Graphical Tool Research Articles

Tri©DB: an integrated platform of knowledgebase and reporting system for cancer precision medicine

BackgroundWith the development of cancer precision medicine, a huge amount of high-dimensional cancer information has rapidly accumulated regarding gene alterations, diseases, therapeutic interventions and various annotations. The information is highly fragmented across multiple different sources, making it highly challenging to effectively utilize and exchange the information. Therefore, it is essential to create a resource platform containing well-aggregated, carefully mined, and easily accessible data for effective knowledge sharing.MethodsIn this study, we have developed “Consensus Cancer Core” (Tri©DB), a new integrative cancer precision medicine knowledgebase and reporting system by mining and harmonizing multifaceted cancer data sources, and presenting them in a centralized platform with enhanced functionalities for accessibility, annotation and analysis.ResultsThe knowledgebase provides the currently most comprehensive information on cancer precision medicine covering more than 40 annotation entities, many of which are novel and have never been explored previously. Tri©DB offers several unique features: (i) harmonizing the cancer-related information from more than 30 data sources into one integrative platform for easy access; (ii) utilizing a variety of data analysis and graphical tools for enhanced user interaction with the high-dimensional data; (iii) containing a newly developed reporting system for automated annotation and therapy matching for external patient genomic data. Benchmark test indicated that Tri©DB is able to annotate 46% more treatments than two officially recognized resources, oncoKB and MCG. Tri©DB was further shown to have achieved 94.9% concordance with administered treatments in a real clinical trial.ConclusionsThe novel features and rich functionalities of the new platform will facilitate full access to cancer precision medicine data in one single platform and accommodate the needs of a broad range of researchers not only in translational medicine, but also in basic biomedical research. We believe that it will help to promote knowledge sharing in cancer precision medicine. Tri©DB is freely available at www.biomeddb.org, and is hosted on a cutting-edge technology architecture supporting all major browsers and mobile handsets.

Oort Cloud and sednoid formation in an embedded cluster. II. Dynamics and orbital evolutions

This paper presents a study of the dynamical mechanisms behind the extraction of Jupiter–Saturn planetesimals into detached orbits belonging to the Oort Cloud or the sednoid population. In an embedded cluster, these are the global cluster tide and gravitational impulses acquired due to stellar encounters. Our study builds on a large set of numerical simulations of Oort Cloud and sednoid formation, whose statistical results are reported in an accompanying paper. The material is extensive, amounting to detailed data on the orbital evolutions of 288000 planetesimals. We have developed two graphical tools for our work: (1) diagrams showing the extraction history of sednoids and Oort Cloud comets for each of 72 solar template stars; and (2) time profiles of the evolution of semi-major axis and perihelion distance for individual planetesimals. These help us identify the main triggers behind individual extractions due to intrinsic differences between the tidal and stellar flyby triggering mechanisms. The time scale of an encounter-based extraction never exceeds the duration of the encounter, while the tide operates on two time scales — the orbital periods of the planetesimal around the star and the star around the cluster centre. These periods are very different for sednoids but often similar for Oort Cloud comets. We note the absence of evidence for synergy between the tide and the encounters or between subsequent encounters, likely due to the fact that each effect depends strongly on the geometrical circumstances, and those are rarely repeatable. The balance between tide and encounters as dominating trigger varies between different cluster types. For clusters which are strongly concentrated with the primordial gas remaining for a few Myr, we discover a previously unnoticed phenomenon, which we call tidal purging. In this case, nearly all Oort Cloud comets with semi-major axes exceeding 7000astronomical units are ejected from the solar system on hyperbolic orbits due to the non-conservative nature of the cluster tide. In a separate study of the end states reached by all planetesimals, we find that an overwhelming majority undergo hyperbolic ejections, remain in orbits similar to the initial ones, or get physically removed from the solar system due to collisions with a planet or the Sun.

The Influences of Mind-Map on Cultivating Students' Metacognitive Capacity

Mind mapping is an effective graphic thinking tool for expressing divergent thinking proposed by Tony Buzan, a world-renowned psychologist and educator. It is a practical thinking tool that is simple, yet effective and efficient at the same time. Mind mapping develops students thinking skills, logical skills, etc. This study aims to investigate the development of metacognitive ability of students through the production of mind mapping. Through a review of related literature, the study found that mind mapping can promote students categorization and organization skills, help students discover and understand new relationships, improve problem-solving skills, and facilitate the deposition of learning outcomes. In addition, mind mapping production requires student participation, thereby improving students metacognitive ability. The literature access suggests that the production of mind mapping has a significant effect on the development of students metacognitive ability, and it should be introduced into education. In the future, the production method of mind mapping should be further optimized, and its application scenarios should be studied to improve students learning effectiveness and metacognitive ability development.

A bibliometric analysis of intra-articular injection therapy for knee osteoarthritis from 2012 to 2022.

Knee osteoarthritis (KOA) is the most common joint disease worldwide and, with the progression of an aging population, is one of the most important causes of disability worldwide. Its main symptoms include articular cartilage damage, periarticular pain, swelling, and stiffness. Intra-articular (IA) injections offer many advantages over systemic administration and surgical treatment, including direct action on the target joint to improve local bioavailability, reduce systemic toxicity, and lower costs. This study analyzed KOA intra-articular injection treatment and its hot literature and research horizons using bibliometric methodologies and graphical tools to aid future research. We performed a bibliometric analysis of 2360 publications in the Web of Science core collection using CiteSpace software. The United States (28.26% of publications) and China (18%) had the biggest publications. Rush University was the most active institution, but Boston University had the greatest citation/publication rate (65.77), suggesting a high literature standard. The majority of publications were in Osteoarthritis and cartilage. Bannuru RR was the most referenced author, while Filardo, Giuseppe was the most productive author. Studies in platelet-rich plasma (PRP), mesenchymal stem cells (MSCs), and microsphere formulation are likely to be future research hotspots. The current scientometric study provides an overview of KOA intra-articular injection therapy studies from 2012 to 2022. This study outlines the current research hotspots and potential future research hotspots in the field of intra-articular injection treatment for KOA and may serve as a resource for researchers interested in this topic.

RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.

RegulonDB is a database that contains the most comprehensive corpus of knowledge of the regulation of transcription initiation of Escherichia coli K-12, including data from both classical molecular biology and high-throughput methodologies. Here, we describe biological advances since our last NAR paper of 2019. We explain the changes to satisfy FAIR requirements. We also present a full reconstruction of the RegulonDB computational infrastructure, which has significantly improved data storage, retrievaland accessibility and thus supports a more intuitive and user-friendly experience. The integration of graphical tools provides clear visual representations of genetic regulation data, facilitating data interpretation and knowledge integration. RegulonDB version 12.0can be accessed at https://regulondb.ccg.unam.mx.

An AI‐based platform to investigate African large carnivore dispersal and demography across broad landscapes: A case study and future directions using African wild dogs

AbstractUnderstanding dispersal patterns and demographic processes is crucial for the development of evidence‐based conservation practices. Obtaining such information relies on the ability to identify and track individuals across spatial and temporal scales relevant to the life‐history events under investigation. This knowledge can be achieved by combining photographic and sighting data collected by various sources with a high accuracy automated individual identification platform. Here, we present the African Carnivore Wildbook (ACW), an AI‐based graphical user interface tool capable of identifying individuals of several African carnivore species and specifically developed to accommodate the above outlined needs. We showcase the ACW functionality using the endangered African wild dog as an example. Pictures collected over an area >56,000 km2 and submitted to ACW allowed inferences on movement patterns and dispersal at regional and international scales; for instance, transboundary dispersal events >200 km were documented. ACW furthermore enabled monitoring some individuals for >4 years; such information is invaluable for reliable survival analyses. We discuss how the ACW can contribute to data collection at appropriate spatial and temporal scales to support population monitoring, scientific research and management of African wild dogs and other apex carnivores and to the conservation of these charismatic species.

Graphical tools for selecting conditional instrumental sets

Summary We consider the efficient estimation of total causal effects in the presence of unmeasured confounding using conditional instrumental sets. Specifically, we consider the two-stage least-squares estimator in the setting of a linear structural equation model with correlated errors that is compatible with a known acyclic directed mixed graph. To set the stage for our results, we characterize the class of linearly valid conditional instrumental sets that yield consistent two-stage least-squares estimators for the target total effect and derive a new asymptotic variance formula for these estimators. Equipped with these results, we provide three graphical tools for selecting more efficient linearly valid conditional instrumental sets: first, a graphical criterion that, for certain pairs of linearly valid conditional instrumental sets, identifies which of the two corresponding estimators has the smaller asymptotic variance second, an algorithm that greedily adds covariates that reduce the asymptotic variance to a given linearly valid conditional instrumental set and, third, a linearly valid conditional instrumental set for which the corresponding estimator has the smallest asymptotic variance that can be ensured with a graphical criterion.

A multi-criteria review of mean radiant temperature evaluation models for urban thermal comfort

This article reviews the main tools used to simulate the mean radiant temperature (T mrt ) under outdoor conditions. Urban environment complexity and the multiplicity of the radiative fluxes force models’ developers to simplify the problem. To summarize the common assumptions of these models, a graphical tool is proposed. In addition to the physical description, effective coherence of models as a tool for urban decision-making is analyzed. Based on this double vision, this article achieves a multi-criteria analysis of T mrt calculation. Nine tools (ENVI-met, Solene-microclimat, SOLWEIG, RayMan, CitySim, Ladybug-Grasshopper, VTUF, DART and LASER/F) are evaluated against five criteria. Three criteria relate to physics implementation: completeness of the considered radiative phenomena, representation of the environment and surface temperature modeling. Two criteria deal with the operational capabilities: consistency with the needs of city-planners and practical accessibility. These criteria highlight various issues, and in particular the conflict between user-friendly practicality and an accurate description of physical phenomena.

Scarred Flesh and the X of Law

This essay responds to and expands the concept of the X for trans studies, theorized by Marquis Bey, as a graphic tool for thinking the intersection of gender, race, law, and crime. In doing so, the essay reads Howard Hawks's 1932 film Scarface, a work crossed throughout by the symbology of the X. Rather than providing a simple visual cue for death and closure, the X is vitalized, through a reading of Bey and Scarface together, as the (un)graphing of law that both inscribes and defaces the biopolitical state, which predicates itself on legislating the difference between genders, races, species, spaces, and criminals and law enforcement. The essay thereby moves toward a criminal reading of the Law, in which it becomes possible to see how the state's apparatus betrays its populous and itself, and to sketch out a vision of pluralized life otherwise, figured in the transgressions of a film in which crime becomes law, law becomes crime, and the riotously raced and gendered protagonist weave together the terms that the biopolitical state desperately attempts to hold apart.

Optimizing the Performance of the Sparse Matrix-Vector Multiplication Kernel in FPGA Guided by the Roofline Model.

The widespread adoption of massively parallel processors over the past decade has fundamentally transformed the landscape of high-performance computing hardware. This revolution has recently driven the advancement of FPGAs, which are emerging as an attractive alternative to power-hungry many-core devices in a world increasingly concerned with energy consumption. Consequently, numerous recent studies have focused on implementing efficient dense and sparse numerical linear algebra (NLA) kernels on FPGAs. To maximize the efficiency of these kernels, a key aspect is the exploration of analytical tools to comprehend the performance of the developments and guide the optimization process. In this regard, the roofline model (RLM) is a well-known graphical tool that facilitates the analysis of computational performance and identifies the primary bottlenecks of a specific software when executed on a particular hardware platform. Our previous efforts advanced in developing efficient implementations of the sparse matrix-vector multiplication (SpMV) for FPGAs, considering both speed and energy consumption. In this work, we propose an extension of the RLM that enables optimizing runtime and energy consumption for NLA kernels based on sparse blocked storage formats on FPGAs. To test the power of this tool, we use it to extend our previous SpMV kernels by leveraging a block-sparse storage format that enables more efficient data access.

Model Uncertainty and Selection of Risk Models for Left-Truncated and Right-Censored Loss Data

Insurance loss data are usually in the form of left-truncation and right-censoring due to deductibles and policy limits, respectively. This paper investigates the model uncertainty and selection procedure when various parametric models are constructed to accommodate such left-truncated and right-censored data. The joint asymptotic properties of the estimators have been established using the Delta method along with Maximum Likelihood Estimation when the model is specified. We conduct the simulation studies using Fisk, Lognormal, Lomax, Paralogistic, and Weibull distributions with various proportions of loss data below deductibles and above policy limits. A variety of graphic tools, hypothesis tests, and penalized likelihood criteria are employed to validate the models, and their performances on the model selection are evaluated through the probability of each parent distribution being correctly selected. The effectiveness of each tool on model selection is also illustrated using well-studied data that represent Wisconsin property losses in the United States from 2007 to 2010.

The Impact of Media and Technology in Christian Religious Education Strategy

This research aims to describe the impact of media and technology in Christian Religious Education strategies. This impact is to build social change and to convey messages from God. Media is a communication tool in the form of graphic, photographic and electronic tools to capture, process and reconstruct visual or audio information. Technology is the practice of knowledge in the form of useful tasks to increase effectiveness and efficiency. Christian religious education is not against developments in media and technology. The background of this article is the impact of media and technology on Christian Religious Education strategies. The research method used is descriptive qualitative research. The result of this article is that media and technology in Christian religious education strategies have an impact on building social change and conveying God's message.

The importance of geometric algebra in the language of physics

Geometric algebra has emerged as the preferred mathematical framework for physics because it provides compact and intuitive descriptions in many areas including classical and quantum mechanics, electromagnetic theory and relativity. Geometric algebra has also found prolific applications as a computational tool in computer graphics and robotics. Leading exponents of this extensive mathematical apparatus are fervently insisting its inclusion in the undergraduate physics curriculum.

THE USAGE OF AUGMENTEDCLASS APPLICATION FOR GRAPHIC COMPETENCE DEVELOPMENT OF STUDENTS OF THE 5th-7th GRADES IN THE PROCESS OF CREATING AUGMENTED REALITY PROJECTS

The article examines the usage of the AugmentedClass application for graphic competence development of students of the 5th-7th grades while creating augmented reality projects. The application’s main functions and interface are described. Methods and techniques that contribute to students’ graphic skills development are presented as well. The advantages of using augmented reality technology in the educational process are considered, in particular, increasing students’ interest in learning and stimulating their creativity. The need to integrate the AugmentedClass application into the educational process is emphasized, which will improve the quality of education and provide active and exciting educational activities for students of the 5th-7th grades. Attention is focused on the fact that the main aspects of graphic competence development are interest, creativity, and skills in using graphic tools, which can be successfully developed with the help of the AugmentedClass application.
 It has been found that the usage of augmented reality in the field of education provides students with a significant number of advantages: augmented reality stimulates students’ interest in educational material thanks to interactive content and expands the educational process by providing new competencies and innovative forms of working with the audience, gamification, competitive elements, and cognitive stimuli used in augmented reality activate and motivate students to more independent educational and cognitive activities. Also, the usage of innovative educational tasks, including augmented reality, helps to stimulate students’ educational activity and makes the learning process more exciting and attractive, as well as the usage of augmented reality promotes students’ personal quality development, which is of particular importance for Ukrainian general secondary education institutions, helping to increase their self-esteem and positive attitude to learning.

SECONDARY SCHOOL STUDENTS’ GRAPHIC COMPETENCE FORMATION WHILE CREATING SKETCHES OF GRAPHIC MATERIAL IN CONDITIONS OF DIGITIZATION

The study is devoted to the analysis of the process of secondary school students’ graphic competence formation in the context of modern transformations caused by the process of education digitization. The article examines the importance of graphic competence formation in creating sketches of graphic material in the context of the growing role of digital technologies in the educational process. The article analyzes scientific research aimed at understanding graphic competence and its role in the modern educational process.
 The author has analyzed various approaches to defining the category «competence» and revealed the main components of graphic competence. It is shown that this competence includes not only the technical skills of creating graphic materials but also creativity, the ability to analyze and visualize information, as well as the ability to work with various tools and resources that are opened up thanks to the digital transformation of education.
 The influence of digitalization on students’ creative potential and their ability to translate ideas into graphic material has been studied. A comprehensive approach to the educational process that takes into account traditional methods and modern information technologies is proposed. The advantages associated with the effectiveness of pedagogical approaches and methods aimed at graphic competence formation are highlighted. In particular, the teacher’s role in this competence formation has been investigated and the importance of an individual approach to each student has been emphasized.
 Examples of pedagogical practices aimed at creating conditions for the development of creative thinking and secondary school students’ graphic competence formation are considered. The author has considered the possibilities of using various software tools and online resources to increase the level of students’ graphic competence.
 Based on the analysis, recommendations aimed at further improving students’ graphic competence in the conditions of digitization of education are proposed. These recommendations are aimed at increasing the quality level of education and development of students so that they can successfully form graphic competence in the modern information society.
 The article highlights the significant topic of secondary school students’ graphic competence formation in the conditions of the digital transformation of education. It offers specific practical recommendations and examples for usage in pedagogical practice and promotes the further development of this key educational field. The study emphasizes the need to acquire competencies that allow the effective usage of graphic tools in the modern information society. The author emphasizes the importance of introducing digital tools into the educational process aimed at increasing the level of students’ graphic literacy and developing their creative competence.

Unsteady Casson fluid flow on MHD with an internal heat source

The present paper investigates the heat transfer features of a viscous fluid in an unsteady incompressible Casson fluid flow through a porous medium with an internal heat source under the influence of a magnetic field. A Casson fluid passes through the given porous medium using Darcy model. The study involves simulating the flow using mathematical models based on conservation laws and similarity transformations. The resulting highly nonlinear coupled ordinary differential equations are solved using the Bernoulli wavelet numerical approach. The study utilizes graphical tools to illustrate the flow behaviour under different physical factors, including the effect of the internal heat source. The normalization of the flow behaviour by the magnetic field suggests that it could potentially be used to control various flows. The study finds that various physical parameters which affects the velocity and temperature profiles of the fluid.

Assessing the risk of using hazardous drugs in Hospital-at-Home Units: a big data study protocol

ObjectiveThis article describes a study protocol for the implementation of quality and traceability control in the hazardous medication circuit through an analysis of risks and the development and introduction of a Big Data-based software application aimed at performing a continuous and dynamic audit of the whole system. MethodA standardized graphical modeling tool called Business Process Model Notation will be used to generate a detailed description of each of the stages in the hazardous medication circuit with a view to ensuring full traceability of the system. The information on each stage will be collected in a flowchart, which will be used —together with each event's likelihood of occurrence and severity— as a basis to calculate the criticality index of the different control points established and to determine any control measures that may be required. The flowcharts will also be used to develop the technological support needed to capture all such data as may be relevant to the model. Proper quality control of the process will be ensured by client software agents intended to allow automatic application of efficient data processing tools at the different phases. In addition, Big Data methodologies, in particular machine learning, will be used to develop algorithms based on the repository of generated data to come up with patterns capable of improving the protocols to be applied. Lastly, proper operation of the process will be ensured by means of clinical-pharmaceutical verification and a full technical-documentary review of control and registration systems. ConclusionsThe development of a risk management system based on mobile technology will allow integration of hazardous drugs into a standardized system, ensuring the safety, quality, and traceability of the hazardous medication handling process.

Development and evaluation of patient information leaflet for liver cirrhosis patients

Problem consideredThe present study aimed at developing and validating patient information leaflet (PIL) for liver cirrhosis patients. MethodologyPIL was prepared using canvas (an online design graphic tool). Up-to-date and Micromedex were used to gather information on liver cirrhosis. Before user testing, PIL readability was assessed by using the Flesch Reading Ease Score (FR-ES). Additionally, user opinion on the legibility and content of the PIL was also determined. Baker Able Leaflet Design (BALD) method was employed to assess the layout and design characteristics of the PIL. ResultsA total of 52 participants with liver cirrhosis with a mean age of 53.04 ± 11.89 were enrolled in the study. A score of 22.2 was achieved for Flesch Reading Ease Score (FR-ES). The BALD scores for English and Kannada PIL were 25 and 23, respectively. User testing showed significant improvement (p-value: <0.05) in disease knowledge from 12 (6–20) to 16 (12–22). Spearman's correlation showed the disease duration as a significant factor affecting disease knowledge (rs:0.498; p-value: <0.001). Concerning user opinion, 48.1% (n,25) of patients reported the legibility and content of PIL as good. ConclusionPIL met the standard criteria of readability and layout design. Pictogram-based PIL was found to be an effective patient education tool in improving patient disease knowledge in liver cirrhosis patients.

Design and implementation of hybrid logic based MAC unit using 45 nm technology

Digital signal processing algorithms, at times, necessitate the execution of a substantial quantity of mathematical operations to speed up and iterate upon a particular data set. Numerous digital signal processing (DSP) applications impose limitations on delay, necessitating the accomplishment of DSP operations within a predetermined timeframe, hence rendering deferred processing not feasible. Therefore, digital signal processing (DSP) necessitates a multiplier and accumulator (MAC) unit that exhibits fast speed, high throughput, and low power consumption. This research aims to develop and execute a low-power MAC unit utilising a hybrid logic technique to achieve power efficiency. A MAC unit has been purposefully designed with suitable geometries to provide optimised power, area, and delay characteristics. Estimating the delay in the MAC unit depends upon data flow analysis between the MAC blocks, explicitly focusing on low-power concerns. The developed hybrid adder cell possesses several advantageous characteristics, including a high operational speed, low power consumption, minimal transistor count. The MAC architecture uses a 45 nm CMOS technology with the Mentor Graphics tool. This research additionally examines different designs of multipliers and adders that are well-suited for the execution of high throughput signal processing while simultaneously achieving low power consumption. The registers in the MAC have been implemented in GDI logic using Multi Bit Flip flops technique to achieve low power operation. The entire MAC circuitry operates on a voltage supply of 1 V. The hybrid logic MAC architecture that has been developed demonstrates a significant decrease in area consumption, amounting to a reduction of 68 % when compared to the typical CMOS logic design. Hybrid logic demonstrates a power consumption that is 92 % better compared to CMOS logic.

A New Set of in Silico Tools to Support the Interpretation of ATM Missense Variants Using Graphical Analysis

Establishing the pathogenic nature of variants in ATM, a gene associated with breast cancer and other hereditary cancers, is crucial for providing patients with adequate care. Unfortunately, achieving good variant classification is still difficult. To address this challenge, we extended the range of in silico tools with a series of graphical tools devised for the analysis of computational evidence by health care professionals. We propose a family of fast and easy-to-use graphical representations in which the impact of a variant is considered relative to other pathogenic and benign variants. To illustrate their value, the representations are applied to three problems in variant interpretation. The assessment of computational pathogenicity predictions showed that the graphics provide an intuitive view of prediction reliability, complementing and extending conventional numerical reliability indexes. When applied to variant of unknown significance populations, the representations shed light on the nature of these variants and can be used to prioritize variants of unknown significance for further studies. In a third application, the graphics were used to compare the two versions of the ATM-adapted American College of Medical Genetics and Genomics and Association for Molecular Pathology guidelines, obtaining valuable information on their relative virtues and weaknesses. Finally, a server [ATMision (ATM missense in silico interpretation online)] was generated for users to apply these representations in their variant interpretation problems, to check the ATM-adapted guidelines' criteria for computational evidence on their variant(s) and access different sources of information.