tbuckley/cabot-search huggingface dataset:
Acute exacerbations of chronic type B hepatitis are accompanied by increased T cell responses to hepatitis B core and e antigens. Implications for hepatitis B e antigen seroconversion.
Authors: S L Tsai, P J Chen, M Y Lai, P M Yang, J L Sung, J H Huang, L H Hwang, T H Chang, D S Chen
Journal: Journal of Clinical Investigation (1992)

T cell proliferative responses to hepatitis B virus-encoded envelope antigen (S + preS2 + preS1), recombinant core antigen (HBcAg), and natural hepatitis B e antigen (HBeAg) were examined in 22 HBeAg-positive patients with chronic type B hepatitis and 17 healthy hepatitis B surface antigen (HBsAg) carriers. The results showed that HBeAg-positive patients had (a) higher levels of T cell responses to HBcAg/HBeAg than those of healthy HBsAg carriers (P less than 0.001 and P less than 0.01, respectively); (b) a further increase in these T cell responses during acute exacerbations (P less than 0.05 and P less than 0.05, respectively); (c) subsidence in the T cell responses to HBcAg/HBeAg after recovery from acute exacerbations and HBeAg seroconversion, whereas the responses would persist at high levels if the patients did not enter a clinical remission; and (d) low levels of T cell responses to S + preS2 + preS1 either before or after HBeAg seroconversion. The appearance of increasing T cell responses to HBcAg/HBeAg usually occurred in the early phase of acute exacerbations. These findings imply that HBcAg/HBeAg-specific T cells play an important role in the exacerbations of chronic hepatitis B and in HBeAg seroconversion. HBcAg/HBeAg-specific precursor T cell frequencies were serially studied in selected cases by limiting dilution assay. Elevation (two- to fourfold) of HBcAg/HBeAg-specific precursor T cell frequencies contributed to the increase of HBcAg/HBeAg-specific T cell proliferation during acute exacerbations.
Cardiac troponin I release and cytokine response during experimental human endotoxaemia
Authors: Esther A. P. van Bockel, Jaap E. Tulleken, Anneke C. Muller Kobold, Jack J. M. Ligtenberg, Tjip S. van der Werf, Rob Spanjersberg, Jan G. Zijlstra
Journal: Intensive Care Medicine (2003)
Review of the Health Effects of Sulfur Oxides
Authors: David P. Rall
Journal: Environmental Health Perspectives (1974)

The pollution in the air is a complex mixture of chemical substances of varying toxicity of which the sulfur oxides are a principal component. Those components which pose the primary hazards to human health have not yet been fully identified, nor have their respective contributions to human disease been fully determined. Efficient and effective control strategies are dependent upon the identification and understanding of these toxic components. Ultimately, the goal of standard-setting should be the development of composite pollution indices rather than control of individual pollutants. Concentrations of SO(2) in the ambient air twice the current standards are associated with adverse health effects. A considerable body of evidence suggests that there may be discernible human health effects from exposure to concentrations approximating the current standards. There is therefore no basis for relaxation of the present standards for sulfur oxides at this time. Since the scientific basis for this judgment is incomplete, further scientific information will be required either to validate the present standards or to justify alteration of these standards.
Respirators in respiratory failure
Authors: W. H. Kelleher
Journal: BMJ (1969)

BRnTnS 369 raises the point that the presence of the prune-belly syndrome in an older child should be unacceptable because it represents failure to apply early preventive treatment.In addition to the psychological and cos- metic benefit it might well be that the stronger abdominal wall would also be a positive advantage in the child's urinary dynamics.-Iam, etc.,
Human Leukocyte Antigen Class I Antigen Expression Is an Independent Prognostic Factor in Ovarian Cancer
Authors: Phil Rolland, Suha Deen, Ian Scott, Lindy Durrant, Ian Spendlove
Journal: Clinical Cancer Research (2007)

Abstract Purpose: Despite improvements in cancer treatment, the prognosis of ovarian cancer remains low and imperfectly predicted by traditional pathologic criteria. Biomarkers that predict prognosis independently of such criteria shed light on important molecular variations, aiding in the development and targeting of novel therapies. Previous work has shown human leukocyte antigen (HLA) class I antigen expression to be independently predictive of prognosis in colorectal and breast cancer. We investigated the prognostic potential of HLA class I antigen expression by studying a large series of ovarian cancers. Experimental Design: A tissue microarray of 339 ovarian cancer cases linked to prospectively recorded clinicopathologic and follow-up data was constructed. This was stained following a standard immunohistochemical protocol for HLA class I heavy chain (HC-10) and β2-microglobulin (β2-m). HLA class I antigen expression was compared with clinicopathologic factors and overall disease-specific survival using the Pearson χ2 test, Kaplan-Meier curves, and the log-rank test. Cox regression was used to test for the independence and magnitude of effects. Results: There were no univariate correlations between HLA class I antigen expression and clinicopathologic factors. Deviation from an HC-10+/β2-m+ phenotype correlated with reduced survival in univariate analysis (log-rank, 5.69; P = 0.017); a retained HC-10+/β2-m+ phenotype predicted improved prognosis independently of age, stage, level of cytoreduction, and chemotherapy usage on multivariate analysis (hazard ratio, 0.587; 95% confidence interval, 0.442-0.781; P &amp;lt; 0.001). Conclusions: HLA class I antigen expression is an independent prognostic marker in ovarian cancer, its loss correlating with a poor prognostic outcome.
Recent developments in computer assisted rehabilitation environments
Authors: Rob van der Meer
Journal: Military Medical Research (2014)

Computer Assisted Rehabilitation Environment (CAREN) is a system that integrates a training platform (motion base), a virtual environment, a sensor system (motion capture) and D-flow software. It is useful for both diagnostic and therapeutic use. The human gait pattern can be impaired due to disease, trauma or natural decline. Gait analysis is a useful tool to identify impaired gait patterns. Traditional gait analysis is a very time consuming process and therefore only used in exceptional cases. With new systems a quick and extensive analysis is possible and provides useful tools for therapeutic purposes. The range of systems will be described in this paper, highlighting both their diagnostic use and the therapeutic possibilities. Because wounded warriors often have an impaired gait due to amputations or other extremity trauma, these systems are very useful for military rehabilitative efforts. Additionally, the virtual reality environment creates a very challenging situation for the patient, enhancing their rehabilitation experience. For that reason several Armed Forces have these systems already in use. The most recent experiences will be discussed; including new developments both in the extension of the range of systems and the improvement and adaptation of the software. A new and promising development, the use of CAREN in a special application for patients with post-traumatic stress disorder (PTSD), will also be reviewed.
Frequency of 13q Abnormalities Among 203 Patients With Retinoblastoma
Authors: G. R. Bunin, B. S. Emanuel, A. T. Meadows, J. D. Buckley, W. G. Woods, G. D. Hammond
Journal: JNCI Journal of the National Cancer Institute (1989)

Journal Article Frequency of 13q Abnormalities Among 203 Patients With Retinoblastoma Get access Greta R. Bunin, Greta R. Bunin 1Children's Hospital of Philadelphia and the University of Pennsylvania School of MedicinePhiladelphia, PA Correspondence to: Childrens Cancer Study Group, Operations Office, Third Floor, 199 North Lake Ave. Pasadena, CA 91101. Search for other works by this author on: Oxford Academic PubMed Google Scholar Beverly S. Emanuel, Beverly S. Emanuel 1Children's Hospital of Philadelphia and the University of Pennsylvania School of MedicinePhiladelphia, PA Search for other works by this author on: Oxford Academic PubMed Google Scholar Anna T. Meadows, Anna T. Meadows 1Children's Hospital of Philadelphia and the University of Pennsylvania School of MedicinePhiladelphia, PA Search for other works by this author on: Oxford Academic PubMed Google Scholar Jonathan D. Buckley, Jonathan D. Buckley 2University of Southern California School of MedicineLos Angeles, CA Search for other works by this author on: Oxford Academic PubMed Google Scholar William G. Woods, William G. Woods 3University of Minnesota, MinneapolisMN Search for other works by this author on: Oxford Academic PubMed Google Scholar G. Denman Hammond G. Denman Hammond 2University of Southern California School of MedicineLos Angeles, CA Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 81, Issue 5, 1 March 1989, Pages 370–374, https://doi.org/10.1093/jnci/81.5.370 Published: 01 March 1989 Article history Received: 08 September 1988 Revision received: 14 December 1988 Accepted: 27 December 1988 Published: 01 March 1989
FATE OF STAPHYLOCOCCI WITHIN HUMAN LEUKOCYTES
Authors: Marian Ann Melly, John B. Thomison, David E. Rogers
Journal: The Journal of Experimental Medicine (1960)

Direct observations by phase microscopy have demonstrated that small numbers of pathogenic staphylococci survive prolonged periods of time within living human polymorphonuclear leukocytes. Non-pathogenic microorganisms are rapidly destroyed in similar preparations. Leukocytes in which staphylococci remained viable often appeared less vigorous after ingesting microorganisms, but intracellular survival could not be correlated with obvious leukocyte damage with any consistency. Both pathogenic and non-pathogenic cocci were seen to divide within living granulocytes during the first few minutes after ingestion. Occasionally pathogenic staphylococci multiplied in dying cells after long periods of intracellular residence. Phagocytosis of more than one pair of staphylococci by a single leukocyte appeared to act as a stimulus to bacterial destruction. Multiple ingestions of pathogenic staphylococci reduced the incidence of survival of the total microbiol population contained within the cell.
Transposable elements reveal a stem cell-specific class of long noncoding RNAs
Authors: David Kelley, John Rinn
Journal: Genome biology (2012)

Abstract Background Numerous studies over the past decade have elucidated a large set of long intergenic noncoding RNAs (lincRNAs) in the human genome. Research since has shown that lincRNAs constitute an important layer of genome regulation across a wide spectrum of species. However, the factors governing their evolution and origins remain relatively unexplored. One possible factor driving lincRNA evolution and biological function is transposable element (TE) insertions. Here, we comprehensively characterize the TE content of lincRNAs relative to genomic averages and protein coding transcripts. Results Our analysis of the TE composition of 9,241 human lincRNAs revealed that, in sharp contrast to protein coding genes, 83% of lincRNAs contain a TE, and TEs comprise 42% of lincRNA sequence. lincRNA TE composition varies significantly from genomic averages - L1 and Alu elements are depleted and broad classes of endogenous retroviruses are enriched. TEs occur in biased positions and orientations within lincRNAs, particularly at their transcription start sites, suggesting a role in lincRNA transcriptional regulation. Accordingly, we observed a dramatic example of HERVH transcriptional regulatory signals correlating strongly with stem cell-specific expression of lincRNAs. Conversely, lincRNAs devoid of TEs are expressed at greater levels than lincRNAs with TEs in all tissues and cell lines, particularly in the testis. Conclusions TEs pervade lincRNAs, dividing them into classes, and may have shaped lincRNA evolution and function by conferring tissue-specific expression from extant transcriptional regulatory signals.
Effect of vasoactive agents on intestinal oxygen consumption and blood flow in dogs.
Authors: W Pawlik, A P Shepherd, E D Jacobson
Journal: Journal of Clinical Investigation (1975)

A comparison study of several vasoconstrictor and vasodilator agents was conducted measuring changes in intestinal blood flow and oxygen consumption during 10-min periods of intra-arterial infusion. Blood flow was measured in a branch of the superior mesenteric artery of anesthetized dogs with an electromagnetic blood flow meter, and the arteriovenous oxygen content difference across the gut segment was determined photometrically. Vasopressin (4 x 10(-3) and 7x 10(-4) U/kg-min) diminished blood flow 60 and 28% and reduced oxygen consumption 54 and 22%, respectively (all P less than 0.001). In a dose which did not lower blood flow, vasopressin still caused a decline in oxygen consumption (P less than 0.01). Epinephrine (5 x 10(-2) mug/kg-min) decreased blood flow 19% (P less than 0.001) but did not reduce oxygen consumption. After beta-adrenergic blockade, however, the same dose of epinephrine decreased blood flow 41% and oxygen consumption 33% (both P less than 0.001). Responses to angiotension II, calcium chloride, and prostaglandin F2alpha resembled effects of vasopressin rather than those of epinephrine, namely decreased blood flow and decreased oxygen consumption. The vasodilator agents, prostaglandin E1, is isoproterenol, and histamine, increased (P less than 0.001) both blood flow (130, 80, and 98%, respectively) and oxygen consumption (98, 64, and 70%, respectively). Vasopressin, angiotensin II, calcium chloride, and prostaglandin F2alpha appear to contract arteriolar and precapillary sphincteric smooth muscle indiscriminately to evoke both intestinal ischemia and hypoxia. Epinephrine is the exceptional constrictor in this case, producing diminished blood flow without a reduction in oxygen uptake.
The Molecular Genetics of the T-Cell Antigen Receptor and T-Cell Antigen Recognition
Authors: M Kronenberg, G Siu, L E Hood, N Shastri
Journal: Annual Review of Immunology (1986)

Exhausted CD8 T (Tex) cells are a distinct cell lineage that arise during chronic infections and cancers in animal models and humans. Tex cells are characterized by progressive loss of effector functions, high and sustained inhibitory receptor expression, ...Read More
BiDiBlast: Comparative Genomics Pipeline for the PC
Authors: João M.G.C.F. de Almeida
Journal: Genomics Proteomics & Bioinformatics (2010)

Abstract Bi-directional BLAST is a simple approach to detect, annotate, and analyze candidate orthologous or paralogous sequences in a single go. This procedure is usually confined to the realm of customized Perl scripts, usually tuned for UNIX-like environments. Porting those scripts to other operating systems involves refactoring them, and also the installation of the Perl programming environment with the required libraries. To overcome these limitations, a data pipeline was implemented in Java. This application submits two batches of sequences to local versions of the NCBI BLAST tool, manages result lists, and refines both bi-directional and simple hits. GO Slim terms are attached to hits, several statistics are derived, and molecular evolution rates are estimated through PAML. The results are written to a set of delimited text tables intended for further analysis. The provided graphic user interface allows a friendly interaction with this application, which is documented and available to download at http://moodle.fct.unl.pt/course/view.php?id=2079 or https://sourceforge.net/projects/bidiblast/ under the GNU GPL license.
Risk of Adverse Pregnancy Outcomes in Women with CKD
Authors: Giorgina Barbara Piccoli, Gianfranca Cabiddu, Rossella Attini, Federica Neve Vigotti, Stefania Maxia, Nicola Lepori, Milena Tuveri, Marco Massidda, Cecilia Marchi, Silvia Mura, Alessandra Coscia, Marilisa Biolcati, Pietro Gaglioti, Michele Nichelatti, Luciana Pibiri, Giuseppe Chessa, Antonello Pani, Tullia Todros
Journal: Journal of the American Society of Nephrology (2015)

CKD is increasingly prevalent in pregnancy. In the Torino-Cagliari Observational Study (TOCOS), we assessed whether the risk for adverse pregnancy outcomes is associated with CKD by comparing pregnancy outcomes of 504 pregnancies in women with CKD to outcomes of 836 low-risk pregnancies in women without CKD. The presence of hypertension, proteinuria (&gt;1 g/d), systemic disease, and CKD stage (at referral) were assessed at baseline. The following outcomes were studied: cesarean section, preterm delivery, and early preterm delivery; small for gestational age (SGA); need for neonatal intensive care unit (NICU); new onset of hypertension; new onset/doubling of proteinuria; CKD stage shift; “general” combined outcome (preterm delivery, NICU, SGA); and “severe” combined outcome (early preterm delivery, NICU, SGA). The risk for adverse outcomes increased across stages (for stage 1 versus stages 4–5: “general” combined outcome, 34.1% versus 90.0%; “severe” combined outcome, 21.4% versus 80.0%; P &lt;0.001). In women with stage 1 CKD, preterm delivery was associated with baseline hypertension (odds ratio [OR], 3.42; 95% confidence interval [95% CI], 1.87 to 6.21), systemic disease (OR, 3.13; 95% CI, 1.51 to 6.50), and proteinuria (OR, 3.69; 95% CI, 1.63 to 8.36). However, stage 1 CKD remained associated with adverse pregnancy outcomes (general combined outcome) in women without baseline hypertension, proteinuria, or systemic disease (OR, 1.88; 95% CI, 1.27 to 2.79). The risk of intrauterine death did not differ between patients and controls. Findings from this prospective study suggest a “baseline risk” for adverse pregnancy-related outcomes linked to CKD.
Immunoglobulin Allotypes Influence Antibody Responses to Mucin 1 in Patients with Gastric Cancer
Authors: Janardan P. Pandey, Paul J. Nietert, Silvia von Mensdorff-Pouilly, Kersti Klaamas, Oleg Kurtenkov
Journal: Cancer Research (2008)

Abstract There are significant interindividual differences in naturally occurring antibody responses to the tumor-associated antigen mucin 1 (MUC1), but the host genetic factors that might contribute to these differences have not been identified. The aim of the present investigation was to determine whether the variation in naturally occurring antibody levels to MUC1 in patients with gastric cancer is associated with GM and KM allotypes, genetic markers of IgG heavy chains and κ-type light chains, respectively. A total of 169 Caucasian subjects with gastric cancer were allotyped for several GM and KM markers. These subjects were also characterized for IgG and IgM antibodies to MUC1. GM 3 23 5,13 phenotype was highly significantly associated with MUC1 IgG levels; subjects with this phenotype had lower antibody levels compared with those lacking this phenotype (median IgG level 65.5 relative units versus 91.0 relative units, P = 0.0058). In addition, this phenotype had an interactive effect with KM phenotypes on the levels of IgG antibodies to this antigen (P = 0.0081). Levels of MUC1 IgM antibodies were not associated with these genetic markers. These results show, for the first time, that GM and KM allotypes contribute to the interindividual differences in humoral immunity to MUC1. [Cancer Res 2008;68(11):4442–6]
Randomized Phase III Trial of Gemcitabine Compared With Pegylated Liposomal Doxorubicin in Patients With Platinum-Resistant Ovarian Cancer
Authors: David G. Mutch, Mauro Orlando, Tiana Goss, Michael G. Teneriello, Alan N. Gordon, Scott D. McMeekin, Yanping Wang, Dennis R. Scribner, Martin Marciniack, R. Wendel Naumann, Angeles Alvarez Secord
Journal: Journal of Clinical Oncology (2007)

Ovarian cancer (OC) patients experiencing progressive disease (PD) within 6 months of platinum-based therapy in the primary setting are considered platinum resistant (Pt-R). Currently, pegylated liposomal doxorubicin (PLD) is a standard of care for treatment of recurrent Pt-R disease. On the basis of promising phase II results, gemcitabine was compared with PLD for efficacy and safety in taxane-pretreated Pt-R OC patients.Patients (n = 195) with Pt-R OC were randomly assigned to either gemcitabine 1,000 mg/m2 (days 1 and 8; every 21 days) or PLD 50 mg/m2 (day 1; every 28 days) until PD or undue toxicity. Optional cross-over therapy was allowed at PD or at withdrawal because of toxicity. Primary end point was progression-free survival (PFS). Additional end points included tumor response, time to treatment failure, survival, and quality of life.In the gemcitabine and PLD groups, median PFS was 3.6 v 3.1 months; median overall survival was 12.7 v 13.5 months; overall response rate (ORR) was 6.1% v 8.3%; and in the subset of patients with measurable disease, ORR was 9.2% v 11.7%, respectively. None of the efficacy end points showed a statistically significant difference between treatment groups. The PLD group experienced significantly more hand-foot syndrome and mucositis; the gemcitabine group experienced significantly more constipation, nausea/vomiting, fatigue, and neutropenia but not febrile neutropenia.Although this was not designed as an equivalency study, gemcitabine and PLD seem to have a comparable therapeutic index in this population of Pt-R taxane-pretreated OC patients. Single-agent gemcitabine may be an acceptable alternative to PLD for patients with Pt-R OC.
BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach
Authors: Andrea Riebler, Mirco Menigatti, Jenny Z Song, Aaron L Statham, Clare Stirzaker, Nadiya Mahmud, Charles A Mein, Susan J Clark, Mark D Robinson
Journal: Genome biology (2014)

Affinity capture of DNA methylation combined with high-throughput sequencing strikes a good balance between the high cost of whole genome bisulfite sequencing and the low coverage of methylation arrays. We present BayMeth, an empirical Bayes approach that uses a fully methylated control sample to transform observed read counts into regional methylation levels. In our model, inefficient capture can readily be distinguished from low methylation levels. BayMeth improves on existing methods, allows explicit modeling of copy number variation, and offers computationally efficient analytical mean and variance estimators. BayMeth is available in the Repitools Bioconductor package.
Liver/biliary injuries following chemoembolisation of endocrine tumours and hepatocellular carcinoma: Lipiodol vs. drug-eluting beads
Authors: Boris Guiu, Frédéric Deschamps, Serge Aho, Flore Munck, Clarisse Dromain, Valérie Boige, David Malka, Sophie Leboulleux, Michel Ducreux, Martin Schlumberger, Eric Baudin, Thierry de Baere
Journal: Journal of Hepatology (2011)