Linking common human diseases to their phenotypes; development of a resource for human phenomics.

BackgroundIn recent years a large volume of clinical genomics data has become available due to rapid advances in sequencing technologies. Efficient exploitation of this genomics data requires linkage to patient phenotype profiles. Current resources providing disease-phenotype associations are not comprehensive, and they often do not have broad coverage of the disease terminologies, particularly ICD-10, which is still the primary terminology used in clinical settings.MethodsWe developed two approaches to gather disease-phenotype associations. First, we used a text mining method that utilizes semantic relations in phenotype ontologies, and applies statistical methods to extract associations between diseases in ICD-10 and phenotype ontology classes from the literature. Second, we developed a semi-automatic way to collect ICD-10-phenotype associations from existing resources containing known relationships.ResultsWe generated four datasets. Two of them are independent datasets linking diseases to their phenotypes based on text mining and semi-automatic strategies. The remaining two datasets are generated from these datasets and cover a subset of ICD-10 classes of common diseases contained in UK Biobank. We extensively validated our text mined and semi-automatically curated datasets by: comparing them against an expert-curated validation dataset containing disease-phenotype associations, measuring their similarity to disease-phenotype associations found in public databases, and assessing how well they could be used to recover gene-disease associations using phenotype similarity.ConclusionWe find that our text mining method can produce phenotype annotations of diseases that are correct but often too general to have significant information content, or too specific to accurately reflect the typical manifestations of the sporadic disease. On the other hand, the datasets generated from integrating multiple knowledgebases are more complete (i.e., cover more of the required phenotype annotations for a given disease). We make all data freely available at https://doi.org/10.5281/zenodo.4726713

AlGaAs film growth using thermionic vacuum arc (TVA) and determination of its physical properties

In this research, an AlGaAs film was deposited on a microscope slide by means of the thermionic vacuum arc (TVA) technique which is a novel plasma production technique. AlGaAs structures were grown by this deposition technique for the first time and this process occurred in a very short period of time. In order to characterize the produced film, nano-structural, nano-mechanical, optical, and surface properties were determined by field emission scanning electron microscope (FESEM), atomic force microscope (AFM), X-ray diffractometer (XRD) and interferometer. According to the results of the measurements, the mean thickness value of the produced film was obtained as 1.8 ?m. The band gap value was determined as 2eV from the Kubelka-Munk plot. The refractive index value was obtained as approximately 3.4. Hardness value was determined as 2 GPa from the Oliver-Pharr method. All these values are consistent with the reported values in the literature for the AlGaAs films produced by different methods. TVA technique appeared as a suitable and promising technique for the production of AlGaAs films. © 2015, Società Italiana di Fisica and Springer-Verlag Berlin Heidelberg

A study on some physical properties of a Pb-doped GaAs thin film produced by thermionic vacuum arc

A 155 nm Pb-doped GaAs thin film was deposited on a glass substrate by means of the thermionic vacuum arc technique in 30 s using GaAs and Pb pellets as source materials. Tools and techniques such as an optical reflectometer, UV-VIS-NIR spectrophotometer, FESEM, EDX, AFM and optical tensiometer were employed to investigate the physical properties of the produced film. From the optical investigations, the refractive index at the wavelength of 632.8 nm and optical band gap of the film were found to be 4.03 and 1.13 eV respectively. It was observed that Pb doping increased the value of refractive index and decreased the band gap value. A uniform surface morphology with fine grain covering the entire surface was observed through the FESEM and AFM studies while 50–80 nm grain size and 2.22 nm root mean square roughness values were obtained. The EDX analysis confirmed the presence of Ga, As and Pb elements in the film. The wetting experiments revealed that the contact angle value was dependent on the liquid used. The surface free energy calculated with OWRK/Fowkes and Equation of State approaches were about 26 mN/m. © 2017 Elsevier B.V

Optical and surface properties of the in doped GaAs layer deposition using thermionic vacuum arc method

A broadband optical transparent InGaAs semiconductor layer production of micron thicknesses was produced in only 75 s by thermionic vacuum arc (TVA) method at the first time. The optical and surface properties of the produced layers have been investigated. InGaAs structure is using in electronics and optoelectronics devices. The main advantage of TVA method is its fast deposition rate, without any loss in the quality of the films. Doping is a very simple and fast according to common production methods. InGaAs is an alloy of indium arsenide (InAs) and gallium arsenide (GaAs). InAs with (220) crystallographic direction and GaAs with (024)/(022) crystallographic directions were detected using by XRD analysis. GaAs and InAs are in the cubic and zinc blende crystal system, respectively. According to the transmittance spectra, sample has a broadband transparency in the range of 1000–3300 nm. According to results, defined TVA method for In doping to GaAs is proper fast and friendly method. SCANNING 38:297–302, 2016. © 2015 Wiley Periodicals, Inc. © Wiley Periodicals, Inc

Investigation of the surface free energy of the ITO thin films deposited under different working pressure

9th International Physics Conference of the Balkan Physical Union, BPU 2015This study discusses the influence of working pressure on the surface energy of the ITO thin films produced by radio frequency magnetron sputtering method. Optical tensiometer (Attension Theta Lite) is used for evaluating wetting behavior of the water droplet on the film surface and Equation of State method was selected to determine surface free energy for this study. Equation of state method does not divide the surface tension into different components such as polar, dispersive, acid-base. It is calculated the surfaces' free energy measuring the contact angle with a single liquid. The surface free energy value was in the range of 15-31 mN/m. Also, the transmittances were determined in the wavelength range between 200 and 1000 nm using the UNICO 4802 UV-Vis double beam spectrophotometer. Transmittances of the produced ITO thin films are greater than %70 in the visible range. © 2016 AIP Publishing LLC

Characterization of a fast grown GaAs:Sn thin film by thermionic vacuum arc

In this research, a tin doped gallium arsenide thin film was grown on a glass substrate by means of the TVA technique in a very short period of time (70 s) and it’s morphological, compositional, and optical properties were examined. The deposited GaAs:Sn structures were characterized via both atomic force microscope (AFM) and field emission scanning electron microscope (FESEM). In this context, current research aims to reach a conclusion about the structure of the produced GaAs:Sn film by combining AFM, FESEM and energy dispersive X-ray spectroscopy data. From the optical investigation, the refractive index and extinction coefficient values for the produced film were obtained as 3.68 and 0.03 at the wavelength of 632.8 nm, respectively. The direct optical band gap energy of the deposited thin film was determined by two different models. Estimated optical band gap values were compared with each other. The results showed that TVA technique is suitable for a GaAs:Sn coating on glass substrate. © 2015, Springer Science+Business Media New York

Seasonal variations of NOM composition and their reactivity in a low humic water

Natural organic matter (NOM) and its potential to form disinfection by-products (DBPs) during water treatment are of great public health concern. Understanding the seasonal changes in NOM composition and their reactivity in DBP formation could lead to a better treatment of drinking water and a more consistent water quality. NOM from the Terkos Lake was fractionated and characterized by XAD resin adsorption and ultrafiltration (UF) techniques during four different seasons within a year. XAD fraction analysis indicates that the HPI (38%) and the TPI (21%) were the dominant chemical fractions as DOC masses across the sampling period. Moreover, the fractions contributing to the most UV254 absorbance were HPO, which accounted for more than 72% of total UV254. It was found that the percentages of UV254 of HPI and TPI showed significant amount of variation with coefficients of variation of 48% (HPI) and 35% (TPI), respectively. Moreover, it was concluded that the HPO fraction was the primary THM precursor, which contributed more than 48%, and while the primary fraction of HAA precursors was found to be TPI, accounting for more than 47% of total HAAFP with exceptions in January 2011. As obviously seen in this study, the hydrophobic constituents in Terkos Lake water are on the low end of the spectrum in terms of their reactivity to form HAAs. In the context of THM reactivity, the physical properties (i.e., moleculer size) of Terkos Lake NOM are more important than their chemical properties (i.e., aromaticity). On the other hand, the predominant fraction as the source of HAAs precursors was found to be with the TPI and HPI chemical fractions. © 2013 American Institute of Chemical Engineers

Heavily carbon doped GaAs nanocrystalline thin film deposited by thermionic vacuum arc method

In this paper, we introduced a new different thin film deposition method for heavily carbon doped GaAs. Used method is thermionic vacuum arc (TVA) and first used for the carbon doping process. The method is very fast deposition process for the other growth method such as metal organic chemical vapor deposition, molecular beam epitaxy, molecular organic molecular beam epitaxy. The smallest grain size of GaAs and doped GaAs were obtained by carbon doping process. Mean crystalline size and height of crystalline size were found to be 3.4 nm and 4 nm, respectively. Crystal direction was found to be (022) plane and (024) plane for the sample at 45.322° and 75.060°, respectively. The production process and obtained results show that used methods is very simple, low cost, eco friendly and very fast method for the carbon doped GaAs. © 2015 Elsevier B.V

Optical, structural, morphological and compositional characterization of a Co-doped GaAs semiconducting thin film produced by thermionic vacuum arc

A 80 nm 2 at% Co-doped GaAs thin film was deposited on a glass substrate under a high vacuum condition by means of the thermionic vacuum arc technique using GaAs and Co pellets as source materials. Tools and techniques such as an optical reflectometer, XRD, UV-VIS-NIR spectrophotometer, FESEM, EDX, and AFM were employed to investigate some of the physical properties of the produced film. From the optical investigations, the refractive index at 632.8 nm and optical band gap of the film were determined to be 3.60 and 1.42 eV respectively. XRD characterization indicated that the film contained GaAs and Co phases. A uniform surface morphology with fine grain covering the entire surface was observed through the FESEM and AFM studies, while 30 nm grain size and 2.72 nm root mean square roughness were obtained. The EDX analysis also confirmed the presence of Ga, As and Co in the film. © 2015 Elsevier B.V. All rights reserved

Direct and fast growth of GaAs thin films on glass and polyethylene terephthalate substrates using a thermionic vacuum arc

Using a thermionic vacuum arc, single?crystal gallium arsenide (GaAs) layers of micron thickness were grown on PET and glass substrates in 2 min. We present a new deposition mechanism and parameters for GaAs thin films produced in a very short time. Crystal direction was found to be (111) plane for the GaAs/PET sample and (022) plane and (133) plane for the GaAs/glass sample, respectively. The average roughness values of the deposited thin films were determined to be approximately 30 nm for GaAs/PET and 60 nm for GaAs/glass. The structures can be seen clearly in field emission scanning electron microscopy and atomic force microscopy. The obtained optical band is nearly the same with literatures values of the GaAs. Although produced structures in different crystal formations, only aggregations dimensions and absorbance of the layers were changed. Obtained refractive index values are nearly same with database info. © 2015, Springer Science+Business Media New York