File Processing Research Articles

Metandem: An online software tool for mass spectrometry-based isobaric labeling metabolomics

Mass spectrometry-based stable isotope labeling provides the advantages of multiplexing capability and accurate quantification but requires tailored bioinformatics tools for data analysis. Despite the rapid advancements in analytical methodology, it is often challenging to analyze stable isotope labeling-based metabolomics data, particularly for isobaric labeling using MS/MS reporter ions for quantification. We report Metandem, a novel online software tool for isobaric labeling-based metabolomics, freely available at http://metandem.com/web/. Metandem provides a comprehensive data analysis pipeline integrating feature extraction, metabolite quantification, metabolite identification, batch processing of multiple data files, online parameter optimization for custom datasets, data normalization, and statistical analysis. Systematic evaluation of the Metandem tool was demonstrated on UPLC-MS/MS, nanoLC-MS/MS, CE-MS/MS and MALDI-MS platforms, via duplex, 4-plex, 10-plex, and 12-plex isobaric labeling experiments and the application to various biological samples.

Impact of digital video analytics on accuracy of chemobehavioural phenotyping in aquatic toxicology.

Chemobehavioural phenotypic analysis using small aquatic model organisms is becoming an important toolbox in aquatic ecotoxicology and neuroactive drug discovery. The analysis of the organisms’ behavior is usually performed by combining digital video recording with animal tracking software. This software detects the organisms in the video frames, and reconstructs their movement trajectory using image processing algorithms. In this work we investigated the impact of video file characteristics, video optimization techniques and differences in animal tracking algorithms on the accuracy of quantitative neurobehavioural endpoints. We employed larval stages of a free-swimming euryhaline crustacean Artemia franciscana,commonly used for marine ecotoxicity testing, as a proxy modelto assess the effects of video analytics on quantitative behavioural parameters. We evaluated parameters such as data processing speed, tracking precision, capability to perform high-throughput batch processing of video files. Using a model toxicant the software algorithms were also finally benchmarked against one another. Our data indicates that variability in video file parameters; such as resolution, frame rate, file containers types, codecs and compression levels, can be a source of experimental biases in behavioural analysis. Similarly, the variability in data outputs between different tracking algorithms should be taken into account when designing standardized behavioral experiments and conducting chemobehavioural phenotyping.

Proteogenomic Analysis of Protein Sequence Alterations in Breast Cancer Cells

Cancer evolves as a result of an accumulation of mutations and chromosomal aberrations. Developments in sequencing technologies have enabled the discovery and cataloguing of millions of such mutations. The identification of protein-level alterations, typically by using reversed-phase protein arrays or mass spectrometry, has lagged, however, behind gene and transcript-level observations. In this study, we report the use of mass spectrometry for detecting the presence of mutations-missense, indels and frame shifts-in MCF7 and SKBR3 breast cancer, and non-tumorigenic MCF10A cells. The mutations were identified by expanding the database search process of raw mass spectrometry files by including an in-house built database of mutated peptides (XMAn-v1) that complemented a minimally redundant, canonical database of Homo sapiens proteins. The work resulted in the identification of nearly 300 mutated peptide sequences, of which ~50 were characterized by quality tandem mass spectra. We describe the criteria that were used to select the mutated peptide sequences, evaluate the parameters that characterized these peptides, and assess the artifacts that could have led to false peptide identifications. Further, we discuss the functional domains and biological processes that may be impacted by the observed peptide alterations, and how protein-level detection can support the efforts of identifying cancer driving mutations and genes. Mass spectrometry data are available via ProteomeXchange with identifier PXD014458.

Sistem Pengolahan Data Jamaah Umroh Berbasis Web Menggunakan Metode Interpolation Seacrh pada PT. Kaisa Rossie Semarang

The use of software as a supporting tool to input data in a company is needed. The software that is used of course must also be able to work effectively and efficiently so that it can support the performance of administrative staff. Every company, private institution or government has certainly done a filing process to store files or data that are considered important. Archiving data on pilgrims performed at this company is still centralized in several Microsoft Excel files for all staff staff. Search is needed to find specific information from a table when the exact location of that information was previously unknown.When the array data is ordered with key values,searching data can be useful using method interpolation search for efficient to find a key value from data array. The system development method used in this system is the Research And Development (R & D) method. This study purpose is intended to be able to assist the task of the cashier in inputting data and admin in making reports given to the leadership, and information appropriate to the position of the employee.

Hydrogen storage properties of filings of the ZK60 alloy modified with 2.5 wt% mischmetal

In this study, a commercial Mg-based ZK60 alloy was modified with 2.5 wt% mischmetal (ZK60-2.5 wt%Mm) and further processed by cold rolling followed by manual filing. The chips obtained by manual filing process were collected from the as cast (AC) and the cold rolled (CR) materials. The hydrogen storage properties were evaluated by kinetics measurements at 350 °C. A full microstructural characterization including optical, scanning and transmission electron microscopy (MO, MEV and TEM), X-ray diffraction (XRD) and differential scanning calorimetry (DSC) was performed in the samples. For the first absorption of both filed samples the H storage capacity showed a value around 6.0 wt% after 1 h while for the CR sample it was close to 1.25 wt% after the same time. The manual filing produced samples with higher hydrogenation kinetics compared with that of the CR sample. Besides, their hydrogen storage capacity was maintained close to the theoretical value (6.75 wt%). The breakage and pulverization of the intermetallic phases gave the chips from the CR alloy the faster hydrogenation kinetics, especially for H-desorption.

FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files

BackgroundExploration and processing of FASTQ files are the first steps in state-of-the-art data analysis workflows of Next Generation Sequencing (NGS) platforms. The large amount of data generated by these technologies has put a challenge in terms of rapid analysis and visualization of sequencing information. Recent integration of the R data analysis platform with web visual frameworks has stimulated the development of user-friendly, powerful, and dynamic NGS data analysis applications.ResultsThis paper presents FastqCleaner, a Bioconductor visual application for both quality-control (QC) and pre-processing of FASTQ files. The interface shows diagnostic information for the input and output data and allows to select a series of filtering and trimming operations in an interactive framework. FastqCleaner combines the technology of Bioconductor for NGS data analysis with the data visualization advantages of a web environment.ConclusionsFastqCleaner is an user-friendly, offline-capable tool that enables access to advanced Bioconductor infrastructure. The novel concept of a Bioconductor interactive application that can be used without the need for programming skills, makes FastqCleaner a valuable resource for NGS data analysis.

Land use and land cover mapping in wetlands one step closer to the ground: Sentinel-2 versus landsat 8

Environmental studies with Landsat images have revealed many of the problems faced by wetland ecosystem, which are crucial for the conservation of biodiversity and the natural values of our planet. The study of LULC changes in wetlands through remote sensing constantly helps to identify and combat their main environmental threats improving the conservation of these natural habitats. Starting in mid-2015, the Sentinel-2 satellite opens new possibilities in the field of earth observation thanks to its higher spatial, spectral and temporal resolution becoming a powerful source of information for LULC monitoring in wetland areas. However, researchers may ask them selves to what extent Sentinel-2 is an improvement over Landsat 8 for general purposes. This research test if there is a real difference in the quality of the results delivered by both Sentinel-2 and Landsat 8 imagery when basic classification methods are applied.The study uses Sentinel-2 and Landsat 8 imagery to produce LULC maps in a Mediterranean wetland area applying an object based classification method in order to compare the accuracy and reliability in the surface detected by both satellites. The results show that an object based classification using only the Sentinel-2 and Landsat 8 image information, without band indexes or ancillary data, offers very similar results for most LULC classes, being the overall accuracy around 87–88% with slightly better results when using Sentinel-2. Although using Sentinel-2 leads to an increase in file size and processing times, the analysis of certain LULC classes presents an improvement compared to Landsat 8, detecting more linear and small size elements with a better delineation of image features in the classified map. However, these improvements should not underestimate the value of Landsat imagery in the future since both satellites provide high precision information, so they can and should coexist and be used together to increase data availability in order to have the best possible results in remote sensing research.

Distributed File Sharing and Retrieval Model for Cloud Virtual Environment

Cloud-based storage services are multiplying and are being adapted mostly for data storage. At the same time, many potential problems pertaining to data storage and security are being addressed. This research provides the architecture for splitting user data and the solution in retrieving different data chunks, stored on different cloud storages. By doing this, not only the load on a single server is reduced but security and storage are efficiently used. Data would be stored and retrieved in slices, hence the chances of data forgery are diminishing. File processing will be faster as split parts would be fetched from different clouds, enabling parallel processing.

OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes.

Organellar (plastid and mitochondrial) genomes play an important role in resolving phylogenetic relationships, and next-generation sequencing technologies have led to a burst in their availability. The ongoing massive sequencing efforts require software tools for routine assembly and annotation of organellar genomes as well as their display as physical maps. OrganellarGenomeDRAW (OGDRAW) has become the standard tool to draw graphical maps of plastid and mitochondrial genomes. Here, we present a new version of OGDRAW equipped with a new front end. Besides several new features, OGDRAW now has access to a local copy of the organelle genome database of the NCBI RefSeq project. Together with batch processing of (multi-)GenBank files, this enables the user to easily visualize large sets of organellar genomes spanning entire taxonomic clades. The new OGDRAW server can be accessed at https://chlorobox.mpimp-golm.mpg.de/OGDraw.html.

Interpreting Viral Deep Sequencing Data with GLUE.

Using deep sequencing technologies such as Illumina’s platform, it is possible to obtain reads from the viral RNA population revealing the viral genome diversity within a single host. A range of software tools and pipelines can transform raw deep sequencing reads into Sequence Alignment Mapping (SAM) files. We propose that interpretation tools should process these SAM files, directly translating individual reads to amino acids in order to extract statistics of interest such as the proportion of different amino acid residues at specific sites. This preserves per-read linkage between nucleotide variants at different positions within a codon location. The samReporter is a subsystem of the GLUE software toolkit which follows this direct read translation approach in its processing of SAM files. We test samReporter on a deep sequencing dataset obtained from a cohort of 241 UK HCV patients for whom prior treatment with direct-acting antivirals has failed; deep sequencing and resistance testing have been suggested to be of clinical use in this context. We compared the polymorphism interpretation results of the samReporter against an approach that does not preserve per-read linkage. We found that the samReporter was able to properly interpret the sequence data at resistance-associated locations in nine patients where the alternative approach was equivocal. In three cases, the samReporter confirmed that resistance or an atypical substitution was present at NS5A position 30. In three further cases, it confirmed that the sofosbuvir-resistant NS5B substitution S282T was absent. This suggests the direct read translation approach implemented is of value for interpreting viral deep sequencing data.

Development of an E-Training Model to Reduce Errors in Claims Presented to the U.S. Department of Veterans' Affairs

The objectives of this study are: (1) Investigate and suggest ways to employ e-training to inform and educate anyone [including U.S. military veterans] filing disability or pension claims; (2) Determine ways to improve current training methods and techniques to assist Veteran Service Organizations (VSO) better understand the nuances of filing a successful claim though e-training; (3) Simplify access to information, laws and regulations required by law to submit an accurate disability or pension claim by use of smart dialog-based interaction during claims preparation. This research will be based on the collection of data from primary, secondary and expert sources. These resources will include, research papers, digital studies, journals, and VSO online documents. In addition, data will be collected using a survey, questionnaires, and interviews of persons serving as VSOs and employees working at authorized Veteran Administration (VA) Regional Offices in Hawaii and the Philippines. The main contribution of this research will include the development of an e-training module to make the VSO benefit filing process error-free and more efficient.

Radtools: R utilities for convenient extraction of medical image metadata

The radiology community has adopted several widely used standards for medical image files, including the popular DICOM (Digital Imaging and Communication in Medicine) and NIfTI (Neuroimaging Informatics Technology Initiative) standards. These file formats include image intensities as well as potentially extensive metadata. The NIfTI standard specifies a particular set of header fields describing the image and minimal information about the scan. DICOM headers can include any of >4,000 available metadata attributes spanning a variety of topics. NIfTI files contain all slices for an image series, while DICOM files capture single slices and image series are typically organized into a directory. Each DICOM file contains metadata for the image series as well as the individual image slice. The programming environment R is popular for data analysis due to its free and open code, active ecosystem of tools and users, and excellent system of contributed packages. Currently, many published radiological image analyses are performed with proprietary software or custom unpublished scripts. However, R is increasing in popularity in this area due to several packages for processing and analysis of image files. While these R packages handle image import and processing, no existing package makes image metadata conveniently accessible. Extracting image metadata, combining across slices, and converting to useful formats can be prohibitively cumbersome, especially for DICOM files. We present radtools, an R package for convenient extraction of medical image metadata. Radtools provides simple functions to explore and return metadata in familiar R data structures. For convenience, radtools also includes wrappers of existing tools for extraction of pixel data and viewing of image slices. The package is freely available under the MIT license at GitHub and is easily installable from the Comprehensive R Archive Network.

ZF-Mapper: Simple and Complete Freeware for Fluorescence Quantification in Zebrafish Images.

Zebrafish embryos and larvae have become popular vertebrate models because their body walls are transparent, which enables live imaging of target organs using fluorescent protein transgenes or dye staining. Software packages for the quantification of these fluorescent signals are available from both commercial and noncommercial sources; however, their algorithms are complicated and their resources (code) have mostly not been openly shared. In this study, we developed a simple and robust open-source software tool named "ZF-Mapper" for the quantification of the fluorescence intensity of each pixel in zebrafish images with batch image file processing capability. Using this software, we can evaluate the three-dimensional (3D) distribution of fluorescence intensity among zebrafish cells by analyzing each image pixel. We tested ZF-Mapper for the analysis of zebrafish with macrophage-specific enhanced green fluorescent protein (EGFP) and obtained results that were equivalent to those acquired using the conventional image analysis software ImageJ. We further applied ZF-Mapper to the analysis of zebrafish with cancer cell xenografts and quantified the amount of implanted melanoma cells labeled with a tdTomato red fluorescent protein in the whole body and the tail region. In addition, by combining ZF-Mapper with R freeware, we created an interactive 3D scatter plot of the fluorescence intensities of macrophage-EGFPs in zebrafish. In summary, we developed the Python-based freeware ZF-Mapper for the quantification of fluorescent signals in multiple zebrafish images, which enables fluorescence-based zebrafish screening. We provide the source code and the executable application software for Windows (.exe) and macOS (.app).

Circulating cell-free methylated DNA (cfmeDNA) to predict postoperative recurrence in patients with muscle-invasive bladder cancer (MIBC).

454 Background: CfmeDNA is a promising non-invasive biomarker to assess solid tumor burden: i) CpG island methylation changes in cfDNA are stable ii) methylation is tissue- and tumor- specific iii) methylation target size is larger and more sensitively detected than genomic alterations. CfmeDNA Immunoprecipitation and high throughput sequencing (cfMeDIP-seq) is an innovative assay for genome-wide bisulfite-free plasma DNA methylation profiling, that permits CpG enrichment. We tested the feasibility of cfmeDNA to predict recurrence of MIBC post- radical cystectomy (RC). Methods: We selected 12 pts who underwent RC for MIBC: 6 pts who had recurrent disease within 2-3yrs after RC (A) and 6 pts who did not (B). 119 healthy pts without BC were controls. cfDNA isolated from 1ml of plasma samples collected after RC and before recurrence (A) or during follow-up in those who did not recur (B) was analyzed by the cfMeDIP-seq using 10ng cfDNA. The data were analyzed using the MEDIPS program and differentially methylated regions (DMR) between the cohorts were studied. ENCODE ChIP-seq analytical pipeline was used for fastq file processing and peak calling. Results: The average cfDNA isolated from 1ml of plasma was 13.1 ng (6.4-19.7) in A and 17.1 ng (13.6-21.2) in B. The median time from RC to plasma collection were respectively 9.3 mos (3.4-91.3) vs 12.3 mos (2.9-150). Median time from plasma collection to recurrence was 21.9 mos (0.25-141.3). We identified ~137,000 peaks in ≥1 sample. The supervised classification identified 61 DMR (FDR<0.050), predominantly located in intergenic region, which distinguished A from B. Randomized sample tests proved the discriminatory power of the identified set. Supervised analysis comparing the status of the identified DMRs relative to healthy controls showed 28 regions were differentially methylated (logFC > +/- 1, FDR < 0.05). The study is limited by retrospective design and sample size. Conclusions: This is the first study to demonstrate that cfmeDNA can be readily harvested from MIBC pts to detect cancer-specific methylation patterns and predict recurrence post-RC. Prospective validation will enable the selection of suitable pts for adjuvant therapy.

English

A computer program is a set of electronic instructions executed from within the computer memory by the computer central processing unit. Its purpose is to control the functionalities of the computer allowing it to perform various tasks. Basically, a computer program is written by humans using a programming language. A programming language is the set of grammatical rules and vocabulary that governs the correct writing of a computer program. In practice, the majority of the existing programming languages are written in English-speaking countries and thus they all use the English language to express their syntax and vocabulary. However, many other programming languages were written in non-English languages, for instance, the Chinese BASIC, the Chinese Python, the Russian Rapira, and the Arabic Loughaty. This paper discusses the design and implementation of a new programming language, called Phoenix. It is a General-Purpose, High-Level, Imperative, Object-Oriented, and Compiled Arabic programming language that uses the Arabic language as syntax and vocabulary. The core of Phoenix is a compiler system made up of six components, they are the Preprocessor, the scanner, the parser, the semantic analyzer, the code generator, and the linker. The experiments conducted have illustrated the several powerful features of the Phoenix language including functions, while-loop, and arithmetic operations. As future work, more advanced features are to be developed including inheritance, polymorphism, file processing, graphical user interface, and networking.

On the Lifecycle of the File

Users and Operating Systems (OSs) have vastly different views of files. OSs use files to persist data and structured information. To accomplish this, OSs treat files as named collections of bytes managed in hierarchical file systems. Despite their critical role in computing, little attention is paid to the lifecycle of the file, the evolution of file contents, or the evolution of file metadata. In contrast, users have rich mental models of files: they group files into projects, send data repositories to others, work on documents over time, and stash them aside for future use. Current OSs and Revision Control Systems ignore such mental models, persisting a selective, manually designated history of revisions. Preserving the mental model allows applications to better match how users view their files, making file processing and archiving tools more effective. We propose two mechanisms that OSs can adopt to better preserve the mental model: File Lifecycle Events (FLEs) that record a file’s progression and Complex File Events (CFEs) that combine them into meaningful patterns. We present the Complex File Events Engine (CoFEE), which uses file system monitoring and an extensible rulebase (Drools) to detect FLEs and convert them into complex ones. CFEs are persisted in NoSQL stores for later querying.

About comprehensive edition on the culture of Belarusian speech

The introduction of this paper depicts the issues related to the creation of the first in Belarusian linguistics “Pronouncing dictionary of the Belarusian language”, prepared at the junction of interdisciplinary research by specialists of two academic institutions. The dictionary proposes literary pronunciation for 117,000 words with full transcription taking into account existing orthoepic options that do not contradict the norm. It also describes the methodological basis of the work associated with the consolidation of the norms of the literary pronunciation. the main part describes in detail the structure and mechanism of algorithms for generating spelling words in phonetic transcription.The main types of combinatorial consonant changes that determine the specificity of the phonetic system of the Belarusian literary language are shown. The authors provide examples and results of instrumental processing of sound files to explain orthoepical controversial points mainly related to the phonetic adaptation of borrowed vocabulary, as well as clarification of certain phonetic positions. In particular, there are specific cases of operation for the new literary language of the opposition “voiceless fricative [ф] – voiced fricative [в]ˮ with a description of the physical characteristics of these sounds. The reasonability of displaying phonetic variations in the dictionary as a consequence of the development of language is also substantiated.Conclusion draws attention to the innovation, economic and social importance of the publication. It provides guidance on its practical use, the expediency of further interdisciplinary research in linguistics and information technology.

Radtools: R utilities for convenient extraction of medical image metadata.

The radiology community has adopted several widely used standards for medical image files, including the popular DICOM (Digital Imaging and Communication in Medicine) and NIfTI (Neuroimaging Informatics Technology Initiative) standards. These file formats include image intensities as well as potentially extensive metadata. The NIfTI standard specifies a particular set of header fields describing the image and minimal information about the scan. DICOM headers can include any of >4,000 available metadata attributes spanning a variety of topics. NIfTI files contain all slices for an image series, while DICOM files capture single slices and image series are typically organized into a directory. Each DICOM file contains metadata for the image series as well as the individual image slice. The programming environment R is popular for data analysis due to its free and open code, active ecosystem of tools and users, and excellent system of contributed packages. Currently, many published radiological image analyses are performed with proprietary software or custom unpublished scripts. However, R is increasing in popularity in this area due to several packages for processing and analysis of image files. While these R packages handle image import and processing, no existing package makes image metadata conveniently accessible. Extracting image metadata, combining across slices, and converting to useful formats can be prohibitively cumbersome, especially for DICOM files. We present radtools, an R package for convenient extraction of medical image metadata. Radtools provides simple functions to explore and return metadata in familiar R data structures. For convenience, radtools also includes wrappers of existing tools for extraction of pixel data and viewing of image slices. The package is freely available under the MIT license at https://github.com/pamelarussell/radtools and is easily installable from the Comprehensive R Archive Network ( https://cran.r-project.org/package=radtools).

Radtools: R utilities for convenient extraction of medical image metadata

The radiology community has adopted several widely used standards for medical image files, including the popular DICOM (Digital Imaging and Communication in Medicine) and NIfTI (Neuroimaging Informatics Technology Initiative) standards. These file formats include image intensities as well as potentially extensive metadata. The NIfTI standard specifies a particular set of header fields describing the image and minimal information about the scan. DICOM headers can include any of >4,000 available metadata attributes spanning a variety of topics. NIfTI files contain all slices for an image series, while DICOM files capture single slices and image series are typically organized into a directory. Each DICOM file contains metadata for the image series as well as the individual image slice. The programming environment R is popular for data analysis due to its free and open code, active ecosystem of tools and users, and excellent system of contributed packages. Currently, many published radiological image analyses are performed with proprietary software or custom unpublished scripts. However, R is increasing in popularity in this area due to several packages for processing and analysis of image files. While these R packages handle image import and processing, no existing package makes image metadata conveniently accessible. Extracting image metadata, combining across slices, and converting to useful formats can be prohibitively cumbersome, especially for DICOM files. We present radtools, an R package for convenient extraction of medical image metadata. Radtools provides simple functions to explore and return metadata in familiar R data structures. For convenience, radtools also includes wrappers of existing tools for extraction of pixel data and viewing of image slices. The package is freely available under the MIT license at GitHub and is easily installable from the Comprehensive R Archive Network.

Pengamanan Aplikasi Menggunakan Algoritma Camelia


 Safeguarding Applications Using the Camelia Algorithm is a software that can assist in securing or locking an application file, where the file can no longer be opened by anyone except the owner of the file. In this research the locking and reopening process of the application file is performed using the Camelia Algorithm , So that it produces a software that can lock and open an application file.