Search results for: genomic tools

Authors: Angel Daniel Muñoz Guzmán

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E-learning is becoming more and more common every day. For online, hybrid or traditional face-to-face programs, there are some e-teaching platforms like Google classroom, Blackboard, Moodle and Canvas, and there are platforms for full e-learning like Coursera, edX or Udemy. These tools are changing the way students acquire knowledge at schools; however, in today’s changing world that is not enough. As students’ needs and skills change and become more complex, new tools will need to be added to keep them engaged and potentialize their learning. This is especially important in the current global situation that is changing everything: the Covid-19 pandemic. Due to Covid-19, education had to make an unexpected switch from face-to-face courses to digital courses. In this study, the students’ learning experience is analyzed by applying different e-tools and following the Tec21 Model and a flexible and digital model, both developed by the Tecnologico de Monterrey University. The evaluation of the students’ learning experience has been made by the quantitative PrEmo method of emotions. Findings suggest that the quantity of e-tools used during a course does not affect the students’ learning experience as much as how a teacher links every available tool and makes them work as one in order to keep the student engaged and motivated.

Keywords: student, experience, e-learning, e-teaching, e-tools, technology, education

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Authors: Yi Anson Lam, Siu Ming Yiu, Kam Pui Chow

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Digital evidence has been tendering to courts at an exponential rate in recent years. As an industrial practice, most digital evidence is extracted and preserved using specialized and well-accepted forensics tools. On the other hand, the advancement in technologies enables the creation of quite a few emerging platforms such as Telegram, Signal etc. Existing (well-accepted) forensics tools were not designed to extract evidence from these emerging platforms. While new forensics tools require a significant amount of time and effort to be developed and verified, this paper tries to address how to fill this gap using quick-fix alternative methods for digital evidence collection (e.g., based on APIs provided by Apps) and discuss issues related to the admissibility of this evidence to courts with support from international courts’ stance and the circumstances of accepting digital evidence using these proposed alternatives.

Keywords: extraction, digital evidence, laws, investigation

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Authors: H. Bahbahani, H. Musa, F. Al Mathen

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The dromedary camels (Camelus dromedarius) are single-humped even-toed ungulates populating the African Sahara, Arabian Peninsula, and Southwest Asia. The genome of this desert-adapted species has been minimally investigated using autosomal microsatellite and mitochondrial DNA markers. In this study, the genomes of 33 dromedary camel samples from different parts of the Arabian Peninsula were sequenced using Illumina Next Generation Sequencing (NGS) platform. These data were combined with Genotyping-by-Sequencing (GBS) data from African (Sudanese) dromedaries to investigate the genomic relationship between African and Arabian Peninsula dromedary camels. Principle Component Analysis (PCA) and average genome-wide admixture analysis were be conducted on these data to tackle the objectives of these studies. Both of the two analyses conducted revealed phylogeographic distinction between these two camel populations. However, no breed-wise genetic classification has been revealed among the African (Sudanese) camel breeds. The Arabian Peninsula camel populations also show higher heterozygosity than the Sudanese camels. The results of this study explain the evolutionary history and migration of African dromedary camels from their center of domestication in the southern Arabian Peninsula. These outputs help scientists to further understand the evolutionary history of dromedary camels, which might impact in conserving the favorable genetic of this species.

Keywords: dromedary, genotyping-by-sequencing, Arabian Peninsula, Sudan

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Authors: Jinu Phonamontham

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Coronavirus, also referred to as COVID-19, is a virus caused by the SARS-Cov-2 virus. The pandemic has caused over 10 million cases and 500,000 deaths worldwide through the end of June 2020. In a previous study, HLA-DQA1*01:02 allele was associated with COVID-19 disease (p-value = 0.0121). Furthermore, there was a statistical significance between HLA- DQB1*06:02 and COVID-19 in the Italian population by Bonferroni’s correction (p-value = 0.0016). Nevertheless, there is no data describing the distribution of HLA alleles as a valid marker for prediction of COVID-19 in the Thai population. We want to investigate the prevalence of HLA-DQA1*01:02 and HLA-DQB1*06:02 alleles that are associated with severe COVID-19 in the Thai population. In this study, we recruited 200 healthy Thai individuals. Genomic DNA samples were isolated from EDTA blood using Genomic DNA Mini Kit. HLA genotyping was conducted using the Lifecodes HLA SSO typing kits (Immucor, West Avenue, Stamford, USA). The frequency of HLA-DQA1 alleles in Thai population, consisting of HLA-DQA1*01:01 (27.75%), HLA-DQA1*01:02 (24.50%), HLA-DQA1*03:03 (13.00%), HLA-DQA1*06:01 (10.25%) and HLA-DQA1*02:01 (6.75%). Furthermore, the distributions of HLA-DQB1 alleles were HLA-DQB1*05:02 (21.50%), HLA-DQB1*03:01 (15.75%), HLA-DQB1*05:01 (14.50%), HLA-DQB1*03:03 (11.00%) and HLA-DQB1*02:02 (8.25%). Particularly, HLA- DQA1*01:02 (29.00%) allele was the highest frequency in the NorthEast group, but there was not significant difference when compared with the other regions in Thais (p-value = 0.4202). HLA-DQB1*06:02 allele was similarly distributed in Thai population and there was no significant difference between Thais and China (3.8%) and South Korea (6.4%) and Japan (8.2%) with p-value > 0.05. Whereas, South Africa (15.7%) has a significance with Thais by p-value of 0.0013. This study supports the specific genotyping of the HLA-DQA1*01:02 and HLA-DQB1*06:02 alleles to screen severe COVID-19 in Thai and many populations.

Keywords: HLA-DQA1*01:02, HLA-DQB1*06:02, Asian, Thai population

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Authors: Eurico Lima Basto, Ofélia Pinto, Anabela Silva, Amélia Ferreira-Da-Silva

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The purpose if this study is two-fold: on the one hand, to identify the accounting information systems implemented in third sector organizations, as well as its components, its tools and the decisions and control purposes they serve; on the other hand, and by confronting these two theories - institutional theory versus rational choice – we intent to go further by understanding the reasons behind the adoption of the aforementioned tools. Data has been collected from third sector organizations operating in Portugal. Our sample includes all juridical types of organizations such as foundations, cooperative, associations or private institutions of social solidarity. The questionnaire contained sixteen close-ended questions and four open-questions. Results confirm the theoretical perspective of institutionalism. Most third sector organizations operating in Portugal implemented only traditional accounting tools like standard accounting statements, cost accounting, budgeting. Moreover, there is clear evidence that the decisions about the implementation of these tools were coercive oriented. With this study it is intended to contribute to a better understanding of the context of third sector organizations in Portugal, in particular the role that accounting plays in this sector, with a special focus on management accounting tools, and the factors that influence their use and the degree of their usefulness in the process of decision making.

Keywords: third sector, accounting tools, institutional theory, Portugal, descriptive research

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Authors: Maria Lopez-Ibarra, Ana Velazquez-Wong, Lucelli Yañez-Gutierrez, Maria Araujo-Solis, Fabio Salamanca-Gomez, Alfonso Mendez-Tenorio, Haydeé Rosas-Vargas

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Congenital heart diseases (CHD) are the most common congenital abnormalities. These conditions can occur as both an element of distinct chromosomal malformation syndromes or as non-syndromic forms. Their etiology is not fully understood. Genetic variants such copy number variants have been associated with CHD. The aim of our study was to analyze these genomic variants in peripheral blood from Mexican children diagnosed with non-syndromic CHD. We included 16 children with atrial and ventricular septal defects and 5 healthy subjects without heart malformations as controls. To exclude the most common heart disease-associated syndrome alteration, we performed a fluorescence in situ hybridization test to identify the 22q11.2, responsible for congenital heart abnormalities associated with Di-George Syndrome. Then, a microarray based comparative genomic hybridization was used to identify global copy number variants. The identification of copy number variants resulted from the comparison and analysis between our results and data from main genetic variation databases. We identified copy number variants gain in three chromosomes regions from pediatric patients, 4q13.2 (31.25%), 9q34.3 (25%) and 20q13.33 (50%), where several genes associated with cellular, biosynthetic, and metabolic processes are located, UGT2B15, UGT2B17, SNAPC4, SDCCAG3, PMPCA, INPP6E, C9orf163, NOTCH1, C20orf166, and SLCO4A1. In addition, after a hierarchical cluster analysis based on the fluorescence intensity ratios from the comparative genomic hybridization, two congenital heart disease groups were generated corresponding to children with atrial or ventricular septal defects. Further analysis with a larger sample size is needed to corroborate these copy number variants as possible biomarkers to differentiate between heart abnormalities. Interestingly, the 20q13.33 gain was present in 50% of children with these CHD which could suggest that alterations in both coding and non-coding elements within this chromosomal region may play an important role in distinct heart conditions.

Keywords: aCGH, bioinformatics, congenital heart diseases, copy number variants, fluorescence in situ hybridization

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Authors: Zeynep Turhan

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Digital tools can improve knowledge and awareness of strategies and skills for healthy and respectful intimate relationships. The website of the Healthy and Respectful Relationship Program has been developed and included five key videos about how to build healthy intimate relationships. This study examined the perspectives about informative videos by focusing on how individuals learn new information or challenge their preconceptions or attitudes regarding male privilege and women's oppression. Five individuals who received no-contact orders and attended group intervention were the sample of this study. The observation notes were the major methodology examining how participants responded to video tools. The data analysis method was the interpretative phenomenological analysis. The results showed that many participants found the tools useful in learning the types of violence and communication strategies. Nevertheless, obstacles to implementing some techniques were found in their relationships. These digital tools might enhance healthy and respectful relationships despite some limitations.

Keywords: healthy relationship, digital tools, intimate partner violence, perpetrators, video interventions

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Authors: Omar Alshehri, Vic Lally

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This paper examined the attitudes of using social media tools to support learning at a university in Saudi Arabia. Moreover, it investigated the students’ current usage of these tools and examined the barriers they could face during the use of social media tools in the education process. Participants in this study were 42 university students. A web-based survey was used to collect data for this study. The results indicate that all of the students were familiar with social media and had used at least one type of social media for learning. It was found out that all students had very positive attitudes towards the use of social media and welcomed using these tools as a supplementary to the curriculum. However, the results indicated that the major barriers to using these tools in learning were distraction, opposing Islamic religious teachings, privacy issues, and cyberbullying. The study recommended that this study could be replicated at other Saudi universities to investigate factors and barriers that might affect Saudi students’ attitudes toward using social media to support learning.

Keywords: barriers to social media use, benefits of social media use, higher education, Saudi Arabia, social media

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Authors: M. Błoch, P. Karpiński, P. Gasperowicz, R. Płoski, A. Lebioda, P. Skiba, A. Rozensztrauch, D. Patkowski, R. Śmigiel

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Introduction: The cause of the isolated form of esophageal atresia has been yet unknown. Objectives: The primary objective of this study was to indicate epigenetic factors which may play an important role in the etiopathogenesis of esophageal atresia. Methods: We recruited a group of 6 pairs of twins, among whom one of the twins developed EA. The selection of such a group for testing allows for excluding external factors (e.g., infections, drugs, toxins) as the cause of the birth defect. The analyzes were performed with the use of genetic material isolated from the whole blood and esophagus tissue of a patient with EA. The reduced representation bisulphite sequencing (RRBS) technique was used to study the change in the genomic imprinting -a change in the expression of genes, which may be the epigenetic cause of EA. Results: In the course of the analyzes, significant hypomethylation and hypermethylation regions were identified. 65 genes with probably increased expression and 65 with decreased expression were selected. These genes have not been marked in literature as possibly pathogenic in esophageal atresia. However, their participation in the pathogenesis of esophageal atresia cannot be clearly excluded. Conclusion: We suggest a role of hypomethylation or hypermethylation of selected genes as one of the possible epigenetic factors in EA pathogenesis. The use of the RRBS technique in the search for the cause of EA is pioneer research; therefore, it seems necessary to extend the research group to new patients with EA. Acknowledgment: The work was supported by the National Science Centre, Poland, under research project 2016/21/N/NZ5/01927.

Keywords: esophageal atresia, epigenetics, embryonic development, surgery, genes expression, twins

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Authors: Abdul Sattar Jamali, Imdad Ali Memon, Maqsood Ahmed Memon

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Quality of production near to zero defects is an objective of every manufacturing and service organization. In order to maintain and improve the quality by reduction in defects, Statistical tools are being used by any organizations. There are many statistical tools are available to assess the quality. Keeping in view the importance of many statistical tools, traditional 7QC tools has been used in any manufacturing and automobile Industry. Therefore, the 7QC tools have been successfully applied at one of the Automobile Company Pakistan. Preliminary survey has been done for the implementation of 7QC tool in the assembly line of Automobile Industry. During preliminary survey two inspection points were decided to collect the data, which are Chassis line and trim line. The data for defects at Chassis line and trim line were collected for reduction in defects which ultimately improve productivity. Every 7QC tools has its benefits observed from the results. The flow charts developed for better understanding about inspection point for data collection. The check sheets developed for helps for defects data collection. Histogram represents the severity level of defects. Pareto charts show the cumulative effect of defects. The Cause and Effect diagrams developed for finding the root causes of each defects. Scatter diagram developed the relation of defects increasing or decreasing. The P-Control charts developed for showing out of control points beyond the limits for corrective actions. The successful implementation of 7QC tools at the inspection points at Automobile Industry concluded that the considerable amount of reduction on defects level, as in Chassis line from 132 defects to 13 defects. The total 90% defects were reduced in Chassis Line. In Trim line defects were reduced from 157 defects to 28 defects. The total 82% defects were reduced in Trim Line. As the Automobile Company exercised only few of the 7 QC tools, not fully getting the fruits by the application of 7 QC tools. Therefore, it is suggested the company may need to manage a mechanism for the application of 7 QC tools at every section.

Keywords: check sheet, cause and effect diagram, control chart, histogram

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Authors: Takwa Belwakess

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With the wave of the digitization that invades the modern world, communication tools took their place in the world of business. As for organizations, being part of the digital era necessarily involves an evolution of the management style, mainly in processes management, knowing also as quality management system (QMS). For more than 50 years quality management standards have been adopted by organizations to prove their operational and financial performances. We believe that achieving a high-level of communication can lead to better quality management and greater customer satisfaction, which is essential to make sure long-term competitiveness. In this paper, a questionnaire survey was developed to investigate the use of collaboration tools such as Content Management System and Social Networks. Data from more than 100 companies based in France was analyzed, the results show that adopting new digital communication tools while applying quality management practices over a reasonable period, contributed to delivering a better implementation of the QMS for a better business performance.

Keywords: communication tools, content management system, digital, effectiveness, French companies, quality management system, quality management practices, social networks

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Authors: Nur Azemah Aminludin, Osman Mohd Tahir

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A dynamic landscape development is important for providing healthy ecosystem which supports all life. Nowadays, many initiatives towards sustainable development have been published. They lead to better living and more efficient use of natural resources in sustaining long-term ecological, economics and social benefits. To date, many assessment tools related to built environment have been established and practiced in this region, which mostly has the purpose assessing the environment performance of buildings. Hence, an assessment tool focusing on the sustainable landscape development itself is a necessity. This paper reviews the assessment criteria and indicators that are suitable for sustainable landscape development practices. The local and global assessment tools for landscape development are investigated, analyzed and discussed critically. Consideration also is given to the integration of the assessment tools with the surrounding environmental, social, and economical aspects. In addition, the assessment criteria and indicators for assessing the landscape development in Malaysia are also reviewed and discussed. In conclusion, this paper reviews, analyzes and discusses on available local and global landscape development assessment tools for sustainability.

Keywords: assessment tool, sustainable landscape development, assessment criteria, assessment indicator

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Authors: Esteban Alejandro Armas Vega, Ana Lucila Sandoval Orozco, Luis Javier García Villalba

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The benchmarking of tools for dynamic analysis of vulnerabilities in web applications is something that is done periodically, because these tools from time to time update their knowledge base and search algorithms, in order to improve their accuracy. Unfortunately, the vast majority of these evaluations are made by software enthusiasts who publish their results on blogs or on non-academic websites and always with the same evaluation methodology. Similarly, academics who have carried out this type of analysis from a scientific approach, the majority, make their analysis within the same methodology as well the empirical authors. This paper is based on the interest of finding answers to questions that many users of this type of tools have been asking over the years, such as, to know if the tool truly test and evaluate every vulnerability that it ensures do, or if the tool, really, deliver a real report of all the vulnerabilities tested and exploited. This kind of questions have also motivated previous work but without real answers. The aim of this paper is to show results that truly answer, at least on the tested tools, all those unanswered questions. All the results have been obtained by changing the common model of benchmarking used for all those previous works.

Keywords: cybersecurity, IDS, security, web scanners, web vulnerabilities

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Authors: Ki-Yeo Kim

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Trends in genetics are transforming in order to identify differential coexpressions of correlated gene expression rather than the significant individual gene. Moreover, it is known that a combined biomarker pattern improves the discrimination of a specific cancer. The identification of the combined biomarker is also necessary for the early detection of invasive oral squamous cell carcinoma (OSCC). To identify the combined biomarker that could improve the discrimination of OSCC, we explored an appropriate number of genes in a combined gene set in order to attain the highest level of accuracy. After detecting a significant gene set, including the pre-defined number of genes, a combined expression was identified using the weights of genes in a gene set. We used the Principal Component Analysis (PCA) for the weight calculation. In this process, we used three public microarray datasets. One dataset was used for identifying the combined biomarker, and the other two datasets were used for validation. The discrimination accuracy was measured by the out-of-bag (OOB) error. There was no relation between the significance and the discrimination accuracy in each individual gene. The identified gene set included both significant and insignificant genes. One of the most significant gene sets in the classification of normal and OSCC included MMP1, SOCS3 and ACOX1. Furthermore, in the case of oral dysplasia and OSCC discrimination, two combined biomarkers were identified. The combined genomic expression achieved better performance in the discrimination of different conditions than in a single significant gene. Therefore, it could be expected that accurate diagnosis for cancer could be possible with a combined biomarker.

Keywords: oral squamous cell carcinoma, combined biomarker, microarray dataset, correlated genes

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Authors: A. Capodieci, G. Del Fiore, L. Mainetti

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Recently, the use of web 2.0 tools has increased in companies and public administration organizations. This phenomenon, known as "Enterprise 2.0", has, de facto, modified common organizational and operative practices. This has led “knowledge workers” to change their working practices through the use of Web 2.0 communication tools. Unfortunately, these tools have not been integrated with existing enterprise information systems, a situation that could potentially lead to a loss of information. This is an important problem in an organizational context, because knowledge of information exchanged within the organization is needed to increase the efficiency and competitiveness of the organization. In this article we demonstrate that it is possible to capture this knowledge using collaboration processes, which are processes of abstraction created in accordance with design patterns and applied to new organizational operative practices.

Keywords: business practices, business process patterns, collaboration tools, enterprise 2.0, knowledge workers

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Authors: Tung-Hui Hsu, Wen-Yuh Jywe

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Five-axis computer numerical control (CNC) machine tools (three linear and two rotary axes) are ideally suited to the fabrication of complex work pieces, such as dies, turbo blades, and cams. The locations of the axis average line and centerline of the rotary axes strongly influence the performance of these machines; however, techniques to compensate for eccentric error in the rotary axes remain weak. This paper proposes optical (Non-Bar) techniques capable of calibrating five-axis CNC machine tools and compensating for eccentric error in the rotary axes. This approach employs the measurement path in ISO/CD 10791-6 to determine the eccentric error in two rotary axes, for which compensatory measures can be implemented. Experimental results demonstrate that the proposed techniques can improve the performance of various five-axis CNC machine tools by more than 90%. Finally, a result of the cutting test using a B-type five-axis CNC machine tool confirmed to the usefulness of this proposed compensation technique.

Keywords: calibration, compensation, rotary axis, five-axis computer numerical control (CNC) machine tools, eccentric error, optical calibration system, ISO/CD 10791-6

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Authors: Rohaya Abdul Wahab, Raja Mohd Fuad Tengku Aziz, Nazaliza Othman, Sharifah Saleh, Nabihah Razali, Rozaimah Baharim, M. Hanif M. Nasir

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This paper will discuss how EDA tools are integrated and automated in an Integrated Circuit Design Environment. Some of the problems face in our current environment is that users need to configure manually on the library paths, start-up files and project directories. Certain manual processes that happen between the users and applications can be automated but they must be transparent to the users. For example, the users can run the applications directly after login without knowing the library paths and start-up files locations. The solution to these problems is to automate the processes using standard configuration files which will benefit the users and EDA support. This paper will discuss how the implementation is done to automate the process using scripting languages such as Perl, Tcl, Scheme and Shell Script. These scripting tools are great assets for design engineers to build a robust and powerful design flow and this technique is widely used to integrate all the tools together.

Keywords: EDA tools, Integrated Circuits, scripting, integration, automation

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Authors: Ugo Rovigatti

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Neuroblastoma (NBL) has epitomized for at least 40 years our understanding of cancer cellular and molecular biology and its potential applications to novel therapeutic strategies. This includes the discovery of the very first oncogene aberrations and tumorigenesis suppression by differentiation in the 80s; the potential role of suppressor genes in the 90s; the relevance of immunotherapy in the millennium first, and the discovery of additional mutations by NGS technology in the millennium second decade. Similar discoveries were achieved in the majority of human cancers, and similar therapeutic interventions were obtained subsequently to NBL discoveries. Unfortunately, targeted therapies suggested by specific mutations (such as MYCN amplification –MNA- present in ¼ or 1/5 of cases) have not elicited therapeutic successes in aggressive NBL, where the prognosis is still dismal. The reasons appear to be linked to Tumor Heterogeneity, which is particularly evident in NBL but also a clear hallmark of aggressive human cancers generally. The new avenue of cancer immunotherapy (CIT) provided new hopes for cancer patients, but we still ignore the cellular or molecular targets. CIT is emblematic of high-risk disease (HR-NBL) since the mentioned GD2 passive immunotherapy is still providing better survival. We recently critically reviewed and evaluated the literature depicting the genomic landscapes of HR-NBL, coming to the qualified conclusion that among hundreds of affected genes, potential targets, or chromosomal sites, none correlated with anti-GD2 sensitivity. A better explanation is provided by the Micro-Foci inducing Virus (MFV) model, which predicts that neuroblasts infection with the MFV, an RNA virus isolated from a cancer-cluster (space-time association) of HR-NBL cases, elicits the appearance of MNA and additional genomic aberrations with mechanisms resembling chromothripsis. Neuroblasts infected with low titers of MFV amplified MYCN up to 100 folds and became highly transformed and malignant, thus causing neuroblastoma in young rat pups of strains SD and Fisher-344 and larger tumor masses in nu/nu mice. An association was discovered with GD2 since this glycosphingolipid is also the receptor for the family of MFV virus (dsRNA viruses). It is concluded that a dsRNA virus, MFV, appears to provide better explicatory mechanisms for the genesis of i) specific genomic aberrations such as MNA; ii) extensive tumor heterogeneity and chromothripsis; iii) the effects of passive immunotherapy with anti-GD2 monoclonals and that this and similar models should be further investigated in both pediatric and adult cancers.

Keywords: neuroblastoma, MYCN, amplification, viruses, GD2

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Authors: David J. Foran, Nhan Do, Samuel Ajjarapu, Wenjin Chen, Tahsin Kurc, Joel H. Saltz

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The large-scale data and computational requirements of investigators throughout the clinical and research communities demand an informatics infrastructure that supports both existing and new investigative and translational projects in a robust, secure environment. In some subspecialties of medicine and research, the capacity to generate data has outpaced the methods and technology used to aggregate, organize, access, and reliably retrieve this information. Leading health care centers now recognize the utility of establishing an enterprise-wide, clinical data warehouse. The primary benefits that can be realized through such efforts include cost savings, efficient tracking of outcomes, advanced clinical decision support, improved prognostic accuracy, and more reliable clinical trials matching. The overarching objective of the work presented here is the development and implementation of a flexible Intelligent Retrieval and Interrogation System (IRIS) that exploits the combined use of computational imaging, genomics, and data-mining capabilities to facilitate clinical assessments and translational research in oncology. The proposed System includes a multi-modal, Clinical & Research Data Warehouse (CRDW) that is tightly integrated with a suite of computational and machine-learning tools to provide insight into the underlying tumor characteristics that are not be apparent by human inspection alone. A key distinguishing feature of the System is a configurable Extract, Transform and Load (ETL) interface that enables it to adapt to different clinical and research data environments. This project is motivated by the growing emphasis on establishing Learning Health Systems in which cyclical hypothesis generation and evidence evaluation become integral to improving the quality of patient care. To facilitate iterative prototyping and optimization of the algorithms and workflows for the System, the team has already implemented a fully functional Warehouse that can reliably aggregate information originating from multiple data sources including EHR’s, Clinical Trial Management Systems, Tumor Registries, Biospecimen Repositories, Radiology PAC systems, Digital Pathology archives, Unstructured Clinical Documents, and Next Generation Sequencing services. The System enables physicians to systematically mine and review the molecular, genomic, image-based, and correlated clinical information about patient tumors individually or as part of large cohorts to identify patterns that may influence treatment decisions and outcomes. The CRDW core system has facilitated peer-reviewed publications and funded projects, including an NIH-sponsored collaboration to enhance the cancer registries in Georgia, Kentucky, New Jersey, and New York, with machine-learning based classifications and quantitative pathomics, feature sets. The CRDW has also resulted in a collaboration with the Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC) at the U.S. Department of Veterans Affairs to develop algorithms and workflows to automate the analysis of lung adenocarcinoma. Those studies showed that combining computational nuclear signatures with traditional WHO criteria through the use of deep convolutional neural networks (CNNs) led to improved discrimination among tumor growth patterns. The team has also leveraged the Warehouse to support studies to investigate the potential of utilizing a combination of genomic and computational imaging signatures to characterize prostate cancer. The results of those studies show that integrating image biomarkers with genomic pathway scores is more strongly correlated with disease recurrence than using standard clinical markers.

Keywords: clinical data warehouse, decision support, data-mining, intelligent databases, machine-learning.

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Authors: A. Pontrandolfi, G. Enjolras, F. Capitanio

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The study analyses the strategies Italian farmers use to cope with the risks that face their production. We specifically explore the potential and the limitations of the economic tools for climatic risk management in agriculture of the Common Agricultural Policy 2014-2020, that foresees contributions for economic tools for risk management, in relation to farms’ needs, exposure and vulnerability of agricultural areas to climatic risk. We consider at the farm level approaches to hedge risks in terms of the use of technical tools (agricultural practices, pesticides, fertilizers, irrigation) and economic/financial instruments (insurances, etc.). We develop cross-sectional and longitudinal analyses as well as analyses of correlation that underline the main differences between the way farms adapt their structure and management towards risk. The results show a preference for technical tools, despite the presence of important public aids on economic tools such as insurances. Therefore, there is a strong need for a more effective and integrated risk management policy scheme. Synergies between economic tools and risk reduction actions of a more technical, structural and management nature (production diversification, irrigation infrastructures, technological and management innovations and formation-information-consultancy, etc.) are emphasized.

Keywords: agriculture and climate change, climatic risk management, insurance schemes, farmers' approaches to risk management

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Authors: Gaurav D. Sonawane, Vikas G. Sargade

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The present investigation is a study of the effect of advanced Physical Vapor Deposition (PVD) coatings on cutting temperature residual stresses and surface roughness during Duplex Stainless Steel (DSS) 2205 turning. Austenite stabilizers like nickel, manganese, and molybdenum reduced the cost of DSS. Surface Integrity (SI) plays an important role in determining corrosion resistance and fatigue life. Resistance to various types of corrosion makes DSS suitable for applications with critical environments like Heat exchangers, Desalination plants, Seawater pipes and Marine components. However, lower thermal conductivity, poor chip control and non-uniform tool wear make DSS very difficult to machine. Cemented carbide tools (M grade) were used to turn DSS in a dry environment. AlTiN and AlTiCrN coatings were deposited using advanced PVD High Pulse Impulse Magnetron Sputtering (HiPIMS) technique. Experiments were conducted with cutting speed of 100 m/min, 140 m/min and 180 m/min. A constant feed and depth of cut of 0.18 mm/rev and 0.8 mm were used, respectively. AlTiCrN coated tools followed by AlTiN coated tools outperformed uncoated tools due to properties like lower thermal conductivity, higher adhesion strength and hardness. Residual stresses were found to be compressive for all the tools used for dry turning, increasing the fatigue life of the machined component. Higher cutting temperatures were observed for coated tools due to its lower thermal conductivity, which results in very less tool wear than uncoated tools. Surface roughness with uncoated tools was found to be three times higher than coated tools due to lower coefficient of friction of coating used.

Keywords: cutting temperature, DSS2205, dry turning, HiPIMS, surface integrity

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Authors: Anna Solovyeva, Ivan Levakin, Nickolai Galaktionov, Olga Podgornaya

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Animals that reproduce asexually were thought to have the same genotypes within generations for a long time. However, some refuting examples were found, and mobile genetic elements (MGEs) or transposons are considered to be the most probable source of genetic instability. Dispersed nature and the ability to change their genomic localization enables MGEs to be efficient mutators. Hence the study of MGEs genomic impact requires an appropriate object which comprehends both representative amounts of various MGEs and options to evaluate the genomic influence of MGEs. Animals that reproduce asexually seem to be a decent model to study MGEs impact in genomic variability. We found a small marine trematode Himasthla elongata (Himasthlidae) to be a good model for such investigation as it has a small genome size, diverse MGEs and parthenogenetic stages in the lifecycle. In the current work, clonal diversity of cercaria was traced with an AFLP (Amplified fragment length polymorphism) method, diverse zones from electrophoretic patterns were cloned, and the nature of the fragments explored. Polymorphic patterns of individual cercariae AFLP-based fingerprints are enriched with retrotransposons of different families. The bulk of those sequences are represented by open reading frames of non-Long Terminal Repeats containing elements(non-LTR) yet Long-Terminal Repeats containing elements (LTR), to a lesser extent in variable figments of AFLP array. The CR1 elements expose both in polymorphic and conservative patterns are remarkably more frequent than the other non-LTR retrotransposons. This data was confirmed with shotgun sequencing-based on Illumina HiSeq 2500 platform. Individual cercaria of the same clone (i.e., originated from a single miracidium and inhabiting one host) has a various distribution of MGE families detected in sequenced AFLP patterns. The most numerous are CR1 and RTE-Bov retrotransposons, typical for trematode genomes. Also, we identified LTR-retrotransposons of Pao and Gypsy families among DNA transposons of CMC-EnSpm, Tc1/Mariner, MuLE-MuDR and Merlin families. We detected many of them in H. elongata transcriptome. Such uneven MGEs distribution in AFLP sequences’ sets reflects the different patterns of transposons spreading in cercarial genomes as transposons affect the genome in many ways (ectopic recombination, gene structure interruption, epigenetic silencing). It is considered that they play a key role in the origins of trematode clonal polymorphism. The authors greatly appreciate the help received at the Kartesh White Sea Biological Station of the Russian Academy of Sciences Zoological Institute. This work is funded with RSF 19-74-20102 and RFBR 17-04-02161 grants and the research program of the Zoological Institute of the Russian Academy of Sciences (project number AAAA-A19-119020690109-2).

Keywords: AFLP, clonal polymorphism, Himasthla elongata, mobile genetic elements, NGS

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Authors: Faheema Khan

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In order to investigate the influence of genetic background on salt tolerance in Soybean (Glycine max) ten soybean genotypes released/notified in India were selected. (Pusa-20, Pusa-40, Pusa-37, Pusa-16, Pusa-24, Pusa-22, BRAGG, PK-416, PK-1042, and DS-9712). The 10-day-old seedlings were subjected to 0, 25, 50, 75, 100, 125, and 150 mM NaCl for 15 days. Plant growth, leaf osmotic adjustment, and RAPD analysis were studied. In comparison to control plants, the plant growth in all genotypes was decreased by salt stress, respectively. Salt stress decreased leaf osmotic potential in all genotypes however the maximum reduction was observed in genotype Pusa-24 followed by PK-416 and Pusa-20. The difference in osmotic adjustment between all the genotypes was correlated with the concentrations of ion examined such as Na+ and the leaf proline concentration. These results suggest that the genotypic variation for salt tolerance can be partially accounted for by plant physiological measures. The genetic polymorphisms between soybean genotypes differing in response to salt stress were characterized using 25 RAPD primers. These primers generated a total of 1640 amplification products, among which 1615 were found to be polymorphic. A very high degree of polymorphism (98.30%) was observed. UPGMA cluster analysis of genetic similarity indices grouped all the genotypes into two major clusters. Intra-clustering within the two clusters precisely grouped the 10 genotypes in sub-cluster as expected from their physiological findings. Our results show that RAPD technique is a sensitive, precise and efficient tool for genomic analysis in soybean genotypes.

Keywords: glycine max, NaCl, RAPD, proteomics

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Authors: M. Ramadan, B. Salah

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This paper introduces a framework to digitalize lean manufacturing tools to enhance smart lean-based manufacturing environments or Lean 4.0 manufacturing systems. The paper discusses the integration between lean tools and the powerful features of recent real-time data capturing systems with the help of Information and Communication Technologies (ICT) to develop an intelligent real-time monitoring and controlling system of production operations concerning lean targets. This integration is represented in the Lean 4.0 system called Dynamic Value Stream Mapping (DVSM). Moreover, the paper introduces the practice of Radio Frequency Identification (RFID) and ICT to smartly support lean tools and practices during daily production runs to keep the lean system alive and effective. This work introduces a practical description of how the lean method tools 5S, standardized work, and poka-yoke can be digitalized and smartly monitored and controlled through DVSM. A framework of the three tools has been discussed and put into practice in a German switchgear manufacturer.

Keywords: lean manufacturing, Industry 4.0, radio frequency identification, value stream mapping

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Authors: Harold Jideofor

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The application of Project Management (PM) tools and techniques in the public sector is gradually becoming an important issue in developing economies, especially in a country like Nigeria where projects of different size and structures are undertaken. The paper examined the application of the project management practice in the public sector in Nigeria. The PM lifecycles, tools, and techniques were presented. The study was carried out in Lagos because of its metropolitan nature and rapidly growing economy. Twenty-three copies of questionnaire were administered to 23 public institutions in Lagos to generate primary data. The descriptive analysis techniques using percentages and table presentations coupled with the coefficient of correlation were used for data analysis. The study revealed that application of PM tools and techniques is an essential management approach that tends to achieve specified objectives within specific time and budget limits through the optimum use of resources. Furthermore, the study noted that there is a lack of in-depth knowledge of PM tools and techniques in public sector institutions sampled, also a high cost of the application was also observed by the respondents. The study recommended among others that PM tools and techniques should be applied gradually especially in old government institutions where resistance to change is perceived to be high.

Keywords: project management, public sector, practice, Nigeria

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Authors: Sandisiwe Mangali, Graeme Bradley

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Genome is complete set of the organism's hereditary information encoded as either deoxyribonucleic acid or ribonucleic acid in most viruses. The three different types of genomes are nuclear, mitochondrial and the plastid genome and their sequences which are uncovered by genome sequencing are known as an archive for all genetic information and enable researchers to understand the composition of a genome, regulation of gene expression and also provide information on how the whole genome works. These sequences enable researchers to explore the population structure, genetic variations, and recent demographic events in threatened species. Particularly, genome sequencing refers to a process of figuring out the exact arrangement of the basic nucleotide bases of a genome and the process through which all the afore-mentioned genomes are sequenced is referred to as whole or complete genome sequencing. Gelidium pristoides is South African endemic Rhodophyta species which has been harvested in the Eastern Cape since the 1950s for its high economic value which is one motivation for its sequencing. Its endemism further motivates its sequencing for conservation biology as endemic species are more vulnerable to anthropogenic activities endangering a species. As sequencing, mapping and annotating the Gelidium pristoides genome is the aim of this study. To accomplish this aim, the genomic DNA was extracted and quantified using the Nucleospin Plank Kit, Qubit 2.0 and Nanodrop. Thereafter, the Ion Plus Fragment Library was used for preparation of a 600bp library which was then sequenced through the Ion S5 sequencing platform for two runs. The produced reads were then quality-controlled and assembled through the SPAdes assembler with default parameters and the genome assembly was quality assessed through the QUAST software. From this assembly, the plastid and the mitochondrial genomes were then sampled out using Gelidiales organellar genomes as search queries and ordered according to them using the Geneious software. The Qubit and the Nanodrop instruments revealed an A260/A280 and A230/A260 values of 1.81 and 1.52 respectively. A total of 30792074 reads were obtained and produced a total of 94140 contigs with resulted into a sequence length of 217.06 Mbp with N50 value of 3072 bp and GC content of 41.72%. A total length of 179281bp and 25734 bp was obtained for plastid and mitochondrial respectively. Genomic data allows a clear understanding of the genomic constituent of an organism and is valuable as foundation information for studies of individual genes and resolving the evolutionary relationships between organisms including Rhodophytes and other seaweeds.

Keywords: Gelidium pristoides, genome, genome sequencing and assembly, Ion S5 sequencing platform

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Authors: Olivia Kurucz

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Gamification is one of the outstanding new methodological possibilities of urban public participation processes to make the most informed decision possible for the future steps of urban development. This paper examines four Hungarian experimental projects in which gamified tools were applied during the public participation progresses by the Urban Future Laboratory (UFLab) research workshop of Budapest University of Technology and Economics (BUTE). The recently implemented future planning projects (in the cities of Pécel, Kistarcsa, Budapest, and Salgótarján) were initiated by various motives, but the multi-stakeholder dialogues were facilitated through physical gamified tools in all cases. Based on the urban gamification hypothesis, the use of gamified tools supported certain steps of participatory processes in several aspects: it helped to increase the attractiveness of public events, to create a more informal atmosphere, to ensure equal conditions for actors, to recall a design mindset, to bridge contrasting social or cultural differences, to fix opinions and to assist dialogue between city actors, designers, and residents. This statement is confirmed by assessing the applied tools, analyzing the case studies, and comparing them to perceive their effects and interrelations.

Keywords: experimental projects, future planning, gamification, gamified tools, Hungary, public participation, UFLab, urban gamification

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Authors: Leo Nnamdi Ozurumba-Dwight

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Messenger ribooxynucleic acid (mRNA) molecules are compositional, protein-based. These proteins, encoding mRNA molecules (which collectively connote the transcriptome), when analyzed by RNA sequencing (RNAseq), unveils the nature of gene expression in the RNA. The obtained gene expression provides clues of cellular traits and their dynamics in presentations. These can be studied in relation to function and responses. RNAseq is a practical concept in Genomics as it enables detection and quantitative analysis of mRNA molecules. Single cell and spatial transcriptomics both present varying avenues for expositions in genomic characteristics of single cells and pooled cells in disease conditions such as cancer, auto-immune diseases, hematopoietic based diseases, among others, from investigated biological tissue samples. Single cell transcriptomics helps conduct a direct assessment of each building unit of tissues (the cell) during diagnosis and molecular gene expressional studies. A typical technique to achieve this is through the use of a single-cell RNA sequencer (scRNAseq), which helps in conducting high throughput genomic expressional studies. However, this technique generates expressional gene data for several cells which lack presentations on the cells’ positional coordinates within the tissue. As science is developmental, the use of complimentary pre-established tissue reference maps using molecular and bioinformatics techniques has innovatively sprung-forth and is now used to resolve this set back to produce both levels of data in one shot of scRNAseq analysis. This is an emerging conceptual approach in methodology for integrative and progressively dependable transcriptomics analysis. This can support in-situ fashioned analysis for better understanding of tissue functional organization, unveil new biomarkers for early-stage detection of diseases, biomarkers for therapeutic targets in drug development, and exposit nature of cell-to-cell interactions. Also, these are vital genomic signatures and characterizations of clinical applications. Over the past decades, RNAseq has generated a wide array of information that is igniting bespoke breakthroughs and innovations in Biomedicine. On the other side, spatial transcriptomics is tissue level based and utilized to study biological specimens having heterogeneous features. It exposits the gross identity of investigated mammalian tissues, which can then be used to study cell differentiation, track cell line trajectory patterns and behavior, and regulatory homeostasis in disease states. Also, it requires referenced positional analysis to make up of genomic signatures that will be sassed from the single cells in the tissue sample. Given these two presented approaches to RNA transcriptomics study in varying quantities of cell lines, with avenues for appropriate resolutions, both approaches have made the study of gene expression from mRNA molecules interesting, progressive, developmental, and helping to tackle health challenges head-on.

Keywords: transcriptomics, RNA sequencing, single cell, spatial, gene expression.

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Authors: W. S. Thulasitha, N. Umasuthan, G. I. Godahewa, Jehee Lee

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In fish, innate immune defense is the first immune response against microbial pathogens which consists of several antimicrobial components. Galectins are one of the carbohydrate binding lectins that have the ability to identify pathogen by recognition of pathogen associated molecular patterns. Galectins play a vital role in the regulation of innate and adaptive immune responses. Rock bream Oplegnathus fasciatus is one of the most important cultured species in Korea and Japan. Considering the losses due to microbial pathogens, present study was carried out to understand the molecular and functional characteristics of a galectin in normal and pathogenic conditions, which could help to establish an understanding about immunological components of rock bream. Complete cDNA of rock bream galectin like protein B (rbGal like B) was identified from the cDNA library, and the in silico analysis was carried out using bioinformatic tools. Genomic structure was derived from the BAC library by sequencing a specific clone and using Spidey. Full length of rbGal like B (contig14775) cDNA containing 517 nucleotides was identified from the cDNA library which comprised of 435 bp in the open reading frame encoding a deduced protein composed of 145 amino acids. The molecular mass of putative protein was predicted as 16.14 kDa with an isoelectric point of 8.55. A characteristic conserved galactose binding domain was located from 12 to 145 amino acids. Genomic structure of rbGal like B consisted of 4 exons and 3 introns. Moreover, pairwise alignment showed that rock bream rbGal like B shares highest similarity (95.9 %) and identity (91 %) with Takifugu rubripes galectin related protein B like and lowest similarity (55.5 %) and identity (32.4 %) with Homo sapiens. Multiple sequence alignment demonstrated that the galectin related protein B was conserved among vertebrates. A phylogenetic analysis revealed that rbGal like B protein clustered together with other fish homologs in fish clade. It showed closer evolutionary link with Takifugu rubripes. Tissue distribution and expression patterns of rbGal like B upon immune challenges were performed using qRT-PCR assays. Among all tested tissues, level of rbGal like B expression was significantly high in gill tissue followed by kidney, intestine, heart and spleen. Upon immune challenges, it showed an up-regulated pattern of expression with Edwardsiella tarda, rock bream irido virus and poly I:C up to 6 h post injection and up to 24 h with LPS. However, In the presence of Streptococcus iniae rbGal like B showed an up and down pattern of expression with the peak at 6 - 12 h. Results from the present study revealed the phylogenetic position and role of rbGal like B in response to microbial infection in rock bream.

Keywords: galectin like protein B, immune response, Oplegnathus fasciatus, molecular characterization

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Authors: Muhammad Iqbal, Edi Istiyono

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Misconceptions are one of the problems in physics learning where students' understanding is not in line with scientific theory. The aim of this research is to find diagnostic tools to identify misconceptions and how to remediate physics misconceptions. In this research, the articles that will be reviewed come from the Scopus database related to physics misconceptions from 2013-2023. The articles obtained from the Scopus database were then selected according to the Prisma model, so 29 articles were obtained that focused on discussing physics misconceptions, especially regarding diagnostic tools and remediation methods. Currently, the most widely used diagnostic tool is the four-tier test, which is able to measure students' misconceptions in depth by knowing whether students are guessing or not and from then on, there is also a trend toward five-tier diagnostic tests with additional sources of information obtained. So that the origin of students' misconceptions is known. There are several ways to remediate student misconceptions, namely 11 ways and one of the methods used is digital practicum so that abstract things can be visualized into real ones. This research is limited to knowing what tools are used to diagnose and remediate misconceptions, so it is not yet known how big the effect of remediation methods is on misconceptions. The researcher recommends that in the future further research can be carried out to find out the most appropriate remediation method for remediating student misconceptions.

Keywords: misconception, remediation, systematic review, tools

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