Journal articles on the topic 'Biology Research Computer programs'
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1
Ofria, Charles, and Claus O. Wilke. "Avida: A Software Platform for Research in Computational Evolutionary Biology." Artificial Life 10, no. 2 (March 2004): 191–229. http://dx.doi.org/10.1162/106454604773563612.
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Avida is a software platform for experiments with self-replicating and evolving computer programs. It provides detailed control over experimental settings and protocols, a large array of measurement tools, and sophisticated methods to analyze and post-process experimental data. We explain the general principles on which Avida is built, as well as its main components and their interactions. We also explain how experiments are set up, carried out, and analyzed.
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Caudill, Lester, April Hill, Kathy Hoke, and Ovidiu Lipan. "Impact of Interdisciplinary Undergraduate Research in Mathematics and Biology on the Development of a New Course Integrating Five STEM Disciplines." CBE—Life Sciences Education 9, no. 3 (September 2010): 212–16. http://dx.doi.org/10.1187/cbe.10-03-0020.
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Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a course for first-year students that integrates the material in the first course of the major in each of biology, chemistry, mathematics, computer science, and physics.
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Reeves, Aaron. "MicroMeasure: A new computer program for the collection and analysis of cytogenetic data." Genome 44, no. 3 (June 1, 2001): 439–43. http://dx.doi.org/10.1139/g01-037.
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The ability to identify individual chromosomes in cytological preparations is an essential component of many investigations. While several computer software applications have been used to facilitate such quantitative karyotype analysis, most of these programs are limited by design for specific types of analyses, or can be used only with specific hardware configurations. MicroMeasure is a new image analysis application that may be used to collect data for a wide variety of chromosomal parameters from electronically captured or scanned images. Unlike similar applications, MicroMeasure may be individually configured by the end user to suit a wide variety of research needs. This program can be used with most common personal computers, and requires no unusual or specific hardware. MicroMeasure is made available to the research community without cost by the Department of Biology at Colorado State University via the World Wide Web at http://www.biology.colostate.edu/MicroMeasure.Key words: MicroMeasure, computer program, chromosome measurement, cytogenetics.
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Krilowicz, Beverly, Wendie Johnston, Sandra B. Sharp, Nancy Warter-Perez, and Jamil Momand. "A Summer Program Designed to Educate College Students for Careers in Bioinformatics." CBE—Life Sciences Education 6, no. 1 (March 2007): 74–83. http://dx.doi.org/10.1187/cbe.06-03-0150.
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A summer program was created for undergraduates and graduate students that teaches bioinformatics concepts, offers skills in professional development, and provides research opportunities in academic and industrial institutions. We estimate that 34 of 38 graduates (89%) are in a career trajectory that will use bioinformatics. Evidence from open-ended research mentor and student survey responses, student exit interview responses, and research mentor exit interview/survey responses identified skills and knowledge from the fields of computer science, biology, and mathematics that are critical for students considering bioinformatics research. Programming knowledge and general computer skills were essential to success on bioinformatics research projects. General mathematics skills obtained through current undergraduate natural sciences programs were adequate for the research projects, although knowledge of probability and statistics should be strengthened. Biology knowledge obtained through the didactic phase of the program and prior undergraduate education was adequate, but advanced or specific knowledge could help students progress on research projects. The curriculum and assessment instruments developed for this program are available for adoption by other bioinformatics programs at http://www.calstatela.edu/SoCalBSI .
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Oxford, Julia Thom, Ken A. Cornell, Jared J. Romero, Diane B. Smith, Tracy L. Yarnell, Rhiannon M. Wood, Cheryl L. Jorcyk, et al. "Center of Biomedical Research Excellence in Matrix Biology: Building Research Infrastructure, Supporting Young Researchers, and Fostering Collaboration." International Journal of Molecular Sciences 21, no. 6 (March 20, 2020): 2141. http://dx.doi.org/10.3390/ijms21062141.
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The Center of Biomedical Research Excellence in Matrix Biology strives to improve our understanding of extracellular matrix at molecular, cellular, tissue, and organismal levels to generate new knowledge about pathophysiology, normal development, and regenerative medicine. The primary goals of the Center are to i) support junior investigators, ii) enhance the productivity of established scientists, iii) facilitate collaboration between both junior and established researchers, and iv) build biomedical research infrastructure that will support research relevant to cell–matrix interactions in disease progression, tissue repair and regeneration, and v) provide access to instrumentation and technical support. A Pilot Project program provides funding to investigators who propose applying their expertise to matrix biology questions. Support from the National Institute of General Medical Sciences at the National Institutes of Health that established the Center of Biomedical Research Excellence in Matrix Biology has significantly enhanced the infrastructure and the capabilities of researchers at Boise State University, leading to new approaches that address disease diagnosis, prevention, and treatment. New multidisciplinary collaborations have been formed with investigators who may not have previously considered how their biomedical research programs addressed fundamental and applied questions involving the extracellular matrix. Collaborations with the broader matrix biology community are encouraged.
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Laudel, Grit, and Jana Bielick. "The Emergence of Individual Research Programs in the Early Career Phase of Academics." Science, Technology, & Human Values 43, no. 6 (March 19, 2018): 972–1010. http://dx.doi.org/10.1177/0162243918763100.
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Scientific communities expect early career researchers (ECRs) to become intellectually independent and to develop longer-term research plans (individual research programs [IRPs]). How such programs emerge during the early career phase is still poorly understood. Drawing on semistructured interviews with German ECRs in plant biology, experimental physics, and early modern history, we show that the development of such a plan is a research process in itself. The processes leading to IRPs are conditioned by the fields’ epistemic practices for producing new knowledge. By linking the conditions under which ECRs work to the epistemic properties of their IRPs, we identify mechanisms that produce these programs and conditions facilitating or hindering the operation of these mechanisms.
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Kowalski, Charles J. "Data Analysis in Craniofacial Biology with Special Emphasis on Longitudinal Studies." Cleft Palate-Craniofacial Journal 30, no. 2 (March 1993): 111–20. http://dx.doi.org/10.1597/1545-1569_1993_030_0111_daicbw_2.3.co_2.
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Recommendations are made for strengthening data description and analysis in craniofacial biology. Special emphasis is placed on longitudinal data, and PC programs for accomplishing appropriate analyses in this context are described and made available to interested readers. Some more general recommendations are treated in less detail. These include the effective description of data using stem-and-leaf displays and/or boxplots, the use of decision-analytic methods in the management of patients with dentofacial deformities, and the valid application of certain statistical methods in single-subject studies. Finally, it is conjectured that computer-intensive methods such as randomization tests and jackknifing will play an increasingly prominent role in craniofacial research.
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Looney, C. R., and J. H. Pryor. "Practical applications of new research information in the practice of bovine embryo transfer." Reproduction, Fertility and Development 22, no. 1 (2010): 145. http://dx.doi.org/10.1071/rd09223.
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For more than 40 years, practitioners have sought to improve all aspects of commercial bovine embryo transfer. The development of new technologies for this industry has been substantial, with recent focus on cryopreservation techniques and the in vitro production of embryos fertilised with sexed spermatozoa. When these and other new technologies are developed, the following questions remain: (1) is said technology regulated or does it require licensing; and (2) is it applicable and, if so, is it financially feasible? Computer access to published research and the advancement of data software programs conducive to the industry for data procurement have been essential for helping practitioners answer these questions by enhancing their ability to analyse and apply data. The focus of the present paper is to aid commercial embryo transfer practitioners in determining new technologies that are available and whether they can be implemented effectively, benefiting their programs.
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Sipper, Moshe. "Fifty Years of Research on Self-Replication: An Overview." Artificial Life 4, no. 3 (July 1998): 237–57. http://dx.doi.org/10.1162/106454698568576.
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The study of artificial self-replicating structures or machines has been taking place now for almost half a century. My goal in this article is to present an overview of research carried out in the domain of self-replication over the past 50 years, starting from von Neumann's work in the late 1940s and continuing to the most recent research efforts. I shall concentrate on computational models, that is, ones that have been studied from a computer science point of view, be it theoretical or experimental. The systems are divided into four major classes, according to the model on which they are based: cellular automata, computer programs, strings (or strands), or an altogether different approach. With the advent of new materials, such as synthetic molecules and nanomachines, it is quite possible that we shall see this somewhat theoretical domain of study producing practical, real-world applications.
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KEARNEY, P., and P. THIBAULT. "BIOINFORMATICS MEETS PROTEOMICS — BRIDGING THE GAP BETWEEN MASS SPECTROMETRY DATA ANALYSIS AND CELL BIOLOGY." Journal of Bioinformatics and Computational Biology 01, no. 01 (April 2003): 183–200. http://dx.doi.org/10.1142/s021972000300023x.
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Proteomics research programs typically comprise the identification of protein content of any given cell, their isoforms, splice variants, post-translational modifications, interacting partners and higher-order complexes under different conditions. These studies present significant analytical challenges owing to the high proteome complexity and the low abundance of the corresponding proteins, which often requires highly sensitive and resolving techniques. Mass spectrometry plays an important role in proteomics and has become an indispensable tool for molecular and cellular biology. However, the analysis of mass spectrometry data can be a daunting task in view of the complexity of the information to decipher, the accuracy and dynamic range of quantitative analysis, the availability of appropriate bioinformatics software and the overwhelming size of data files. The past ten years have witnessed significant technological advances in mass spectrometry-based proteomics and synergy with bioinformatics is vital to fulfill the expectations of biological discovery programs. We present here the technological capabilities of mass spectrometry and bioinformatics for mining the cellular proteome in the context of discovery programs aimed at trace-level protein identification and expression from microgram amounts of protein extracts from human tissues.
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Klyushkin, I. V., M. F. Tukhbatullin, and R. F. Bakhtiozin. "III All-Asian Congress on Ultrasound Research in Medicine and Biology (Seoul, August 30 - September 4, 1992)." Kazan medical journal 74, no. 3 (June 15, 1993): 238–39. http://dx.doi.org/10.17816/kazmj64731.
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A qualitative leap in the echoscanning of internal organs took place after the introduction of computers and the development of special programs for them. The development of new, more advanced and special sensors with high sensitivity is also of great importance. In this regard, organs such as the stomach and intestines become available for research, the diagnosis of intravascular and intraductal pathologies of organs is improved. Doppler sonography plays an important role in assessing the state of a particular organ, which occupies a special place in the differential diagnosis of liver and kidney neoplasms (Miron L. Poznaik, USA; Zai-Zsng-Ksu, China).
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Zhang, Lan, Min Yuan, Tao Liu, Li Wang, and Peng Gao. "Research on Program Calling and File Sharing between Windows and Linux." Applied Mechanics and Materials 214 (November 2012): 721–24. http://dx.doi.org/10.4028/www.scientific.net/amm.214.721.
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There is often more than one kind of operating systems in enterprises’ and organizations’ local area network. Therefore, exchanging visits under different operating systems would be very meaningful and important. Especially in the field of bioinformatics, in order to meet the requirements of researchers from various disciplines, such as mathematics, biology and computer science, we develop a new, intuitive and convenient system for exchanging resources between Windows and Linux.
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Lamanauskas, Vincentas, Violeta Šlekienė, and Loreta Ragulienė. "COMPUTER-BASED TECHNOLOGIES IN THE PROCESS OF NATURAL SCIENCE EDUCATION: SOCIO-EDUCATIONAL ASPECTS." GAMTAMOKSLINIS UGDYMAS / NATURAL SCIENCE EDUCATION 6, no. 3 (December 5, 2009): 8–23. http://dx.doi.org/10.48127/gu-nse/09.6.08b.
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It is obvious that ICT makes the process of teaching/learning more effective and beneficial whereas the education system starts functioning faster. The development of ICT and the process of globalization determine alteration in the education system as well as in the whole society. The implementation of new technologies in the educational process raises new possibilities for both teacher and learner, enhances educa-tion quality and makes the educational process more versatile. Hence, the object of research is the use of computer-based technologies in the process of teach-ing/learning sciences. Research is aimed at establishing the positions of 1st year students on applying com-puter-based technologies in comprehensive school learning sciences and at disclosing the frequency of us-ing these technologies in the classroom during the lessons on sciences, and also to find out some infor-mation about students` own skills in using computer technologies. Pilot research Student and Computer-Based Technologies was conducted in October – November, 2009. To collect the required data, an anonymous questionnaire was prepared. Research sample consisted of 211 respondents who were 1st year university students (freshmen). To collect the required data, an anonymous questionnaire including four main blocks was prepared. • The level of ability to use computer (in total, 30 parameters were included, for example, ability to use programs and documents, ability to operate fail search system etc.). • The methods of using computers (5 parameters were included, for example, learned during in-formatics classes; during classes in other subjects; during extracurricular activities; helped family members, friends etc.; individual learning). • The evaluation of the frequency of applying computer-based technologies during the classes of sciences (5 parameters were included, for example, the frequency of using a computer projector by the teacher; the frequency of demonstrations done by the teacher, the frequency of applying computer-based technologies by the students for the purpose of practical experimentation; the frequency of communication between students and teachers outside the classroom etc.). • Opinions on applying computer-based technologies during the classes of sciences at school. 20 closed type questions were addressed, for example, using computer-based technologies to make lessons more interesting, to increase motivation, for communication purposes etc. In the majority of cases, the students learn to use computer independently, whereas next comes help provided by friends and family members. The lessons of informatics have a higher impact on the learners from regional centres and female students. The classes on other subjects and extracurricular activities have no significant impact on increasing knowledge of work at computer. It has been established that computer-based technologies are very rarely used during the lessons of other subjects. The teachers relatively fre-quently used computer during the lessons of physics and biology, les frequently - during the classes of chemistry and physics. The teachers of sciences very rarely use computer-based technologies outside the classroom, i.e. for tutoring, giving advice, performing different tasks. The respondents think that using computer-based technologies in the classroom during the lessons of sciences has the highest impact on cog-nitive abilities (knowledge acquisition, self-sufficient studies etc.). However, they do not find important the impact of technologies on motivation for learning, practical use, communication and collaboration between students. Moreover, applying computer-based technologies in the classroom helps with concentration, pre-vents from distracting attention and does not lead to stressful situations, i.e. has no negative impact on the state of health and personal development. The level of ability to use computer (for example, ability to use programs and documents, ability to operate fail search system etc.) Computer knowledge and abilities does not depend on the duration of com-puter usage per day. The best skills are demonstrated in ability to carry out the simple functions of editing of the text, to use search systems and e-mail. The weakest skills, according to respondents, are connected with abilities to create websites, to establish and change parametres of computer programs, and also to instal new computer programs. Some differences depending on the sex of respondents are established also. For example, male students are better in ability to use complex functions of operating systems, than female students. Key words: computer-based technologies, science education, skills, science lessons.
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Xu, Xingjian, Lijun Sun, and Fanjun Meng. "Distributed Big Data Storage Infrastructure for Biomedical Research Featuring High-Performance and Rich-Features." Future Internet 14, no. 10 (September 24, 2022): 273. http://dx.doi.org/10.3390/fi14100273.
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The biomedical field entered the era of “big data” years ago, and a lot of software is being developed to tackle the analysis problems brought on by big data. However, very few programs focus on providing a solid foundation for file systems of biomedical big data. Since file systems are a key prerequisite for efficient big data utilization, the absence of specialized biomedical big data file systems makes it difficult to optimize storage, accelerate analysis, and enrich functionality, resulting in inefficiency. Here we present F3BFS, a functional, fundamental, and future-oriented distributed file system, specially designed for various kinds of biomedical data. F3BFS makes it possible to boost existing software’s performance without modifying its main algorithms by transmitting raw datasets from generic file systems. Further, F3BFS has various built-in features to help researchers manage biology datasets more efficiently and productively, including metadata management, fuzzy search, automatic backup, transparent compression, etc.
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Procko, Carl, Steven Morrison, Courtney Dunar, Sara Mills, Brianna Maldonado, Carlee Cockrum, Nathan Emmanuel Peters, Shao-shan Carol Huang, and Joanne Chory. "Big Data to the Bench: Transcriptome Analysis for Undergraduates." CBE—Life Sciences Education 18, no. 2 (June 2019): ar19. http://dx.doi.org/10.1187/cbe.18-08-0161.
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Next-generation sequencing (NGS)-based methods are revolutionizing biology. Their prevalence requires biologists to be increasingly knowledgeable about computational methods to manage the enormous scale of data. As such, early introduction to NGS analysis and conceptual connection to wet-lab experiments is crucial for training young scientists. However, significant challenges impede the introduction of these methods into the undergraduate classroom, including the need for specialized computer programs and knowledge of computer coding. Here, we describe a semester-long, course-based undergraduate research experience at a liberal arts college combining RNA-sequencing (RNA-seq) analysis with student-driven, wet-lab experiments to investigate plant responses to light. Students derived hypotheses based on analysis of RNA-seq data and designed follow-up studies of gene expression and plant growth. Our assessments indicate that students acquired knowledge of big data analysis and computer coding; however, earlier exposure to computational methods may be beneficial. Our course requires minimal prior knowledge of plant biology, is easy to replicate, and can be modified to a shorter, directed-inquiry module. This framework promotes exploration of the links between gene expression and phenotype using examples that are clear and tractable and improves computational skills and bioinformatics self-efficacy to prepare students for the “big data” era of modern biology.
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Kankaanpää, Pasi, Kalle Pahajoki, Varpu Marjomäki, Jyrki Heino, and Daniel White. "BioImageXD - New Open Source Free Software for the Processing, Analysis and Visualization of Multidimensional Microscopic Images." Microscopy Today 14, no. 3 (May 2006): 12–17. http://dx.doi.org/10.1017/s1551929500057606.
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With the recent success of the human genome project, researchers must now discover biological functions of the tens of thousands of proteins encoded in the genome. Molecular cell biology and structural biology methods are required for this work.Modern multidimensional bioimaging methods, such as laser scanning confocal microscopy and other light microscopic techniques, have emerged as a major research methodology in this new era of informational biology. These methods all produce vast amounts of digital information and require specialized computer software to process and analyze it. Several programs intended for this purpose have become available in recent years, but microscopists around the world frequently discover them unsuitable for many of their required tasks. The reasons for this are varied, and include: extensive bugs that take too long to fix, prohibitively high prices (also for updates and bug fixes), algorithms that are undisclosed and as such unacceptable for accurate scientific work, limited sets of features dispersed into separate “modules”, complex and difficult user interfaces, and lack of flexibility in adapting to specific research situations.
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Maldonado-Alconada, Ana María, María Ángeles Castillejo, María-Dolores Rey, Mónica Labella-Ortega, Marta Tienda-Parrilla, Tamara Hernández-Lao, Irene Honrubia-Gómez, et al. "Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for and How." International Journal of Molecular Sciences 23, no. 17 (September 1, 2022): 9980. http://dx.doi.org/10.3390/ijms23179980.
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The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, “dehesa.” It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors’ group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.
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Harris, Michelle A., Ronald F. Peck, Shannon Colton, Jennifer Morris, Elias Chaibub Neto, and Julie Kallio. "A Combination of Hand-held Models and Computer Imaging Programs Helps Students Answer Oral Questions about Molecular Structure and Function: A Controlled Investigation of Student Learning." CBE—Life Sciences Education 8, no. 1 (March 2009): 29–43. http://dx.doi.org/10.1187/cbe.08-07-0039.
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We conducted a controlled investigation to examine whether a combination of computer imagery and tactile tools helps introductory cell biology laboratory undergraduate students better learn about protein structure/function relationships as compared with computer imagery alone. In all five laboratory sections, students used the molecular imaging program, Protein Explorer (PE). In the three experimental sections, three-dimensional physical models were made available to the students, in addition to PE. Student learning was assessed via oral and written research summaries and videotaped interviews. Differences between the experimental and control group students were not found in our typical course assessments such as research papers, but rather were revealed during one-on-one interviews with students at the end of the semester. A subset of students in the experimental group produced superior answers to some higher-order interview questions as compared with students in the control group. During the interview, students in both groups preferred to use either the hand-held models alone or in combination with the PE imaging program. Students typically did not use any tools when answering knowledge (lower-level thinking) questions, but when challenged with higher-level thinking questions, students in both the control and experimental groups elected to use the models.
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Magana, Alejandra J., Manaz Taleyarkhan, Daniela Rivera Alvarado, Michael Kane, John Springer, and Kari Clase. "A Survey of Scholarly Literature Describing the Field of Bioinformatics Education and Bioinformatics Educational Research." CBE—Life Sciences Education 13, no. 4 (December 2014): 607–23. http://dx.doi.org/10.1187/cbe.13-10-0193.
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Bioinformatics education can be broadly defined as the teaching and learning of the use of computer and information technology, along with mathematical and statistical analysis for gathering, storing, analyzing, interpreting, and integrating data to solve biological problems. The recent surge of genomics, proteomics, and structural biology in the potential advancement of research and development in complex biomedical systems has created a need for an educated workforce in bioinformatics. However, effectively integrating bioinformatics education through formal and informal educational settings has been a challenge due in part to its cross-disciplinary nature. In this article, we seek to provide an overview of the state of bioinformatics education. This article identifies: 1) current approaches of bioinformatics education at the undergraduate and graduate levels; 2) the most common concepts and skills being taught in bioinformatics education; 3) pedagogical approaches and methods of delivery for conveying bioinformatics concepts and skills; and 4) assessment results on the impact of these programs, approaches, and methods in students’ attitudes or learning. Based on these findings, it is our goal to describe the landscape of scholarly work in this area and, as a result, identify opportunities and challenges in bioinformatics education.
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Marinicheva, K. V., L. V. Pchelinskaya, and D. А. Zubritsky. "DARPA programs and biological technologies – in the interests of national security." Scientific Messenger of LNU of Veterinary Medicine and Biotechnologies 20, no. 91 (November 16, 2018): 9–13. http://dx.doi.org/10.32718/nvlvet9102.
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The purpose of our article is to review and analyze the main areas, projects and developments in the management of promising research projects of the US Department of Defense DARPA. The dynamics of funding revealed an increase in interest in such areas as materials technology and biotechnology, promising aerospace systems, technology centric armed struggle, etc. The object of the research is – the development of the DARPA agency, and its influence on world scientific activity. As a subject of research in the article the possibilities of the DARPA Biological Technology Department and the perspective directions of research are considered. The Agency for Advanced Defense Research Projects DARPA (USA) was established in 1958. Over the past decade, success has led to the creation of analogues of this organizational structure in other countries: DRDO (India), MAFAT (Israel), SASTIND (China), GDA (France). DARPA Technology Priorities for 2020: 1. human technology; 2. technology of robotics; 3. network technologies; 5. technologies of automatic switching of events of real and virtual worlds; 6. technologies of integration and mutual empowerment of human and computer networks; 7. integrated network technologies for the transformation of the real world through the interaction of man and robots. In 2014, DARPA announced the creation of a new department – Biological Technology. The Department of Biological Technologies (DBT) is created to study the complex mechanisms of natural processes, and to implement their use in solving the problems of national defense. The task of DBT is to put biology at the service of national security. Among the priorities of the new department: 1) Survivability and ability to survive military service; 2) Synthetic biology of animals and living systems; 3) Integration of biochemical and omics data on human health. A feature of the direct line will be the overcoming of moral and ethical constraints on the way to improving the physical and intellectual abilities of a person. The appearance in Ukraine of the DARPA analogue is of the utmost importance for future technological development. Such a structure, called GARDA, should become a platform that brings together developers, startups, investment funds and military. The GARDA project was developed last year, but it requires professional expertise, resources, and serious political support at the government level.The creation in Ukraine of the domestic prototype of the DARPA Agency has a number of prerequisites: 1) the presence of high-tech institutions in the areas of defense and dual use; 2) the need for technological advantages of the Armed Forces of Ukraine and other armed formations of the state; 3) the importance of high-tech export on the world market of armaments and consolidation of the image of Ukraine as a high-tech state.
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Al Hijji, Khalfan Zahran Hamed, and Khaled Ateeq Saeed Abdullah. "The Specialization of Information Science and its Relationship with other Specializations: The Experience of the Department of Information Studies at Sultan Qaboos University." Journal of Arts and Social Sciences [JASS] 7, no. 3 (December 1, 2016): 141. http://dx.doi.org/10.24200/jass.vol7iss3pp141-154.
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This study aims to explore the interdisciplinary research and courses of the Department of Information Studies (DIS) at Sultan Qaboos University with other disciplines in the university, and to explore its impact on the management and development of various academic programs of the department. To achieve this objective, the study utilized qualitative research methods such as: content analysis of documents, written plans, and course syllabi of the department and open interviews with faculty members to identify kinds of relations with other scientific disciplines they seek when building their academic programs. The study revealed that the interdisciplinary relations of the department exist in all its programs. The DIS PhD program was initiated as an interdisciplinary program in cooperation with departments of Information Systems, Management, and Computer Science. Further, the interdisciplinary path of the Masters’ program is clearly seen in the variation of topics that dissertations have discussed, which include human resources, marketing, bibliometric studies, social media, e-government, information literacy, manuscripts, and technology acceptance. The Higher Diploma in Medical Libraries is directed towards qualifying specialist librarians for health and medical libraries. Students admitted in this program are usually selected from those who apply from biology and health sciences. Lastly, in the undergraduate level, DIS provides the bachelor of Learning Resource Centers in Faculty of Education with number of specialized courses. In the main time there are many electives and required courses from different disciplines that are included in the department’s undergraduate study plan.
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Sánchez-Jaramillo, Esteban Andrés, Luz Elena Gasca-Lozano, José María Vera-Cruz, Luis Daniel Hernández-Ortega, and Adriana María Salazar-Montes. "Automated Computer-Assisted Image Analysis for the Fast Quantification of Kidney Fibrosis." Biology 11, no. 8 (August 17, 2022): 1227. http://dx.doi.org/10.3390/biology11081227.
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Chronic kidney disease (CKD) is a common and worldwide health problem and one of the most important causes of morbidity and mortality. Most primary research on this disease requires evaluating the fibrosis index in animal model kidneys, specifically using Masson’s trichrome stain. Different programs are used to calculate the percentage of fibrosis; however, the analysis is time-consuming since one image must be performed at a time. CellProfiler™ is a program designed to analyze data obtained from biological samples and can process multiple images through pipelines, and the results can be exported to databases. This article explains how CellProfiler™ can be used to automatically analyze kidney histology photomicrographs from samples stained with Masson’s trichrome stain to assess the percentage of fibrosis in an experimental animal model of CKD. A pipeline was created to analyze Masson’s trichrome-stained slides in a model of CDK induced by adenine at doses of 50 mg/kg and 100 mg/kg, in addition to samples with the vehicle (75% glycerin). The results were compared with those obtained by ImageJ, and no significant differences were found between both programs. The CellProfiler™ pipeline made here is a reliable, fast, and easy alternative for kidney fibrosis analysis and quantification in experimental animal models.
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Tse, William T., Kevin K. Duh, and Morris Kletzel. "A Low-Cost, Open-Source Informatics Framework for Clinical Trials and Outcomes Research." Blood 118, no. 21 (November 18, 2011): 4763. http://dx.doi.org/10.1182/blood.v118.21.4763.4763.
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Abstract Abstract 4763 Data collection and analysis in clinical studies in hematology often require the use of specialized databases, which demand extensive information technology (IT) support and are expensive to maintain. With the goal of reducing the cost of clinical trials and promoting outcomes research, we have devised a new informatics framework that is low-cost, low-maintenance, and adaptable to both small- and large-scale clinical studies. This framework is based on the idea that most clinical data are hierarchical in nature: a clinical protocol typically entails the creation of sequential patient files, each of which documents multiple encounters, during which clinical events and data are captured and tagged for later retrieval and analysis. These hierarchical trees of clinical data can be easily stored in a hypertext mark-up language (HTML) document format, which is designed to represent similar hierarchical data on web pages. In this framework, the stored clinical data will be structured according to a web standard called Document Object Model (DOM), for which powerful informatics techniques have been developed to allow efficient retrieval and collation of data from the HTML documents. The proposed framework has many potential advantages. The data will be stored in plain text files in the HTML format, which is both human and machine readable, hence facilitating data exchange between collaborative groups. The framework requires only a regular web browser to function, thereby easing its adoption in multiple institutions. There will be no need to set up or maintain a relational database for data storage, thus minimizing data fragmentation and reducing the demand for IT support. Data entry and analysis will be performed mostly on the client computer, requiring the use of a backend server only for central data storage. Utility programs for data management and manipulation will be written in Javascript and JQuery, computer languages that are free, open-source and easy to maintain. Data can be captured, retrieved, and analyzed on different devices, including desktop computers, tablets or smart phones. Encryption and password protection can be applied in document storage and data transmission to ensure data security and HIPPA compliance. In a pilot project to implement and test this informatics framework, we designed prototype programming modules to perform individual tasks commonly encountered in clinical data management. The functionalities of these modules included user-interface creation, patient data entry and retrieval, visualization and analysis of aggregate results, and exporting and reporting of extracted data. These modules were used to access simulated clinical data stored in a remote server, employing standard web browsers available on all desktop computers and mobile devices. To test the capability of these modules, benchmark tests were performed. Simulated datasets of complete patient records, each with 1000 data items, were created and stored in the remote server. Data were retrieved via the web using a gzip compressed format. Retrieval of 100, 300, 1000 such records took only 1.01, 2.45, and 6.67 seconds using a desktop computer via a broadband connection, or 3.67, 11.39, and 30.23 seconds using a tablet computer via a 3G connection. Filtering of specific data from the retrieved records was equally speedy. Automated extraction of relevant data from 300 complete records for a two-sample t-test analysis took 1.97 seconds. A similar extraction of data for a Kaplan-Meier survival analysis took 4.19 seconds. The program allowed the data to be presented separately for individual patients or in aggregation for different clinical subgroups. A user-friendly interface enabled viewing of the data in either tabular or graphical forms. Incorporation of a new web browser technique permitted caching of the entire dataset locally for off-line access and analysis. Adaptable programming allowed efficient export of data in different formats for regulatory reporting purposes. Once the system was set up, no further intervention from IT department was necessary. In summary, we have designed and implemented a prototype of a new informatics framework for clinical data management, which should be low-cost and highly adaptable to various types of clinical studies. Field-testing of this framework in real-life clinical studies will be the next step to demonstrate its effectiveness and potential benefits. Disclosures: No relevant conflicts of interest to declare.
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Tangen, Uwe. "Enzyme-like Replication de Novo in a Microcontroller Environment." Artificial Life 16, no. 4 (October 2010): 311–28. http://dx.doi.org/10.1162/artl_a_00012.
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The desire to start evolution from scratch inside a computer memory is as old as computing. Here we demonstrate how viable computer programs can be established de novo in a Precambrian environment without supplying any specific instantiation, just starting with random bit sequences. These programs are not self-replicators, but act much more like catalysts. The microcontrollers used in the end are the result of a long series of simplifications. The objective of this simplification process was to produce universal machines with a human-readable interface, allowing software and/or hardware evolution to be studied. The power of the instruction set can be modified by introducing a secondary structure-folding mechanism, which is a state machine, allowing nontrivial replication to emerge with an instruction width of only a few bits. This state-machine approach not only attenuates the problems of brittleness and encoding functionality (too few bits available for coding, and too many instructions needed); it also enables the study of hardware evolution as such. Furthermore, the instruction set is sufficiently powerful to permit external signals to be processed. This information-theoretic approach forms one vertex of a triangle alongside artificial cell research and experimental research on the creation of life. Hopefully this work helps develop an understanding of how information—in a similar sense to the account of functional information described by Hazen et al.—is created by evolution and how this information interacts with or is embedded in its physico-chemical environment.
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Pizzolante, Antonio, Federico Nicodemo, Andrea Pierri, Amedeo Ferro, Biancamaria Pierri, Carlo Buonerba, Eleonora Beccaloni, Stefano Albanese, Bruno Basso, and Pellegrino Cerino. "Development of a municipality index of environmental pressure in Campania, Italy." Future Science OA 7, no. 7 (August 2021): FSO720. http://dx.doi.org/10.2144/fsoa-2021-0055.
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The Experimental Zooprophylactic Institute of Southern Italy (Istitituto Zooprofilattico Sperimentale del Mezzogiorno, IZSM) is a public health institution operating within the Italian National Health Service. Over the past 5 years [IZSM] has promoted several research studies and interventions in an effort to tackle the ‘Land of Fires’ phenomenon, caused by the continued trafficking and uncontrolled incineration of waste that has affected some areas of Campania for decades. In this article, a mathematical model that generates a municipality index of environmental pressure is presented. The model was developed by a multidisciplinary team led by an environmental engineer and included researchers in the fields of veterinary and human medicine, biology and computer science. This model may serve as a geostratification tool useful for the design of human biomonitoring studies, although it may also be employed for strategic planning of remediation programs and public health interventions.
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Ilie, Constantin Ovidiu, Octavian Alexa, Ion Lespezeanu, Marin Marinescu, and Dănuț Grosu. "Recurrence Plot Analysis to Study Parameters of a Gasoline Engine." Applied Mechanics and Materials 823 (January 2016): 323–28. http://dx.doi.org/10.4028/www.scientific.net/amm.823.323.
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Modern data analysis techniques has been successfully applied in many technical disciplines to understand the complexity of the system. The growing volume of theoretical knowledge about systems dynamic's offered researchers the opportunity to look for non-linear dynamics in data whose evolution linear models are unable to explain in a satisfactory manner. One of the most recent approach in this respect is Recurrence Analysis - RA. It is a graphical method designed to locate hidden recurring patterns, nonstationarity and structural changes. RA approach have first been applied in natural sciences like physics and biology. Quickly, was adopted in economics and engineering. Meanwhile, the fast development of computer resources has provided powerful tools to perform this new and complex model. One free software which we used to perform the analysis is Visual Recurrence Analysis - VRA developed by Eugene Kononov. As is presented in this paper, the recurrence plot investigation for the analyzing of the gasoline engine shows some of the its capabilities in this domain. We chose two specific engine parameters measured in two different tests to perform the RPA. These parameters are ignition angle and engine angular speed. There were computed graphs for each of them. Graphs were analyzed and compared to obtain a conclusion. This work is an incipient research, being one of the first attempt of using recurrence plot for analyzing automotive dynamics. It opens a wide field of action for future research programs.
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Hacisalihoglu, Gokhan, Uwe Hilgert, E. Bruce Nash, and David A. Micklos. "An Innovative Plant Genomics and Gene Annotation Program for High School, Community College, and University Faculty." CBE—Life Sciences Education 7, no. 3 (September 2008): 310–16. http://dx.doi.org/10.1187/cbe.07-08-0061.
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Today's biology educators face the challenge of training their students in modern molecular biology techniques including genomics and bioinformatics. The Dolan DNA Learning Center (DNALC) of Cold Spring Harbor Laboratory has developed and disseminated a bench- and computer-based plant genomics curriculum for biology faculty. In 2007, a five-day “Plant Genomics and Gene Annotation” workshop was held at Florida A&M University in Tallahassee, FL, to enhance participants' knowledge and understanding of plant molecular genetics and assist them in developing and honing their laboratory and computer skills. Florida A&M University is a historically black university with over 95% African-American student enrollment. Sixteen participants, including high school (56%) and community college faculty (25%), attended the workshop. Participants carried out in vitro and in silico experiments with maize, Arabidopsis, soybean, and food products to determine the genotype of the samples. Benefits of the workshop included increased awareness of plant biology research for high school and college level students. Participants completed pre- and postworkshop evaluations for the measurement of effectiveness. Participants demonstrated an overall improvement in their postworkshop evaluation scores. This article provides a detailed description of workshop activities, as well as assessment and long-term support for broad classroom implementation.
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Rodríguez Gutiérrez, Daniel, and Anna Biason-Lauber. "Pluripotent Cell Models for Gonadal Research." International Journal of Molecular Sciences 20, no. 21 (November 4, 2019): 5495. http://dx.doi.org/10.3390/ijms20215495.
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Sex development is a complex process involving many genes and hormones. Defects in this process lead to Differences of Sex Development (DSD), a group of heterogeneous conditions not as rare as previously thought. Part of the obstacles in proper management of these patients is due to an incomplete understanding of the genetics programs and molecular pathways involved in sex development and DSD. Several challenges delay progress and the lack of a proper model system for the single patient severely hinders advances in understanding these diseases. The revolutionary techniques of cellular reprogramming and guided in vitro differentiation allow us now to exploit the versatility of induced pluripotent stem cells to create alternatives models for DSD, ideally on a patient-specific personalized basis.
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Orazaliyeva, Elmira, and Fauziya Orazbayeva. "Multilingual Content in Teaching the Kazakh Language Courses." ATHENS JOURNAL OF PHILOLOGY 8, no. 4 (September 9, 2021): 269–82. http://dx.doi.org/10.30958/ajp.8-4-2.
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According to the second state program on the development and functioning of languages until 2020, Kazakhstan concentrates on consolidating the Kazakh language as the state language, where Russian, English or others are foreign languages. New educational programs of the country assume a step-by-step implementation of communicative language skills. Students receive a possibility of relaying certain knowledge in the field of natural, human and technical sciences. The mission of Abai Kazakh National Pedagogical University as the educational center of transforming the results of advanced research in the field of pedagogy, teaching methods are implemented to prepare teachers in order to support multilingual content approaches in education. It is expected that in high schools four natural subjects like chemistry, biology, computer science, and physics will be taught in English, Kazakh, and Russian, while history, language, literature and other art sciences will be the subjects of the Kazakh or Russian languages. The school programs with general educational standards are aimed at creating a base of modernly demanded and replenished knowledge. It explains the creation of the International Nazarbayev University which is unique in Kazakhstan. High admission requirements characterize selection quality, and targets in mastering foreign languages. Keywords: multi-academic content, multilingualism, cross-cultural expertises, educational methods and strategies, educational approaches
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MA, BIN, LIEYU WU, and KAIZHONG ZHANG. "IMPROVING THE SENSITIVITY AND SPECIFICITY OF PROTEIN HOMOLOGY SEARCH BY INCORPORATING PREDICTED SECONDARY STRUCTURES." Journal of Bioinformatics and Computational Biology 04, no. 03 (June 2006): 709–20. http://dx.doi.org/10.1142/s0219720006002119.
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In this paper, we improve the homology search performance by the combination of the predicted protein secondary structures and protein sequences. Previous research suggested that the straightforward combination of predicted secondary structures did not improve the homology search performance, mostly because of the errors in the structure prediction. We solved this problem by taking into account the confidence scores output by the prediction programs.
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Matteson, S. R., S. T. Deahl, M. E. Alder, and P. V. Nummikoski. "Advanced Imaging Methods." Critical Reviews in Oral Biology & Medicine 7, no. 4 (October 1996): 346–95. http://dx.doi.org/10.1177/10454411960070040401.
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Recent developments in imaging sciences have enabled dental researchers to visualize structural and biophysical changes effectively. New approaches for intra-oral radiography allow investigators to conduct densitometric assessments of dento-alveolar structures. Longitudinal changes in alveolar bone can be studied by computer-assisted image analysis programs. These techniques have been applied to dimensional analysis of the alveolar crest, detection of gain or loss of alveolar bone density, peri-implant bone healing, and caries detection. Dental applications of computed tomography (CT) include the detailed radiologic anatomy of alveolar processes, orofacial soft tissues and air spaces, and developmental defects. Image analysis software permits bone mass mineralization to be quantified by means of CT data. CT has also been used to study salivary gland disease, injuries of the facial skeleton, and dental implant treatment planning. Magnetic resonance imaging (MRI) has been used extensively in retrospective and prospective studies of internal derangements of the temporomandibular joint. Assessments based on MRI imaging of the salivary glands, paranasal sinuses, and cerebrovascular disease have also been reported. Magnetic resonance spectroscopy (MRS) has been applied to the study of skeletal muscle, tumors, and to monitor the healing of grafts. Nuclear imaging provides a sensitive technique for early detection of physiological changes in soft tissue and bone. It has been used in studies of periodontitis, osteomyelitis, oral and maxillofacial tumors, stress fractures, bone healing, temporomandibular joint, and blood flow. This article includes brief descriptions of the technical principles of each imaging modality, reviews their previous uses in oral biology research, and discusses potential future applications in research protocols.
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Sanchez, Alejandro, Fengshen Kuo, Stacey Petruzella, Oguz Akin, Michael Paris, Paul Russo, Timothy An-thy Chan, Marina Mourtzakis, A. Ari Hakimi, and Helena Furberg. "Mechanisms underlying the association between sarcopenia and poor oncologic outcomes in clear cell renal cell carcinoma." Journal of Clinical Oncology 37, no. 7_suppl (March 1, 2019): 662. http://dx.doi.org/10.1200/jco.2019.37.7_suppl.662.
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662 Background: Sarcopenia (low skeletal muscle mass) is associated with poor outcomes in patients with ccRCC. The mechanisms underlying this association are unclear. To understand this association, we examined gene expression differences by sarcopenic status in patients with ccRCC. Methods: The cohort consisted of 62 ccRCC patients treated by nephrectomy and previously transcriptomically-profiled in the Cancer Genome Atlas. Computed tomography scans without contrast performed within two months of surgery were reviewed to determine skeletal muscle cross-sectional area. Sarcopenia (yes/no) was defined according to gender-specific international consensus definitions. Baseline differences in clinicopathologic characteristics were assessed using the Chi-squared test for categorical and t-test for continuous variables. Differential expression analyses were performed using the R package “DESeq2.” Gene set enrichment analyses (GSEA) and single-set GSEA were used to evaluate differences in MSigDB Hallmark gene sets and estimate immune cell infiltration, respectively. P-values were corrected for multiple testing (p-adjust). Results: The cohort was predominantly male (82%), white (97%) and had localized disease (58%). Median age was 58.9 years (SD: 12.1). Sarcopenic (47%) patients were older (p < 0.001), obese (p < 0.001), and presented with higher AJCC stage (p = 0.006). In primary tumor specimens, sarcopenic patients demonstrated increased expression of angiogenic, inflammatory (e.g., IL-6, TNF-alpha), and epithelial mesenchymal transition programs (p-adjust < 0.05). Furthermore, sarcopenic patients had higher macrophage (p = 0.003) and Th17 immune cell infiltration (p = 0.003). Conclusions: Our findings suggest that ccRCC patients who are sarcopenic harbor gene expression programs associated with more aggressive biology. Increased macrophage infiltration and decreased Th17 immune cell infiltration have been previously associated with worse prognosis in ccRCC. It is not clear whether sarcopenia is a cause or consequence of tumor aggressiveness. Validation of these results in a larger cohort of patients and orthogonal validation are ongoing.
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Madsen, Ralitsa R., and Bart Vanhaesebroeck. "Cracking the context-specific PI3K signaling code." Science Signaling 13, no. 613 (January 7, 2020): eaay2940. http://dx.doi.org/10.1126/scisignal.aay2940.
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Specificity in signal transduction is determined by the ability of cells to “encode” and subsequently “decode” different environmental signals. Akin to computer software, this “signaling code” governs context-dependent execution of cellular programs through modulation of signaling dynamics and can be corrupted by disease-causing mutations. Class IA phosphoinositide 3-kinase (PI3K) signaling is critical for normal growth and development and is dysregulated in human disorders such as benign overgrowth syndromes, cancer, primary immune deficiency, and metabolic syndrome. Despite decades of PI3K research, understanding of context-dependent regulation of the PI3K pathway and of the underlying signaling code remains rudimentary. Here, we review current knowledge on context-specific PI3K signaling and how technological advances now make it possible to move from a qualitative to quantitative understanding of this pathway. Insight into how cellular PI3K signaling is encoded or decoded may open new avenues for rational pharmacological targeting of PI3K-associated diseases. The principles of PI3K context-dependent signal encoding and decoding described here are likely applicable to most, if not all, major cell signaling pathways.
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Hammersley, A. P. "FIT2D: a multi-purpose data reduction, analysis and visualization program." Journal of Applied Crystallography 49, no. 2 (March 1, 2016): 646–52. http://dx.doi.org/10.1107/s1600576716000455.
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FIT2D is one of the principal area detector data reduction, analysis and visualization programs used at the European Synchrotron Radiation Facility and is also used by more than 400 research groups worldwide, including many other synchrotron radiation facilities. It has been developed for X-ray science, but is applicable to other structural techniques and is used in analysing electron diffraction data and microscopy, and neutron diffraction and scattering data. FIT2D works for both interactive and `batch'-style data processing. Calibration and correction of detector distortions, integration of two-dimensional data to a variety of one-dimensional scans, and one- and two-dimensional model fitting are the main uses. Many other general-purpose image processing and image visualization operations are available. Commands are available through a `graphical user interface' and operations common to certain types of analysis are grouped within `interfaces'. Executable versions for most workstation and personal computer systems, and web page documentation, are available at http://www.esrf.eu/computing/scientific/FIT2D.
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Ibrahim, Ibrahim, Nurul Akmal, and Marwan Marwan. "Problem-based Learning and Student Critical Thinking to Improve Learning Achievement at Private Universities in Aceh." AL-ISHLAH: Jurnal Pendidikan 13, no. 2 (August 24, 2021): 1142–51. http://dx.doi.org/10.35445/alishlah.v13i2.698.
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This study aimed to determine the effectiveness of problem-based teaching and learning models to increase learning achievement and the relationship with students' critical thinking skills. This study used an experimental method with a design pretest-posttest control group. The population in this study were all semester four students of the Biology Education Department. Analysis of experimental data to measure the achievement of student learning outcomes with t-test and critical thinking skills using percentage description analysis, using statistical computer software programs. The research results show an increase in learning achievement, with an average N-gain for problem-based learning units is 70.9 (moderate) and 57.93 (moderate) for conventional classes. The t-test results show that the t-count value is 3.61 and the t-table is 1.991, so t-count t-table. The conclusion is that there are differences in learning outcomes in implementing problem-based teaching and learning models to increase learning outcomes with critical thinking skills of four at the Private University of Aceh Province, Indonesia.
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Akhavan, Peyman, Maryam Dehghani, Amir Rajabpour, and Amir Pezeshkan. "An investigation of the effect of extroverted and introverted personalities on knowledge acquisition techniques." VINE Journal of Information and Knowledge Management Systems 46, no. 2 (May 9, 2016): 194–206. http://dx.doi.org/10.1108/vjikms-06-2014-0043.
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Purpose This paper aims to explore the relationship between personality traits (introversion versus extroversion) and knowledge acquisition (KA) techniques. Design/methodology/approach The major methodology of the current study is survey. Results are based on 152 usable responses provided by experts in different industries including electronic, communication, information technology, computer and biology. The major analytical technique used is Pearson correlation analysis. Findings According to the results, there are significant relationships between personality traits (i.e. introversion versus extroversion) and KA techniques. Research limitations/implications This study was conducted on data from 152 Iranian experts which limits the generalizability of the results. This limitation can be addressed by future studies conducting similar studies on cross-country samples. Further, due to the analytical technique adopted in this study, causality implications cannot be drawn from the results. Originality/value This study reveals linkages between personality traits (i.e. introversion versus extroversion) and KA techniques. Results shed light on the KA process for both scholars and practitioners involved in KA programs in the organizations.
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Suzumori, Koichi, Ryuma Niiyama, Kenjiro Fukuda, and Kohei Nakajima. "Special Issue on Science of Soft Robots." Journal of Robotics and Mechatronics 34, no. 2 (April 20, 2022): 193–94. http://dx.doi.org/10.20965/jrm.2022.p0193.
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The science of soft robots, or soft robotics, is currently one of the most active fields in robotics. While traditional robots consist of rigid bodies, powerful servomotors, and carefully coded programs to realize power, precision, and reliability, soft robots consist of soft and flexible bodies, actuators, and intelligence for adaptability. They are not rigid, but instead flexible toward their surroundings. These differences have the potential to make soft robotics a great new field in robotics. A JSPS KAKENHI project “Science of Soft Robots” has been in progress in Japan since 2018. Part of this special issue is made in collaboration with this project. This special issue consists of 46 works in total: 2 review papers, 29 letters, and 15 papers. One review paper, 29 letters, and 3 research papers report research activities from the JSPS KAKENHI project, and the other review paper and 12 research papers have been contributed from outside the project. As this issue will make clear, the science of soft robots is a very interdisciplinary academic field, a collaboration of many researchers from various fields, such as mechanical/electrical engineering, computer science, material sciences, biology, zoology, medicine, and nursing, among others. We believe interdisciplinary work to be a key point for the exploration of soft robotics. The editors thank all of the authors and reviewers of the contributions, and are confident that this special issue will greatly contribute to further progress in robotics.
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Sulimov, V. B., E. V. Katkova, I. V. Oferkin, A. V. Sulimov, A. N. Romanov, A. I. Roschin, I. B. Beloglazova, O. S. Plekhanova, V. A. Tkachuk, and V. A. Sadovnichiy. "Application of Molecular Modeling to Urokinase Inhibitors Development." BioMed Research International 2014 (2014): 1–15. http://dx.doi.org/10.1155/2014/625176.
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Urokinase-type plasminogen activator (uPA) plays an important role in the regulation of diverse physiologic and pathologic processes. Experimental research has shown that elevated uPA expression is associated with cancer progression, metastasis, and shortened survival in patients, whereas suppression of proteolytic activity of uPA leads to evident decrease of metastasis. Therefore, uPA has been considered as a promising molecular target for development of anticancer drugs. The present study sets out to develop the new selective uPA inhibitors using computer-aided structural based drug design methods. Investigation involves the following stages: computer modeling of the protein active site, development and validation of computer molecular modeling methods: docking (SOL program), postprocessing (DISCORE program), direct generalized docking (FLM program), and the application of the quantum chemical calculations (MOPAC package), search of uPA inhibitors among molecules from databases of ready-made compounds to find new uPA inhibitors, and design of new chemical structures and their optimization and experimental examination. On the basis of known uPA inhibitors and modeling results, 18 new compounds have been designed, calculated using programs mentioned above, synthesized, and testedin vitro. Eight of them display inhibitory activity and two of them display activity about 10 μM.
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Yubero, Dèlia, Daniel Natera-de Benito, Jordi Pijuan, Judith Armstrong, Loreto Martorell, Guerau Fernàndez, Joan Maynou, et al. "The Increasing Impact of Translational Research in the Molecular Diagnostics of Neuromuscular Diseases." International Journal of Molecular Sciences 22, no. 8 (April 20, 2021): 4274. http://dx.doi.org/10.3390/ijms22084274.
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The diagnosis of neuromuscular diseases (NMDs) has been progressively evolving from the grouping of clinical symptoms and signs towards the molecular definition. Optimal clinical, biochemical, electrophysiological, electrophysiological, and histopathological characterization is very helpful to achieve molecular diagnosis, which is essential for establishing prognosis, treatment and genetic counselling. Currently, the genetic approach includes both the gene-targeted analysis in specific clinically recognizable diseases, as well as genomic analysis based on next-generation sequencing, analyzing either the clinical exome/genome or the whole exome or genome. However, as of today, there are still many patients in whom the causative genetic variant cannot be definitely established and variants of uncertain significance are often found. In this review, we address these drawbacks by incorporating two additional biological omics approaches into the molecular diagnostic process of NMDs. First, functional genomics by introducing experimental cell and molecular biology to analyze and validate the variant for its biological effect in an in-house translational diagnostic program, and second, incorporating a multi-omics approach including RNA-seq, metabolomics, and proteomics in the molecular diagnosis of neuromuscular disease. Both translational diagnostics programs and omics are being implemented as part of the diagnostic process in academic centers and referral hospitals and, therefore, an increase in the proportion of neuromuscular patients with a molecular diagnosis is expected. This improvement in the process and diagnostic performance of patients will allow solving aspects of their health problems in a precise way and will allow them and their families to take a step forward in their lives.
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Dharma, Arie Satia, and Veronika Tambunan. "Penerapan Model Pembelajaran dengan Metode Reinforcement Learning Menggunakan Simulator Carla." JURNAL MEDIA INFORMATIKA BUDIDARMA 5, no. 4 (October 26, 2021): 1405. http://dx.doi.org/10.30865/mib.v5i4.3169.
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Artificial Intelligence is the study of how to make machines or computer programs have the intelligence or ability to do things that humans can do. The application of AI is currently in various ways, one of which is for self-driving cars. To be able to do a self-driving car, the AI that is implanted in a car must applied to the method to be able to walk on its path and be able to adapt to its environment. Reinforcement learning is one type of machine learning where agents learn something by doing certain actions and the results of those actions and try to maximize the gifts received through interactions with the environment that are reward negative or positive. In this research, we applied of the reinforcement learning method on the Carla Car simulator. The simulator is used to collect data using an RGB sensor, then modeling experiments which produce several models to be used in simulation experiments. The model is obtained by using the Convolutional Neural Network (CNN) algorithm with the NVIDIA architectural model. From the results of research based on experiments conducted obtained the best model obtained from the experimental model by comparing the maximum reward value, high accuracy and low loss is model 1 in the experimental model A with 100 episodes and model 4 in model B experiment with 150 episodes
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Dill-McFarland, Kimberly A., Stephan G. König, Florent Mazel, David C. Oliver, Lisa M. McEwen, Kris Y. Hong, and Steven J. Hallam. "An integrated, modular approach to data science education in microbiology." PLOS Computational Biology 17, no. 2 (February 25, 2021): e1008661. http://dx.doi.org/10.1371/journal.pcbi.1008661.
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We live in an increasingly data-driven world, where high-throughput sequencing and mass spectrometry platforms are transforming biology into an information science. This has shifted major challenges in biological research from data generation and processing to interpretation and knowledge translation. However, postsecondary training in bioinformatics, or more generally data science for life scientists, lags behind current demand. In particular, development of accessible, undergraduate data science curricula has the potential to improve research and learning outcomes as well as better prepare students in the life sciences to thrive in public and private sector careers. Here, we describe the Experiential Data science for Undergraduate Cross-Disciplinary Education (EDUCE) initiative, which aims to progressively build data science competency across several years of integrated practice. Through EDUCE, students complete data science modules integrated into required and elective courses augmented with coordinated cocurricular activities. The EDUCE initiative draws on a community of practice consisting of teaching assistants (TAs), postdocs, instructors, and research faculty from multiple disciplines to overcome several reported barriers to data science for life scientists, including instructor capacity, student prior knowledge, and relevance to discipline-specific problems. Preliminary survey results indicate that even a single module improves student self-reported interest and/or experience in bioinformatics and computer science. Thus, EDUCE provides a flexible and extensible active learning framework for integration of data science curriculum into undergraduate courses and programs across the life sciences.
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Jaworek-Korjakowska, Joanna, and Paweł Kłeczek. "Automatic Classification of Specific Melanocytic Lesions Using Artificial Intelligence." BioMed Research International 2016 (2016): 1–17. http://dx.doi.org/10.1155/2016/8934242.
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Background. Given its propensity to metastasize, and lack of effective therapies for most patients with advanced disease, early detection of melanoma is a clinical imperative. Different computer-aided diagnosis (CAD) systems have been proposed to increase the specificity and sensitivity of melanoma detection. Although such computer programs are developed for different diagnostic algorithms, to the best of our knowledge, a system to classify different melanocytic lesions has not been proposed yet.Method. In this research we present a new approach to the classification of melanocytic lesions. This work is focused not only on categorization of skin lesions as benign or malignant but also on specifying the exact type of a skin lesion including melanoma, Clark nevus, Spitz/Reed nevus, and blue nevus. The proposed automatic algorithm contains the following steps: image enhancement, lesion segmentation, feature extraction, and selection as well as classification.Results. The algorithm has been tested on 300 dermoscopic images and achieved accuracy of 92% indicating that the proposed approach classified most of the melanocytic lesions correctly.Conclusions. A proposed system can not only help to precisely diagnose the type of the skin mole but also decrease the amount of biopsies and reduce the morbidity related to skin lesion excision.
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Hwang, Ki Woo. "The Use of Computer Algorithms and the Possibility of Historical Simulation in Digital History in Germany." Korean Society For German History 50 (August 31, 2022): 187–217. http://dx.doi.org/10.17995/kjgs.2022.8.50.187.
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In relation to history simulation, the difference between the technical principle of operating it and the actual use is very large at the current stage of digital history. However, the reason for such a difference is that while the technology of programs with complex and massive capacities such as human perception is already beyond our expectations, there is no history-optimized program yet to grasp historical events as a whole. Although the aforementioned text mining or network analysis methods have a device that can process high-dimensional areas such as human perception as data, it can only identify one aspect of the relationship between actors, and the level of development of a kind of historical simulation program that integrates them into one program is at an early stage, even abroad. The big difference between this theory and reality stems from the need for knowledge other than history in the process of constructing the simulation rather than a technical problem. For example, among the various factors that constitute the actor's attributes, there are many cases that require special knowledge of the psychological part or the external natural environment. Of course, the contents constituting the attribute can be limited to the scope covered by the historian, but in order to precisely construct the simulation model, the contents other than the history of the attribute must be very detailed, and for this, the help of the specialized area must be obtained.
Historical simulations have recently attracted attention for a new leap forward in digital history. In particular, the various expertise required in history simulation will expand the scope of history, thereby reaffirming the achievements of existing history and reducing unnecessary arguments, as well as triggering new and productive debates as the extension of expanded history. To do so, we first need to recognize two facts. The first is the fact that detailed technical environments for historical simulation are already in place, and the other is that research on simulation models optimized for historical studies by integrating these detailed results is insufficient. Fortunately, an integrated model for historical simulation has recently been introduced, such as German digital historian Shoeermann. Although the programs for building integrated historical simulation models are in the early stages, their applicability in the field of “history education” is at least significant, given that there is a device in place to identify the results produced by existing historical studies.
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Madeddu, Manuela, Stefano Marelli, Ahmad Abdel Sayed, Fabio Mosca, Silvia Cerolini, and Luisa Zaniboni. "Assessment of Sperm Viability and Computer-Assisted Motility Analysis in Budgerigars (Melopsittacus undulatus): Effect of Several In Vitro Processing Conditions." Veterinary Medicine International 2022 (March 22, 2022): 1–8. http://dx.doi.org/10.1155/2022/5997320.
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In order to preserve endangered psittacine species, more basic and applied research in reproductive biology is required. Assisted reproductive technologies such as artificial insemination play an important role in parrots species conservation programs to overcome the problem of infertile eggs and male infertility. The aim of this study was to define an effective in vitro protocol in order to standardize the sperm quality evaluation in psittacines, studying Melopsittacus undulatus as model species. Semen was collected from twenty adult males by massage technique from May to June. Sperm concentration was measured by the spectrophotometric method. Sperm quality (sperm membrane integrity (SMI), motility, and kinetic parameters) was assessed on fresh semen. Three different experimental protocols were performed to compare the effects of various processing conditions on SMI, motility, and kinetic parameters. In protocol 1, test was performed by Lake extender with three different pH, 7.4 versus 8.2 versus 8.4, and two different equilibration temperatures after dilution of fresh semen (4°C versus 25°C). In protocol 2, two dilution rates of semen after collection were valuated, 1 : 3 versus 1 : 4, as well as three different semen storage temperatures (4°C versus 25°C versus 38°C) before sperm motility analysis with the computer-assisted sperm analysis (CASA). In protocol 3, two different Makler chamber temperatures (38 versus 41°C) during motility analysis were tested. A significant progressive improvement in spermatozoa motility and kinetic parameters was registered with pH 8.4. Progressive motility and all kinetic parameters were higher at 4°C equilibration temperature. Straightness (STR) kinetic parameter was better with 1 : 4 dilution rate. Total motile sperm was higher in 41°C Makler chamber. In this study, for the first time, the effects of different processing protocols on psittacines seminal quality analysis were investigated. Significant differences conditioning the effectiveness of analysis protocols have been described.
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Lazarus, David B., Johan Renaudie, Dorina Lenz, Patrick Diver, and Jens Klump. "Raritas: a program for counting high diversity categorical data with highly unequal abundances." PeerJ 6 (October 9, 2018): e5453. http://dx.doi.org/10.7717/peerj.5453.
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Acquiring data on the occurrences of many types of difficult to identify objects are often still made by human observation, for example, in biodiversity and paleontologic research. Existing computer counting programs used to record such data have various limitations, including inflexibility and cost. We describe a new open-source program for this purpose—Raritas. Raritas is written in Python and can be run as a standalone app for recent versions of either MacOS or Windows, or from the command line as easily customized source code. The program explicitly supports a rare category count mode which makes it easier to collect quantitative data on rare categories, for example, rare species which are important in biodiversity surveys. Lastly, we describe the file format used by Raritas and propose it as a standard for storing geologic biodiversity data. ‘Stratigraphic occurrence data’ file format combines extensive sample metadata and a flexible structure for recording occurrence data of species or other categories in a series of samples.
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Wercelens, Polyane, Waldeyr da Silva, Fernanda Hondo, Klayton Castro, Maria Emília Walter, Aletéia Araújo, Sergio Lifschitz, and Maristela Holanda. "Bioinformatics Workflows With NoSQL Database in Cloud Computing." Evolutionary Bioinformatics 15 (January 2019): 117693431988997. http://dx.doi.org/10.1177/1176934319889974.
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Scientific workflows can be understood as arrangements of managed activities executed by different processing entities. It is a regular Bioinformatics approach applying workflows to solve problems in Molecular Biology, notably those related to sequence analyses. Due to the nature of the raw data and the in silico environment of Molecular Biology experiments, apart from the research subject, 2 practical and closely related problems have been studied: reproducibility and computational environment. When aiming to enhance the reproducibility of Bioinformatics experiments, various aspects should be considered. The reproducibility requirements comprise the data provenance, which enables the acquisition of knowledge about the trajectory of data over a defined workflow, the settings of the programs, and the entire computational environment. Cloud computing is a booming alternative that can provide this computational environment, hiding technical details, and delivering a more affordable, accessible, and configurable on-demand environment for researchers. Considering this specific scenario, we proposed a solution to improve the reproducibility of Bioinformatics workflows in a cloud computing environment using both Infrastructure as a Service (IaaS) and Not only SQL (NoSQL) database systems. To meet the goal, we have built 3 typical Bioinformatics workflows and ran them on 1 private and 2 public clouds, using different types of NoSQL database systems to persist the provenance data according to the Provenance Data Model (PROV-DM). We present here the results and a guide for the deployment of a cloud environment for Bioinformatics exploring the characteristics of various NoSQL database systems to persist provenance data.
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De Greve, Jean-Pierre. "Challenges in Astronomy Education." Proceedings of the International Astronomical Union 5, H15 (November 2009): 642–67. http://dx.doi.org/10.1017/s1743921310010884.
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AbstractAstronomy is an attractive subject for education. It deals with fascination of the unknown and the unreachable, yet is uses tools, concepts and insights from various fundamental sciences such as mathematics, physics, chemistry, biology. Because of this it can be well used for introducing sciences to young people and to raise their interest in further studies in that direction. It is also an interesting subject for teaching as its different aspects (observation techniques, theory, data sampling and analysis, modelling,?) offer various didactical approaches towards different levels of pupils, students and different backgrounds. And it gives great opportunities to teach and demonstrate the essence of scientific research, through tutorials and projects. In this paper we discuss some of the challenges education in general, and astronomy in particular, faces in the coming decades, given the major geophysical and technological changes that can be deducted from our present knowledge. This defines a general, but very important background in terms of educational needs at various levels, and in geographical distribution of future efforts of the astronomical community. Special emphasis will be given to creative approaches to teaching, to strategies that are successful (such as the use of tutorials with element from computer games), and to initiatives complementary to the regular educational system. The programs developed by the IAU will be briefly highlighted.
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Chiu, Wei-Chiao, Da-Liang Ou, and Ching-Ting Tan. "Mouse Models for Immune Checkpoint Blockade Therapeutic Research in Oral Cancer." International Journal of Molecular Sciences 23, no. 16 (August 16, 2022): 9195. http://dx.doi.org/10.3390/ijms23169195.
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The most prevalent oral cancer globally is oral squamous cell carcinoma (OSCC). The invasion of adjacent bones and the metastasis to regional lymph nodes often lead to poor prognoses and shortened survival times in patients with OSCC. Encouraging immunotherapeutic responses have been seen with immune checkpoint inhibitors (ICIs); however, these positive responses to monotherapy have been limited to a small subset of patients. Therefore, it is urgent that further investigations into optimizing immunotherapies are conducted. Areas of research include identifying novel immune checkpoints and targets and tailoring treatment programs to meet the needs of individual patients. Furthermore, the advancement of combination therapies against OSCC is also critical. Thus, additional studies are needed to ensure clinical trials are successful. Mice models are advantageous in immunotherapy research with several advantages, such as relatively low costs and high tumor growth success rate. This review paper divided methods for establishing OSCC mouse models into four categories: syngeneic tumor models, chemical carcinogen induction, genetically engineered mouse, and humanized mouse. Each method has advantages and disadvantages that influence its application in OSCC research. This review comprehensively surveys the literature and summarizes the current mouse models used in immunotherapy, their advantages and disadvantages, and details relating to the cell lines for oral cancer growth. This review aims to present evidence and considerations for choosing a suitable model establishment method to investigate the early diagnosis, clinical treatment, and related pathogenesis of OSCC.
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Hernández-Vázquez, Rosa Alicia, Guillermo Urriolagoitia-Sosa, Rodrigo Arturo Marquet-Rivera, Beatriz Romero-Ángeles, Octavio Alejandro Mastache-Miranda, Juan Alejandro Vázquez-Feijoo, and Guillermo Urriolagoitia-Calderón. "High-Biofidelity Biomodel Generated from Three-Dimensional Imaging (Cone-Beam Computed Tomography): A Methodological Proposal." Computational and Mathematical Methods in Medicine 2020 (January 28, 2020): 1–14. http://dx.doi.org/10.1155/2020/4292501.
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Experimental research on living beings faces several obstacles, which are more than ethical and moral issues. One of the proposed solutions to these situations is the computational modelling of anatomical structures. The present study shows a methodology for obtaining high-biofidelity biomodels, where a novel imagenological technique is used, which applies several CAM/CAD computer programs that allow a better precision for obtaining a biomodel, with highly accurate morphological specifications of the molar and tissues that shape the biomodel. The biomodel developed is the first lower molar subjected to a basic chewing simulation through the application of the finite element method, resulting in a viable model, able to be subjected to various simulations to analyse molar biomechanical characteristics, as well as pathological conditions to evaluate restorative materials and develop treatment plans. When research is focused in medical and dental investigation aspects, numerical analyses could allow the implementation of several tools commonly used by mechanical engineers to provide new answers to old problems in these areas. With this methodology, it is possible to perform high-fidelity models no matter the size of the anatomical structure, nor the complexity of its structure and internal tissues. So, it can be used in any area of medicine.
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Roc, Anne C., Julie M. Vose, Susan M. O'Brien, and Wendy Turell. "Addressing Challenges in Chronic Lymphocytic Leukemia with Continuing Education: Impact on Practice Behaviors and Knowledge." Blood 132, Supplement 1 (November 29, 2018): 5851. http://dx.doi.org/10.1182/blood-2018-99-120174.
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Abstract Background: As the era of personalized medicine draws ever closer for patients with CLL, advances in understanding of prognostic factors, biomarkers, drug classes and new agents pose a continuing challenge for clinicians to remain informed and competent in managing CLL. Clinicians must be able to determine the best treatment regimens for their patients based on cytogenetic profiles and in accordance with current treatment guidelines, evaluate recent efficacy and safety data and how they apply in practice for individual patients, anticipate and manage adverse effects, and address barriers to adherence. To address these challenges, we created continuing medical education (CME) activities focused on: 1) determination of optimal treatment strategy through use of prognostic and patient criteria, including mutations and abnormalities; 2) stratification of regimens, 3) assessment of emerging agents, sequential and combination regimens, and use of clinical trial data pertaining to patients with relapsed/refractory CLL; 4) planning individualized treatment algorithms; and, 5) addressing treatment barriers. Learner responses were evaluated to assess the influence of education. Methods: Two sets of consecutive online video-based programs were developed in January 2016 and January 2018 to address the identified knowledge and practice needs. Each respective program consisted of two 1-hour CME activities (4 hours overall) with slides, polling and live questions; programs were initially live and immediately made available on-demand at www.OMedLive.com for 6 months. CME test questions were administered at 3 time points (pre-activity, immediate post-activity, and 8-weeks post). Data from these questions, live polling responses, and learner-submitted questions during live Q&A were analyzed to determine engagement, lessons learned and continuing education gaps. Tests of statistical significance were conducted using the McNemar test for matched pairs (learners who completed both pre/post & pre/follow-up post, respectively). Effect size was computed using Cohen's d. Results: In total, 869 learners took part in the 2016 and 2018 programs (561 and 308). Overall, 103 out of 437 learners (25% at the point of evaluation) completed all pre, post, and follow-up surveys. 71% reported the educational activity positively influenced patient experience or outcome, and 76% reported it played a role in positively altering their clinical practice. As the result of education, learners reported commitments to change regarding: medical/practice knowledge (88%), care attitudes (84%), practice behavior (84%) and patient clinical outcomes (79%). Learners showed improvements on 8 knowledge questions and 4 competence questions, including statistically significant lifts in 3 case questions and 2 knowledge questions. Specifically, they demonstrated significantly improved competence via 3 case scenarios which required identifying the optimal next step for various patients with del17p, with and without IgHV unmutated CLL. They also showed significantly improved knowledge on patient-specific criteria for selecting treatment strategies for patients with CLL, and clinical staging of CLL. Although this study is limited by lack of access to practice data, outcomes results and participant questions indicate clinicians benefit from online continuing education on CLL. Conclusions: Ongoing education on CLL can yield immediate and sustained gains in knowledge, competence, and performance, and improve the ability to provide individualized treatment for patients. Disclosures Vose: Kite Pharma: Research Funding; Legend Pharmaceuticals: Honoraria; Merck Sharp & Dohme Corp.: Research Funding; Novartis: Honoraria, Research Funding; Bristol Myers Squibb: Research Funding; Celgene: Research Funding; Abbvie: Honoraria; Seattle Genetics, Inc.: Research Funding; Incyte Corp.: Research Funding; Acerta Pharma: Research Funding; Epizyme: Honoraria; Roche: Honoraria. O'Brien:Acerta: Research Funding; Gilead: Consultancy, Research Funding; Kite Pharma: Research Funding; Abbvie: Consultancy; Aptose Biosciences Inc.: Consultancy; TG Therapeutics: Consultancy, Research Funding; Regeneron: Research Funding; Sunesis: Consultancy, Research Funding; Astellas: Consultancy; Vaniam Group LLC: Consultancy; GlaxoSmithKline: Consultancy; Janssen: Consultancy; Pharmacyclics: Consultancy, Research Funding; Alexion: Consultancy; Pfizer: Consultancy, Research Funding; Celgene: Consultancy; Amgen: Consultancy.