Search results for: Silvaco ATLAS

Authors: Gabriela Prins, Quinette Louw, Dawn Ernstzen

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Background: Access to rehabilitation services is a major challenge globally, especially in low-and-middle income countries (LMICs) where resources and infrastructure are extremely limited. Telerehabilitation (TR) has emerged in recent decades as a highly promising method to dramatically expand accessibility to rehabilitation services globally. TR provides rehabilitation care remotely using communication technologies such as video conferencing, smartphones, and internet-connected devices. This boosts accessibility to underprivileged regions and allows for greater flexibility for patients. Despite this, TR is hindered by several factors, including limited technological resources, high costs, lack of digital access, and the unavailability of healthcare systems, which are major barriers to widespread adoption among LMIC patients. These barriers have collectively hindered the potential implementation and adoption of TR services in LMICs healthcare settings. Adoption of TR will also require the buy-in of end users and limited information is known on the perspectives of the SA population. Aim: The study aimed to understand patients' perspectives regarding the use of digital technology as part of their OA rehabilitation at a public community healthcare centre in the Cape Metropole Area. Methods: A qualitative descriptive study design was used on 10 OA patients from a public community rehabilitation centre in South Africa. Data collection included semi-structured interviews and patient-reported outcome measures (PSFS, ASES-8, and EuroQol EQ-5D-5L) on functioning and quality of life. Transcribed interview data were coded in Atlas.ti. 22.2 and analyzed using thematic analysis. The results were narratively documented. Results: Four themes arose from the interviews. The themes were Telerehabilitation awareness (Use of Digital Technology Information Sources and Prior Experience with Technology /TR), Telerehabilitation Benefits (Access to healthcare providers, Access to educational information, Convenience, Time and Resource Efficiency and Facilitating Family Involvement), Telerehabilitation Implementation Considerations (Openness towards TR Implementation, Learning about TR and Technology, Therapeutic relationship, and Privacy) and Future use of Telerehabilitation (Personal Preference and TR for the next generation). The ten participants demonstrated limited awareness and exposure to TR, as well as minimal digital literacy and skills. Skepticism was shown when comparing the effectiveness of TR to in-person rehabilitation and valued physical interactions with health professionals. However, some recognized potential benefits of TR for accessibility, convenience, family involvement and improving community health in the long term. Willingness existed to try TR with sufficient training. Conclusion: With targeted efforts addressing identified barriers around awareness, technological literacy, clinician readiness and resource availability, perspectives on TR may shift positively from uncertainty towards endorsement of this expanding approach for simpler rehabilitation access in LMICs.

Keywords: digital technology, osteoarthritis, primary health care, telerehabilitation

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Authors: Ivy Chen XQ

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This research places a much-needed focus on the conservation of the Blue Economy (BE) by focusing on the design and development of monitoring systems to track critical indicators on the status of the BE. In this process, local experiences provide an insight into important community issues, as well as the necessity to cooperate and collaborate in order to achieve sustainable options. Researchers worldwide and industry initiatives over the last decade show that the exploitation of marine resources has resulted in a significant decrease in the share of total allowable catch (TAC). The result has been strengthening law enforcement, yet the results have shown that problems were related to poor policies, a lack of understanding of over-exploitation, biological uncertainty and political pressures. This reality and other statistics that show a significant negative impact on the attainment of the Sustainable Development Goals (SDGs), warrant an emphasis on the development of national M&E systems, in order to provide evidence-based information, on the nature and scale of especially transnational fisheries crime and under-sea marine resources in the BE. In particular, a need exists to establish a compendium of relevant BE indicators to assess such impact against the SDGs by using selected SDG indicators for this purpose. The research methodology consists of ATLAS.ti qualitative approach and a case study will be developed of Illegal, unregulated and unreported (IUU) poaching and Illegal Wildlife Trade (IWT) as component of the BE as it relates to the case of abalone in southern Africa and Far East. This research project will make an original contribution through the analysis and comparative assessment of available indicators, in the design process of M&E systems and developing indicators and monitoring frameworks in order to track critical trends and tendencies on the status of the BE, to ensure specific objectives to be aligned with the indicators of the SDGs framework. The research will provide a set of recommendations to governments and stakeholders involved in such projects on lessons learned, as well as priorities for future research. The research findings will enable scholars, civil society institutions, donors and public servants, to understand the capability of the M&E systems, the importance of showing multi-level governance, in the coordination of information management, together with knowledge management (KM) and M&E at the international, regional, national and local levels. This coordination should focus on a sustainable development management approach, based on addressing socio-economic challenges to the potential and sustainability of BE, with an emphasis on ecosystem resilience, social equity and resource efficiency. This research and study focus are timely as the opportunities of the post-Covid-19 crisis recovery package will be grasped to set the economy on a path to sustainable development in line with the UN 2030 Agenda. The pandemic raises more awareness for the world to eliminate IUU poaching and illegal wildlife trade (IWT).

Keywords: Blue Economy (BE), transnational governance, Monitoring and Evaluation (M&E), Sustainable Development Goals (SDGs).

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Authors: Melanie Girdharilall, Anjli Himraj, Shivan Bhagwandin, Marike Venter De Villiers

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The allure of luxury has long been attractive, fashionable, mystifying, and complex. As globalisation and the popularity of social media continue to evolve, consumers are seeking status products. However, in emerging economies like South Africa, where 60% of the country lives in poverty, this desire is often far-fetched and out of reach to most of the consumers. As a result, luxury brands are introducing masstige products: products that are associated with luxury and status but within financial reach to the middle-class consumer. The biggest challenge that this industry faces is the lack of knowledge and expertise on black female’s hair composition and offering products that meet their intricate requirements. African consumers have unique hair types, and global brands often do not accommodate for the complex nature of their hair and their product needs. By gaining insight into this phenomenon, global cosmetic brands can benefit from brand expansion, product extensions, increased brand awareness, brand knowledge, and brand equity. The purpose of this study is to determine how cosmetic brands can leverage the concept of masstige products to cater to the needs of middle-income black African woman. This study explores the 18- to 35-year-old black female cohort, which comprises approximately 17% of the South African population. The black hair care industry in Africa is expected a 6% growth rate over the next 5 years. The study is grounded in Paul’s (2019) 3-phase model for masstige marketing. This model demonstrates that product, promotion, and place strategies play a significant role in masstige value creation and the impact of these strategies on the branding dimensions (brand trust, brand association, brand positioning, brand preference, etc.).More specifically, this theoretical framework encompasses nine stages, or dimensions, that are of critical importance to companies who plan to infiltrate the masstige market. In short, the most critical components to consider are the positioning of the product and its competitive advantage in comparison to competitors. Secondly, advertising appeals and use of celebrities, and lastly, distribution channels such as online or in-store while maintain the exclusivity of the brand. By means of an exploratory study, a qualitative approach was undertaken, and focus groups were conducted among black African woman. The focus groups were voice recorded, transcribed, and analysed using Atlas software. The main themes were identified and used to provide brands with insight and direction for developing a comprehensive marketing mix for effectively entering the masstige market. The findings of this study will provide marketing practitioners with in-depth insight into how to effectively position masstige brands in line with consumer needs. It will give direction to both existing and new brands aiming to enter this market, by giving a comprehensive marketing mix for targeting the growing black hair care industry in Africa.

Keywords: africa, masstige, cosmetics, hard care, black females

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Authors: Sahar Nasr, Lin Li, Edwin Wang

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Bladder cancer (BLCA) is known as the 13th cause of death among cancer patients worldwide, and ~575,000 new BLCA cases are diagnosed each year. Urothelial carcinoma (UC) is the most prevalent subtype among BLCA patients, which can be categorized into muscle-invasive bladder cancer (MIBC) and non-muscle-invasive bladder cancer (NMIBC). Currently, various therapeutic options are available for UC patients, including (1) transurethral resection followed by intravesical instillation of chemotherapeutics or Bacillus Calmette-Guérin for NMIBC patients, (2) neoadjuvant platinum-based chemotherapy (NAC) plus radical cystectomy is the standard of care for localized MIBC patients, and (3) systematic chemotherapy for metastatic UC. However, conventional treatments may lead to several challenges for treating patients. As an illustration, some patients may suffer from recurrence of the disease after the first line of treatment. Recently, immune checkpoint therapy (ICT) has been introduced as an alternative treatment strategy for the first or second line of treatment in advanced or metastatic BLCA patients. Although ICT showed lucrative results for a fraction of BLCA patients, ~80% of patients were not responsive to it. Therefore, novel treatment methods are required to augment the ICI response rate within BLCA patients. It has been shown that the infiltration of T-cells into the tumor microenvironment (TME) is positively correlated with the response to ICT within cancerous patients. Therefore, the goal of this study is to enhance the infiltration of cytotoxic T-cells into TME through the identification of target genes within the tumor that are responsible for the non-T-cell inflamed TME and their inhibition. BLCA bulk RNA-sequencing data from The Cancer Genome Atlas (TCGA) and immune score for TCGA samples were used to determine the Pearson correlation score between the expression of different genes and immune score for each sample. The genes with strong negative correlations were selected (r < -0.2). Thereafter, the correlation between the expression of each gene and survival in BLCA patients was calculated using the TCGA data and Cox regression method. The genes that are common in both selected gene lists were chosen for further analysis. Afterward, BLCA bulk and single-cell RNA-sequencing data were ranked based on the expression of each selected gene and the top and bottom 25% samples were used for pathway enrichment analysis. If the pathways related to the T-cell infiltration (e.g., antigen presentation, interferon, or chemokine pathways) were enriched within the low-expression group, the gene was included for downstream analysis. Finally, the selected genes will be used to calculate the correlation between their expression and the infiltration rate of the activated CD+8 T-cells, natural killer cells and the activated dendric cells. A list of potential target genes has been identified and ranked based on the above-mentioned analysis and criteria. SUN-1 got the highest score within the gene list and other identified genes in the literature as benchmarks. In conclusion, inhibition of SUN1 may increase the tumor-infiltrating lymphocytes and the efficacy of ICI in BLCA patients. BLCA tumor cells with and without SUN-1 CRISPR/Cas9 knockout will be injected into the syngeneic mouse model to validate the predicted SUN-1 effect on increasing tumor-infiltrating lymphocytes.

Keywords: data analysis, gene expression analysis, gene identification, immunoinformatic, functional genomics, transcriptomics

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Authors: Chevonne Reynolds, Res Altwegg, Andrew Balmford, Claire N. Spottiswoode

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Modern agriculture has revolutionised the planet’s capacity to support humans, yet has simultaneously had a greater negative impact on biodiversity than any other human activity. Balancing the demand for food with the conservation of biodiversity is one of the most pressing issues of our time. Biodiversity-friendly farming (‘land sharing’), or alternatively, separation of conservation and production activities (‘land sparing’), are proposed as two strategies for mediating the trade-off between agriculture and biodiversity. However, there is much debate regarding the efficacy of each strategy, as this trade-off has typically been addressed by short term studies at fine spatial scales. These studies ignore processes that are relevant to biodiversity at larger scales, such as meta-population dynamics and landscape connectivity. Therefore, to better understand species response to agricultural land-use and provide evidence to underpin the planning of better production landscapes, we need to determine the merits of each strategy at larger scales. In South Africa, a remarkable citizen science project - the South African Bird Atlas Project 2 (SABAP2) – collates an extensive dataset describing the occurrence of birds at a 5-min by 5-min grid cell resolution. We use these data, along with fine-resolution data on agricultural land-use, to determine which strategy optimises the agriculture-biodiversity trade-off in a southern African context, and at a spatial scale never considered before. To empirically test this trade-off, we model bird species population density, derived for each 5-min grid cell by Royle-Nicols single-species occupancy modelling, against both the amount and configuration of different types of agricultural production in the same 5-min grid cell. In using both production amount and configuration, we can show not only how species population densities react to changes in yield, but also describe the production landscape patterns most conducive to conservation. Furthermore, the extent of both the SABAP2 and land-cover datasets allows us to test this trade-off across multiple regions to determine if bird populations respond in a consistent way and whether results can be extrapolated to other landscapes. We tested the land sparing/sharing trade-off for 281 bird species across three different biomes in South Africa. Overall, a higher proportion of species are classified as losers, and would benefit from land sparing. However, this proportion of loser-sparers is not consistent and varies across biomes and the different types of agricultural production. This is most likely because of differences in the intensity of agricultural land-use and the interactions between the differing types of natural vegetation and agriculture. Interestingly, we observe a higher number of species that benefit from agriculture than anticipated, suggesting that agriculture is a legitimate resource for certain bird species. Our results support those seen at smaller scales and across vastly different agricultural systems, that land sparing benefits the most species. However, our analysis suggests that land sparing needs to be implemented at spatial scales much larger than previously considered. Species persistence in agricultural landscapes will require the conservation of large tracts of land, and is an important consideration in developing countries, which are undergoing rapid agricultural development.

Keywords: agriculture, birds, land sharing, land sparing

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Authors: Guilherme Oliveira

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The assimilation of images and their potential symbolism into lived experiences is inherent. It is through this exercise of recognition via imagistic records that the questioning of the origins of a constant narrative stimulated by the media arises. The construction of the "Man" archetype and the reflections of active masculine imagery in the 21st century, when conveyed through media channels, could potentially have detrimental effects. Addressing this systematic behavioral chronology of virile cisgender, permeated imagistically through these means, involves exploring potential resolutions. Thus, an investigation process is initiated into the potential representation of the 'hero' in this media emulation through idols contextualized in the political sphere, with the purpose of elucidating the processes of simulation and emulation of narratives based on mythical, historical, and sacred accounts. In this process of sharing, the narratives contained in the imagistic structuring offered by information dissemination channels seek validation through a process of public acceptance. To achieve this consensus, a visual set adorned with mythological and sacred symbolisms adapted to the intended environment is promoted, thus utilizing sociocultural characteristics in favor of political marketing. Visual recognition, therefore, becomes a direct reflection of a cultural heritage acquired through lived human experience, stimulated by continuous representations throughout history. Echoes of imagery and narratives undergo a constant process of resignification of their concepts, sharpened by their premises, and adapted to the environment in which they seek to establish themselves. Political figures analyzed in this article employ the practice of taking possession of symbolisms, mythological stories, and heroisms and adapt their visual construction through a continuous praxis of emulation. Thus, they utilize iconic mythological narratives to gain credibility through belief. Utilizing iconic mythological narratives for credibility through belief, the idol becomes the very act of release of trauma, offering believers liberation from preconceived concepts and allowing for the attribution of new meanings. To dissolve this issue and highlight the subjectivities within the intention of the image, a linguistic, semiotic, and anthropological methodology is created. Linguistics uses expressions like 'Blaming the Image' to create a mechanism of expressive action in questioning why to blame a construction or visual composition and thus seek answers in the first act. Semiotics and anthropology develop an imagistic atlas of graphic analysis, seeking to make connections, comparisons, and relations between modern and sacred/mystical narratives, emphasizing the different subjective layers of embedded symbolism. Thus, it constitutes a performative act of disarming the image. It creates a disenchantment of the superficial gaze under the constant reproduction of visual content stimulated by virtual networks, enabling a discussion about the acceptance of caricatures characterized by past fables.

Keywords: image, heroic narrative, media heroism, virile politics, political, myth, sacred performance, visual mythmaking, characterization dynamics

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Authors: Leander Van Neste, Kirk Wojno

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The innate immune system reacts to foreign insult in several unique ways, one of which is phagocytosis of perceived threats such as cancer, bacteria, and viruses. The goal of this study was to look for evidence of phagocytosed RNA from tumor cells in circulating monocytes. While all monocytes possess phagocytic capabilities, the non-classical CD14+/FCGR3A+ monocytes and the intermediate CD14++/FCGR3A+ monocytes most actively remove threatening ‘external’ cellular materials. Purified CD14-positive monocyte samples from fourteen patients recently diagnosed with clinically localized prostate cancer (PCa) were investigated by single-cell RNA sequencing using the 10X Genomics protocol followed by paired-end sequencing on Illumina’s NovaSeq. Similarly, samples were processed and used as controls, i.e., one patient underwent biopsy but was found not to harbor prostate cancer (benign), three young, healthy men, and three men previously diagnosed with prostate cancer that recently underwent (curative) radical prostatectomy (post-RP). Sequencing data were mapped using 10X Genomics’ CellRanger software and viable cells were subsequently identified using CellBender, removing technical artifacts such as doublets and non-cellular RNA. Next, data analysis was performed in R, using the Seurat package. Because the main goal was to identify differences between PCa patients and ‘control’ patients, rather than exploring differences between individual subjects, the individual Seurat objects of all 21 patients were merged into one Seurat object per Seurat’s recommendation. Finally, the single-cell dataset was normalized as a whole prior to further analysis. Cell identity was assessed using the SingleR and cell dex packages. The Monaco Immune Data was selected as the reference dataset, consisting of bulk RNA-seq data of sorted human immune cells. The Monaco classification was supplemented with normalized PCa data obtained from The Cancer Genome Atlas (TCGA), which consists of bulk RNA sequencing data from 499 prostate tumor tissues (including 1 metastatic) and 52 (adjacent) normal prostate tissues. SingleR was subsequently run on the combined immune cell and PCa datasets. As expected, the vast majority of cells were labeled as having a monocytic origin (~90%), with the most noticeable difference being the larger number of intermediate monocytes in the PCa patients (13.6% versus 7.1%; p<.001). In men harboring PCa, 0.60% of all purified monocytes were classified as harboring PCa signals when the TCGA data were included. This was 3-fold, 7.5-fold, and 4-fold higher compared to post-RP, benign, and young men, respectively (all p<.001). In addition, with 7.91%, the number of unclassified cells, i.e., cells with pruned labels due to high uncertainty of the assigned label, was also highest in men with PCa, compared to 3.51%, 2.67%, and 5.51% of cells in post-RP, benign, and young men, respectively (all p<.001). It can be postulated that actively phagocytosing cells are hardest to classify due to their dual immune cell and foreign cell nature. Hence, the higher number of unclassified cells and intermediate monocytes in PCa patients might reflect higher phagocytic activity due to tumor burden. This also illustrates that small numbers (~1%) of circulating peripheral blood monocytes that have interacted with tumor cells might still possess detectable phagocytosed tumor RNA.

Keywords: circulating monocytes, phagocytic cells, prostate cancer, tumor immune response

Procedia PDF Downloads 162

Authors: Majed Al Otaibi, Melissa Lessard-Beaudoin, Amel Loudghi, Raphael Chouinard-Watkins, Melanie Plourde, Frederic Calon, C. Alexandre Castellano, Stephen Cunnane, Helene Payette, Pierrette Gaudreau, Denis Gris, Rona K. Graham

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Introduction: Alzheimer disease (AD) is a chronic disorder that affects millions of individuals worldwide. Symptoms include memory dysfunction, and also alterations in attention, planning, language and overall cognitive function. Olfactory dysfunction is a common symptom of several neurological disorders including AD. Studying the mechanisms underlying the olfactory dysfunction may therefore lead to the discovery of potential biomarkers and/or treatments for neurodegenerative diseases. Objectives: To determine if olfactory dysfunction predicts future cognitive impairment in the aging population and to characterize the olfactory system in a murine model expressing a genetic factor of AD. Method: For the human study, quantitative olfactory tests (UPSIT and OMT) have been done on 93 subjects (aged 80 to 94 years) from the Quebec Longitudinal Study on Nutrition and Successful Aging (NuAge) cohort accepting to participate in the ORCA secondary study. The telephone Modified Mini Mental State examination (t-MMSE) was used to assess cognition levels, and an olfactory self-report was also collected. In a separate cohort, olfactory cortical volume was calculated using MRI results from healthy old adults (n=25) and patients with AD (n=18) using the AAL single-subject atlas and performed with the PNEURO tool (PMOD 3.7). For the murine study, we are using Western blotting, RT-PCR and immunohistochemistry. Result: Human Study: Based on the self-report, 81% of the participants claimed to not suffer from any problem with olfaction. However, based on the UPSIT, 94% of those subjects showed a poor olfactory performance and different forms of microsmia. Moreover, the results confirm that olfactory function declines with age. We also detected a significant decrease in olfactory cortical volume in AD individuals compared to controls. Murine study: Preliminary data demonstrate there is a significant decrease in expression levels of the proform of caspase-3 and the caspase substrate STK3, in the olfactory bulb of mice expressing human APOE4 compared with controls. In addition, there is a significant decrease in the expression level of the caspase-9 proform and caspase-8 active fragment. Analysis of the mature neuron marker, NeuN, shows decreased expression levels of both isoforms. The data also suggest that Iba-1 immunostaining is increased in the olfactory bulb of APOE4 mice compared to wild type mice. Conclusions: The activation of caspase-3 may be the cause of the decreased levels of STK3 through caspase cleavage and may play role in the inflammation observed. In the clinical study, our results suggest that seniors are unaware of their olfactory function status and therefore it is not sufficient to measure olfaction using the self-report in the elderly. Studying olfactory function and cognitive performance in the aging population will help to discover biomarkers in the early stage of the AD.

Keywords: Alzheimer's disease, APOE4, cognition, caspase, brain atrophy, neurodegenerative, olfactory dysfunction

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Authors: Ahmedou Moulaye Idriss, Yahya Tfeil

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Medical imaging technology has become an indispensable tool in many branches of the biomedical, health area, and research and is vitally important for the training of professionals in these fields. It is not only about the tools, technologies, and knowledge provided but also about the community that this training project proposes. In order to be able to raise the level of anatomy teaching in the medical school of Nouakchott in Mauritania, it is necessary and even urgent to facilitate access to modern technology for African countries. The role of technology as a key driver of justifiable development has long been recognized. Anatomy is an essential discipline for the training of medical students; it is a key element for the training of medical specialists. The quality and results of the work of a young surgeon depend on his better knowledge of anatomical structures. The teaching of anatomy is difficult as the discipline is being neglected by medical students in many academic institutions. However, anatomy remains a vital part of any medical education program. When anatomy is presented in various planes medical students approve of difficulties in understanding. They do not increase their ability to visualize and mentally manipulate 3D structures. They are sometimes not able to correctly identify neighbouring or associated structures. This is the case when they have to make the identification of structures related to the caudate lobe when the liver is moved to different positions. In recent decades, some modern educational tools using digital sources tend to replace old methods. One of the main reasons for this change is the lack of cadavers in laboratories with poorly qualified staff. The emergence of increasingly sophisticated mathematical models, image processing, and visualization tools in biomedical imaging research have enabled sophisticated three-dimensional (3D) representations of anatomical structures. In this paper, we report our current experience in the Faculty of Medicine in Nouakchott Mauritania. One of our main aims is to create a local learning community in the fields of anatomy. The main technological platform used in this project is called 3D Slicer. 3D Slicer platform is an open-source application available for free for viewing, analysis, and interaction with biomedical imaging data. Using the 3D Slicer platform, we created from real medical images anatomical atlases of parts of the human body, including head, thorax, abdomen, liver, and pelvis, upper and lower limbs. Data were collected from several local hospitals and also from the website. We used MRI and CT-Scan imaging data from children and adults. Many different anatomy atlases exist, both in print and digital forms. Anatomy Atlas displays three-dimensional anatomical models, image cross-sections of labelled structures and source radiological imaging, and a text-based hierarchy of structures. Open and free online anatomical atlases developed by our anatomy laboratory team will be available to our students. This will allow pedagogical autonomy and remedy the shortcomings by responding more fully to the objectives of sustainable local development of quality education and good health at the national level. To make this work a reality, our team produced several atlases available in our faculty in the form of research projects.

Keywords: anatomy, education, medical imaging, three dimensional

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Authors: A. Peyvan, D. Li, J. Komperda, F. Mashayek

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Turbulence can be observed in a variety fluid motions in nature and industrial applications. Recent investment in high-speed aircraft and propulsion systems has revitalized fundamental research on turbulent flows. In these systems, capturing chaotic fluid structures with different length and time scales is accomplished through the Direct Numerical Simulation (DNS) approach since it accurately simulates flows down to smallest dissipative scales, i.e., Kolmogorov’s scales. The discontinuous spectral element method (DSEM) is a high-order technique that uses spectral functions for approximating the solution. The DSEM code has been developed by our research group over the course of more than two decades. Recently, the code has been improved to run large cases in the order of billions of solution points. Running big simulations requires a considerable amount of RAM. Therefore, the DSEM code must be highly parallelized and able to start on multiple computational nodes on an HPC cluster with distributed memory. However, some pre-processing procedures, such as determining global element information, creating a global face list, and assigning global partitioning and element connection information of the domain for communication, must be done sequentially with a single processing core. A separate code has been written to perform the pre-processing procedures on a local machine. It stores the minimum amount of information that is required for the DSEM code to start in parallel, extracted from the mesh file, into text files (pre-files). It packs integer type information with a Stream Binary format in pre-files that are portable between machines. The files are generated to ensure fast read performance on different file-systems, such as Lustre and General Parallel File System (GPFS). A new subroutine has been added to the DSEM code to read the startup files using parallel MPI I/O, for Lustre, in a way that each MPI rank acquires its information from the file in parallel. In case of GPFS, in each computational node, a single MPI rank reads data from the file, which is specifically generated for the computational node, and send them to other ranks on the node using point to point non-blocking MPI communication. This way, communication takes place locally on each node and signals do not cross the switches of the cluster. The read subroutine has been tested on Argonne National Laboratory’s Mira (GPFS), National Center for Supercomputing Application’s Blue Waters (Lustre), San Diego Supercomputer Center’s Comet (Lustre), and UIC’s Extreme (Lustre). The tests showed that one file per node is suited for GPFS and parallel MPI I/O is the best choice for Lustre file system. The DSEM code relies on heavily optimized linear algebra operation such as matrix-matrix and matrix-vector products for calculation of the solution in every time-step. For this, the code can either make use of its matrix math library, BLAS, Intel MKL, or ATLAS. This fact and the discontinuous nature of the method makes the DSEM code run efficiently in parallel. The results of weak scaling tests performed on Blue Waters showed a scalable and efficient performance of the code in parallel computing.

Keywords: computational fluid dynamics, direct numerical simulation, spectral element, turbulent flow

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Authors: Abouchouaib Belahmira, Joerg W. Schneider, Hafid Saber, Sara Akboub

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The lithofacies analyzed herein were reported from the interbedded fluvial and lacustrine deposits of the Oued Issene and El Menizla formations. These formations are part of the sedimentary fill of the Carboniferous (Stephanian) submontaneous Souss basin. The latter is situated in the western High Atlas Mountains, south-central Morocco, about 50km east of Agadir. The Souss basin started as a single basin but was separated into sub-basins called Ida Ou Zal and Ida Ou Ziki by sinistral displacement along the west branch of the Tizi N'Test Fault during the end of the Mauritanid phase of the Variscan orogeny in Morocco, after the early Stephanian (Kasimovian) and before the late middle Permian (Capitanian). The studied succession is a monotonous finning-upward sequence of 1800 m thick. It consists of fine-grained sandstone, finely bedded siltstone and thinly laminated claystone, and black shale. Herein we provide a detailed characterization of lithofacies of the upper El Menizla and Oued Issène formations, with a focus on the prevailing overbank to flood plain fine-grained lithofacies. The studied facies are capping the Stephanian alluvial fan basal clast-supported conglomerates that are intercalated bedded coarse-grained sandstones of Ikhourba Formation in the Ou Zal subbasin and Tajgaline Formation in the Ida Ou Ziki subbasin, respectively. Within the fluvial elements, only two main facies have been observed. It comprises channel-fill and channel-bar deposits, mostly occur as lenticular –shape sand bodies or sheet-like sand greenish to gray fine-to medium (Fm), massive internally structureless, or very locally exhibits a medium to large scale trough-cross bedding medium to coarse sandstone (St), observable in relatively thicker bed. These facies are laterally extensive, with a thickness varying from a few to several meters. Finer-grained sediments such as mud can be present as drapes over bedforms. Whilst the fluvial association FA1, the overbank elements are represented by a relatively wide range of 5 facies. This exhibit mostly a cm scale horizontally bedded greenish fine- to medium sand and silt, and mm scale fossiliferous thinly laminated dark gray- black Corganic-rich clays to siltstone associated with black shale. Thus, FA2 includes flood plain fines (Fh, R) associated with the paleosols and back swamp coaly clay facies (C). The floodplain lake element comprises only laminated organic-rich dark gray facies of claystone, black shale, and graded siltstone. Bedsets are dm to several meters thick (typically < 1 m thick). They are intercalated between several m-thick fluvial sandstone, extend over a few meters, and are poorly bioturbated. The lacustrine facies described in this study have been divided into two sub-facies (Fl, B) based on field observations that indicate differing environmental conditions of formation. Thus, the thorough analysis of the lithofacies of the Souss basin units allows us to reconstruct the original environment that was interpreted as a typical fluvial-dominated braided to anastomosing wide distributary channel system and surrounding deep to shallow freshwater floodplain lakes and back swamps.

Keywords: Souss, carboniferous, facies, depositional setting

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Authors: Manon Frédout, Laëtitia Bucari, Mathias Aloui, Gaëtan Duhamel, Olivier Rovellotti, Javier Blanco

Abstract:

Ecosystems must be resilient to ensure cleaner air, better water and soil quality, and thus healthier citizens. Technology can be an excellent tool to support urban ecosystem restoration projects, especially when based on Open Source and promoting Open Data. This is the goal of the ecoTeka application: one single digital tool for tree management which allows decision-makers to improve their urban forestry practices, enabling more responsible urban planning and climate change adaptation. EcoTeka provides city councils with three main functionalities tackling three of their challenges: easier biodiversity inventories, better green space management, and more efficient planning. To answer the cities’ need for reliable tree inventories, the application has been first built with open data coming from the websites OpenStreetMap and OpenTrees, but it will also include very soon the possibility of creating new data. To achieve this, a multi-source algorithm will be elaborated, based on existing artificial intelligence Deep Forest, integrating open-source satellite images, 3D representations from LiDAR, and street views from Mapillary. This data processing will permit identifying individual trees' position, height, crown diameter, and taxonomic genus. To support urban forestry management, ecoTeka offers a dashboard for monitoring the city’s tree inventory and trigger alerts to inform about upcoming due interventions. This tool was co-constructed with the green space departments of the French cities of Alès, Marseille, and Rouen. The third functionality of the application is a decision-making tool for urban planning, promoting biodiversity and landscape connectivity metrics to drive ecosystem restoration roadmap. Based on landscape graph theory, we are currently experimenting with new methodological approaches to scale down regional ecological connectivity principles to local biodiversity conservation and urban planning policies. This methodological framework will couple graph theoretic approach and biological data, mainly biodiversity occurrences (presence/absence) data available on both international (e.g., GBIF), national (e.g., Système d’Information Nature et Paysage) and local (e.g., Atlas de la Biodiversté Communale) biodiversity data sharing platforms in order to help reasoning new decisions for ecological networks conservation and restoration in urban areas. An experiment on this subject is currently ongoing with Montpellier Mediterranee Metropole. These projects and studies have shown that only 26% of tree inventory data is currently geo-localized in France - the rest is still being done on paper or Excel sheets. It seems that technology is not yet used enough to enrich the knowledge city councils have about biodiversity in their city and that existing biodiversity open data (e.g., occurrences, telemetry, or genetic data), species distribution models, landscape graph connectivity metrics are still underexploited to make rational decisions for landscape and urban planning projects. This is the goal of ecoTeka: to support easier inventories of urban biodiversity and better management of urban spaces through rational planning and decisions relying on open databases. Future studies and projects will focus on the development of tools for reducing the artificialization of soils, selecting plant species adapted to climate change, and highlighting the need for ecosystem and biodiversity services in cities.

Keywords: digital software, ecological design of urban landscapes, sustainable urban development, urban ecological corridor, urban forestry, urban planning

Procedia PDF Downloads 70

Authors: Oluwaseun Adeleke, Samuel O. Ikani, Simeon Christian Chukwu, Fidelis Edet, Anthony Nwala, Mopelola Raji, Simeon Christian Chukwu

Abstract:

Background: Health service providers are offered in-service training periodically to strengthen their ability to deliver services that are ethical, quality, timely and safe. Not all capacity-building courses have successfully resulted in intended service delivery outcomes because of poor training content, design, approach, and ambiance. The Delivering Innovations in Selfcare (DISC) project developed a Moment of Truth innovation, which is a proven training model focused on improving consumer/provider interaction that leads to an increase in the voluntary uptake of subcutaneous depot medroxyprogesterone acetate (DMPA-SC) self-injection among women who opt for injectable contraception. Methodology: Six months after training on a moment of truth (MoT) training manual, the project conducted two intensive rounds of qualitative data collection and triangulation that included provider, client, and community mobilizer interviews, facility observations, and routine program data collection. Respondents were sampled according to a convenience sampling approach, and data collected was analyzed using a codebook and Atlas-TI. Providers and clients were interviewed to understand their experience, perspective, attitude, and awareness about the DMPA-SC self-inject. Data were collected from 12 health facilities in three states – eight directly trained and four cascades trained. The research team members came together for a participatory analysis workshop to explore and interpret emergent themes. Findings: Quality-of-service delivery and performance outcomes were observed to be significantly better in facilities whose providers were trained directly trained by the DISC project than in sites that received indirect training through master trainers. Facilities that were directly trained recorded SI proportions that were twice more than in cascade-trained sites. Direct training comprised of full-day and standalone didactic and interactive sessions constructed to evoke commitment, passion and conviction as well as eliminate provider bias and misconceptions in providers by utilizing human interest stories and values clarification exercises. Sessions also created compelling arguments using evidence and national guidelines. The training also prioritized demonstration sessions, utilized job aids, particularly videos, strengthened empathetic counseling – allaying client fears and concerns about SI, trained on positioning self-inject first and side effects management. Role plays and practicum was particularly useful to enable providers to retain and internalize new knowledge. These sessions provided experiential learning and the opportunity to apply one's expertise in a supervised environment where supportive feedback is provided in real-time. Cascade Training was often a shorter and abridged form of MoT training that leveraged existing training already planned by master trainers. This training was held over a four-hour period and was less emotive, focusing more on foundational DMPA-SC knowledge such as a reorientation to DMPA-SC, comparison of DMPA-SC variants, counseling framework and skills, data reporting and commodity tracking/requisition – no facility practicums. Training on self-injection was not as robust, presumably because they were not directed at methods in the contraceptive mix that align with state/organizational sponsored objectives – in this instance, fostering LARC services. Conclusion: To achieve better performance outcomes, consideration should be given to providing training that prioritizes practice-based and emotive content. Furthermore, a firm understanding and conviction about the value training offers improve motivation and commitment to accomplish and surpass service-related performance outcomes.

Keywords: training, performance outcomes, innovation, family planning, contraception, DMPA-SC, self-care, self-injection.

Procedia PDF Downloads 85