Miracle-dz/UniFAR-FTUs huggingface dataset:
Genotype–phenotype correlation and functional studies in patients with cystic fibrosis bearing CFTR complex alleles

Background The effect of complex alleles in cystic fibrosis (CF) is poorly defined for the lack of functional studies. Objectives To describe the genotype–phenotype correlation and the results of either in vitro and ex vivo studies performed on nasal epithelial cells (NEC) in a cohort of patients with CF carrying cystic fibrosis transmembrane conductance regulator (CFTR) complex alleles. Methods We studied 70 homozygous, compound heterozygous or heterozygous for CFTR mutations: p.[Arg74Trp;Val201Met;Asp1270Asn], n=8; p.[Ile148Thr;Ile1023_Val1024del], n=5; p.[Arg117Leu;Leu997Phe], n=6; c. [1210-34TG[12];1210-12T[5];2930C>T], n=3; p.[Arg74Trp;Asp1270Asn], n=4; p.Asp1270Asn, n=2; p.Ile148Thr, n=6; p.Leu997Phe, n=36. In 39 patients, we analysed the CFTR gating activity on NEC in comparison with patients with CF (n=8) and carriers (n=4). Finally, we analysed in vitro the p.[Arg74Trp;Val201Met;Asp1270Asn] complex allele. Results The p.[Ile148Thr;Ile1023_Val1024del] caused severe CF in five compound heterozygous with a class I–II mutation. Their CFTR activity on NEC was comparable with patients with two class I–II mutations (mean 7.3% vs 6.9%). The p.[Arg74Trp;Asp1270Asn] and the p.Asp1270Asn have scarce functional effects, while p.[Arg74Trp;Val201Met;Asp1270Asn] caused mild CF in four of five subjects carrying a class I–II mutation in trans, or CFTR-related disorders (CFTR-RD) in three having in trans a class IV–V mutation. The p.[Arg74Trp;Val201Met;Asp1270Asn] causes significantly (p<0.001) higher CFTR activity compared with compound heterozygous for class I–II mutations. Furthermore, five of six compounds heterozygous with the p.[Arg117Leu;Leu997Phe] had mild CF, whereas the p.Leu997Phe, in trans with a class I–II CFTR mutation, caused CFTR-RD or a healthy status (CFTR activity: 21.3–36.9%). Finally, compounds heterozygous for the c. [1210-34TG[12];1210-12T[5];2930C>T] and a class I–II mutation had mild CF or CFTR-RD (gating activity: 18.5–19.0%). Conclusions The effect of complex alleles partially depends on the mutation in trans. Although larger studies are necessary, the CFTR activity on NEC is a rapid contributory tool to classify patients with CFTR dysfunction.
Plasma NT‐proBNP and Cell‐Free DNA Concentrations after Prolonged Strenuous Exercise in Working Farm Dogs

Background Plasma N‐terminal pro–B‐type natriuretic peptide (NT‐proBNP) concentration is increased in dogs with myocardial dysfunction, and cell‐free DNA (cfDNA) increases in numerous disease states. In humans, both of these biomarkers can be altered after endurance exercise. Objective To investigate the effect of prolonged strenuous exercise on circulating NT‐proBNP and cfDNA concentrations in working farm dogs. Animals Six healthy, privately owned working farm dogs (4 Huntaways and 2 heading dogs) from the same hill country farm in New Zealand. Methods Prospective, nonrandomised cohort study. Venous blood samples were collected before and after the dogs worked over 4 days. Plasma NT‐proBNP concentrations were measured by a commercially available ELISA assay and cfDNA concentrations were determined by fluorometry without prior DNA extraction. Results The baseline (before work, Day 1) median plasma NT‐proBNP concentration was 664 pmol/L. A linear mixed‐effects model showed that work increased plasma NT‐proBNP concentrations by 101 ± 9% (P < 0.001), but with each consecutive day of work, NT‐proBNP concentrations declined by 16 ± 4% (P < 0.001). The baseline median plasma cfDNA concentration was 653 ng/mL, and plasma cfDNA concentrations increased by 138 ± 45 ng/mL after work (P = 0.004). Conclusions and Clinical Importance The plasma concentration of NT‐proBNP in healthy Huntaways and heading dogs after work can exceed the upper limit of the reference range. Results in dogs sampled on the day of prolonged strenuous exercise should be interpreted with caution. Plasma concentrations of cfDNA also increase with exercise, but further studies are needed to establish reference ranges in healthy dogs.
Effect of Continuous versus Intermittent Subglottic Suctioning on Tracheal Mucosa by the Mallinckrodt TaperGuard Evac Oral Tracheal Tube in Intensive Care Unit Ventilated Patients: A Prospective Randomized Study

Background and Aims: A risk of tracheal mucosa injury induced by subglottic suctioning has been raised. Therefore, this prospective randomized study aims to compare the effect of continuous suctioning of subglottic secretions versus intermittent suctioning of subglottic secretions (CSSS vs. ISSS) secretions on tracheal mucosa in front of the suctioning port of the endotracheal tube. Patients and Methods: Patients requiring intubation or reintubation in Intensive Care Unit with an expected ventilation duration > 24 h were eligible. Participants received CSSS at −20 mmHg or ISSS at −100 mmHg during 15 s and no suction during 8 s. The effect on tracheal mucosa in front of the suction port was assessed after intubation (T0) and before extubation (T1) using bronchoscopy. Tracheal mucosa damages were graded into five categories (no injury, erythema, edema, ulceration, or necrosis). The occurrence (no injury observed at T0 but present at T1) or the worsening (injury observed at T0 exacerbating at T1) was studied. Results: Seventy-three patients were included and 53 patients (CSSS, n = 26 and ISSS, n = 27) were evaluable on the primary endpoint. The occurrence or worsening of tracheal mucosal damages did not differ between the two groups (CSSS, n = 7 [27%] vs. ISSS, n = 5 [17%], P = 0.465). Daily average volume of suctioned secretion was higher with ISSS (74 ± 100 ml vs. 20 ± 25 ml, P < 0.001). Impossibility to aspirate was higher with CSSS (0.14 ± 0.16 per day vs. 0.03 ± 0.07 per day, P < 0.001). Conclusions: Our results suggest that tracheal mucosal damages did not differ between CSSS and ISSS. The aspirated volume was higher and impossibility to aspirate was lower with ISSS. Clinical Trial Registration: ClinicalTrials.gov Identifier: NCT01555229.
OKULLARIN ÖRGÜTSEL KÜLTÜRÜ İLE AKADEMİK İYİMSERLİĞİ ARASINDAKİ İLİŞKİ

Genis olcude paylasilan ve guclu bir sekilde tutulan degerler olarak tanimlanan orgut kulturu ayni zamanda etkili bir okul olusturma surecinde etkin bir rol oynamaktadir. Ogrencilerle ve ogrencilerin ebeveynleri ile birlikte calisilabilecegine iliskin guven duygusu ve ogrencilerin akademik olarak basarili olabileceklerine iliskin olumlu inanc ve davranislarin okul kulturu ile iliskili oldugu dusunulmektedir. Iliskisel tarama yontemi ile yapilan bu calisma okul kulturu ile akademik iyimserlik arasindaki iliskiyi ve okul kulturunun akademik iyimserligi yordama derecesini betimlemek amaciyla yapilmistir. Arastirmanin evreni Konya ili merkez ilceleri Meram, Karatay ve Selcuklu’da bulunan 7269 ogretmenden, orneklemi ayni ilcelerde calisan 352 ogretmenden olusmaktadir. Orneklemin belirlenmesinde oranli ornekleme yontemi kullanilmistir. Arastirmada orgut kulturunun guc kulturu ve rol kulturu alt boyutlari ile akademik iyimserligin guven ve akademik alt boyutlari arasinda negatif yonlu ve anlamli duzeyde, basari kulturu alt boyutu ile akademik iyimserligin guven ve akademik vurgu alt boyutlari arasinda pozitif yonlu ve anlamli duzeyde iliski bulunmustur. Destek kulturu alt boyutu ile akademik iyimserligin tum alt boyutlari arasinda ise pozitif yonlu ve anlamli duzeyde iliski bulunmustur.
The Dynamics of Incomplete and Inconsistent Information : Applications of logic, algebra and coalgebra. (La dynamique de l'information incomplète et incohérente : applications de la logique, de l'algèbre et de la coalgèbre)

In this Ph.D. dissertation we investigate reasoning about information change in the presence of incomplete or inconsistent information, and the characterisation of notions of bisimulation on models encoding such reasoning patterns. Modal logics for incomplete and inconsistent information are typically weaker than the standard modal logics, such as the modal logic of contingency. We use logical, algebraic and co-algebraic methods to achieve our aims. The dissertation consists of two main parts. The first part focusses on reasoning about information change, and the second part focusses on expressivity and bisimulation. In the following, we give an overview of the contents of this dissertation
Screening for lung cancer: Diagnosis and management of lung cancer, 3rd ed: American College of Chest Physicians evidence-based clinical practice guidelines.

BACKGROUND Lung cancer is by far the major cause of cancer deaths largely because in the majority of patients it is at an advanced stage at the time it is discovered, when curative treatment is no longer feasible. This article examines the data regarding the ability of screening to decrease the number of lung cancer deaths. METHODS A systematic review was conducted of controlled studies that address the effectiveness of methods of screening for lung cancer. RESULTS Several large randomized controlled trials (RCTs), including a recent one, have demonstrated that screening for lung cancer using a chest radiograph does not reduce the number of deaths from lung cancer. One large RCT involving low-dose CT (LDCT) screening demonstrated a significant reduction in lung cancer deaths, with few harms to individuals at elevated risk when done in the context of a structured program of selection, screening, evaluation, and management of the relatively high number of benign abnormalities. Whether other RCTs involving LDCT screening are consistent is unclear because data are limited or not yet mature. CONCLUSIONS Screening is a complex interplay of selection (a population with sufficient risk and few serious comorbidities), the value of the screening test, the interval between screening tests, the availability of effective treatment, the risk of complications or harms as a result of screening, and the degree with which the screened individuals comply with screening and treatment recommendations. Screening with LDCT of appropriate individuals in the context of a structured process is associated with a significant reduction in the number of lung cancer deaths in the screened population. Given the complex interplay of factors inherent in screening, many questions remain on how to effectively implement screening on a broader scale.
Inverse transport modeling of volcanic sulfur dioxide emissions using large-scale simulations

Abstract. An inverse transport modeling approach based on the concepts of sequential importance resampling and parallel computing is presented to reconstruct altitude-resolved time series of volcanic emissions, which often cannot be obtained directly with current measurement techniques. A new inverse modeling and simulation system, which implements the inversion approach with the Lagrangian transport model Massive-Parallel Trajectory Calculations (MPTRAC) is developed to provide reliable transport simulations of volcanic sulfur dioxide (SO2). In the inverse modeling system MPTRAC is used to perform two types of simulations, i.e., unit simulations for the reconstruction of volcanic emissions and final forward simulations. Both types of transport simulations are based on wind fields of the ERA-Interim meteorological reanalysis of the European Centre for Medium Range Weather Forecasts. The reconstruction of altitude-dependent SO2 emission time series is also based on Atmospheric InfraRed Sounder (AIRS) satellite observations. A case study for the eruption of the Nabro volcano, Eritrea, in June 2011, with complex emission patterns, is considered for method validation. Meteosat Visible and InfraRed Imager (MVIRI) near-real-time imagery data are used to validate the temporal development of the reconstructed emissions. Furthermore, the altitude distributions of the emission time series are compared with top and bottom altitude measurements of aerosol layers obtained by the Cloud–Aerosol Lidar with Orthogonal Polarization (CALIOP) and the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) satellite instruments. The final forward simulations provide detailed spatial and temporal information on the SO2 distributions of the Nabro eruption. By using the critical success index (CSI), the simulation results are evaluated with the AIRS observations. Compared to the results with an assumption of a constant flux of SO2 emissions, our inversion approach leads to an improvement of the mean CSI value from 8.1 to 21.4 % and the maximum CSI value from 32.3 to 52.4 %. The simulation results are also compared with those reported in other studies and good agreement is observed. Our new inverse modeling and simulation system is expected to become a useful tool to also study other volcanic eruption events.
Evolution of resistance to chytridiomycosis is associated with a robust early immune response

Potentiating the evolution of immunity is a promising strategy for addressing biodiversity diseases. Assisted selection for infection resistance may enable the recovery and persistence of amphibians threatened by chytridiomycosis, a devastating fungal skin disease threatening hundreds of species globally. However, knowledge of the mechanisms involved in the natural evolution of immunity to chytridiomycosis is limited. Understanding the mechanisms of such resistance may help speed‐assisted selection. Using a transcriptomics approach, we examined gene expression responses of endangered alpine tree frogs (Litoria verreauxii alpina) to subclinical infection, comparing two long‐exposed populations with a naïve population. We performed a blinded, randomized and controlled exposure experiment, collecting skin, liver and spleen tissues at 4, 8 and 14 days postexposure from 51 wild‐caught captively reared infection‐naïve adult frogs for transcriptome assembly and differential gene expression analyses. We analysed our results in conjunction with infection intensity data, and the results of a large clinical survival experiment run concurrently with individuals from the same clutches. Here, we show that frogs from an evolutionarily long‐exposed and phenotypically more resistant population of the highly susceptible alpine tree frog demonstrate a more robust innate and adaptive immune response at the critical early subclinical stage of infection when compared with two more susceptible populations. These results are consistent with the occurrence of evolution of resistance against chytridiomycosis, help to explain underlying resistance mechanisms, and provide genes of potential interest and sequence data for future research. We recommend further investigation of cell‐mediated immunity pathways, the role of interferons and mechanisms of lymphocyte suppression.
Cross-cultural adaptation and psychometric evaluation of oral health impact profile among school teacher community

AIM: To translate OHIP-14 into Hindi and test its psychometric properties among school teacher community. METHODS: The OHIP-14 was translated to OHIP-14-H using WHO recommended translation protocol. During pre-testing, an expert panel assessed content validity of the questionnaire. Face validity was assessed on a sample of 10 individuals. The OHIP-14-H was administered on a random sample of 170 primary school teachers. Internal consistency and test-retest reliability were assessed using Cronbach's alpha and Intra-class correlation coefficient (ICC) respectively, with 2 weeks interval. Predictive validity was tested by comparing OHIP-14-H scores with clinical parameters. The concurrent validity was assessed using self-reported oral health and discriminant validity was ascertained through negative association with sociodemographic variables. RESULTS: The mean OHIP-14-H score was 9.57 (S.D = 4.58). ICC and Cronbach's alpha for OHIP-14-H was 0.96 and 0.92 respectively. Concurrent validity using binomial regression model indicated that good (OR = 0.56, 95% CI = 0.55 – 4.47) and moderate (OR = 0.25, 95% CI = 0.17 – 1.87) OHIP-14-H scores were negative but significant risk indicators of poor self reported oral health (P < 0.009). Significant predictive validity was observed between OHIP-14-H scores and clinical parameters (P < 0.000). CONCLUSION: Translated and culturally adapted OHIP-14-H indicates good reliability and validity among primary school teachers.
The association between proton pump inhibitor use and the risk of adverse kidney outcomes: a systematic review and meta-analysis

Background Existing epidemiological studies illustrate that proton pump inhibitors (PPIs) may be related to adverse kidney outcomes. To date, no comprehensive meta-analysis has been conducted to evaluate and quantify this association. Methods We performed a systematic review and meta-analysis of studies to assess the association between PPI use and the risk of adverse kidney outcomes. We searched MEDLINE, Embase, SCOPUS, Web of Science, CINAHL, Cochrane Library and grey literature with no language restrictions (through 31 October 2016). Adverse kidney outcomes were acute interstitial nephritis (AIN), acute kidney injury (AKI), chronic kidney disease (CKD) and end-stage renal disease (ESRD). The risk ratios (RRs) and confidence intervals (CIs) were pooled using a random effects model. The strength of evidence (SOE) for each outcome was assessed using the Grading of Recommended Assessment, Development and Evaluation system. Results Of 2037 identified studies, four cohort and five case-control studies with ∼2.6 million patients were included. Of these, 534 003 (20.2%) were PPI users. Compared with non-PPI users, PPI users experienced a significantly higher risk of AKI [RR 1.44 (95% CI 1.08-1.91); P = 0.013; SOE, low] and CKD [RR 1.36 (95% CI 1.07-1.72); P = 0.012; SOE, low]. Moreover, PPIs increased the risk of AIN [RR 3.61 (95% CI 2.37-5.51); P < 0.001; SOE, insufficient] and ESRD [RR 1.42 (95% CI 1.28-1.58); P < 0.001; SOE, insufficient]. Conclusion PPI usage was associated with adverse kidney outcomes; however, these findings were based on observational studies and low-quality evidence. Additional rigorous studies are needed for further clarification.
Expression of Matrix Metalloproteinases and Tissue Inhibitor of Matrix Metalloproteinases in Non-Small-Cell Lung Cancer

Expression of matrix metalloproteinase (MMP)-2, MMP-9, tissue inhibitor of metalloproteinases (TIMP)-1, and TIMP-2 was studied in non-small-cell lung cancer (NSCLC). Activity of MMP-2 and MMP-9 by gelatin zymography and expression of MMP-2, MMP-9, TIMP-1, and TIMP-2 mRNAs were examined in 11 lung cancer cell lines which included six small-cell lung cancer (SCLC) cell lines. Localization of MMP-2, MMP-9, TIMP-1, and TIMP-2 was examined by immunohistochemistry in 43 resected NSCLC (22 adenocarcinomas, 17 squamous cell carcinomas, 4 large cell carcinomas) using specific anti-human monoclonal antibodies. Expression of MMP-2 mRNA was detected in 5 (100%), MMP-9 in 1 (20%), TIMP-1 in 4 (80%), and TIMP-2 in 5 (100%) of 5 NSCLC cell lines examined. MMP-2 gelatinolytic activity also was detected in all five NSCLC cell lines, whereas MMP-9 activity was detected in only one cell line. In 43 patients, MMP-2, MMP-9, TIMP-1, and TIMP-2 immunoreactivity was demonstrated in 19 (44%), 9 (21%), 15 (35%), and 29 (67%) excised tumors, respectively. All stromal fibroblasts in tumor samples stained positive for MMP-2. There was a correlation between TIMP-2 immunoreactivity and disease stage (42% stage I versus 88% stages II, III, and IV) (p = 0.0024). Both cancer cell lines and NSCLC tumor samples frequently expressed MMP-2, MMP-9, TIMP-1, and TIMP-2; MMP-2 in particular was highly expressed in malignant cells and surrounding fibroblasts. These findings suggest that MMP-2 plays a more important role in invasion of NSCLC than MMP-9 and that TIMP-2 may have clinical relevance in NSCLC.
Performance Evaluation of SHA-3 Final Round Candidate Algorithms on ARM Cortex-M4 Processor

SHA-3 was an open competition initiated by NIST to design new generation of hash functions. This competition was a necessity to overcome the challenges imposed by multiple attacks on MDx family of hash functions including SHA-0 and SHA-1. For this competition, NIST announced a reference platform which did not cover Embedded and Mobile machines. This paper compares the performance of SHA-3 final round candidate algorithms on ARM Cortex-M4 processor embedded processor and presents the results. Cycles per Byte is used as performance metric. Cortex-M4 based Stellaris® LM4F232 Evaluation Board EK-LM4F232 from Texas Instruments is used for performance evaluation.
Cell-free and in vivo characterization of Lux, Las, and Rpa quorum activation systems in E. coli

Synthetic biologists have turned towards quorum systems as a path for building sophisticated microbial consortia that exhibit group decision making. Currently, however, even the most complex consortium circuits rely on only one or two quorum sensing systems, greatly restricting the available design space. High-throughput characterization of available quorum sensing systems is useful for finding compatible sets of systems that are suitable for a defined circuit architecture. Recently, cell–free systems have gained popularity as a test-bed for rapid prototyping of genetic circuitry. We take advantage of the transcription-translation cell-free system to characterize three commonly used Lux-type quorum activators, Lux, Las, and Rpa. We then compare the cell-free characterization to results obtained in vivo. We find significant genetic crosstalk in both the Las and Rpa systems and substantial signal crosstalk in Lux activation. We show that cell-free characterization predicts crosstalk observed in vivo.
Consumer Preferences in Format and Type of Community-Based Weight Control Programs

Purpose. The purpose of this study was to provide further information about preferences for types and formats (e.g., correspondence vs. face to face) of eating and exercise programs, actual participation rates in a variety of offered programs, and characteristics of program participants vs. nonparticipants. Design. Over a 3-year period, a large sample of community volunteers was given the opportunity to participate in various forms of diet and exercise programs as part of a weight gain prevention study. Setting. The study was conducted at a university and three local health department sites. Subjects. Subjects in the study were 616 individuals participating in the Pound of Prevention study (POP), a 3-year randomized evaluation of an intervention for preventing weight gain.1 Measures. The primary outcomes assessed were participation rates for each program offering. Program participants were also compared to those who did not participate on demographic characteristics, smoking, diet behavior, exercise behavior, and weight concern. Results. Survey results indicated that correspondence formats for delivery of health education programs were rated as more desirable than face-to-face formats. Participation for program offerings ranged from 0 to 16% of the study population. Participation data were consistent with survey results and showed participants' preference for correspondence formats even more strongly. Program offerings attracted health-conscious participants with higher education and income levels. Conclusions. These data suggest that some community members will get interested and take part in low-cost, minimal contact programs for exercise and weight control. Future research efforts should focus on investigating ways to increase participation in brief or minimal contact programs, particularly among groups that may be difficult to reach and at high risk for the development of obesity.