tbuckley/cabot-search huggingface dataset:
Overexpression of transcripts containing LINE-1 in the synovia of patients with rheumatoid arthritis
Authors: M Ali
Journal: Annals of the Rheumatic Diseases (2003)

To identify novel diagnostic markers by comparing gene expression in rheumatoid (RA) and reactive arthritis (ReA) synovium.Synovial biopsy specimens were obtained by needle arthroscopy from the knees of 10 patients with either RA or ReA. RNA was isolated from the biopsy specimens and cDNA synthesised for analysis using a customised cDNA macroarray. Confirmatory analysis was performed using in situ hybridisation on a second set of synovial samples.Two unique transcripts (ReXS1 and fibronectin) were consistently more abundant in ReA and three homologous transcripts were more abundant in RA. The latter all mapped within long interspersed nucleotide elements (LINE-1), that form one of the families of repetitive sequences in the human genome.The abundance of transcripts containing LINE-1 in the RA synovium may be an epiphenomenon or may have pathogenic significance. Further work is required to determine the identity of the full length transcript(s) before its use as a diagnostic marker in RA can be assessed.
Expansion of inflammatory innate lymphoid cells in patients with common variable immune deficiency
Authors: Montserrat Cols, Adeeb Rahman, Paul J. Maglione, Yolanda Garcia-Carmona, Noa Simchoni, Huai-Bin M. Ko, Lin Radigan, Andrea Cerutti, Derek Blankenship, Virginia Pascual, Charlotte Cunningham-Rundles
Journal: Journal of Allergy and Clinical Immunology (2015)
Polyclonal Immunoglobulin E Levels Are Correlated with Hemoglobin Values and Overall Survival in Patients with Multiple Myeloma
Authors: Giorgia Maria Elena Matta, Silvano Battaglio, Cristiana DiBello, Patrizia Napoli, Cristina Baldi, Giovannino Ciccone, Marta Coscia, Mario Boccadoro, Massimo Massaia
Journal: Clinical Cancer Research (2007)

Abstract Purpose: Polyclonal IgG, IgA, and IgM immunoglobulins are often decreased in sera of patients with multiple myeloma (MM), whereas very few data are available on polyclonal IgE levels. We have determined IgE levels in a large series of MM patients at diagnosis and subjects with monoclonal gammopathy of undetermined significance (MGUS) and correlated IgE levels with survival and prognostic factors in MM. Experimental Design: IgE were determined with a commercially available ELISA kit in 201 MM patients at diagnosis, 144 subjects with MGUS, and 77 age-matched controls. Results: IgE levels progressively decreased from controls to MGUS and from MGUS to MM (P = 0.001). MM patients with IgE levels of &amp;gt;11.5 IU/mL (median) had a better survival than patients with IgE of &amp;lt;11.5 IU/mL (P = 0.048). The difference was even more significant when MM patients were divided according to clinical cutoff values. Patients with elevated IgE levels (&amp;gt;100 IU/mL) had from 2 to 3 years longer survival than those with low (&amp;lt;10 IU/mL) or intermediate values (10-100 IU/mL; P &amp;lt; 0.01). IgE levels were positively and negatively correlated with hemoglobin (P = 0.006) and β2-microglobulin levels (P = 0.007), respectively. Univariate and multivariate analyses confirmed that high IgE levels are positive predictors of overall survival (P = 0.03 and 0.08, respectively) and strongly correlated with hemoglobin values. Conclusions: Because IgE levels are dependent on Th2 responses, these data open new perspectives in the interpretation of antitumor immune responses and pathogenesis of anemia in MM.
Newly Diagnosed Type 2 Diabetic Population in Belgium
Authors: Johan Wens, Viviane Van Casteren, Etienne Vermeire, Paul Van Royen, Joke Denekens
Journal: Diabetes Care (2002)

We read with interest the article by Hillier and Pedula (1). The authors stated that, so far, no study has evaluated baseline metabolic profiles in a newly diagnosed type 2 diabetic population. However, in Belgium a few years ago, a registration of newly diagnosed people with type 2 diabetes was performed in a network of ∼130 sentinel general practices throughout the country. Due to lack of inscription lists by the family physician in our liberal health care system, the free choice of physician within primary, secondary, and tertiary health care and the dissemination of parts of the medical file over the various health care providers that resulted, it was not easy to collect basic population data about sickness and health. Therefore, this method of registration by volunteering family physicians is the only validated (2,3) method to gather at least some epidemiological primary care figures in Belgium.

Data of 651 patients were registered in two consecutive years, 1997 and 1998. After diagnosis of a new patient with type 2 diabetes, the participating family physician ticked a weekly …
Identification of Necrosis-Associated Genes in Glioblastoma by cDNA Microarray Analysis
Authors: Shaan M. Raza, Gregory N. Fuller, Chang Hun Rhee, Suyun Huang, Kenneth Hess, Wei Zhang, Raymond Sawaya
Journal: Clinical Cancer Research (2004)

Abstract Purpose: In the field of cancer research, there has been a paucity of interest in necrosis, whereas studies focusing on apoptosis abound. In neuro-oncology, this is particularly surprising because of the importance of necrosis as a hallmark of glioblastoma (GBM), the most malignant and most common primary brain tumor, and the fact that the degree of necrosis has been shown to be inversely related to patient survival. It is therefore of considerable interest and importance to identify genes and gene products related to necrosis formation. Experimental Design: We used a nylon cDNA microarray to analyze mRNA expression of 588 universal cellular genes in 15 surgically resected human GBM samples with varying degrees of necrosis. Gene expression was correlated with the degree of necrosis using rank correlation coefficients. The expression of identified genes was compared with their expression in tissue samples from 5 anaplastic astrocytomas (AAs). Immunostaining was used to determine whether genes showing the most positive correlation with necrosis were increasingly expressed in tumor tissues, as grade of necrosis increased. Results: The hybridization results indicated that 26 genes showed significant correlation with the amount of necrosis. All 26 genes had functions associated with either Ras, Akt, tumor necrosis factor α, nuclear factor κB, apoptosis, procoagulation, or hypoxia. Nine genes were positively correlated with necrosis grade, and 17 genes were negatively correlated with necrosis grade. There were significant differences in the median expression levels of 3 of the 26 genes between grade III necrosis GBM and anaplastic astrocytoma (AA) samples; all but 1 of the genes had elevated expression when comparing necrosis grade III with AA samples. Two factors, the ephrin type A receptor 1 and the prostaglandin E2 receptor EP4 subtype, not previously considered in this context, were highlighted because of their particularly high (positive) correlation coefficients; immunostaining showed the products of these two genes to be localized in perinecrotic and necrotic regions and to be overexpressed in grade III GBMs, but not AAs. These two molecules also showed significant correlation with survival of GBM patients (P = 0.0034) in a combined model. Conclusions: The application of cDNA expression microarray analysis has identified specific genes and patterns of gene expression that may help elucidate the molecular basis of necrogenesis in GBM. Additional studies will be required to further investigate and confirm these findings.
Microbial Origins of Chronic Diseases
Authors: Lisa M. Gargano, James M. Hughes
Journal: Annual Review of Public Health (2013)

Chronic diseases such as cardiovascular disease and cancer are among the leading causes of death worldwide and have been on the rise over the past decade. Associations between microbial agents and development of chronic diseases have been made in the past, and new connections are currently being assessed. Investigators are examining the relationship between infectious agents and chronic disease using new technologies with more rigor and specificity. This review examines microbial agents' links to and associations with cardiovascular diseases, cancer, neurodegenerative diseases, renal diseases, psychiatric disorders, and obesity and addresses the important role of the human microbiome in maintenance of health and its potential role in chronic diseases. These associations and relationships will impact future research priorities, surveillance approaches, treatment strategies, and prevention programs for chronic diseases.
Mapping of a Novel Ocular and Cutaneous Malignant Melanoma Susceptibility Locus to Chromosome 9q21.32
Authors: Göran Jönsson, Pär-Ola Bendahl, Therese Sandberg, Azra Kurbasic, Johan Staaf, Lone Sunde, Dorthe G. Crüger, Christian Ingvar, Håkan Olsson, Åke Borg
Journal: JNCI Journal of the National Cancer Institute (2005)

An estimated 10% of all cutaneous malignant melanoma (CMM) cases are inherited, but the genetics of familial CMM are largely unknown. Ocular malignant melanoma (OMM), which is rare, may be associated with familial CMM. We performed a genome-wide scan of two Danish pedigrees with multiple cases of OMM (N = 10) and CMM (N = 3) and other malignancies (with no germline mutations in CDKN2A, CDK4, BRCA1, and BRCA2) to identify melanoma susceptibility genes. Results of parametric linkage analysis are presented as logarithm of the odds (LOD) scores, and all P values are two-sided. Peak two-point parametric LOD score of 2.2 (P = .0007) at D9S167 on chromosome 9q21 was observed. Targeted analysis of a third Danish family with OMM and CMM patients confirmed 9q21 linkage, providing a combined four-point parametric LOD score of 3.02 (nominal P = .00003 and genome-wide P = .086). Two families shared a common haplotype comprising three adjacent and highly polymorphic markers, limiting the region to less than 5 cM and 3 Mbp at 9q21.32. Expression of RASEF, a known gene in this region, was examined in tumor tissue from 10 sporadic CMM lesions and was found to be decreased in 70% of these tumors compared with RASEF expression in a human reference RNA pool from 10 different cell types and in 10 breast tumors.
Fatal outcomes in patients with community acquired pneumonia
Authors: Rustem Khamitov
Journal: European Respiratory Journal (2013)

The community acquired pneumonia (CAP) is one of the frequent respiratory diseases and the leading cause of death in structure of infectious pathology in Russia. Objective. Fatal outcomes from community acquired pneumonia (CAP) for a year were analyzed in the main hospitals of Kazan (big Russian industrial center with the population more than 1 million people).  Methods. The objects of research were case histories of 56 inpatients with lethal outcomes from a severe CAP (45 men and 11 women) at the age of 44 years on the average.  Results. Patients have been hospitalized on 5th day of disease. Outpatient treatment was provided only on 9%. The bilateral pneumonia was in 59% of cases. 80% of patients had the signs of accompanying gastrointestinal diseases of alcohol genesis. Cardiovascular pathology was on the 2nd place (52%). Drug dependent patients compiled 23%. 12% patients were HIV infected. Patient9s severity was estimated without using of severity indexes and was inadequate in 50%. Defects of antibacterial treatment were important: monotherapy in 27% of cases, inadequate daily doses – 25%, inadequacy of the antibiotic changing - 5%, inadequate ways of introduction – 49 %. The late patient9s arriving in the Intensive Care Unite was in 45%.  Conclusions. In the course of the research threatening factors of fatal outcomes were revealed: late hospitalization, inadequate estimation of patient9s severity, accompanying diseases, and defects of antibacterial therapy. All of these factors should be foreseen in the treatment of the patients with a severe CAP.
Revising Expectations from Rapid HIV Tests in the Emergency Department
Authors: Rochelle P. Walensky, Christian Arbelaez, William M. Reichmann, Ron M. Walls, Jeffrey N. Katz, Brian L. Block, Matthew Dooley, Adam Hetland, Simeon Kimmel, Jessica D. Solomon, Elena Losina
Journal: Annals of Internal Medicine (2008)

Background: Expanded HIV screening efforts in the United States have increased the use of rapid HIV tests in emergency departments. The reported sensitivity and specificity of rapid HIV tests exceed 99%. Objective: To assess whether a reactive rapid oral HIV test result correctly identifies adults with HIV infection in the emergency department. Design: Diagnostic test performance assessment within the framework of a randomized, clinical trial. Setting: Brigham and Women's Hospital emergency department (Boston, Massachusetts) from 7 February to 1 October 2007. Patients: 849 adults with valid rapid oral HIV test results. Intervention: Rapid HIV testing with the OraQuick ADVANCE Rapid HIV-1/2 Antibody Test (OraSure Technologies, Bethlehem, Pennsylvania). Patients with reactive rapid test results were offered enzyme-linked immunoassay, Western blot, and plasma HIV-1 RNA testing for confirmation. Measurements: Specificity and positive likelihood ratio. Results: 39 patients had reactive results (4.6% [95% CI, 3.2% to 6.0%]). On confirmation, 5 patients were HIV-infected (prevalence, 0.6% [CI, 0.1% to 1.1%]) and 26 were non–HIV-infected (8 patients declined confirmation). The estimated rapid test specificity was 96.9% (CI, 95.7% to 98.1%). Sensitivity analyses of the true HIV status of unconfirmed cases and test sensitivity resulted in a positive likelihood ratio of 8 to 32. Western blot alone as a confirmation test provided conclusive HIV status in only 50.0% (CI, 30.8% to 69.2%) of patients at first follow-up. The addition of HIV-1 RNA testing to the confirmation protocol improved this rate to 96.2% (CI, 88.8% to 100.0%). Limitation: Test sensitivity cannot be assessed because nonreactive OraQuick test results were not confirmed. Conclusion: Although patients with a reactive oral OraQuick HIV screening test in the emergency department had an 8- to 32-fold increased odds of HIV infection compared with the pretest odds, the specificity of the test was lower than anticipated.
Gallstones after ileostomy and ileal resection.
Authors: G L Hill, W S Mair, J C Goligher
Journal: Gut (1975)

One hundred and eight patients with ileostomies were investigated for cholelithiasis at routine annual review in a large Ileostomy Clinic. Gallstones were demonstrated in 24-5%, which is three times the incidence that might have been expected in a population of this age and sex distribution. The frequency of cholelithiasis was significantly increased in those patients who had lost more than 10 cm of ileum at operation, regardless of whether the primary condition had been ulcerative colitis or Crohn9s disease. It was significantly increased in those patients who had had a resection of less than 10 cm of ileum if the original condition had been Crohn9s disease, but not if it had been colitis.
An enhancer factor defect in a mutant Burkitt lymphoma cell line.
Authors: W Koch, S Candeias, J Guardiola, R Accolla, C Benoist, D Mathis
Journal: The Journal of Experimental Medicine (1988)

RJ 2.2.5 is an immunoselected mutant of the Burkitt lymphoma line Raji. It fails to display MHC class II antigens at the cell surface due to a transcriptional defect. We have identified the function of a regulatory factor that is defective in RJ 2.2.5 cells; this factor is absolutely required for the activity of an MHC class II gene enhancer.
WT1, a Multiform Protein. Contribution of Genetic Models to the Understanding of its Various Functions
Authors: Marie Claire Gubler
Journal: Journal of the American Society of Nephrology (2002)

WT1 was initially identified as a Wilms tumour suppressor gene through the study of children presenting the contiguous gene syndrome WAGR ( W ilms tumor, A niridia, G enitourinary malformations, mental R etardation) due to large constitutional deletions of DNA in band 11p13 ([1][1],[2][2]). This 10-
The challenge and promise of anti-epileptic therapy development in animal models
Authors: Michele Simonato, Amy R Brooks-Kayal, Jerome Engel, Aristea S Galanopoulou, Frances E Jensen, Solomon L Moshé, Terence J O'Brien, Asla Pitkanen, Karen S Wilcox, Jacqueline A French
Journal: The Lancet Neurology (2014)
Prevalence of atopy, asthma symptoms and diagnosis, and the management of asthma: comparison of an affluent and a non-affluent country
Authors: A. O. Faniran, J. K Peat, A. J Woolcock
Journal: Thorax (1999)

<h3>BACKGROUND</h3> The prevalence of childhood asthma and of atopy varies widely between countries. However, few studies have compared the pattern of diagnosis and management of asthma, or the role of atopy in predisposing to asthma between a less affluent country and a more affluent country. The aim of this study was to compare the prevalence of symptoms, diagnosis, and management of asthma, and the prevalence of atopy as measured by skin prick tests in Nigeria and Australia using a standardised methodology. <h3>METHODS</h3> Respiratory history was collected using a validated questionnaire administered to parents, and atopy was measured with skin prick tests in 654 Australian and 566 Nigerian children aged 8–11 years (70% consent rate in Australia, 60% in Nigeria). <h3>RESULTS</h3> Wheeze and persistent cough were less prevalent in Nigeria (10.2% and 5.1%, respectively) than in Australia (21.9% and 9.6%, respectively), caused less morbidity, and were less likely to be labelled or treated as asthma than in Australia. There was no significant difference in the overall prevalence of atopy between the two countries (Australia 32.5%, Nigeria 28.2%). Atopy was a strong risk for wheeze in both countries (odds ratio (OR) 3.4 (95% CI 2.3 to 5.1) in Australia, 1.8 (95% CI 1.0 to 3.3) in Nigeria), especially atopy to house dust mites (OR 3.1 (95% CI 2.1 to 4.7) in Australia, 2.4 (95% CI 1.3 to 4.3) in Nigeria). <h3>CONCLUSION</h3> Although there was a similar prevalence of atopy in both countries, Australian children had a higher prevalence of asthma symptoms. Further studies are needed to determine why atopic children in Australia are more at risk of developing asthma. Such studies will have important implications for the prevention of asthma.
Perioperative chemotherapy with FOLFOX4 and surgery versus surgery alone for resectable liver metastases from colorectal cancer (EORTC Intergroup trial 40983): a randomised controlled trial
Authors: Bernard Nordlinger, Halfdan Sorbye, Bengt Glimelius, Graeme J Poston, Peter M Schlag, Philippe Rougier, Wolf O Bechstein, John N Primrose, Euan T Walpole, Meg Finch-Jones, Daniel Jaeck, Darius Mirza, Rowan W Parks, Laurence Collette, Michel Praet, Ullrich Bethe, Eric Van Cutsem, Werner Scheithauer, Thomas Gruenberger
Journal: The Lancet (2008)
Ligand-Binding Proteins: Their Potential for Application in Systems for Controlled Delivery and Uptake of Ligands
Authors: Frits A. de Wolf, Gary M. Brett
Journal: Pharmacological Reviews (2000)

Unstable or harmful agents, such as drugs, vitamins, flavors, pheromones, and catalysts, for use in pharmaceutics, personal care, functional foods, crop protection, laboratories, offices, and industrial processes, require stabilization against oxidation and degradation or shielding from sensitive environments. Therefore, binding them to carriers with high affinity and selectivity for targeting to the right environment and subsequent controlled release is beneficial, especially if this allows improved control of (stimulus-induced) release. Proteins often possess one or more of these properties, whereas modern biotechnology and bioinformatics provide an increasing number of tools to engineer and adapt these properties. Carrier systems are now developed that incorporate proteins as the central ligand-binding component, e.g., lectins for glucose-triggered release of glycosylated insulin and bispecific antibodies for brain targeting of drugs, but ligand-binding proteins can potentially be used in many other applications. Collectively, the proteins available in nature bind an impressive variety of ligands and non-natural analogs. In this light, various ligand-binding protein classes are surveyed, including biotin-, lipid-, immunosuppressant-, insect pheromone-, phosphate-, and sulfate-binding proteins, as well as bacterial periplasmic proteins, lectins, serum albumins, immunoglobulins, and inactivated enzymes. Disadvantages, such as enzymatic degradation or immunogenicity, associated with the pharmaceutical use of certain proteins can be avoided by incorporating these proteins in more complex carrier and targeting systems. In other applications, this may not be necessary. The enclosure of high-affinity (potentially stimulus-sensitive) binding proteins within an envelope that acts as a diffusion barrier for the ligand may provide excellent slow release. Many possibilities seem to be as yet unexplored.
HBsAg seroclearance with NUCs: rare but important
Authors: Markus Cornberg, Christoph Höner zu Siederdissen
Journal: Gut (2014)

A major breakthrough in the treatment of chronic hepatitis B virus (HBV) infection had been the approval of nucleoside and nucleotide analogues (NUCs), which inhibit the reverse transcriptase and, thereby, dramatically suppress HBV DNA. To date, five NUCs are approved for the treatment of hepatitis B, with tenofovir and entecavir considered as first-line therapy.1 Treatment with tenofovir or entecavir leads to viral suppression below the limit of detection in almost 100% of adherent patients.1 This is associated with regression of fibrosis or even cirrhosis.2 ,3 Furthermore, some studies suggest a lowered incidence of hepatocellular carcinoma (HCC) with long-term NUC treatment. However, a significant risk for HCC development remains despite low HBV DNA, especially in patients with cirrhosis.4 Data from the REVEAL study suggest that higher HBsAg in low viremic patients is associated with an increased risk for HCC, underlining the importance of HBsAg as a complement to HBV DNA in risk stratification.5 One important limitation of NUC therapy is that treatment duration is indefinite in most cases. Guidelines suggest that NUCs can only safely be stopped 12 months after anti-HBe seroconversion in HBeAg-positive patients, or if HBsAg seroclearance is achieved.1 However, relapse after anti-HBe seroconversion can be frequent, and limited data exist if NUC-induced HBsAg seroclearance is stable and associated with an improved outcome.1 So far, only reports on spontaneous or interferon α (IFN)-induced HBsAg …