tbuckley/cabot-search huggingface dataset:
The significance of the number of submitted samples and patient-related factors for faecal bacterial diagnostics
Authors: S. Ethelberg, K.E.P. Olsen, P. Gerner-Smidt, K. Mølbak
Journal: Clinical Microbiology and Infection (2007)

The sensitivity of bacteriological testing of faecal samples from patients with diarrhoea has not been properly determined. The present study analysed the association between the results of stool sample examinations and the number of samples examined per patient and other patient-related factors. Data concerning faecal specimens referred for culture for enteric bacterial pathogens (Campylobacter, Salmonella, Shigella and Yersinia) to the central microbiological laboratory in Denmark between 1995 and 2003 were analysed. In total, 620 000 samples were sorted into 277 000 sample-series, i.e., samples submitted from the same individual on the same day. Data were analysed by multivariate logistic regression, with the outcome being a positive sample-series, i.e., one or more positive samples per series. Overall, 11.9% of the sample-series were positive. For adults (aged > or =18 years), the OR for a positive diagnosis was 1.20 (95% CI 1.18-1.21) for each additional sample. Positive diagnoses were also more likely during summer, if the patient was male, or if the patient was neither very young nor very old. The added diagnostic effect of additional samples was more pronounced for the group of patients with persistent (>2 weeks) diarrhoea. Overall, the probability of finding common pathogenic bacteria in faecal samples was found to vary according to the number of samples, the season and the patient's age and gender. Analysis of more than one sample improves the sensitivity of faecal culture by at least 20% for each additional sample.
Immunologic Induction of Malignant Lymphoma: Genetic Factors in the Graft-Versus-Host Model&lt;xref ref-type="fn" rid="FN1"&gt;2&lt;/xref&gt;
Authors: Ernst Gleichmann, Helga Gleichmann, Robert S. Schwartz
Journal: JNCI Journal of the National Cancer Institute (1972)

The development of malignant lymphomas was studied in 47 different donor-recipient pairs undergoing a chronic graft-versus-host reaction, which was induced in F1 hybrid mice by the injection of parental spleen cells. None of the H-2 compatible combinations developed lymphomas. The development of neoplasms in H-2 incompatible pairs was inhibited by maneuvers designed to diminish the immunologic response of the graft against the host. Whether lymphomas developed in a given donorrecipient pair appeared to depend on: a) a major antigenic (H-2) difference between donor and recipient; b) the inherent (genetic?) ability of the donor' s immunocytes to respond to the recipient' s antigens; and c) a factor in the recipient, which probably determines susceptibility to oncogenic viruses.
SAR650984 directly induces multiple myeloma cell death via lysosomal-associated and apoptotic pathways, which is further enhanced by pomalidomide
Authors: H Jiang, C Acharya, G An, M Zhong, X Feng, L Wang, N Dasilva, Z Song, G Yang, F Adrian, L Qiu, P Richardson, N C Munshi, Y-T Tai, K C Anderson
Journal: Leukemia (2015)
Comparison of SAPADIA and ECCS lung function normal values in a Swiss hospital setting
Authors: Jochen Rüdiger, Florent Baty, Andreas Bloch, Lukas Kern, Tino Schneider, Martin Brutsche
Journal: European Respiratory Journal (2012)

The SAPALDIA survey observed better lung function in healthy volunteers than the common ECCS normal values (ECCS) predicted. We thus introduced the SAPADIA normal values (SAP) for lung function interpretation at the Kantonsspital St. Gallen. We currently analyzed the distribution of FVC and FEV1 in non-pulmonary patients with a normal lung function comparing SAP and ECCS (so far 379 lung functions). Data was analyzed using descriptive statistics, Bland-Altman (BA) analysis and linear regression. Estimated bias and precision were calculated.  For FEV1 we observed a significant difference between ECCS and SAP only in elderly men (>59 y.o.) (7±336 vs. 122±336 ml/s). When comparing FVC using SAP, the Bland Altman analysis revealed a bias, which was significantly lower using ECCS (e.g. in men bias of SAP was 0.33 l (0.27-0.39), bias of ECCS was 0.18 l (0.11-0.24), (fig.1, lower panels).  In summary, SAP tended to overestimate FVC and FEV1 in eldery men compared to ECCS. However, absence of a pulmonary consultation in our population does not exclude a slight impact of the underlying disease on lung function.  We consider SAP for FEV1 and FVC appropriate for the measurement of lung function of our population. Cut-off values require special attention especially in elderly.
IL‐33 facilitates oncogene‐induced cholangiocarcinoma in mice by an interleukin‐6‐sensitive mechanism
Authors: Daisaku Yamada, Sumera I. Ilyas, Nataliya Razumilava, Steven F. Bronk, Jaime I. Davila, Mia D. Champion, Mitesh J. Borad, Jorge A. Bezerra, Xin Chen, Gregory J. Gores
Journal: Hepatology (2015)

Cholangiocarcinoma (CCA) is a lethal hepatobiliary neoplasm originating from the biliary apparatus. In humans, CCA risk factors include hepatobiliary inflammation and fibrosis. The recently identified interleukin (IL)−1 family member, IL‐33, has been shown to be a biliary mitogen which also promotes liver inflammation and fibrosis. Our aim was to generate a mouse model of CCA mimicking the human disease. Ectopic oncogene expression in the biliary tract was accomplished by the Sleeping Beauty transposon transfection system with transduction of constitutively active AKT (myr‐AKT) and Yes‐associated protein. Intrabiliary instillation of the transposon–transposase complex was coupled with lobar bile duct ligation in C57BL/6 mice, followed by administration of IL‐33 for 3 consecutive days. Tumors developed in 72% of the male mice receiving both oncogenes plus IL‐33 by 10 weeks but in only 20% of the male mice transduced with the oncogenes alone. Tumors expressed SOX9 and pancytokeratin (features of CCA) but were negative for HepPar1 (a marker of hepatocellular carcinoma). Substantive overlap with human CCA specimens was revealed by RNA profiling. Not only did IL‐33 induce IL‐6 expression by human cholangiocytes but it likely facilitated tumor development in vivo by an IL‐6–sensitive process as tumor development was significantly attenuated in Il‐6–/– male animals. Furthermore, tumor formation occurred at a similar rate when IL‐6 was substituted for IL‐33 in this model. Conclusion : The transposase‐mediated transduction of constitutively active AKT and Yes‐associated protein in the biliary epithelium coupled with lobar obstruction and IL‐33 administration results in the development of CCA with morphological and biochemical features of the human disease; this model highlights the role of inflammatory cytokines in CCA oncogenesis. (H epatology 2015;61:1627–1642)
Modeling Spontaneous Metastasis following Surgery: An <i>In Vivo-In Silico</i> Approach
Authors: Sebastien Benzekry, Amanda Tracz, Michalis Mastri, Ryan Corbelli, Dominique Barbolosi, John M.L. Ebos
Journal: Cancer Research (2015)

Rapid improvements in the detection and tracking of early-stage tumor progression aim to guide decisions regarding cancer treatments as well as predict metastatic recurrence in patients following surgery. Mathematical models may have the potential to further assist in estimating metastatic risk, particularly when paired with in vivo tumor data that faithfully represent all stages of disease progression. Herein, we describe mathematical analysis that uses data from mouse models of spontaneous metastasis developing after surgical removal of orthotopically implanted primary tumors. Both presurgical (primary tumor) growth and postsurgical (metastatic) growth were quantified using bioluminescence and were then used to generate a mathematical formalism based on general laws of the disease (i.e., dissemination and growth). The model was able to fit and predict pre/postsurgical data at the level of the individual as well as the population. Our approach also enabled retrospective analysis of clinical data describing the probability of metastatic relapse as a function of primary tumor size. In these data-based models, interindividual variability was quantified by a key parameter of intrinsic metastatic potential. Critically, our analysis identified a highly nonlinear relationship between primary tumor size and postsurgical survival, suggesting possible threshold limits for the utility of tumor size as a predictor of metastatic recurrence. These findings represent a novel use of clinically relevant models to assess the impact of surgery on metastatic potential and may guide optimal timing of treatments in neoadjuvant (presurgical) and adjuvant (postsurgical) settings to maximize patient benefit.
Defects in Plasmacytoid Dendritic Cell Expression of Inducible Costimulator Ligand and IFN-α Are Associated in Asthma with Disease Persistence
Authors: Antoine Froidure, Olivier Vandenplas, Vinciane D’Alpaos, Geneviève Evrard, Charles Pilette
Journal: American Journal of Respiratory and Critical Care Medicine (2015)
Carotid Body Tumors in Humans: Genetics and Epidemiology
Authors: D. M. Parry, F. P. Li, Louise C Strong, J. A. Carney, D. Schottenfeld, R. R. Reimer, S. Grufferman
Journal: JNCI Journal of the National Cancer Institute (1982)

Genetic factors in the etiology of carotid body tumors (CBT) were sought in a medical record review of 222 histologically diagnosed cases at 12 U.S. medical centers. Patients in the series, which had a marked female predominance (146 females:76 males), usually developed tumors between the fourth and seventh decades of life (mean, 44.7 yr). In 16 patients who also had other extra-adrenal paragangliomas, suggesting a multiple primary tumor syndrome, CBT were diagnosed significantly earlier (mean, 35.4 yr; P less than 0.01). The occurrence of thyroid cancer in 5 other patients appeared to be excessive. Familial CBT was recognized in 16 patients from 13 affected families, including 9 newly ascertained kindreds. Compared with non-familial lesions, familial CBT tended to develop bilaterally (38% vs. 8% unilaterally) and at slightly earlier ages (41.6 vs. 44.9 yr). CBT was reported to occur in an autosomal dominant pattern in some families and within sibships in others; relatives were not examined for confirmation. The familial findings are generally consistent with a two-step mutation model of the development of hereditary and nonhereditary CBT; apparent deviations from the model might be clarified with additional data on this rare neoplasm.
Tissue-Specific Antibodies Against Human Lung and Breast Carcinoma Dehistonized Chromatins2
Authors: Jen-Fu Chiu, Lubomir S. Hnilica, Frank Chytil, John T. Orrahood, Lowell W. Rogers
Journal: JNCI Journal of the National Cancer Institute (1977)

Tissue-specific antisera against human lung and breast carcinoma dehistonized chromatins were obtained. The specificity of these antisera was determined by complement fixation. In the presence of antiserum against human lung carcinoma, only chromatins from lung carcinoma fixed complement significantly, whereas chromatins isolated from human breast carcinoma, HeLa cells, normal lung tissue, breast tissue, or term placenta were negative (i.e., inactive). In a similar assay with the use of antiserum against dehistonized breast carcinoma chromatins, only breast carcinoma chromatins fixed complement. Immunohistochemical localization of the antigens by the horseradish peroxidase bridge method demonstrated their presence in the nuclei.
Effect of Ovariectomy at Different Ages on Development of Mammary Tumors in (C3H X RIII)F&lt;sub&gt;1&lt;/sub&gt; Mice&lt;xref ref-type="fn" rid="FN1"&gt;2&lt;/xref&gt;
Authors: F L Richardson
Journal: JNCI Journal of the National Cancer Institute (1967)

The rate of development of mammary tumors in (C3H X RIII)F1 hybrid mice ovariectomized at 2 months of age was similar to that of mice ovariectomized at 3 months. The increased rate of tumor development in many females ovariectomized at 4 or 5 months over that of females ovariectomized at 2 or 3 months indicates that the ovaries before their removal affected the subsequent development of mammary tumors. In the controls, the mean tumor age was much lower and the tumor incidence higher than in the ovariectomized females. Nodular hyperplasia of the adrenals was present in all tumor-bearing mice spayed at 2 or 3 months of age and in many of those spayed at 4 or 5 months. These findings, with the use of F1 hybrids of C3H female X RIII hermaphrodite, agree with the postulate that hyperplastic adrenals of spayed mice of the C3H strain secrete estrogenic substances capable of inducing mammary tumors.
Abstract 3110: Prevalence and Covariates of Low Left Ventricular Midwall Shortening in Patients with Asymptomatic Aortic Valve Stenosis. A SEAS Substudy
Authors: Dana Cramariuc, Ashild E Rieck, Eva M Staal, Erlend Eriksen, Kristian Wachtell, Eva Gerdts
Journal: Circulation (2006)
Dual TaqMan probes for the detection of rifampin resistance in Mycobacterium tuberculosis
Authors: Veronika Slizen, Larisa Surkova
Journal: European Respiratory Journal (2012)

Mutations (SNP) at codons 526, 531 of rpoB gene of MTB are considered to be biomarkers of resistance to rifampin (RMP). The aim of the study was to develop 96-well plate qPCR platform with dual TaqMan probes for the prediction of RMP resistance in MTB.    Methods.  A total number of 122 DNA extracts from MTB cultures were studied. SNPs in 516, 526, 531 codons of rpoB gene were detected by autosequencing and qPCR with dual TaqMan probes (labeled with FAM and JOE for identification of wild and mutated codons correspondingly).    Results . We present a 96-well PCR plate method for identification of SNPs in rpoB gene of MTB. Each 96-well PCR plate is organized as follows: 1) 12 DNA extracts can be investigated collectively; 2) four wells are used for each DNA extract to identify MTB and mutations in 516, 526, 531 codons; 3) one set of controls per 6 DNA extracts is provided including positive, and negative (with and without mutations), and no-template controls for each codon tested. The entire assay includes the following steps:1) filling wells with DNA-extracts and PCR reaction mixtures using repeater pipette; 2) amplification and data bioanalysis including: a) detection of fluorescence threshold using method of negatives with 20% tolerance; b) allele discrimination analysis based on detection of differences in JOE and FAM fluorescence. The results obtained with this real time PCR design agreed well with DNA sequencing data. Out of 122 DNA extracts (488 reactions) 8 samples were false negative (7%) versus sequencing data. This 96-well PCR plates diagnostic platform resembles ELISA and represents an adequate method for the specific and rapid detection of RMP resistance in MTB cultures.
Neuropeptide blood levels correlate with mast cell load in patients with mastocytosis
Authors: L. Maintz, E. Wardelmann, K. Walgenbach, R. Fimmers, T. Bieber, U. Raap, N. Novak
Journal: Allergy (2011)

To cite this article: Maintz L, Wardelmann E, Walgenbach K, Fimmers R, Bieber T, Raap U, Novak N. Neuropeptide blood levels correlate with mast cell load in patients with mastocytosis. Allergy 2011; 66: 862–869. Abstract Background: Mastocytosis is characterized by abnormal growth and accumulation of mast cells (MCs) in different organs. MCs have been shown to express receptors for neuropeptides. Furthermore, neuropeptides can activate MCs inducing cytokine production and MC mediator release, which further contribute to MC chemotaxis and stimulate the release of vasoactive peptides from sensory nerves. Thus, a contribution of neuropeptides to mastocytosis seems highly conceivable, but has not been investigated sufficiently yet. This study aimed to analyse blood levels of the neuropeptides substance P (SP), somatostatin (SST), vasoactive intestinal peptide (VIP), calcitonine gene–related peptide (CGRP) and expression of the SP receptor NK-1R in the skin of patients with mastocytosis (n = 46) compared to healthy controls (n = 69). Methods: Substance P, SST, VIP and CGRP plasma levels were analysed by ELISA, serum tryptase levels with the UniCAP System and NK-1R expression in the skin by immunohistochemistry. Results: Plasma levels of SP (P < 0.0001), SST, (P = 0.007), VIP (P < 0.0001) and CGRP (P = 0.003) were significantly increased in patients with mastocytosis compared to controls. Tryptase serum levels correlated significantly with neuropeptide levels, implying a link between MC load and neuropeptide blood levels in mastocytosis. NK-1R was expressed on the majority of MCs, and NK-1R-positive cells were increased in lesional mastocytosis skin compared to control skin (P = 0.01). Conclusions: Elevated blood levels of the neuropeptides SP, SST, VIP and CGRP correlate with MC load and together with an increased expression of NK-1R in the skin of patients with mastocytosis indicate a role of neuropeptides in the pathophysiology of mastocytosis.
A newly developed sublingual tonometer and its validation in patients with chronic obstructive pulmonary disease
Authors: Zoltán Rózsavölgyi, Andrea Hajnal, Domokos Boda, Krisztina Boda, Attila Somfay
Journal: European Respiratory Journal (2013)

INTRODUCTION: chronic obstructive pulmonary disease (COPD) is a progressive, insidious disease with slow decline in lung function over many years. Respiratory failure is common in severe stage of COPD and blood gas analysis is required to asses this condition.  AIM: in order to monitor the efficiency of ventilation, a simple, non–invasive, new sublingual method was developed.  METHODS: to validate this method, measurements of carbon dioxide equilibration time using a sublingual tonometer were performed in vitro and in vivo. Tonometric values in volunteers under hyperventilation were also analysed as well as the agreement of parallel data in 42 COPD patients. The sublingual partial pressure of carbon dioxide (PslCO2) was compared to the partial pressure of carbon dioxide of arterialized blood samples (PaCO2) and exhaled breath carbon dioxide (PETCO2) in 10 healthy volunteers and 54 COPD patients.  RESULTS: there was a close agreement (mean ± SD) between PslCO2 and PaCO2 (44.4±9.3 versus 42.7±7.7 mmHg) which did not change across disease severity (GOLD I–IV.) stages (PslCO2–PaCO2: I+II.: 0.8±4.5; III.: 2.3±6.7; IV.: 1.6±4.2 mmHg.). The agreement between the PslCO2 and PaCO2 was confirmed by Bland and Altman analysis (bias: 1.75 mmHg). Parallel measurements of PslCO2 proved the reproducibility of the method.  CONCLUSION: this initial study demonstrates the feasibility of the method suggesting that sublingual tonometry deserves further consideration to be applied in clinical practice in COPD patients with respiratory failure.
Growth of Rous Sarcomas in Bursectomized Chickens&lt;xref ref-type="fn" rid="FN1"&gt;2&lt;/xref&gt;
Authors: William P. McArthur, Elizabeth A. Carswell, G. Jeanette Thorbecke
Journal: JNCI Journal of the National Cancer Institute (1972)

Growth of Rous sarcomas in severely hypogammaglobulinemic and agammaglobulinemic chickens was compared to that in normal chickens. The incidence or development of the tumor did not differ between the 2 groups. These results suggest that “blocking” or “enhancing” antibody is not an important factor in the growth of Rous sarcomas in chickens under the conditions used.
Why are local recurrences after breast-conserving therapy more frequent in younger patients?
Authors: J M Kurtz, J Jacquemier, R Amalric, H Brandone, Y Ayme, D Hans, C Bressac, J M Spitalier
Journal: Journal of Clinical Oncology (1990)

The influence of patient age on risk of recurrence in the breast was retrospectively studied in 496 stage I-II invasive ductal carcinomas treated by macroscopically complete primary tumor excision followed by radiotherapy. With a median follow-up of 71 months, local recurrence occurred in 13 of 62 (21%) patients younger than 40 years, compared with 48 of 434 (11%) older patients (P less than .025). Cox multivariate analysis of 18 parameters identified four that significantly determined risk: major lymphocytic stromal reaction (MCR), unsatisfactory resection margins, increasing histologic grade, and extensive intraductal cancer (DCIS) within the primary tumor. Compared with older patients, those younger than 40 years had tumors that more often exhibited MCR (36% v 20%, P less than .01), histologic grade 3 (42% v 28%, P less than .025), and very extensive DCIS (21% v 6%, P less than .001). The status of resection margins did not differ significantly between younger and older patients. Restriction of Cox analysis to patients younger than 40 indicated that risk was adequately described by MCR and percentage of DCIS, without consideration of grade or margins. For patients younger than 40, local failure occurred in four of five (80%) tumors with both MCR and more than 50% DCIS, in eight of 25 (32%) with either, and one of 32 (3.1%) with neither of these morphologic features. This study suggests that the higher local failure risk observed in patients younger than 40 years reflects the greater prevalence of certain morphologic characteristics in breast cancers in younger patients. Age itself does not appear to be an independent determinate of risk.
Investigation on the effectiveness of the Mostgraph and fractional exhaled nitric oxide measurement in chronic cough
Authors: Chihiro Nakano, Nobuyuki Hatanaka, Toru Yamagishi, Hirotaka Kamemura, Norio Kodaka, Atsuo Miura, Asako Kitahara, Yoshiyuki Kurose, Kayo Sugawa, Kumiko Kashiwa, Yuuki Kamata, Haruhi Hayashi, Manabu Toyoda, Kanako Hirayama, Ken Sanno
Journal: European Respiratory Journal (2012)

Objectives: Mostgraph, Fractional exhaled nitric oxide(FeNO) measurement, and pulmonary function tests were conducted in patients with chronic cough. The effectiveness of Mostgraph, FeNO measurement, and pulmonary function tests were examined in elucidation of pathology, differential diagnosis, and therapy evaluation of chronic cough.

Method s : The subjects were 120 patients who presented with chronic cough. The respiratory resistance measuring device Mostgraph (Chest MI, Inc) was used. For FeNO, NIOX-MINO (Aerocrine) was used. Pulmonary function tests used spirometry. Imaging and blood tests were performed as diagnostic aids. Patients treated with combination of β stimulants and inhaled corticosteroid.

Results : Airway resistance at 5 Hz (Rrs5) and 20 Hz (Rrs20) as well as FeNO tended to increase in patients with chronic cough. Airway resistance and FeNO showed a significant reduction as symptoms improved. Pulmonary function tests showed no significant changes.

Conclusion s : In patients with chronic cough, Rrs5 and Rrs20 increased, and FeNO tended to increase, but decreased with treatment. A combination of Mostgraph and FeNO measurement can be conducted quickly and noninvasively, and this study suggests that this combination may be useful in diagnosis of chronic cough, and in assessing the effectiveness of treatment.