Search results for: integrated bioinformatics analysis

Authors: Mohamed Aniss El-Gamal

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For decades, the Global South has been facing many challenges in the fields of heritage conservation and local development. These challenges continue to increase due to rapid urbanization in historical cities, thus resulting in complicated juxtaposed contexts of heritage resources and deteriorated dwellings, where slum areas are dotted with heritage structures. While the majority of cases show the incapacity of national and local governments to deal with such contexts, few others managed to demonstrate how different levels of government can play complementary roles in the cooperation with local and international institutions as well as involving local community to achieve an integrated strategy and overcome the challenge. This paper discusses heritage conservation and local development strategies in reference to a number of case studies in cities of the Global south, i.e. Porto Alegre, Agra, Cairo and Mumbai. It further investigates main key aspects of success and failure through cross case studies analysis (Matrix). This study could help create a delineation of an integrated strategy for undertaking future interventions in similar contexts. Integrated strategies are needed to overcome the gap between heritage conservation and local development, maintaining the value of heritage structures and ensuring the quality of life for communities residing in its surroundings.

Keywords: heritage conservation, local development, the global south, regional development

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Authors: Geraldine O’Neill

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Work-integrated learning is a valuable learning experience for students in higher education. However, the fairness of the assessment process has been identified as a challenge. This study explored solutions to this challenge through interviews with expert authors in the field and workshops across nine different disciplines in Ireland. In keeping with the use of a participatory and action research methodology, the key stakeholders in the process, the students, educators, and practitioners, identified some solutions. The solutions included the need to: clarify the assessments’ expectations; enhance the flexibility of the competencies, reduce the number of competencies; use grading scales with lower specificity; support practitioner training, and empower students in the assessment process. The results are discussed as they relate to interactional, procedural, and distributive fairness.

Keywords: competencies, fairness, grading scales, work-integrated learning

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Authors: Nafiseh Noormohammadi, Ahmad Sobhani Najafabadi

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Hypericins (hypericin and pseudohypericin) are natural napthodianthrone derivatives produced by Hypericum perforatum (St. John’s Wort), which have many medicinal properties such as antitumor, antineoplastic, antiviral, and antidepressant activities. Production and accumulation of hypericin in the plant are influenced by both genetic and environmental conditions. Despite the existence of different high-throughput data on the plant, genetic dimensions of hypericin biosynthesis have not yet been completely understood. In this research, 21 high-quality RNA-seq data on different parts of the plant were integrated into metabolic data to reconstruct a coexpression network. Results showed that a cluster of 30 transcripts was correlated with total hypericin. The identified transcripts were divided into three main groups based on their functions, including hypericin biosynthesis genes, transporters, detoxification genes, and transcription factors (TFs). In the biosynthetic group, different isoforms of polyketide synthase (PKSs) and phenolic oxidative coupling proteins (POCPs) were identified. Phylogenetic analysis of protein sequences integrated into gene expression analysis showed that some of the POCPs seem to be very important in the biosynthetic pathway of hypericin. In the TFs group, six TFs were correlated with total hypericin. qPCR analysis of these six TFs confirmed that three of them were highly correlated. The identified genes in this research are a rich resource for further studies on the molecular breeding of H. perforatum in order to obtain varieties with high hypericin production.

Keywords: hypericin, St. John’s Wort, data mining, transcription factors, secondary metabolites

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Authors: S. O. Obasa, J. A. Soaga, O. I. Afolabi, N. A. Bamidele, O. E. Babalola

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Attempt to improve the income of the rural population is a welcome development in Nigeria. Integrated fish-crop farming has been suggested as a means of raising farm income, reducing wastage and mitigating the risk component in production through the complementarity gain. A feeding trial was carried out to investigate the replacement of maize with fermented unripe plantain (Musa paradisiaca) peel meal in the diet of Nile tilapia, Oreochromis niloticus. The economics of the integrated enterprise was assessed using budgetary analysis techniques. The analysis incorporated the material and labour costs as well as the returns from sale of matured fish and plantain. A total of 60 fingerlings of Nile tilapia (1.70±0.1 g) were stocked at 10 per plastic tank. Two iso-nitrogenous diets containing 35% crude protein in which maize meal was replaced by fermented unripe plantain peel meal at 0% (FUP0/Control diet), and 100% (FUP100) were formulated and prepared. The fingerlings were fed at 5% body weight per day for 56 days. Lowest feed conversion ratio of 1.39 in fish fed diet FUP100 was not significantly different (P > 0.05) from the highest 1.42 of fish fed the Control diet. The highest percentage profit of 88.85% in fish fed diet FUP100 was significantly higher than 66.68% in fish fed diet FUP0, while the profit index of 1.89 in fish fed diet FUP100 was significantly different from 1.67 in fish fed diet FUP0. Therefore, fermented unripe plantain peel meal can completely replace maize in the diet of O. niloticus fingerlings. Profitability assessment shows that the net income from the integration was ₦ 463,000 per hectare and the integration resulted to an increase of ₦ 87,750.00 representing a 12.2% increase than in separate production.

Keywords: fish-crop, income, Nile tilapia, waste management

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Authors: Jacqui Robertson

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The sustainable governance of groundwater is of the utmost importance in an arid country like Australia. Groundwater has been relied on by our agricultural and pastoral communities since the State was settled by European colonialists. Nevertheless, the rapid establishment of a coal seam gas (CSG) industry in Queensland, Australia, has had extensive impacts on the pre-existing groundwater users. Managed aquifer recharge of important aquifers in Queensland, Australia, using treated coal seam gas produced water has been used to reduce the impacts of CSG development in Queensland Australia. However, the process has not been widely adopted. Negative environmental outcomes are now acknowledged as not only engineering, scientific or technical problems to be solved but also the result of governance failures. An analysis of the regulatory context for aquifer injection using treated CSG water in Queensland, Australia, using Ostrom’s Common Pool Resource (CPR) theory and a ‘heat map’ designed by the author, highlights the importance of governance arrangements. The analysis reveals the costs and benefits for relevant stakeholders of artificial recharge of groundwater resources in this context. The research also reveals missed opportunities to further active management of the aquifer and resolve existing conflicts between users. The research illustrates the importance of strategically and holistically evaluating innovations in technology that impact water resources to reveal incentives that impact resource user behaviors. The paper presents a proactive step that can be adapted to support integrated water resource management and sustainable groundwater development.

Keywords: managed aquifer recharge, groundwater regulation, common-pool resources, integrated water resource management, Australia

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Authors: Maryvone Cunha de Morais, Lilian Cristine Hübner

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Based on a translanguaging theoretical approach, which considers language not as separate entities but as an entire repertoire available to bilingual individuals, this systematic review aimed at analyzing the methods (aims, samples investigated, type of stimuli, and analyses) adopted by studies on translanguaging practices associated with written and oral tasks (separately or integrated) in bilingual education. The PRISMA criteria for systematic reviews were adopted, with the descriptors "translanguaging", "bilingual education" and/or “written and oral tasks" to search in Pubmed/Medline, Lilacs, Eric, Scopus, PsycINFO, and Web of Science databases for articles published between 2017 and 2021. 280 registers were found, and after following the inclusion/exclusion criteria, 24 articles were considered for this analysis. The results showed that translanguaging practices were investigated on four studies focused on written production analyses, ten focused on oral production analysis, whereas ten studies focused on both written and oral production analyses. The majority of the studies followed a qualitative approach, while five studies have attempted to study translanguaging with quantitative statistical measures. Several types of methods were used to investigate translanguaging practices in written and oral production, with different approaches and tools indicating that the methods are still in development. Moreover, the findings showed that students’ interactions have received significant attention, and studies have been developed not just in language classes in bilingual education, but also including diverse educational and theoretical contexts such as Content and Language Integrated Learning, task repetition, Science classes, collaborative writing, storytelling, peer feedback, Speech Act theory and collective thinking, language ideologies, conversational analysis, and discourse analyses. The studies, whether focused either on writing or oral tasks or in both, have portrayed significant research and pedagogical implications, grounded on the view of integrated languages in bi-and multilinguals.

Keywords: bilingual education, oral production, translanguaging, written production

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Authors: M. Ndeley

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The performance of global manufacturing supply chains depends on the interaction of production and transport processes. Currently, the scheduling of these processes is done separately without considering mutual requirements, which leads to no optimal solutions. An integrated scheduling of both processes enables the improvement of supply chain performance. The integrated production and transport scheduling problem (PTSP) is NP-hard, so that heuristic methods are necessary to efficiently solve large problem instances as in the case of global manufacturing supply chains. This paper presents a heuristic scheduling approach which handles the integration of flexible production processes with intermodal transport, incorporating flexible land transport. The method is based on a graph that allows a reformulation of the PTSP as a shortest path problem for each job, which can be solved in polynomial time. The proposed method is applied to a supply chain scenario with a manufacturing facility in South Africa and shipments of finished product to customers within the Country. The obtained results show that the approach is suitable for the scheduling of large-scale problems and can be flexibly adapted to different scenarios.

Keywords: production and transport scheduling problem, graph based scheduling, integrated scheduling

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Authors: E. Behmanesh, J. Pannek

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Logistics network design is known as one of the strategic decision problems. As these kinds of problems belong to the category of NP-hard problems, traditional ways are failed to find an optimal solution in short time. In this study, we attempt to involve reverse flow through an integrated design of forward/reverse supply chain network that formulated into a mixed integer linear programming. This Integrated, multi-stages model is enriched by three different delivery path which makes the problem more complex. To tackle with such an NP-hard problem a revised random path direct encoding method based memetic algorithm is considered as the solution methodology. Each algorithm has some parameters that need to be investigate to reveal the best performance. In this regard, Taguchi method is adapted to identify the optimum operating condition of the proposed memetic algorithm to improve the results. In this study, four factors namely, population size, crossover rate, local search iteration and a number of iteration are considered. Analyzing the parameters and improvement in results are the outlook of this research.

Keywords: integrated logistics network, flexible path, memetic algorithm, Taguchi method

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Authors: Mohammad Hossein Habibi, Atena Sadat Hosseini

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Colorectal cancer is the third leading cause of cancer-related death in the world. Colorectal cancer screening, early detection, and treatment programs could benefit from the most up-to-date information on the disease's burden, given the present worldwide trend of increasing colorectal cancer incidence. Tumor recurrence and resistance are exacerbated by the presence of chemotherapy-resistant cancer stem cells that can generate rapidly proliferating tumor cells. In addition, tumor cells can evolve chemoresistance through adaptation mechanisms. In this work, we used in silico analysis to select suitable GEO datasets. In this study, we compared slow-growing cancer stem cells with high-growth colorectal cancer-derived cancer stem cells. We then evaluated the signal pathways, transcription factors, and kinases associated with these two types of cancer stem cells. A total of 980 upregulated genes and 870 downregulated genes were clustered. MAPK signaling pathway, AGE-RAGE signaling pathway in diabetic complications, Fc gamma R-mediated phagocytosis, and Steroid biosynthesis signaling pathways were observed in upregulated genes. Also, caffeine metabolism, amino sugar and nucleotide sugar metabolism, TNF signaling pathway, and cytosolic DNA-sensing pathway were involved in downregulated genes. In the next step, we evaluated the best transcription factors and kinases in two types of cancer stem cells. In this regard, NR2F2, ZEB2, HEY1, and HDGF as transcription factors and PRDM5, SMAD, CBP, and KDM2B as critical kinases in upregulated genes. On the other hand, IRF1, SPDEF, NCOA1, and STAT1 transcription factors and CTNNB1 and CDH7 kinases were regulated low expression genes. Using bioinformatics analysis in the present study, we conducted an in-depth study of colorectal cancer stem cells at low and high growth rates so that we could take further steps to detect and even target these cells. Naturally, more additional tests are needed in this direction.

Keywords: colorectal cancer, bioinformatics analysis, transcription factor, kinases, cancer stem cells

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Authors: Cheng Li, Jie Shen, Yutian Tang

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Embracing the upcoming era of urbanization with the challenges of limitation of resources, disappearing cultural identities and conflicts among different groups of stakeholders, new integrated approaches are offered in our urban practice to help decision-makers and stakeholders frame and develop well-conceived, practical strategies for urban developing trajectories to approach urban-level sustainability in multiple social, cultural, ecological dimensions. Through bottom-up participation, we take advantage of tourism and leisure industries as driving forces for urbanization in China to promote integrated sustainable systems, with the hope of approaching both historical and ecological aspects of urban sustainability; and also thanks to top-down participation, we have codes, standards and rules established by the governments to strengthen the implementation of ecological urban sustainability. The results are monitored and evaluated experimentally and multidimensionally and the sustainable systems we constructed with local stakeholder groups turned out to be effective. The presentation of our selected projects would indicate our different focuses on urban sustainability.

Keywords: urban sustainability, integrated urban strategy, tourism and leisure industries, history, modern technology

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Authors: Craig Mertens

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Teaching art history or any other academic subject to EFL students can be done successfully. A course called Western Images was created to teach Japanese students art history while only using English in the classroom. An approach known as Content and Language Integrated Learning (CLIL) was used as a basis for this course. This paper’s purpose is to state the reasons why learning about art history is important, go through the process of creating content for the course, and suggest multiple tasks to help students practice the critical thinking skills used in analyzing and drawing conclusions of works of art from western culture. As a guide for this paper, Brown’s (1995) six elements of a language curriculum will be used. These stages include needs analysis, goals and objectives, assessment, materials, teaching method and tasks, and evaluation of the course. The goal here is to inspire debate and discussion regarding CLIL and its pros and cons, and to question current curriculum in university language courses.

Keywords: art history, EFL, content and language integration learning, critical thinking

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Authors: Moien Mojabi, Aurelien Hospital, Daniel Potts, Chris Young, Albert Leung

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The wave analysis is an integral part of the hydrotechnical assessment carried out during the permitting and design phases for coastal structures, such as marinas. This analysis aims in quantifying: i) the Suitability of the coastal structure design against Small Craft Harbour wave tranquility safety criterion; ii) Potential environmental impacts of the structure (e.g., effect on wave, flow, and sediment transport); iii) Mooring and dock design and iv) Requirements set by regulatory agency’s (e.g., WSA section 11 application). While a complex three-dimensional hydrodynamic modelling approach can be applied on large-scale projects, the need for an efficient and reliable wave analysis method suitable for smaller scale marina projects was identified. As a result, Tetra Tech has developed and applied an integrated analysis framework (hereafter TT approach), which takes the advantage of the state-of-the-art numerical models while preserving the level of simplicity that fits smaller scale projects. The present paper aims to describe the TT approach and highlight the key advantages of using this integrated framework in lake marina projects. The core of this methodology is made by integrating wind, water level, bathymetry, and structure geometry data. To respond to the needs of specific projects, several add-on modules have been added to the core of the TT approach. The main advantages of this method over the simplified analytical approaches are i) Accounting for the proper physics of the lake through the modelling of the entire lake (capturing real lake geometry) instead of a simplified fetch approach; ii) Providing a more realistic representation of the waves by modelling random waves instead of monochromatic waves; iii) Modelling wave-structure interaction (e.g. wave transmission/reflection application for floating structures and piles amongst others); iv) Accounting for wave interaction with the lakebed (e.g. bottom friction, refraction, and breaking); v) Providing the inputs for flow and sediment transport assessment at the project site; vi) Taking in consideration historical and geographical variations of the wind field; and vii) Independence of the scale of the reservoir under study. Overall, in comparison with simplified analytical approaches, this integrated framework provides a more realistic and reliable estimation of wave parameters (and its spatial distribution) in lake marinas, leading to a realistic hydrotechnical assessment accessible to any project size, from the development of a new marina to marina expansion and pile replacement. Tetra Tech has successfully utilized this approach since many years in the Okanagan area.

Keywords: wave modelling, wind-wave, extreme value analysis, marina

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Authors: Abdon O. Makore

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The study analyses policy and institutional implications with regard to the successful implementation of IPTS in Harare. IPTS has widely been recommended as a rich solution to chaotic public transport operations, yet studies to determine the suitability or applicability of this concept have not been done in light of the existing transport institutions and policy framework in Harare. A predominantly qualitative research approach was employed backed by a deep scrutiny of the NTP and other subsidiary legislations and plans in place so as to ascertain the views and perceptions of various stakeholders regarding the proposed concept. As such, key informant interviews, unstructured interviews, and questionnaires were vital tools in gathering data and these were effectively buttressed by observations, photography, and documentary analysis. The study revealed from a policy perspective that there are high prospects for the implementation of IPTS in Harare as the existing NTP, subsidiary legislations and plans do have provisions for the concept backed by keen interest of all responsible urban public transport authorities. However, there is lack of coherent and systematic approach among other responsible institutions, as such recommendations formulated advocated for institutional integration and strong political will for the ultimate success of the concept.

Keywords: integrated public transport system, policy, legislation, institutions

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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: Ahmed Guerine, Ali El Hafidi, Bruno Martin, Philippe Leclaire

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In this paper, we propose a method for the dynamic response of multi-storey structures with uncertain-but-bounded parameters. The effectiveness of the proposed method is demonstrated by a numerical example of three-storey structures. This equation is integrated numerically using Newmark’s method. The numerical results are obtained by the proposed method. The simulation accounting the interval analysis method results are compared with a probabilistic approach results. The interval analysis method provides a mean curve that is between an upper and lower bound obtained from the probabilistic approach.

Keywords: multi-storey structure, dynamic response, interval analysis method, random parameters

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Authors: S. Fahiminiya, J. Nadaf, F. Rauch, L. Jerome-Majewska, J. Majewski

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Background: Sequencing of protein coding regions of human genome (Whole Exome Sequencing; WES), has demonstrated a great success in the identification of causal mutations for several rare genetic disorders in human. Generally, most of WES studies have focused on rare variants in coding exons and splicing-sites where missense substitutions lead to the alternation of protein product. Although focusing on this category of variants has revealed the mystery behind many inherited genetic diseases in recent years, a subset of them remained still inconclusive. Here, we present the result of our WES studies where analyzing only rare variants in coding regions was not conclusive but further investigation revealed the involvement of non-coding variants and copy number variations (CNV) in etiology of the diseases. Methods: Whole exome sequencing was performed using our standard protocols at Genome Quebec Innovation Center, Montreal, Canada. All bioinformatics analyses were done using in-house WES pipeline. Results: To date, we successfully identified several disease causing mutations within gene coding regions (e.g. SCARF2: Van den Ende-Gupta syndrome and SNAP29: 22q11.2 deletion syndrome) by using WES. In addition, we showed that variants in non-coding regions and CNV have also important value and should not be ignored and/or filtered out along the way of bioinformatics analysis on WES data. For instance, in patients with osteogenesis imperfecta type V and in patients with glucocorticoid deficiency, we identified variants in 5'UTR, resulting in the production of longer or truncating non-functional proteins. Furthermore, CNVs were identified as the main cause of the diseases in patients with metaphyseal dysplasia with maxillary hypoplasia and brachydactyly and in patients with osteogenesis imperfecta type VII. Conclusions: Our study highlights the importance of considering non-coding variants and CNVs during interpretation of WES data, as they can be the only cause of disease under investigation.

Keywords: whole exome sequencing data, non-coding variants, copy number variations, rare diseases

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Authors: Hande Aladağ, Gökçe Aydın

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The world’s population is increasing continuously and rapidly. Moreover, there are other problems such as the decline of natural energy resources, global warming, and environmental pollution. These facts have made sustainability an important and primary topic from future planning perspective. From this perspective, constituting sustainable cities and communities can be considered as one of the key issues in terms of sustainable development goals. The concept of sustainable cities can be evaluated under three headings such as green/sustainable buildings, self – contained cities and sustainable transportation. This study only concentrates on how to form and support a sustainable urban transportation system to contribute to the sustainable urbanization. Urban transportation system inevitably requires many engineering projects with various sizes. Engineering projects generally have four phases, in the following order: Planning, design, construction, operation. The order is valid but there are feedbacks from every phase to every phase in its upstream. In this regard, engineering projects are iterative processes. Sustainability is an integrated and comprehensive concept thus it should be among the primary concerns in every phase of transportation projects. In the study, a meta-analysis will be performed on the related studies in the literature. It is targeted and planned that, as a result of the findings of this meta-analysis, a framework for the list of principles and actions for sustainable transport will be formed. The meta-analysis will be performed to point out and clarify sustainability approaches in every phase of the related engineering projects, with also paying attention to the iterative nature of the process and relative contribution of the action for the outcomes of the sustainable transportation system. However, the analysis will not be limited to the engineering projects, non-engineering solutions will also be included in the meta-analysis. The most important contribution of this study is a determination of the outcomes of a sustainable urban transportation system in terms of energy efficiency, resource preservation and related social, environmental and economic factors. The study is also important because it will give light to the engineering and management approaches to achieve these outcomes.

Keywords: meta-analysis, sustainability, sustainable cities, sustainable urban transportation, urban transportation

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Authors: Nikhat Nawaz, S. Srinivasulu, P. Kesava Rao

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Feature extraction plays an important role in many remote sensing applications. Automatic extraction of water bodies is of great significance in many remote sensing applications like change detection, image retrieval etc. This paper presents a procedure for automatic extraction of water information from remote sensing images. The algorithm uses the relative location of R-colour component of the chromaticity diagram. This method is then integrated with the effectiveness of the spatial scale transformation of whole method. The whole method is based on water index fitted from spectral library. Experimental results demonstrate the improved accuracy and effectiveness of the integrated method for automatic extraction of water bodies.

Keywords: feature extraction, remote sensing, image retrieval, chromaticity, water index, spectral library, integrated method

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Authors: Mohammad Reza Oftadeh

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The purpose of the article is to describe project objective structure (POS) concept that was developed on research activities and experiences about project management, Balanced Scorecard (BSC) and European Foundation Quality Management Excellence Model (EFQM Excellence Model). Furthermore, this paper tries to define a balanced, systematic, and integrated measurement approach to meet project objectives and project strategic goals based on a process-oriented model. In this paper, POS is suggested in order to measure project performance in the project life cycle. After using the POS model, the project manager can ensure in order to achieve the project objectives on the project charter. This concept can help project managers to implement integrated and balanced monitoring and control project work.

Keywords: project objectives, project performance management, PMBOK, key performance indicators, integration management

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Authors: Danyi Wang, Andrew Schriefer, Dennis O'Rourke, Brajendra Kumar, Yang Liu, Fei Zhong, Juergen Scheuenpflug, Zheng Feng

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Purpose: It has been recognized that the microbiome plays critical roles in disease pathogenesis, including cancer, autoimmune disease, and multiple sclerosis. To develop a clinical-grade assay for exploring microbiome-derived clinical biomarkers across disease areas, a two-phase approach is implemented. 1) Identification of the optimal sample preparation reagents using pre-mixed bacteria and healthy donor stool samples coupled with proprietary Sigma-Aldrich® bioinformatics solution. 2) Exploratory analysis of patient samples for enabling precision medicine. Study Procedure: In phase 1 study, we first compared the 16S sequencing results of two ATCC® microbiome standards (MSA 2002 and MSA 2003) across five different extraction kits (Kit A, B, C, D & E). Both microbiome standards samples were extracted in triplicate across all extraction kits. Following isolation, DNA quantity was determined by Qubit assay. DNA quality was assessed to determine purity and to confirm extracted DNA is of high molecular weight. Bacterial 16S ribosomal ribonucleic acid (rRNA) amplicons were generated via amplification of the V3/V4 hypervariable region of the 16S rRNA. Sequencing was performed using a 2x300 bp paired-end configuration on the Illumina MiSeq. Fastq files were analyzed using the Sigma-Aldrich® Microbiome Platform. The Microbiome Platform is a cloud-based service that offers best-in-class 16S-seq and WGS analysis pipelines and databases. The Platform and its methods have been extensively benchmarked using microbiome standards generated internally by MilliporeSigma and other external providers. Data Summary: The DNA yield using the extraction kit D and E is below the limit of detection (100 pg/µl) of Qubit assay as both extraction kits are intended for samples with low bacterial counts. The pre-mixed bacterial pellets at high concentrations with an input of 2 x106 cells for MSA-2002 and 1 x106 cells from MSA-2003 were not compatible with the kits. Among the remaining 3 extraction kits, kit A produced the greatest yield whereas kit B provided the least yield (Kit-A/MSA-2002: 174.25 ± 34.98; Kit-A/MSA-2003: 179.89 ± 30.18; Kit-B/MSA-2002: 27.86 ± 9.35; Kit-B/MSA-2003: 23.14 ± 6.39; Kit-C/MSA-2002: 55.19 ± 10.18; Kit-C/MSA-2003: 35.80 ± 11.41 (Mean ± SD)). Also, kit A produced the greatest yield, whereas kit B provided the least yield. The PCoA 3D visualization of the Weighted Unifrac beta diversity shows that kits A and C cluster closely together while kit B appears as an outlier. The kit A sequencing samples cluster more closely together than both the other kits. The taxonomic profiles of kit B have lower recall when compared to the known mixture profiles indicating that kit B was inefficient at detecting some of the bacteria. Conclusion: Our data demonstrated that the DNA extraction method impacts DNA concentration, purity, and microbial communities detected by next-generation sequencing analysis. Further microbiome analysis performance comparison of using healthy stool samples is underway; also, colorectal cancer patients' samples will be acquired for further explore the clinical utilities. Collectively, our comprehensive qualification approach, including the evaluation of optimal DNA extraction conditions, the inclusion of positive controls, and the implementation of a robust qualified bioinformatics pipeline, assures accurate characterization of the microbiota in a complex matrix for deciphering the deep biology and enabling precision medicine.

Keywords: 16S rRNA sequencing, analytical validation, bioinformatics pipeline, metagenomics

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Authors: Hana Barak, Alex Sivan, Ariel Kushmaro

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Microorganisms are the most diverse and abundant life forms on Earth and account for a large portion of the Earth’s biomass and biodiversity. To date though, our knowledge regarding microbial life is lacking, as it is based mainly on information from cultivated organisms. Indeed, microbiologists have borrowed from astrophysics and termed the ‘uncultured microbial majority’ as ‘microbial dark matter’. The realization of how diverse and unexplored microorganisms are, actually stems from recent advances in molecular biology, and in particular from novel methods for sequencing microbial small subunit ribosomal RNA genes directly from environmental samples termed next-generation sequencing (NGS). This has led us to use NGS that generates several gigabases of sequencing data in a single experimental run, to identify and classify environmental samples of microorganisms. In metagenomics sequencing analysis (both 16S and shotgun), sequences are compared to reference databases that contain only small part of the existing microorganisms and therefore their taxonomy assignment may reveal groups of unknown microorganisms or origins. These unknowns, or the ‘microbial sequences dark matter’, are usually ignored in spite of their great importance. The goal of this work was to develop an improved bioinformatics method that enables more complete analyses of the microbial communities in numerous environments. Therefore, NGS was used to identify previously unknown microorganisms from three different environments (industrials wastewater, Negev Desert’s rocks and water wells at the Arava valley). 16S rRNA gene metagenome analysis of the microorganisms from those three environments produce about ~4 million reads for 75 samples. Between 0.1-12% of the sequences in each sample were tagged as ‘Unassigned’. Employing relatively simple methodology for resequencing of original gDNA samples through Sanger or MiSeq Illumina with specific primers, this study demonstrates that the mysterious ‘Unassigned’ group apparently contains sequences of candidate phyla. Those unknown sequences can be located on a phylogenetic tree and thus provide a better understanding of the ‘sequences dark matter’ and its role in the research of microbial communities and diversity. Studying this ‘dark matter’ will extend the existing databases and could reveal the hidden potential of the ‘microbial dark matter’.

Keywords: bacteria, bioinformatics, dark matter, Next Generation Sequencing, unknown

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Authors: Su Mon Saw, Joe Rothnagel

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Short open reading frames (sORFs) located in 5’UTR of mRNAs are known as uORFs. Characterization of uORF-encoded peptides (uPEPs) i.e., a subset of short open reading frame encoded peptides (sPEPs) and their translation regulation lead to understanding of causes of genetic disease, proteome complexity and development of treatments. Existence of uORFs within cellular proteome could be detected by LC-MS/MS. The ability of uORF to be translated into uPEP and achievement of uPEP identification will allow uPEP’s characterization, structures, functions, subcellular localization, evolutionary maintenance (conservation in human and other species) and abundance in cells. It is hypothesized that a subset of sORFs are translatable and that their encoded sPEPs are functional and are endogenously expressed contributing to the eukaryotic cellular proteome complexity. This project aimed to investigate whether sORFs encode functional peptides. Liquid chromatography-mass spectrometry (LC-MS) and bioinformatics were thus employed. Due to probable low abundance of sPEPs and small in sizes, the need for efficient peptide enrichment strategies for enriching small proteins and depleting the sub-proteome of large and abundant proteins is crucial for identifying sPEPs. Low molecular weight proteins were extracted using SDS-PAGE from Human Embryonic Kidney (HEK293) cells and Strong Cation Exchange Chromatography (SCX) from secreted HEK293 cells. Extracted proteins were digested by trypsin to peptides, which were detected by LC-MS/MS. The MS/MS data obtained was searched against Swiss-Prot using MASCOT version 2.4 to filter out known proteins, and all unmatched spectra were re-searched against human RefSeq database. ProteinPilot v5.0.1 was used to identify sPEPs by searching against human RefSeq, Vanderperre and Human Alternative Open Reading Frame (HaltORF) databases. Potential sPEPs were analyzed by bioinformatics. Since SDS PAGE electrophoresis could not separate proteins <20kDa, this could not identify sPEPs. All MASCOT-identified peptide fragments were parts of main open reading frame (mORF) by ORF Finder search and blastp search. No sPEP was detected and existence of sPEPs could not be identified in this study. 13 translated sORFs in HEK293 cells by mass spectrometry in previous studies were characterized by bioinformatics. Identified sPEPs from previous studies were <100 amino acids and <15 kDa. Bioinformatics results showed that sORFs are translated to sPEPs and contribute to proteome complexity. uPEP translated from uORF of SLC35A4 was strongly conserved in human and mouse while uPEP translated from uORF of MKKS was strongly conserved in human and Rhesus monkey. Cross-species conserved uORFs in association with protein translation strongly suggest evolutionary maintenance of coding sequence and indicate probable functional expression of peptides encoded within these uORFs. Translation of sORFs was confirmed by mass spectrometry and sPEPs were characterized with bioinformatics.

Keywords: bioinformatics, HEK293 cells, liquid chromatography-mass spectrometry, ProteinPilot, Strong Cation Exchange Chromatography, SDS-PAGE, sPEPs

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Authors: Penelope Paliadelis, Asheley Jones, Glenn Campbell

Abstract:

This paper discusses the development of co-designed capability frameworks for two large multinational organizations led by a university department. The aim was to create evidence-based, integrated capability frameworks that could define, identify, and measure human skill capabilities independent of specific work roles. The frameworks capture and cluster human skills required in the workplace and capture their application at various levels of mastery. Identified capability gaps inform targeted learning opportunities for workers to enhance their employability skills. The paper highlights the value of this evidence-based framework development process in capturing, defining, and assessing desired human-focused capabilities for organizational growth and success.

Keywords: capability framework, human skills, work-integrated learning, credentialing, digital badging

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Authors: Matheus Fonseca Durães, Bruno da Silva Pereira, Bruna Stewart

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The concept of Brazil’s water governance has been the topic of discussion and has undergone legal and organizational improvements due to the need to promote a more effective and sustainable relationship with natural resources and stemming from conflicts related to shortcomings in decision-making. The Waters Act has enabled Brazil to create interesting mechanisms for integrated management, but, on the other hand, it has created a challenge that involves the implementation of the principles established in this legal framework. This study aims to evaluate some challenges and opportunities for water governance in two watersheds based on data collection and analysis of concessions, the water use register, and flow data. The elements presented demonstrated, via an analysis of legally instituted criteria, that the level of commitment of water resources is high, especially to public supply, and the adoption of the reference flow constituted one of the main barriers to implementing an efficient system, demonstrating the need for a regulatory policy that considers the hydrological behavior of the watersheds. Finally, the current water management model presents challenges to be addressed to achieve the objectives proposed by the water policy, such as ensuring sustainable, rational, and integrated use of water resources.

Keywords: management, hydrology, public policies, Brazil

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Authors: Shairn Hollis-Turner

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The changing demands of workplace practice in the field of business information and administration have placed considerable pressure on educators to prepare students for the world of work. In this paper, we argue that appropriate forms of work-integrated learning (WIL) could enhance learning experiences in higher education and support educators to meet industry needs for changing times. The study aims to enhance business information and administration education from a practice perspective. The guiding research question is: How can a systematic understanding of work-integrated learning practices enhance learning experiences in higher education? The research design comprised comparative case studies across three countries and was framed by Activity Theory. Analysis of the findings highlighted the similarities across WIL systems for higher education practices and the differences within the activity systems. The findings showed similarities in program practice, content, placement, and in the struggles of students to find placements. The findings also showed misalignments between WIL preparation, delivery, and future focus of WIL at these institutions. The findings suggest that employment requirements vary across countries and that systems could be improved to meet the demands of workplace practice for changing times for the benefit of students’ learning and employability.

Keywords: business administration, business information, knowledge, post graduate diploma

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Authors: Firdous Nizar, Carmela Cucuzzella

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This paper explores how the integrated design process (IDP) was adopted for an architectural project. The IDP is a relatively new approach to collaborative design in architectural design projects in Canada. It has gained much traction recently as the closest possible approach to the successful management of low energy building projects and has been advocated as a productive method for multi-disciplinary collaboration within complex projects. This study is based on the premise that there are explicit and implicit dimensions of power within the integrated design process (IDP) in the green building industry that may or may not lead to irreconcilable differences in a process that demands consensus. To gain insight on the potential gap between the theoretical promises and practical realities of the IDP, a review of existing IDP literature is compared with a case study analysis of a competition-based architectural project in Canada, a first to incorporate the IDP in its overall design format. This paper aims to address the undertheorized power relations of the IDP in a real project. It presents a critical assessment through the lens of the combined theories of deliberative democracy by Jürgen Habermas, with that of agonistic pluralism by political theorist Chantal Mouffe. These two theories are intended to more appropriately embrace the conflictual situations in collaborative environments, and shed light on the relationships of power, between engineers, city officials, architects, and designers in this conventional consensus-based model. In addition, propositions for a shift in approach that embraces conflictual differences among its participants are put forth based on concepts of critical spatial practice by Markus Meissen. As IDP is a relatively new design process, it requires much deliberation on its structure from the theoretical framework built in this paper in order to unlock its true potential.

Keywords: agonistic pluralism, critical spatial practice, deliberative democracy, integrated design process

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Authors: A. Mohammed, A. Babatunde

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This study investigated the integrated removal of heavy metals, organic matter and nitrogen from landfill leachate using a novel laboratory scale constructed wetland system. The main objectives of this study were: (i) to assess the overall effectiveness of the constructed wetland system for treating landfill leachate; (ii) to examine the interactions and impact of key leachate constituents (heavy metals, organic matter and nitrogen) on the overall removal dynamics and efficiency. The constructed wetland system consisted of four stages operated in tidal flow and anoxic conditions. Results obtained from 215 days of operation have demonstrated extraordinary heavy metals removal up to 100%. Analysis of the physico- chemical data reveal that the controlling factors for metals removal were the anoxic condition and the use of the novel media (dewatered ferric sludge which is a by-product of drinking water treatment process) as the main substrate in the constructed wetland system. Results show that the use of the ferric sludge enhanced heavy metals removal and brought more flexibility to simultaneous nitrification and denitrification which occurs within the microbial flocs. Furthermore, COD and NH₄-N were effectively removed in the system and this coincided with enhanced aeration in the 2nd and 3rd stages of the constructed wetland system. Overall, the results demonstrated that the ferric dewatered sludge constructed wetland system would be an effective solution for integrated removal of pollutants from landfill leachates.

Keywords: constructed wetland, ferric dewatered sludge, heavy metals, landfill leachate

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Authors: A. Buruzs, M. F. Hatwágner, A. Torma, L. T. Kóczy

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Recently, an increasing number of researchers have been focusing on working out realistic solutions to sustainability problems. As sustainability issues gain higher importance for organisations, the management of such decisions becomes critical. Knowledge representation is a fundamental issue of complex knowledge based systems. Many types of sustainability problems would benefit from models based on experts’ knowledge. Cognitive maps have been used for analyzing and aiding decision making. A cognitive map can be made of almost any system or problem. A fuzzy cognitive map (FCM) can successfully represent knowledge and human experience, introducing concepts to represent the essential elements and the cause and effect relationships among the concepts to model the behavior of any system. Integrated waste management systems (IWMS) are complex systems that can be decomposed to non-related and related subsystems and elements, where many factors have to be taken into consideration that may be complementary, contradictory, and competitive; these factors influence each other and determine the overall decision process of the system. The goal of the present paper is to construct an efficient IWMS which considers various factors. The authors’ intention is to propose an expert based system design approach for implementing expert decision support in the area of IWMSs and introduces an appropriate methodology for the development and analysis of group FCM. A framework for such a methodology consisting of the development and application phases is presented.

Keywords: factors, fuzzy cognitive map, group decision, integrated waste management system

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Authors: Ankan Roy, Niharika, Samir Kumar Patra

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

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

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Authors: Nicolas Haber

Abstract:

The study addresses the design process of integrated product-service offerings as a measure of answering environmental sustainability concerns by replacing stand-alone physical artefacts with comprehensive solutions relying on functional results rather than conventional product sales. However, views regarding this transformation are dissimilar and differentiated: The study discusses the importance and requirements of product-service systems before analysing the theoretical studies accomplished in the extent of their design and development processes. Based on this, a framework, built on a design science approach, is proposed, where the distinct approaches from the literature are merged towards a unified structure serving as a generic methodology to designing product-service systems. Each stage of this model is then developed to present a holistic design proposal called the Functional Engineered Product-Service System (FEPSS) model. Product-service systems are portrayed as customisable solutions tailored to specific settings and defined circumstances. Moreover, the approaches adopted to guide the design process are diversified. A thorough analysis of the design strategies and development processes however, allowed the extraction of a design backbone, valid to varied situations and contexts whether they are product-oriented, use-oriented or result-oriented. The goal is to guide manufacturers towards an eased adoption of these integrated offerings, given their inherited environmental benefits, by proposing a robust all-purpose design process.

Keywords: functional product, integrated product-service offerings, product-service systems, sustainable design

Procedia PDF Downloads 267