BlenderPhotonics - a versatile environment for 3-D complex bio-tissue modeling and light transport simulations based on Blender

Significance: Rapid advances in biophotonics techniques require quantitative, model-based computational approaches to obtain functional and structural information from increasingly complex and multi-scaled anatomies. The lack of efficient tools to accurately model tissue structures and subsequently perform quantitative multi-physics modeling greatly impedes the clinical translation of these modalities. Aim: While the mesh-based Monte Carlo (MMC) method expands our capabilities in simulating complex tissues by using tetrahedral meshes, the generation of such domains often requires specialized meshing tools such as Iso2Mesh. Creating a simplified and intuitive interface for tissue anatomical modeling and optical simulations is essential towards making these advanced modeling techniques broadly accessible to the user community. Approach: We responded to the above challenge by combining the powerful, open-source 3-D modeling software, Blender, with state-of-the-art 3-D mesh generation and MC simulation tools, utilizing the interactive graphical user interface (GUI) in Blender as the front-end to allow users to create complex tissue mesh models, and subsequently launch MMC light simulations. Results: We have developed a Python-based Blender add-on -- BlenderPhotonics -- to interface with Iso2Mesh and MMC, allowing users to create, configure and refine complex simulation domains and run hardware-accelerated 3-D light simulations with only a few clicks. In this tutorial, we provide a comprehensive introduction to this new tool and walk readers through 5 examples, ranging from simple shapes to sophisticated realistic tissue models. Conclusion: BlenderPhotonics is user-friendly and open-source, leveraging the vastly rich ecosystem of Blender. It wraps advanced modeling capabilities within an easy-to-use and interactive interface. The latest software can be downloaded at http://mcx.space/bp.

Method for Calculating the Shape of Rolls for Helical Rolling

The paper is devoted to solving the problem of determining the shape of the rolls of helical rolling mills, depending on the specified profile of the deformation zone. A universal calculation method has been proposed, thanks to which it is possible to determine the shape of the working surface of a roll for all types of helical rolling mills (with mushroom-shaped, cup-shaped, barrel-shaped and disc rolls), any relative arrangement of the rolling axis and rolls axes, and various locations of the deformation zone on the rolling axis. The proposed method is implemented as a standalone exe-application with a simple intuitive interface. The application allows you to output the calculation results into txt-files, which can then be imported into CAD systems to create 3D roll models.

TextQ—A User Friendly Tool for Exploratory Text Analysis

As the amount of textual data available on the Internet grows substantially each year, there is a need for tools to assist with exploratory data analysis. Furthermore, to democratize the process of text analytics, tools must be usable for those with a non-technical background and those who do not have the financial resources to outsource their data analysis needs. To that end, we developed TextQ, which provides a simple, intuitive interface for exploratory analysis of textual data. We also tested the efficacy of TextQ using two case studies performed by subject matter experts—one related to a project on the detection of cyberbullying communication and another related to the user of Twitter for influence operations. TextQ was able to efficiently process over a million social media messages and provide valuable insights that directly assisted in our research efforts on these topics. TextQ is built using an open access platform and object-oriented architecture for ease of use and installation. Additional features will continue to be added to TextQ, based on the needs and interests of the installed base.

ViaFuse: Fiji macros to calculate skeletal muscle cell viability and fusion index

Background Measuring biological features of skeletal muscle cells is difficult because of their unique morphology and multinucleate nature upon differentiation. Here, we developed a new Fiji macro package called ViaFuse (that stands for viability and fusion) to measure skeletal muscle cell viability and differentiation. To test ViaFuse, we utilized immunofluorescence images of differentiated myotubes where the capping actin protein of muscle z-line subunit beta (CAPZB) was depleted in comparison with control cells. Results We compared the values achieved using the ViaFuse macros first with manual quantification performed by researchers and second with those obtained utilizing the MATLAB muscle-centric software MyoCount. We observed a high degree of correlation between all methods of quantification. Conclusions ViaFuse can detect the borders of myotubes and identify nuclear clumps which have been limitations of previous muscle-centric imaging software. The ViaFuse macros require little computer power or space to run and user inputs to the ViaFuse macros are minimal, thereby automating the analysis process in a quick, easy, and accurate fashion. Additionally, the ViaFuse macros work with Fiji, an existing imaging software widely used by skeletal muscle researchers. Furthermore, ViaFuse is compatible with many computer systems, has a very intuitive interface, and does not require prior complex mathematical knowledge. Therefore, we propose ViaFuse as a robust and meticulous method to quantify skeletal muscle cell viability and differentiation.

Una introducción a los estudios de atribución de autoría en el ámbito disciplinario de la Lingüística Forense y al programa de análisis de textos ALTXA

RESUMEN Este artículo presenta un caso de atribución de autoría en el ámbito de la lingüística forense a partir de la herramienta ALTXA. Primeramente, se aportará una definición general de la lingüística forense y una breve explicación de sus principales áreas de estudio con el propósito de acotar progresivamente el foco de la investigación hasta llegar a los estudios de atribución de autoría, los cuales serán abordados con mayor profundidad. En segundo lugar, el artículo evaluará las principales herramientas computacionales empleadas para determinar de forma cuantitativa la autoría de textos anónimos o disputados y presentará el software ALTXA, el cual ha sido creado por el presente grupo investigador. Dicha herramienta computacional pretende aunar las funcionalidades de distintos programas informáticos en una interfaz accesible que permita la implementación de los estudios de atribución de autoría en contextos educativos y facilite la labor del lingüista forense. El artículo concluirá con una demostración práctica de ALTXA en la que se realizará un estudio de atribución de autoría de un fragmento indubitado de William Shakespeare para demostrar la validez del programa, así como de los estudios de n-grams, una de las funcionalidades que ofrece dicha herramienta y que constituyen un procedimiento metodológico consolidado en el campo de la lingüística forense. PALABRAS CLAVE Lingüística forense, lingüística computacional, atribución de autoría, William Shakespeare, n-grams. ABSTRACT This article will present a case of authorship attribution within the framework of forensic linguistics with the computational tool ALTXA. For such end, a general definition of forensic linguistics and an explanation of its main areas of study will be offered with the aim of narrowing down progressively the scope of the article until authorship attribution studies are presented and discussed in more depth. Afterwards, a review of the main computational tools with which the authorship of disputed or anonymous texts are analysed will be provided, and ALTXA, a software that has been developed by the researcher, will be presented. Such tool combines many of the functionalities offered by other programs in an intuitive interface that allows for the implementation of authorship attribution studies in educational settings and facilitates the labour of the forensic linguist. Lastly, the article will provide a practical demonstration of ALTXA in which the authorship of an undisputed text written by William Shakespeare will be analysed to prove its reliability. Such analysis will consist of an n-gram study, which is one of the functionalities of ALTXA and constitutes a solid methodological procedure within the framework of forensic linguistics. KEYWORDS Forensic linguistics, computational linguistics, authorship attribution, William Shakespeare, n-grams.

Comparison of two platforms for distance learning students of Moscow Aviation Institute: Microsoft Teams and LMS Moodle

Microsoft Teams platform is a kind of messenger created on the basis of Microsoft Skype for Business in 2017. It implements the concept of a collaborative workspace and allows group members to organize joint online meetings, hold audio and video conferences and connect additional Microsoft services. Microsoft Teams implements the possibility of individual interaction between the teacher and the student through audio and video calls. In relation to the pandemic of coronavirus infection, on March 17, 2020, MAI completely switched to the distance learning mode. For the organization of distance educational process, LMS MAI website, based on the Moodle platform, is mainly used, but the range of its capabilities is limited. In order to expand opportunities and share the flow of students using the website for e-learning, many classes with students began to be held at Microsoft Teams. It has an intuitive interface and meets all the requirements of confidentiality and security: encryption, multi-factor authentication and device management are used to protect information; necessary protection mechanisms against unauthorized access are implemented. When this platform was studied a number of its advantages were identified compared to LMS Moodle platform, also there were system vulnerabilities correlated with LMS and suggestions to eliminate them.

Designing a Collaborative Virtual Conference Application: Challenges, Requirements and Guidelines

Due to the recent COVID-19 pandemic that has swept the globe, more people are working from home. People use synchronous applications to communicate remotely because they are not able to meet face-to-face. However, few research studies on the issues surrounding the virtual conference application, particularly those that include collaborative activities, have been conducted. The usability study recruited 16 participants (in four groups of four) to communicate synchronously while performing collaborative activities, such as drawing together on a shared screen. According to the findings of the usability study, users do not often use the collaborative tools provided by the current virtual conference application. This is due to low exposure and unfamiliarity with the use of collaborative tools. The findings also show that users frequently do not turn on the web camera due to several reasons, including privacy, connectivity issues, the environment, and background distraction. Turning on the web camera can also cause anxiety due to shyness in front of the camera. However, some participants prefer to turn on the web camera so that they can see each other’s reactions when performing collaborative activities. The article provides several guidelines to assist in the design of virtual conference applications, including a simple familiar intuitive interface to encourage the use of collaborative tools and also introduces the use of virtual avatars as a way to represent oneself during online meetings to allow affective sharing while respecting the privacy of its users.

A Wearable IMU System for Flexible Teleoperation of a Collaborative Industrial Robot

Increasing the accessibility of collaborative robotics requires interfaces that support intuitive teleoperation. One possibility for an intuitive interface is offered by wearable systems that measure the operator’s movement and use the information for robot control. Such wearable systems should preserve the operator’s movement capabilities and, thus, their ability to flexibly operate in the workspace. This paper presents a novel wireless wearable system that uses only inertial measurement units (IMUs) to determine the orientation of the operator’s upper body parts. An algorithm was developed to transform the measured orientations to movement commands for an industrial collaborative robot. The algorithm includes a calibration procedure, which aligns the coordinate systems of all IMUs, the operator, and the robot, and the transformation of the operator’s relative hand motions to the movement of the robot’s end effector, which takes into account the operator’s orientation relative to the robot. The developed system is demonstrated with an example of an industrial application in which a workpiece needs to be inserted into a fixture. The robot’s motion is compared between the developed system and a standard robot controller. The results confirm that the developed system is intuitive, allows for flexible control, and is robust enough for use in industrial collaborative robotic applications.

FIVEx: an interactive eQTL browser across public datasets

Summary Expression quantitative trait loci (eQTLs) characterize the associations between genetic variation and gene expression to provide insights into tissue-specific gene regulation. Interactive visualization of tissue-specific eQTLs or splice QTLs (sQTLs) can facilitate our understanding of functional variants relevant to disease-related traits. However, combining the multi-dimensional nature of eQTLs/sQTLs into a concise and informative visualization is challenging. Existing QTL visualization tools provide useful ways to summarize the unprecedented scale of transcriptomic data but are not necessarily tailored to answer questions about the functional interpretations of trait-associated variants or other variants of interest. We developed FIVEx, an interactive eQTL/sQTL browser with an intuitive interface tailored to the functional interpretation of associated variants. It features the ability to navigate seamlessly between different data views while providing relevant tissue- and locus-specific information to offer users a better understanding of population-scale multi-tissue transcriptomic profiles. Our implementation of the FIVEx browser on the EBI eQTL catalogue, encompassing 16 publicly available RNA-seq studies, provides important insights for understanding potential tissue-specific regulatory mechanisms underlying trait-associated signals. Availability and implementation A FIVEx instance visualizing EBI eQTL catalogue data can be found at https://fivex.sph.umich.edu. Its source code is open source under an MIT license at https://github.com/statgen/fivex. Supplementary information Supplementary data are available at Bioinformatics online.

DETERMINING WHETHER THE PROTOTYPE HACKATHON ECOSYSTEM FOR TECHNOLOGY TRANSFER IN A HIGHER EDUCATION INSTITUTION MEETS THE NEEDS OF STAKEHOLDERS

BACKGROUND AND OBJECTIVES. The development of the innovation ecosystem is one of the main vectors of development of the Ukrainian economy. One of the main elements of such policy are higher education institutions. Organizational method is an effective transition to the project approach of technology transfer management. The use of the organizational method implies the creation of a new organizational structure in the higher education institution. Such structure can be the creation of organizational unit – Hackathon-ecosystem of technology transfer, the main task of which will be the management of technology transfer projects.METHODS. The study used methods of expert evaluation and questionnaire survey of stakeholders using closed and open-ended questions; feedback grids – to diagnose the effectiveness of the created prototype of the Hackathon ecosystem; Pareto diagrams – to analyze the information by determining the total score of the survey results; A / B testing – to choose between the existing version of the site and the created prototype; usability testing – to determine the degree of convenience and intuitive interface prototype.FINDINGS. The method of creating a hackathon-ecosystem of technology transfer in higher education institution with elements of design thinking is proposed. The work of new structural unit allows to determine the needs, interest, preferences and priorities of university stakeholders. Such stakeholders are university's employees, business representatives and the state. Tools of design-thought (observation, survey, generation and selection of ideas, prototyping) of stakeholders allow to build an optimal prototype of Hackathon-ecosystem of technology transfer in higher education institution.CONCLUSION. Determination of compliance of the prototype of Hackathon-ecosystem of technology transfer in higher education institution with the needs of stakeholders allows to get feedback on directions of improvement of innovative work of university in general and new organizational structure, in particular. Questioning of technology transfer stakeholders in Kyiv National University of Technologies and Design allowed to create an optimal user-friendly and intuitive interface of Hackathon ecosystem prototype, corresponding to stakeholder needs.