Search results for: integrative bioinformatics

Authors: Agostinho Antunes

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The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of selected marine animal species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

Keywords: comparative genomics, adaptive evolution, bioinformatics, phylogenetics, genome mining

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Authors: Said Abdullah Al Saifi

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The goal of this research is to examine the impact of trust, motivation, and national culture on knowledge sharing within the context of electronic mail. This study is quantitative and survey based. In order to conduct the research, 200 students from a leading university in New Zealand were chosen randomly to participate in a questionnaire survey. Motivation and trust were found to be significantly and positively related to knowledge sharing. The research findings illustrated that face saving, face gaining, and individualism positively moderates the relationship between motivation and knowledge sharing. In addition, collectivism culture negatively moderates the relationship between motivation and knowledge sharing. Moreover, the research findings reveal that face saving, individualism, and collectivism culture positively moderate the relationship between trust and knowledge sharing. In addition, face gaining culture negatively moderates the relationship between trust and knowledge sharing. This study sets out several implications for researchers and practitioners. The study produces an integrative model that shows how attributes of national culture impact knowledge sharing through the use of emails. A better understanding of the relationship between knowledge sharing and trust, motivation, and national culture differences will increase individuals’ ability to make wise choices when sharing knowledge with those from different cultures.

Keywords: knowledge sharing, motivation, national culture, trust

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Authors: A. Luft, S. Bremen, N. Balc

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The task of flexibility planning and design, just like factory planning, for example, is to create the long-term systemic framework that constitutes the restriction for short-term operational management. This is a strategic challenge since, due to the decision defect character of the underlying flexibility problem, multiple types of flexibility need to be considered over the course of various scenarios, production programs, and production system configurations. In this context, an evaluation model has been developed that integrates both conventional and additive resources on a basic task level and allows the quantification of flexibility enhancement in terms of mix and volume flexibility, complexity reduction, and machine capacity. The model helps companies to decide in early decision-making processes about the potential gains of implementing additive manufacturing technologies on a strategic level. For companies, it is essential to consider both additive and conventional manufacturing beyond pure unit costs. It is necessary to achieve an integrative view of manufacturing that incorporates both additive and conventional manufacturing resources and quantifies their potential with regard to flexibility and manufacturing complexity. This also requires a structured process for the strategic production systems design that spans the design of various scenarios and allows for multi-dimensional and comparative analysis. A respective guideline for the planning of additive resources on a strategic level is being laid out in this paper.

Keywords: additive manufacturing, production system design, flexibility enhancement, strategic guideline

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Authors: Agostinho Antunes

Abstract:

The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of selected marine animal species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

Keywords: marine genomics, evolutionary bioinformatics, human genome sequencing, genomic analyses

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Authors: P. Priya Madhuri, J. Kamini, S. C. Jayanthi

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Assessment of land use and transportation networks is essential for sustainable urban growth, urban planning, efficient public transportation systems, and reducing traffic congestion. The study focuses on land use, population density, and their correlation with the road network for future development. The scope of the study covers inventory and assessment of the road network dataset (line) at the city, zonal, or ward level, which is extracted from very high-resolution satellite data (spatial resolution < 0.5 m) at 1:4000 map scale and ground truth verification. Road network assessment is carried out by computing various indices that measure road coverage and connectivity. In this study, an assessment of the road network is carried out for the study region at the municipal and ward levels. In order to identify gaps, road coverage and connectivity were associated with urban land use, built-up area, and population density in the study area. Ward-wise road connectivity and coverage maps have been prepared. To assess the relationship between road network metrics, correlation analysis is applied. The study's conclusions are extremely beneficial for effective road network planning and detecting gaps in the road network at the ward level in association with urban land use, existing built-up, and population.

Keywords: road connectivity, road coverage, road network, urban land use, transportation analysis

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Authors: Alexandre Barbosa de Almeida, Telma Woerle de Lima Soares

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Protein structure prediction is a challenging task in the bioinformatics field. The biological function of all proteins majorly relies on the shape of their three-dimensional conformational structure, but less than 1% of all known proteins in the world have their structure solved. This work proposes a deep learning model to address this problem, attempting to predict some aspects of the protein conformations. Throughout a process of multiobjective dominance, a recurrent neural network was trained to abstract the particular bias of each individual multiobjective algorithm, generating a heuristic that could be useful to predict some of the relevant aspects of the three-dimensional conformation process formation, known as protein folding.

Keywords: Ab initio heuristic modeling, multiobjective optimization, protein structure prediction, recurrent neural network

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Authors: Z. Aziz, S. Terkhi, Y. Sefir, R. Djelti, S. Bentata

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The effect of a uniform electric field across multi-barrier systems (InAs/InxGa1-xAs) is exhaustively explored by a computational model using exact Airy function formalism and the transfer-matrix technique. In the case of biased DFHBSL structure a strong reduction in transmission properties was observed and the width of the mini-band structure linearly decreases with the increase of the applied bias. This is due to the confinement of the states in the mini-band structure, which becomes increasingly important (Wannier-Stark Effect).

Keywords: dimer fibonacci height barrier superlattices, singular extended state, exact Airy function and transfer matrix formalism, bioinformatics

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Authors: José Maria, Vânia Laranjo, Luís Abrunhosa, António Inês

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The occurrence of mycotoxigenic moulds such as Aspergillus, Penicillium and Fusarium in food and feed has an important impact on public health, by the appearance of acute and chronic mycotoxicoses in humans and animals, which is more severe in the developing countries due to lack of food security, poverty and malnutrition. This mould contamination also constitutes a major economic problem due the lost of crop production. A great variety of filamentous fungi is able to produce highly toxic secondary metabolites known as mycotoxins. Most of the mycotoxins are carcinogenic, mutagenic, neurotoxic and immunosuppressive, being ochratoxin A (OTA) one of the most important. OTA is toxic to animals and humans, mainly due to its nephrotoxic properties. Several approaches have been developed for decontamination of mycotoxins in foods, such as, prevention of contamination, biodegradation of mycotoxins-containing food and feed with microorganisms or enzymes and inhibition or absorption of mycotoxin content of consumed food into the digestive tract. Some group of Gram-positive bacteria named lactic acid bacteria (LAB) are able to release some molecules that can influence the mould growth, improving the shelf life of many fermented products and reducing health risks due to exposure to mycotoxins. Some LAB are capable of mycotoxin detoxification. Recently our group was the first to describe the ability of LAB strains to biodegrade OTA, more specifically, Pediococcus parvulus strains isolated from Douro wines. The pathway of this biodegradation was identified previously in other microorganisms. OTA can be degraded through the hydrolysis of the amide bond that links the L-β-phenylalanine molecule to the ochratoxin alpha (OTα) a non toxic compound. It is known that some peptidases from different origins can mediate the hydrolysis reaction like, carboxypeptidase A an enzyme from the bovine pancreas, a commercial lipase and several commercial proteases. So, we wanted to have a better understanding of this OTA degradation process when LAB are involved and identify which molecules where present in this process. For achieving our aim we used some bioinformatics tools (BLAST, CLUSTALX2, CLC Sequence Viewer 7, Finch TV). We also designed specific primers and realized gene specific PCR. The template DNA used came from LAB strains samples of our previous work, and other DNA LAB strains isolated from elderberry fruit, silage, milk and sausages. Through the employment of bioinformatics tools it was possible to identify several proteins belonging to the carboxypeptidase family that participate in the process of OTA degradation, such as serine type D-Ala-D-Ala carboxypeptidase and membrane carboxypeptidase. In conclusions, this work has identified carboxypeptidase proteins being one of the molecules present in the OTA degradation process when LAB are involved.

Keywords: carboxypeptidase, lactic acid bacteria, mycotoxins, ochratoxin a.

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Authors: Jolien Rijlaarsdam, Charlotte A. M. Cecil, J. Marieke Buil, Pol A. C. Van Lier, Edward D. Barker

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Although there is mounting evidence that the experience of being bullied associates with both internalizing and externalizing symptoms, it is not known yet whether the identified associations are specific to these symptoms or shared between them. The primary focus of this study is to assess the prospective associations of bullying exposure with both general and specific (i.e., internalizing, externalizing) factors of psychopathology. This study included data from 6,210 children participating in the Avon Longitudinal Study of Parents and Children (ALSPAC). Child bullying was measured by self-report at ages 8 and 10 years. Child psychopathology symptoms were assessed by parent-interview, using the Development and Well-being Assessment (DAWBA) at ages 7 and 13 years. Bullying exposure is significantly associated with the general psychopathology factor in early adolescence. In particular, chronically victimized youth exposed to multiple forms of bullying (i.e., both overt and relational) showed the highest levels of general psychopathology. Bullying exposure is also associated with both internalizing and externalizing factors from the correlated-factors model. However, the effect estimates for these factors decreased considerably in size and dropped to insignificant for the internalizing factor after extracting the shared variance that belongs to the general factor of psychopathology. In an integrative longitudinal model, higher levels of general psychopathology at age seven are associated with bullying exposure at age eight, which, in turn, is associated with general psychopathology at age 13 through its two-year continuity. Findings suggest that exposure to bullying is a risk factor for a more general vulnerability to psychopathology through mutually influencing relationships.

Keywords: bullying exposure, externalizing, general psychopathology, internalizing, longitudinal

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Authors: Mijoh A. Gbededo, Kapila Liyanage, Sabuj Mallik

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The emerging approaches to sustainable manufacturing are considered to be solution-oriented with the aim of addressing the environmental, economic and social issues holistically. However, the analysis of the interdependencies amongst the three sustainability dimensions has not been fully captured in the literature. In a recent review of approaches to sustainable manufacturing, two categories of techniques are identified: 1) Sustainable Product Development (SPD), and 2) Sustainability Performance Assessment (SPA) techniques. The challenges of the approaches are not only related to the arguments and misconceptions of the relationships between the techniques and sustainable development but also to the inability to capture and integrate the three sustainability dimensions. This requires a clear definition of some of the approaches and a road-map to the development of a holistic approach that supports sustainability decision-making. In this context, eco-innovation, social impact assessment, and life cycle sustainability analysis play an important role. This paper deployed an integrative approach that enabled amalgamation of sustainable manufacturing approaches and the theories of reciprocity and motivation into a holistic simulation-based impact analysis framework. The findings in this research have the potential to guide sustainability analysts to capture the aspects of the three sustainability dimensions into an analytical model. Additionally, the research findings presented can aid the construction of a holistic simulation model of a sustainable manufacturing and support effective decision-making.

Keywords: life cycle sustainability analysis, sustainable manufacturing, sustainability performance assessment, sustainable product development

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Authors: Tripti Singhal, C. Tara Satyavathi, S. P. Singh, Aruna Kumar, Mukesh Sankar S., C. Bhardwaj, Mallik M., Jayant Bhat, N. Anuradha, Nirupma Singh

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Pearl millet is a climate-resilient nutritious crop. We report iron and zinc content QTLs from 3 divergent locations. The content of grain Fe in the RILs ranged between 36 and 114 mg/kg, and that of Zn from 20 to 106 mg/kg across the three years at over 3 locations (Delhi, Dharwad, and Jodhpur). We used SSRs to generate a linkage map using 210 F₆ RIL derived from the (PPMI 683 × PPMI 627) cross. The linkage map of 151 loci was 3403.6 cM in length. QTL analysis revealed a total of 22 QTLs for both traits at all locations. Inside QTLs, candidate genes were identified using bioinformatics approaches.

Keywords: yield, pearl millet, QTL mapping, multi-environment, RILs

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Authors: Lauren Provost

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The digital world remains increasingly vulnerable, making the development of effective cybersecurity approaches even more critical in supporting the success of the digital economy and national security. Although approaches to cybersecurity have shifted and improved in the last decade with new models, especially with cloud computing and mobility, a record number of high severity vulnerabilities were recorded in the National Institute of Standards and Technology (NIST), and its National Vulnerability Database (NVD) in 2020. This is due, in part, to the increasing complexity of cyber ecosystems. Security must be approached with a more comprehensive, multi-tool strategy that addresses the complexity of cyber ecosystems, including the human factor. Ethical hacking has emerged as such an approach: a more effective, multi-strategy, comprehensive approach to cyber security's most pressing needs, especially understanding the human factor. Research on ethical hacking, however, is limited in scope. The two main objectives of this work are to (1) provide highlights of case studies in ethical hacking, (2) provide a conceptual framework for research in ethical hacking that embraces and addresses both technical and nontechnical security measures. Recommendations include an improved conceptual framework for research centered on ethical hacking that addresses many factors and attributes of significant attacks that threaten computer security; a more robust, integrative multi-layered framework embracing the complexity of cybersecurity ecosystems.

Keywords: ethical hacking, literature review, penetration testing, social engineering

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Authors: Jui-Hung Hung, Ching-Liang Hsieh, Yi-Wen Lin

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Modern medicine highly emphasizes the importance of palliative treatment. The inception of palliative and hospice care recently developed into the concept of caring for the patients’ and families’ physical, psychological and spiritual problems. There are several benefits related to palliative care such as reducing medical expenses, decreasing patients’ suffer, and supporting patient go through the finale of the life. Nowadays, in Taiwan, over 60-70% terminal cancer patients were covered in hospice care, and the coverage rate increased annually. Acupuncture is a well-known therapy used more than thousand years to relieve symptoms of cancer patient. Many reports showed that, even in the Western society, many reputable medical centers can provide Acupuncture therapy for patients. Accordingly, using Acupuncture for cancer patient care is a global trend. There are increased evidences indicate that Acupuncture can relieve the symptoms for cancer patients including pain, reduce the dosage of anesthetic, improve the cancer-related fatigue, relieve the chemotherapy-related nausea and vomiting, ease anxiety mood and even improving the quality of life. Furthermore, some trials show that Acupuncture may help relieve xerostomia, hot flash, sleep disorders, and some GI discomfort and so on. Acupuncture therapy has many advantages for clinical use with effective, low-cost, minimal side effect, suitable for cancer patients and even for elderly population. Especially in nowadays, there are more diversified challenges in modern medicine, all of them will make the higher medical budget. We suggest that Acupuncture will be one of methods for palliative care for cancer patients.

Keywords: Acupuncture, cancer, integrative medicine, palliative care

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Authors: Elnaz Sabzehparvar, Pouya Rabiei, Houman Rezaei

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Few studies have been conducted about the effects of compound exercises emphasizing local stability and global stabilization subsystems on the performance of athletes. The present research aimed to study the effect of 6 weeks of compound exercises emphasizing local and global stability on the dynamic balance of elite male Taekwondo athletes. Twenty-seven elite male Taekwondo athletes (with a mean age, mass, and height of 24.4 ± 4.9 years, 75.7 ± 15.1kg, and 181.4 ± 7.8 cm, respectively) were assigned to two groups of control (n=12) and exercise (n=15). 6 weeks of compound exercises in 2 local and global phases. The first phase included activation exercises which were done separately and locally for 3 weeks. Then, integrative exercises specific to the global stabilization subsystems (longitudinal-depth, posterior oblique and anterior, and lateral) was carried out for next 3 weeks. The dynamic balance of subjects was measured in the pre-test and post-test using the Y Balance Test (YBT). After 6 weeks of compound exercises, scores of the YBT in the exercise group showed a significant improvement in all three anterior (p=0.035), posterolateral (p=0.017) and medial (p=0.001) directions in the post-test compared to the control group (p ≤ 0.05 for all comparisons). The findings of the present study suggested that compound exercises focusing on muscle as separate units and then as interdependent chains (muscular subsystems) can significantly increase YBT on elite male Taekwondo athletes in all three directions.

Keywords: Taekwondo, compound exercises, local and global stability, muscular subsystems

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Authors: Donatella Cimini, Sergio D’ambrosio, Saba Sadiq, Chiara Schiraldi

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Chondroitin sulfate (CS), as well as modified CS, and unsulfated chondroitin, are largely applied in research today. CS is a linear glycosaminoglycan normally present in cartilage-rich tissues and bones in the form of proteoglycans decorated with sulfate groups in different positions. CS is used as an effective non-pharmacological alternative for the treatment of osteoarthritis, and other potential applications in the biomedical field are being investigated. Some bacteria, such as E. coli K4, produce a polysaccharide that is a precursor of CS (unsulfated chondroitin). This work focused on the construction of integrative E. coli K4 recombinant strains overexpressing genes (kfoA, kfoF, pgm and galU in different combinations) involved in the biosynthesis of the nucleotide sugars necessary for polysaccharide synthesis. Strain growth and polymer production were evaluated using renewable waste materials as substrates in shake flasks and small-scale batch fermentation processes. Results demonstrated the potential to replace pure sugars with cheaper medium components to establish environmentally sustainable and cost-effective production routes for potential industrial development. In fact, although excellent fermentation results have been described so far by employing strains that naturally produce chondroitin-like polysaccharides on semi-defined media, there is still the need to reduce manufacturing costs by providing a cost-effective biotechnological alternative to currently used animal-based extraction procedures.

Keywords: E. coli K4, chondroitin, microbial cell factories, glycosaminoglycans, renewable resources

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Authors: K. H. Reeta, Bhavana Prasher, Mitali Mukerji, Dhwani Dholakia, Sangeeta Khanna, Archana Vats, Shivam Pandey, Sandeep Seth, Subir Kumar Maulik

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Introduction Research has demonstrated a connection between coronary artery disease (CAD) and genetics. We did a deep literature mining using both bioinformatics and manual efforts to identify the susceptible polymorphisms in coronary artery disease. Further, the study sought to validate these findings in an Asian population. Methodology In first phase, we used an automated pipeline which organizes and presents structured information on SNPs, Population and Diseases. The information was obtained by applying Natural Language Processing (NLP) techniques to approximately 28 million PubMed abstracts. To accomplish this, we utilized Python scripts to extract and curate disease-related data, filter out false positives, and categorize them into 24 hierarchical groups using named Entity Recognition (NER) algorithms. From the extensive research conducted, a total of 466 unique PubMed Identifiers (PMIDs) and 694 Single Nucleotide Polymorphisms (SNPs) related to coronary artery disease (CAD) were identified. To refine the selection process, a thorough manual examination of all the studies was carried out. Specifically, SNPs that demonstrated susceptibility to CAD and exhibited a positive Odds Ratio (OR) were selected, and a final pool of 324 SNPs was compiled. The next phase involved validating the identified SNPs in DNA samples of 96 CAD patients and 37 healthy controls from Indian population using Global Screening Array. ResultsThe results exhibited out of 324, only 108 SNPs were expressed, further 4 SNPs showed significant difference of minor allele frequency in cases and controls. These were rs187238 of IL-18 gene, rs731236 of VDR gene, rs11556218 of IL16 gene and rs5882 of CETP gene. Prior researches have reported association of these SNPs with various pathways like endothelial damage, susceptibility of vitamin D receptor (VDR) polymorphisms, and reduction of HDL-cholesterol levels, ultimately leading to the development of CAD. Among these, only rs731236 had been studied in Indian population and that too in diabetes and vitamin D deficiency. For the first time, these SNPs were reported to be associated with CAD in Indian population. Conclusion: This pool of 324 SNP s is a unique kind of resource that can help to uncover risk associations in CAD. Here, we validated in Indian population. Further, validation in different populations may offer valuable insights and contribute to the development of a screening tool and may help in enabling the implementation of primary prevention strategies targeted at the vulnerable population.

Keywords: coronary artery disease, single nucleotide polymorphism, susceptible SNP, bioinformatics

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Authors: Jimoh Olumide Yusuf

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Various factors have continued to bedevil the effective teaching and learning of English Language in Nigeria and prominent among these factors are learners’ characteristics. Unfortunately, these particular factors seem to have recorded paucity of research efforts by scholars and the problem of lack of proficiency in the target language continues to linger. This study therefore investigates the relationship between specific learners’ characteristics and effective teaching of English as a Second Language (ESL) in senior secondary schools in Nigeria. To this end, Self-Determination, and Integrative Motivation Theories were applied to investigate motivation, language learning, learners’ characteristics and its relationship to language proficiency. A survey of 500 students and 100 English Language teachers across 20 schools was conducted. Descriptive statistics was used to analyze the data and findings revealed that; specific learners’ characteristics such as learners’ age, learning style and motivation significantly determine the performance of students in English Language. Specifically, students with appropriate school age, visual learning style and intrinsic motivation, demonstrated English Language proficiency; as they performed better than students with extrinsic motivation, audio and kinaesthetic learning styles. Moreover, teachers related factors such as teaching experience; teaching strategies and teachers’ extrinsic motivation also emerged as essential correlates of effective language teaching. The findings conclude that learning characteristics are significant factors that should be considered by the teachers and education planners for adequate, sequential and effective implementation of the ESL curriculum in Nigeria.

Keywords: senior secondary school, English as a second language, intrinsic motivation, Kinaesthetic learning style

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Authors: Jiang Yuqi

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Aims: The aim is to analyze the facilitators and barriers of family resilience in cancer patients based on the theoretical domain framework, provide a basis for intervention in the family resilience of cancer patients, and identify the progress and enlightenment of existing intervention projects. Methods: NVivo software was used to code the influencing factors using the framework of 14 theoretical domains as primary nodes; secondary nodes were then refined using thematic analysis, and specific influencing factors were aggregated and analyzed for evaluator reliability. Data sources: PubMed, Embase, CINAHL, Web of Science, Cochrane Library, MEDLINE, CNKI, and Wanfang (search dates: from construction to November 2023). Results: A total of 35 papers were included, with 142 coding points across 14 theoretical domains and 38 secondary nodes. The three most relevant theoretical domains are social influences (norms), the environment and resources, and emotions (mood). The factors with the greatest impact were family support, mood, confidence and beliefs, external support, quality of life, economic circumstances, family adaptation, coping styles with illness, and management. Conclusion: The factors influencing family resilience in cancer patients cover most of the theoretical domains in the Theoretical Domains Framework and are cross-cutting, multi-sourced, and complex. Further in-depth exploration of the key factors influencing family resilience is necessary to provide a basis for intervention research.

Keywords: cancer, survivors, family resilience, theoretical domains framework, literature review

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Authors: Yasaman Mohammadi

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Executive functions are a critical component of goal-directed behavior, encompassing a diverse set of cognitive processes such as working memory, cognitive flexibility, and inhibitory control. These functions are known to decline with age, but the precise mechanisms underlying this decline remain unclear. This paper provides an in-depth review of recent research investigating age-related changes in executive functions, drawing on insights from neuroimaging, genetics, and cognitive neuroscience. Through an interdisciplinary approach, this paper offers a nuanced understanding of the complex interplay between neural mechanisms, genetic factors, and cognitive processes that contribute to executive function decline in aging. Here, we investigate how different neuroimaging methods, like functional magnetic resonance imaging (fMRI) and positron emission tomography (PET), have helped scientists better understand the brain bases for age-related declines in executive function. Additionally, we discuss the role of genetic factors in mediating individual differences in executive functions across the lifespan, as well as the potential for cognitive interventions to mitigate age-related decline. Overall, this paper presents a comprehensive and integrative view of the current state of knowledge regarding age-related changes in executive functions. It underscores the need for continued interdisciplinary research to fully understand the complex and dynamic nature of executive function decline in aging, with the ultimate goal of developing effective interventions to promote healthy cognitive aging.

Keywords: executive functions, aging, neuroimaging, cognitive neuroscience, working memory, cognitive training

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Authors: Siti Ayu Ningsih

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This study aims to find the differences outcomes in learning reading comprehension with text and film as media on Indonesian Language for foreign speaker (BIPA) learning at intermediate level. By using quantitative and qualitative research methods, the respondent of this study is a single respondent from D'Royal Morocco Integrative Islamic School in grade nine from secondary level. Quantitative method used to calculate the learning outcomes that have been given the appropriate action cycle, whereas qualitative method used to translate the findings derived from quantitative methods to be described. The technique used in this study is the observation techniques and testing work. Based on the research, it is known that the use of the text media is more effective than the film for intermediate level of Indonesian Language for foreign speaker learner. This is because, when using film the learner does not have enough time to take note the difficult vocabulary and don't have enough time to look for the meaning of the vocabulary from the dictionary. While the use of media texts shows the better effectiveness because it does not require additional time to take note the difficult words. For the words that are difficult or strange, the learner can immediately find its meaning from the dictionary. The presence of the text is also very helpful for Indonesian Language for foreign speaker learner to find the answers according to the questions more easily. By matching the vocabulary of the question into the text references.

Keywords: Indonesian language for foreign speaker, learning outcome, media, reading comprehension

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Authors: B. Parchem, M. Watanabe, D. Modrakovic, L. Mathew, A. Franklin, M. Cao, R. E. Broudy

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Objective: Executive functioning (EF) deficits underlie several mental health diagnoses including ADHD, anxiety, and depression. Community mental health clinics face extensive waitlists for services with many referrals involving EF deficits. A pilot trial of a four-week group therapy was developed using key components from Cognitive-Behavioral Therapy (CBT), Dialectical Behavior Therapy (DBT), and mindfulness with an aim to improve EF skills and offer low-fee services. Method: Eight adults (M = 34.5) waiting for services at a community clinic were enrolled in a four-week group therapy at an in-house training clinic for doctoral trainees. Baseline EF, pre-/post-intervention ADHD and distress symptoms, group satisfaction, and curriculum helpfulness were assessed. Results: Downward trends in ADHD and distress symptoms pre/post-intervention were not significant. Favorable responses on group satisfaction and helpfulness suggest clinical utility. Conclusion: Preliminary pilot data from a brief group therapy to improve EF may be an efficacious, acceptable, and feasible intervention for adults waiting for services at community mental health and training clinics where there are high demands and limits to services and staffs.

Keywords: executive functioning, cognitive-behavioral therapy, dialectical behavior therapy, mindfulness, adult group therapy

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Authors: Atef Ibrahim, Hamed Elsimary, Abdullah Aljumah, Fayez Gebali

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This paper presents a novel semi-systolic array architecture for an optimized parallel sequence alignment algorithm. This architecture has the advantage that it can be modified to be reused for multiple pass processing in order to increase the number of processing elements that can be packed into a single FPGA and to increase the number of sequences that can be aligned in parallel in a single FPGA. This resolves the potential problem of many FPGA resources left unused for designs that have large values of short read length. When using the previously published conventional hardware design. FPGA implementation results show that, for large values of short read lengths (M>128), the proposed design has a slightly higher speed up and FPGA utilization over the the conventional one.

Keywords: bioinformatics, genome sequence alignment, re-sequencing applications, systolic array

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Authors: Danny Barash

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Riboswitches are RNA genetic control elements that were originally discovered in bacteria and provide a unique mechanism of gene regulation. They work without the participation of proteins and are believed to represent ancient regulatory systems in the evolutionary timescale. One of the biggest challenges in riboswitch research is that many are found in prokaryotes but only a small percentage of known riboswitches have been found in certain eukaryotic organisms. The few examples of eukaryotic riboswitches were identified using sequence-based bioinformatics search methods that include some slight structural considerations. These pattern-matching methods were the first ones to be applied for the purpose of riboswitch detection and they can also be programmed very efficiently using a data structure called affix arrays, making them suitable for genome-wide searches of riboswitch patterns. However, they are limited by their ability to detect harder to find riboswitches that deviate from the known patterns. Several methods have been developed since then to tackle this problem. The most commonly used by practitioners is Infernal that relies on Hidden Markov Models (HMMs) and Covariance Models (CMs). Profile Hidden Markov Models were also carried out in the pHMM Riboswitch Scanner web application, independently from Infernal. Other computational approaches that have been developed include RMDetect by the use of 3D structural modules and RNAbor that utilizes Boltzmann probability of structural neighbors. We have tried to incorporate more sophisticated secondary structure considerations based on RNA folding prediction using several strategies. The first idea was to utilize window-based methods in conjunction with folding predictions by energy minimization. The moving window approach is heavily geared towards secondary structure consideration relative to sequence that is treated as a constraint. However, the method cannot be used genome-wide due to its high cost because each folding prediction by energy minimization in the moving window is computationally expensive, enabling to scan only at the vicinity of genes of interest. The second idea was to remedy the inefficiency of the previous approach by constructing a pipeline that consists of inverse RNA folding considering RNA secondary structure, followed by a BLAST search that is sequence-based and highly efficient. This approach, which relies on inverse RNA folding in general and our own in-house fragment-based inverse RNA folding program called RNAfbinv in particular, shows capability to find attractive candidates that are missed by Infernal and other standard methods being used for riboswitch detection. We demonstrate attractive candidates found by both the moving-window approach and the inverse RNA folding approach performed together with BLAST. We conclude that structure-based methods like the two strategies outlined above hold considerable promise in detecting riboswitches and other conserved RNAs of functional importance in a variety of organisms.

Keywords: riboswitches, RNA folding prediction, RNA structure, structure-based methods

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Authors: Elizelle Juaneé Cilliers

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The green hype is becoming stronger within various disciplines, modern practices and academic thinking, enforced by concepts such as eco-health, eco-tourism, eco-cities, and eco-engineering. There is currently also an expanded scientific understanding regarding the value and benefits relating to green infrastructure, for both communities and their host cities, linked to broader sustainability and resilience thinking. The integration and implementation of green infrastructure as part of spatial planning approaches and municipal planning, are, however, more complex, especially in South Africa, inflated by limitations of budgets and human resources, development pressures, inequities in terms of green space availability and political legacies of the past. The prevailing approach to spatial planning is further contributing to complexity, linked to misguided perceptions of the function and value of green infrastructure. As such, green spaces are often considered a luxury, and green infrastructure a costly alternative, resulting in green networks being susceptible to land-use changes and under-prioritized in local authority decision-making. Spatial planning, in this sense, may well be a valuable tool to realise the green agenda, encapsulating various initiatives of sustainability as provided by a range of disciplines. This paper aims to clarify the importance and value of green infrastructure planning as a component of spatial planning approaches, in order to inform and encourage local authorities to embed sustainability thinking into city planning and decision-making approaches. It reflects on the decisive role of land-use management to guide the green agenda and refers to some recent planning initiatives. Lastly, it calls for trans-disciplinary planning approaches to build a case towards green(er) cities.

Keywords: green infrastructure, spatial planning, transdisciplinary, integrative

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Authors: Fan Gao, Lior Pachter

Abstract:

The primary tool currently used to pre-process 10X Chromium single-cell ATAC-seq data is Cell Ranger, which can take very long to run on standard datasets. To facilitate rapid pre-processing that enables reproducible workflows, we present a suite of tools called scATAK for pre-processing single-cell ATAC-seq data that is 15 to 18 times faster than Cell Ranger on mouse and human samples. Our tool can also calculate chromatin interaction potential matrices, and generate open chromatin signal and interaction traces for cell groups. We use scATAK tool to explore the chromatin regulatory landscape of a healthy adult human brain and unveil cell-type specific features, and show that it provides a convenient and computational efficient approach for pre-processing single-cell ATAC-seq data.

Keywords: single-cell, ATAC-seq, bioinformatics, open chromatin landscape, chromatin interactome

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Authors: Duc Dong Do, Ngoc Ha Tran, Thanh Hai Dang, Cao Cuong Dang, Xuan Huan Hoang

Abstract:

Global aligning two protein-protein interaction networks is an essentially important task in bioinformatics/computational biology field of study. It is a challenging and widely studied research topic in recent years. Accurately aligned networks allow us to identify functional modules of proteins and/ororthologous proteins from which unknown functions of a protein can be inferred. We here introduce a novel efficient heuristic global network alignment algorithm called FASTAn, including two phases: the first to construct an initial alignment and the second to improve such alignment by exerting a local optimization repeated procedure. The experimental results demonstrated that FASTAn outperformed the state-of-the-art global network alignment algorithm namely SPINAL in terms of both commonly used objective scores and the run-time.

Keywords: FASTAn, Heuristic algorithm, biological network alignment, protein-protein interaction networks

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Authors: Vildan Cırık, Emine Efe

Abstract:

Complementary health approaches are growing in popularity worldwide and play a substantial role in health care. It is very important for paediatric nurses to have knowledge of practices affecting the medical conditions of patients and to communicate with them through integrative nursing care. The purpose of this study was to determine paediatric nurses’ knowledge and experiences of complementary health approaches (CHA) and their personal and professional attitudes to the use of complementary health approaches. This multicentre study was conducted with 1450 paediatric nurses in 18 hospitals in Turkey. Paediatric nurses included in the study were working in the following clinics: Paediatric Service, Paediatric Intensive Care, Paediatric Haematology/Oncology. Data collection focused on the paediatric nurses’ knowledge and experiences of CHA. A high proportion of our sample of paediatric nurses reported that they had used some form of CHA themselves; the most popular choices of CHA were prayer, massage, and vitamins techniques. Paediatric nurses reported positive experiences (drawing/music/art/dance therapies, prayer, herbs, thermal springs, massage, and reflexology) and negative experiences (herbs, thermal springs, prayer, and massage). This study may contribute to increased awareness of the potentially important role of paediatric nurses in the delivery of CHA. Paediatric nurses play important roles in helping patients to use complementary health approaches safely and accurately. Trainings on CHA should be organised, data collection forms including CHA should be created, and evidence-based studies should be focused towards improving the clinical practice of paediatric nurses.

Keywords: complementary health approaches, paediatric nurses, knowledge, experience, attitude, Turkey

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Authors: Vishnu Pratap Singh Kirar, Madhuri Saxena

Abstract:

Advancement in sequence data generation technologies is churning out voluminous omics data and posing a massive challenge to annotate the biological functional features. With so much data available, the use of machine learning methods and tools to make novel inferences has become obvious. Machine learning methods have been successfully applied to a lot of disciplines, including computational biology and bioinformatics. Researchers in computational biology are interested to develop novel machine learning frameworks to classify the huge amounts of biological data. In this proposal, it plan to employ novel machine learning approaches to aid the understanding of how apparently innocuous mutations (in intergenic DNA and at synonymous sites) cause diseases. We are also interested in discovering novel functional sites in the genome and mutations in which can affect a phenotype of interest.

Keywords: genome wide association studies (GWAS), next generation sequencing (NGS), deep learning, omics

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Authors: Ankan Roy, Niharika, Samir Kumar Patra

Abstract:

Anomalous nexus of complex topological assemblies and spatiotemporal epigenetic choreography at chromosomal territory may forms the most sophisticated regulatory layer of gene expression in cancer. Colon cancer is one of the leading malignant neoplasms of the lower gastrointestinal tract worldwide. There is still a paucity of information about the complex molecular mechanisms of colonic cancerogenesis. Bioinformatics prediction and analysis helps to identify essential genes and significant pathways for monitoring and conquering this deadly disease. The present study investigates and explores potential hub genes as biomarkers and effective therapeutic targets for colon cancer treatment. Colon cancer patient sample containing gene expression profile datasets, such as GSE44076, GSE20916, and GSE37364 were downloaded from Gene Expression Omnibus (GEO) database and thoroughly screened using the GEO2R tool and Funrich software to find out common 2 differentially expressed genes (DEGs). Other approaches, including Gene Ontology (GO) and KEGG pathway analysis, Protein-Protein Interaction (PPI) network construction and hub gene investigation, Overall Survival (OS) analysis, gene correlation analysis, methylation pattern analysis, and hub gene-Transcription factors regulatory network construction, were performed and validated using various bioinformatics tool. Initially, we identified 166 DEGs, including 68 up-regulated and 98 down-regulated genes. Up-regulated genes are mainly associated with the Cytokine-cytokine receptor interaction, IL17 signaling pathway, ECM-receptor interaction, Focal adhesion and PI3K-Akt pathway. Downregulated genes are enriched in metabolic pathways, retinol metabolism, Steroid hormone biosynthesis, and bile secretion. From the protein-protein interaction network, thirty hub genes with high connectivity are selected using the MCODE and cytoHubba plugin. Survival analysis, expression validation, correlation analysis, and methylation pattern analysis were further verified using TCGA data. Finally, we predicted COL1A1, COL1A2, COL4A1, SPP1, SPARC, and THBS2 as potential master regulators in colonic cancerogenesis. Moreover, our experimental data highlights that disruption of lipid raft and RAS/MAPK signaling cascade affects this gene hub at mRNA level. We identified COL1A1, COL1A2, COL4A1, SPP1, SPARC, and THBS2 as determinant hub genes in colon cancer progression. They can be considered as biomarkers for diagnosis and promising therapeutic targets in colon cancer treatment. Additionally, our experimental data advertise that signaling pathway act as connecting link between membrane hub and gene hub.

Keywords: hub genes, colon cancer, DNA methylation, epigenetic engineering, bioinformatic predictions

Procedia PDF Downloads 128

Authors: Merkouche Wassila, Marchand Alain, Renaud Stéphane

Abstract:

Organizations are facing competitive pressures constraining them to modify their practices and change initial work conditions of employees, however, these modifications have to sustain initial quality of work and engagements toward the workforce. We focus on the importance of promises in the perspective of psychological contract. According to this perspective, employees perceiving a breach of the expected obligations from the employer may become unsatisfied at work and develop organizational withdrawal behaviors. These are negative counterproductive behaviours aiming to damage the organisation according to the principle of reciprocity and social exchange. We present an integrative model of the determinants and manifestations of organizational withdrawal (OW), a set of behaviors allowing the employee to leave his job or avoid his assigned work. OW contains two main components often studied in silos: work withdrawal (delays, absenteeism and other adverse behaviors) and job withdrawal (turnover). We use the systemic micro, meso and macro sociological approach designing the individual at the heart of a system containing individual, organizational, and environmental determinants. Under the influence of these different factors, the individual assesses the type of behavior to adopt. We provide better lighting for understanding OW using both psychological contract approach through the perception of its respect by the organization and job embeddedness approach which explains why the employee does not leave the organization and then remains in his post while practicing negative and counterproductive behaviors such as OW. We study specifically cynicism as a type of OW as it is a dimension of burnout. We focus on the antecedents of cynicism to try to prevent it in the workplace.

Keywords: burnout, cynicism, job embeddedness, organizational withdrawal, psychological contract

Procedia PDF Downloads 252