Windows OS Research Articles

JOES: An application software for Judd-Ofelt analysis from Eu3+ emission spectra

In this paper we will be presenting JOES (Judd-Ofelt from Emission Spectra), an application software for calculation of the Judd-Ofelt intensity parameters and derived quantities from the emission spectra of Eu3+ doped materials. The program is written to be user friendly and it requires no previous experience in the field of study. This Free and Open-Source program written in JAVA, works on Windows, Linux and MAC OS operating systems. Program has been tested on three europium doped oxides with good luminescent properties: TiO2:Eu3+, ZrO2:Eu3+ and Nb2O5:Eu3+. We wish to give to the researchers this theoretical tool which can make the calculations easier, faster and more reliable.

Installing, Maintaining, and Using a Local Copy of BLAST for Compute Cluster or Workstation Use.

The Basic Local Alignment Search Tool (BLAST) is the first resource to computationally characterize a novel amino acid or nucleic acid sequence. BLAST plays important roles in genomics, transcriptomics, and protein science. For numerous academic and commercial researchers, neither BLAST Web servers nor cloud resources satisfy the requirements of high-throughput comparative genomic pipelines or company policies. For such users, this unit describes how to install BLAST locally, either on a standalone workstation, or preferably on a compute cluster. We provide practical guidance for the planning and the installation under the LINUX, Windows, and Mac OS X operating systems. We propose strategies for downloading existing and generating new sequence databases in BLAST format. © 2018 by John Wiley & Sons, Inc.

Instant Clue: A Software Suite for Interactive Data Visualization and Analysis

The development of modern high-throughput instrumentation and improved core facility infrastructures leads to an accumulation of large amounts of scientific data. However, for a majority of scientists the comprehensive analysis and visualization of their data goes beyond their expertise. To reduce this hurdle, we developed a software suite called Instant Clue that helps scientists to visually analyze data and to gain insights into biological processes from their high-dimensional dataset. Instant Clue combines the power of visual and statistical analytics using a straight forward drag & drop approach making the software highly intuitive. Additionally, it offers a comprehensive portfolio of statistical tools for systematic analysis such as dimensional reduction, (un)-supervised learning, clustering, multi-block (omics) integration and curve fitting. Charts can be combined with high flexibility into a main figure template for direct usage in scientific publications. Even though Instant Clue was developed with the omics-sciences in mind, users can analyze any kind of data from low to high dimensional data sets. The open-source software is available for Windows and Mac OS (http://www.instantclue.uni-koeln.de) and is accompanied by a detailed video tutorial series.

IsiKnock: in silico knockouts in signaling pathways.

isiKnock is a new software that automatically conducts in silico knockouts for mathematical models of signaling pathways. The software allows for the prediction of the behavior of biological systems after single or multiple knockout. The implemented algorithm applies transition invariants and the novel concept of Manatee invariants. A knockout matrix visualizes the results. The tool enables the analysis of dependencies, for example, in signal flows from the receptor activation to the cell response at steady state. isiKnock is an open-source tool, freely available at http://www.bioinformatik.uni-frankfurt.de/tools/isiKnock/. It requires at least Java 8 and runs under Microsoft Windows, Linux, and Mac OS.

Creamino: A Cost-Effective, Open-Source EEG-Based BCI System.

This paper presents an open source framework called Creamino. It consists of an Arduino-based cost-effective quick-setup EEG platform built with off-the-shelf components and a set of software modules that easily allow users to connect this system to Simulink or BCI-oriented tools (such as BCI2000 or OpenViBE) and set up a wide number of neuroscientific experiments. Creamino is capable of processing multiple EEG channels in real-time and operates under Windows, Linux, and Mac OS X in real-time on a standard PC. Its objective is to provide a system that can be readily fabricated and used for neurophysiological experiments and, at the same time, can serve as the basis for development of novel BCI platforms by accessing and modifying its open source hardware and software libraries. Schematics, gerber files, bill of materials, source code, software modules, demonstration videos, and instructions on how to use these modules are available free of charge for research and educational purposes online at https://github.com/ArcesUnibo/creamino. Application cases show how the system can be used for neuroscientific or BCI experiments. Thanks to its low production cost and its compatibility with open-source BCI tools, the system presented is particularly suitable for use in BCI research and educational applications.

Calculation of The Stability of the Form of Equilibrium of Discrete Systems

The paper presents an algorithm for calculating the stability of the equilibrium form of the first kind of compressed discrete systems by the displacements method in combination with the methods of iterations and bisection. The use of the methods makes it possible to effectively determine the minimum critical stress or strain at the first bifurcation and their corresponding form of stability loss, both for statically determined and statically undetermined systems. This approach, using matrix forms, makes it possible to significantly simplify the calculations of the analytical condition for the stability loss of compressed discrete systems (the stability loss equation), which has high orders, as well as to construct the form of stability loss corresponding to a critical load, that is, to solve the problem of loss of equilibrium stability. The calculation actually leads to solving a nonlinear transcendental equation, which is the equation of stability loss. The difficulty lies in the absence of an analytical solution of such an equation due to the presence of complex of Zhukovsky functions, which have transcendental functions in their structure. Such solution can be performed only with the use of numerical methods. This algorithm for calculating the loss of equilibrium of the first kind of compressed discrete systems by displacement in combination with the methods of iteration and bisection is implemented in the software complex "Persist" for PC in Windows OS. The program was approbated and implemented in the educational process at the Department of Structural and Theoretical Mechanics of Poltava National Technical Yuri Kondratyuk University during the training of specialists in engineering specialties.

Modern information technologies in organization of geophysical studies

The features of geo-electrical surveying on permanent geophysical stations and in field conditions are described in this article. Modern approaches to geophysical study with IT-technology application, which require an automatic or semiautomatic data recording, express analysis of current experimental results, in a on-line or off-line mode, automatic data acquisition and transmission by GSM net are represented. Described approaches are realized using ftp-server with appropriate settings on a base of standard server’s tools i. e. LAMPP (Linux, Apache, MySQL, PHP, Python) and web techniques: HTML, CGI, SSI, JavaScript, DHTML, CSS. The described approaches were tested on the permanent geophysical station “Nyzhne Selyshche” (Zakarpatska oblast) for a natural electrical field variations monitoring study and during in field study of the shallow layers resistivity by the transient electromagnetic method (TEM). The express analysis of experimental TEM data is shown and illustrated by screenshots demonstrating the operation of program modules developed and handled by OS Windows. Such application can also be used for any other data as where the mobile Internet is available as well as the off-line mode is possible too.

Rqc: A Bioconductor Package for Quality Control of High-Throughput Sequencing Data

As sequencing costs drop with the constant improvements in the field, next-generation sequencing becomes one of the most used technologies in biological research. Sequencing technology allows the detailed characterization of events at the molecular level, including gene expression, genomic sequence and structural variants. Such experiments result in billions of sequenced nucleotides and each one of them is associated to a quality score. Several software tools allow the quality assessment of whole experiments. However, users need to switch between software environments to perform all steps of data analysis, adding an extra layer of complexity to the data analysis workflow. We developed Rqc, a Bioconductor package designed to assist the analyst during assessment of high-throughput sequencing data quality. The package uses parallel computing strategies to optimize large data sets processing, regardless of the sequencing platform. We created new data quality visualization strategies by using established analytical procedures. That improves the ability of identifying patterns that may affect downstream procedures, including undesired sources technical variability. The software provides a framework for writing customized reports that integrates seamlessly to the R/Bioconductor environment, including publication-ready images. The package also offers an interactive tool to generate quality reports dynamically. Rqc is implemented in R and it is freely available through the Bioconductor project (https://bioconductor.org/packages/Rqc/) for Windows, Linux and Mac OS X operating systems.

Клинические типы биполярного аффективного расстройства в позднем возрасте

The aim : was to analize the prevalence of clinical types of bipolar disorder (BD) according to bipolar spectrum concept in geriatric in-patients. Study design : comparative study of the prevalence of different types of BD in aged patients with regard to the age of disease onset (before and after 60 years) in accordance with bipolar spectrum concept. Methods : all the patients included to the study were examined by psychopathological, clinical and psychometrical method (Hamilton Depression Rating Scale — HAM–D, Hamilton Anxiety Rating Scale — HARS, Young Mania Rating Scale — YMRS, MiniMental State Examination — MMSE, Montreal Cognitive Assessment — MoCA and Bipolarity Index by G. Sachs). Statistical data processing was held by STATISTICA 10.0 for Windows OS. Results : according to bipolar spectrum concept the 1st type of BD occurred in 42,7% (n = 50) examined patients, the 2nd type — in 40,2% (n = 47), the 3rd type — in 8,5% (n = 10), the 4th type — in 3,4% (n = 4), the 5th type — in 1,7% (n = 2) and the 6th type — in 3,4% (n = 4). The 1st type of BD was more often presented in patients with disease onset in young and adult age (54,0%) and in men (45,5%). The 2nd type of BD was more common for patients with disease onset in involution period (56,0%) and with late-onset BD after 60 years (50,0%), also this type more often occurred in women (46,8%). The 3rd and the 4th types were presented rarely, although, like the 1st type of BD they occurred predominantly in patients with early-onset BD (9,2 and 3,9% consequently) and in men (10,9 and 5,5% consequently). The rarest type of BD was the 5th type. The 6th type of BD was presented only in a cohort of patients with late-onset of BD (25,0%) with the same frequency in men and women. Among approximately 1/3 of examined patients the disease had its onset in the second life half (after 50 years). New onset BD occuring in the involution period (50–59 years) was more common for women, late-onset BD at the age of 60 anf older — for men. The occurrence rate of mixed affecteive states and hypomanic states increases in case of BD onset during the involution period. For late-onset BD (age 60 and older) depressive episodes with signs of transitoral cognitive disfunction were more common. Conclusion : every type of bipolar spectrum concept may occur in aged patients. New-onset BD in elderly has some special characteristics: during the involution period BD more ofter onsets in women, at the age of 60 and older — in men. Progressively as aging the frequency of new-onset BD with predominant depressive disturbances and cognitive performance disturbances increases.

Effects of Bilateral Nasal Packing on Oxygen Saturation and Blood Pressure

Nasal packing is one of the most common rhinological procedures in ENT practice exerting local in nose and systemic effects. Systemic effects may be due to poor sleep quality, respiratory difficulty, decreased oxygen saturation, circulatory problems and toxic shock syndrome which can threaten the life of a person.The study was done to investigate the effect on bilateral nasal packing on blood oxygen saturation and blood pressure changes. A cross-sectional prospective study was undertaken in Kathmandu Medical College from January 2017 to June 2017. The ethical approval was taken from institutional review committee of KMC and verbal consent was taken from each patient. Thirty patients were included in the study by simple randomized sampling. The association between nasal packing and oxygen saturation and blood pressure was done using ANNOVA and Fisher Exact test. P value of <0.005 was considered statistically significant. SPSS version 20 for windows OS was used for analysis. Blood oxygen saturation on four different days was compared using ANNOVA and paired sample tests. It showed a significant dip on the day of bilateral nasal packing compared to other readings (P value <0.001). Likewise, systolic and diastolic blood pressures showed a significant rise on the day of bilateral nasal packing compared to readings on other days (P value <0.001). Bilateral nasal packing can lead to significant rise in systolic and diastolic blood pressure and a dip in blood oxygen saturation. Thus care has to be taken while performing bilateral nasal packing in normal patients but much more in high risk patients.

ChronQC: a quality control monitoring system for clinical next generation sequencing.

ChronQC is a quality control (QC) tracking system for clinical implementation of next-generation sequencing (NGS). ChronQC generates time series plots for various QC metrics to allow comparison of current runs to historical runs. ChronQC has multiple features for tracking QC data including Westgard rules for clinical validity, laboratory-defined thresholds and historical observations within a specified time period. Users can record their notes and corrective actions directly onto the plots for long-term recordkeeping. ChronQC facilitates regular monitoring of clinical NGS to enable adherence to high quality clinical standards. ChronQC is freely available on GitHub (https://github.com/nilesh-tawari/ChronQC), Docker (https://hub.docker.com/r/nileshtawari/chronqc/) and the Python Package Index. ChronQC is implemented in Python and runs on all common operating systems (Windows, Linux and Mac OS X). tawari.nilesh@gmail.com or pauline.c.ng@gmail.com. Supplementary data are available at Bioinformatics online.

NMπ-improved re-implementation of NM+, a software for estimating gene dispersal and mating patterns.

This study introduces the NMπ computer program designed for estimation of plant mating system and seed and pollen dispersal kernels. NMπ is a re-implementation of the NM+ program and provides new features such as support for multicore processors, explicit treatment of dioecy, the possibility of incorporating uniparentally cytoplasmic markers, the possibility of assessing assortative mating due to phenotypic similarity and inference about offspring genealogies. The probability model of parentage (the neighbourhood model) accounts for missing data and genotyping errors, which can be estimated along with regular parameters of the mating system. The program has virtually no restrictions with respect to a number of individuals, markers or phenotypic characters. A console version of NMπ can be run under a wide variety of operating systems, including Windows, Linux or Mac OS. For Windows users, a graphical user interface is provided to facilitate operating the software. The program, user manual and example data are available on http://www.ukw.edu.pl/pracownicy/plik/igor_chybicki/3694/.

SgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters

BackgroundsgnesR (Stochastic Gene Network Expression Simulator in R) is an R package that provides an interface to simulate gene expression data from a given gene network using the stochastic simulation algorithm (SSA). The package allows various options for delay parameters and can easily included in reactions for promoter delay, RNA delay and Protein delay. A user can tune these parameters to model various types of reactions within a cell. As examples, we present two network models to generate expression profiles. We also demonstrated the inference of networks and the evaluation of association measure of edge and non-edge components from the generated expression profiles.ResultsThe purpose of sgnesR is to enable an easy to use and a quick implementation for generating realistic gene expression data from biologically relevant networks that can be user selected.ConclusionssgnesR is freely available for academic use. The R package has been tested for R 3.2.0 under Linux, Windows and Mac OS X.

A portable platform to collect and review behavioral data simultaneously with neurophysiological signals.

This paper presents a portable platform to collect and review behavioral data simultaneously with neurophysiological signals. The whole system is comprised of four parts: a sensor data acquisition interface, a socket server for real-time data streaming, a Simulink system for real-time processing and an offline data review and analysis toolbox. A low-cost microcontroller is used to acquire data from external sensors such as accelerometer and hand dynamometer. The micro-controller transfers the data either directly through USB or wirelessly through a bluetooth module to a data server written in C++ for MS Windows OS. The data server also interfaces with the digital glove and captures HD video from webcam. The acquired sensor data are streamed under User Datagram Protocol (UDP) to other applications such as Simulink/Matlab for real-time analysis and recording. Neurophysiological signals such as electroencephalography (EEG), electrocorticography (ECoG) and local field potential (LFP) recordings can be collected simultaneously in Simulink and fused with behavioral data. In addition, we developed a customized Matlab Graphical User Interface (GUI) software to review, annotate and analyze the data offline. The software provides a fast, user-friendly data visualization environment with synchronized video playback feature. The software is also capable of reviewing long-term neural recordings. Other featured functions such as fast preprocessing with multithreaded filters, annotation, montage selection, power-spectral density (PSD) estimate, time-frequency map and spatial spectral map are also implemented.

PET of the Brain with 2-18F-2-desoxi-D-Glucose in Differential Diagnosis of Dystonia and Essential Tremor

The purpose.The purpous of the present study is to compare the data of brain PET wih 2-18F-2-desoxi-D-glucose (18-FDG) of patients with dystonia with the results of patients with essential tremor (ET) by analyzing the data with the help of the new calculation method of Z-score of PET results.Materials and methods. In 2010 in journal “Medical Visualization” we published results of PET study with 18-FDG of brain of 11 patients, which have been divided in two groups: the group with dystonia – 7 patients and the group with essential tremor – 4 patients. Glucose metabolism was studied by means of Siemens Exacthigh resolution tomograph. The results were presented in semi quantitative form of percentage of change of glucose metabolism, without comparison with the healthy control. The calculation has been done by means of software package SPM2, installated to the personal computer (OS Windows 2000). Later the Advantage Workstation of the same tomograph, used for the study, was equipped by software package Cortex ID that allows automatic structural and functional analyzes of PET visualization of the brain in comparison with the scans of control group of the same age. The results of such comparison are calculated by this program in the equation of Z-score, that is calculated automatically by special program for each brain zone. In present study we applied Z-score for analyzing again the comparison of the PET results of these two disorders. The group of essential tremor remained the same and included 4 patients studied before. As to the second group of dystonia, we added to it 3 new patients, studied since aforementioned study of 2010, the whole group of D rising up to ten patients. In order to level the conditions of our research, we also compared the former group of dystonia of 7 patients with the group of essential tremor by means of Z-score method.Results. We have detected reliable difference between the group of dystonia and the group of essential tremor, presented in the form of different changes of glucose metabolism in 4 brain zones – left thalamus, right nucleus lentiformis, girus cingularis and the pons. Such result has not changed when we also compared the former staff of dystonia group of 7 patients with essential tremor group.Conclusion.The study has confirmed efficacy PET in differential diagnosis of extrapyramidal disorders and of Z-score method in PET investigations by means of establishing of the correspondence of cinical heterogeneity to PET heterogeneity.

SpecPad: device-independent NMR data visualization and processing based on the novel DART programming language and Html5 Web technology.

SpecPad is a new device-independent software program for the visualization and processing of one-dimensional and two-dimensional nuclear magnetic resonance (NMR) time domain (FID) and frequency domain (spectrum) data. It is the result of a project to investigate whether the novel programming language DART, in combination with Html5 Web technology, forms a suitable base to write an NMR data evaluation software which runs on modern computing devices such as Android, iOS, and Windows tablets as well as on Windows, Linux, and Mac OS X desktop PCs and notebooks. Another topic of interest is whether this technique also effectively supports the required sophisticated graphical and computational algorithms. SpecPad is device-independent because DART's compiled executable code is JavaScript and can, therefore, be run by the browsers of PCs and tablets. Because of Html5 browser cache technology, SpecPad may be operated off-line. Network access is only required during data import or export, e.g. via a Cloud service, or for software updates. A professional and easy to use graphical user interface consistent across all hardware platforms supports touch screen features on mobile devices for zooming and panning and for NMR-related interactive operations such as phasing, integration, peak picking, or atom assignment. Copyright © 2017 John Wiley & Sons, Ltd.

The other guys: automated analysis of marginalized malware

In order to thwart dynamic analysis and bypass protection mechanisms, malware have been using several file formats and evasive techniques. While publicly available dynamic malware analysis systems are one of the main sources of information for researchers, security analysts and incident response professionals, they are unable to cope with all types of threats. Therefore, it is difficult to gather information from public systems about CPL, .NET/Mono, 64-bits, reboot-dependent, or malware targeting systems newer than Windows XP, which result in a lack of understanding about how current malware behave during infections on modern operating systems. In this paper, we discuss the challenges and issues faced during the development of this type of analysis system, mainly due to security features available in NT 6.x kernel versions of Windows OS. We also introduce a dynamic analysis system that addresses the aforementioned types of malware as well as present results obtained from their analyses.

WinPSSP: a revamp of the computer program PSSP and its performance solving the crystal structures of small organic compounds and solids of biological and pharmaceutical interest

The direct-space methods software Powder Structure Solution Program (PSSP) [Pagola &amp; Stephens (2010). J. Appl. Cryst. 43, 370–376] has been migrated to the Windows OS and the code has been optimized for fast runs. WinPSSP is a user-friendly graphical user interface that allows the input of preliminary crystal structure information, integrated intensities of the reflections and FWHM, the definition of structural parameters and a simulated annealing schedule, and the visualization of the calculated and experimental diffraction data overlaid for each individual solution. The solutions are reported as filename.cif files, which can be used to analyze packing motifs and chemical bonding, and to input the atomic coordinates into the Rietveld analysis software GSAS. WinPSSP performance in straightforward crystal structure determinations has been evaluated using 18 molecular solids with 6–20 degrees of freedom. The free-distribution program as well as multimedia tutorials can be accessed at http://users.uoi.gr/nkourkou/winpssp/.

The Role of Economic Efficiency in Competition Law

The main focus of the paper is the function of economics in the current application of competition law. While advocating further economization of the law, it is seen as necessary to widen the extent to which aspects of economic efficiency encompassing static and dynamic efficiency are taken into consideration in an antitrust analysis. Much attention is devoted to these issues, while clarifying what is meant by them, how they are to be understood and implemented in the practice of antitrust authorities, as well as discussing their importance for the promotion of innovation. It is noted that accounting for the economic efficiency aspects differently in the light of competition law allows for the assessment of the market behavior of dominant companies, which traditionally has been seen as anticompetitive. This main issue of the paper is analyzed extensively and explained using the case of Microsoft, a company accused by the US and EU antitrust authorities of abusing its dominant position on the market of operating systems in that it integrated the sale of its base product Windows OS exclusively with other applications (Media Player and Internet Explorer). The differences presented in the research part of the paper as to the way Microsoft was treated by these authorities originated in their different methodology of analysis and assessment of the effects of the sales model launched by Microsoft for products offered to the PC manufacturers and their users, in spite of the US and EU antitrust authorities adopting the same evaluation standard – consumer welfare. Aspects of dynamic efficiency adequate in the assessment of the behavior of innovative firms holding a dominant position proved to be deciding. On the other side of the Atlantic, taking into account the aspects of dynamic efficiency was crucial in coming up with a lighter assessment of Microsoft’s tying compared to the European authorities’ assessment which was based largely on the structural analysis, where the benefits arising from dynamic efficiency are not visible. It is clear from the decisions made by the Commission that it favours regulation over effects generated by competition forces at a later time.

An Embedded Iris Image Acquisition Research

&lt;p&gt;In view of the limitation of traditional identification, it is easy to lose and copy keys, cards or ID cards, and it is easy to forget the password. Here, an embedded application system was designed based on the iris identification technology, the functions of gathering, inputing, and registering the iris information and identification can be realized. The system architecture was designed by using the embedded microprocessor of advanced RISC machines (ARM), which is used as the core. The iris sensor was used to gather the iris information, and the development of software was accomplished with the embedded OS Windows CE. The system can be used on the company entrance guard system, customs security of airport and criminal identification.&lt;/p&gt;