues surrounding the active site in catalysis by mutagenesis. The ensemble of hMTHFS structures and the mutagenesis data yield a coherent picture of the MTHFS active site, determinants of substrate specificity, and new insights into the mechanism of inhibition of hMTHFS.
Effects of Systematic Prone Positioning in Hypoxemic Acute Respiratory Failure
Authors: Claude Guerin, Sandrine Gaillard, Stephane Lemasson, Louis Ayzac, Raphaele Girard, Pascal Beuret, Bruno Palmier, Quoc Viet Le, Michel Sirodot, Sylvaine Rosselli, Vincent Cadiergue, Jean-Marie Sainty, Philippe Barbe, Emmanuel Combourieu, Daniel Debatty, Jean Rouffineau, Eric Ezingeard, Olivier Millet, Dominique Guelon, Luc Rodriguez, Olivier Martin, Anne Renault, Jean-Paul Sibille, Michel Kaidomar
Journal: JAMA (2004)

cated 30 years ago 1 to improve oxygenation in patients with hypoxemic acute respiratory failure (ARF) receiving mechanical ventilation.Dramatic oxygenation improvement using prone positioning was reported in severely hypoxemic patients. 2e mechanism of how the prone position improves oxygenation in this setting is still unclear.Postulated hypotheses in humans include alveolar recruitment, 3 redistribution of ventilation 4 toward dorsal areas that remain well
Dietary Fats Do Not Contribute to Hyperlipidemia in Children and Adolescents With Type 1 Diabetes
Authors: Esko J. Wiltshire, Craig Hirte, Jennifer J. Couper
Journal: Diabetes Care (2003)

OBJECTIVE—To determine the relative influence of diet, metabolic control, and familial factors on lipids in children with type 1 diabetes and control subjects. RESEARCH DESIGN AND METHODS—We assessed fasting serum cholesterol, LDL cholesterol, HDL cholesterol, triglycerides, lipoprotein(a), apolipoprotein (apo)-A1, and apoB in 79 children and adolescents with type 1 diabetes and 61 age- and sex-matched control subjects, together with dietary intakes using a quantitative food frequency questionnaire. RESULTS—Total cholesterol, LDL cholesterol, apoB, HDL cholesterol, and apoA1 were significantly higher in children with diabetes. Children with diabetes had higher percentage energy intake from complex carbohydrates (P = 0.001) and fiber intake (P = 0.02), and they had lower intake of refined sugar (P &amp;lt; 0.001) and percentage energy from saturated fat (P = 0.045) than control subjects. Total cholesterol (β = 0.43, P &amp;lt; 0.001), LDL cholesterol (β = 0.4, P &amp;lt; 0.001), and apoB (β = 0.32, P = 0.006) correlated independently with HbA1c but not dietary intake. HDL cholesterol (β = 0.24, P = 0.05) and apoA1 (β = 0.32, P = 0.004) correlated independently with HbA1c, and HDL cholesterol (β = −0.34, P = 0.009) correlated with percentage energy intake from complex carbohydrates. Triglycerides correlated independently with percentage energy intake from complex carbohydrates (β = 0.33, P = 0.01) and insulin dose (β = 0.26, P = 0.04). Subjects with diabetes and elevated LDL (&amp;gt;3.35 mmol/l, &amp;gt;130 mg/dl), for whom dietary therapy would be recommended, had significantly higher HbA1c (P = 0.007), but they had higher intake of complex carbohydrates than subjects with LDL cholesterol &amp;lt;3.35 mmol/l. CONCLUSIONS—Lipid abnormalities remain common in children and adolescents with type 1 diabetes who adhere to current dietary recommendations, and they relate to metabolic control but not dietary intake.
Phylogenetic inference under the pure drift model.
Authors: S Xu, W R Atchley, W M Fitch
Journal: Molecular Biology and Evolution (1994)

When pairwise genetic distances are used for phylogenetic reconstruction, it is usually assumed that the genetic distance between two taxa contains information about the time after the two taxa diverged. As a result, upon an appropriate transformation if necessary, the distance usually can be fitted to a linear model such that it is expressed as the sum of lengths of all branches that connect the two taxa in a given phylogeny. This kind of distance is referred to as "additive distance." For a phylogenetic tree exclusively driven by random genetic drift, genetic distances related to coancestry coefficients (theta XY) between any two taxa are more suitable. However, these distances are fundamentally different from the additive distance in that coancestry does not contain any information about the time after two taxa split from a common ancestral population; instead, it reflects the time before the two taxa diverged. In other words, the magnitude of theta XY provides information about how long the two taxa share the same evolutionary pathways. The fundamental difference between the two kinds of distances has led to a different algorithm of evaluating phylogenetic trees when theta XY and related distance measures are used. Here we present the new algorithm using the ordinary-least-squares approach but fitting to a different linear model. This treatment allows genetic variation within a taxon to be included in the model. Monte Carlo simulation for a rooted phylogeny of four taxa has verified the efficacy and consistency of the new method. Application of the method to human population was demonstrated.
Authors’ response to: primary healthcare factors and hospital admission rates for COPD: no association
Authors: Michael Soljak, Amaia Calderón-Larrañaga, Derek Bell, Azeem Majeed
Journal: Thorax (2014)

evidence that GP supply or treatment factors are predictive of rates of COPD admissions at practice or PCT level.All of this suggests that the claim in the editorial published alongside this paper that the inverse care law is alive and well with respect to hospital admission rates for COPD needs to be reconsidered.
Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade
Authors: Katarzyna Zaremba-Niedzwiedzka, Johan Viklund, Weizhou Zhao, Jennifer Ast, Alexander Sczyrba, Tanja Woyke, Katherina McMahon, Stefan Bertilsson, Ramunas Stepanauskas, Siv G E Andersson
Journal: Genome biology (2013)

Abstract Background The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt- and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet. Results We isolated ten single SAR11 cells from three freshwater lakes and sequenced and assembled their genomes. A phylogeny based on 57 proteins indicates that the cells are organized into distinct microclusters. We show that the freshwater genomes have evolved primarily by the accumulation of nucleotide substitutions and that they have among the lowest ratio of recombination to mutation estimated for bacteria. In contrast, members of the marine SAR11 clade have one of the highest ratios. Additional metagenome reads from six lakes confirm low recombination frequencies for the genome overall and reveal lake-specific variations in microcluster abundances. We identify hypervariable regions with gene contents broadly similar to those in the hypervariable regions of the marine isolates, containing genes putatively coding for cell surface molecules. Conclusions We conclude that recombination rates differ dramatically in phylogenetic sister groups of the SAR11 clade adapted to freshwater and marine ecosystems. The results suggest that the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade. The low recombination frequencies of the LD12 clade resemble the low genetic divergence of host-restricted pathogens that have recently shifted to a new host.
Effect of exacerbations on quality of life in patients with chronic obstructive pulmonary disease: a 2 year follow up study
Authors: M Miravitlles
Journal: Thorax (2004)

<b>Background:</b> A study was undertaken to evaluate exacerbations and their impact on the health related quality of life (HRQL) of patients with chronic obstructive pulmonary disease (COPD). <b>Methods:</b> A 2 year follow up study was performed in 336 patients with COPD of mean (SD) age 66 (8.2) years and mean (SD) forced expiratory volume in 1 second (FEV<sub>1</sub>) 33 (8)% predicted. Spirometric tests, questions regarding exacerbations of COPD, and HRQL measurements (St George's Respiratory Questionnaire (SGRQ) and SF-12 Health Survey) were conducted at 6 month intervals. <b>Results:</b> A total of 1015 exacerbations were recorded, and 103 (30.7%) patients required at least one hospital admission during the study. After adjustment for baseline characteristics and season of assessment, frequent exacerbations had a negative effect on HRQL in patients with moderate COPD (FEV<sub>1</sub> 35–50% predicted); the change in SGRQ total score of moderate patients with ⩾3 exacerbations was almost two points per year greater (worse) than those with &lt;3 exacerbations during the follow up (p = 0.042). For patients with severe COPD (FEV<sub>1</sub> &lt;35% predicted) exacerbations had no effect on HRQL. The change in SGRQ total score of patients admitted to hospital was almost 2 points per year greater (worse) than patients not admitted, but this effect failed to show statistical significance in any severity group. There was a significant and independent seasonal effect on HRQL since SGRQ total scores were, on average, 3 points better in measurements performed in spring/summer than in those measured in the winter (p&lt;0.001). <b>Conclusions:</b> Frequent exacerbations significantly impair HRQL of patients with moderate COPD. A significant and independent effect of seasonality was also observed.
Achieving integrated care is a slow and difficult process
Authors: A. O'Dowd
Journal: BMJ (2011)

The government’s aim to encourage more integrated care services across the whole NHS is a slow process full of “hurdles” but an achievable one, concludes a leading health policy think tank.

The study by the Nuffield Trust found that achieving more integration by redesigning healthcare services is not a simple matter and that it can take three years before improvements and financial benefits are visible.

Towards Integrated Care in Trafford , published on 10 November, looks at the work carried out by clinicians and managers in Trafford, Greater Manchester, since 2008 to develop an integrated care system as an example of how the rest of England could change.

The Nuffield Trust and the fellow think tank …
Meta-analysis and imputation refines the association of 15q25 with smoking quantity
Authors: Jason Z Liu, Federica Tozzi, Dawn M Waterworth, Sreekumar G Pillai, Pierandrea Muglia, Lefkos Middleton, Wade Berrettini, Christopher W Knouff, Xin Yuan, Gérard Waeber, Peter Vollenweider, Martin Preisig, Nicholas J Wareham, Jing Hua Zhao, Ruth J F Loos, Inês Barroso, Kay-Tee Khaw, Scott Grundy, Philip Barter, Robert Mahley, Antero Kesaniemi, Ruth McPherson, John B Vincent, John Strauss, James L Kennedy, Anne Farmer, Peter McGuffin, Richard Day, Keith Matthews, Per Bakke, Amund Gulsvik, Susanne Lucae, Marcus Ising, Tanja Brueckl, Sonja Horstmann, H-Erich Wichmann, Rajesh Rawal, Norbert Dahmen, Claudia Lamina, Ozren Polasek, Lina Zgaga, Jennifer Huffman, Susan Campbell, Jaspal Kooner, John C Chambers, Mary Susan Burnett, Joseph M Devaney, Augusto D Pichard, Kenneth M Kent, Lowell Satler, Joseph M Lindsay, Ron Waksman, Stephen Epstein, James F Wilson, Sarah H Wild, Harry Campbell, Veronique Vitart, Muredach P Reilly, Mingyao Li, Liming Qu, Robert Wilensky, William Matthai, Hakon H Hakonarson, Daniel J Rader, Andre Franke, Michael Wittig, Arne Schäfer, Manuela Uda, Antonio Terracciano, Xiangjun Xiao, Fabio Busonero, Paul Scheet, David Schlessinger, David St Clair, Dan Rujescu, Gonçalo R Abecasis, Hans Jörgen Grabe, Alexander Teumer, Henry Völzke, Astrid Petersmann, Ulrich John, Igor Rudan, Caroline Hayward, Alan F Wright, Ivana Kolcic, Benjamin J Wright, John R Thompson, Anthony J Balmforth, Alistair S Hall, Nilesh J Samani, Carl A Anderson, Tariq Ahmad, Christopher G Mathew, Miles Parkes, Jack Satsangi, Mark Caulfield, Patricia B Munroe, Martin Farrall, Anna Dominiczak, Jane Worthington, Wendy Thomson, Steve Eyre, Anne Barton, Vincent Mooser, Clyde Francks, Jonathan Marchini
Journal: Nature Genetics (2010)
AVISPA: a web tool for the prediction and analysis of alternative splicing
Authors: Yoseph Barash, Jorge Vaquero-Garcia, Juan González-Vallinas, Hui Yuan Xiong, Weijun Gao, Leo J Lee, Brendan J Frey
Journal: Genome biology (2013)

Transcriptome complexity and its relation to numerous diseases underpins the need to predict in silico splice variants and the regulatory elements that affect them. Building upon our recently described splicing code, we developed AVISPA, a Galaxy-based web tool for splicing prediction and analysis. Given an exon and its proximal sequence, the tool predicts whether the exon is alternatively spliced, displays tissue-dependent splicing patterns, and whether it has associated regulatory elements. We assess AVISPA's accuracy on an independent dataset of tissue-dependent exons, and illustrate how the tool can be applied to analyze a gene of interest. AVISPA is available at http://avispa.biociphers.org .
Chronic lymphocytic leukemia cells induce changes in gene expression of CD4 and CD8 T cells
Authors: Güllü Görgün, Tobias A.W. Holderried, David Zahrieh, Donna Neuberg, John G. Gribben
Journal: Journal of Clinical Investigation (2005)

To examine the impact of tumors on the immune system, we compared global gene expression profiles of peripheral blood T cells from previously untreated patients with B cell chronic lymphocytic leukemia (CLL) with those from age-matched healthy donors. Although the cells analyzed were not part of the malignant clone, analysis revealed differentially expressed genes, mainly involved in cell differentiation in CD4 cells and defects in cytoskeleton formation, vesicle trafficking, and cytotoxicity in CD8 cells of the CLL patients. In coculture experiments using CLL cells and T cells from healthy allogeneic donors, similar defects developed in both CD4 and CD8 cells. These changes were induced only with direct contact and were not cytokine mediated. Identification of the specific pathways perturbed in the T cells of cancer-bearing patients will allow us to assess steps to repair these defects, which will likely be required to enhance antitumor immunity.
Acute hiatal hernia after Heller's operation.
Authors: M Y Rabau, I Avigad, A Czerniak, Y Liberman, I Wolfstein
Journal: Thorax (1981)

A modified Heller's operation is the surgical treatment of choice for oesophageal achalasia.Oesophageal reflux (with or without hernia) has been reported as an in- frequent complication of this operation.However, acute diaphragmatic hernia after Heller's operation is a rare complication.Routine anatomical restoration of the hiatus upon completion of the oesophagomyotomy will further reduce its occurrence.Once the diagnosis has been made, surgery is indicated to prevent additional compli- cations. Case reportA 60-year-old woman was operated on for achalasia of 10 years' duration.Routine transthoracic oesophagomyo- tomy was performed.The oesophageal muscle was
Suicidality in Body Dysmorphic Disorder: A Prospective Study
Authors: Katharine Phillips
Journal: American Journal of Psychiatry (2006)

Objective: Cross-sectional/retrospective data have indicated that individuals with body dysmorphic disorder (BDD) have high rates of suicidal ideation and attempts. However, no study, to the authors' knowledge, has prospectively examined suicidality in BDD. Method: In the first prospective study of BDD's course, the authors examined suicidality in 185 subjects for up to 4 years. Results: Suicidal ideation was reported by a mean of 57.8% of the subjects per year, and a mean of 2.6% attempted suicide per year. Two subjects (0.3% per year) completed suicide. Conclusions: Individuals with BDD have high rates of suicidal ideation and attempts. The completed suicide rate is preliminary but suggests that the rate of completed suicide in BDD is markedly high.
Effect of biologically active coating on biocompatibility of Nitinol devices designed for the closure of intra-atrial communications
Authors: Xiangqing Kong, R.G Grabitz, W van Oeveren, D Klee, T.G van Kooten, F Freudenthal, Ma Qing, G von Bernuth, M.-C Seghaye
Journal: Biomaterials (2002)