Search results for: gene regulation

Authors: Berk Ecer, Ebru Akcapinar Sezer

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Traditional management models of intersections, such as no-light intersections or signalized intersection, are not the most effective way of passing the intersections if the vehicles are intelligent. To this end, Dresner and Stone proposed a new intersection control model called Autonomous Intersection Management (AIM). In the AIM simulation, they were examining the problem from a multi-agent perspective, demonstrating that intelligent intersection control can be made more efficient than existing control mechanisms. In this study, autonomous intersection management has been investigated. We extended their works and added a potential-based lane organization layer. In order to distribute vehicles evenly to each lane, this layer triggers vehicles to analyze near lanes, and they change their lane if other lanes have an advantage. We can observe this behavior in real life, such as drivers, change their lane by considering their intuitions. Basic intuition on selecting the correct lane for traffic is selecting a less crowded lane in order to reduce delay. We model that behavior without any change in the AIM workflow. Experiment results show us that intersection performance is directly connected with the vehicle distribution in lanes of roads of intersections. We see the advantage of handling lane management with a potential approach in performance metrics such as average delay of intersection and average travel time. Therefore, lane management and intersection management are problems that need to be handled together. This study shows us that the lane through which vehicles enter the intersection is an effective parameter for intersection management. Our study draws attention to this parameter and suggested a solution for it. We observed that the regulation of AIM inputs, which are vehicles in lanes, was as effective as contributing to aim intersection management. PLO-AIM model outperforms AIM in evaluation metrics such as average delay of intersection and average travel time for reasonable traffic rates, which is in between 600 vehicle/hour per lane to 1300 vehicle/hour per lane. The proposed model reduced the average travel time reduced in between %0.2 - %17.3 and reduced the average delay of intersection in between %1.6 - %17.1 for 4-lane and 6-lane scenarios.

Keywords: AIM project, autonomous intersection management, lane organization, potential-based approach

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Authors: Dimakatso B. Gumede, Nicolette N. Houreld

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Diabetic foot ulcers (DFUs) are a complication of diabetes mellitus (DM), a metabolic disease caused by insulin resistance or insufficiency, resulting in hyperglycaemia and low-grade chronic inflammation. Current therapies for treating DFUs include wound debridement, glycaemic control, and wound dressing. However, these therapies are moderately effective as there is a recurrence of these ulcers and an increased risk of lower limb amputations. Photobiomodulation (PBM), which is the application of non-invasive low-level light for wound healing at the spectrum of 660-1000 nm, has shown great promise in accelerating the healing of chronic wounds. However, its underlying mechanisms are not clearly defined. Studies have indicated that PBM induces wound healing via the activation of signaling pathways that are involved in tissue repair, such as the transforming growth factor-β (TGF-β). However, other signaling pathways, such as the WNT/β-catenin pathway, which is also critical for wound repair, have not been investigated. This study aimed to elucidate if PBM at 660 nm and a fluence of 5 J/cm² activates the WNT/β-catenin signaling pathway for wound healing in a diabetic cellular model. Human dermal fibroblasts (WS1) were continuously cultured high-glucose (26.5 mM D-glucose) environment to create a diabetic cellular model. A central scratch was created in the diabetic model to ‘wound’ the cells. The diabetic wounded (DW) cells were thereafter irradiated at 660 nm and a fluence of 5 J/cm². Cell migration, gene expression and protein assays were conducted at 24- and 48-h post-PBM. The results showed that PBM at 660 nm and a fluence of 5 J/cm² significantly increased cell migration in diabetic wounded cells at 24-h post-PBM. The expression of CTNNB1, ACTA2, COL1A1 and COL3A1 genes was also increased in DW cells post-PBM. Furthermore, there was increased cytoplasmic accumulation and nuclear localization of β-catenin at 24 h post-PBM. The findings in this study demonstrate that PBM activates the WNT/β-catenin signaling pathway by inducing the accumulation of β-catenin in diabetic wounded cells, leading to increased cell migration and expression of wound repair markers. These results thus indicate that PBM has the potential to improve wound healing in diabetic ulcers via activation of the WNT/β-catenin signaling pathway.

Keywords: wound healing, diabetic ulcers, photobiomodulation, WNT/β-catenin, signalling pathway

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Authors: Max Plotnikov, Arkadius Schier

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To counteract climate change, the European Commission adopted the European Green Deal (EDG) in 2019. Some of the main objectives of the EDG are climate neutrality by 2050, decarbonization, sustainable mobility, and the shift from a linear economy to a circular economy in the European Union. The mobility turnaround envisages, among other things, the switch from classic internal combustion vehicles to electromobility. The aforementioned goals are therefore accompanied by increased demand for lithium-ion batteries (LIBs) and the associated logistics. However, this inevitably gives rise to challenges that need to be addressed. Depending on whether the LIB is transported by road, rail, air, or sea, there are different regulatory frameworks in the European Union that relevant players in the value chain must adhere to. LIBs are classified as Dangerous Goods Class 9, and against this backdrop, there are various restrictions that need to be adhered to when transporting them for various actors. Currently, the exchange of information in the value chain between the various actors is almost entirely paper-based. Especially in the transport of dangerous goods, this often leads to a delay in the transport or to incorrect data. The exchange of information with the authorities is particularly essential in this context. A solution for the digital exchange of information is currently being developed. Electronic freight transport information (eFTI) enables fast and secure exchange of information between the players in the freight transport process. This concept is to be used within the supply chain from 2025. Another initiative that is expected to improve the monitoring of LIB in this context, among other things, is the battery pass. In July 2023, the latest battery regulation was adopted in the Official Journal of the European Union. This battery pass gives different actors static as well as dynamic information about the batteries depending on their access rights. This includes master data such as battery weight or battery category or information on the state of health or the number of negative events that the battery has experienced. The integration of the battery pass with the eFTI platform will be investigated for synergy effects in favor of the actors for battery transport.

Keywords: battery logistics, battery passport, data sharing, eFTI, sustainability

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Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Patrice Conner

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Nanotechnologies have enormous potential to contribute to human flourishing in responsible and sustainable ways. They are rapidly developing field of science, technology and innovation. As enabling technologies, their full scope of applications is potentially very wide. Major implications are expected in many areas, e.g. healthcare, information and communication technologies, energy production and storage, materials science/chemical engineering, manufacturing, environmental protection, consumer products, etc. However, nanotechnologies are unlikely to realize their full potential unless their associated societal and ethical issues are adequately attended. Namely nanotechnologies and nanoparticles may expose humans and the environment to new health risks, possibly involving quite different mechanisms of interference with the physiology of human and environmental species. One of the building blocks of the ‘safe, integrated and responsible’ approach is standardization. Both the Economic and Social Committee and the European Parliament have highlighted the importance to be attached to standardization as a means to accompany the introduction on the market of nanotechnologies and nanomaterials, and a means to facilitate the implementation of regulation. ISO and CEN have respectively started in 2005 and 2006 to deal with selected topics related to this emerging and enabling technology. In the beginning of 2010, EC DG ‘Enterprise and Industry’ addressed the mandate M/461 to CEN, CENELEC and ETSI for standardization activities regarding nanotechnologies and nanomaterials. Thus CEN/TC 352 ‘Nanotechnologies’ has been asked to take the leadership for the coordination in the execution of M/461 (46 topics to be standardized) and to contact relevant European and International Technical committees and interested stakeholders as appropriate (56 structures have been identified). Prior requests from M/461 deal with characterization and exposure of nanomaterials and any matters related to Health, Safety and Environment. Answers will be given to: - What are the structures and how they work? - Where are we right now and how work is going from now onwards? - How CEN’s work and targets deal with and interact with global matters in this field?

Keywords: characterization, environmental protection, exposure, health risks, nanotechnologies, responsible and sustainable ways, safety

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Authors: Marjan Moradi fard, Hossein Rassi, Masoud Houshmand

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Aim: Breast cancer is one of the most common cancers affecting the morbidity and mortality of Iranian women. This disease is a result of collective alterations of oncogenes and tumor suppressor genes. Studies have produced conflicting results concerning the role of p53 codon 72 polymorphism (G>C) and miR-146a rs2910164 polymorphism (G>C) on the risk of several cancers; therefore, a research was performed to estimate the association between the p53 codon 72 polymorphism and miR-146a rs2910164 polymorphism in breast cancer. Methods and Materials: A total of 45 archival breast cancer samples from Khatam hospital and 40 healthy samples were collected. Verification of each cancer reported in a relative was sought through the pathology reports of the hospital records. Then, DNA extracted from all samples by standard methods and p53 codon 72 polymorphism genotypes and miR-146a rs2910164 polymorphism genotypes were analyzed using multiplex PCR. The tubules, mitotic activity, necrosis, polymorphism and grade of breast cancer were staged by Nottingham histological grading and immunohistochemical staining of the sections from the paraffin wax embedded tissues for the expression of ER, PR and p53 was carried out using a standard method. Finally, data analysis was performed using the 7 version of the Epi Info(TM) 2012 software and test chi-square(x2) for trend. Results: Successful DNA extraction was assessed by PCR amplification of b-actin gene (99 bp). According to the results, p53 GG genotype and miR-146a rs2910164 CC genotype was significantly associated with increased risk of breast cancer in the study population. In this study, we established that tumors of p53 GG genotype and miR-146a rs2910164 CC genotype exhibited higher mitotic activity, higher polymorphism, lower necrosis, lower tubules, higher ER- and PR-negatives and lower TP53-positives than the other genotypes. Conclusion: The present study provided preliminary evidence that a p53 GG genotype may effect breast cancer risk in the study population, interacting synergistically with miR-146a rs2910164 CC genotype. Our results demonstrate that the testing of p53 codon 72 polymorphism genotypes and miR-146a rs2910164 polymorphism genotypes in combination with clinical parameters can serve as major risk factors in the early identification of breast cancers.

Keywords: breast cancer, miR-146a rs2910164 polymorphism, p53 codon 72 polymorphism, tumors, pathology reports

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Authors: Zeina Bourhane, Anders Lanzen, Christine Cagnon, Olfa Ben Said, Cristiana Cravo-Laureau, Robert Duran

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The anthropogenic pressure in coastal areas increases dramatically with the exploitation of environmental resources. Biomonitoring coastal areas are crucial to determine the impact of pollutants on bacterial communities in soils and sediments since they provide important ecosystem services. However, relevant biomonitoring tools allowing fast determination of the ecological status are yet to be defined. Microbial ecology approaches provide useful information for developing such microbial monitoring tools reporting on the effect of environmental stressors. Chemical and microbial molecular approaches were combined in order to determine microbial bioindicators for assessing the ecological status of soil and river ecosystems around the Ichkeul Lake (Tunisia), an area highly impacted by human activities. Samples were collected along soil/river/lake continuums in three stations around the Ichkeul Lake influenced by different human activities at two seasons (summer and winter). Contaminant pressure indexes (PI), including PAHs (Polycyclic aromatic hydrocarbons), alkanes, and OCPs (Organochlorine pesticides) contents, showed significant differences in the contamination level between the stations with seasonal variation. Bacterial communities were characterized by 16S ribosomal RNAs (rRNA) gene metabarcoding. Although microgAMBI indexes, determined from the sequencing data, were in accordance with contaminant contents, they were not sufficient to fully explain the PI. Therefore, further microbial indicators are still to be defined. The comparison of bacterial communities revealed the specific microbial assemblage for soil, river, and lake sediments, which were significantly correlated with contaminant contents and PI. Such observation offers the possibility to define a relevant set of bioindicators for reporting the effects of human activities on the microbial community structure. Such bioindicators might constitute useful monitoring tools for the management of microbial communities in coastal areas.

Keywords: bacterial communities, biomonitoring, contamination, human impacts, microbial bioindicators

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Authors: Jin-Hyeong Park, Hong-Seok Kim, Jin-Hyeok Yim, Young-Ji Kim, Dong-Hyeon Kim, Jung-Whan Chon, Kun-Ho Seo

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Salmonella contamination in chicken samples can cause major health problems in humans. However, not only the effects of antibiotic treatment during growth but also the impacts of poultry slaughter line on the prevalence of Salmonella in final chicken meat sold to consumers are unknown. In this study, we compared the isolation rates and antimicrobial resistance of Salmonella between antibiotic-free, conventional, conventional Korean native retail chicken meat samples and clonal divergence of Salmonella isolates by multilocus sequence typing. In addition, the distribution of extended-spectrum β-lactamase (ESBL) genes in ESBL-producing Salmonella isolates was analyzed. A total of 72 retail chicken meat samples (n = 24 antibiotic-free broiler [AFB] chickens, n = 24 conventional broiler [CB] chickens, and n = 24 conventional Korean native [CK] chickens) were collected from local retail markets in Seoul, South Korea. The isolation rates of Salmonella were 66.6% in AFB chickens, 45.8% in CB chickens, and 25% in CK chickens. By analyzing the minimum inhibitory concentrations of β -lactam antibiotics with the disc-diffusion test, we found that 81.2% of Salmonella isolates from AFB chickens, 63.6% of isolates from CB chickens, and 50% of isolates from CK chickens were ESBL producers; all ESBL-positive isolates had the CTX-M-15 genotype. Interestingly, all ESBL-producing Salmonella were revealed as ST16 by multilocus sequence typing. In addition, all CTX-M-15-positive isolates had the genetic platform of blaCTX-M gene (IS26-ISEcp1-blaCTX-M-15-IS903), to the best of our knowledge, this is the first report in Salmonella around the world. The Salmonella ST33 strain (S. Hadar) isolated in this study has never been reported in South Korea. In conclusion, our findings showed that antibiotic-free retail chicken meat products were also largely contaminated with ESBL-producing Salmonella and that their ESBL genes and genetic platforms were the same as those isolated from conventional retail chicken meat products.

Keywords: antibiotic-free poultry, conventional poultry, multilocus sequence typing, extended-spectrum β-lactamase, antimicrobial resistance

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Authors: Radovan Čobanović, Milica Rankov Šicar

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The fresh cheese is in the group of perishable food which cannot be kept a long period of time. The study of sustainability have been done in order to extend the shelf-life of the product which was 15 days. According to the plan of sustainability it was defined that 35 samples had to be stored for 30 days at 2°C−6°C and analyzed every 7th day from the day of reception until 30th day. Shelf life of the cheese has expired during the study of sustainability in the period between 15th and 30th day of analyses. Cheese samples were subjected to sensory analysis (appearance, odor, taste, color, aroma) and bacteriological analyzes (Listeria monocytogenes, Salmonella spp., Bacillus cereus, Staphylococcus aureus and total plate count) according to Serbian state regulation. All analyses were tested according to ISO methodology: sensory analysis ISO 6658, Listeria monocytogenes ISO 11 290-1, Salmonella spp ISO 6579, Bacillus cereus ISO 7932, Staphylococcus aureus ISO 6888-1, and total plate count ISO 4833. Analyses showed that after fifteen days of storage at a temperature defined by the manufacturers and within the product's shelf life, the cheese did not have any noticeable changes in sensory characteristics. Smell and taste are unaffected there was no separation of whey and there was not presence of strange smell or taste. As far as microbiological analyses are concerned neither one pathogen was detected and total plate count was at level of 103 cfu/g. After expiry of shelf life in a period of 15th and 30th day of storage, the analysis showed that there was a separation of whey on the surface. Along the edge of the container was present a dried part of cheese and sour-milky smell and taste were very weakly expressed. Concerning the microbiological analyses there still were not positive results for pathogen microorganisms but the total plate count was at a level of 106cfu/g. Based on the obtained results it can be concluded that this product cannot have longer shelf life than shelf life which is already defined because there are a sensory changes that would certainly have influence on decision of customers when purchase of this product is concerned.

Keywords: sustainability, fresh cheese, shelf-life, product

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Authors: Payal Maheshwari, Maheaswari Brindavan

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The present study aimed at studying the level of perceived self-efficacy of children with learning disability and their mother’s perception about the efficacy of the child and the relationship between the two. The study further aimed at finding out the relationship between the level of perceived self-efficacy of children with learning disability and their academic achievement and their mother’s perception about the Efficacy of the child and child’s Academic Achievement. The sample comprised of 80 respondents (40 children with learning disability and their mothers). Children with learning disability as their primary condition, belonging to middle or upper middle class, living with both the parents, residing in Mumbai and their mothers were selected. Purposive or judgmental and snowball sampling technique was used to select the sample for the present study. Proformas in the form of questionnaires were used to obtain the background information of the children with learning disability and their mother’s. A self-constructed Mother’s Perceived Efficacy of their Child Assessment Scale was used to measure mothers perceived level of efficacy of their child with learning disability. Self-constructed Child’s Perceived Self-Efficacy Assessment Scale was used to measure the level of child’s perceived self-efficacy. Academic scores of the child were collected from the child’s parents or teachers and were converted into percentage. The data were analyzed quantitatively using frequencies, mean and standard deviation. Correlations were computed to ascertain the relationships between the different variables. The findings revealed that majority of the mother’s perceived efficacy about their child with learning disability was above average as well as majority of the children with learning disability also perceived themselves as having above average level of self-efficacy. Further in the domains of self-regulated learning and emotional self-efficacy majority of the mothers perceived their child as having average or below average efficacy, 50% of the children also perceived their self-efficacy in the two domains at average or below average level. A significant (r=.322, p < .05) weak correlation (Spearman’s rho) was found between mother’s perceived efficacy about their child, and child’s perceived self-efficacy and a significant (r=.377, p < .01) weak correlation (Pearson Correlation) was also found between mother’s perceived efficacy about their child and child’s academic achievement. Significant weak positive correlation was found between child’s perceived self-efficacy and academic achievement (r=.332, p < .05). Based on the findings, the study discussed the need for intervention program for children in non-academic skills like self-regulation and emotional competence.

Keywords: learning disability, perceived self efficacy, academic achievement, mothers, children

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Authors: Nurjannatul Naim Kamaruddin, Tengku Sifziuzl Tengku Muhammad, Aina Farahiyah Abdul Manan, Habsah Mohamad

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Atherosclerosis which leads to cardiovascular diseases such as myocardial infarction, unstable angina (ischemic heart pain), sudden cardiac death and stroke is the principal cause of death worldwide. It has been a very critical issue as current common drug treatment, statin therapy has left bad side effects like rhabdomyolysis, atrial fibrillation, liver disease, abdominal and chest pain. Interestingly, the discoveries of proprotein convertase subtilisin-kexin type 9 have paved a new way in the treatment of atherosclerosis. This serine protease is believed to involve in the regulation of LDL- uptake by LDL-receptor. Therefore, this study was conducted to evaluate the potential of Acanthaster plancii fractions to reduce the transcriptional activity of the PCSK9 promoter. In this study, the marine organism which is Acanthaster plancii has been used as the source for marine compounds in inhibiting PCSK9. The cytotoxicity activity of ten fractions from the methanol extracts of Acanthaster plancii was investigated on HepG2 cell lines using MTS assay and dual glo luciferase assay was carried out later to analyses the effects of the samples in reducing the transcriptional activity of the PCSK9 promoter. Both assays used fractions with five different concentrations, 3.13µg/mL, 6.25µg/mL, 12.5µg/mL, 25µg/mL, and 50µg/mL. MTS assay indicated that the fractions are non-cytotoxic towards HepG2 cell lines as their IC50 value is greater than 30µg/mL. Whilst, for the dual glo luciferase assay, among all the fractions, Enhance Fraction 2 (EF2) showed the best potential in reducing the transcriptional activity of the PCSK9 promoter. The results indicated that this EF2 gave the lowest PCSK9 promoter expression at low concentration which is 0.2 fold change at 6.25µg/mL. This finding suggested that further analysis should be done to validate the potential of Acanthaster plancii as the source of anti-atherosclerotic agent.

Keywords: Acanthaster plancii, atherosclerosis, luciferase assay, PCSK9

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Authors: Sheraz Gul

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The requirements for progressing a compound to clinical trials is well established and relies on the results from in-vitro and in-vivo animal tests to indicate that it is likely to be safe and efficacious when testing in humans. The typical data package required will include demonstrating compound safety, toxicity, bioavailability, pharmacodynamics (potential effects of the compound on body systems) and pharmacokinetics (how the compound is potentially absorbed, distributed, metabolised and eliminated after dosing in humans). If the desired criteria are met and the compound meets the clinical Candidate criteria and is deemed worthy of further development, a submission to regulatory bodies such as the US Food & Drug Administration for an exploratory Investigational New Drug Study can be made. The purpose of this study is to collect data to establish that the compound will not expose humans to unreasonable risks when used in limited, early-stage clinical studies in patients or normal volunteer subjects (Phase I). These studies are also designed to determine the metabolism and pharmacologic actions of the drug in humans, the side effects associated with increasing doses, and, if possible, to gain early evidence on their effectiveness. In order to reach the above goals, we have developed a pre-clinical high throughput Absorption, Distribution, Metabolism and Excretion–Toxicity (ADME–Toxicity) panel of assays to identify compounds that are likely to meet the Lead and Candidate compound acceptance criteria. This panel includes solubility studies in a range of biological fluids, cell viability studies in cancer and primary cell-lines, mitochondrial toxicity, off-target effects (across the kinase, protease, histone deacetylase, phosphodiesterase and GPCR protein families), CYP450 inhibition (5 different CYP450 enzymes), CYP450 induction, cardio-toxicity (hERG) and gene-toxicity. This panel of assays has been applied to multiple compound series developed in a number of projects delivering Lead and clinical Candidates and examples from these will be presented.

Keywords: absorption, distribution, metabolism and excretion–toxicity , drug discovery, food and drug administration , pharmacodynamics

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Authors: Nur Syahidatul Idany Abdul Ghani, Rahizar Ramli, Jamilah Mohamad, Ahmad Saifizul, Mohamed Rehan Karim

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Increasing fatalities in road accidents in Malaysia over the last 10 years are quite alarming. Based on Malaysian Institute of Road Safety Research (Miros) latest research ‘Predicting Malaysian Road Fatalities for year 2020; it is predicted that road fatalities in Malaysia for 2015 is 8,780 and 10,716 for the year 2020 which 30 percent of fatalities were caused by accidents involving commercial vehicles. Government, related agencies and NGOs have continuously and persistently work to reduce the statistics through enforcement, educating the public, training to drivers, road safety campaigns, advertisements etc. However, the trend of casualties does not show encouraging pattern but instead, steadily growing. Thus, this comparative study reviews the literature pertaining on method of measurement used to evaluate commercial drivers competency. In several studies driving competency has been assessed with different assessment based on the license procedures and requirements according to the country regulation. The assessment criteria that has been establish for commercial drivers generally focus on driving tasks and assessment e.g. theory test, medical test and road assessment rather than driving competency test or physical test. Realizing the importance of specific assessment test for drivers competency this comparative study reviews the most discussed literature related to competency assessment method to identify competency of the drivers include (1. judgement and reaction, 2. skill of drivers, 3. experiences and fatigue). The concluding analysis of this paper is a comparative table for assessment methodology to access driver’s competency. A comparative study is a further discussion reviewing past literature to provide an overview on existing assessment test and potential subject matters that can be identified for further studies to increase awareness of the drivers, passengers as well as the authorities about the importance of competent drivers in order to improve safety in commercial vehicles.

Keywords: commercial vehicles, driver’s competency, specific assessment

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Authors: Mark Lin, Periklis Papadopoulos

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This paper explores the aerodynamics of the formula racecar when a ‘halo’ driver-protection device is added to the chassis. The halo protection device was introduced at the start of the 2018 racing season as a safety measure against foreign object impacts that a driver may encounter when driving an open-wheel racecar. In the one-year since its introduction, the device has received wide acclaim for protecting the driver on two separate occasions. The benefit of such a safety device certainly cannot be disputed. However, by adding the halo device to a car, it changes the airflow around the vehicle, and most notably, to the engine air-intake and the rear wing. These negative effects in the air supply to the engine, and equally to the downforce created by the rear wing are studied in this paper using numerical technique, and the resulting CFD outputs are presented and discussed. Comparing racecar design prior to and after the introduction of the halo device, it is shown that the design of the air intake and the rear wing has not followed suit since the addition of the halo device. The reduction of engine intake mass flow due to the halo device is computed and presented for various speeds the car may be going. Because of the location of the halo device in relation to the air intake, airflow is directed away from the engine, making the engine perform less than optimal. The reduction is quantified in this paper to show the correspondence to reduce the engine output when compared to a similar car without the halo device. This paper shows that through aerodynamic arguments, the engine in a halo car will not receive unobstructed, clean airflow that a non-halo car does. Another negative effect is on the downforce created by the rear wing. Because the amount of downforce created by the rear wing is influenced by every component that comes before it, when a halo device is added upstream to the rear wing, airflow is obstructed, and less is available for making downforce. This reduction in downforce is especially dramatic as the speed is increased. This paper presents a graph of downforce over a range of speeds for a car with and without the halo device. Acknowledging that although driver safety is paramount, the negative effect of this safety device on the performance of the car should still be well understood so that any possible redesign to mitigate these negative effects can be taken into account in next year’s rules regulation.

Keywords: automotive aerodynamics, halo device, downforce. engine intake

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Authors: Irena Maus, Katharina Gabriella Cibis, Andreas Bremges, Yvonne Stolze, Geizecler Tomazetto, Daniel Wibberg, Helmut König, Alfred Pühler, Andreas Schlüter

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Within the agricultural sector, the production of biogas from organic substrates represents an economically attractive technology to generate bioenergy. Complex consortia of microorganisms are responsible for biomass decomposition and biogas production. Recently, species belonging to the phylum Thermotogae were detected in thermophilic biogas-production plants utilizing renewable primary products for biomethanation. To analyze adaptive genome features of representative Thermotogae strains, Defluviitoga tunisiensis L3 was isolated from a rural thermophilic biogas plant (54°C) and completely sequenced on an Illumina MiSeq system. Sequencing and assembly of the D. tunisiensis L3 genome yielded a circular chromosome with a size of 2,053,097 bp and a mean GC content of 31.38%. Functional annotation of the complete genome sequence revealed that the thermophilic strain L3 encodes several genes predicted to facilitate growth of this microorganism on arabinose, galactose, maltose, mannose, fructose, raffinose, ribose, cellobiose, lactose, xylose, xylan, lactate and mannitol. Acetate, hydrogen (H2) and carbon dioxide (CO2) are supposed to be end products of the fermentation process. The latter gene products are metabolites for methanogenic archaea, the key players in the final step of the anaerobic digestion process. To determine the degree of relatedness of dominant biogas community members within selected digester systems to D. tunisiensis L3, metagenome sequences from corresponding communities were mapped on the L3 genome. These fragment recruitments revealed that metagenome reads originating from a thermophilic biogas plant covered 95% of D. tunisiensis L3 genome sequence. In conclusion, availability of the D. tunisiensis L3 genome sequence and insights into its metabolic capabilities provide the basis for biotechnological exploitation of genome features involved in thermophilic fermentation processes utilizing renewable primary products.

Keywords: genome sequence, thermophilic biogas plant, Thermotogae, Defluviitoga tunisiensis

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Authors: Yanqun Li, Hong Geng

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The rapid urbanization process taking big cities as the main body leads to the unequal configuration of urban and rural areas in the aspects of land supply, industrial division of labor, service supply and space allocation, and induces the shrinking characterization of service energy, industrial system and population vitality in small towns. As an important spatial unit in the spectrum of urbanization that serves, connects and couples urban and rural areas, the shrinking phenomenon faced by small towns has an important influence on the healthy development of urbanization. Based on the census of small towns in Wuhan metropolitan area, we have found that the shrinking of small towns is a passive contraction of elastic tension under the squeeze in cities. Once affected by the external forces such as policy regulation, planning guidance, and population return, small towns will achieve expansion and growth. Based on the theory of complex adaptive systems, this paper comprehensively constructs the development index evaluation system of small towns from five aspects of population, economy, space, society and ecology, measures the shrinking level of small towns, further analyzes the shrinking characteristics of small towns, and identifies whether the shrinking is elastic or not. And then this paper measures the resilience ability index of small town contract from the above-mentioned five aspects. Finally, this paper proposes an adaptive mechanism of urban-rural interaction evolution under fine division of labor to response the passive shrinking in small towns of Wuhan. Based on the above, the paper creatively puts forward the planning response measures of the small towns on the aspects of spatial layout, function orientation and service support, which can provide reference for other regions.

Keywords: complex adaptive systems, resiliency shrinking, adaptation mechanism, planning response

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Authors: Sumedha Ganjoo, Santosh Goswami

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The rising reliance on technology places national security at the forefront of 21st-century issues. It complicates the efforts of emerging and developed countries to combat cyber threats and increases the inherent risk factors connected with technology. The inability to preserve data securely might have devastating repercussions on a massive scale. Consequently, it is vital to establish national, regional, and global data protection rules and regulations that penalise individuals who participate in immoral technology usage and exploit the inherent vulnerabilities of technology. This study paper seeks to analyse GDPR-inspired Bills in the South Asian Region and determine their suitability for the development of a worldwide data protection framework, considering that Asian countries are much more diversified than European ones. In light of this context, the objectives of this paper are to identify GDPR-inspired Bills in the South Asian Region, identify their similarities and differences, as well as the obstacles to developing a regional-level data protection mechanism, thereby satisfying the need to develop a global-level mechanism. Due to the qualitative character of this study, the researcher did a comprehensive literature review of prior research papers, journal articles, survey reports, and government publications on the aforementioned topics. Taking into consideration the survey results, the researcher conducted a critical analysis of the significant parameters highlighted in the literature study. Many nations in the South Asian area are in the process of revising their present data protection measures in accordance with GDPR, according to the primary results of this study. Consideration is given to the data protection laws of Thailand, Malaysia, China, and Japan. Significant parallels and differences in comparison to GDPR have been discussed in detail. The conclusion of the research analyses the development of various data protection legislation regimes in South Asia.

Keywords: data privacy, GDPR, Asia, data protection laws

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Authors: Neda Safari, Jacob Petersen-Perlman

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There are more than two million dams in the United States, and a considerable portion of them are either non-operational or approaching the end of their designed lifespan. However, this emerging trend is new, and the majority of dam sites have not undergone thorough research and assessments after their removal to determine the overall effectiveness of restoration initiatives, particularly in the case of large-scale dams that may significantly impact their surrounding areas. A crucial factor to consider is the lack of specific regulations pertaining to dam removal at the federal level. Consequently, other environmental regulations that were not originally designed with dam removal considerations are used to execute these projects. This can result in delays or challenges for dam removal initiatives. The process of removing dams is usually the most important first step to restore the ecological and biological health of the river, but often there is a lack of measurable indicators to assess if it has achieved its intended objectives. In addition, the majority of studies on dam removal are only short-term and focus on a particular measure of response. Therefore, it is essential to conduct extensive and continuous monitoring to analyze the river's response throughout every aspect. Our study is divided into two sections. The first section of my research will analyze the establishment and utilization of dam removal laws and regulations in the Condit Dam removal process. We will highlight the areas where the frameworks for policy and dam removal projects remain in need of improvement in order to facilitate successful dam removals in the future. In this part, We will review the policies and plans that affected the decision-making process to remove the Condit dam while also looking at how they impacted the physical changes to the river after the dam was removed. In the second section, we will look at the effects of the dam removal over a decade later and attempt to determine how the river's physical response has been impacted by this modification. Our study aims to investigate the Condit dam removal process and its impact on the ecological response of the river. We anticipate identifying areas for improvement in policies pertaining to dam removal projects and exploring ways to enhance them to ensure improved project outcomes in the future.

Keywords: dam removal, ecolocgical change, water related regulation, water resources

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Authors: Ahmet Erdoğan, Şahin Kesici, Mustafa Baloğlu

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Information technologies have lead to changes in the areas of communication, learning, and teaching. Besides offering many opportunities to the learners, these technologies have changed the teaching methods and beliefs of teachers. What the Technological Pedagogical Content Knowledge (TPACK) means to the teachers is considerably important to integrate technology successfully into teaching processes. It is necessary to understand how to plan and apply teacher training programs in order to balance students’ pedagogical and technological knowledge. Because of many inefficient teacher training programs, teachers have difficulties in relating technology, pedagogy and content knowledge each other. While providing an efficient training supported with technology, understanding the three main components (technology, pedagogy and content knowledge) and their relationship are very crucial. The purpose of this study is to determine whether motivational beliefs and self-regulated learning strategies are significant predictors of mathematics teacher candidates' TPACK perceptions. A hundred seventy five Turkish mathematics teachers candidates responded to the Motivated Strategies for Learning Questionnaire (MSLQ) and the Technological Pedagogical And Content Knowledge (TPACK) Scale. Of the group, 129 (73.7%) were women and 46 (26.3%) were men. Participants' ages ranged from 20 to 31 years with a mean of 23.04 years (SD = 2.001). In this study, a multiple linear regression analysis was used. In multiple linear regression analysis, the relationship between the predictor variables, mathematics teacher candidates' motivational beliefs, and self-regulated learning strategies, and the dependent variable, TPACK perceptions, were tested. It was determined that self-efficacy for learning and performance and intrinsic goal orientation are significant predictors of mathematics teacher candidates' TPACK perceptions. Additionally, mathematics teacher candidates' critical thinking, metacognitive self-regulation, organisation, time and study environment management, and help-seeking were found to be significant predictors for their TPACK perceptions.

Keywords: candidate mathematics teachers, motivational beliefs, self-regulated learning strategies, technological and pedagogical knowledge, content knowledge

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Authors: Irena Lucy Ishimora, Eva Maria Putri Salsabila

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The constellation on Indonesian Legal System that varies shows a structural injustice – as a result of patriarchy – exists from the biggest range as a country to the smallest such as a family. Women in their lives, carry out excessive responsibilities in the community. However, the unequal positions between men and women in the society restrain women to fulfill their constructed role. Therefore, increasing the chance for women to become the victim of structural injustice. The lack of authority given to women and its effects can be seen through a case study of the Cirompang Indigenous Women’s involvement in natural resources management. The decision to make the Mount Halimun-Salak as a National Park and the expansion itself did not involve nor consider the existence of indigenous people (Kasepuhan Ciromopang) – especially the women’s experience regarding natural resources management – has been significantly impacting the fulfillment of the indigenous women’s rights. Moreover, the adat law that still reflects patriarchy, made matters worse because women are restricted from expressing their opinion. The writers explored the experience of Cirompang indigenous women through in-depth interviews with them and analyzed it with several theories such as ecofeminism, woman’s access to land and legal pluralism. This paper is important to show how the decision and expansion of the National Park reduced the rights of access to land, natural resources, expressing an opinion, and participating in development. Reflecting on the Cirompang Indigenous Women’s conditions on natural resources management, this paper aims to present the implications of the regulations that do not acknowledge Indigenous women’s experience and the proposed solutions. First, there should be an integration between the law regarding indigenous people and traditional rights in a regulation to align the understanding of indigenous people and their rights. Secondly, Indonesia as a country that’s rich with diversity should ratify the ILO Convention no 169 to reaffirm the protection of Indigenous people’s rights. Last, considering the position of indigenous women that still experienced unjustness in the community, the government and NGOs must collaborate to provide adequate assistance for them.

Keywords: Cirompang indigenous women, indigenous women’s rights, structural injustice, women access to land

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Authors: Vitor Rafael Regiani, Carlos Henrique Viesi Do Nascimento Filho, Patricia Matos Biselli-Chicote, Claudia Aparecida Rainho, Luiz Sergio Raposo, José Victor Maniglia, Eny Maria Goloni-Bertollo, Erika Cristina Pavarino

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Promoter hypermethylation of tumor-related genes has been associated with prognosis in early-stage head-and-neck cancers, providing strong evidence that these hypermethylated genes are valuable biomarkers for prognostic evaluation. Hence, we selected the MGMT and RASSF1A genes to examine the methylation status in head and neck squamous cell carcinomas (HNSCC) samples matched with non-tumor tissues (tumor-surrounding tissues or peripheral blood samples). DNA methylation analysis was based on Methylation-Sensitive High Resolution Melting, and the methylation status was correlated with clinic-pathological characteristics of the patients. RASSF1A and MGMT promoter methylation was detected in 43.24% (16/37) and in 44.44% (16/36) of the tumors, respectively. RASSF1A and MGMT methylation was significantly more frequent in tumor tissue than non-tumor tissues, as well as, simultaneous methylation of RASSF1A and MGMT also was higher in tumor tissue than non-tumor tissues. In relation to anatomic site, larynx cancer presented significant methylation of MGMT gene compared to tumor-surrounding tissue. The frequency of RASSF1A and MGMT promoter methylated was higher in tumor tissues in relation to peripheral blood from the same patient. No association was found between methylation and the variables analyzed, including gender, age, smoking or alcohol drinking habits. Clinic-pathological characteristics also showed no association in the presence of methylation. The Kaplan–Meier's method showed no association of methylation and both disease-free and overall survival. In conclusion, the presence of epigenetic abnormalities in normal-appearing tissue corroborates the hypothesis of the ‘field cancerization', or it can reflect preneoplastic and/or preinvasive. Moreover, MGMT methylation may serve as an important laryngeal cancer biomarker because it showed significant difference between laryngeal cancer and surrounding tumor tissues.

Keywords: head and neck cancer, DNA methylation, MGMT promoter methylation, RASSF1A promoter methylation

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Authors: Nefzi Ahlem, Aydi Ben Abdallah Rania, Jabnoun-Khiareddine Hayfa, Ammar Nawaim, Mejda Daami-Remadi

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Fusarium Crown and Root Rot (FCRR) caused by Fusarium oxysporum f. sp. radicis-lycopersici (FORL) is a serious tomato (Solanum lycopersicum L.) disease in Tunisia. Its management is very difficult due to the long survival of its resting structures and to the luck of genetic resistance. In this work, we explored the wild Solanaceae species Withania somnifera, growing in the Tunisian Centre-East, as a potential source of biocontrol agents effective in FCRR suppression and tomato growth promotion. Seven fungal isolates were shown able to colonize tomato roots, crowns, and stems. Used as conidial suspensions or cell-free culture filtrates, all tested fungal treatments significantly enhanced tomato growth parameters by 21.5-90.3% over FORL-free control and by 27.6-93.5% over pathogen-inoculated control. All treatments significantly decreased the leaf and root damage index by 28.5-92.8 and the vascular browning extent 9.7-86.4% over FORL-inoculated and untreated control. The highest disease suppression ability (decrease by 86.4-92.8% in FCRR severity) over pathogen-inoculated control and by 81.3-88.8 over hymexazol-treated control) was expressed by I6 based treatments. This endophytic fungus was morphologically characterized and identified using rDNA sequencing gene as Fusarium sp. I6 (MG835371). This fungus was shown able to reduce FORL radial growth by 58.5–83.2% using its conidial suspension or cell-free culture filtrate. Fusarium sp. I6 showed chitinolytic, proteolytic and amylase activities. The current study clearly demonstrated that Fusarium sp. (I6) is a promising biocontrol candidate for suppressing FCRR severity and promoting tomato growth. Further investigations are required for elucidating its mechanism of action involved in disease suppression and plant growth promotion.

Keywords: antifungal activity, associated fungi, Fusarium oxysporum f. sp. radicis-lycopersici, Withania somnifera, tomato growth

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Authors: Mohammed H. Abu-Dieyeh, Mohammad M. Zalloum

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Plant growth-promoting rhizobacteria (PGPR) are known to enhance plant growth and/or reduce plant damage due to soil-borne pathogens. Tomato is the highest consumable vegetable world-wide including Jordan. Fusarium oxysporum is a pathogen that causes well-known damages and losses to many vegetable crops including tomato. In this study, purification of 112 isolates of PGPR strains from rhizosphere environment of different regions in Jordan was accomplished. All bacterial isolates were In-vitro screened for antagonistic effects against F. oxysporum. The eleven most effective isolates that caused 30%-50% in-vitro growth reduction of F. oxysporum were selected. 8 out of 11 of these isolates were collected from Al-Halabat (arid-land). 7 isolates of Al-Halabat exerted 40-54% In-vitro growth reduction of F. oxysporum. Four-week-old seedlings of tomato cultivar (Anjara, the most susceptible indigenous cultivar to F. oxysporum) treated with PGPR5 (Bacillus amyloliquefaciens), and exposed to F. oxysporum, showed no disease symptoms and no significant changes in biomasses or chlorophyll contents indicating a non-direct mechanism of action of PGPR on tomato plants. However PGPR3 (Bacillus sp.), PGPR4 (Bacillus cereus), and PGPR38 (Paenibacillus sp.) treated plants or PGPR treated and exposed to F. oxysporum showed a significant increasing growth of shoot and root biomasses as well as chlorophyll contents of leaves compared to control untreated plants or plants exposed to the fungus without PGPR treatment. A significant increase in number of flowers per plant was also recorded in all PGPR treated plants. The characterization of rhizobacterial strains were accomplished using 16S rRNA gene sequence analysis in addition to microscopic characterization. Further research is necessary to explore the potentiality of other collected PGPR isolates on tomato plants in addition to investigate the efficacy of the identified isolates on other plant pathogens and then finding a proper and effective methods of formulation and application of the successful isolates on selected crops.

Keywords: antagonism, arid land, growth promoting, rhizobacteria, tomato

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Authors: Mohamed Shafi Bin Mahboob Ali

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Introduction: Synchronous tumor is defined as the presence of more than one primary malignant lesion in the same patient at the indexed diagnosis. It is a rare occurrence, especially in the spectrum of colorectal cancer, which accounts for less than 4%. The underlying pathology of a synchronous tumor is thought to be due to a genomic factor, which is microsatellite instability (MIS) with the involvement of BRAF, KRAS, and the GSRM1 gene. There are no specific sites of occurrence for the synchronous colorectal tumor, but many studies have shown that a synchronous tumor has about 43% predominance in the ascending colon with rarity in the sigmoid colon. Case Report: We reported a case of a young lady in the middle of her 30's with no family history of colorectal cancer that was diagnosed with a synchronous adenocarcinoma at the descending colon and rectosigmoid region. The lady's presentation was quite perplexing as she presented to the district hospital initially with simple, uncomplicated hemorrhoids and constipation. She was then referred to our center for further management as she developed a 'football' sized right gluteal swelling with a complete intestinal obstruction and bilateral lower-limb paralysis. We performed a CT scan and biopsy of the lesion, which found that the tumor engulfed the sacrococcygeal region with more than one primary lesion in the colon as well as secondaries in the liver. The patient was operated on after a multidisciplinary meeting was held. Pelvic exenteration with tumor debulking and anterior resection were performed. Postoperatively, she was referred to the oncology team for chemotherapy. She had a tremendous recovery in eight months' time with a partial regain of her lower limb power. The patient is still under our follow-up with an improved quality of life post-intervention. Discussion: Synchronous colon cancer is rare, with an incidence of 2.4% to 12.4%. It has male predominance and is pathologically more advanced compared to a single colon lesion. Down staging the disease by means of chemoradiotherapy has shown to be effective in managing this tumor. It is seen commonly on the right colon, but in our case, we found it on the left colon and the rectosigmoid. Conclusion: Managing a synchronous colon tumor could be challenging to surgeons, especially in deciding the extent of resection and postoperative functional outcomes of the bowel; thus, individual treatment strategies are needed to tackle this pathology.

Keywords: synchronous, colon, tumor, adenocarcinoma

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Authors: Yassir Adam Shuaib, Stefan Niemann, Eltahir Awad Khalil, Ulrich Schaible, Lothar Heinz Wieler, Mohammed Ahmed Bakhiet, Abbashar Osman Mohammed, Mohamed Abdelsalam Abdalla, Elvira Richter

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Tuberculosis (TB) is a chronic bacterial disease of humans and animals and it is characterized by the progressive development of specific granulomatous tubercle lesions in affected tissues. In a six-month study, from June to November 2014, a total of 2,304 carcasses of cattle, camel, sheep, and goats slaughtered at East and West Gaash slaughterhouses, Kassala, were investigated during postmortem, in parallel, 101 sputum samples from TB suspected patients at Kassala and El-Gadarif Teaching Hospitals were collected in order to investigate tuberculosis in animals and humans. Only 0.1% carcasses were found with suspected TB lesions in the liver and lung and peritoneal cavity of two sheep and no tuberculous lesions were found in the carcasses of cattle, goats or camels. All samples, tissue lesions and sputum, were decontaminated by the NALC-NaOH method and cultured for mycobacterial growth at the NRZ for Mycobacteria, Research Center Borstel, Germany. Genotyping and molecular characterization of the grown strains were done by line probe assay (GenoType CM and MTBC) and 16S rDNA, rpoB gene, and ITS sequencing, spoligotyping, MIRU-VNTR typing and next generation sequencing (NGS). Culture of the specimens revealed growth of organisms from 81.6% of all samples. Mycobacterium tuberculosis (76.2%), M. intracellulare (14.2%), mixed infection with M. tuberculosis and M. intracellulare (6.0%) and mixed infection with M. tuberculosis and M. fortuitum and with M. intracellulare and unknown species (1.2%) were detected in the sputum samples and unknown species (1.2%) were detected in the samples of one of the animals tissues. From the 69 M. tuberculosis strains, 25 (36.2%) were showing either mono-drug-resistant or multi-drug-resistant or poly-drug-resistant but none was extensively drug-resistant. In conclusion, the prevalence of TB in animals was very low while in humans M. tuberculosis-Delhi/CAS lineage was responsible for most cases and there was an evidence of MDR transmission and acquisition.

Keywords: animal, human, slaughterhouse, Sudan, tuberculosis

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Authors: Suchithra V., Shreedhanya, Kavya Menon, Vidya Niranjan

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Skin metagenomics has a wide range of applications with direct relevance to the health of the organism. It gives us insight to the diverse community of microorganisms (the microbiome) harbored on the skin. In the recent years, it has become increasingly apparent that the interaction between skin microbiome and the human body plays a prominent role in immune system development, cancer development, disease pathology, and many other biological implications. Next Generation Sequencing has led to faster and better understanding of environmental organisms and their mutual interactions. This project is studying the human skin microbiome of different individuals having varied skin conditions. Bacterial 16S rRNA data of skin microbiome is downloaded from SRA toolkit provided by NCBI to perform metagenomics analysis. Twelve samples are selected with two controls, and 3 different categories, i.e., sex (male/female), skin type (moist/intermittently moist/sebaceous) and occlusion (occluded/intermittently occluded/exposed). Quality of the data is increased using Cutadapt, and its analysis is done using FastQC. USearch, a tool used to analyze an NGS data, provides a suitable platform to obtain taxonomy classification and abundance of bacteria from the metagenome data. The statistical tool used for analyzing the USearch result is METAGENassist. The results revealed that the top three abundant organisms found were: Prevotella, Corynebacterium, and Anaerococcus. Prevotella is known to be an infectious bacterium found on wound, tooth cavity, etc. Corynebacterium and Anaerococcus are opportunist bacteria responsible for skin odor. This result infers that Prevotella thrives easily in sebaceous skin conditions. Therefore it is better to undergo intermittently occluded treatment such as applying ointments, creams, etc. to treat wound for sebaceous skin type. Exposing the wound should be avoided as it leads to an increase in Prevotella abundance. Moist skin type individuals can opt for occluded or intermittently occluded treatment as they have shown to decrease the abundance of bacteria during treatment.

Keywords: bacterial 16S rRNA , next generation sequencing, skin metagenomics, skin microbiome, taxonomy

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Authors: Ansari Mohammad Reza, Hiroko Ono, Fakhrullah Sarwari

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Our world is fast heading toward being a predominantly urban planet. This can be a double-edged sword reality where it is as much frightening as it seems interesting. Moreover, a look to the current predictions and taking into the consideration the fact that about 90 percent of the coming urbanization is going to be absorbed by the towns and the cities of the developing countries of Asia and Africa, directly provide us the clues to assume a much more tragic ending to this story than to the happy one. Likewise, in a situation wherein most of these countries are still severely struggling to find the proper answer to their very first initial questions of urbanization—e.g. how to provide the essential structure for their cities, define the regulation, or even design the proper pattern on how the cities should be expanded—thus it is not weird to claim that most of the coming urbanization of the world is going to happen informally. This reality could not only bring the feature, landscape or the picture of the cities of the future under the doubt but at the same time provide the ground for the rise of a bunch of other essential questions of how the facilities would be distributed in these cities, or how fair will this pattern of distribution be. Kabul the capital of Afghanistan, as a city located in the developing world that its process of urbanization has been starting since 2001 and currently hold the position to be the fifth fastest growing city in the world, contained to a considerable slum ratio of 0.7—that means about 70 percent of its population is living in the informal areas—subsequently could be a very good case study to put this questions into the research and find out how the informal development of a city can lead to the unfair and unbalanced distribution of its facilities. Likewise, in this study we tried our best to first propose the ideal model for the fair distribution of the facilities in the Kabul city—where all the citizens have the same equal chance of access to the facilities—and then evaluate the situation of the city based on how fair the facilities are currently distributed therein. We subsequently did it by the comparative analysis between the existing facility rate in the formal and informal areas of the city to the one that was proposed as the fair ideal model.

Keywords: Afghanistan, facility distribution, formal settlements, informal settlements, Kabul

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Authors: Mukolwe D. Lubembe, Odongo O. David, Githaka Naftali, Kanduma Esther, Marinda Oosthuizen, Kgomotso P. Sibeko

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Theileriosis is a tick-borne disease of cattle caused by an apicomplexan protozoan parasite of the genus Theileria. In eastern and southern Africa, Theileria infections in cattle are caused by the species Theileria parva whose natural reservoir is the African buffalo (Syncerus caffer). Currently, East Coast Fever (ECF) caused by the cattle-derived Theileria parva is still a major problem in eastern Africa and some parts of southern Africa but not in South Africa following its eradication in the 1950s. However, Corridor disease (CD) caused by the buffalo-derived Theileria parva still remains a concern in South Africa. The diversity of Theileria parva in South Africa in comparison to other affected countries is poorly defined yet its known to be the survival strategy of this parasite. We assessed the antigenic diversity of Theileria parva isolates from Buffalo and cattle at the wildlife-livestock interface comparing samples from South Africa, Zimbabwe, Kenya, Tanzania, and Uganda. Antigenic epitopes of eight schizont antigen genes (Tp1, Tp3, Tp4, Tp5, Tp6, Tp7, Tp8 and Tp10) were amplified by PCR from genomic DNA extracted from blood samples collected from cattle and buffalo at the wildlife-livestock interface. Amplicons were purified and then sequenced on NGS platform. Full length open reading frames (ORFs) of two schizont antigen genes (Tp2 and Tp9) and one sporozoite antigen gene, p67 were also amplified from genomic DNA. Amplicons were then purified and cloned for sequencing. Analysis was based on sequence differences in the genes. Preliminary results show an extensively diverse population of Theileria parva circulating in buffalo and cattle populations at the wildlife-livestock interface. Diversity of the antigen genes contributes to the evasion of the immune system of the host by Theileria parva. This possess a concern in that, some of the Theileria parva populations may re-assort and become adapted to cattle to cause a form of theileriosis that is as fatal as ECF in areas where ECF was eradicated or is absent

Keywords: Theileria parva, east coast fever, corridor diseases, antigen genes, diversity

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Authors: Feixiong Chen, Naoufel Haddour, Marie Frenea-Robin, Yves MéRieux, Yann Chevolot, Virginie Monnier

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Neonatal thrombopenia occurs when the mother generates antibodies against her baby’s platelet antigens. It is particularly critical for newborns because it can cause coagulation troubles leading to intracranial hemorrhage. In this case, diagnosis must be done quickly to make platelets transfusion immediately after birth. Before transfusion, platelet antigens must be tested carefully to avoid rejection. The majority of thrombopenia (95 %) are caused by antibodies directed against Human Platelet Antigen 1a (HPA-1a) or 5b (HPA-5b). The common method for antigen platelets detection is polymerase chain reaction allowing for identification of gene sequence. However, it is expensive, time-consuming and requires significant blood volume which is not suitable for newborns. We propose to develop a point-of-care device based on double functionalized magnetic colloids with 1) antibodies specific to antigen platelets and 2) highly sensitive electroactive molecules in order to be detected by an electrochemical microsensor. These magnetic colloids will be used first to isolate platelets from other blood components, then to capture specifically platelets bearing HPA-1a and HPA-5b antigens and finally to attract them close to sensor working electrode for improved electrochemical signal. The expected advantages are an assay time lower than 20 min starting from blood volume smaller than 100 µL. Our functionalization procedure based on amine dendrimers and NHS-ester modification of initial carboxyl colloids will be presented. Functionalization efficiency was evaluated by colorimetric titration of surface chemical groups, zeta potential measurements, infrared spectroscopy, fluorescence scanning and cyclic voltammetry. Our results showed that electroactive molecules and antibodies can be immobilized successfully onto magnetic colloids. Application of a magnetic field onto working electrode increased the detected electrochemical signal. Magnetic colloids were able to capture specific purified antigens extracted from platelets.

Keywords: Magnetic Nanoparticles , Electroactive Molecules, Antibody, Platelet

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