Analysis Software Package Research Articles

MetArea: a software package for analysis of the mutually exclusive occurrence in pairs of motifs of transcription factor binding sites based on ChIP-seq data

MetArea: a software package for analysis of the mutually exclusive occurrence in pairs of motifs of transcription factor binding sites based on ChIP-seq data

ChatGPT as a data analyst: an exploratory study on AI-supported quantitative data analysis in empirical research

Social scientists are faced with the challenge of designing complex studies and analyzing collected data via various programs such as R, Stata, SPSS, or Python. This often requires the use of analytical procedures and specific software packages that are beyond an individual’s established skillsets and technical knowledge. To address these challenges, generative artificial intelligence, such as ChatGPT, can now be employed as ‘assistants’—with both associated risks and benefits. Accordingly, this paper explores the potential and pitfalls of using a tool like ChatGPT as an assistant in quantitative data analysis. We investigate the practical use of ChatGPT-3.5 by replicating analyses and findings in everyday scientific research. Unlike previous studies, which have primarily focused optimizing the use of chatbots for code generation, our approach examines an amateur level use of AI tools to support and reference regular research activities, with an emphasis on minimal technical expertise. While we overall conducted three experiments, with the goal to replicate academic papers, the article’s focus is on the methodologically most complex one, by De Wet et al. from 2020. In this case AI is used for the step-by-step replication of the two-dimensional model of value types proposed by Schwartz (2012). The results of this experiment highlight the challenges of using ChatGPT 3.5 for specific, detailed tasks in academic research, as a tendency for responses to repeat in loops when solutions were not readily available emerged at several stages. Thus, we concluded that there are severe limitations in the AI’s ability to provide accurate and comprehensive solutions for complex tasks and emphasize the need for caution and verification when using AI powered tools for complex research procedures.

The effect of blade turning angle on rotation improvement of a small horizontal axis wind turbine

Optimization of wind turbine aerodynamic performances implies solving the problem in the domains such as airfoil selection, blade rotation angle, chord optimization, number of blades, appropriate tip speed ratio, etc. The current paper studies the effect of blade rotation angle [Formula: see text] on power coefficient [Formula: see text], torque [Formula: see text] and mechanical power [Formula: see text] in a small horizontal axis wind turbine ( HAWT). The analysis involves two models of blades ( V and) of the airfoil class SD 7003. The first part of the paper employs numerical analysis, that is, Ansys CFX and Ansys Fluent software packages, to define wind turbine characteristics. The obtained results indicate that as the rotation angle [Formula: see text] increases the [Formula: see text] increases within an appropriate range of tip speed ratio [Formula: see text] change. The second part describes experimental investigation conducted on considered HAWT to define the values of [Formula: see text] and [Formula: see text] for studied blade rotation angles and comparison with the values obtained from Ansys. Existing differences in values are a consequence of the design of the HAWT, that is, the influence of the mass moment of inertia of the rotor and generator as well as the placement of the generator. Experimental setup and methodology allow for investigating the effect of different blade models, rotor and generator structure on wind turbine torque and mechanical power output characteristic.

Application for acoustic assessment: A pilot study in Parkinson’s patients

Background: Patients with Parkinson’s disease (PD) often experience speech impairment that impacts their daily lives. In speech therapy for PD patients, it is important to use instruments to evaluate acoustic characteristics and support rehabilitation programs. However, in Thailand, access to acoustic assessment instruments is limited due to their high price and lack of portability. Objectives: This study’s aim was to develop an application for acoustic assessment (AAA) and to conduct a pilot study of the application among healthy aging (HA) and aging PD subjects. Materials and methods: This study was a developmental research design comprising three distinct phases. Phase one focused on the development of the AAA and evaluation of the accuracy and precision of the application. In phase two, a comparative analysis was conducted between AAA and Praat, a speech analysis software package, among twenty HA. Five acoustic parameters: loudness, jitter, shimmer, high frequency (Hf0), and low frequency (Lf0), were used to determine concurrent validity. Phase three compared both AAA and Praat with twenty aging PD subjects, examining the concurrent validity and reliability, and comparing the acoustic parameters of HA users with those of the aging PD cohort. Results: In phase one, the AAA shows strong accuracy ranging from 96.86% to 99.59% and high precision, with a Coefficient of Variation (%CV) of 1.65%-3.78%. In phase two, the concurrent validity of AAA compared with Praat in HA exhibited significant and very strong correlations (rs ≥ 0.90, p > 0.05) in all acoustic parameters, except for shimmer, which showed significant and strong correlations (rs = 0.73, p = 0.00). In phase three, the concurrent validity of AAA compared with Praat in aging PD subjects exhibited significant and very strong correlations (rs ≥ 0.90, p > 0.05) in loudness, Hf0, and Lf0, whereas significant and strong correlations were shown in jitter (rs = 0.85, p = 0.00) and shimmer (rs = 0.82, p = 0.00). The Intraclass Correlation Coefficient (ICC) exhibited excellent reliability in all acoustic parameters (r > 0.90). When comparing the HA and aging PD subjects using AAA, significant differences (p < 0.05) were observed in all acoustic parameters, except for Lf0 (p < 0.55). Conclusion: The AAA demonstrates high concurrent validity and reliability. It can effectively be utilized for testing in PD groups, serving as an alternative tool for evaluating acoustic characteristics and aiding in treatment planning.

MRSimulator: A cross-platform, object-oriented software package for rapid solid-state NMR spectral simulation and analysis.

The open-source Python package, MRSimulator, is presented as a simple-to-use, fast, versatile, and extendable package capable of simulating one- and higher-dimensional Nuclear Magnetic Resonance (NMR) spectra under static, magic-angle, and variable-angle conditions. High benchmarks in spectral simulations are achieved by assuming that there are no degeneracies in the energy eigenstates, i.e., all dipolar couplings are in the weak limit and that there are no rotational resonances during evolution periods. Under these assumptions, the symmetry pathway formalism is exploited to reduce an NMR method applied to a spin system into a sum of individual transition pathways, whose signals are more efficiently calculated individually than as part of a full-density matrix simulation. To increase numerical efficiencies further, our approach restricts coherence transfer among transitions to pure rotations about an axis in the x-y plane of the rotating frame or through an artificial total mixing operation between selected transitions of adjacent free evolution periods. The assumptions used in this approach are valid for most commonly used solid-state NMR methods. Details of the implementation, along with example code usage, are given, including a least-squares spectral analysis.

"I Haven't Told Other People. I Want to Keep My Dignity": HIV Related Stigma Among the Elderly in Uganda.

Numerous studies focus on stigma, HIV disclosure's impact on treatment compliance, especially in younger groups. Limited research exists about older individuals. We therefore explored issues related to disclosure of HIV status and HIV-related stigma in the elderly. This was an exploratory qualitative study, employing Straussian Grounded Theory. We enrolled individuals aged 60 and above, living with HIV and receiving care from the Infectious Disease Institute, Uganda. We conducted 4 focus group discussions to explore HIV related stigma and self-disclosure in participants using questionnaires that we had developed and pilot-tested. The discussions were audio recorded, transcribed and translated. Using NVivo software package for qualitative analysis, we developed primary and secondary nodes and subsequent emergent themes. We recruited 38 participants for the focus group discussions. Emergent themes were: types of disclosure, reasons for disclosure or non-disclosure, who was disclosed to and the reasons for disclosure, experienced stigma and resolving dissonance in non-disclosure. Our findings reveal HIV-related challenges for the elderly due to stigma and disclosure. There is need to combat this situation by normalizing societal expectations, roles and sexuality in the elderly as a way of fighting HIV/AIDS related stigma.

Handling missing data in longitudinal clinical trials: three examples from the pediatric psychology literature.

Researchers by default tend to choose complex models when analyzing nonindependent response variable data, this may be particularly applicable in the analysis of longitudinal trial data, possibly due to the ability of such models to easily address missing data by default. Both maximum-likelihood (ML) estimation and multiple imputation (MI) are well-known to be acceptable methods for handling missing data, but much of the recently published quantitative literature has addressed questions regarding the research designs and circumstances under which one should be chosen over the other. The purpose of this article is threefold. First, to clearly define the assumptions underlying three common longitudinal trial data analysis models for continuous dependent variable data: repeated measures analysis of covariance (RM-ANCOVA), generalized estimating equation (GEE), and a longitudinal linear mixed model (LLMM). Second, to clarify when ML or MI should be chosen, and to introduce researchers to an easy-to-use, empirically well-validated, and freely available missing data multiple imputation program: BLIMP. Third, to show how missing longitudinal trial data can be handled in the three data analysis models using three popular statistical analysis software packages (SPSS, Stata, and R) while keeping the published quantitative research in mind.

Diagnostic Accuracy and Prognostic Value of Relative Apical Sparing in Cardiac Amyloidosis - Systematic Review and Meta-Analysis.

Although the relative apical sparing (RAPS) pattern of left ventricular (LV) longitudinal strain is a hallmark of cardiac amyloidosis, recent studies have raised concerns about its accuracy. The aim of this systematic review was to investigate diagnostic test accuracy (DTA) and prognostic impact of RAPS in cardiac amyloidosis. We searched PubMed, Embase, and Scopus for manuscripts that could potentially be used in the DTA arm and prognosis arm. Thirty-seven studies were used for DTA analysis. The pooled sensitivity, specificity, and diagnostic odds ratio were 61% (95% confidence interval [CI] 54-68%), 83% (95% CI 80-86%), and 8.9 (95% CI 6.1-13.1), respectively. These values did not differ regardless of the presence of aortic stenosis, but the diagnostic odds ratio differed significantly among analytical software packages. For the prognosis arm, 6 studies were dichotomously assessed for RAPS, and 5 were assessed quantitatively. The pooled proportion of RAPS was 49% and the pooled estimate of the RAPS ratio was 1.40. Although RAPS was associated with outcome (hazard ratio [HR] 1.87; 95% CI 1.15-3.04; P=0.011), its significance disappeared after trim and fill analysis (HR 1.42; 95% CI 0.85-2.38; P=0.184). RAPS has a modest DTA with a significant vendor dependency and does not provide robust prognostic information.

Simulation inversion analysis of simultaneous commutation failure of Zhaoyi and Yindong DC

Abstract Aim at the three times simultaneous commutation failure of two Multi-outfeed and Multi-infeed DC Systems in a Similar Path of Ningxia, the Ningxia power grid model is built in Power System Analysis Software Package (PSASP) with actual parameters, and the accident inversion simulation is carried out based on the operation state of the power grid before the fault. Based on the inversion simulation, the simulation results were compared with the measured PMU data. The results showed that the trend of simulation and the measured curve is consistent, and the simulation was slightly more serious than the actual fault, but the overall error was less than 10%, which verified the accuracy of the simulation model and method, and provided a basis for the subsequent simulation analysis of the power grid operation mode.

Morphology Determination of Luminescent Carbon Nanotubes by Analytical Super-Resolution Microscopy Approaches.

The ability to determine the precise structure of nano-objects is essential for a multitude of applications. This is particularly true of single-walled carbon nanotubes (SWCNTs), which are produced as heterogeneous samples. Current techniques used for their characterization require sophisticated instrumentation, such as atomic force microscopy (AFM), or compromise on accuracy. In this paper, we propose to use super-resolution microscopy (SRM) to accurately determine the morphology (orientation, length, and shape) of individual luminescent SWCNTs. We generate super-resolved images using three recently published SRM analytical software packages (DPR, eSRRF, and MSSR) and metrologically compare their performances to determine the morphological properties of SWCNTs. For this, ground-truth information on nanotube morphologies was obtained using polarization measurements and AFM to directly correlate the results from SRM at the single particle level. We show a more than 4-fold improvement in resolution over standard photoluminescence imaging, revealing hidden morphologies as efficiently as AFM. We finally demonstrate that DPR, and eventually eSRRF, can effectively assess SWCNT length distribution in a much faster and more accessible way than AFM. We believe that this approach can be generalized to other types of luminescent nanostructures and thus become a standard for rapid and accurate characterization of samples.

Autenthity of the indicators of complex visual-motor reaction for trap shooters

The aim of the study was to determine the validity and stability of choice reaction time testing in trap shooters. The following research methods were used: theoretical analysis and summarization of data from scientific and methodological literature and the Internet, medical-biological methods, pedagogical observation, and mathematical statistics methods. Relevant calculations were conducted using the MS Excel analysis software package and functions from the Statistica software package. The study involved 27 athletes of varying qualifications in trap shooting. Each athlete's reaction time was measured in ten attempts. Satisfactory reliability of choice reaction time testing was found among shooters of average skill level (Candidate for Master of Sports, 1st and 2nd categories) with a reliability coefficient of ICC=0.767. Excellent reliability of the test (ICC=0.933) was found in highly qualified shooters (Master of Sports and International Master of Sports). The tested choice reaction time methodology demonstrated acceptable informativeness (validity) and reliability (stability) for the training process of trap shooters.

Analysis of load flow based on power system analysis software package by using the IEEE 30-bus system

Abstract A power-flow study is a numerical analysis to judge the stability of the power system during operation. By analyzing the results of the load flow calculations, the transmission line, the load distribution, the power factor, the equipment capacity, the distribution network, and the power quality and reliability of the distribution network are improved. This paper uses the IEEE 30-Bus system as an example of building a modified system via the power system analysis software package (PSASP) for the power-flow study. Other simulation tools are validated by using the MATPOWER toolbox and MATLAB/Simulink. The result of the load flow calculation for the three simulation tools is almost consistent, so the practicability of the tool is proved. It is verified that the PSASP is one of the reference simulation tools for power system analysis.

Online Monitoring System of Electromechanical Transient Simulation Data of Distribution Network Based on Edge Computing

The current distribution network is developing toward the direction of information and intelligent distribution Internet of Things (IoT). In order to explore the online monitoring system for transient electromechanical simulation of distribution networks, this paper is based on the equivalent model of generator sets. Firstly, it describes the relevant theoretical knowledge of edge computing, designs the distribution IoT based on edge computing, and briefly introduces its network architecture. Secondly, based on the discrete-time domain equivalent model of generators, the electromechanical transient simulation distribution network is constructed by introducing the machine network division of the power network. Finally, the Western System Coordinating Council (WSCC)-3 units and 9 nodes are taken as an example, and simulation experiments are conducted under two fault simulation conditions to verify the effectiveness of the simulation model. The results show that under the two fault simulation conditions, the results of equivalent model simulation of generator terminal voltage and relative power angle change are like those of the Power System Analysis Software Package (PSASP). The changing trend of the two is similar and stable. After the PSASP results are stabilized at a value, the simulation results fluctuate extremely up and down the value. For example, under fault condition 1, the changing trend of the relative power angle of the No. 2 generator is first fluctuating and then becomes stable. After violent fluctuation, the relative power angle tends to be stable from about 20s to -12.35°. The result of PSASP software is stable at -12.35°. The transient electromechanical simulation of the generator equivalent model can provide some ideas for the online monitoring system of the distribution network.

Prevalence and Pattern of Ear Disease Among Primary School Students in Samoa: Preliminary Results from ENT Clinic Outreach to Urban, Rural and Remote Settings.

Objectives: To assess the prevalence and pattern of ear disease among students attending primary school in urban, rural, and remote regions of Samoa in order to develop an evidence-based national school ear and hearing health program. Methods: Retrospective clinical data review of all primary school students seen by the Ear, Nose & Throat Clinic of Samoa during school-based outreach visits from March 2022 to April 2024. A purposefully designed spreadsheet was created to extract the following information from the clinical records: school location (urban, rural, remote), gender (male, female), age (years), age category (0-4, 5-9, 10-14, 15+ years), right ear diagnosis, left ear diagnosis. Data were entered into the SPSS statistical software package for descriptive statistical analysis and association tests of significance. Results: A total of 1491 primary school students were seen for ear health examinations (51.1% male, 48.9% female), with a mean age of 9.1 years (SD = 2.3). Five primary schools were included, representing urban (n = 865), rural (n = 258), and remote (n = 368) settings. Overall, 682 (45.7%) students had normal ear examination results for both ears, 237 (15.9%) had an ear pathology in 1 ear only, and 568 (38.1%) had ear pathology in both ears. Bilateral ear pathology was significantly higher among students who were in the 5 to 9 age group (P < .00001), female (P = .035), and from rural settings (P = .0001). The most common pathology was impacted cerumen (36.8%), followed by otitis media with effusion (7.5%). Overall prevalence of chronic suppurative otitis media (CSOM) was 2.6% (n = 39 students). Following the school visits, no further intervention was required for 1180 students (79%), mostly due to successful cerumen and foreign body removals for 468 students (31.4%). Conclusion: Impacted cerumen is a significant issue among Samoan school-aged students, and future school-based ear health programs should include staff members trained in cerumen removal. CSOM prevalence suggests an avoidable burden of disease that must be addressed.

Determination of the structure of weakly ordered films according to x-ray diffraction data

A method for searching for parameters of structural models of weakly ordered thin films based on X-ray diffraction data containing a small number of reflexes is proposed. The developed method makes it possible to narrow down the number of possible structural models, despite the small number of interference maxima, determine the parameters of possible elementary cells and index the corresponding peaks on diffractograms. It is shown how the use of a priori data makes it possible to obtain physically adequate solutions. The method of determining structural parameters is demonstrated by analyzing an experimental curve containing only 3 diffraction peaks (maxima). The corresponding search algorithms are implemented within the framework of the analytical software package BARD (Basic Analisys of xRay Diffraction).

ColocZStats: a z-stack signal colocalization extension tool for 3D slicer.

Confocal microscopy has evolved to be a widely adopted imaging technique in molecular biology and is frequently utilized to achieve accurate subcellular localization of proteins. Applying colocalization analysis on image z-stacks obtained from confocal fluorescence microscopes is a dependable method of revealing the relationship between different molecules. In addition, despite the established advantages and growing adoption of 3D visualization software in various microscopy research domains, there have been few systems that can support colocalization analysis within a user-specified region of interest (ROI). In this context, several broadly employed biological image visualization platforms are meticulously explored in this study to understand the current landscape. It has been observed that while these applications can generate three-dimensional (3D) reconstructions for z-stacks, and in some cases transfer them into an immersive virtual reality (VR) scene, there is still little support for performing quantitative colocalization analysis on such images based on a user-defined ROI and thresholding levels. To address these issues, an extension called ColocZStats (pronounced Coloc-Zee-Stats) has been developed for 3D Slicer, a widely used free and open-source software package for image analysis and scientific visualization. With a custom-designed user-friendly interface, ColocZStats allows investigators to conduct intensity thresholding and ROI selection on imported 3D image stacks. It can deliver several essential colocalization metrics for structures of interest and produce reports in the form of diagrams and spreadsheets.

Ten quick tips for clinical electroencephalographic (EEG) data acquisition and signal processing.

Electroencephalography (EEG) is a medical engineering technique aimed at recording the electric activity of the human brain. Brain signals derived from an EEG device can be processed and analyzed through computers by using digital signal processing, computational statistics, and machine learning techniques, that can lead to scientifically-relevant results and outcomes about how the brain works. In the last decades, the spread of EEG devices and the higher availability of EEG data, of computational resources, and of software packages for electroencephalography analysis has made EEG signal processing easier and faster to perform for any researcher worldwide. This increased ease to carry out computational analyses of EEG data, however, has made it easier to make mistakes, as well. And these mistakes, if unnoticed or treated wrongly, can in turn lead to wrong results or misleading outcomes, with worrisome consequences for patients and for the advancements of the knowledge about human brain. To tackle this problem, we present here our ten quick tips to perform electroencephalography signal processing analyses avoiding common mistakes: a short list of guidelines designed for beginners on what to do, how to do it, and what not to do when analyzing EEG data with a computer. We believe that following our quick recommendations can lead to better, more reliable and more robust results and outcome in clinical neuroscientific research.

Auto-MuRCiS: a streamlined software package for analysis of multiplex, randomized CRISPR interference sequencing data.

Multiplex, randomized CRISPR interference sequencing (MuRCiS) allows for the simultaneous identification of multiple gene knockouts that together influence microbial processes. Here, we report on an updated analysis tool called Auto-MuRCiS that utilizes Docker to make the analysis of these data rapid and more user-friendly.

Algorithm for the functioning of the analysis and evaluation software package security of software of automated systems internal affairs bodies

Algorithm for the functioning of the analysis and evaluation software package security of software of automated systems internal affairs bodies

Step height measurement of monoatomic silicon crystal lattice steps with a commercial atomic force microscope

Abstract Precise control of advanced materials relies on accurate dimensional metrology at the sub-nanometre scale. At this scale, the accuracy of scanning probe microscopy (SPM) has been limited by the lack of traceable transfer standard artefacts with calibration structures of suitable dimensions. With the adoption in 2019 of the silicon crystal lattice spacing as a secondary realization of the metre in the International System of Units (SI), SPM users have direct access to a realization of the SI metre at the sub-nanometre level by means of the step height of self-assembled monatomic lattice steps that can form on the surface of silicon crystals. A key challenge of successfully adopting this pathway is establishing the need for established protocols to minimize measurement errors and artifacts in routine laboratory use.&amp;#xD;In this study, step height measurements of monoatomic lattice steps in an ordinal/staircase structure on a Si(111) crystal surface have been derived from images acquired with a commercially available, research-level atomic force microscope (AFM). Measurement results derived from AFM images using three different SPM image processing and analysis software packages are compared. Significant sources of measurement uncertainty are identified; principally the contribution from the dependence on scan direction. The calibration of the&amp;#xD;AFM derived from this measurment was used to traceably measure the sub-nanometre lattice steps on a silicon carbide crystal surface to demonstrate the viability of this calibration pathway.&amp;#xD;