Search results for: integrative bioinformatics

Authors: Hediyeh Talebi, Shokoofeh Ghiam, Changiz Eslahchi

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Traditionally, Alzheimer’s disease research has focused on genes with significant fold changes, potentially neglecting subtle but biologically important alterations. Our study introduces an integrative approach that highlights genes crucial to underlying biological processes, regardless of their fold change magnitude. Alzheimer's Single-cell RNA-seq data related to the peripheral blood mononuclear cells (PBMC) was extracted from the Gene Expression Omnibus (GEO). After quality control, normalization, scaling, batch effect correction, and clustering, differentially expressed genes (DEGs) were identified with adjusted p-values less than 0.05. These DEGs were categorized based on cell-type, resulting in four datasets, each corresponding to a distinct cell type. To distinguish between cells from healthy individuals and those with Alzheimer's, an adversarial autoencoder with a classifier was employed. This allowed for the separation of healthy and diseased samples. To identify the most influential genes in this classification, the weight matrices in the network, which includes the encoder and classifier components, were multiplied, and focused on the top 20 genes. The analysis revealed that while some of these genes exhibit a high fold change, others do not. These genes, which may be overlooked by previous methods due to their low fold change, were shown to be significant in our study. The findings highlight the critical role of genes with subtle alterations in diagnosing Alzheimer's disease, a facet frequently overlooked by conventional methods. These genes demonstrate remarkable discriminatory power, underscoring the need to integrate biological relevance with statistical measures in gene prioritization. This integrative approach enhances our understanding of the molecular mechanisms in Alzheimer’s disease and provides a promising direction for identifying potential therapeutic targets.

Keywords: alzheimer's disease, single-cell RNA-seq, neural networks, blood biomarkers

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Authors: Ali M. Al-Shaery

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The purpose of this paper is to address the functions of sustainability dimensions in city information modelling and to present the required sustainability criteria that support establishing a sustainable planning framework for enhancing existing cities and developing future smart cities. The paper is divided into two sections. The first section is based on the examination of a wide and extensive array of cross-disciplinary literature in the last decade and a half to conceptualize the terms ‘sustainable’ and ‘smart city,' and map their associated criteria to city information modelling. The second section is based on analyzing two approaches relating to city information modelling, namely statistical and dynamic approaches, and their suitability in the development of cities’ action plans. The paper argues that the use of statistical approaches to embedding sustainability dimensions in city information modelling have limited value. Despite the popularity of such approaches in addressing other dimensions like utility and service management in development and action plans of the world cities, these approaches are unable to address the dynamics across various city sectors with regards to economic, environmental and social criteria. The paper suggests an integrative dynamic and cross-disciplinary planning approach to embedding sustainability dimensions in city information modelling frameworks. Such an approach will pave the way towards optimal planning and implementation of priority actions of projects and investments. The approach can be used to achieve three main goals: (1) better development and action plans for world cities (2) serve the development of an integrative dynamic and cross-disciplinary framework that incorporates economic, environmental and social sustainability criteria and (3) address areas that require further attention in the development of future sustainable and smart cities. The paper presents an innovative approach for city information modelling and a well-argued, balanced hierarchy of sustainability criteria that can contribute to an area of research which is still in its infancy in terms of development and management.

Keywords: information modelling, smart city, sustainable city, sustainability dimensions, sustainability criteria, city development planning

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Authors: Virginia Chambers, Kamryn York, Mark Marnich

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T.I.M.E. for STEM (Transforming Integrative Maker Education for STEM learning) focuses on improving the quality and effectiveness of STEM education for pre-service teachers through a focus on the integration of maker space pedagogy. This National Science Foundation-funded project primarily focuses on undergraduate pre-service teaching students majoring in elementary education. The study contributes to the knowledge about teaching and learning by developing, implementing, and assessing faculty development, interactive instruction, and STEM lesson plan development. This project offers a valuable opportunity to improve STEM thinking skills by formally integrating STEM concepts throughout the pre-service teacher curriculum using an interdisciplinary approach. T.I.M.E. for STEM utilizes a maker space laboratory at Point Park University in Pittsburgh, PA, USA. However, the project design is such that other institutions of higher education can replicate the program with or without a physical maker space lab as the project’s findings and “maker mindset” are employed. Utilizing qualitative research methodology, the project investigates the following research question: What do pre-service teachers (education students) and faculty members identify as areas of pedagogical growth in STEM learning and teaching in a makerspace environment? This research highlights the impact of makerspace pedagogy on improving STEM education learning outcomes through an interdisciplinary constructivist approach. The project is expected to have a multiplier effect as it impacts STEM disciplinary and higher education faculty, pre-service teachers, and teacher preparation programs at other universities that benefit from what is learned at Point Park University. Ultimately, the future elementary students of the well-prepared pre-service teachers steeped in maker pedagogy and STEM content will have the potential to develop higher-level thinking skills and improve their mathematics and scientific achievement, which are essential for the 21st century STEM workforce.

Keywords: maker education, STEM learning, teacher education, elementary education

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Authors: Abul B. M. M. K. Islam, Mandar Dave, Roderick V. Jensen, Ashok R. Amin

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A systems approach was applied to characterize differentially expressed transcripts, bioinformatics pathways, and proteins and prostaglandins (PGs) from lung fibroblasts procured from wild-type (WT), COX-1-/- and COX-2-/- mice to understand system level control mechanism. Bioinformatics analysis of COX-2 and COX-1 ablated cells induced COX-1 and COX-2 specific signature respectively, which significantly overlapped with an 'IL-1β induced inflammatory signature'. This defined novel cross-talk signals that orchestrated coordinated activation of pathways of sterile inflammation sensed by cellular stress. The overlapping signals showed significant over-representation of shared pathways for interferon y and immune responses, T cell functions, NOD, and toll-like receptor signaling. Gene Ontology Biological Process (GOBP) and pathway enrichment analysis specifically showed an increase in mRNA expression associated with: (a) organ development and homeostasis in COX-1-/- cells and (b) oxidative stress and response, spliceosomes and proteasomes activity, mTOR and p53 signaling in COX-2-/- cells. COX-1 and COX-2 showed signs of functional pathways committed to cell cycle and DNA replication at the genomics level. As compared to WT, metabolomics analysis revealed a significant increase in COX-1 mRNA and synthesis of basal levels of eicosanoids (PGE2, PGD2, TXB2, LTB4, PGF1α, and PGF2α) in COX-2 ablated cells and increase in synthesis of PGE2, and PGF1α in COX-1 null cells. There was a compensation of PGE2 and PGF1α in COX-1-/- and COX-2-/- cells. Collectively, these results support a broader, differential and collaborative regulation of both COX-1 and COX-2 pathways at the metabolic, signaling, and genomics levels in cellular homeostasis and sterile inflammation induced by cellular stress.

Keywords: cyclooxygenases, inflammation, lung fibroblasts, systemic

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Authors: Khadiza Akter, Tammy Greer, Raegan Bishop

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An in-depth study of the psycho-social effects of gynecological health disparities among immigrant women in the USA is the goal of this integrative review paper. Immigrant women frequently encounter unique obstacles that have severe psycho-social repercussions when it comes to receiving high-quality gynecological treatment. The review investigates the interaction of psychological, sociological, and health factors that affect the psycho-social effects that immigrant women experience in recognition of the significance of addressing these imbalances. The difficulties that immigrant women face in providing high-quality gynecological treatment in the USA are examined in this study. These difficulties are caused by a variety of psychological issues, including acculturation stress and stigma, as well as by social problems like prejudice, language hurdles, and cultural norms. Additionally, variations in healthcare access and affordability have a role. This study highlights the particular challenges that immigrant women have in receiving high-quality gynecological treatment in the United States. These difficulties are caused by both social problems like language obstacles, cultural norms, and biases, as well as psychological ones like acculturation stress and stigma. Additionally, variations in gynecological care for immigrant women are greatly influenced by variances in healthcare availability and price. To find pertinent research looking at the psychological effects of gynecological health disparities among immigrant women in the USA, a thorough search of numerous databases was done. Numerous approaches, including mixed, quantitative, and qualitative ones, were used in the studies. The important findings from various investigations were extracted and synthesized after they underwent a careful evaluation. In order to lessen these discrepancies and enhance the overall well-being of immigrant women, healthcare professionals, legislators, and researchers must collaborate to create specialized treatments, regulations, and health system reforms.

Keywords: cultural barriers, gynecological health disparities, health care access, immigrant women, mental health, psycho-social consequences, social stigma

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Authors: Maddalena Arigoni, Maria Luisa Ratto, Raffaele A. Calogero, Luca Alessandri

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The presence of tumor heterogeneity, where distinct cancer cells exhibit diverse morphological and phenotypic profiles, including gene expression, metabolism, and proliferation, poses challenges for molecular prognostic markers and patient classification for targeted therapies. Understanding the causes and progression of cancer requires research efforts aimed at characterizing heterogeneity, which can be facilitated by evolving single-cell sequencing technologies. However, analyzing single-cell data necessitates computational methods that often lack objective validation. Therefore, the establishment of benchmarking datasets is necessary to provide a controlled environment for validating bioinformatics tools in the field of single-cell oncology. Benchmarking bioinformatics tools for single-cell experiments can be costly due to the high expense involved. Therefore, datasets used for benchmarking are typically sourced from publicly available experiments, which often lack a comprehensive cell annotation. This limitation can affect the accuracy and effectiveness of such experiments as benchmarking tools. To address this issue, we introduce omics benchmark experiments designed to evaluate bioinformatics tools to depict the heterogeneity in single-cell tumor experiments. We conducted single-cell RNA sequencing on six lung cancer tumor cell lines that display resistant clones upon treatment of EGFR mutated tumors and are characterized by driver genes, namely ROS1, ALK, HER2, MET, KRAS, and BRAF. These driver genes are associated with downstream networks controlled by EGFR mutations, such as JAK-STAT, PI3K-AKT-mTOR, and MEK-ERK. The experiment also featured an EGFR-mutated cell line. Using 10XGenomics platform with cellplex technology, we analyzed the seven cell lines together with a pseudo-immunological microenvironment consisting of PBMC cells labeled with the Biolegend TotalSeq™-B Human Universal Cocktail (CITEseq). This technology allowed for independent labeling of each cell line and single-cell analysis of the pooled seven cell lines and the pseudo-microenvironment. The data generated from the aforementioned experiments are available as part of an online tool, which allows users to define cell heterogeneity and generates count tables as an output. The tool provides the cell line derivation for each cell and cell annotations for the pseudo-microenvironment based on CITEseq data by an experienced immunologist. Additionally, we created a range of pseudo-tumor tissues using different ratios of the aforementioned cells embedded in matrigel. These tissues were analyzed using 10XGenomics (FFPE samples) and Curio Bioscience (fresh frozen samples) platforms for spatial transcriptomics, further expanding the scope of our benchmark experiments. The benchmark experiments we conducted provide a unique opportunity to evaluate the performance of bioinformatics tools for detecting and characterizing tumor heterogeneity at the single-cell level. Overall, our experiments provide a controlled and standardized environment for assessing the accuracy and robustness of bioinformatics tools for studying tumor heterogeneity at the single-cell level, which can ultimately lead to more precise and effective cancer diagnosis and treatment.

Keywords: single cell omics, benchmark, spatial transcriptomics, CITEseq

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Authors: Nancy Retzlaff, Sarah J. Berkemer, Trudie Strauss

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In the last couple of decades, the advent of digitalization of any kind of data was probably one of the major advances in all fields of study. This paves the way for also analysing these data even though they might come from disciplines where there was no initial computational necessity to do so. Especially in linguistics, one can find a rather manual tradition. Still when considering studies that involve the history of language families it is hard to overlook the striking similarities to bioinformatics (phylogenetic) approaches. Alignments of words are such a fairly well studied example of an application of bioinformatics methods to historical linguistics. In this paper we will not only consider alignments of strings, i.e., words in this case, but also alignments of syntax trees of selected Indo-European languages. Based on initial, crude alignments, a sophisticated scoring model is trained on both letters and syntactic features. The aim is to gain a better understanding on which features in two languages are related, i.e., most likely to have the same root. Initially, all words in two languages are pre-aligned with a basic scoring model that primarily selects consonants and adjusts them before fitting in the vowels. Mixture models are subsequently used to filter ‘good’ alignments depending on the alignment length and the number of inserted gaps. Using these selected word alignments it is possible to perform tree alignments of the given syntax trees and consequently find sentences that correspond rather well to each other across languages. The syntax alignments are then filtered for meaningful scores—’good’ scores contain evolutionary information and are therefore used to train the sophisticated scoring model. Further iterations of alignments and training steps are performed until the scoring model saturates, i.e., barely changes anymore. A better evaluation of the trained scoring model and its function in containing evolutionary meaningful information will be given. An assessment of sentence alignment compared to possible phrase structure will also be provided. The method described here may have its flaws because of limited prior information. This, however, may offer a good starting point to study languages where only little prior knowledge is available and a detailed, unbiased study is needed.

Keywords: alignments, bioinformatics, comparative linguistics, historical linguistics, statistical methods

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Authors: Sampo Tukiainen, Jukka Mattila, Niina Erkama, Erkki Ormala

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During the past decade, calls for more holistic and integrative organizational innovation research have been increasingly voiced. On the one hand, from the theoretical perspective, the reason for this has been the tendency in contemporary innovation studies to focus on disciplinary subfields, often leading to challenges in integrating theories in meaningful ways. For example, we find that during the past three decades the innovation research has evolved into an academic field consisting of several independent research streams, such as studies on organizational learning, project management, and top management teams, to name but a few. The innovation research has also proliferated according to different dimensions of innovation, such as sources, drivers, forms, and the nature of innovation. On the other hand, from the practical perspective the rationale has been the need to develop understanding of the solving of complex, interdisciplinary issues and problems in contemporary and future societies and organizations. Therefore, for advancing theorizing, as well as the practical applicability of organizational innovation research, we acknowledge the need for more integrative and holistic perspectives and approaches. We contribute to addressing this challenge by developing a ‘box transcendent’ perspective to examine interlinkages in and across four key dimensions of organizational innovation processes, which traditionally have been studied in separate research streams. Building on an in-depth, qualitative analysis of 123 interviews of CTOs (or equivalent) and CEOs in top innovative Finnish companies as well as three in-depth case studies, both as part of an EU-level interview study of more than 700 companies, we specify interlinkages in and between i) strategic management, ii) innovation management, iii) implementation and organization, and iv) commercialization, in innovation processes. We contribute to the existing innovation research in multiple ways. Firstly, we develop a cross-dimensional, ‘box transcendent’ conceptual model at the level of organizational innovation process. Secondly, this modeling enables us to extend existing theorizing by allowing us to distinguish specific cross-dimensional innovation ‘profiles’ in two different company categories: large multinational corporations and SMEs. Finally, from the more practical perspective, we consider the implications of such innovation ‘profiles’ for the societal and institutional, policy-making development.

Keywords: holistic research, innovation management, innovation studies, organizational innovation

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Authors: Momoh Omeiza Sheidu

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Finite element method as a method of providing solutions to problems in computational bio mechanics provides a framework for modeling the function of tissues that integrates structurally from cell to organ system and functionally across the physiological processes that affect tissue mechanics or are regulated by mechanical forces. In this paper, we present an integrative finite element strategy for solution to problems in tissue bio mechanics as a case study.

Keywords: finite element, biomechanics, modeling, computational biomechanics

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Authors: Danna Jia, Bin Li

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Background: Atopic dermatitis (AD) is a chronic and refractory inflammatory skin disease characterized by relapsing eczematous and pruritic skin lesions. The global prevalence of AD ranges from 1~ 20%, and its incidence rates are increasing. It affects individuals from infancy to adulthood, significantly impacting their daily lives and social activities. Despite its major health burden, the precise mechanisms underlying AD remain unknown. Understanding the genetic differences associated with AD is crucial for advancing diagnosis and targeted treatment development. This study aims to identify candidate genes of AD by using bioinformatics analysis. Methods: We conducted a comprehensive analysis of four pooled transcriptomic datasets (GSE16161, GSE32924, GSE130588, and GSE120721) obtained from the Gene Expression Omnibus (GEO) database. Differential gene expression analysis was performed using the R statistical language. The differentially expressed genes (DEGs) between AD patients and normal individuals were functionally analyzed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Furthermore, a protein-protein interaction (PPI) network was constructed to identify candidate genes. Results: Among the patient-level gene expression datasets, we identified 114 shared DEGs, consisting of 53 upregulated genes and 61 downregulated genes. Functional analysis using GO and KEGG revealed that the DEGs were mainly associated with the negative regulation of transcription from RNA polymerase II promoter, membrane-related functions, protein binding, and the Human papillomavirus infection pathway. Through the PPI network analysis, we identified eight core genes: CD44, STAT1, HMMR, AURKA, MKI67, and SMARCA4. Conclusion: This study elucidates key genes associated with AD, providing potential targets for diagnosis and treatment. The identified genes have the potential to contribute to the understanding and management of AD. The bioinformatics analysis conducted in this study offers new insights and directions for further research on AD. Future studies can focus on validating the functional roles of these genes and exploring their therapeutic potential in AD. While these findings will require further verification as achieved with experiments involving in vivo and in vitro models, these results provided some initial insights into dysfunctional inflammatory and immune responses associated with AD. Such information offers the potential to develop novel therapeutic targets for use in preventing and treating AD.

Keywords: atopic dermatitis, bioinformatics, biomarkers, genes

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Authors: Balkibekova Venera Serikpaevna

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Background: Autism Spectrum Disorder (ASD) poses significant challenges in both diagnosis and treatment. Existing therapeutic interventions often target specific symptoms, necessitating the exploration of alternative approaches. This study investigates the RITM (Rhythm Integration Tapping Music) developed by Balkibekova, aiming to create imitation, social engagement and a wide range of emotions through brain development. Methods: A randomized controlled trial was conducted with 100 participants diagnosed with ASD, aged 1 to 4 years. Participants were randomly assigned to either the RITM therapy group or a control group receiving standard care. The RITM therapy, rooted in tapping rhythm to music such as: marche on the drums, waltz on bells, lullaby on musical triangle, dancing on tambourine, polka on wooden spoons. Therapy sessions were conducted over a 3 year period, with assessments at baseline, midpoint, and post-intervention. Results: Preliminary analyses reveal promising outcomes in the RITM therapy group. Participants demonstrated significant improvements in social interactions, speech understanding, birth of speech, and adaptive behaviors compared to the control group. Careful examination of subgroup analyses provides insights into the differential effectiveness of the RITM approach across various ASD profiles. Conclusions: The findings suggest that RITM therapy, as developed by Balkibekova, holds promise as intervention for ASD. The integrative nature of the approach, addressing multiple domains simultaneously, may contribute to its efficacy. Further research is warranted to validate these preliminary results and explore the long-term impact of RITM therapy on individuals with ASD. This abstract presents a snapshot of the research, emphasizing the significance, methodology, key findings, and implications of the RITM therapy method for consideration in an autism conference.

Keywords: RITM therapy, tapping rhythm, autism, mirror neurons, bright emotions, social interactions, communications

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Authors: Allison Herlene Du Plessis, Dalena (R.M.) Van Rooyen, Wilma Ten Ham-Baloyi, Sihaam Jardien-Baboo

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Introduction: Women die in pregnancy and childbirth for five main reasons—severe bleeding, infections, unsafe abortions, hypertensive disorders (pre-eclampsia and eclampsia), and medical complications including cardiac disease, diabetes, or HIV/AIDS complicated by pregnancy. In 2015, WHO classified sepsis as the third highest cause for maternal mortalities in the world. Chorioamnionitis is a clinical syndrome of intrauterine infection during any stage of the pregnancy and it refers to ascending bacteria from the vaginal canal up into the uterus, causing infection. While the incidence rates for chorioamnionitis are not well documented, complications related to chorioamnionitis are well documented and midwives still struggle to identify this condition in time due to its complex nature. Few diagnostic methods are available in public health services, due to escalated laboratory costs. Often the affordable biomarkers, such as C-reactive protein CRP, full blood count (FBC) and WBC, have low significance in diagnosing chorioamnionitis. A lack of screening impacts on effective and timeous management of chorioamnionitis, and early identification and management of risks could help to prevent neonatal complications and reduce the subsequent series of morbidities and healthcare costs of infants who are health foci of perinatal infections. Objective: This integrative literature review provides an overview of current best research evidence on the screening of women at risk for chorioamnionitis. Design: An integrative literature review was conducted using a systematic electronic literature search through EBSCOhost, Cochrane Online, Wiley Online, PubMed, Scopus and Google. Guidelines, research studies, and reports in English related to chorioamnionitis from 2008 up until 2020 were included in the study. Findings: After critical appraisal, 31 articles were included. More than one third (67%) of the literature included ranked on the three highest levels of evidence (Level I, II and III). Data extracted regarding screening for chorioamnionitis was synthesized into four themes, namely: screening by clinical signs and symptoms, screening by causative factors of chorioamnionitis, screening of obstetric history, and essential biomarkers to diagnose chorioamnionitis. Key conclusions: There are factors that can be used by midwives to identify women at risk for chorioamnionitis. However, there are a paucity of established sociological, epidemiological and behavioral factors to screen this population. Several biomarkers are available to diagnose chorioamnionitis. Increased Interleukin-6 in amniotic fluid is the better indicator and strongest predictor of histological chorioamnionitis, whereas the available rapid matrix-metalloproteinase-8 test requires further testing. Maternal white blood cells count (WBC) has shown poor selectivity and sensitivity, and C-reactive protein (CRP) thresholds varied among studies and are not ideal for conclusive diagnosis of subclinical chorioamnionitis. Implications for practice: Screening of women at risk for chorioamnionitis by health care providers providing care for pregnant women, including midwives, is important for diagnosis and management before complications arise, particularly in resource-constraint settings.

Keywords: chorioamnionitis, guidelines, best evidence, screening, diagnosis, pregnant women

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Authors: G. Tamilpavai, C. Vishnuppriya

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Studying DNA (deoxyribonucleic acid) sequence is useful in biological processes and it is applied in the fields such as diagnostic and forensic research. DNA is the hereditary information in human and almost all other organisms. It is passed to their generations. Earlier stage detection of defective DNA sequence may lead to many developments in the field of Bioinformatics. Nowadays various tedious techniques are used to identify defective DNA. The proposed work is to analyze and identify the cancer-causing DNA motif in a given sequence. Initially the human DNA sequence is separated as k-mers using k-mer separation rule. The separated k-mers are clustered using Self Organizing Map (SOM). Using Levenshtein distance measure, cancer associated DNA motif is identified from the k-mer clusters. Experimental results of this work indicate the presence or absence of cancer causing DNA motif. If the cancer associated DNA motif is found in DNA, it is declared as the cancer disease causing DNA sequence. Otherwise the input human DNA is declared as normal sequence. Finally, elapsed time is calculated for finding the presence of cancer causing DNA motif using clustering formation. It is compared with normal process of finding cancer causing DNA motif. Locating cancer associated motif is easier in cluster formation process than the other one. The proposed work will be an initiative aid for finding genetic disease related research.

Keywords: bioinformatics, cancer motif, DNA, k-mers, Levenshtein distance, SOM

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Authors: Mohamed Sharof Mostafa, Atefeh Ahmadi

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Most of traditional single modality psychotherapy and counselling approaches to clients’ problems are based on the application of one therapy in all sessions. Modern developments in these sciences focus on eclectic and integrative interventions to consider all dimensions of an issue and all characteristics of the clients. This paper presents and overview eclectic therapy and its pros and cons. In addition, multiple intelligence theory and its application in eclectic therapy approaches are mentioned.

Keywords: eclectic therapy, client, multiple intelligence theory, dimensions

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Authors: L. Matthewman, J. Nowlan

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Background: Holistic or Integrative Psychology emphasizes the interdependence of physiological, spiritual and psychological dynamics. Studying “wholeness and well-being” from a systems perspective combines innovative psychological science interventions with Eastern orientated healing wisdoms and therapies. The literature surrounding holistic/integrative psychology focuses on multi-stage interventions in attempts to enhance the mind-body experiences of well-being for participants. This study proposes a new single stage model as an intervention for UG/PG students, time-constrained workplace employees and managers/leaders for improved well-being and life enhancement. The main research objective was to investigate participants’ experiences of holistic and mindfulness interventions for impact on emotional well-being. The main research question asked was if single stage holistic interventions could impact on psychological well-being. This is of consequence because many people report that a reason for not taking part in mind-body or wellness programmes is that they believe that they do not have sufficient time to engage in such pursuits. Experimental Approach: The study employed a mixed methods pre-test/post-test research design. Data was analyzed using descriptive statistics and interpretative phenomenological analysis. Purposive sampling methods were employed. An adapted mindfulness measurement questionnaire (MAAS) was administered to 20 volunteer final year UG student participants prior to the single stage intervention and following the intervention. A further post-test longitudinal follow-up took place one week later. Intervention: The single stage model intervention consisted of a half hour session of mindfulness, yoga stretches and head and neck massage in the following sequence: Mindful awareness of the breath, yoga stretches 1, mindfulness of the body, head and neck massage, mindfulness of sounds, yoga stretches 2 and finished with pure awareness mindfulness. Results: The findings on the pre-test indicated key themes concerning: “being largely unaware of feelings”, “overwhelmed with final year exams”, “juggling other priorities” , “not feeling in control”, “stress” and “negative emotional display episodes”. Themes indicated on the post-test included: ‘more aware of self’, ‘in more control’, ‘immediately more alive’ and ‘just happier’ compared to the pre-test. Themes from post-test 2 indicated similar findings to post-test 1 in terms of themes. but on a lesser scale when scored for intensity. Interestingly, the majority of participants reported that they would now seek other similar interventions in the future and would be likely to engage with a multi-stage intervention type on a longer-term basis. Overall, participants reported increased psychological well-being after the single stage intervention. Conclusion: A single stage one-off intervention model can be effective to help towards the wellbeing of final year UG students. There is little indication to suggest that this would not be generalizable to others in different areas of life and business. However this study must be taken with caution due to low participant numbers. Implications: Single stage one-off interventions can be used to enhance peoples’ lives who might not otherwise sign up for a longer multi-stage intervention. In addition, single stage interventions can be utilized to help participants progress onto longer multiple stage interventions. Finally, further research into one stage well-being interventions is encouraged.

Keywords: holistic/integrative psychology, mindfulness, well-being, yoga

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Authors: E. Maoz

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Background: As a teaching method, project-based learning is strongly linked to developing students’ critical thinking skills. It combines creative independent thinking, team work, and disciplinary subject-field integration. In the 'Introduction to Nursing Research Methods' course (year 3, Generic Track), project based learning is used to teach the topic of 'Evidence-Based Nursing'. This topic examines a clinical care issue encountered by students in the field. At the end of their project, students present proposals for managing the said issue. Proposals are the product of independent integrative thinking integrating a wide range of factors influencing the issue’s management. Method: Papers by 27 groups of students (165 students) were content analyzed to identify which themes emerged from the students' recommendations for managing the clinical issue. Findings: Five main themes emerged—current management approach; adapting procedures in line with current recent research recommendations; training for change (veteran nursing staff, beginner students, patients, significant others); analysis of 'economic benefit vs. patient benefit'; multidisciplinary team engagement in implementing change in practice. Two surprising themes also emerged: advertising and marketing using new technologies, which reflects how the new generation thinks. Summary and Recommendations: Among the main challenges in nursing education is training nursing graduates to think independently, integratively, and critically. Combining PBL with classical teaching methods stimulates students cognitively while opening new vistas with implications on all levels of the profession: management, research, education, and practice. Advanced students can successfully grasp and interpret the current state of clinical practice. They are competent and open to leading change and able to consider the diverse factors and interconnections that characterize the nurse's work.

Keywords: evidence based nursing, critical thinking skills, project based learning, students education

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Authors: Xiaoxing Ye

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To investigate complex rumen microbial communities, 16S ribosomal RNA (rRNA) sequencing is widely used. Here, we evaluated the impact of bioinformatics pipelines on the observation of OTUs and taxonomic classification of 750 cattle rumen microbial samples by comparing three commonly used pipelines (LotuS, UPARSE, and QIIME) with Usearch. In LotuS-based analyses, 189 archaeal and 3894 bacterial OTUs were observed. The observed OTUs for the Usearch analysis were significantly larger than the LotuS results. We discovered 1495 OTUs for archaea and 92665 OTUs for bacteria using Usearch analysis. In addition, taxonomic assignments were made for the rumen microbial samples. All pipelines had consistent taxonomic annotations from the phylum to the genus level. A difference in relative abundance was calculated for all microbial levels, including Bacteroidetes (QIIME: 72.2%, Usearch: 74.09%), Firmicutes (QIIME: 18.3%, Usearch: 20.20%) for the bacterial phylum, Methanobacteriales (QIIME: 64.2%, Usearch: 45.7%) for the archaeal class, Methanobacteriaceae (QIIME: 35%, Usearch: 45.7%) and Methanomassiliicoccaceae (QIIME: 35%, Usearch: 31.13%) for archaeal family. However, the most prevalent archaeal class varied between these two annotation pipelines. The Thermoplasmata was the top class according to the QIIME annotation, whereas Methanobacteria was the top class according to Usearch.

Keywords: cattle rumen, rumen microbial, 16S rRNA gene sequencing, bioinformatics pipeline

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Authors: I. D. Arroyo

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This article seeks to integrate different concepts from contemporary software engineering with an agile development approach. We seek to clarify some definitions and uses, we make a difference between the Systems Development Life Cycle (SDLC) and the methodologies, we differentiate the types of frameworks such as methodological, philosophical and behavioral, standards and documentation. We define relationships based on the documentation of the development process through formal and ad hoc models, and we define the usefulness of using DevOps and Agile Modeling as integrative methodologies of principles and best practices.

Keywords: methodologies, modeling languages, agile modeling, UML

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Authors: Aakansha Gupta, Neha Vadnere, Tapasvi Soni, M. Anbarsi

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Protein secondary structure prediction is one of the most important goals pursued by bioinformatics and theoretical chemistry; it is highly important in medicine and biotechnology. Some aspects of protein functions and genome analysis can be predicted by secondary structure prediction. This is used to help annotate sequences, classify proteins, identify domains, and recognize functional motifs. In this paper, we represent protein secondary structure as a mathematical model. To extract and predict the protein secondary structure from the primary structure, we require a set of parameters. Any constants appearing in the model are specified by these parameters, which also provide a mechanism for efficient and accurate use of data. To estimate these model parameters there are many algorithms out of which the most popular one is the EM algorithm or called the Expectation Maximization Algorithm. These model parameters are estimated with the use of protein datasets like RS126 by using the Bayesian Probabilistic method (data set being categorical). This paper can then be extended into comparing the efficiency of EM algorithm to the other algorithms for estimating the model parameters, which will in turn lead to an efficient component for the Protein Secondary Structure Prediction. Further this paper provides a scope to use these parameters for predicting secondary structure of proteins using machine learning techniques like neural networks and fuzzy logic. The ultimate objective will be to obtain greater accuracy better than the previously achieved.

Keywords: model parameters, expectation maximization algorithm, protein secondary structure prediction, bioinformatics

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Authors: Long Zhang, Ian Hampson, Loretta O' Donnell

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Practitioners in various industries, especially in the finance industry that conventionally benefit from financial capital and resources, appear to be increasingly aware of the importance of human capital resources (HCR) after the 2008 Global Financial Crisis. Scholars from diverse fields have conducted extensive and fruitful research on HCR within their own disciplines. This review suggests that the mainstream of pure quantitative research alone is insufficient to provide precise or comprehensive understanding of HCR. The complex relationships and interactions in HCR call for more integrative and cross-disciplinary research to more holistically understand complex and intricate HCRs. The complex nature of HCR requires deep qualitative exploration based on in-depth data to capture the everydayness of organizational activities and to register its individuality and variety. Despite previous efforts, a systematic and holistic integration of HCR research among multiple disciplines is lacking. Using a retrospective analysis of articles published in the field of economics, finance and management, including psychology, human resources management (HRM), organizational behaviour (OB), industrial and organizational psychology (I-O psychology), organizational theory, and strategy literatures, this study summaries and compares the major perspectives, theories, and findings on HCR research. A careful examination of the progress of the debates of HCR definitions and measurements in distinct disciplines enables an identification of the limitations and gaps in existing research. It enables an analysis of the interplay of these concepts, as well as that of the related concepts of intellectual capital, social capital, and Chinese guanxi, and how they provide a broader perspective on the HCR-related influences on firms’ competitive advantage. The study also introduces the themes of Environmental, Social and Governance, or ESG based investing, as the burgeoning body of ESG studies illustrates the rising importance of human and non-financial capital in investment process. The ESG literature locates HCR into a broader research context of the value of non-financial capital in explaining firm performance. The study concludes with a discussion of new directions for future research that may help advance our knowledge of HCR.

Keywords: human capital resources, social capital, Chinese guanxi, human resources management

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Authors: Cleiton Pons Ferreira, Diana Francisca Adamatti

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Advancements in computers technology have allowed to obtain information for research in biology and neuroscience. In order to transform the data from these surveys, networks have long been used to represent important biological processes, changing the use of this tools from purely illustrative and didactic to more analytic, even including interaction analysis and hypothesis formulation. Many studies have involved this application, but not directly for interpretation of data obtained from brain functions, asking for new perspectives of development in neuroinformatics using existent models of tools already disseminated by the bioinformatics. This study includes an analysis of neurological data through electroencephalogram (EEG) signals, using the Cytoscape, an open source software tool for visualizing complex networks in biological databases. The data were obtained from a comparative case study developed in a research from the University of Rio Grande (FURG), using the EEG signals from a Brain Computer Interface (BCI) with 32 eletrodes prepared in the brain of a blind and a sighted individuals during the execution of an activity that stimulated the spatial ability. This study intends to present results that lead to better ways for use and adapt techniques that support the data treatment of brain signals for elevate the understanding and learning in neuroscience.

Keywords: neuroinformatics, bioinformatics, network tools, brain mapping

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Authors: Christine Eickhoff, Alyssa Adams, Alaine Duncan

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The Washington, DC Veterans Affairs Medical Center (DC VAMC) offers complementary and integrative health (CIH) services such as acupuncture, yoga, meditation, and nutrition education through a coordinated outpatient clinic. The primary population utilizing CIH services are veterans with chronic pain. Acupuncture is one of the most popular of the CIH services available at the DC VAMC. As interest and availability grows, it is important to measure health outcomes associated with CIH service utilization. The purpose of this study was to investigate pain and mental health outcomes for veterans with chronic pain enrolled in individual acupuncture services in the DC VAMC. Veterans at the DC VAMC with self-identified chronic pain and no prior acupuncture experience were recruited for the study (n=70). Veterans were referred for services by a medical provider and completed baseline assessments at the program orientation prior to participating in any CIH services. Veterans received four individual, full-body acupuncture appointments within four weeks of study enrollment. After the first month, participants were scheduled for six appointments that occurred every two weeks and then eight more sessions that were scheduled one month apart. Follow-up assessments were administered at 2, 4, 6, 8, and 12 months. The findings reported will include completed time points at two and four months. Measures include a demographics survey, the Measure Yourself Medical Outcome Profile-2 (MYMOP-2), The Beck Depression Inventory (BDI-II), the Defense Veterans Pain Rating Scale (DVPRS), and the Pain Disability Questionnaire (PDQ). In this sample, 67% identified a pain condition as their primary health concern. Between baseline and two-month follow-up, there were significant improvements in participants’ primary health concern (MYMOP-2 p=0.010), general wellbeing (MYMOP-2 p=0.011), and a significant decrease in the use of medication (MYMOP-2 p<0.000). Between 2 and 4-month follow-up, pain disability (PDQ p=0.035), pain rating (DVPRS p=0.027), and depression (BDI-II p=0.003) significantly improved. Preliminary findings indicate that individual acupuncture therapy can be effective at improving health outcomes, well-being, and decreasing medication use in U.S. military veterans with chronic pain. Findings also suggest that individual acupuncture therapy can improve pain ratings, pain disability, and depression in veterans with chronic pain.

Keywords: acupuncture, chronic pain, depression, integrative health, medication use, military, pain, veterans, wellbeing

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Authors: Surajit Bhattacharya, Daniel Veltri, Atit A. Patel, Daniel N. Cox

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miRNAs have emerged as key post-transcriptional regulators of gene expression, however identification of biologically-relevant target genes for this epigenetic regulatory mechanism remains a significant challenge. To address this knowledge gap, we have developed a novel tool in R, Intra-miR-ExploreR, that facilitates integrated discovery of miRNA targets by incorporating target databases and novel target prediction algorithms, using statistical methods including Pearson and Distance Correlation on microarray data, to arrive at high confidence intragenic miRNA target predictions. We have explored the efficacy of this tool using Drosophila melanogaster as a model organism for bioinformatics analyses and functional validation. A number of putative targets were obtained which were also validated using qRT-PCR analysis. Additional features of the tool include downloadable text files containing GO analysis from DAVID and Pubmed links of literature related to gene sets. Moreover, we are constructing interaction maps of intragenic miRNAs, using both micro array and RNA-seq data, focusing on neural tissues to uncover regulatory codes via which these molecules regulate gene expression to direct cellular development.

Keywords: miRNA, miRNA:mRNA target prediction, statistical methods, miRNA:mRNA interaction network

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Authors: Hamid Mustafa, Adeela Ajmal, Kim EuiSoo, Noor-ul-Ain

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World wild, buffalo production is considered as most important component of food industry. Efficient buffalo production is related with reproductive performance of this species. Lack of knowledge of reproductive efficiency and its related genes in buffalo species is a major constraint for sustainable buffalo production. In this study, we performed some bioinformatics analysis on Follicle Stimulating Hormone Receptor (FSHR) gene and explored the possible relationship of this gene among different buffalo breeds and with other farm animals. We also found the evolution pattern for this gene among these species. We investigate CDS lengths, Stop codon variation, homology search, signal peptide, isoelectic point, tertiary structure, motifs and phylogenetic tree. The results of this study indicate 4 different motif in this gene, which are Activin-recp, GS motif, STYKc Protein kinase and transmembrane. The results also indicate that this gene has very close relationship with cattle, bison, sheep and goat. Multiple alignment (MA) showed high conservation of motif which indicates constancy of this gene during evolution. The results of this study can be used and applied for better understanding of this gene for better characterization of Follicle Stimulating Hormone Receptor (FSHR) gene structure in different farm animals, which would be helpful for efficient breeding plans for animal’s production.

Keywords: buffalo, FSHR gene, bioinformatics, production

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Authors: Navkiran Kaur, Apoorva Mathur, Abhishree Agarwal, Sakshi Gupta, Tuhin Rashmi

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Aim: Breast cancer is the most common cancer in women worldwide, and resistance to the current therapeutics, often concurrently, is an increasing clinical challenge. Glycosylation of proteins is one of the most important post-translational modifications. It is widely known that aberrant glycosylation has been implicated in many different diseases due to changes associated with biological function and protein folding. Alterations in cell surface glycosylation, can promote invasive behavior of tumor cells that ultimately lead to the progression of cancer. In breast cancer, there is an increasing evidence pertaining to the role of glycosylation in tumor formation and metastasis. In the present study, an attempt has been made to study the disease associated sialoglycoproteins in breast cancer by using bioinformatics tools. The sequence will be retrieved from UniProt database. A database in the form of a word document was made by a collection of FASTA sequences of breast cancer gene sequence. Glycosylation was studied using yinOyang tool on ExPASy and Differential genes expression and protein analysis was done in context of breast cancer metastasis. The number of residues predicted O-glc NAc threshold containing 50 aberrant glycosylation sites or more was detected and recorded for individual sequence. We found that the there is a significant change in the expression profiling of glycosylation patterns of various proteins associated with breast cancer. Differential aberrant glycosylated proteins in breast cancer cells with respect to non-neoplastic cells are an important factor for the overall progression and development of cancer.

Keywords: breast cancer, bioinformatics, cancer, metastasis, glycosylation

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Authors: G. Tamilpavai, C. Vishnuppriya

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Bioinformatics is an active research area which combines biological matter as well as computer science research. The longest common subsequence (LCSS) is one of the major challenges in various bioinformatics applications. The computation of the LCSS plays a vital role in biomedicine and also it is an essential task in DNA sequence analysis in genetics. It includes wide range of disease diagnosing steps. The objective of this proposed system is to find the longest common subsequence which presents in a normal and various disease affected human DNA sequence using Self Organizing Map (SOM) and LCSS. The human DNA sequence is collected from National Center for Biotechnology Information (NCBI) database. Initially, the human DNA sequence is separated as k-mer using k-mer separation rule. Mean and median values are calculated from each separated k-mer. These calculated values are fed as input to the Self Organizing Map for the purpose of clustering. Then obtained clusters are given to the Longest Common Sub Sequence (LCSS) algorithm for finding common subsequence which presents in every clusters. It returns nx(n-1)/2 subsequence for each cluster where n is number of k-mer in a specific cluster. Experimental outcomes of this proposed system produce the possible number of longest common subsequence of normal and disease affected DNA data. Thus the proposed system will be a good initiative aid for finding disease causing sequence. Finally, performance analysis is carried out for different DNA sequences. The obtained values show that the retrieval of LCSS is done in a shorter time than the existing system.

Keywords: clustering, k-mers, longest common subsequence, SOM

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Authors: Alireza Dantism

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Presently, describing the function of a protein sequence is one of the most common problems in biology. Usually, this problem can be facilitated by studying the three-dimensional structure of proteins. In the absence of a protein structure, comparative modeling often provides a useful three-dimensional model of the protein that is dependent on at least one known protein structure. Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) mainly based on its alignment with one or more proteins of known structure (templates). Comparative modeling consists of four main steps 1. Similarity between the target sequence and at least one known template structure 2. Alignment of target sequence and template(s) 3. Build a model based on alignment with the selected template(s). 4. Prediction of model errors 5. Optimization of the built model There are many computer programs and web servers that automate the comparative modeling process. One of the most important advantages of these servers is that it makes comparative modeling available to both experts and non-experts, and they can easily do their own modeling without the need for programming knowledge, but some other experts prefer using programming knowledge and do their modeling manually because by doing this they can maximize the accuracy of their modeling. In this study, a web-based tool has been designed to predict the tertiary structure of proteins using PHP and Python programming languages. This tool is called EasyModel. EasyModel can receive, according to the user's inputs, the desired unknown sequence (which we know as the target) in this study, the protein sequence file (template), etc., which also has a percentage of similarity with the primary sequence, and its third structure Predict the unknown sequence and present the results in the form of graphs and constructed protein files.

Keywords: structural bioinformatics, protein tertiary structure prediction, modeling, comparative modeling, modeller

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Authors: Laura Mion

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Concepts of quality assurance and management are now part of the organizational culture of the Universities. Quality Assurance (QA) systems are, in large part, provided for by national regulatory dictates or supranational indications (such as, for example, at European level are, the ESG Guidelines "European Standard Guidelines"), but their specific definition, in terms of guiding principles, requirements and methodologies, are often delegated to the national evaluation agencies or to the autonomy of individual universities. For this reason, the experiences of implementation of QA systems in different countries and in different universities is an interesting source of information to understand how quality in universities is understood, pursued and verified. The literature often deals with the treatment of the experiences of implementation of QA systems in the individual areas in which the University's activity is carried out - teaching, research, third mission - but only rarely considers quality systems with a systemic and integrated approach, which allows to correlate subjects, actions, and performance in a virtuous circuit of continuous improvement. In particular, it is interesting to understand how to relate the results and uses of the QA in the triple distinction of university activities, identifying how one can cause the performance of the other as a function of an integrated whole and not as an exploit of specific activities or processes conceived in an abstractly atomistic way. The aim of the research is, therefore, to investigate which experiences of "integrated" QA systems are present on the international scene: starting from the experience of European countries that have long shared the Bologna Process for the creation of a European space for Higher Education (EHEA), but also considering experiences from emerging countries that use QA processes to develop their higher education systems to keep them up to date with international levels. The concept of "integration", in this research, is understood in a double meaning: i) between the different areas of activity, in particular between the didactic and research areas, and possibly with the so-called "third mission" "ii) the functional integration between those involved in quality assessment and management and the governance of the University. The paper will present the results of a systematic review conducted according with a method of an integrative review aimed at identifying best practices of quality assurance systems, in individual countries or individual universities, with a high level of integration. The analysis of the material thus obtained has made it possible to grasp common and transversal elements of QA system integration practices or particularly interesting elements and strengths of these experiences that can, therefore, be considered as winning aspects in a QA practice. The paper will present the method of analysis carried out, and the characteristics of the experiences identified, of which the structural elements will be highlighted (level of integration, areas considered, organizational levels included, etc.) and the elements for which these experiences can be considered as best practices.

Keywords: quality assurance, university, integration, country

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Authors: Mahsa Taghavi

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In the treatment of breast cancer, tamoxifen is a regularly prescribed medication. The effect of tamoxifen on breast cancer patients' EMT pathways was studied. In this study to see if it had any effect on the cancer cells' resistance to tamoxifen and to look for specific miRNAs associated with EMT. In this work, we used continuous and integrated bioinformatics analysis to choose the optimal GEO datasets. Once we had sorted the gene expression profile, we looked at the mechanism of signaling, the ontology of genes, and the protein interaction of each gene. In the end, we used the GEPIA database to confirm the candidate genes. after that, I investigated critical miRNAs related to candidate genes. There were two gene expression profiles that were categorized into two distinct groups. Using the expression profile of genes that were lowered in the EMT pathway, the first group was examined. The second group represented the polar opposite of the first. A total of 253 genes from the first group and 302 genes from the second group were found to be common. Several genes in the first category were linked to cell death, focal adhesion, and cellular aging. Two genes in the second group were linked to cell death, focal adhesion, and cellular aging. distinct cell cycle stages were observed. Finally, proteins such as MYLK, SOCS3, and STAT5B from the first group and BIRC5, PLK1, and RAPGAP1 from the second group were selected as potential candidates linked to tamoxifen's influence on the EMT pathway. hsa-miR-1204 and hsa-miR-639 have a very close relationship with the candidates genes according to the node degrees and betweenness index. With this, the action of tamoxifen on the EMT pathway was better understood. It's important to learn more about how tamoxifen's target genes and proteins work so that we can better understand the drug.

Keywords: tamoxifen, breast cancer, bioinformatics analysis, EMT, miRNAs

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Authors: K. M. Kim, S. J. Lee, D. S. Oh, Sadohara Satoru

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The climate change poses a serious challenge to urban sustainability. To alleviate the environmental risk, urban planning has been concentrated on climate adaptation and mitigation, and the sustainable urban model, smart city, has been suggested. However, with regard to sustainable smart city development, a majority of researchers have focused mainly on the aspect of adaptation, which causes the lack of the approaches for mitigation. Therefore, the objective was to identify the planning elements of smart city with integrative reviews about mitigation and adaptation. Moreover, the concepts of smart cities in Sweden, Japan, and Korea were analyzed to find out the country-specific characteristics and strategies for achieving smart city.

Keywords: sustainable urban planning, climate change, mitigating and adaptation, smart city

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