AGScan: a pluggable microarray image quantification software based on the ImageJ library

Challenges and opportunities in modelling of proton exchange membrane fuel cells (PEMFC)

Microarray images, which allow the analysis of hybridization expressions of genes, have been one of the most widely used high-throughput technologies with many different applications. Accurate and automatic microarray image analysis is very important since researchers trust the information provided in these experiments and construct conclusions based on the results produced by the software responsible in analyzing the hybridized arrays. Every microarray image contains thousands of spots, so how to do the spots finding in microarray images accurately and automatically is very meaningful. There are always some problems, such as rotation and distortion, in a microarray image caused by mechanical errors and/or optical errors in the system. All these problems will hinder "doi"ng analysis automatically. Early research has worked out several algorithms to deal with the rotation problem, but those algorithms can not handle microarray images with distortions. In this paper, we propose a robust spots finding method to deal with both rotation and/or distortion in microarray images. The proposed method provides automatic gridding and can handle a microarray image with different type of rotation (global or sub-array rotation) and optical distortions.

Several programs are now available for analyzing the large datasets arising from cDNA microarray experiments. Most programs are expensive commercial packages or require expensive third party software. Some are freely available to academic researchers, but are limited to one operating system. MicroArray Genome Imaging and Clustering Tool (MAGIC Tool) is an open source program that works on all major platforms, and takes users 'from tiff to gif'. Several unique features of MAGIC Tool are particularly useful for research and teaching. http://www.bio.davidson.edu/MAGIC

Image processing is an important stage of every microarray experiment. Reliability of this stage strongly influences the results of data analysis performed on extracted gene expressions. Multiple methods related to array recognition, spot segmentation and measurement extraction have emerged in this area over past several years. Currently there are various commercial and freeware packages available, which perform microarray image analysis. This paper attempts to review microarray image analysis as a whole and to make some experimental comparison of several computational schemes for signal segmentation and measurement extraction. Also we provide a detailed discussion of automated image quality control for use with microarray images.

Porous pavement is a well-documented, low-impact stormwater management technique. When it comes to design of the top layer, the amount of void space (porosity) is often of interest as it influences both infiltration and strength of the pavement. Laboratory equipment can be used to measure the porosity of core samples, but when more detail is required, other equipment or methods must be used. One such method is to scan the entire sample using a computer tomography (CT) machine and then perform some image processing techniques on the scanned data to reconstruct the sample digitally. While the workflow of scanning and processing to produce the 3D digital twin of porous pavement is not new and can be in fact done by open-source or commercial software, there are still some parts of the process that deserve a deeper investigation, for example binarization and segmentation algorithms applied to the solid-and-void space and void space, respectively. This is difficult to do with commercial software which operates like a black-box, and there needs to be more open-source codes that are user-friendly, extendable, and competitive to what commercial software can do. This work presents a MATLAB-based code that allows for a deeper investigation of how one can accurately and efficiently quantify the effective (or connected) void space of a porous pavement sample from a 3D digital model. We demonstrate the effect of dataset coarsening, which can be used to reduce the computational intensity of the algorithm while preserving accuracy. The code is publicly available online to allow for reproducible research and the possibility of extensions for increased functionality and complexity.

The use of exam applications in Kantor Imigrasi Kelas II Sukabumi still uses open sources software, therefore it doesn’t fit the needs. Existing exam applications are still limited in available features. This community service aims to support schools in adopting CBT (Computer Based Test) in administering exams. The problems identified include weaknesses in the existing software and limitations in immigration officer literacy regarding its use. The method of implementing this community service is Service Learning. Activities consist of surveys and CBT software development, training, and mentoring. The implementation of the initial study identified the weaknesses of the existing application, namely regarding aspects of effectiveness and the required features that were unavailable. CBT development is conducted by enhancing usability through adding features and convenience. Training and mentoring are carried out to improve mastery and effectiveness of CBT use. The evaluation showed an increase in the immigration officer understanding of the application, the ability to make evaluations, satisfaction and the effectiveness of using the application. Other outputs were also fulfilled: the CBT application (UHW-CBT Kantor Imigrasi Sukabumi version), training modules, user manuals, intellectual property rights, and publications. This program has increased the adoption of CBT, which can be seen from the aspects of CBT software availability, use, literacy, a form of evaluation and recap, and test score ranking. The follow-up plan for this program is ongoing assistance according to partner needs.

The wind-related processes in the atmospheric roughness layer strongly affect our comfort and health and can have a significant influence on our lives, especially in urban areas. The flow patterns are the main drivers of dispersion and transport of pollutants and particles. However, their evolution in the roughness layer is complex because of disturbances introduced by topology or wind flows in the ABL. Experimental approaches, such as wind-tunnels can significantly improve the understanding of characteristics and be used for the improvement and validation of model approaches. Nevertheless, they are conducted under ideal conditions and do not represent the complex influences occurring in the atmospheric roughness layer. Field measurements are therefore a very practicable approach to study the chaotic behaviour of environmental flow patterns. The effort required to obtain field measurements and their small spatial significance however make it difficult to obtain large spatial monitoring of the phenomena. In the past, numerical studies often used simplified and idealized geometries or methods to model roughness elements and only few studies were conducted in real environments using field measurements to improve the knowledge of roughness layer flows, especially in urban areas. While the different approaches have frequently been used separately, their combination could lead to significant knowledge and new insights into the complex processes. This thesis introduces the theory and major steps taken to model the relevant roughness elements: sub-grid elements, such as surface texture, vegetation elements, such as trees, and impermeable obstacles, such as buildings. The numerical domains were based on real environments where either field or experimental studies had been conducted providing data with which the numerical methods could be validated, highlighting the advantages of a combined, multidisciplinary approach. The bridge between the engineering derived CFD methods and their application in environmental flow case-studies is introduced, as well as methods to model urban areas from a micro to a neighborhood scale. Ways in which to deal with problems, such as meshing complex geometrical data, as well as an alternative approach for obtaining approximate transient results are shown using examples from case studies in different environments. Four case studies, all validated with either experimental wind-tunnel or field measurements were conducted for the relevant roughness elements: sub-grid, porous (e.g. trees) and impermeable (e.g. buildings). The case studies also create a bridge between the engineering dominated CFD methods and today's applications in environmental flows. In each of the case studies, the application of dispersion or transport is studied for gaseous fluids or solid-particle detachment, dispersion and transport. Numerical problems occurring, especially in urban areas, where the topology is complex and heterogeneous, were addressed and the successful solution demonstrated. The implementation used commercial software and OpenFOAM, an open-source code that was found to be an ideal software package for research purposes because of its parallel capabilities and flexibility for future studies.

An enriched finite element method is presented to numerically solve the eigenvalue problem on electromagnetic waveguides governed by the Helmholtz equation. In this work, a highly efficient, simple and precise higher order subparametric method was developed using a 2D automated mesh generator performed with JuliaFEM. The transcendence computerized discretization code in Julia is developed for the present work. For curved waveguide structures, meshes with one side and curving higher orders are proposed with triangular elements with parabolic arcs. The technique is shown for distinct waveguide constructions, and the results are compared with the strongest numerical or analytical results available. The results demonstrate that the proposed methodology is effective and accurate for generating finite element simulations for complex structures with black holes and irregular topology due to no curvature loss. This article presents a finding cutoff frequency performed with JuliaFEM—an open-source program. Analysis results produced by commercial software are considered for the comparison and show that the calculation results between the two programs do not differ significantly. This procedure can be used to achieve the most effective transmission of energy for electromagnetic applications.

: This document is a manual for the application of the computerized Life Cycle Cost (LCC) Model designed for the Full-Scale Engineering Development (FSED) Phase of the SEEK TALK Program. FSED contractors will use the model to perform cost estimates, identify cost drivers and make trade and other cost-related analyses. The manual assists users in establishing input parameter values, making LCC calculations and utilizing results. It also describes how to prepare computer inputs, and run the model in either the interactive or batch mode. Volume I is entitled Life Cycle Cost Management, and Volume II, Model Equations and Model Operations. (Author)

IntroductionMost people who smoke cigarettes begin in their teens and teens may also be attracted to new tobacco, nicotine, and cannabis products. We describe use prevalence among upper-secondary school students in Switzerland, including daily use, of tobacco, nicotine, and cannabis products.MethodsWe invited secondary school students (age 15 to 21) in two Swiss cantons to take an online survey between October 2021 and February 2022. The survey collected demographic information and asked how frequently they used tobacco products (cigarettes in commercial packages, self-rolled cigarettes, hookahs, pipes, cigars and cigarillos, tobacco heating systems, snus, snuff), non-tobacco nicotine products (nicotine pouches, e-cigarettes with and without nicotine), and cannabis products (smoking with and without tobacco, cannabis vaping). Answers were scored on a Likert scale (no use in past month, less than weekly, weekly but not daily, daily use, prefer not to say), then tabulated and reported as descriptive statistics.ResultsOf 32,614 students in the schools we contacted, 9,515 (29.2%) completed the survey; 49.5% identified as female and 48.4% as male; 9.5% were under 16, 47% were 16–17, 27.5% were 18–19, and 16% were over 19. Reported daily use was most frequent for tobacco cigarettes in commercial packages (14.2%), snus (4.1%) and cannabis smoking with tobacco (3.6%). Most participants (54.8%) reported they had used at least one product at least once within the last month.ConclusionStudents who used a product were most likely to smoke cigarettes, but many regularly used new tobacco, nicotine and cannabis products, though use frequency varies.

<div>Abstract<p>Pathology Image Informatics Platform (PIIP) is an NCI/NIH sponsored project intended for managing, annotating, sharing, and quantitatively analyzing digital pathology imaging data. It expands on an existing, freely available pathology image viewer, Sedeen. The goal of this project is to develop and embed some commonly used image analysis applications into the Sedeen viewer to create a freely available resource for the digital pathology and cancer research communities. Thus far, new plugins have been developed and incorporated into the platform for out of focus detection, region of interest transformation, and IHC slide analysis. Our biomarker quantification and nuclear segmentation algorithms, written in MATLAB, have also been integrated into the viewer. This article describes the viewing software and the mechanism to extend functionality by plugins, brief descriptions of which are provided as examples, to guide users who want to use this platform. PIIP project materials, including a video describing its usage and applications, and links for the Sedeen Viewer, plug-ins, and user manuals are freely available through the project web page: <a href="http://pathiip.org" target="_blank">http://pathiip.org</a>. <i>Cancer Res; 77(21); e83–86. ©2017 AACR</i>.</p></div>

Although DEM (Discrete Element Method) was introduced >40 years ago, there are still various challenges in applying it with a certain level of confidence. To develop a realistic material model, calibration, validation, particle shape representation and scaling are well-known challenges that have been studied by various researchers over the past two decades. In addition, once a realistic DEM material model is developed and published in line with open science principles, it is unknown to what extent the calibrated values can be used across software packages. Although a benchmark between 8 open source codes was recently published, it did not cover cohesive materials, rolling friction models, realistic calibrated material behaviour, and commercial software that is widely used in industries.The aim of this study is to investigate the portability of input parameters between different codes and to identify if software independent calibration is possible. We propose a framework to assist DEM users in industry and academia to reach a software independent DEM simulation when required.To compare the results between software packages, the framework considers the following aspects: 1) identical implementation of contact models, 2) single contact modelling, 3) bulk level simulation, and 4) identical post-processing. This framework is demonstrated for two contact models (Hertz-Mindlin and Edinburgh Elasto Plastic Adhesive) with rolling friction model and two commercial software packages (EDEM and PFC) but is applicable for any other (open-source) software. Moreover, two realistic calibrated material models are included to cover a range of material characteristics, from free-flowing incompressible materials to cohesive compressible materials. This study shows that individual particle level simulations give identical results, bulk level simulations show differences for both contact models. In general, users should use parameter values from other software packages with caution, especially where critical or sensitive applications are modelled. This paper also highlights the use of novel computation techniques, such as the GPU engine, to achieve practical computation times when modelling industrial applications.

Purpose The purpose of this paper is to investigate the impact and techniques for mitigating the effects of web robots on usage statistics collected by Open Access (OA) institutional repositories (IRs). Design/methodology/approach A close review of the literature provides a comprehensive list of web robot detection techniques. Reviews of system documentation and open source code are carried out along with personal interviews to provide a comparison of the robot detection techniques used in the major IR platforms. An empirical test based on a simple random sample of downloads with 96.20 per cent certainty is undertaken to measure the accuracy of an IR’s web robot detection at a large Irish University. Findings While web robot detection is not ignored in IRs, there are areas where the two main systems could be improved. The technique tested here is found to have successfully detected 94.18 per cent of web robots visiting the site over a two-year period (recall), with a precision of 98.92 per cent. Due to the high level of robot activity in repositories, correctly labelling more robots has an exponential effect on the accuracy of usage statistics. Research limitations/implications This study is performed on one repository using a single system. Future studies across multiple sites and platforms are needed to determine the accuracy of web robot detection in OA repositories generally. Originality/value This is the only study to date to have investigated web robot detection in IRs. It puts forward the first empirical benchmarking of accuracy in IR usage statistics.

The potential for the use of ad-hoc wireless sensor network technology in experimental investigations in animal welfare was explored in a study of the effect of the immediate environment on the body temperature of pigs. Sensors to simultaneously measure core and surface temperature were implanted in four pigs and monitored for a week using the open source application, TinyDB. Concurrently, a network of environmental sensors measuring predominantly temperature and humidity was placed around the pigs and this network was managed and monitored using a commercial package, Sensicast Developers Version (Sensicast DV). Approximately 100000 data points were gathered during the study. It was found to be significantly easier to develop, deploy and maintain the sensor network using Sensicast DV, and that there were significant problems when TinyDB was faced with large amounts of frequent sampling. However, TinyDB provided greater flexibility than Sensicast DV in its capacity to support more sensor platforms.

This paper aims at presenting the open source and public domain FREEWAT platform capabilities for water resource management, including: (i) pre-processing modules to facilitate the preparation of input data, (ii) modelling tools for the analysis of several processes aimed at supporting water resource management, and (iii) post-processing tools to present results.The FREEWAT platform is based on open source solutions to perform an integrated coupling between the QGIS desktop software, surface and subsurface model engines, mostly based on fully distributed and numerically-based codes developed by the USGS, and other software applications, and the SpatiaLite spatial database. The development of the FREEWAT platform was supported by the main needs and priorities expressed by relevant stakeholders from the water sector involved in the early stage of the project.Extensive testing on the platform is still going on and training material and six User Manuals were prepared to disseminate its use as a standard software for managing surface/sub-surface water quantity and quality dynamics under demand-driven and supply-constrained conditions. The testing phase also includes demonstration of the platform capabilities on 14 case studies at European scale and beyond, to address specific water management issues. Nine of them are devoted to the application of EU water-related Directives, while the others address water management issues in the rural environment under the requirements of EU and/or national/local regulations. Beyond software testing, this demonstration is thought as an experiment on involving stakeholders in the formation of water plans yet during the technical phase of the analysis.