Search results for: integrative bioinformatics

Authors: Victor Prevost, Solene Landerneau, Michel Duhamel, Joel Sternheimer, Olivier Gallet, Pedro Ferrandiz, Marwa Mokni

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The search for homologous proteins is one of the ongoing challenges in biology and bioinformatics. Traditionally, a pair of proteins is thought to be homologous when they originate from the same ancestral protein. In such a case, their sequences share similarities, and advanced scientific research effort is spent to investigate this question. On this basis, we propose the Protein-Wave Alignment Tool (”P-WAT”) developed within the framework of the France Relance 2030 plan. Our work takes into consideration the mass-related wave aspect of protein biosynthesis, by associating specific frequencies to each amino acid according to its mass. Amino acids are then regrouped within their mass category. This way, our algorithm produces specific alignments in addition to those obtained with a common amino acid coding system. For this purpose, we develop the ”P-WAT” original algorithm, able to address large protein databases, with different attributes such as species, protein names, etc. that allow us to align user’s requests with a set of specific protein sequences. The primary intent of this algorithm is to achieve efficient alignments, in this specific conceptual frame, by minimizing execution costs and information loss. Our algorithm identifies sequence similarities by searching for matches of sub-sequences of different sizes, referred to as primers. Our algorithm relies on Boolean operations upon a dot plot matrix to identify primer amino acids common to both proteins which are likely to be part of a significant alignment of peptides. From those primers, dynamic programming-like traceback operations generate alignments and alignment scores based on an adjusted PAM250 matrix.

Keywords: protein, alignment, homologous, Genodic

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Authors: George Kassar, Phillip A. Cartwright

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Based on data collected from The Jones Learning Center (JLC), University of the Ozarks, Arkansas, U.S., this study explores the impact of inclusive classroom practices on neuro-diverse college students’ and their consequent academic performance having participated in integrative therapies designed to support students who are intellectually capable of obtaining a college degree, but who require support for learning challenges owing to disabilities, AD/HD, or ASD. The purpose of this study is two-fold. The first objective is to explore the general process, special techniques, and practices of the (JLC) inclusive program. The second objective is to identify and analyze the effectiveness of the processes, techniques, and practices in supporting the academic performance of enrolled college students with learning disabilities following integration into mainstream university learning. Integrity, transparency, and confidentiality are vital in the research. All questions were shared in advance and confirmed by the concerned management at the JLC. While administering the questionnaire as well as conducted the interviews, the purpose of the study, its scope, aims, and objectives were clearly explained to all participants prior starting the questionnaire / interview. Confidentiality of all participants assured and guaranteed by using encrypted identification of individuals, thus limiting access to data to only the researcher, and storing data in a secure location. Respondents were also informed that their participation in this research is voluntary, and they may withdraw from it at any time prior to submission if they wish. Ethical consent was obtained from the participants before proceeding with videorecording of the interviews. This research uses a mixed methods approach. The research design involves collecting, analyzing, and “mixing” quantitative and qualitative methods and data to enable a research inquiry. The research process is organized based on a five-pillar approach. The first three pillars are focused on testing the first hypothesis (H1) directed toward determining the extent to the academic performance of JLC students did improve after involvement with comprehensive JLC special program. The other two pillars relate to the second hypothesis (H2), which is directed toward determining the extent to which collective and applied knowledge at JLC is distinctive from typical practices in the field. The data collected for research were obtained from three sources: 1) a set of secondary data in the form of Grade Point Average (GPA) received from the registrar, 2) a set of primary data collected throughout structured questionnaire administered to students and alumni at JLC, and 3) another set of primary data collected throughout interviews conducted with staff and educators at JLC. The significance of this study is two folds. First, it validates the effectiveness of the special program at JLC for college-level students who learn differently. Second, it identifies the distinctiveness of the mix of techniques, methods, and practices, including the special individualized and personalized one-on-one approach at JLC.

Keywords: education, neuro-diverse students, program effectiveness, Jones learning center

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Authors: Hai L. Tran

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When covering events and issues, the news media often employ both personal accounts as well as facts and figures. However, the process of using numbers and narratives in the newsroom is mostly operated through trial and error. There is a demonstrated need for the news industry to better understand the specific effects of storytelling and data-driven reporting on the audience as well as explanatory factors driving such effects. In the academic world, anecdotal evidence and statistical evidence have been studied in a mutually exclusive manner. Existing research tends to treat pertinent effects as though the use of one form precludes the other and as if a tradeoff is required. Meanwhile, narratives and statistical facts are often combined in various communication contexts, especially in news presentations. There is value in reconceptualizing and theorizing about both relative and collective impacts of numbers and narratives as well as the mechanism underlying such effects. The current undertaking seeks to link theory to practice by providing a complete picture of how and why people are influenced by information conveyed through quantitative and qualitative accounts. Specifically, the cognitive-experiential theory is invoked to argue that humans employ two distinct systems to process information. The rational system requires the processing of logical evidence effortful analytical cognitions, which are affect-free. Meanwhile, the experiential system is intuitive, rapid, automatic, and holistic, thereby demanding minimum cognitive resources and relating to the experience of affect. In certain situations, one system might dominate the other, but rational and experiential modes of processing operations in parallel and at the same time. As such, anecdotes and quantified facts impact audience response differently and a combination of data and narratives is more effective than either form of evidence. In addition, the present study identifies several media variables and human factors driving the effects of statistics and anecdotes. An integrative model is proposed to explain how message characteristics (modality, vividness, salience, congruency, position) and individual differences (involvement, numeracy skills, cognitive resources, cultural orientation) impact selective exposure, which in turn activates pertinent modes of processing, and thereby induces corresponding responses. The present study represents a step toward bridging theoretical frameworks from various disciplines to better understand the specific effects and the conditions under which the use of anecdotal evidence and/or statistical evidence enhances or undermines information processing. In addition to theoretical contributions, this research helps inform news professionals about the benefits and pitfalls of incorporating quantitative and qualitative accounts in reporting. It proposes a typology of possible scenarios and appropriate strategies for journalists to use when presenting news with anecdotes and numbers.

Keywords: data, narrative, number, anecdote, storytelling, news

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Authors: Manju Kanu, Subrata Sinha, Surabhi Johari

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Viral proteins of Ebola viruses belong to one of the best studied viruses; however no effective prevention against EBOV has been developed. Epitope-based vaccines provide a new strategy for prophylactic and therapeutic application of pathogen-specific immunity. A critical requirement of this strategy is the identification and selection of T-cell epitopes that act as vaccine targets. This study describes current methodologies for the selection process, with Ebola virus as a model system. Hence great challenge in the field of ebola virus research is to design universal vaccine. A combination of publicly available bioinformatics algorithms and computational tools are used to screen and select antigen sequences as potential T-cell epitopes of supertypes Human Leukocyte Antigen (HLA) alleles. MUSCLE and MOTIF tools were used to find out most conserved peptide sequences of viral proteins. Immunoinformatics tools were used for prediction of immunogenic peptides of viral proteins in zaire strains of Ebola virus. Putative epitopes for viral proteins (VP) were predicted from conserved peptide sequences of VP. Three tools NetCTL 1.2, BIMAS and Syfpeithi were used to predict the Class I putative epitopes while three tools, ProPred, IEDB-SMM-align and NetMHCII 2.2 were used to predict the Class II putative epitopes. B cell epitopes were predicted by BCPREDS 1.0. Immunogenic peptides were identified and selected manually by putative epitopes predicted from online tools individually for both MHC classes. Finally sequences of predicted peptides for both MHC classes were looked for common region which was selected as common immunogenic peptide. The immunogenic peptides were found for viral proteins of Ebola virus: epitopes FLESGAVKY, SSLAKHGEY. These predicted peptides could be promising candidates to be used as target for vaccine design.

Keywords: epitope, b cell, immunogenicity, ebola

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Authors: David Nogueiras Blanco, Amir Alwash, Arnaud Gaudinat, René Schneider

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At a time when the access to and the sharing of information are crucial in the world of research, the use of technologies such as persistent identifiers (PIDs), Current Research Information Systems (CRIS), and ontologies may create platforms for information sharing if they respond to the need of disambiguation of their data by assuring interoperability inside and between other systems. INCIPIT-CRIS is a continuation of the former INCIPIT project, whose goal was to set up an infrastructure for a low-cost attribution of PIDs with high granularity based on Archival Resource Keys (ARKs). INCIPIT-CRIS can be interpreted as a logical consequence and propose a research information management system developed from scratch. The system has been created on and around the Schema.org ontology with a further articulation of the use of ARKs. It is thus built upon the infrastructure previously implemented (i.e., INCIPIT) in order to enhance the persistence of URIs. As a consequence, INCIPIT-CRIS aims to be the hinge between previously separated aspects such as CRIS, ontologies and PIDs in order to produce a powerful system allowing the resolution of disambiguation problems using a combination of an ontology such as Schema.org and unique persistent identifiers such as ARK, allowing the sharing of information through a dedicated platform, but also the interoperability of the system by representing the entirety of the data as RDF triplets. This paper aims to present the implemented solution as well as its simulation in real life. We will describe the underlying ideas and inspirations while going through the logic and the different functionalities implemented and their links with ARKs and Schema.org. Finally, we will discuss the tests performed with our project partner, the Swiss Institute of Bioinformatics (SIB), by the use of large and real-world data sets.

Keywords: current research information systems, linked data, ontologies, persistent identifier, schema.org, semantic web

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Authors: Nebojsa Stefanovic, Sasa Milijic, Natasa Danilovic Hristic

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Spatial plan of the special purpose area constitutes a basic tool in the planning of infrastructure corridor of a highway. The aim of the plan is to define the planning basis and provision of spatial conditions for the construction and operation of the highway, as well as for developing other infrastructure systems in the corridor. This paper presents a methodology and approach to the preparation of the Spatial Plan for the special purpose area for the infrastructure corridor of the highway E-80, Section Niš-Merdare in Serbia. The applied methodological approach is based on the combined application of the integrative and participatory method in the decision-making process on the sustainable development of the highway corridor. It was found that, for the planning and management of the infrastructure corridor, a key problem is coordination of spatial and urban planning, strategic environmental assessment and sectoral traffic planning and designing. Through the development of the plan, special attention is focused on increasing the accessibility of the local and regional surrounding, reducing the adverse impacts on the development of settlements and the economy, protection of natural resources, natural and cultural heritage, and the development of other infrastructure systems in the corridor of the highway. As a result of the applied methodology, this paper analyzes the basic features such as coverage, the concept, protected zones, service facilities and objects, the rules of development and construction, etc. Special emphasis is placed to methodology and results of the Strategic Environmental Assessment of the Spatial Plan, and to the importance of protection measures, with the special significance of air and noise protection measures. For evaluation in the Strategic Environmental Assessment, a multicriteria expert evaluation (semi-quantitative method) of planned solutions was used in relation to the set of goals and relevant indicators, based on the basic set of indicators of sustainable development. Evaluation of planned solutions encompassed the significance and size, spatial conditions and probability of the impact of planned solutions on the environment, and the defined goals of strategic assessment. The framework of the implementation of the Spatial Plan is presented, which is determined for the simultaneous elaboration of planning solutions at two levels: the strategic level of the spatial plan and detailed urban plan level. It is also analyzed the relationship of the Spatial Plan to other applicable planning documents for the planning area. The effects of this methodological approach relate to enabling integrated planning of the sustainable development of the infrastructure corridor of the highway and its surrounding area, through coordination of spatial, urban and sectoral traffic planning and design, as well as the participation of all key actors in the adoption and implementation of planned decisions. By the conclusions of the paper, it is pointed to the direction for further research, particularly in terms of harmonizing methodology of planning documentation and preparation of technical-design documentation.

Keywords: corridor, environment, highway, impact, methodology, spatial plan, urban

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Authors: Monisha Isaac

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Biotechnology is a discipline which explains the use of living organisms and systems to construct a product, or we can define it as an application or technology developed to use biological systems and organisms processes for a specific use. Particularly, it includes cells and its components use for new technologies and inventions. The tools developed can be further used in diverse fields such as agriculture, industry, research and hospitals etc. The 21^st century has seen a drastic development and advancement in biotechnology in India. Significant increase in Government of India’s outlays for biotechnology over the past decade has been observed. A sectoral break up of biotechnology-based companies in India shows that most of the companies are agriculture-based companies having interests ranging from tissue culture to biopesticides. Major attention has been given by the companies in health related activities and in environmental biotechnology. The biopharmaceutical, which comprises of vaccines, diagnostic, and recombinant products is the most reliable and largest segment of the Indian Biotech industry. India has developed its vaccine markets and supplies them to various countries. Then there are the bio-services, which mainly comprise of contract researches and manufacturing services. India has made noticeable developments in the field of bio industries including manufacturing of enzymes, biofuels and biopolymers. Biotechnology is also playing a crucial and significant role in the field of agriculture. Traditional methods have been replaced by new technologies that mainly focus on GM crops, marker assisted technologies and the use of biotechnological tools to improve the quality of fertilizers and soil. It may only be a small contributor but has shown to have huge potential for growth. Bioinformatics is a computational method which helps to store, manage, arrange and design tools to interpret the extensive data gathered through experimental trials, making it important in the design of drugs.

Keywords: biotechnology, advancement, agriculture, bio-services, bio-industries, bio-pharmaceuticals

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Authors: Srishty Gulati, Anju Singh, Shrikant Kukreti

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The manifestation of structural polymorphism in DNA depends on the sequence and surrounding environment. Ample of folded DNA structures have been found in the cellular system out of which DNA hairpins are very common, however, are indispensable due to their role in the replication initiation sites, recombination, transcription regulation, and protein recognition. We enumerate this approach in our study, where the two base substitutions and change in temperature embark destabilization of DNA structure and misbalance the equilibrium between two structures of a sequence present at the overlapping region of the human COMT gene and MIR4761 gene. COMT and MIR4761 gene encodes for catechol-O-methyltransferase (COMT) enzyme and microRNAs (miRNAs), respectively. Environmental changes and errors during cell division lead to genetic abnormalities. The COMT gene entailed in dopamine regulation fosters neurological diseases like Parkinson's disease, schizophrenia, velocardiofacial syndrome, etc. A 19-mer deoxyoligonucleotide sequence 5'-AGGACAAGGTGTGCATGCC-3' (COMT19) is located at exon-4 on chromosome 22 and band q11.2 at the intersection of COMT and MIR4761 gene. Bioinformatics studies suggest that this sequence is conserved in humans and few other organisms and is involved in recognition of transcription factors in the vicinity of 3'-end. Non-denaturating gel electrophoresis and CD spectroscopy of COMT sequences indicate the formation of hairpin type DNA structures. Temperature-dependent CD studies revealed an unusual shift in the slipped DNA-Hairpin DNA equilibrium with the change in temperature. Also, UV-thermal melting techniques suggest that the two base substitutions on the complementary strand of COMT19 did not affect the structure but reduces the stability of duplex. This study gives insight about the possibility of existing structurally polymorphic transient states within DNA segments present at the intersection of COMT and MIR4761 gene.

Keywords: base-substitution, catechol-o-methyltransferase (COMT), hairpin-DNA, structural polymorphism

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Authors: Maria L. McLeod

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This study examines the ways in which cancer patient narratives are portrayed and framed on the websites of three leading U.S. cancer care centers –The University of Texas MD Anderson Cancer Center in Houston, Memorial Sloan Kettering Cancer Center in New York, and Seattle Cancer Care Alliance. Thirty patient stories, ten from each cancer center website blog, were analyzed using qualitative and quantitative textual analysis of unstructured data, documenting repeated use of specific metaphors and tropes while charting common themes and other elements of story structure and content. Patient narratives were coded using grounded theory as the basis for conducting emergent qualitative research. As part of a systematic, inductive approach to collecting and analyzing data, recurrent and unique themes were examined and compared in terms of positive and negative framing, patient agency, and institutional praise. All three of these cancer care centers are teaching hospitals with university affiliations, that emphasizes an evidence-based scientific approach to treatment that utilizes the latest research and cutting-edge techniques and technology. Thus, the use of anecdotal evidence presented in patient narratives could be perceived as being in conflict with this evidence-based model, as the patient stories are not an accurate representation of scientific outcomes related to developing cancer, cancer reoccurrence, or cancer outcomes. The representative patient narratives tend to exclude or downplay adverse responses to treatment, survival rates, integrative and/or complementary cancer treatments, cancer prevention and causes, and barriers to treatment, such as the limitation of insurance plans, costs of treatment, and/or other issues related to access, potentially contributing to false narratives and inaccurate notions of cancer prevention, cancer care treatment and the potential for a cure. Both quantitative and qualitative findings demonstrate that cancer patient stories featured on the blogsites of the nation’s top cancer care centers deemphasize patient agency and, instead, emphasize deference and gratitude toward the institutions where the featured patients received treatment. Along these lines, language choices reflect positive framing of the cancer experience. Accompanying portrait photos of healthy appearing subjects as well as positive-framed headlines, subheads, and pull quotes function similarly, reflecting hopeful, transformative experiences and outcomes over hardship and suffering. Although patient narratives include real, factual scientific details and descriptions of actual events, the stories lack references to more negative realities of cancer diagnosis and treatment. Instead, they emphasize the triumph of survival by which the cancer care center, in the savior/hero role, enables the patient’s success, represented as a cathartic medical journey.

Keywords: cancer framing, cancer stories, medical gaze, patient narratives

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Authors: Shelley Zion

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This study examines the longitudinal impact (10 years) of a course for education leaders designed to encourage the development of critical consciousness surrounding issues of equity, oppression, power, and privilege. The ability to resist and challenge oppression across social and cultural contexts can be acquired through the use of transformative pedagogies that create spaces that use the practice of exploration to make connections between pervasive structural and institutional practices and race and ethnicity. This study seeks to extend this understanding by exploring the longitudinal influence of participating in a course that utilizes transformative pedagogies, course materials, exercises, and activities to encourage the practice of exploration of student experiences with racial and ethnic discrimination with the end goal of providing them with the necessary knowledge and skills that foster their ability to resist and challenge oppression and discrimination -critical action- in their lives. To this end, we use the explanatory power of the theories of critical consciousness development, sociopolitical development, and social identity construction that view exploration as a crucial practice in understanding the role ethnic and racial differences play in creating opportunities or barriers in the lives of individuals. When educators use transformative pedagogies, they create a space where students collectively explore their experiences with racial and ethnic discrimination through course readings, in-class activities, and discussions. The end goal of this exploration is twofold: first, to encourage the student’s ability to understand how differences are identified, given meaning to, and used to position them in specific places and spaces in their world; second, to scaffold students’ ability to make connections between their individual and collective differences and particular institutional and structural practices that create opportunities or barriers in their lives. Studies have found the formal exploration of students’ individual and collective differences in relation to their experiences with racial and ethnic discrimination results in developing an understanding of the roles race and ethnicity play in their lives. To trace the role played by exploration in identity construction, we utilize an integrative approach to identity construction informed by multiple theoretical frameworks grounded in cultural studies, social psychology, and sociology that understand social-cultural, racial, and ethnic -identities as dynamic and ever-changing based on context-specific environments. Stuart Hall refers to this practice as taking “symbolic detours through the past” while reflecting on the different ways individuals have been positioned based on their roots (group membership) and also how they, in turn, chose to position themselves through collective sense-making of the various meanings their differences carried through the routes they have taken. The practice of exploration in the construction of ethnic-racial identities has been found to be beneficial to sociopolitical development.

Keywords: political polarization, civic participation, democracy, education

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Authors: Abdorrasoul Malekpour, Mohammad Ghorbani Mojtaba Mortazavi, Mohammadreza Fattahi, Mohammad Hassan Meshkibaf, Ali Fakhrzad, Saeid Salehi, Saeideh Zahedi, Amir Ahmadimoghaddam, Parviz Farzadnia Dr., Mohammadreza Hajyani Asl Bs

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Hepatitis B as an infectious disease has eight main genotypes (A–H). The aim of this study is to Bioinformatically identify Rare Codon Clusters (RCC) in proteins structure of HBV. For detection of protein family accession numbers (Pfam) of HBV proteins; used of uni-prot database and Pfam search tool were used. Obtained Pfam IDs were analyzed in Sherlocc program and RCCs in HBV proteins were detected. In further, the structures of TrEMBL entries proteins studied in PDB database and 3D structures of the HBV proteins and locations of RCCs were visualized and studied using Swiss PDB Viewer software. Pfam search tool have found nine significant hits and 0 insignificant hits in 3 frames. Results of Pfams studied in the Sherlocc program show this program not identified RCCs in the external core antigen (PF08290) and truncated HBeAg protein (PF08290). By contrast the RCCs become identified in Hepatitis core antigen (PF00906) Large envelope protein S (PF00695), X protein (PF00739), DNA polymerase (viral) N-terminal domain (PF00242) and Protein P (Pf00336). In HBV genome, seven RCC identified that found in hepatitis core antigen, large envelope protein S and DNA polymerase proteins and proteins structures of TrEMBL entries sequences that reported in Sherlocc program outputs are not complete. Based on situation of RCC in structure of HBV proteins, it suggested those RCCs are important in HBV life cycle. We hoped that this study provide a new and deep perspective in protein research and drug design for treatment of HBV.

Keywords: rare codon clusters, hepatitis B virus, bioinformatic study, infectious disease

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Authors: Alisa Kazarina, Guntis Gerhards, Elina Petersone-Gordina, Ilva Pole, Viktorija Igumnova, Janis Kimsis, Valentina Capligina, Renate Ranka

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Human body is inhabited by a vast number of microorganisms, collectively known as the human microbiome, and there is a tremendous interest in evolutionary changes in human microbial ecology, diversity and function. The field of paleomicrobiology, study of ancient human microbiome, is powered by modern techniques of Next Generation Sequencing (NGS), which allows extracting microbial genomic data directly from archaeological sample of interest. One of the major techniques is 16S rRNA gene sequencing, by which certain 16S rRNA gene hypervariable regions are being amplified and sequenced. However, some limitations of this method exist including the taxonomic precision and efficacy of different regions used. The aim of this study was to evaluate the phylogenetic sensitivity of different 16S rRNA gene hypervariable regions for microbiome studies in the archaeological samples. Towards this aim, archaeological bone samples and corresponding soil samples from each burial environment were collected in Medieval cemeteries in Latvia. The Ion 16S™ Metagenomics Kit targeting different 16S rRNA gene hypervariable regions was used for library construction (Ion Torrent technologies). Sequenced data were analysed by using appropriate bioinformatic techniques; alignment and taxonomic representation was done using Mothur program. Sequences of most abundant genus were further aligned to E. coli 16S rRNA gene reference sequence using MEGA7 in order to identify the hypervariable region of the segment of interest. Our results showed that different hypervariable regions had different discriminatory power depending on the groups of microbes, as well as the nature of samples. On the basis of our results, we suggest that wider range of primers used can provide more accurate recapitulation of microbial communities in archaeological samples. Acknowledgements. This work was supported by the ERAF grant Nr. 1.1.1.1/16/A/101.

Keywords: 16S rRNA gene, ancient human microbiome, archaeology, bioinformatics, genomics, microbiome, molecular biology, next-generation sequencing

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Authors: Tiptunya Duangsri, Panwilai Chomchid, Natchanok Jansawang

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This research study was to investigate of education decisions must be made which a part of it should be passed on to future generations as obligatory for all members of a chemistry class for students who will prepare themselves for a special position. The descriptions of instructional design were provided and the recent criticisms are discussed. This research study to an outline of an integrative framework for the description of information and the instructional design model give structure to negotiate a semblance of conscious understanding. The aims of this study are to describe the instructional design model for comparisons between students’ genders of their effects on STEM educational learning achievement motives to their science attitudes and logical thinking abilities with a sample size of 18 students at the 11th grade level with the cluster random sampling technique in Mahawichanukul School were designed. The chemistry learning environment was administered with the STEM education method. To build up the 5-instrument lesson instructional plan issues were instructed innovations, the 30-item Logical Thinking Test (LTT) on 5 scales, namely; Inference, Recognition of Assumptions, Deduction, Interpretation and Evaluation scales was used. Students’ responses of their perceptions with the Test Of Chemistry-Related Attitude (TOCRA) were assessed of their attitude in science toward chemistry. The validity from Index Objective Congruence value (IOC) checked by five expert specialist educator in two chemistry classroom targets in STEM education, the E1/E2 process were equaled evidence of 84.05/81.42 which results based on criteria are higher than of 80/80 standard level with the IOC from the expert educators. Comparisons between students’ learning achievement motives with STEM educational model on stoichiometry issue in chemistry classes with different genders were differentiated at evidence level of .05, significantly. Associations between students’ learning achievement motives on their posttest outcomes and logical thinking abilities, the predictive efficiency (R2) values indicate that 69% and 70% of the variances in different male and female student groups of their logical thinking abilities. The predictive efficiency (R2) values indicate that 73%; and 74% of the variances in different male and female student groups of their science attitudes toward chemistry were associated. Statistically significant on students’ perceptions of their chemistry learning classroom environment and their science attitude toward chemistry when using the MCI and TOCRA, the predictive efficiency (R2) values indicated that 72% and 74% of the variances in different male and female student groups of their chemistry classroom climate, consequently. Suggestions that supporting chemistry or science teachers from science, technology, engineering and mathematics (STEM) in addressing complex teaching and learning issues related instructional design to develop, teach, and assess traditional are important strategies with a focus on STEM education instructional method.

Keywords: development, the instructional design model, students learning achievement motives, science attitudes with STEM educational model, stoichiometry issue, chemistry classes, genders

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Authors: Mohammad Faheem, M. Tabish Rehman, Mohd Danishuddin, Asad U. Khan

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The worldwide dissemination of CTX-M type β-lactamases is a threat to human health. Previously, we have reported the spread of blaCTX-M-15 gene in different clinical strains of Enterobacteriaceae from the hospital settings of Aligarh in north India. In view of the varying resistance pattern against cephalosporins and other β-lactam antibiotics, we intended to understand the correlation between MICs and catalytic activity of CTX-M-15. In this study, steady-state kinetic parameters and MICs were determined on E. coli DH5α transformed with blaCTX-M-15 gene that was cloned from Enterobacter cloacae (EC-15) strain of clinical background. The effect of conventional β-lactamase inhibitors (clavulanic acid, sulbactam and tazobactam) on CTX-M-15 was also studied. We have found that tazobactam is the best among these inhibitors against CTX-M-15. The inhibition characteristic of tazobactam is defined by its very low IC50 value (6 nM), high affinity (Ki = 0.017 µM) and better acylation efficiency (k+2/K9 = 0.44 µM-1s-1). It forms an acyl-enzyme covalent complex, which is quite stable (k+3 = 0.0057 s-1). Since increasing resistance has been reported against conventional b-lactam antibiotic-inhibitor combinations, we aspire to design a non-b-lactam core containing b-lactamase inhibitor. For this, we screened ZINC database and performed molecular docking to identify a potential non-β-lactam based inhibitor (ZINC03787097). The MICs of cephalosporin antibiotics in combination with this inhibitor gave promising results. Steady-state kinetics and molecular docking studies showed that ZINC03787097 is a reversible inhibitor which binds non-covalently to the active site of the enzyme through hydrogen bonds and hydrophobic interactions. Though, it’s IC50 (180 nM) is much higher than tazobactam, it has good affinity for CTX-M-15 (Ki = 0.388 µM). This study concludes that ZINC03787097 compound can be used as seed molecule to design more efficient non-b-lactam containing b-lactamase inhibitor that could evade pre-existing bacterial resistance mechanisms.

Keywords: ESBL, non-b-lactam-b-lactamase inhibitor, bioinformatics, biomedicine

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Authors: Lakshmi N. Reddi, Akanksha Varma Sagi

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Studies on biomimetics are largely developed, deriving inspiration from natural processes in our objective world to develop novel technologies. Recent studies are diverse in nature, making their categorization quite challenging. Based on an exhaustive survey, we developed categorizations based on either the essential elements of nature - air, water, land, fire, and space, or on form/shape, functionality, and process. Such diverse studies as aircraft wings inspired by bird wings, a self-cleaning coating inspired by a lotus petal, wetsuits inspired by beaver fur, and search algorithms inspired by arboreal ant path networks lend themselves to these categorizations. Our categorizations of biomimetic studies allowed us to define a different dimension of biomimetics. This new dimension is not restricted to inspiration from the objective world. It is based on the premise that the biological processes observed in the objective world find their reflections in our human bodies in a variety of ways. For example, the lungs provide the most efficient example for liquid-gas phase exchange, the heart exemplifies a very efficient pumping and circulatory system, and the kidneys epitomize the most effective cleaning system. The main focus of this paper is to bring out the magnificence of the cerebro-spinal system (CSS) insofar as it relates to our current computer architecture. In particular, the paper uses four key measures to analyze the differences between CSS and human- engineered computational systems. These are adaptability, sustainability, energy efficiency, and resilience. We found that the cerebrospinal system reveals some important challenges in the development and evolution of our current computer architectures. In particular, the myriad ways in which the CSS is integrated with other systems/processes (circulatory, respiration, etc) offer useful insights on how the human-engineered computational systems could be made more sustainable, energy-efficient, resilient, and adaptable. In our paper, we highlight the energy consumption differences between CSS and our current computational designs. Apart from the obvious differences in materials used between the two, the systemic nature of how CSS functions provides clues to enhance life-cycles of our current computational systems. The rapid formation and changes in the physiology of dendritic spines and their synaptic plasticity causing memory changes (ex., long-term potentiation and long-term depression) allowed us to formulate differences in the adaptability and resilience of CSS. In addition, the CSS is sustained by integrative functions of various organs, and its robustness comes from its interdependence with the circulatory system. The paper documents and analyzes quantifiable differences between the two in terms of the four measures. Our analyses point out the possibilities in the development of computational systems that are more adaptable, sustainable, energy efficient, and resilient. It concludes with the potential approaches for technological advancement through creation of more interconnected and interdependent systems to replicate the effective operation of cerebro-spinal system.

Keywords: cerebrospinal system, computer architecture, adaptability, sustainability, resilience, energy efficiency

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Authors: Asif Mahmood, Yousef Alzeghayer

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The size effects of a precursor Y2BaCuO5 (Y211) powder on the microstructure and critical current density (Jc) of liquid infiltration growth (LIG)-processed YBa2Cu3O7-y (Y123) bulk superconductors were investigated in terms of milling time (t). YBCO bulk samples having high Jc values have been selected for the flywheel energy storage system. Y211 powders were attrition-milled for 0-10 h in 2 h increments at a fixed rotation speed of 400 RPM. Y211 pre-forms were made by pelletizing the milled Y211 powders followed by subsequent sintering, after which an LIG process with top seeding was applied to the Y211/Ba3Cu5O8 (Y035) pre-forms. Spherical pores were observed in all LIG-processed Y123 samples, and the pore density gradually decreased as t increased from 0 h to 8 h. In addition to the reduced pore density, the Y211 particle size in the final Y123 products also decreased with increasing t. As t increased further to 10 h, unexpected Y211 coarsening and large pore evolutions were observed. The magnetic susceptibility-temperature curves showed that the onset superconducting transition temperature (Tc, onset) of all samples was the same (91.5 K), but the transition width became greater as t increased. The Jc of the Y123 bulk superconductors fabricated in this study was observed to correlate well with t of the Y211 precursor powder. The maximum Jc of 1.0×105 A cm-2 (at 77 K, 0 T) was achieved at t = 8 h, which is attributed to the reduction in pore density and Y211 particle size. The prolonged milling time of t = 10 h decreased the Jc of the LIG-processed Y123 superconductor owing to the evolution of large pores and exaggerated Y211 growth. YBCO bulk samples having high Jc (samples prepared using 8 h milled powders) have been used for the energy storage system in flywheel energy storage system.

Keywords: critical current, bulk superconductor, liquid infiltration, bioinformatics

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Authors: Noam Markovitz

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People with physical disabilities constitute a very large and simultaneously a diverse group of general population, as the term physical disabilities is extensive and covers a wide range of disabilities. Therefore, individuals with physical disabilities are often faced with a new, threatening and stressful reality leading possibly to a multi-crisis in their lives due to the great changes they experience in somatic, socio-economic, occupational and psychological level. The current study seeks to advance understanding of the complex adaptation to physical disabilities by expanding the dynamic-adaptational model of the pursuit of happiness in a hostile world with a new conception of physical self-integrity. Physical self-integrity incorporates an objective dimension, namely physical self-functioning (PSF), and a subjective dimension, namely physical self-concept (PSC). Both of these dimensions constitute an experience of wholeness in the individual’s identification with her or his physical body. The model guiding this work is dialectical in nature and depicts two systems in the individual’s sense of happiness: subjective well-being (SWB) and meaning in life (MIL). Both systems serve as self-adaptive agents that moderate the complementary system of the hostile-world scenario (HWS), which integrates one’s perceived threats to one’s integrity. Thus, in situations of increased HWS, the moderation may take a form of joint activity in which SWB and MIL are amplified or a form of compensation in which one system produces a stronger effect while the other system produces a weaker effect. The current study investigated PSC in relations to SWB and MIL through pleasantness and meanings that are physically or metaphorically grounded in one’s body. In parallel, PSC also relates to HWS by activating representations of inappropriateness, deformation and vulnerability. In view of possibly dialectical positions of opposing and complementary forces within the current model, the current field study that aims to explore PSC as appearing in an independent, cross-sectional, design addressing the model’s variables in a focal group of people with physical disabilities. This study delineated the participation of the PSC in the adaptational functions of SWB and MIL vis-à-vis HWS-related life adversities. The findings showed that PSC could fully complement the main variables of the pursuit of happiness in a hostile world model. The assumed dialectics in the form of a stronger relationship between SWB and MIL in the face of physical disabilities was not supported. However, it was found that when HWS increased, PSC and MIL were strongly linked, whereas PSC and SWB were weakly linked. This highlights the compensatory role of MIL. From a conceptual viewpoint, the current investigation may clarify the role of PSC as an adaptational agent of the individual’s positive health in complementary senses of bodily wholeness. Methodologically, the advantage of the current investigation is the application of an integrative, model-based approach within a specially focused design with a particular relevance to PSC. Moreover, from an applicative viewpoint, the current investigation may suggest how an innovative model may be translated to therapeutic interventions used by clinicians, counselors and practitioners in improving wellness and psychological well-being, particularly among people with physical disabilities.

Keywords: older adults, physical disabilities, physical self-concept, pursuit of happiness in a hostile-world

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Authors: Fatemeh Zeinali Sehrig

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Background: miRNAs play an important role in the post-transcriptional regulation of genes, including genes involved in DNA methylation (DNMTs), and are also important regulators of oncogenic pathways. The study of microRNAs and DNMTs in breast cancer allows the development of targeted treatments and early detection of this cancer. Methods and Materials: Clinical Patients and Samples: Institutional guidelines, including ethical approval and informed consent, were followed by the Ethics Committee (Ethics code: IR.IAU.TABRIZ.REC.1401.063) of Tabriz Azad University, Tabriz, Iran. In this study, tissues of 100 patients with breast cancer and tissues of 100 healthy women were collected from Noor Nejat Hospital in Tabriz. The basic characteristics of the patients with breast cancer included: 1)Tumor grade(Grade 3 = 5%, Grade 2 = 87.5%, Grade 1 = 7.5%), 2)Lymph node(Yes = 87.5%, No = 12.5%), 3)Family cancer history(Yes = 47.5%, No = 41.3%, Unknown = 11.2%), 4) Abortion history(Yes = 36.2%).In silico methods (data gathering, process, and build networks): Gene Expression Omnibus (GEO), a high-throughput genomic database, was queried for miRNAs expression profiles in breast cancer. For Experimental protocol Tissue Processing, Total RNA isolation, complementary DNA(cDNA) synthesis, and quantitative real time PCR (QRT-PCR) analysis were performed. Results: In the present study, we found significant (p.value<0.05) changes in the expression level of miRNAs and DNMTs in patients with breast cancer. In bioinformatics studies, the GEO microarray data set, similar to qPCR results, showed a decreased expression of miRNAs and increased expression of DNMTs in breast cancer. Conclusion: According to the results of the present study, which showed a decrease in the expression of miRNAs and DNMTs in breast cancer, it can be said that these genes can be used as important diagnostic and therapeutic biomarkers in breast cancer.

Keywords: gene expression omnibus, microarray dataset, breast cancer, miRNA, DNMT (DNA methyltransferases)

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Authors: D. Anderlini, G. Wallis

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Background: The number of people experiencing stroke is steadily increasing due to changes in diet and lifestyle, to longer life expectancy resulting in older population, to higher survival rates as a consequence of improvements during the acute phase. This study considers what risk factors might contribute to delayed entry to hospital for treatment. Methods: We analyzed data from 2472 patients admitted to the Stroke Unit of the Royal Brisbane Women's Hospital, Australia, between 2002 to 2011. Results: Previous studies have reported that factors which can contribute to delay include the patient’s age, the time of day, physical location, visit the GP instead of going to the emergency, means of transport, severity of symptoms and type of stroke. Contrary to findings of other studies, we found a strong correlation between side of lesion and delay in admission: patients with right hemisphere lesions had an average delay of 3.78 days, while patients with left hemisphere lesions had an average delay of 1.49 days. Damage to the right hemisphere generally ends in motor impairment in the non-dominant hand and no speech impediment. In contrast, left hemisphere lesions can result in deficit to; dominant hand function and aphasia which will be noticed even if their impact on performance is relatively minor. A finding which goes against many previous studies, is the fact that women get to the hospital much sooner than men, showing an average delay of 0.92 days in women vs. 3.36 days in men. Conclusion: Acute surgical-pharmacological therapies are most effective if applied immediately after stroke. Hence delays to admission can be crucial to the degree of recovery. The tendency of patients to overlook symptoms of right hemisphere lesion should be the target of information campaigns both for the general public and GPs. Why do men go to hospital so late? We don't know yet! Nevertheless an awareness plan specifically direct to male population should be on the agenda of Health Departments.

Keywords: gender, admission delay, stroke location, bioinformatics, biomedicine

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Authors: Mouna Baassi, Mohamed Moussaoui, Sanchaita Rajkhowa, Hatim Soufi, Said Belaaouad

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The objective of this paper is to address the challenging task of targeting Human Immunodeficiency Virus type 1 Reverse Transcriptase (HIV-1 RT) in the treatment of AIDS. Reverse Transcriptase inhibitors (RTIs) have limitations due to the development of Reverse Transcriptase mutations that lead to treatment resistance. In this study, a combination of statistical analysis and bioinformatics tools was adopted to develop a mathematical model that relates the structure of compounds to their inhibitory activities against HIV-1 Reverse Transcriptase. Our approach was based on a series of compounds recognized for their HIV-1 RT enzymatic inhibitory activities. These compounds were designed via software, with their descriptors computed using multiple tools. The most statistically promising model was chosen, and its domain of application was ascertained. Furthermore, compounds exhibiting comparable biological activity to existing drugs were identified as potential inhibitors of HIV-1 RT. The compounds underwent evaluation based on their chemical absorption, distribution, metabolism, excretion, toxicity properties, and adherence to Lipinski's rule. Molecular docking techniques were employed to examine the interaction between the Reverse Transcriptase (Wild Type and Mutant Type) and the ligands, including a known drug available in the market. Molecular dynamics simulations were also conducted to assess the stability of the RT-ligand complexes. Our results reveal some of the new compounds as promising candidates for effectively inhibiting HIV-1 Reverse Transcriptase, matching the potency of the established drug. This necessitates further experimental validation. This study, beyond its immediate results, provides a methodological foundation for future endeavors aiming to discover and design new inhibitors targeting HIV-1 Reverse Transcriptase.

Keywords: QSAR, ADMET properties, molecular docking, molecular dynamics simulation, reverse transcriptase inhibitors, HIV type 1

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Authors: Liang-Jen Wang, Sung-Chou Li, Yuan-Ming Yeh, Sheng-Yu Lee, Ho-Chang Kuo, Chia-Yu Yang

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Background: Dysbiosis in the gut microbial community might be involved in the pathophysiology of attention deficit/hyperactivity disorder (ADHD). The fungal component of the gut microbiome, namely the mycobiota, is a hyperdiverse group of multicellular eukaryotes that can influence host intestinal permeability. This study therefore aimed to investigate the impact of fungal mycobiome dysbiosis and intestinal permeability on ADHD. Methods: Faecal samples were collected from 35 children with ADHD and from 35 healthy controls. Total DNA was extracted from the faecal samples, and the internal transcribed spacer (ITS) regions were sequenced using high-throughput next-generation sequencing (NGS). The fungal taxonomic classification was analysed using bioinformatics tools, and the differentially expressed fungal species between the ADHD and healthy control groups were identified. An in vitro permeability assay (Caco-2 cell layer) was used to evaluate the biological effects of fungal dysbiosis on intestinal epithelial barrier function. Results: The β-diversity (the species diversity between two communities), but not α-diversity (the species diversity within a community), reflected the differences in fungal community composition between ADHD and control groups. At the phylum level, the ADHD group displayed a significantly higher abundance of Ascomycota and significantly lower abundance of Basidiomycota than the healthy control group. At the genus level, the abundance of Candida (especially Candida albicans) was significantly increased in ADHD patients compared to the healthy controls. In addition, the in vitro cell assay revealed that C. albicans secretions significantly enhanced the permeability of Caco-2 cells. Conclusions: The current study is the first to explore altered gut mycobiome dysbiosis using the NGS platform in ADHD. The findings from this study indicated that dysbiosis of the fungal mycobiome and intestinal permeability might be associated with susceptibility to ADHD.

Keywords: ADHD, fungus, gut–brain axis, biomarker, child psychiatry

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Authors: Saqib Aziz, Brad Alexander, Christoph Gengnagel, Stefan Weinzierl

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This paper explores a generative design, simulation, and optimization workflow for the integration of acoustical diffuser and/or absorber geometry with embedded coupled Helmholtz-resonators for full-scale 3D printed building components. Large-scale additive manufacturing in conjunction with algorithmic CAD design tools enables a vast amount of control when creating geometry. This is advantageous regarding the increasing demands of comfort standards for indoor spaces and the use of more resourceful and sustainable construction methods and materials. The presented methodology highlights these new technological advancements and offers a multimodal and integrative design solution with the potential for an immediate application in the AEC-Industry. In principle, the methodology can be applied to a wide range of structural elements that can be manufactured by additive manufacturing processes. The current paper focuses on a case study of an application for a biaxial load-bearing beam grillage made of reinforced concrete, which allows for a variety of applications through the combination of additive prefabricated semi-finished parts and in-situ concrete supplementation. The semi-prefabricated parts or formwork bodies form the basic framework of the supporting structure and at the same time have acoustic absorption and diffusion properties that are precisely acoustically programmed for the space underneath the structure. To this end, a hybrid validation strategy is being explored using a digital and cross-platform simulation environment, verified with physical prototyping. The iterative workflow starts with the generation of a parametric design model for the acoustical geometry using the algorithmic visual scripting editor Grasshopper3D inside the building information modeling (BIM) software Revit. Various geometric attributes (i.e., bottleneck and cavity dimensions) of the resonator are parameterized and fed to a numerical optimization algorithm which can modify the geometry with the goal of increasing absorption at resonance and increasing the bandwidth of the effective absorption range. Using Rhino.Inside and LiveLink for Revit, the generative model was imported directly into the Multiphysics simulation environment COMSOL. The geometry was further modified and prepared for simulation in a semi-automated process. The incident and scattered pressure fields were simulated from which the surface normal absorption coefficients were calculated. This reciprocal process was repeated to further optimize the geometric parameters. Subsequently the numerical models were compared to a set of 3D concrete printed physical twin models, which were tested in a .25 m x .25 m impedance tube. The empirical results served to improve the starting parameter settings of the initial numerical model. The geometry resulting from the numerical optimization was finally returned to grasshopper for further implementation in an interdisciplinary study.

Keywords: acoustical design, additive manufacturing, computational design, multimodal optimization

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Authors: Faride Hashemiannejad, Shima Oloomi

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Imagination is one of the important elements of creative thinking which as a skill needs attention by the educational system. Although most students learn reading, writing, and arithmetic skills well, they lack high level thinking skills like creative thinking. Therefore, in the information age and in the beginning of entry to knowledge-based society, the educational system needs to think over its goals and mission, and concentrate on creativity-based curriculum. From among curriculum elements-goals, content, method and evaluation “method” is a major domain whose reform can pave the way for fostering imagination and creativity. The purpose of this study was examining the relationship between creativity development and curriculum. Research questions were: (1) is there a relationship between the cognitive-emotional structure of the classroom and creativity development? (2) Is there a relationship between the environmental-social structure of the classroom and creativity development? (3) Is there a relationship between the thinking structure of the classroom and creativity development? (4) Is there a relationship between the physical structure of the classroom and creativity development? (5) Is there a relationship between the instructional structure of the classroom and creativity development? Method: This research is a applied research and the research method is Correlational research. Participants: The total number of participants in this study included 894 students from High school through 11th grade from seven schools of seven zones in Mashad city. Sampling Plan: Sampling was selected based on Random Multi State. Measurement: The dependent measure in this study was: (a) the Test of Creative Thinking, (b) The researcher-made questionnaire includes five fragments, cognitive, emotional structure, environmental social structure, thinking structure, physical structure, and instructional structure. The Results Show: There was significant relationship between the cognitive-emotional structure of the classroom and student’s creativity development (sig=0.139). There was significant relationship between the environmental-social structure of the classroom and student’s creativity development (sig=0.006). There was significant relationship between the thinking structure of the classroom and student’s creativity development (sig=0.004). There was not significant relationship between the physical structure of the classroom and student’s creativity development (sig=0.215). There was significant relationship between the instructional structure of the classroom and student’s creativity development (sig=0.003). These findings denote if students feel secure, calm and confident, they can experience creative learning. Also the quality of coping with students’ questions, imaginations and risks can influence on their creativity development.

Keywords: imagination, creativity, curriculum, bioinformatics, biomedicine

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Authors: Zakieh Rostamzadeh, Zahra Shirmohammadi

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Human cytomegalovirus is a species of the cytomegalovirus family of viruses, which in turn is a member of the viral family known as herpesviridae or herpesviruses. Although they may be found throughout the body, HCMV infections are frequently associated with the salivary glands. HCMV infection is typically unnoticed in healthy people, but can be life-threatening for the immunocompromised such as HIV-infected persons, organ transplant recipients, or newborn infants. After infection, HCMV has an ability to remain latent within the body over long periods. Cytomegalovirus (CMV) causes infection in immunocompromised, hemophilia patients and those who received blood transfusion frequently. This study aimed at determining the prevalence of cytomegalovirus (CMV) antibodies in hemophilia patients. Materials and Methods: A retrospective observational study was carried out in Urmia, North West of Iran. The study population comprised a sample of 50 hemophilic patients born after 1985 and have received blood factors in West Azerbaijan. The exclusion criteria include: drug abusing, high risk sexual contacts, vertical transmission of mother to fetus and suspicious needling. All samples were evaluated with the method of ELISA, with a certain kind of kit and by a certain laboratory. Results: Fifty hemophiliacs from 250 patients registered with Urmia Hemophilia Society were enrolled in the study including 43 (86%) male, and 7 (14%) female. The mean age of patients was 10.3 years, range 3 to 25 years. None of patients had risk factors mentioned above. Among our studied population, 34(68%) had hemophilia A, 1 (2%) hemophilia B, 8 (16%) VWF, 3(6%) factor VII deficiency, 1 (2%) factor V deficiency, 1 (2%) factor X deficiency, 1 (2%). Sera of 50 Hemodialysis patients were investigated for CMV-specific immunoglobulin G (IgG) and IgM. % 91.89 patients were anti-CMV IgG positive and %40.54 was seropositive for anti-CMV IgM. 37.8% patient had serological evidence of reactivation and 2.7% of patients had the primary infection. Discussion: There was no relationship between the antibody titer and: drug abusing, high risk sexual contacts, vertical transmission of mother to fetus and suspicious needling.

Keywords: bioinformatics, biomedicine, cytomegalovirus, immunocompromise

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Authors: Felix Lankester, Alicia Davis, Safari Kinung'hi, Catherine Bunga, Shayo Alkara, Imam Mzimbiri, Jonathan Yoder, Sarah Cleaveland, Guy H. Palmer

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Achieving the London Declaration goal of a 90% reduction in neglected tropical diseases (NTDs) by 2030 requires cost-effective strategies that attain high and comprehensive coverage. The first objective of this trial was to assess the impact on cost and coverage of employing a novel integrative One Health approach linking two NTD control programs: mass drug administration (MDA) for soil-transmitted helminths in humans (STH) and mass dog rabies vaccination (MDRV). The second objective was to compare the coverage achieved by the MDA, a community-wide deworming intervention, with that of the existing national primary school-based deworming program (NSDP), with particular focus on the proportion of primary school-age children reached and their school enrolment status. Our approach was unconventional because, in line with the One Health approach to disease control, it coupled the responsibilities and resources of the Ministries responsible for human and animal health into one program with the shared aim of preventing multiple NTDs. The trial was carried out in hard-to-reach pastoral communities comprising 24 villages of the Ngorongoro District, Tanzania, randomly allocated to either Arm A (MDA and MDRV), Arm B (MDA only) or Arm C (MDRV only). Objective one: The percentage of people in each target village that received treatment through MDA in Arms A and B was 63% and 65%, respectively (χ2 = 1, p = 0.32). The percentage of dogs vaccinated in Arm A and C was 70% and 81%, respectively (χ2 =9, p = 0.003). It took 33% less time for a single person and a dog to attend the integrated delivery than two separate events. Cost per dose (including delivery) was lower under the integrated strategy, with delivery of deworming and rabies vaccination reduced by $0.13 (54%) and $0.85 (19%) per dose, respectively. Despite a slight reduction in the proportion of village dogs vaccinated in the integrated event, both the integrated and non-integrated strategies achieved the target threshold of 70% required to eliminate rabies. Objective two: The percentages of primary school age children enrolled in school that was reached by this trial (73%) and the existing NSDP (80%) were not significantly different (F = 0.9, p = 0.36). However, of the primary school age children treated in this trial, 46% were not enrolled in school. Furthermore, 86% of the people treated would have been outside the reach of the NSDP because they were not primary school age or were primary school age children not enrolled in school. The comparable reach, the substantial reductions in cost per dose delivered and the decrease in participants’ time support this integrated One Health approach to control multiple NTDs. Further, the recorded level of non-enrolment at primary school suggests that, in remote areas, school-based delivery strategies could miss a large fraction of school-age children and that programs that focus delivery solely at the level of the primary school will miss a substantial proportion of both primary school age children as well as other individuals from the community. We have shown that these populations can be effectively reached through extramural programs.

Keywords: canine mediated human rabies, integrated health interventions, mass drug administration, neglected tropical disease, One Health, soil-transmitted helminths

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Authors: Frida Carrillo Morales, Maria Maricela Carrasco Yépez, Saúl Rojas Hernández

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Naegleria fowleri is the causative agent of primary amebic meningoencephalitis, this disease is acute and fulminant that affects humans. It has been reported that despite the existence of therapeutic options against this disease, its mortality rate is 97%. Therefore, the need arises to have vaccines that confer protection against this disease and, in addition to developing adjuvants to enhance the immune response. In this regard, in our work group, we obtained a peptide designed from the membrane protein MP2CL5 of Naegleria fowleri called Smp145 that was shown to be immunogenic; however, it would be of great importance to enhance its immunological response, being able to co-administer it with a non-toxic adjuvant. Therefore, the objective of this work was to carry out the bioinformatic design of a peptide of the Naegleria fowleri membrane protein MP2CL5 conjugated with a non-toxic modified adjuvant from the native A1 structure of Cholera Toxin. For which different bioinformatics tools were used to obtain a model with a modification in amino acid 61 of the A1 subunit of the CT (CTA1), to which the Smp145 peptide was added and both molecules were joined with a 13-glycine linker. As for the results obtained, the modification in CTA1 bound to the peptide produces a reduction in the toxicity of the molecule in in silico experiments, likewise, the prediction in the binding of Smp145 to the receptor of B cells suggests that the molecule is directed in specifically to the BCR receptor, decreasing its native enzymatic activity. The stereochemical evaluation showed that the generated model has a high number of adequately predicted residues. In the ERRAT test, the confidence with which it is possible to reject regions that exceed the error values was evaluated, in the generated model, a high score was obtained, which determines that the model has a good structural resolution. Therefore, the design of the conjugated peptide in this work will allow us to proceed with its chemical synthesis and subsequently be able to use it in the mouse meningitis protection model caused by N. fowleri.

Keywords: immunology, vaccines, pathogens, infectious disease

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Authors: Iyd Eqqab Maree, Moouyad Ibrahim Abbood

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The purpose behind this study is to predict damping effect for steel cantilever beam by using two methods of passive viscoelastic constrained layer damping. First method is Matlab Program, this method depend on the Ross, Kerwin and Unger (RKU) model for passive viscoelastic damping. Second method is experimental lab (frequency domain method), in this method used the half-power bandwidth method and can be used to determine the system loss factors for damped steel cantilever beam. The RKU method has been applied to a cantilever beam because beam is a major part of a structure and this prediction may further leads to utilize for different kinds of structural application according to design requirements in many industries. In this method of damping a simple cantilever beam is treated by making sandwich structure to make the beam damp, and this is usually done by using viscoelastic material as a core to ensure the damping effect. The use of viscoelastic layers constrained between elastic layers is known to be effective for damping of flexural vibrations of structures over a wide range of frequencies. The energy dissipated in these arrangements is due to shear deformation in the viscoelastic layers, which occurs due to flexural vibration of the structures. The theory of dynamic stability of elastic systems deals with the study of vibrations induced by pulsating loads that are parametric with respect to certain forms of deformation. There is a very good agreement of the experimental results with the theoretical findings. The main ideas of this thesis are to find the transition region for damped steel cantilever beam (4mm and 8mm thickness) from experimental lab and theoretical prediction (Matlab R2011a). Experimentally and theoretically proved that the transition region for two specimens occurs at modal frequency between mode 1 and mode 2, which give the best damping, maximum loss factor and maximum damping ratio, thus this type of viscoelastic material core (3M468) is very appropriate to use in automotive industry and in any mechanical application has modal frequency eventuate between mode 1 and mode 2.

Keywords: 3M-468 material core, loss factor and frequency, domain method, bioinformatics, biomedicine, MATLAB

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Authors: Misty Attwood, Helgi Schioth

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Transmembrane proteins are important components in many essential cell processes such as signal transduction, cell-cell signalling, transport of solutes, structural adhesion activities, and protein trafficking. Due to their involvement in diverse critical activities, transmembrane proteins are implicated in different disease pathways and hence are the focus of intense interest in understanding functional activities, their pathogenesis in disease, and their potential as pharmaceutical targets. Further, as the structure and function of proteins are correlated, investigating a group of proteins with the same tertiary structure, i.e., the same number of transmembrane regions, may give understanding about their functional roles and potential as therapeutic targets. In this in silico bioinformatics analysis, we identify and comprehensively characterize the previously unstudied group of proteins with five transmembrane-spanning regions (5TM). We classify nearly 60 5TM proteins in which 31 are members of ten families that contain two or more family members and all members are predicted to contain the 5TM architecture. Furthermore, nine singlet proteins that contain the 5TM architecture without paralogues detected in humans were also identifying, indicating the evolution of single unique proteins with the 5TM structure. Interestingly, more than half of these proteins function in localization activities through movement or tethering of cell components and more than one-third are involved in transport activities, particularly in the mitochondria. Surprisingly, no receptor activity was identified within this family in sharp contrast with other TM families. Three major 5TM families were identified and include the Tweety family, which are pore-forming subunits of the swelling-dependent volume regulated anion channel in astrocytes; the sidoreflexin family that acts as mitochondrial amino acid transporters; and the Yip1 domain family engaged in vesicle budding and intra-Golgi transport. About 30% of the proteins have enhanced expression in the brain, liver, or testis. Importantly, 60% of these proteins are identified as cancer prognostic markers, where they are associated with clinical outcomes of various tumour types, indicating further investigation into the function and expression of these proteins is important. This study provides the first comprehensive analysis of proteins with 5TM regions and provides details of the unique characteristics and application in pharmaceutical development.

Keywords: 5TM, cancer prognostic marker, drug targets, transmembrane protein

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Authors: Anil Kumar, Diwakar Aggarwal, M. Sudhakara Reddy

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The wood of Eucalyptus, Populus and bamboos are some important species used as raw material for the manufacture of pulp. However, higher levels of lignin pose a problem during Kraft pulping and yield of pulp is also lower. In order to increase the yield of pulp per unit wood and reduce the use of chemicals during kraft pulping it is important to reduce the lignin content and/or increase cellulose content in wood. Cellulose biosynthesis in wood takes place by the coordinated action of many enzymes. The two important enzymes are KORRIGAN and SUCROSE SYNTHASE. KORRIGAN (Endo-1,4--glucanase) is implicated in the process of editing growing cellulose chains and improvement of the crystallinity of produced cellulose, whereas SUCROSE SYNTHASE is involved in providing substrate (UDP-glucose) for growing cellulose chains. The present study was aimed at the cloning, characterization and overexpression of these genes in Eucalyptus and Populus. An efficient shoot organogenesis protocol from leaf explants taken from micro shoots of the species has been developed. Agrobacterium mediated genetic transformation using Agrobacterium tumefaciens strain EHA105 and LBA4404 harboring binary vector pBI121 was achieved. Both the genes were cloned from cDNA library of Populus deltoides. These were subsequently characterized using various bioinformatics tools. The cloned genes were then inserted into pBI121 under the CaMV35S promotors replacing GUS gene. The constructs were then mobilized into above strains of Agrobacterium and used for the transformation work. Subsequently, genetic transformation of these clones with target genes following already developed protocol is in progress. Four transgenic lines of Eucalyptus tereticornis overexpressing Korrigan gene under the strong constitutive promoters CaMV35S have been developed, which are being further evaluated. Work on development of more transgenic lines overexpressing these genes in Populus and Eucalyptus is also in progress. This presentation will focus on important developments in this direction.

Keywords: Eucalyptus tereticornis, genetic transformation, Kraft pulping Populus deltoides

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Authors: Sonika Raj, Amarjeet Singh, Vijay Lakshmi Sharma

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Introduction: In 21st century, due to revolution in Information and Communication Technologies (ICTs), there has been phenomenal development in quality and quantity of knowledge in the field of medical science. So, the access to relevant information to physicians is critical to the delivery of effective healthcare services to patients. The study was conducted to assess the information needs and attitudes of the medical professionals; to determine the sources and channels of information used by them; to ascertain the current usage of ICTs and the barriers faced by them in utilization of ICTs in health information access. Methodology: This descriptive cross-sectional study was carried in 2015 on hundred medical professionals working in public and private sectors of Chandigarh. The study used both quantitative and qualitative method for data collection. A semi structured questionnaire and interview schedule was used to collect data on information seeking needs, access to ICTs and barriers to healthcare information access. Five Data analysis was done using SPSS-16 and qualitative data was analyzed using thematic approach. Results: The most preferred sources to access healthcare information were internet (85%), trainings (61%) and communication with colleagues (57%). They wanted information on new drug therapy and latest developments in respective fields. All had access to computer with but almost half assessed their computer knowledge as average and only 3% had received training regarding usage. Educational status (p=0.004), place of work (p=0.004), number of years in job (p=0.004) and sector of job (p=0.04) of doctors were found to be significantly associated with their active search for information. The major themes that emerged from in-views were need; types and sources of healthcare information; exchange of information among different levels of healthcare providers; usage of ICTs to obtain and share information; barriers to access of healthcare information and quality of health information materials and involvement in their development process Conclusion and Recommendations: The medical professionals need information in their in their due course of work. However, information needs of medical professionals were not being adequately met. There should be training of professional regarding internet skills and the course on bioinformatics should be incorporated in the curricula of medical students. The policy framework must be formulated that will encourage and promote the use of ICTs as tools for health information access and dissemination.

Keywords: health information, ICTs, medical professionals, qualitative

Procedia PDF Downloads 337