Search results for: genome scale model

Authors: Dora Vajda, Somayyeh Mohammadi, Sandor Rozsa

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Predicting the relationship satisfaction based on the personality characteristics of both partners has a long history. The association between relationship quality and personality traits has been previously demonstrated. Personality traits are most commonly assessed using the Five-Factor Model. The present study has focused on Cloninger's psychobiological model of personality that accounts for dimensions of both temperament and character. The goal of this study was to examine the actor and partner effect of couple's personality on relationship outcomes. In total, 184 heterosexual couples completed the Temperament and Character Inventory (TCI) and the Dyadic Adjustment Scale. The analysis was based on Actor-Partner Interdependence Model (APIM) using multilevel modeling (MLwiN). Results showed that character dimensions Self-Directedness and Cooperativeness had a statistically meaningful actor and partner effect on both partner's relationship quality. However, male's personality temperament dimension Reward Dependence had an only actor effect on his relationship quality. The findings contribute to the literature by highlighting the role of character dimensions of personality in romantic relationships.

Keywords: APIM (actor-partner interdependence model), MLwiN, personality, relationship quality

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Authors: Alsu F. Saifitdinova, Alexey S. Komissarov, Svetlana A. Galkina, Elena I. Koshel, Maria M. Kulak, Stephen J. O'Brien, Elena R. Gaginskaya

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The mystery of sex determination is one of the most ancient and still not solved until the end so far. In many species, sex determination is genetic and often accompanied by the presence of dimorphic sex chromosomes in the karyotype. Genomic sequencing gave the information about the gene content of sex chromosomes which allowed to reveal their origin from ordinary autosomes and to trace their evolutionary history. Female-specific W chromosome in birds as well as mammalian male-specific Y chromosome is characterized by the degeneration of gene content and the accumulation of repetitive DNA. Tandem repeats complicate the analysis of genomic data. Despite the best efforts chicken W chromosome assembly includes only 1.2 Mb from expected 55 Mb. Supplementing the information on the sex chromosome composition not only helps to complete the assembly of genomes but also moves us in the direction of understanding of the sex-determination systems evolution. A whole-genome survey to the assembly Gallus_gallus WASHUC 2.60 was applied for repeats search in assembled genome and performed search and assembly of high copy number repeats in unassembled reads of SRR867748 short reads datasets. For cytogenetic analysis conventional methods of fluorescent in situ hybridization was used for previously cloned W specific satellites and specifically designed directly labeled synthetic oligonucleotide DNA probe was used for bioinformatically identified repetitive sequence. Hybridization was performed with mitotic chicken chromosomes and manually isolated giant meiotic lampbrush chromosomes from growing oocytes. A novel chicken W specific satellite (GGAAA)n which is not co-localizes with any previously described classes of W specific repeats was identified and mapped with high resolution. In the composition of autosomes this repeat units was found as a part of upstream regions of gonad specific protein coding sequences. These findings may contribute to the understanding of the role of tandem repeats in sex specific differentiation regulation in birds and sex chromosome evolution. This work was supported by the postdoctoral fellowships from St. Petersburg State University (#1.50.1623.2013 and #1.50.1043.2014), the grant for Leading Scientific Schools (#3553.2014.4) and the grant from Russian foundation for basic researches (#15-04-05684). The equipment and software of Research Resource Center “Chromas” and Theodosius Dobzhansky Center for Genome Bioinformatics of Saint Petersburg State University were used.

Keywords: birds, lampbrush chromosomes, sex chromosomes, tandem repeats

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Authors: J. R. Dinsmore, R. W. Hood

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Experiences of a divine or mystical light are frequently reported in religious/spiritual experiences today, most notably in the context of mystical and near-death experiences. Light of a transcendental nature and its experiences of it are also widely present and highly valued in many religious and mystical traditions. Despite the significance of this luminosity to the topic of religious experience, efforts to study the phenomenon empirically have been minimal and scattered. This mixed methods study developed and validated a questionnaire for the measurement of numinous luminosity experience and investigated the dimensions and effects of this novel construct using both quantitative and qualitative methodologies. A sequential explanatory design (participant selection model) was used, which involved a scale development phase, followed by a correlational study testing hypotheses about its effects on beliefs and well-being derived from the literature, and lastly, a phenomenological study of a sample selected from the correlational phase results. The outcomes of the study are a unified theoretical model of numinous luminosity experience across multiple experiential contexts, initial correlational findings regarding the possible mechanism of its reported positive transformational effects, and a valid and reliable instrument for its further empirical study.

Keywords: religious experience, mystical experience, near-death experience, scale development, questionnaire, divine light, mystical light, mystical luminosity

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Authors: Muhammad Adeel Arshad, Faiz-Ul Hassan, Yanfen Cheng

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According to FAO, enteric methane (CH4) production is about 44% of all greenhouse gas emissions from the livestock sector. Ruminants produce CH4 as a result of fermentation of feed in the rumen especially from roughages which yield more CH4 per unit of biomass ingested as compared to concentrates. Efficient ruminal fermentation is not possible without abating CO2 and CH4. Methane abatement strategies are required to curb the predicted rise in emissions associated with greater ruminant production in future to meet ever increasing animal protein requirements. Ecology of ruminal methanogenesis and avenues for its mitigation can be identified through various genomic and transcriptomic techniques. Programs such as Hungate1000 and the Global Rumen Census have been launched to enhance our understanding about global ruminal microbial communities. Through Hungate1000 project, a comprehensive reference set of rumen microbial genome sequences has been developed from cultivated rumen bacteria and methanogenic archaea along with representative rumen anaerobic fungi and ciliate protozoa cultures. But still many species of rumen microbes are underrepresented especially uncultivable microbes. Lack of sequence information specific to the rumen's microbial community has inhibited efforts to use genomic data to identify specific set of species and their target genes involved in methanogenesis. Metagenomic and metatranscriptomic study of entire microbial rumen populations offer new perspectives to understand interaction of methanogens with other rumen microbes and their potential association with total gas and methane production. Deep understanding of methanogenic pathway will help to devise potentially effective strategies to abate methane production while increasing feed efficiency in ruminants.

Keywords: Genome sequences, Hungate1000, methanogens, ruminal fermentation

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Authors: Folasade Adegbaju, Olusola Arowolo, Olufisayo Onawumi

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Owolowo ile – ege garri processing industry which is a small scale cassava processing industry, located in Ilesha, Osun State was purposively selected as a case study because it is a cooperative business. This industry was established in 1991 by eight men (8) who were mostly retirees. A researcher made questionnaire was used to collect information from thirty (30) respondents: the manager, four official staffs and 25 randomly selected processors in the industry. The study found that within twelve years of the utilization of their self raised initial capital of N240, 000 naira (Two hundred and forty thousand naira) this cassava – based industry had impacted on and attracted the involvement of many more people because within the period of the study (i.e. 2007-2011) the processors had quadrupled in number (e.g. 8 to 30), the facilities (equipment) in use had increased from one machine and a frying pot to many, this translated into being able to produce large quantities of fried garri, fufu and also starch for marketing to the people in Ilesha and neighbouring cities like Ibadan, Lagos, etc. This is indicative of economic growth. The industry also became a source of employment for community members in the sense that, as at the time of study four staffs were employed to work and coordinate the industry. It was observed that despite all odds of small-scale industry and the problem of people migrating from rural to urban area, this agro-based industry still existed successfully in the community, and many of such industry can be replicated by such agricultural cooperative groups nationwide so as to further boost the productivity as well as the economy of the area and nation at large. However, government and individual still have major roles to play in ensuring the growth and development of the nation in this respect.The local agricultural cooperative groups should form regional cooperative consortium with more networking for the farmers, in order to create more jobs for the young ones and to increase agricultural productivity in the country thus resulting in a better and more sustainable economy.

Keywords: agricultural cooperative, cassava processing industry, model, small scale enterprise

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Authors: Faisal Nouroz, Mukaramin Mukaramin

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Of the transposable elements (TEs), the retrotransposons are the most copious elements identified from many sequenced genomes. They have played a major role in genome evolution, rearrangement, and expansions based on their copy and paste mode of proliferation. They are further divided into LTR and Non-LTR retrotransposons. The purpose of the current study was to identify the LTR REs in sequenced Phoenix dactylifera genome and to study their structural diversity. A total of 150 P. dactylifera BAC sequences with > 60kb sizes were randomly retrieved from National Center for Biotechnology Information (NCBI) database and screened for the presence of LTR retrotransposons. Seven bacterial artificial chromosomes (BAC) sequences showed full-length LTR Retrotransposons with 4 Copia and 3 Gypsy families having variable copy numbers in respective families. Reverse transcriptase (RT) domain was found as the most conserved domain among Copia and Gypsy superfamilies and was used to deduce evolutionary analysis. The amino acid residues among various RT sequences showed variability in their percentages indicating post divergence evolution. Amino acid Leucine was found in highest proportions followed by Lysine, while Methionine and Tryptophan were in lowest percentages. The phylogenetic analysis based on RT domains confirmed that although having most conserved RT regions, several evolutionary events occurred causing nucleotide polymorphisms and hence clustering of Gypsy and Copia superfamilies into their respective lineages. The study will be helpful in identification and annotation of these elements in other species and genera and their distribution patterns on chromosomes by fluorescent in situ hybridization techniques.

Keywords: transposable elements, Phoenix dactylifera, retrotransposons, phylogenetic analysis

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Authors: Akram Farhadi, Mahshid Froughan, Farahnaz Mohammadi, Maryam Rassouli, Maryam Noroozian, Leila Sadeghmoghaddam

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Background: The caregivers’ assessment of their own caregiving is considered the most important concept in exploring their experiences and has a major role in care outcomes. The rising number of people with dementia and their need for care makes family caregiving really important matter to consider and evaluate. Objectives: This study was conducted with the aim to naturalize and validate the Persian version of the Revised Caregiving Appraisal Scale (RCAS) in family caregivers of older adults with dementia. Patients and Method: In this cross-sectional methodological study, the Revised Caregiving Appraisal Scale (RCAS) was translated using International Quality of Life Assessment (IQOLA) protocol, and then a panel of experts examined its face and content validities. To ensure construct validity, the translated Revised Caregiving Appraisal Scale (RCAS) was completed by 236 family caregivers, and factor construct of the scale was assessed with 5 initial factors using confirmatory factor analysis. Internal consistency was found using Cronbach's alpha, and test-retest using intraclass correlation coefficient. Confirmatory factor analysis was performed in LISREL-8.8 software in Windows®. Results: Participating caregivers' mean age was 53.5±13.13 years. Content and face validities of the scale were confirmed according to the views expressed by family caregivers and panel of experts. The confirmatory factor analysis (CFA) results showed appropriate values for all fitness indices (RMSEA=0.046, df/X2=2.428, CFI=0.98, AGFI=0.84, GFI=0.9), and the 5-factor model was confirmed with 27 items. Overall Cronbach's alpha was reported 0.894, and test retest showed overall ICC=0.94. Conclusion: The Persian version of RCAS is a valid and reliable tool for family caregivers' assessment of their caregiving of older adults with dementia, and can be useful in assessing family caregiving interventions.

Keywords: psychometric, family caregivers, reliability and validity, elderly, dementia, self-appraisal

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Authors: Fatemeh Nokhodchi Bonab

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Bioinformatics, in its broad sense, involves application of computer processes to solve biological problems. A wide range of computational tools are needed to effectively and efficiently process large amounts of data being generated as a result of recent technological innovations in biology and medicine. A number of computational tools have been developed or adapted to deal with the experimental riches of complex and multivariate data and transition from data collection to information or knowledge. These bioinformatics tools are being evaluated and applied in various medical areas including early detection, risk assessment, classification, and prognosis of cancer. The goal of these efforts is to develop and identify bioinformatics methods with optimal sensitivity, specificity, and predictive capabilities. The recent flood of data from genome sequences and functional genomics has given rise to new field, bioinformatics, which combines elements of biology and computer science. Bioinformatics is conceptualizing biology in terms of macromolecules (in the sense of physical-chemistry) and then applying "informatics" techniques (derived from disciplines such as applied maths, computer science, and statistics) to understand and organize the information associated with these molecules, on a large-scale. Here we propose a definition for this new field and review some of the research that is being pursued, particularly in relation to transcriptional regulatory systems.

Keywords: methods, applications, transcriptional regulatory systems, techniques

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Authors: Z. Mowafy Emam Mowafy, Ahmed R. Sayed, M. El Sayed Mohmmed Hassan

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Purpose: to evaluate the effect of low intensity laser on severe tinnitus in idiopathic sudden hearing loss patients. Methods of evaluation (Visual analogue scale and tinnitus handicap inventory scale):- Thirty patients who had unilateral tinnitus with sensorineural hearing loss were participated in the study. Subjects aged from 40 to 50 were randomly divided into two equal groups: group (A): composed of 15 patients who received the routine medical care (Systemic steroids) in addition to the low-intensity laser therapy (LILT) while group (B): composed of 15 patients who received only the routine medical care. Continuous 632.8nm He-Ne laser was used with 5mW power for 15 min\day, 3 days per week for 3 months. Results and conclusion: Results showed that application of the LILT had a valuable effect on severe tinnitus in idiopathic sudden hearing loss patients as evidenced by the highly decreased visual analogue scale and tinnitus handicap inventory scale.

Keywords: idiopathic sudden hearing loss, low intensity laser, tinnitus, tinnitus handicap inventory scale and visual analogue scale

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Authors: Nadereh Sohrabi Shegefti, Siamak Samani

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Level of adjustment is the first index to check mental health. The aim of this study was developing a valid and reliable Multidimensional Adjustment Scale (MAS). The sample consisted of 150 college students. Multidimensional adjustment scale and Depression, Anxiety, and stress scale (DASS) were used in this study. Principle factor analysis, Pearson correlation coefficient, and Cornbach's Alpha were used to check the validity and reliability of the MAS. Principle component factor analysis showed a 5 factor solution for the MAS. Alpha coefficients for the MAS sub scales were ranged between .69 to .83. Test-retest reliability for MAS was .88 and the mean of sub scales- total score correlation was .88. All these indexes revealed an acceptable reliability and validity for the MAS. The MAS is a short assessment instrument with good acceptable psychometric properties to use in clinical filed.

Keywords: psychological adjustment, psychometric properties, validity, Pearson correlation

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Authors: Morten Brøgger, Kim Wittchen

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Focus on reducing energy consumption in existing buildings at large scale, e.g. in cities or countries, has been increasing in recent years. In order to reduce energy consumption in existing buildings, political incentive schemes are put in place and large scale investments are made by utility companies. Prioritising these investments requires a comprehensive overview of the energy consumption in the existing building stock, as well as potential energy-savings. However, a building stock comprises thousands of buildings with different characteristics making it difficult to model energy consumption accurately. Moreover, the complexity of the building stock makes it difficult to convey model results to policymakers and other stakeholders. In order to manage the complexity of the building stock, building archetypes are often employed in building stock energy models (BSEMs). Building archetypes are formed by segmenting the building stock according to specific characteristics. Segmenting the building stock according to building type and building age is common, among other things because this information is often easily available. This segmentation makes it easy to convey results to non-experts. However, using a single archetypical building to represent all buildings in a segment of the building stock is associated with loss of detail. Thermal characteristics are aggregated while other characteristics, which could affect the energy efficiency of a building, are disregarded. Thus, using a simplified representation of the building stock could come at the expense of the accuracy of the model. The present study evaluates the accuracy of a conventional archetype-based BSEM that segments the building stock according to building type- and age. The accuracy is evaluated in terms of the archetypes’ ability to accurately emulate the average energy demands of the corresponding buildings they were meant to represent. This is done for the buildings’ energy demands as a whole as well as for relevant sub-demands. Both are evaluated in relation to the type- and the age of the building. This should provide researchers, who use archetypes in BSEMs, with an indication of the expected accuracy of the conventional archetype model, as well as the accuracy lost in specific parts of the calculation, due to use of the archetype method.

Keywords: building stock energy modelling, energy-savings, archetype

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Authors: İsmail Seçer

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Although depression and anxiety disorders are considered to be adult disorders, the evidence obtained from several studies conducted recently shows that the roots of depression and anxiety disorders go back to childhood years. Thus, it is thought that analyzing depressive symptoms and anxiety disorders observed in the childhood is an important necessity. In the direction of the problem status of the study, the purpose of this study is to adapt anxiety and depression questionnaire for children into Turkish culture and analyze the psychometric characteristics of it on clinical and nonclinical samples separately. The study is a descriptive survey research. The study was conducted on two different sample groups, clinical and nonclinical. The clinical sample is formed of 205 individuals and the nonclinical sample is formed of 630 individuals. Through the study, anxiety and depression questionnaire for children, anxiety sensitivity index and obsessive compulsive disorder questionnaire for children were used. Experts’ opinions were asked to provide language validity of the scale. Confirmatory factor analysis and criterion-related validity to analyze construct validity and internal consistency and split-half reliability analyses were done for reliability. In the direction of experts’ opinions, construct validity of the scale was analyzed with simple confirmatory factor analysis and it was determined that the model fit of the two-factor structure of the scale gives good fit on both the clinical and nonclinical samples after determining that the language validity of the scale is provided. In criterion-related validity, it was determined that there are positive and significant relations between anxiety and depression questionnaire for children and anxiety sensitivity and obsessive compulsive disorder. The results of internal consistency and half-split reliability analyses also show that the scale has adequate reliability value. It can be said that depression and anxiety questionnaire for children which was adapted to determine depressive symptoms and anxiety disorders observed in childhood has adequate reliability and validity values and it can be used in future studies. It can be recommended that the psychometric characteristics of the scale can be analyzed and reported on new samples in the future studies.

Keywords: scale adapting, construct validity, confirmatory factor analysis, childhood depression

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Authors: Rituparna Pal, Faiz Ahmed

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Neighbourhood energy efficiency is a newly emerged term to address the quality of urban strata of built environment in terms of various covariates of sustainability. The concept of sustainability paradigm in developed nations has encouraged the policymakers for developing urban scale cities to envision plans under the aegis of urban scale sustainability. The concept of neighbourhood energy efficiency is realized a lot lately just when the cities, towns and other areas comprising this massive global urban strata have started facing a strong blow from climate change, energy crisis, cost hike and an alarming shortfall in the justice which the urban areas required. So this step of urban sustainability can be easily referred more as a ‘Retrofit Action’ which is to cover up the already affected urban structure. So even if we start energy efficiency for existing cities and urban areas the initial layer remains, for which a complete model of urban sustainability still lacks definition. Urban sustainability is a broadly spoken off word with end number of parameters and policies through which the loop can be met. Out of which neighbourhood energy efficiency can be an integral part where the concept and index of neighbourhood scale indicators, block level indicators and building physics parameters can be understood, analyzed and concluded to help emerge guidelines for urban scale sustainability. The future of neighbourhood energy efficiency not only lies in energy efficiency but also important parameters like quality of life, access to green, access to daylight, outdoor comfort, natural ventilation etc. So apart from designing less energy-hungry buildings, it is required to create a built environment which will create less stress on buildings to consume more energy. A lot of literary analysis has been done in the Western countries prominently in Spain, Paris and also Hong Kong, leaving a distinct gap in the Indian scenario in exploring the sustainability at the urban strata. The site for the study has been selected in the upcoming capital city of Amaravati which can be replicated with similar neighbourhood typologies in the area. The paper suggests a methodical intent to quantify energy and sustainability indices in detail taking by involving several macro, meso and micro level covariates and parameters. Several iterations have been made both at macro and micro level and have been subjected to simulation, computation and mathematical models and finally to comparative analysis. Parameters at all levels are analyzed to suggest the best case scenarios which in turn is extrapolated to the macro level finally coming out with a proposal model for energy efficient neighbourhood and worked out guidelines with significance and correlations derived.

Keywords: energy quantification, macro scale parameters, meso scale parameters, micro scale parameters

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Authors: Tuba Tekin, Nurcan Baglam, Emine Dincer

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This study aimed to examine the effects of nutrition education received by university students on sustainable healthy eating behaviors and adherence to the Mediterranean diet. The 2nd, 3rd, and 4th-grade university students studying at the Faculty of Health Sciences, Nutrition and Dietetics, Midwifery, Nursing, Physical Therapy, and Rehabilitation departments of universities in Turkey were included in the study. Students' adherence to the Mediterranean diet was evaluated using the Mediterranean Diet Adherence Scale, and their sustainable and healthy eating behaviors were evaluated using the Sustainable and Healthy Eating Behaviors Scale. In addition, the body weight and height of the students were measured by the researchers, and the Body Mass Index (BMI) value was calculated. A total of 181 students, 85 of whom were studying in the Department of Nutrition and Dietetics and 96 of whom were educated in other departments, were included in the study. 75.7% of the students in the sample are female, while 24.3% are male. The average body weight of the students was 61.17±10.87 kg, and the average BMI was 22.04±3.40 kg/m2. While the mean score of the Mediterranean Diet Adherence Scale was 6.72±1.84, in the evaluation of adherence to the Mediterranean diet, it was determined that 25.4% of the students had poor adherence and 66.9% needed improvement. When the adherence scores of students who received and did not receive nutrition education were compared, it was discovered that the students who received nutrition education had a higher score (p<0.05). Students who received nutrition education had a higher total score on the Sustainable and Healthy Eating Behaviors scale (p<0.05). A moderately positive correlation was found between the Sustainable and Healthy Eating Behaviors scale total score and the Mediterranean Diet Adherence scores (p<0.05). As a result of the linear regression analysis, it was revealed that a 1-unit increase in the Mediterranean diet adherence score would result in a 1.3-point increase in the total score of the Sustainable and Healthy Eating Behaviors scale. Sustainable and healthy diets are important for improving and developing health and the prevention of diseases. The Mediterranean diet is defined as a sustainable diet model. The findings revealed the relationship between the Mediterranean diet and sustainable nutrition and showed that nutrition education increased knowledge and awareness about sustainable nutrition and increased adherence to the Mediterranean diet. For this reason, courses or seminars on sustainable nutrition can be organized during educational periods.

Keywords: healthy eating, Mediterranean diet, nutrition education, sustainable nutrition

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Authors: Ming-Hong Chen

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In the study, the mechanical and financial feasibility for the compressed air energy storage (CAES) system in the porous media reservoir in Taiwan is evaluated. In 2035, Taiwan aims to install 16.7 GW of wind power and 40 GW of photovoltaic (PV) capacity. However, renewable energy sources often generate more electricity than needed, particularly during winter. Consequently, Taiwan requires long-term, large-scale energy storage systems to ensure the security and stability of its power grid. Currently, the primary large-scale energy storage options are Pumped Hydro Storage (PHS) and Compressed Air Energy Storage (CAES). Taiwan has not ventured into CAES-related technologies due to geological and cost constraints. However, with the imperative of achieving net-zero carbon emissions by 2050, there's a substantial need for the development of a considerable amount of renewable energy. PHS has matured, boasting an overall installed capacity of 4.68 GW. CAES, presenting a similar scale and power generation duration to PHS, is now under consideration. Taiwan's geological composition, being a porous medium unlike salt caves, introduces flow field resistance affecting gas injection and extraction. This study employs a program analysis model to establish the system performance analysis capabilities of CAES. The finite volume model is then used to assess the impact of porous media, and the findings are fed back into the system performance analysis for correction. Subsequently, the financial implications are calculated and compared with existing literature. For Taiwan, the strategic development of CAES technology is crucial, not only for meeting energy needs but also for decentralizing energy allocation, a feature of great significance in regions lacking alternative natural resources.

Keywords: compressed-air energy storage, efficiency, porous media, financial feasibility

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Authors: Naoki Yamamoto, Hidenobu Ozaki, Taiichiro Ookawa, Youming Liu, Kazunori Okada, Aiping Zheng

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Rice sheath blight is one of the destructive fungal diseases in rice. We have thought that rice sheath blight resistance is a polygenic trait. Host-pathogen interactions and secondary metabolites such as lignin and phytoalexins are likely to be involved in defense against R. solani. However, to our knowledge, it is still unknown how sheath blight resistance can be enhanced in rice breeding. To seek for an alternative genetic factor that contribute to sheath blight resistance, we mined relevant allelic variations from rice core collections created in Japan. Based on disease lesion length on detached leaf sheath, we selected 30 varieties of the top tail-end and the bottom tail-end, respectively, from the core collections to perform genome-wide association mapping. Re-sequencing reads for these varieties were used for calling single nucleotide polymorphisms among the 60 varieties to create a SNP panel, which contained 1,137,131 homozygous variant sites after filitering. Association mapping highlighted a locus on the long arm of chromosome 11, which is co-localized with three sheath blight QTLs, qShB11-2-TX, qShB11, and qSBR-11-2. Based on the localization of the trait-associated alleles, we identified an ankyryn repeat-containing protein gene (ANK-M) as an uncharacterized candidate factor for rice sheath blight resistance. Allelic distributions for ANK-M in the whole rice population supported the reliability of trait-allele associations. Gene expression characteristics were checked to evaluiate the functionality of ANK-M. Since an ANK-M homolog (OsPIANK1) in rice seems a basal defense regulator against rice blast and bacterial leaf blight, ANK-M may also play a role in the rice immune system.

Keywords: allele mining, GWAS, QTL, rice sheath blight

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Authors: Yulin Zhang, Kaixi Dong, Guozhen Zhao

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Background: Different levels of life satisfaction are associated with some individual differences. Understanding the mechanism between them will help to enhance an individual’s well-being. On the one hand, traditional personality such as extraversion has been considered as the most stable and effective factor in predicting life satisfaction to the author’s best knowledge. On the other, individual emotional difference, such as alexithymia (difficulties identifying and describing one’s own feelings), is also closely related to life satisfaction. With the development of positive psychology, positive personalities such as virtues attract wide attention. And according to the broaden-and-build theory, social connectivity may mediate between emotion and life satisfaction. Therefore, the current study aims to explore the mediating role of social connectivity in the effect of positive personality and alexithymia on life satisfaction. Method: This study was conducted with 318 healthy Chinese college students whose age range from 18 to 30. Positive personality (including interpersonal, vitality, and cautiousness) was measured by the Chinese version of Values in Action Inventory of Strengths (VIA-IS). Alexithymia was measured by the Toronto Alexithymia Scale (TAS), and life satisfaction was measured by Satisfaction With Life Scale (SWLS). And social connectivity was measured by six items which have been used in previous studies. Each scale showed high reliability and validity. The mediating model was examined in Mplus 7.2 within a structural equation modeling (SEM) framework. Findings: The model fitted well and results revealed that both positive personality (95% confidence interval of indirect effect was [0.023, 0.097]) and alexithymia (95% confidence interval of indirect effect was [-0.270, -0.089]) predicted life satisfaction level significantly through social connectivity. Also, only positive personality significantly and directly predicted life satisfaction compared to alexithymia (95% confidence interval of direct effect was [0.109, 0.260]). Conclusion: Alexithymia predicts life satisfaction only through social connectivity, which emphasizes the importance of social bonding in enhancing the well-being of Chinese college students with alexithymia. And the positive personality can predict life satisfaction directly or through social connectivity, which provides implications for enhancing the well-being of Chinese college students by cultivating their virtue and positive psychological quality.

Keywords: alexithymia, life satisfaction, positive personality, social connectivity

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Authors: Rossella Arcucci, Luisa D'Amore, Simone Celestino, Giuseppe Scotti, Giuliano Laccetti

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This work is the first dowel in a rather wide research activity in collaboration with Euro Mediterranean Center for Climate Changes, aimed at introducing scalable approaches in Ocean Circulation Models. We discuss designing and implementation of a parallel algorithm for solving the Variational Data Assimilation (DA) problem on Graphics Processing Units (GPUs). The algorithm is based on the fully scalable 3DVar DA model, previously proposed by the authors, which uses a Domain Decomposition approach (we refer to this model as the DD-DA model). We proceed with an incremental porting process consisting of 3 distinct stages: requirements and source code analysis, incremental development of CUDA kernels, testing and optimization. Experiments confirm the theoretic performance analysis based on the so-called scale up factor demonstrating that the DD-DA model can be suitably mapped on GPU architectures.

Keywords: data assimilation, GPU architectures, ocean models, parallel algorithm

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Authors: Joseph Fitoussi, Mohammadali Shirinbayan, Abbas Tcharkhtchi

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Due to material flow during processing, short fiber reinforced composites structures obtained by injection or compression molding generally present strong spatial microstructure variation. On the other hand, quasi-static, dynamic, and fatigue behavior of these materials are highly dependent on microstructure parameters such as fiber orientation distribution. Indeed, because of complex damage mechanisms, SFRC structures design is a key challenge for safety and reliability. In this paper, we propose a micromechanical model allowing prediction of damage behavior of real structures as a function of microstructure spatial distribution. To this aim, a statistical damage criterion including strain rate and fatigue effect at the local scale is introduced into a Mori and Tanaka model. A critical local damage state is identified, allowing fatigue life prediction. Moreover, the multi-scale model is coupled with an experimental intrinsic link between damage under monotonic loading and fatigue life in order to build an abacus giving Tsai-Wu failure criterion parameters as a function of microstructure and targeted fatigue life. On the other hand, the micromechanical damage model gives access to the evolution of the anisotropic stiffness tensor of SFRC submitted to complex thermomechanical loading, including quasi-static, dynamic, and cyclic loading with temperature and amplitude variations. Then, the latter is used to fill out microstructure dependent material cards in finite element analysis for design optimization in the case of complex loading history. The proposed methodology is illustrated in the case of a real automotive component made of sheet molding compound (PSA 3008 tailgate). The obtained results emphasize how the proposed micromechanical methodology opens a new path for the automotive industry to lighten vehicle bodies and thereby save energy and reduce gas emission.

Keywords: short fiber reinforced composite, structural design, damage, micromechanical modelling, fatigue, strain rate effect

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Authors: Azadeh Malekan, Shahin Rouhani

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Superlubricity is a phenomenon where two surfaces in contact show negligible friction;this may be because the asperities of the two surfaces do not interlock. Two rough surfaces, when pressed against each other, can get into a formation where the summits of asperities of one surface lock into the valleys of the other surface. The amount of interlock depends on the geometry of the two surfaces. We suggest the friction force may then be proportional to the amount of interlock; this explains Superlubricity as the situation where there is little interlock. Then the friction force will be directly proportional to the normal force as it is related to the work necessary to lift the upper surface in order to clear the interlock. To investigate this model, we simulate the contact of two surfaces. In order to validate our model, we first investigate Amontons‘ law. Assuming that asperities retain deformations in the time scale while the top asperity moves across the lattice spacing Amonton’s law is observed. Structural superlubricity is examined by the hypothesis that surfaces are very rigid and there is no deformation in asperities. This may happen at small normal forces. When two identical surfaces come into contact, rotating the top surface we observe a peak in friction force near the angle of orientation where the two surfaces can interlock.

Keywords: friction, amonton`s law, superlubricity, contact model

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Authors: Sofia Sehli, Zainab El Ouafi, Casey Eddington, Soumaya Jbara, Kasambula Arthur Shem, Islam El Jaddaoui, Ayorinde Afolayan, Olaitan I. Awe, Allissa Dillman, Hassan Ghazal

Abstract:

The ability to promptly sequence whole genomes at a relatively low cost has revolutionized the way we study the microbiome. Microbiologists are no longer limited to studying what can be grown in a laboratory and instead are given the opportunity to rapidly identify the makeup of microbial communities in a wide variety of environments. Analyzing whole genome sequencing (WGS) data is a complex process that involves multiple moving parts and might be rather unintuitive for scientists that don’t typically work with this type of data. Thus, to help lower the barrier for less-computationally inclined individuals, TAXAPRO was developed at the first Omics Codeathon held virtually by the African Society for Bioinformatics and Computational Biology (ASBCB) in June 2021. TAXAPRO is an advanced metagenomics pipeline that accurately assembles organelle genomes from whole-genome sequencing data. TAXAPRO seamlessly combines WGS analysis tools to create a pipeline that automatically processes raw WGS data and presents organism abundance information in both a tabular and graphical format. TAXAPRO was evaluated using COVID-19 patient gut microbiome data. Analysis performed by TAXAPRO demonstrated a high abundance of Clostridia and Bacteroidia genera and a low abundance of Proteobacteria genera relative to others in the gut microbiome of patients hospitalized with COVID-19, consistent with the original findings derived using a different analysis methodology. This provides crucial evidence that the TAXAPRO workflow dispenses reliable organism abundance information overnight without the hassle of performing the analysis manually.

Keywords: metagenomics, shotgun metagenomic sequence analysis, COVID-19, pipeline, bioinformatics

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Authors: Jianshu Yang, Delphine Sordes, Marek Kolmer, Christian Joachim

Abstract:

Nanoelectronics, for example the calculating circuits integrating at molecule scale logic gates, atomic scale circuits, has been constructed and investigated recently. A major challenge is their functional properties characterization because of the connecting problem from atomic scale to micrometer scale. New experimental instruments and new processes have been proposed therefore. To satisfy a precisely measurement at atomic scale and then connecting micrometer scale electrical integration controller, the technique improvement is kept on going. Our new machine, a low temperature high vacuum four scanning tunneling microscope, as a customer required instrument constructed by Omicron GmbH, is expected to be scaling down to atomic scale characterization. Here, we will present our first testified results about the performance of this new instrument. The sample we selected is Au(111) surface. The measurements have been taken at 4.2 K. The atomic resolution surface structure was observed with each of four scanners with noise level better than 3 pm. With a tip-sample distance calibration by I-z spectra, the sample conductance has been derived from its atomic locally I-V spectra. Furthermore, the surface conductance measurement has been performed using two methods, (1) by landing two STM tips on the surface with sample floating; and (2) by sample floating and one of the landed tips turned to be grounding. In addition, single atom manipulation has been achieved with a modified tip design, which is comparable to a conventional LT-STM.

Keywords: low temperature ultra-high vacuum four scanning tunneling microscope, nanoelectronics, point contact, single atom manipulation, tunneling resistance

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Authors: Ahmed M. Debela, Mayreli Ortiz , Ciara K. O´Sullivan

Abstract:

The completion of the human genome Project (HGP) has paved the way for mapping the diversity in the overall genome sequence which helps to understand the genetic causes of inherited diseases and susceptibility to drugs or environmental toxins. Arrayed primer extension (APEX) is a microarray based minisequencing strategy for screening disease causing mutations. It is derived from Sanger DNA sequencing and uses fluorescently dideoxynucleotides (ddNTPs) for termination of a growing DNA strand from a primer with its 3´- end designed immediately upstream of a site where single nucleotide polymorphism (SNP) occurs. The use of DNA polymerase offers a very high accuracy and specificity to APEX which in turn happens to be a method of choice for multiplex SNP detection. Coupling the high specificity of this method with the high sensitivity, low cost and compatibility for miniaturization of electrochemical techniques would offer an excellent platform for detection of mutation as well as sequencing of DNA templates. We are developing an electrochemical APEX for the analysis of SNPs found in the MYH7 gene for group of cardiomyopathy patients. ddNTPs were labeled with four different redox active compounds with four distinct potentials. Thiolated oligonucleotide probes were immobilised on gold and glassy carbon substrates which are followed by hybridisation with complementary target DNA just adjacent to the base to be extended by polymerase. Electrochemical interrogation was performed after the incorporation of the redox labelled dedioxynucleotide. The work involved the synthesis and characterisation of the redox labelled ddNTPs, optimisation and characterisation of surface functionalisation strategies and the nucleotide incorporation assays.

Keywords: array based primer extension, labelled ddNTPs, electrochemical, mutations

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Authors: Ammar Maziz, Mostapha Tarfaoui, Said Rechak

Abstract:

The high mechanical performance of composite pipes can be adversely affected by their low resistance to impact loads. Loads in dynamic origin are dangerous and cause consequences on the operation of pipes because the damage is often not detected and can affect the structural integrity of composite pipes. In this work, an advanced 3-D finite element (FE) model, based on the use of intralaminar damage models was developed and used to predict damage under low-velocity impact. The performance of the numerical model is validated with the confrontation with the results of experimental tests. The results show that at low impact energy, the damage happens mainly by matrix cracking and delamination. The model capabilities to simulate the low-velocity impact events on the full-scale composite structures were proved.

Keywords: composite materials, low velocity impact, FEA, dynamic behavior, progressive damage modeling

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Authors: Prajwal Prakash Vasisht, Sharath Rajamurthy, Nishanth Dara

Abstract:

In a supervised machine learning approach, metrics such as precision, accuracy, and coverage can be calculated using ground truth labels to help in model tuning, evaluation, and selection. In an unsupervised setting, however, where the data has no ground truth, there are few interpretable metrics that can guide us to do the same. Our approach creates a framework to adapt the Intersection over Union metric, referred to as Adapted IoU, usually used to evaluate supervised learning models, into the unsupervised domain, which solves the problem by factoring in subject matter expertise and intuition about the ideal output from the model. This metric essentially provides a scale that allows us to compare the performance across numerous unsupervised models or tune hyper-parameters and compare different versions of the same model.

Keywords: general metric, unsupervised learning, classification, intersection over union

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Authors: Simiso Fisokuhle Nyandeni

Abstract:

Climate change has turned out to be a pandemic that has drawn the attention of many countries’ households around the globe, especially those whose livelihood and economic status depend on agricultural productivity. Hence, the agricultural sector is regarded as the sector that is most dependent on climate conditions for its productivity/harvest, yet in recent years this sector has been experiencing drought. However, adaptation seems to be a tool that every farmer looks upon as a solution to their challenges as their productivity keeps on being vulnerable to climate effects. Thus, exposure/access to the market seems to be a major challenge that faces especially small-scale farmers. We, therefore, examine the small-scale farmers’ constraints or challenges towards getting access to the market for them to get proper sales of their farming products. As a result, the adaptation capacity of every farm household varies on the financial status.

Keywords: climate change, small-scale farming, agriculture sector, adaptation

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Authors: Gayatri Ghosh

Abstract:

In this work, a flavour theory of a neutrino mass model based on A_4 symmetry is considered to explain the phenomenology of neutrino mixing. The spontaneous symmetry breaking of A_4 symmetry in this model leads to tribimaximal mixing in the neutrino sector at a leading order. We consider the effect of Z_2 × Z_2 invariant perturbations in neutrino sector and find the allowed region of correction terms in the perturbation matrix that is consistent with 3σ ranges of the experimental values of the mixing angles. We study the entanglement of this formalism on the other phenomenological observables, such as δ_CP phase, the neutrino oscillation probability P(νµ → νe), the effective Majorana mass |mee| and |meff νe |. A Z_2 × Z_2 invariant perturbations in this model is introduced in the neutrino sector which leads to testable predictions of θ_13 and CP violation. By changing the magnitudes of perturbations in neutrino sector, one can generate viable values of δ_CP and neutrino oscillation parameters. Next we investigate the feasibility of charged lepton flavour violation in type-I seesaw models with leptonic flavour symmetries at high energy that leads to tribimaximal neutrino mixing. We consider an effective theory with an A_4 × Z_2 × Z_2 symmetry, which after spontaneous symmetry breaking at high scale which is much higher than the electroweak scale leads to charged lepton flavour violation processes once the heavy Majorana neutrino mass degeneracy is lifted either by renormalization group effects or by a soft breaking of the A_4 symmetry. In this context the implications for charged lepton flavour violation processes like µ → eγ, τ → eγ, τ → µγ are discussed.

Keywords: Z2 × Z2 invariant perturbations, CLFV, delta CP phase, tribimaximal neutrino mixing

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Authors: Muhammad Yusuf Abduh, Robert Manurung, Hero Jan Heeres

Abstract:

Biodiesel can be produced in small scale mobile units which are designed with local input and demand. Unlike the typical biodiesel production plants, mobile biodiesel unit consiss of a biodiesel production facility placed inside a standard cargo container and mounted on a truck so that it can be transported to a region near the location of raw materials. In this paper, we review the existing concept and unit for the development of community-scale and mobile production of biodiesel. This includes the main reactor technology to produce biodiesel as well as the pre-treatment prior to the reaction unit. The pre-treatment includes the oil-expeller unit to obtain oil from the oilseeds as well as the quality control of the oil before it enters the reaction unit. This paper also discusses the post-treatment after the production of biodiesel. It includes the refining and purification of biodiesel to meet the product specification set by the biodiesel industry.

Keywords: biodiesel, community scale, mobile biodiesel unit, reactor technology

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Authors: Golden J. Zhang, Dongbao Zhou

Abstract:

Darcy’s law is the fundamental theory in fluid dynamics and engineering applications. Although Darcy linearity was found to be valid for slow, viscous flow, non-linear and non-Darcian flow has been well documented under both small and large velocity fluid flow. Various classical models were proposed and used widely to quantify non-Darcian flow, including the well-known Forchheimer, Izbash, and Swartzendruber models. Applications, however, revealed limitations of these models. Here we propose a general model built upon the Caputo fractional derivative to quantify non-Darcian flow for various flows (laminar to turbulence).Real-world applications and model comparisons showed that the new fractional-derivative model, which extends the fractional model proposed recently by Zhou and Yang (2018), can capture the non-Darcian flow in the relatively small velocity in low-permeability deposits and the relatively high velocity in high-permeability sand. A scale effect was also identified for non-Darcian flow in fractured rocks. Therefore, fractional calculus may provide an efficient tool to improve classical models to quantify fluid dynamics in aquatic environments.

Keywords: fractional derivative, darcy’s law, non-darcian flow, fluid dynamics

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Authors: Janos Juhasz, Sandor Pongor, Balazs Ligeti

Abstract:

Next-generation sequencing, especially whole genome shotgun sequencing, is becoming a common approach to gain insight into the microbiomes in a culture-independent way, even in clinical practice. It does not only give us information about the species composition of an environmental sample but opens the possibility to detect antimicrobial resistance and novel, or currently unknown, pathogens. Accurately and reliably detecting the microbial strains is a challenging task. Here we present a sensitive approach for detecting pathogens in metagenomics samples with special regard to detecting novel variants of known pathogens. We have developed a pipeline that uses fast, short read aligner programs (i.e., Bowtie2/BWA) and comprehensive nucleotide databases. Taxonomic binning is based on the lowest common ancestor (LCA) principle; each read is assigned to a taxon, covering the most significantly hit taxa. This approach helps in balancing between sensitivity and running time. The program was tested both on experimental and synthetic data. The results implicate that our method performs as good as the state-of-the-art BLAST-based ones, furthermore, in some cases, it even proves to be better, while running two orders magnitude faster. It is sensitive and capable of identifying taxa being present only in small abundance. Moreover, it needs two orders of magnitude less reads to complete the identification than MetaPhLan2 does. We analyzed an experimental anthrax dataset (B. anthracis strain BA104). The majority of the reads (96.50%) was classified as Bacillus anthracis, a small portion, 1.2%, was classified as other species from the Bacillus genus. We demonstrate that the evaluation of high-throughput sequencing data is feasible in a reasonable time with good classification accuracy.

Keywords: metagenomics, taxonomy binning, pathogens, microbiome, B. anthracis

Procedia PDF Downloads 137