tbuckley/cabot-search huggingface dataset:
Eosinophilia predicts poor outcome after lung transplantation
Authors: Stijn Verleden, David Ruttens, Elly Vandermeulen, Bart Vanaudenaerde, Dirk Van Raemdonck, Robin Vos, Geert Verleden
Journal: European Respiratory Journal (2013)

Eosinophils are involved in the pathophysioloy of many respiratory diseases but the role of eosinophilia in lung transplantation has never been investigated in full. Our aim was to investigate the impact of BAL eosinophilia on outcome.  A retrospective analysis of our BAL and patient database was performed for all patients transplanted between 2001 and 2011 with follow-up until 2012. Using a cut-off ≥2% eosinophilia in BAL, BOS free survival and overall survival was compared between 66 patients having a BAL with eosinophils ≥2% and 253 control patients (never BAL ≥2%).  Patients with eosinophilic BAL had worse BOS-free survival and overall survival (both p  BAL eosinophilia ≥2% predicted poor outcome in our lung transplant cohort. BOS-free survival and overall survival were significantly lower compared to controls (never BAL eosinophilia ≥2%). Eosinophils especially predisposed to RAS, which implicates that RAS might work via another immunological mechanism.
First Insights into the Viral Communities of the Deep-Sea Anoxic Brines of the Red Sea
Authors: André Antunes, Intikhab Alam, Marta Filipa Simões, Camille Daniels, Ari J.S. Ferreira, Rania Siam, Hamza El-Dorry, Vladimir B. Bajic
Journal: Genomics Proteomics & Bioinformatics (2015)

Abstract The deep-sea brines of the Red Sea include some of the most extreme and unique environments on Earth. They combine high salinities with increases in temperature, heavy metals, hydrostatic pressure, and anoxic conditions, creating unique settings for thriving populations of novel extremophiles. Despite a recent increase of studies focusing on these unusual biotopes, their viral communities remain unexplored. The current survey explores four metagenomic datasets obtained from different brine–seawater interface samples, focusing specifically on the diversity of their viral communities. Data analysis confirmed that the particle-attached viral communities present in the brine–seawater interfaces were diverse and generally dominated by Caudovirales, yet appearing distinct from sample to sample. With a level of caution, we report the unexpected finding of Phycodnaviridae, which infects algae and plants, and trace amounts of insect-infecting Iridoviridae. Results from Kebrit Deep revealed stratification in the viral communities present in the interface: the upper-interface was enriched with viruses associated with typical marine bacteria, while the lower-interface was enriched with haloviruses and halophages. These results provide first insights into the unexplored viral communities present in deep-sea brines of the Red Sea, representing one of the first steps for ongoing and future sampling efforts and studies.
<scp>ALK</scp>‐positive anaplastic large cell lymphoma presenting with hemophagocytic lymphohistiocytosis
Authors: Mili Shah, Leena Karnik, Elizabet Nadal‐Melsió, Alistair Reid, Radia Ahmad, Barbara J. Bain
Journal: American Journal of Hematology (2015)

ALK-positive anaplastic T cell lymphoma (ALCL) is more common in children than in adults and more common in males than in females 1. Leukemic manifestations, as seen in this patient, are more common in the small cell variant 1. Hemophagocytic lymphohistiocytosis is a life-threatening disorder that can occur in a familial primary form or be a response to infections, rheumatological disorders or neoplasms, particularly T-lineage lymphomas. It has occasionally been reported in association with ALCL.
Fire-eater's lung.
Authors: PE Brander, E Taskinen, B Stenius-Aarniala
Journal: European Respiratory Journal (1992)

Acute pneumonitis following aspiration of petroleum products is usually related to accidental poisonings in children. We describe here two cases of hydrocarbon pneumonitis in fire-eaters, caused by accidental aspiration of petroleum during the performance of fire-eating. Both patients had cough, dyspnoea, chest pain and fever. Chest X-rays showed basal lung infiltrates and, 2 weeks later, pneumatocele formations. Reversible bronchial hyperresponsiveness and restrictive ventilatory limitation were demonstrated in one of the patients. The bronchoalveolar lavage specimen showed cytoplasmic vacuolation of the macrophages and neutrophilia. After treatment with antibiotics and corticosteroids the symptoms disappeared and the lung function values returned to normal within 2-3 weeks. Radiological resolution of the pneumatoceles occurred within 2-12 months.
Postural changes in children with non-cystic fibrosis bronchiectasis
Authors: Baki Umut Tugay, Hülya Arikan, Ugur Özçelik, Nazan Tugay
Journal: European Respiratory Journal (2012)

Bronchiectasis not caused by cystic fibrosis (CF) is often perceived to be rare in western societies, but remains an important cause of chronic suppurative lung disease in the developing world among children. Although, the clinical features, radiological, and histological findings in these children was investigated there is not enough knowledge about the musculoskeletal consequences of the disease. Therefore the aim of this study is to document the musculoskeletal affects of the disease process. 24 patients with non-CF bronchiectasis (mean age 13,2(3,4) years) participated in the study. Anterior, posterior and lateral postural analyses was performed and thoracic kyphosis angle was measured from lateral chest X-Rays. 4 (16.7%) patients had kyphosis (over 35 degrees) and mean angle of thoracic curve was 28.5(5.1) degrees. There was scoliosis in 3 (12.5 %) of the children. Bilateral pes planus was present in 8 (33.3 %) patients. There was barrel chest deformity in 7 (29.2 %), pectus carinatum deformity in 2 (8.3 %) and pectus excavatum deformity in 4 (16.7 %) patients. 17 (70 %) patients had also protracted shoulders. Our results indicate a high rate of postural deformities or adaptations especially in the upper body of the patients with non-CF bronchiectasis. Since the upper body posture is carefully related to the pulmonary functions these changes should be closely monitored as soon as the patients are diagnosed and necessary preventive and corrective physiotherapy programs must be initiated.
Ultrastructural Analysis of the Early Development of Teratocarcinomas&lt;xref ref-type="fn" rid="FN1"&gt;2&lt;/xref&gt;
Authors: G. B. Pierce, L. C. Stevens, P. K. Nakane
Journal: JNCI Journal of the National Cancer Institute (1967)

Genital ridges of 12-day embryos of strain 129 mice were transplanted into the testes of adult mice of the same strain. Of the transplants that differentiated into fetal testes, 80% contained intratubular teratocarcinomas by the 7th day after transplantation. These teratocarcinomas were studied ultrastructurally, daily from the 7th-14th day following transplantation, to gain information about the histogenesis of the tumors and the mode of development of multipotent cells. The embryonal carcinoma cells, which are the stem cells of teratocarcinomas, so closely resembled primordial germ cells that the former appeared to be derived from the latter. The cytoplasm of these multipotential cells was characterized by large numbers of dispersed ribosomes and polysomes with few membranous organelles other than mitochondria. Among the earliest signs of differentiation was the development of rough-surfaced endoplasmic reticulum and Golgi complexes, followed by modification of the plasma membrane.
A phase II study of bortezomib added to standard daunorubicin and cytarabine during induction therapy and to intermediate-dose cytarabine (Int-DAC) for consolidation in patients with previously untreated acute myeloid leukemia (AML) age 60-75 years: CALGB study 10502.
Authors: Eyal C. Attar, Jeffrey L. Johnson, Philip C. Amrein, Gerard Lozanski, Martha Wadleigh, Daniel J. DeAngelo, Jonathan E. Kolitz, Bayard L. Powell, Peter Michael Voorhees, Eunice S. Wang, William G. Blum, Guido Marcucci, Clara D. Bloomfield, Barry K Moser, Richard M. Stone, Richard A. Larson
Journal: Journal of Clinical Oncology (2012)

6526 Background: We conducted a clinical trial to determine the complete remission (CR) rate in older AML patients treated with bortezomib (Bz) plus daunorubicin and cytarabine induction therapy and the maximal tolerated dose (MTD) of Bz when added to Int-DAC consolidation therapy. Methods: Ninety-five adults (60-75 yrs old; median, 67) with previously untreated AML (including therapy-related and prior MDS) received Bz 1.3 mg/m 2 IV on days 1, 4, 8 and 11 with daunorubicin 60 mg/m 2 on days 1-3 and cytarabine 100 mg/m 2 by continuous IV infusion on days 1-7. Patients who achieved a CR received 2 courses of consolidation chemotherapy with cytarabine 2 gm/m 2 over 3 hours on days 1-5 (Int-DAC) with Bz administered on days 1, 4, 8 and 11. Three cohorts with escalating dose levels of Bz were tested (0.7, 1.0, and 1.3 mg/m 2 ). Dose limiting toxicities were assessed during the first cycle of consolidation. Predictors of response, including CD74 expression, were assessed. Results: The CR frequency was 65% (62/95). An additional 4% (4/95) achieved CR with incomplete platelet recovery. The CR rate according to ELN Genetic Groups was 90% (9/10) for favorable, 71% (12/17) for Int-I, 52% (17/33) for Int-II, and 46% (5/11) for adverse. Six patients had grade 3 sensory neuropathy. There were 6 treatment-related deaths during cycle 1 of induction and 2 during cycle 2. Bz plus Int-DAC proved tolerable at the highest dose tested. The median disease-free (DFS) and overall survivals (OS) for patients on this study were 8.2 and 12.1 months, respectively. Lower CD74 expression was associated with CR/CRp (p=.04) but not with DFS or OS. Conclusions: The addition of Bz 1.3 mg/m 2 IV on days 1, 4, 8, and 11 to standard “3 + 7” daunorubicin and cytarabine induction chemotherapy for AML is well tolerated and results in a remission rate at least as high as would be expected with ”3+7” alone in older patients. The maximum tested dose of Bz given in combination with Int-DAC for remission consolidation was 1.3 mg/m 2 and proved to be tolerable. Further testing of this regimen in a phase III study is planned.
The Engineering of Gene Regulatory Networks
Authors: Mads Kærn, William J. Blake, J.J. Collins
Journal: Annual Review of Biomedical Engineering (2003)

▪ Abstract The rapid accumulation of genetic information and advancement of experimental techniques have opened a new frontier in biomedical engineering. With the availability of well-characterized components from natural gene networks, the stage has been set for the engineering of artificial gene regulatory networks with sophisticated computational and functional capabilities. In these efforts, the ability to construct, analyze, and interpret qualitative and quantitative models is becoming increasingly important. In this review, we consider the current state of gene network engineering from a combined experimental and modeling perspective. We discuss how networks with increased complexity are being constructed from simple modular components and how quantitative deterministic and stochastic modeling of these modules may provide the foundation for accurate in silico representations of gene regulatory network function in vivo.
Determinants of prediction of post-operative lung function in patients undergoing surgical lobectomy
Authors: Mariarosaria Calvello, Carola Condoluci, Giuliano Montemurro, Alessandro Di Marco Berardino, Andrea Smargiassi, Riccardo Inchingolo, Anna Rita Larici, Ersilia Devicenti, Giuseppe Corbo, Salvatore Valente
Journal: European Respiratory Journal (2013)

Aim: to evaluate contribution of both CT-virtual lobectomy and anatomic compute in prediction of post-operative FEV1 (poFEV1).

Methods: 31 NSCLC (15 COPD) patients, candidate for surgical lobectomy, underwent lung function tests and CT-scan. CT resected and total lung volumes, without (RLV, TLV) and with emphysema extent correction (RLVe, TLVe), number of resected segments and pre-operative FEV1 (preFEV1) were considered to estimate predicted post-operative FEV1 (ppoFEV1).

We adopted general formula: ppoFEV1= preFEV1 x [1-(resected volume/total volume)] in both anatomic and radiological computing.

Radiological and anatomic methods were performed and the resulting values were compared with poFEV1.

Results: Linear regression analysis of poFEV1 showed significative relationships with ppoFEV1 estimated by anatomic method (R2:0,73) and different radiological approaches considering:

RLVe and TLVe (R2:0,75); RLVe and TLV (R2:0,76); RLV and TLV (R2:0,79).

Multiple regression analysis considering patients with airflow obstruction (FEV1/FVC < 70%) and the numbers of days occurring between surgery and first post-resection functional evaluation (VISITIME) showed:

- anatomic method: R2:0,82;

- RLVe and TLVe: R2:0,81;

- RLVe and TLV: R2:0,82;

- RLV and TLV: R2:0,81.

Conclusions: anatomic and radiological methods to estimate poFEV1 show similar results. Predictive power for poFEV1 of all methods ameliorates considering VISITIME and airflow obstruction.
Consistent Chromosome Abnormalities Associated With Mouse Bladder Epithelial Cell Lines Transformed In Vitro
Authors: John Kenneth Cowell
Journal: JNCI Journal of the National Cancer Institute (1980)

Nine epithelial tumor cell lines that were derived from inbred C57BL/lcrf-at adult male mouse bladder and were transformed in vitro were cytogenetically analyzed. Most cell lines were near-diploid and showed only minor karyotypic deviations from normal. Tetraploid cell lines showed duplication of chromosome markers, which suggested that they arose originally as near-diploid cell lines with minor karyotypic changes. Chromosome abnormalities were consistent among different cell lines and involved chromosomes #6, #3, and #15. The Y-chromosome was frequently missing. Identical chromosome abnormalities were present in cell lines that arose in control, dimethyl sulfoxide-treated, or 7,12-dimethylbenz[a]anthracene-treated cultures. The most frequent abnormality was the presence of three copies (trisomy) of chromosome #6. Few structural chromosome abnormalities were detected, although a marker chromosome derived from chromosome #3 was present in several cell lines. Two cell lines had excesses of chromosome #15. These results suggest that excesses of individual chromosomes or parts of chromosomes, particularly chromosome #6, may be important in the expression of the malignant phenotype in mouse bladder epithelium.
Quantitation of Secretory Component Levels in Cyst Fluids, Ascitic Fluids, and Sera From Ovarian Adenocarcinoma Patients2
Authors: Jerry L. Klein, Stanley A. Gall, Jeffrey R. Dawson
Journal: JNCI Journal of the National Cancer Institute (1978)

A secretory component (SC) was detected by radioimmunoassay in the cyst fluids, ascitic fluids, and sera from patients with ovarian adenocarcinomas. Serous cyst fluids and ascitic fluids showed lower levels (expressed as means± se) of SC (1.37±0.37 and 1.24±0.24 μg/ml, respectively) than mucinous cyst fluids (181.50±50.40 μg/ml). SC levels in the sera of all patients with ovarian adenocarcinoma were high (12.67±1.43 μg/ml) when compared to SC levels in the sera of normal individuals (2.34±0.41 μg/ml). Sera from patients with ovarian cancers diagnosed as serous, mucinous, papillary, and poorly differentiated adenocarcinomas showed SC levels of 9.93±1.68, 22.44±3.24, 7.35±1.13, and 10.1011.58 μg/ml, respectively.
Effect of high-flow nasal cannula on nasopharyngeal airway pressure, respiratory muscles loading and respiratory distress symptoms in young infants with severe acute viral bronchiolitis
Authors: Stefan Matecki, Christophe Milesie, Julien Baleine, Aurélien Jacquot, Gilles Cambonie
Journal: European Respiratory Journal (2012)

Objective: To determine the efficacy of high-flow nasal cannula (HFNC) at different flow level on respiratory distress symptoms, nasopharyngeal airway pressure (NAP) and respiratory effort in young infants with acute respiratory syncytial virus bronchiolitis.  Patients: 21 less than six month/old infants, with severe respiratory distress.  Interventions: Oesophageal pressure (Pes) and NAP was measured simultaneously after 5 different flow of 1,4,6 and 7 l/mn delivered through a HFNC.  Measurements and results: Respiratory distress was quantified with a specific scoring system (m-WCAS). Mean respiratory rate (RR), inspiratory time over total time or respiratory cycle (Ti/Tot), NAP, Swing Pes and respiratory effort with the Pes-derived inspiratory muscles pressure-time product (PTPes) was calculated from the pressure curves.  Results are presented in Table 1.  Conclusion: In young infants with severe acute respiratory syncytial virus bronchiolitis NAP progressively increase with flow delivery through HFNC. We observed a negative correlation between flow delivery, NAP and PTPes. HFNC are able to increase NAP, decrease PTPes and improve ventilatory function of infant with severe acute viral bronchiolitis.  Funding by APARD and CHU Montpellier.
Hydrogen Sulfide Promotes Tet1- and Tet2-Mediated Foxp3 Demethylation to Drive Regulatory T Cell Differentiation and Maintain Immune Homeostasis
Authors: Ruili Yang, Cunye Qu, Yu Zhou, Joanne E. Konkel, Shihong Shi, Yi Liu, Chider Chen, Shiyu Liu, Dawei Liu, Yibu Chen, Ebrahim Zandi, Wanjun Chen, Yanheng Zhou, Songtao Shi
Journal: Immunity (2015)
Genes that Affect Brain Structure and Function Identified by Rare Variant Analyses of Mendelian Neurologic Disease
Authors: Ender Karaca, Tamar Harel, Davut Pehlivan, Shalini N. Jhangiani, Tomasz Gambin, Zeynep Coban Akdemir, Claudia Gonzaga-Jauregui, Serkan Erdin, Yavuz Bayram, Ian M. Campbell, Jill V. Hunter, Mehmed M. Atik, Hilde Van Esch, Bo Yuan, Wojciech Wiszniewski, Sedat Isikay, Gozde Yesil, Ozge O. Yuregir, Sevcan Tug Bozdogan, Huseyin Aslan, Hatip Aydin, Tulay Tos, Ayse Aksoy, Darryl C. De Vivo, Preti Jain, B. Bilge Geckinli, Ozlem Sezer, Davut Gul, Burak Durmaz, Ozgur Cogulu, Ferda Ozkinay, Vehap Topcu, Sukru Candan, Alper Han Cebi, Mevlit Ikbal, Elif Yilmaz Gulec, Alper Gezdirici, Erkan Koparir, Fatma Ekici, Salih Coskun, Salih Cicek, Kadri Karaer, Asuman Koparir, Mehmet Bugrahan Duz, Emre Kirat, Elif Fenercioglu, Hakan Ulucan, Mehmet Seven, Tulay Guran, Nursel Elcioglu, Mahmut Selman Yildirim, Dilek Aktas, Mehmet Alikaşifoğlu, Mehmet Ture, Tahsin Yakut, John D. Overton, Adnan Yuksel, Mustafa Ozen, Donna M. Muzny, David R. Adams, Eric Boerwinkle, Wendy K. Chung, Richard A. Gibbs, James R. Lupski
Journal: Neuron (2015)
Features and treatment outcome in caseous pneumonia
Authors: Evelina Lesnic, Olga Caraiani, Vasile Zlepca
Journal: European Respiratory Journal (2012)

Caseous pneumonia is a clinical X-ray form of infiltrative TB or a complication of the acute progression of fibro-cavitary TB.  Aim of stady is evaluation of features and treatment outcome in CP. A retrospective study included 95 patients with CP. Most of them (84%), were new cases of infiltrative TB and 16% fibro-cavitary TB. New-onset TB were 70% cases, relapse cases were 21%, after treatment failure 7% and after default 2%. Male/female ratio was 2/1, average age 42,6 yrs, unemployed 64%, disease disabled 11%, with bad living conditions 72%, homeless 10%, with medium level of education 59%. Regarding the way of detection, all were detected passively, 68% were late detected (average time 6 weeks). Regarding clinical picture, 77% had well-defined respiratory syndrome and 85% intoxication syndrome. Co-morbidities had 40% cases (alcoholism 19%, hepatitis 11%, diabetes 7%, HIV-infection 4%). Hematological predominates anemia in 61% cases, lymphocytosis 48%, lymphopenia 51%, increased ADA 42%. Radiological were revealed destructive lesions in 90% with bilateral localization in 89%, involving more 3 lobes in all cases. At the detection, smear positive for acid-fast bacilli were 83%, culture positive 84%. Primary drug resistance was identified in 34% cases. Conversion rate of smear positive patients at 2 months of treatment was 56%. DOTS received 91%, individualized treatment 9%, compliant with treatment were 84% cases. Treatment outcome: anti-TB treatment completed 61%, dead 23%, treatment failure 12%, default 4%. Features that affect the outcome of CP are: late detection, co-morbidities (associated with low economical status), previous anti-TB treatment, high rate of primary resistance, bilateral involving.
Role of cryptic genes in microbial evolution.
Authors: B G Hall, S Yokoyama, D H Calhoun
Journal: Molecular Biology and Evolution (1984)

Cryptic genes are phenotypically silent DNA sequences, not normally expressed during the life cycle of an individual. They may, however, be activated in a few individuals of a large population by mutation, recombination, insertion elements, or other genetic mechanisms. A consideration of the microbial literature concerning biochemical evolution, physiology, and taxonomy provides the basis for a hypothesis of microbial adaptation and evolution by mutational activation of cryptic genes. Evidence is presented, and a mathematical model is derived, indicating that powerful and biologically important mechanisms exist to prevent the loss of cryptic genes. We propose that cryptic genes persist as a vital element of the genetic repertoire, ready for recall by mutational activation in future generations. Cryptic genes provide a versatile endogenous genetic reservoir that enhances the adaptive potential of a species by a mechanism that is independent of genetic exchange.
Factors associated with compliance with palivizumab treatment in the Canadian rSV evaluation study for synagis (CARESS) registry (32005-2011)
Authors: Ian Mitchell, Bosco Paes, Abby Li, Krista Lanctot
Journal: European Respiratory Journal (2012)

Objective: Determine factors affecting compliance in palivizumab use.  Methods: Registry of infants who received >1 dose of palivizumab during 6 RSV seasons. Demographic data collected at enrolment. Data on palivizumab utilization, compliance, and outcomes (respiratory illness - RI) collected monthly. Complianc interval between doses, and percentage of expected injections received.  Results: 10,452 infants enrolled, 7492 (71.7%) complied with timing of doses. 91.9%±27.1% of expected injections received. Greater proportion of non-compliant infants were hospitalized for RI (7.5% versus 6.0%, p=0.005), compliance did not affect RSV-positive hospitalizations (1.79% versus 1.53%, p=0.177). Compliant infants (all [ 5 household individuals (23.9% versus 21.7). More non-compliant infants had smoke exposure (30.5% versus 28.4%, p=0.033). Six factors influenced compliance in regression analysis: age (HR=0.989, 95%CI 0.982-0.996, p=0.002), siblings (HR=1.104, 95%CI 1.007-1.211, p=0.034), >5 household individuals (HR=1.114, 95%CI 1.001-1.241, p=0.047), smoke exposure (HR=0.891, 95%CI 0.811-0.980, p=0.018) and CHD (HR=0.805, 95%CI 0.700-0.927, p=0.002), and RI-related hospitalization (HR=0.837, 95%CI 0.705-0.903, p=0.041).  Conclusions: Siblings and >5 household individuals is associated with increased treatment compliance; being older, smoke exposure, having CHD and being hospitalized with decreased compliance.
Decrease of Tumor Growth in Mice After Intravenous Thymosin-Treated Bone Marrow Cell Injection&lt;xref ref-type="fn" rid="FN2"&gt;2&lt;/xref&gt;
Authors: Didier Cupissol, Augustin Rey, Allan L. Goldstein, Bernard Serrou
Journal: JNCI Journal of the National Cancer Institute (1982)

The effect of iv injection in C57BL/6 mice of 3×107 bone marrow cells preincubated in either thymosin fraction V or thymosin α-1 was evaluated on the growth of a 3-methylcholanthrene-induced transplantable tumor in a syngeneic system. The effect was then compared to that elicited by theophylline or levamisole, which both demonstrated thymosin-like action in vitro. The results showed significantly retarded tumor growth (P<0.001) and prolonged survival time (P<0.001) when thymosin fraction V was used. The same results were obtained with thymosin α-1 with use of the same protocol but only one-twentieth of the concentration of fraction V. Theophylline and levamisole demonstrated no antitumor effect.