Bridging data management platforms and visualization tools to enable ad-hoc and smart analytics in life sciences

Core facilities have to offer technologies that best serve the needs of their users and provide them a competitive advantage in research. They have to set up and maintain instruments in the range of ten to a hundred, which produce large amounts of data and serve thousands of active projects and customers. Particular emphasis has to be given to the reproducibility of the results. More and more, the entire process from building the research hypothesis, conducting the experiments, doing the measurements, through the data explorations and analysis is solely driven by very few experts in various scientific fields. Still, the ability to perform the entire data exploration in real-time on a personal computer is often hampered by the heterogeneity of software, the data structure formats of the output, and the enormous data sizes. These impact the design and architecture of the implemented software stack. At the Functional Genomics Center Zurich (FGCZ), a joint state-of-the-art research and training facility of ETH Zurich and the University of Zurich, we have developed the B-Fabric system, which has served for more than a decade, an entire life sciences community with fundamental data science support. In this paper, we sketch how such a system can be used to glue together data (including metadata), computing infrastructures (clusters and clouds), and visualization software to support instant data exploration and visual analysis. We illustrate our in-daily life implemented approach using visualization applications of mass spectrometry data

A Multiagent System for the Reliable Execution of Automatically Composed Ad-hoc Processes

This article presents an architecture to automatically create ad-hoc processes for complex value-added services and to execute them in a reliable way. The uniqueness of ad-hoc processes is to support users not only in standardized situations like traditional workflows do, but also in unique non-recurring situations. Based on user requirements, a service composition engine generates such ad-hoc processes, which integrate individual services in order to provide the desired functionality. Our infrastructure executes ad-hoc processes by transactional agents in a peer-to-peer style. The process execution is thereby performed under transactional guarantees. Moreover, the service composition engine is used to re-plan in the case of execution failure

Postoperative pain intensity after using different instrumentation techniques: a randomized clinical study

Postoperative pain is a frequent complication associated with root canal treatment, especially during apical instrumentation of tooth with preexisting periradicular inflammation Objectives The aim of this clinical study was to evaluate the influence of the instrumentation techniques on the incidence and intensity of postoperative pain in single-visit root canal treatment. Material and Methods Ninety patients with single root/canal and non-vital pulps were included. The patients were assigned into 3 groups according to root canal instrumentation technique used; modified step-back, reciprocal, and rotational techniques. Root canal treatment was carried out in a single visit and the severity of postoperative pain was assessed via 4-point pain intensity scale. All the participants were called through the phone at 12, 24 and 48 h to obtain the pain scores. Data were analyzed through the Kruskal–Wallis test. Results There was significant difference between all groups (

Effects of Partial or Total Replacement of Fish Oil by Unrefined Peanut Oil on Growth and Chemical Composition of Common Carp (Cyprinus carpio)

Abstract Unrefined peanut oil was evaluated as a partial or total replacement of fish oil in diets for common carp (Cyprinus carpio) and growth performance, feed utilization, and biochemical status were examined. Three isonitrogenous (34.5% protein) and isolipidic (12.8% lipid) experimental diets were fed to satiation to triplicate groups of 10 common carp (29.57±0.44 g), each, for 60 days. At the end of the experiment, total replacement of the fish oil by peanut oil did not affect growth, feed utilization, or ash, protein, or moisture content in the carp body. Hepatosomatic and viscerasomatic indices increased as the content of peanut oil increased but did not significantly differ between treatments (p<0.05). Serum total protein, globulin, and triglyceride significantly increased as the content of peanut oil increased while glucose decreased. There was no definable trend in cholersterol. In conclusion, replacement of 50% dietary fish oil with unrefined peanut oil had no adverse effect on the growth performance, biochemical parameters, or general health (survival) of common carps

Evaluation of patients with fibrotic interstitial lung disease: Preliminary results from the Turk-UIP study

OBJECTIVE: Differential diagnosis of idiopathic pulmonary fibrosis (IPF) is important among fibrotic interstitial lung diseases (ILD). This study aimed to evaluate the rate of IPF in patients with fibrotic ILD and to determine the clinical-laboratory features of patients with and without IPF that would provide the differential diagnosis of IPF. MATERIAL AND METHODS: The study included the patients with the usual interstitial pneumonia (UIP) pattern or possible UIP pattern on thorax high-resolution computed tomography, and/or UIP pattern, probable UIP or possible UIP pattern at lung biopsy according to the 2011 ATS/ERSARS/ALAT guidelines. Demographics and clinical and radiological data of the patients were recorded. All data recorded by researchers was evaluated by radiology and the clinical decision board. RESULTS: A total of 336 patients (253 men, 83 women, age 65.8 +/- 9.0 years) were evaluated. Of the patients with sufficient data for diag-nosis (n=300), the diagnosis was IPF in 121 (40.3%), unclassified idiopathic interstitial pneumonia in 50 (16.7%), combined pulmonary fibrosis and emphysema (CPFE) in 40 (13.3%), and lung involvement of connective tissue disease (CTD) in 16 (5.3%). When 29 patients with definite IPF features were added to the patients with CPFE, the total number of IPF patients reached 150 (50%). Rate of male sex (p<0.001), smoking history (p<0.001), and the presence of clubbing (p=0.001) were significantly high in patients with IPE None of the women <50 years and none of the men <50 years of age without a smoking history were diagnosed with IPE Presence of at least 1 of the symptoms suggestive of CTD, erythrocyte sedimentation rate (ESR), and antinuclear antibody (FANA) positivity rates were significantly higher in the non-IPF group (p<0.001, p=0.029, p=0.009, respectively). CONCLUSION: The rate of IPF among patients with fibrotic ILD was 50%. In the differential diagnosis of IPF, sex, smoking habits, and the presence of clubbing are important. The presence of symptoms related to CTD, ESR elevation, and EANA positivity reduce the likelihood of IPF

In a real-life setting, direct-acting antivirals to people who inject drugs with chronic hepatitis c in Turkey

Background: People who inject drugs (PWID) should be treated in order to eliminate hepatitis C virus in the world. The aim of this study was to compare direct-acting antivirals treatment of hepatitis C virus for PWID and non-PWID in a real-life setting. Methods: We performed a prospective, non-randomized, observational multicenter cohort study in 37 centers. All patients treated with direct-acting antivirals between April 1, 2017, and February 28, 2019, were included. In total, 2713 patients were included in the study among which 250 were PWID and 2463 were non-PWID. Besides patient characteristics, treatment response, follow-up, and side effects of treatment were also analyzed. Results: Genotype 1a and 3 were more prevalent in PWID-infected patients (20.4% vs 9.9% and 46.8% vs 5.3%). The number of naïve patients was higher in PWID (90.7% vs 60.0%), while the number of patients with cirrhosis was higher in non-PWID (14.1% vs 3.7%). The loss of follow-up was higher in PWID (29.6% vs 13.6%). There was no difference in the sustained virologic response at 12 weeks after treatment (98.3% vs 98.4%), but the end of treatment response was lower in PWID (96.2% vs 99.0%). In addition, the rate of treatment completion was lower in PWID (74% vs 94.4%). Conclusion: Direct-acting antivirals were safe and effective in PWID. Primary measures should be taken to prevent the loss of follow-up and poor adherence in PWID patients in order to achieve World Health Organization’s objective of eliminating viral hepatitis

Postoperative pain intensity after using different instrumentation techniques: a randomized clinical study

Postoperative pain is a frequent complication associated with root canal treatment, especially during apical instrumentation of tooth with preexisting periradicular inflammation OBJECTIVES: The aim of this clinical study was to evaluate the influence of the instrumentation techniques on the incidence and intensity of postoperative pain in single-visit root canal treatment. MATERIAL AND METHODS: Ninety patients with single root/canal and non-vital pulps were included. The patients were assigned into 3 groups according to root canal instrumentation technique used; modified step-back, reciprocal, and rotational techniques. Root canal treatment was carried out in a single visit and the severity of postoperative pain was assessed via 4-point pain intensity scale. All the participants were called through the phone at 12, 24 and 48 h to obtain the pain scores. Data were analyzed through the Kruskal–Wallis test. RESULTS: There was significant difference between all groups (p<0.05). The modified step-back technique produced postoperative pain significantly lower than the rotational (p=0.018) and reciprocal (p=0.020) techniques. No difference was found between the reciprocal and rotational techniques (p=0.868). Postoperative pain in the first 12 h period (p=0.763) and in the 24 h period (p=0.147) was not significantly different between the groups. However, the difference in the 48 h period was statistically different between the groups (p=0.040). CONCLUSION: All instrumentation techniques caused postoperative pain. The modified step-back technique produced less pain compared to the rotational and reciprocal techniques

An Approach to Supporting Semantic Integrity of Federated Databases

In this paper, a very flexible way to realize global integrity enforcement in federated database systems is proposed. By integrating the active rule paradigm into a federated database framework global integrity constraints which refer to multiple component database systems can be supported. Active rules well-known from active databases can be used as a powerful mechanism for enforcing integrity constraints in case of violations

Maddi duran varlıkların bağımsız denetimi ve bir uygulama

ÖZET MADDİ DURAN VARLIKLARIN BAĞIMSIZ DENETİMİ VE BİR UYGULAMAÜretimin ve idari işlerin yapılabilmesi için gerekli olan maddi duran varlıklar, günümüzde şirketler için büyük önem taşımaktadır. Bu açıdan maddi duran varlıklar, şirketlerin elinde bulundurduğu varlıkların büyük bir bölümünü oluşturmaktadır. Bunun en büyük sebebi de yüksek tutarlı olmalarıdır. Yüksek tutarlı olmaları itibariyle kasten ya da bilmeyerek yapılan hata ve hileler mali tablo kullanıcılarının yanlış kararlar vermelerine neden olacaktır. Bu çalışma ile, mali tablo kullanıcılarına maddi duran varlıklarla ilgili nasıl güvenilir bilgi sunulacağı anlatılmaya çalışılmıştır. Güvenilir bilgi temin etmenin en kolay yolunun ise mali tabloların şirketlerden bağımsız kişiler tarafından denetlenmesi ile sağlanabileceği, günümüz dünyasında kanıtlarla ispatlanmış bir olgudur. Çalışmamızda maddi duran varlıklarla ilgili bağımsız denetimin hangi aşamalardan geçmesi gerektiği, bu aşamaları uygularken hangi yöntemlerin kullanılması gerektiği hakkında detaylı bilgiler verilmiştir. Bu aşamalar aynı zamanda uygulamalı bir örnek ile açıklanmıştır. ABSTRACT INDEPENDENT AUDIT OF TANGIBLE FIXED ASSETS AND AN APPLICATIONNowadays tangible fixed assets are so important for the companies to do the production and administrative functions. In that point, tangible fixed assets are presented in assets. The highest amounts of assets are always comprised tangible fixed assets. Because of that reason, third parties make wrong decisions due to the mistakes and frauds on tangible fixed assets. How the reliable information should be shown in the financial statements for investors are tried to explain in this work. Easy way to provide reliable information for investors is independent audit, and this is certified with evidences. This work related with the independent audit of tangible fixed assets includes which stages will pass and which methods should be used for these stages. These stages are supported with the application