Search results for: spatial gene

Authors: Isobel Hambleton, Mark Carrington

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Trypanosoma brucei, the causal agent of a range of diseases in humans and livestock, evades the mammalian immune system through a population survival strategy based on the expression of a series of antigenically distinct variant surface glycoproteins (VSGs). RNAi mediated knockdown of the active VSG gene triggers a precytokinesis cell cycle arrest. To determine whether this phenotype is the result of reduced VSG transcript or depleted VSG protein, we used morpholino antisense oligonucleotides to block translation of VSG mRNA. The same precytokinesis cell cycle arrest was observed, suggesting that VSG protein abundance is monitored closely throughout the cell cycle. An inducible expression system has been developed to test various GPI-anchored proteins for their ability to rescue this cell cycle arrest. This system has been used to demonstrate that wild-type VSG expressed from a T7 promoter rescues this phenotype. This indicates that VSG expression from one of the specialised bloodstream expression sites (BES) is not essential for cell division. The same approach has been used to define the minimum essential features of a VSG necessary for function.

Keywords: bloodstream expression site, morpholino, precytokinesis cell cycle arrest, variant surface glycoprotein

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Authors: Khaled M. Khleifat

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An extracellular methanol and ethanol tolerant lipase producing bacterial strain K5b4 was isolated from soil samples contaminated with hydrocarbon residues. It was identified by using morphological and biochemical characteristics and 16srRNA technique as Acinetobacter species. The immobilized lipase from Acinetobacter sp. K5b4 retained more than 98% of its residual activity after incubation with pure methanol and ethanol for 24 hours. The highest hydrolytic activity of the immobilized enzyme was obtained in the presence of 75% (v/v) methanol in the assay solution. In contrary, the enzyme was able to maintain its original activity up to only 25% (v/v) ethanol whereas at elevated concentrations of 50 and 75% (v/v) the enzyme activity was reduced to 10 and 40%, respectively. Maximum lipase activity of 31.5 mU/mL was achieved after 48 hr cultivation when the optimized medium (pH 7.0) that composed of 1.0% (w/v) olive oil, 0.2% (w/v) glycerol, 0.15% (w/v) yeast extract, and 0.05% (w/v) NaCl was inoculated with 0.4% (v/v) seed culture and incubated at 30°C and 150 rpm agitation speed. However, the presence of CaCl2 in the growth media did not show any inhibitory or stimulatory effect on the enzyme production as it compared to the control experiment. Meanwhile, the other mineral salts MgCl2, MnCl2, KCl and CoCl2 were negatively affected the production of lipase enzyme. The inhibition of lipase production from Acinetobacter sp. K5b4 in presence of glucose suggesting that lipase gene expression is prone to catabolic repression.

Keywords: K5B4, methanol and ethanol, acinetobacter, morphological

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Authors: Narin Ozturk, Xiao-Mei Li, Sylvie Giachetti, Francis Levi, Alper Okyar

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P-glycoprotein (P-gp, MDR1, ABCB1) is a transmembrane protein acting as an ATP-dependent efflux pump and functions as a biological barrier by extruding drugs and xenobiotics out of cells in healthy tissues especially in intestines, liver and brain as well as in tumor cells. The circadian timing system controls a variety of biological functions in mammals including xenobiotic metabolism and detoxification, proliferation and cell cycle events, and may affect pharmacokinetics, toxicity and efficacy of drugs. Selective mTOR (mammalian target of rapamycin) inhibitor everolimus is an immunosuppressant and anticancer drug that is active against many cancers, and its pharmacokinetics depend on P-gp. The aim of this study was to investigate the dosing time-dependent toxicity of everolimus with respect to the intestinal P-gp expression rhythms in mdr1a::Luc mice using Real Time-Biolumicorder (RT-BIO) System. Mdr1a::Luc male mice were synchronized with 12 h of Light and 12 h of Dark (LD12:12, with Zeitgeber Time 0 – ZT0 – corresponding Light onset). After 1-week baseline recordings, everolimus (5 mg/kg/day x 14 days) was administered orally at ZT1-resting period- and ZT13-activity period- to mdr1a::Luc mice singly housed in an innovative monitoring device, Real Time-Biolumicorder units which let us monitor real-time and long-term gene expression in freely moving mice. D-luciferin (1.5 mg/mL) was dissolved in drinking water. Mouse intestinal mdr1a::Luc oscillation profile reflecting P-gp gene expression and locomotor activity pattern were recorded every minute with the photomultiplier tube and infrared sensor respectively. General behavior and clinical signs were monitored, and body weight was measured every day as an index of toxicity. Drug-induced body weight change was expressed relative to body weight on the initial treatment day. Statistical significance of differences between groups was validated with ANOVA. Circadian rhythms were validated with Cosinor Analysis. Everolimus toxicity changed as a function of drug timing, which was least following dosing at ZT13, near the onset of the activity span in male mice. Mean body weight loss was nearly twice as large in mice treated with 5 mg/kg everolimus at ZT1 as compared to ZT13 (8.9% vs. 5.4%; ANOVA, p < 0.001). Based on the body weight loss and clinical signs upon everolimus treatment, tolerability for the drug was best following dosing at ZT13. Both rest-activity and mdr1a::Luc expression displayed stable 24-h periodic rhythms before everolimus and in both vehicle-treated controls. Real-time bioluminescence pattern of mdr1a revealed a circadian rhythm with a 24-h period with an acrophase at ZT16 (Cosinor, p < 0.001). Mdr1a expression remained rhythmic in everolimus-treated mice, whereas down-regulation was observed in P-gp expression in 2 of 4 mice. The study identified the circadian pattern of intestinal P-gp expression with an unprecedented precision. The circadian timing depending on the P-gp expression rhythms may play a crucial role in the tolerability/toxicity of everolimus. The circadian changes in mdr1a genes deserve further studies regarding their relevance for in vitro and in vivo chronotolerance of mdr1a-transported anticancer drugs. Chronotherapy with P-gp-effluxed anticancer drugs could then be applied according to their rhythmic patterns in host and tumor to jointly maximize treatment efficacy and minimize toxicity.

Keywords: circadian rhythm, chronotoxicity, everolimus, mdr1a::Luc mice, p-glycoprotein

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Authors: Fekir Youcef, Mederbal Khalladi, M. A. Hamadouche, D. Anteur

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Algeria is one of the countries that are highly affected by desertification which is the consequence of several factors. For this purpose, there is a need to study this problem by quantitative approaches. In this study, we apply the MEDALUS method (Mediterranean Desertification and Land Use) to a watershed located in Saida town in semi-arid environment in the south west of Algeria. The method is based on sensitive areas identification by making use of the different parameters that may affect the desertification process such as vegetation, soil, climate and management. Spatial analyses are strong tools that allow modelization of each indicator. Results show that according to European standards, a large scale of the watershed falls into critical classes. And therefore, the modelization approach can be an effective way to study and understand the desertification showing an example of the project of the green dam that limits the desertification process to affect the north areas off Algeria.

Keywords: Algeria, desertification, MEDALUS, modelization

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Authors: Jessica A. Soto-Bear, Virginia González-Vélez, Norma Castañeda-Villa, Amparo Gil

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Glutamate release of the cochlear inner hair cell (IHC) ribbon synapse is a fundamental step in transferring sound information in the auditory pathway. Otoferlin is the calcium sensor in the IHC and its activity has been related to many auditory disorders. In order to simulate secretion dynamics occurring in the IHC in a few milliseconds timescale and with high spatial resolution, we proposed an active-zone model solved with Monte Carlo algorithms. We included models for calcium buffered diffusion, calcium-binding schemes for vesicle fusion, and L-type voltage-gated calcium channels. Our results indicate that calcium influx and calcium binding is managing IHC secretion as a function of voltage depolarization, which in turn mean that IHC response depends on sound intensity.

Keywords: inner hair cells, Monte Carlo algorithm, Otoferlin, secretion

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Authors: Zahra Solgi, Hossein Rassi

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Colorectal cancer (CRC) is a multi-step disease, and chronic gastric infection with H. pylori could play a role in one or more of the steps in this pathogenic process. Polymorphisms in several miRNAs are considered to increase the risk for the development of CRC by controlling proliferation, apoptosis and H. pylori pathogenesis. Therefore, the aim of this study was to investigate miRNA146a rs2910164 polymorphism and Helicobacter pylori infection in CRC. A total of 65 patients with CRC were divided into 2 groups: 28 patients < 50 years of age and 37 patients ≥ 50 years of age. DNA was extracted from all samples by a standard method and H. pylori cagA and miRNA146a rs2910164 genotypes were determined by PCR method. The results show that there was no significant difference in the frequency of H. pylori cagA gene between the two groups but there was a significant difference in the distribution of rs2910164 genotypes in patients < 50 years of age with the p-value of 0.05 and odds ratio equal to 2.69. On other hand, patients < 50 years of age with genotype CC of miRNA146a showed a significant difference in CRC risk. Furthermore, there was a significant correlation between rs2910164 CC genotype with Helicobacter pylori infection in patients < 50 years of age. The present study suggests that the CC genotype of miRNA146a in combination with H. pylori infection can be effective as risk factors and molecular markers for early diagnosis and treatment of CRC.

Keywords: colorectal cancer, Helicobacter pylori, miRNA146a, rs2910164 polymorphism

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Authors: Kanchan Vishwakarma, Shivesh Sharma, Nitin Kumar

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Soil is incoherent matter on Earth’s surface having organic and mineral content. The spatial variation of 4 soil enzyme activities and microbial biomass were assessed for two seasons’ viz. monsoon and winter along the latitudinal gradient in North-central India as the area of this study is fettered with respect to national status. The study was facilitated to encompass the effect of climate change, enzyme activity and biomass on nutrient cycling. Top soils were sampled from 4 sites in North-India. There were significant correlations found between organic C, N & P wrt to latitude gradient in two seasons. This distribution of enzyme activities and microbial biomass was consequence of alterations in temperature and moisture of soil because of which soil properties change along the latitude transect.

Keywords: latitude gradient, microbial biomass, moisture, soil, organic carbon, temperature

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Authors: Anastasia K. Eleftheriadou, Athanasios Sfetsos, Nikolaos Gounaris

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The present work examines the suitability of a seasonal forecasting model downscaled with a very high spatial resolution in order to assess the energy performance and requirements of buildings. The application of the developed model is applied on Greece for a period and with a forecast horizon of 5 months in the future. Greece, as a country in the middle of a financial crisis and facing serious societal challenges, is also very sensitive to climate changes. The commonly used method for the correlation of climate change with the buildings energy consumption is the concept of Degree Days (DD). This method can be applied to heating and cooling systems for a better management of environmental, economic and energy crisis, and can be used as medium (3-6 months) planning tools in order to predict the building needs and country’s requirements for residential energy use.

Keywords: downscaled seasonal models, degree days, energy performance

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Authors: Hasmithaa Neha, Atul Kumar Patidar, Girish Ch Kothyari

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The northward convergence of the Indian plate has a dominating influence over the structural and geomorphic development of the Himalayan region. The highly deformed and complex stratigraphy in the area arises from a confluence of exogenic and endogenetic geological processes. This region frequently experiences natural hazards such as debris flows, flash floods, avalanches, landslides, and earthquakes due to its harsh and steep topography and fragile rock formations. Therefore, remote sensing technique-based examination and real-time monitoring of tectonically sensitive regions may provide crucial early warnings and invaluable data for effective hazard mitigation strategies. In order to identify unusual changes in the river gradients, the current study demonstrates a spatial quantitative geomorphic analysis of the upper Alaknanda River basin, Uttarakhand Himalaya, India, using gradient length anomaly analysis (GLAA). This basin is highly vulnerable to ground creeping and landslides due to the presence of active faults/thrusts, toe-cutting of slopes for road widening, development of heavy engineering projects on the highly sheared bedrock, and periodic earthquakes. The intersecting joint sets developed in the bedrocks have formed wedges that have facilitated the recurrence of several landslides. The main objective of current research is to identify abnormal gradient lengths, indicating potential landslide-prone zones. High-resolution digital elevation data and geospatial techniques are used to perform this analysis. The results of GLAA are corroborated with the historical landslide events and ultimately used for the generation of landslide susceptibility maps of the current study area. The preliminary results indicate that approximately 3.97% of the basin is stable, while about 8.54% is classified as moderately stable and suitable for human habitation. However, roughly 19.89% fall within the zone of moderate vulnerability, 38.06% are classified as vulnerable, and 29% fall within the highly vulnerable zones, posing risks for geohazards, including landslides, glacial avalanches, and earthquakes. This research provides valuable insights into the spatial distribution of landslide-prone areas. It offers a basis for implementing proactive measures for landslide risk reduction, including land-use planning, early warning systems, and infrastructure development techniques.

Keywords: landslide vulnerability, geohazard, GLA, upper Alaknanda Basin, Uttarakhand Himalaya

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Authors: S. Rostampour Yasouri, M. Ghane

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Leptospirosis is one the most important common diseases between human and live stock occurred by different species of Leptospira. This disease has been construed as the native in the northern provinces of Iran and risk of the infection with pathogenic is high. One hundred fifteen samples of water (67), soil (36) and feces of rodents (12) were collected from the rice fields of the suburbs of Tonekabon Township situated in northern part of Iran in 2012. The samples, after passage from membranous filters, were cultured in the liquid and solid EMJH medium and incubated at 30°C for 1 month. Leptospira spp. were isolated using culture technique, and the plates were studied from viewpoint of colony formation, microscopic observations and then identified by phenotyping tests. Finally, the identification of Leptospira genus was verified by PCR technique and 16S rRNA gene sequencing. Of 115 samples totally, 55 samples (47.82%) became positive by use of the culture technique which the positive cases included 47 water samples (70.14%) and 8 soil samples (22.22%), while the isolation was not accomplished from the sample of the rodents feces. Overall, according to these data, Leptospira spp. exists with high frequency in North Iran. Hence, based on foregoing evidence environments in the north of Iran are vehicles of Leptospira spp.

Keywords: EMJH Medium, Leptospira, Northern of Iran, rice fields

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Authors: Daniel Osorio, Janneth Gonzalez, Andres Pinzon

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In this work, proteins and metabolic pathways associated with the neuroprotective response mediated by the synthetic neurosteroid tibolone under a palmitate-induced inflammatory model were identified by flux balance analysis (FBA). Three different metabolic scenarios (‘healthy’, ‘inflamed’ and ‘medicated’) were modeled over a gene expression data-driven constructed tissue-specific metabolic reconstruction of mature astrocytes. Astrocyte reconstruction was built, validated and constrained using three open source software packages (‘minval’, ‘g2f’ and ‘exp2flux’) released through the Comprehensive R Archive Network repositories during the development of this work. From our analysis, we predict that tibolone executes their neuroprotective effects through a reduction of neurotoxicity mediated by L-glutamate in astrocytes, inducing the activation several metabolic pathways with neuroprotective actions associated such as taurine metabolism, gluconeogenesis, calcium and the Peroxisome Proliferator Activated Receptor signaling pathways. Also, we found a tibolone associated increase in growth rate probably in concordance with previously reported side effects of steroid compounds in other human cell types.

Keywords: astrocytes, flux balance analysis, genome scale metabolic reconstruction, inflammation, neuroprotection, tibolone

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Authors: Ibtissem Hosni, Lilia Bennaceur Farah, Saber Mohamed Naceur

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In order to assess the water availability in the soil, it is crucial to have information about soil distributed moisture content; this parameter helps to understand the effect of humidity on the exchange between soil, plant cover and atmosphere in addition to fully understanding the surface processes and the hydrological cycle. On the other hand, aerodynamic roughness length is a surface parameter that scales the vertical profile of the horizontal component of the wind speed and characterizes the surface ability to absorb the momentum of the airflow. In numerous applications of the surface hydrology and meteorology, aerodynamic roughness length is an important parameter for estimating momentum, heat and mass exchange between the soil surface and atmosphere. It is important on this side, to consider the atmosphere factors impact in general, and the natural erosion in particular, in the process of soil evolution and its characterization and prediction of its physical parameters. The study of the induced movements by the wind over soil vegetated surface, either spaced plants or plant cover, is motivated by significant research efforts in agronomy and biology. The known major problem in this side concerns crop damage by wind, which presents a booming field of research. Obviously, most models of soil surface require information about the aerodynamic roughness length and its temporal and spatial variability. We have used a bi-dimensional multi-scale (2D MLS) roughness description where the surface is considered as a superposition of a finite number of one-dimensional Gaussian processes each one having a spatial scale using the wavelet transform and the Mallat algorithm to describe natural surface roughness. We have introduced multi-layer aspect of the humidity of the soil surface, to take into account a volume component in the problem of backscattering radar signal. As humidity increases, the dielectric constant of the soil-water mixture increases and this change is detected by microwave sensors. Nevertheless, many existing models in the field of radar imagery, cannot be applied directly on areas covered with vegetation due to the vegetation backscattering. Thus, the radar response corresponds to the combined signature of the vegetation layer and the layer of soil surface. Therefore, the key issue of the numerical estimation of soil moisture is to separate the two contributions and calculate both scattering behaviors of the two layers by defining the scattering of the vegetation and the soil blow. This paper presents a synergistic methodology, and it is for estimating roughness and soil moisture from C-band radar measurements. The methodology adequately represents a microwave/optical model which has been used to calculate the scattering behavior of the aerodynamic vegetation-covered area by defining the scattering of the vegetation and the soil below.

Keywords: aerodynamic, bi-dimensional, vegetation, synergistic

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Authors: Ahmed M. Hjazi, Bader M. Hjazi

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Protein 4.1 is a crucial component of complex interactions between the cytoskeleton and other junctional complex proteins. When the gene encoding this protein is altered, resulting in reduced expression, or when the protein is absent, the red cell undergoes a significant structural change. This research aims to achieve a deeper comprehension of the biochemical effects of red cell protein deficiency. A Tandem Mass Spectrometry Analysis (TMT-MS/MS) of patient cells lacking protein 4.1 compared to three healthy controls was achieved by the Proteomics Institute of the University of Bristol. The SDS-PAGE and Western blotting were utilized on the original patient sample and controls to partially confirm TMT MS/MS data analysis of the protein-4.1-deficient cells. Compared to healthy controls, protein levels in samples lacking protein 4.1 had a significantly higher concentration of proteins that probably originated from reticulocytes. This could occur if the patient has an elevated reticulocyte count. The increase in chaperone and reticulocyte-associated proteins was most notable in this study. This may result from elevated quantities of reticulocytes in patients with hereditary elliptocytosis.

Keywords: hereditary elliptocytosis, protein 4.1, red cells, tandem mass spectrometry data.

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

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

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

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Authors: Billel Kenidra, Mohamed Benmohammed

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Data mining technique used in the field of clustering is a subject of active research and assists in biological pattern recognition and extraction of new knowledge from raw data. Clustering means the act of partitioning an unlabeled dataset into groups of similar objects. Each group, called a cluster, consists of objects that are similar between themselves and dissimilar to objects of other groups. Several clustering methods are based on partitional clustering. This category attempts to directly decompose the dataset into a set of disjoint clusters leading to an integer number of clusters that optimizes a given criterion function. The criterion function may emphasize a local or a global structure of the data, and its optimization is an iterative relocation procedure. The K-Means algorithm is one of the most widely used partitional clustering techniques. Since K-Means is extremely sensitive to the initial choice of centers and a poor choice of centers may lead to a local optimum that is quite inferior to the global optimum, we propose a strategy to initiate K-Means centers. The improved K-Means algorithm is compared with the original K-Means, and the results prove how the efficiency has been significantly improved.

Keywords: microarray data mining, biological pattern recognition, partitional clustering, k-means algorithm, centroid initialization

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Authors: Albert K. Chong, Jasim Ahmed Ali Al-Baghdadi, Peter B. Milburn

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Precise capture of plantar 3D surface of the foot at the loading gait phases on rigid substrate was found to be valuable for the assessment of the physiology, health and problems of the feet. Photogrammetry, a precision 3D spatial data capture technique is suitable for this type of dynamic application. In this research, the technique is utilised to study of the effect on the plantar deformation for having a strip of kinesiology tape on the plantar surface while going through the loading phase of gait. For this pilot study, one healthy adult male subject was recruited under the USQ University human research ethics guidelines for this preliminary study. The 3D plantar deformation data of both with and without applying the tape were analysed. The results and analyses are presented together with the detail of the findings.

Keywords: gait, human plantar, plantar loading, photogrammetry, kinesiology tape

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Authors: Halina Veloso e Zarate, Manuela Triggianese

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The urban challenges posed by rapid population growth, climate adaptation, and sustainable living have compelled Dutch cities to reimagine their built environment and transportation systems. As a pivotal contributor to CO₂ emissions, the transportation sector in the Netherlands demands innovative solutions for transitioning to low-carbon mobility. This study investigates the potential of transit oriented development (TOD) as a strategy for achieving carbon reduction and sustainable urban transformation. Focusing on the Lombardijen station area in Rotterdam, which is targeted for significant densification, this paper presents a design-oriented exploration of a low-carbon transport node. By employing a research-by-design methodology, this study delves into multifaceted factors and scales, aiming to propose future scenarios for Lombardijen. Drawing from a synthesis of existing literature, applied research, and practical insights, a robust design framework emerges. To inform this framework, governmental data concerning the built environment and material embodied carbon are harnessed. However, the restricted access to crucial datasets, such as property ownership information from the cadastre and embodied carbon data from De Nationale Milieudatabase, underscores the need for improved data accessibility, especially during the concept design phase. The findings of this research contribute fundamental insights not only to the Lombardijen case but also to TOD studies across Rotterdam's 13 nodes and similar global contexts. Spatial data related to property ownership facilitated the identification of potential densification sites, underscoring its importance for informed urban design decisions. Additionally, the paper highlights the disparity between the essential role of embodied carbon data in environmental assessments for building permits and its limited accessibility due to proprietary barriers. Although this study lays the groundwork for sustainable urbanization through TOD-based design, it acknowledges an area of future research worthy of exploration: the socio-economic dimension. Given the complex socio-economic challenges inherent in the Lombardijen area, extending beyond spatial constraints, a comprehensive approach demands integration of mobility infrastructure expansion, land-use diversification, programmatic enhancements, and climate adaptation. While the paper adopts a TOD lens, it refrains from an in-depth examination of issues concerning equity and inclusivity, opening doors for subsequent research to address these aspects crucial for holistic urban development.

Keywords: Rotterdam zuid, transport oriented development, carbon emissions, low-carbon design, cross-scale design, data-supported design

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Authors: Gaby Fahmy

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The last decades have seen a rise in metabolic disorders like diabetes, obesity, and fatty liver disease around the world. Environmental factors, especially nutrition, have contributed to this increase. Additionally, pre-conceptional parental nutritional choices have been shown to result in epigenetic modifications affecting gene expression during the developmental process in-utero. These epigenetic modifications have also been seen to extend to the following offspring in a trans-generational effect. This further highlights the significance and relevance of epigenetics and epigenetic tags, which were previously thought to be stripped in newly formed embryos. Suitable prenatal nutrition may partially counteract adverse outcomes caused by exposures to environmental contaminants, ultimately resulting in improved metabolic profiles like body weight and glucose homeostasis. This was seen in patients who were given dietary interventions like restrictive caloric intake, intermittent fasting, and time-restricted feeding. Changes in nutrition are pivotal in the regulation of epigenetic modifications that are transgenerational. For example, dietary choices such as fatty foods vs. vegetables and nuts in fathers were shown to significantly affect sperm motility and volume. This was pivotal in understanding the importance of paternal inheritance. Further research in the field is needed as it remains unclear how many generations are affected by these changes.

Keywords: epigenetics, transgenerational, diet, fasting

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Authors: Hyeon Su Kim, Sungjin Park, Hae Ryung Chang, Hae Rim Jung, Young Zoo Ahn, Yon Hui Kim, Seungyoon Nam

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Ependymoma, one of the most common parenchymal spinal cord tumor, represents 3-6% of all CNS tumor. Especially intracranial ependymomas, which are more frequent in childhood, have a more poor prognosis and more malignant than spinal ependymomas. Although there are growing needs to understand pathogenesis, detailed molecular understanding of pathogenesis remains to be explored. A cancer cell is composed of complex signaling pathway networks, and identifying interaction between genes and/or proteins are crucial for understanding these pathways. Therefore, we explored each ependymoma in terms of differential expressed genes and signaling networks. We used Microsoft Excel™ to manipulate microarray data gathered from NCBI’s GEO Database. To analyze and visualize signaling network, we used web-based PATHOME algorithm and Cytoscape. We show HOX family and NEFL are down-regulated but SCL family is up-regulated in cerebrum and posterior fossa cancers over a spinal cancer, and JAK/STAT signaling pathway and Chemokine signaling pathway are significantly different in the both intracranial ependymoma comparing to spinal ependymoma. We are considering there may be an age-dependent mechanism under different histological pathogenesis. We annotated mutation data of each gene subsequently in order to find potential target genes.

Keywords: systems biology, ependymoma, deg, network analysis

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Authors: Humayun Kabir, Amirul Hasan, Yu Miyaoka, Makiko Yamaguchi, Chisaki Kadota, Kazuaki Takehara

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From field isolates of Newcastle disease virus (NDV) in Japan, one avirulent strain, APMV/northern pintail/Japan/Aomori/2003 (dk-Aomori/03, NDV 261), was selected for its excellent thermostability, and the strain was heat-treated at 56℃ temperatures for 30 min with each passage into Vero cells to maintain thermostability and to adapt Vero cells. After serial 20 passages in Vero cells, it was named NDV Vero20. When growth curves were tested in Vero cells, NDV Vero20 grew well to compare the original NDV261. The HN gene was sequenced, and found motifs that show thermostability. The intracerebral pathogenicity index (ICPI) test score was 0. The thermostability of the virus was confirmed by storing it at different temperatures, including at 37°C. When susceptible chicks were inoculated with NDV Vero20 through eye drops, induced adequate levels of antibody were measured using a serum neutralization test. The results showed that NDV Vero20, a vaccine candidate strain is thermostable, Vero cell adapted, and has immunogenic potential, which would make as an alternative to the traditional embryonated chicken eggs-based vaccine.

Keywords: Newcastle disease virus, thermostability, vaccine, Vero cell adaptability

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Authors: Saadoun Abd Errazak, Hafssaoui Abdallah, Fredj Mohamed

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Mining operations open induce risks of instability that can cause landslides and collapse at the bleachers slope. These risks may occur both during and after the operation phase. The magnitude of these risks depends on the mechanical and physical characteristics of the rock mass, the geometrical dimensions of ore bodies, their spatial arrangement, and the state of the operated area. If security and technology measures are not taken into account for this purpose, the environment will be affected. The main objective of this work is to assess these risks by analytical and numerical methods. The study is based on the geological, hydrogeological and geotechnical rock mass of the open pit quarry of Chouf Amar M'sila. The results obtained have allowed us to obtain an acceptable factor of safety and stability study of the open pit.

Keywords: stability, land sliding, numerical modeling, safety factor, open-pit quarry

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Authors: João Pereira Dos Santos

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The uneven spatial distribution of start-ups and their respective survival may reflect comparative advantages resulting from the local institutional background. For the first time, we explore this idea using Data Envelopment Analysis (DEA) to assess relative efficiency of Portuguese municipalities in this specific context. We depart from the related literature where expenditure is perceived as a desirable input by choosing a measure of fiscal responsibility and infrastructural variables in the first stage. Comparing results for 2006 and 2010, we find that mean performance decreased substantially with 1) the effects of the Global Financial Crisis; 2) as municipal population increases and 3) as financial independence decreases. A second stage is then computed employing a double-bootstrap procedure to evaluate how the regional context outside the control of local authorities (e.g. demographic characteristics and political preferences) impacts on efficiency.

Keywords: entrepreneurship, political economy, public finance, accountability, crisis, efficiency, Portuguese municipalities

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Authors: M. Helen

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Chemical graph serves as a convenient model for any real or abstract chemical system. Dendrimers are novel three dimensional hyper branched globular nanopolymeric architectures. Drug delivery scientists are especially enthusiastic about possible utility of dendrimers as drug delivery tool. Dendrimers like poly L lysine (PLL), poly-propylene imine (PPI) and poly-amidoamine (PAMAM), etc., are used as gene carrier in drug delivery system because of their chemical characteristics. These characteristics of chemical compounds are analysed using topological indices (invariants under graph isomorphism) such as Wiener index, Zagreb index, etc., Prof. V. R. Kulli motivated by the application of Zagreb indices in finding the total π energy and derived Gourava indices which is an improved version over Zagreb indices. In this paper, we study the structure of PLL-Dendrimer that has the following applications: reduction in toxicity, colon delivery, and topical delivery. Also, we determine first and second Gourava indices, first and second hyper Gourava indices, product and sum connectivity Gourava indices for PLL-Dendrimer. Gourava Indices have found applications in Quantitative Structure-Property Relationship (QSPR)/ Quantitative Structure-Activity Relationship (QSAR) studies.

Keywords: connectivity Gourava indices, dendrimer, Gourava indices, hyper GouravaG indices

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Authors: Fangwen Ni, Hongpeng Xu

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When disasters occur, it is important to provide temporary shelters to protect victims from their environment and to comfort them with privacy and dignity. However, the commonly used shelters like tents and shanties can not ensure a comfortable condition. Furthermore, the demand for more energy and less pollution has become a major challenge. Focusing on the sustainable of temporary shelters, this study intends to clarify the essential role of temporary shelters before the reconstruction work is done. The paper also identifies the main problems from three aspects including spatial layout, thermal comfort and utilization of passive technology. Moreover, it expounds the passive strategies of ecological design by case study and simulation. It is found that the living condition of shelters can be improved from the perspective of architectural space, ventilation theory and construction techniques. Regardless of being temporary, these shelters are crucial elements in emergency situations and should be taken more seriously.

Keywords: architectural space, construction technique, sustainable strategy, temporary shelter

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Authors: Ravinder Singh, C Rajesh, Saroj Badhan, Shailendra Mishra, Ranjit Singh Kataria

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Heat shock protein 60 and 70 are crucial chaperones that guide appropriate folding of denatured proteins under heat stress conditions. HSP60 and HSP70 provide assistance in correct folding of a multitude of denatured proteins. The heat shock factors are the family of some transcription factors which controls the regulation of gene expression of proteins involved in folding of damaged or improper folded proteins during stress conditions. Under normal condition heat shock proteins bind with HSF-1 and act as its repressor as well as aids in maintaining the HSF-1’s nonactive and monomeric confirmation. The experimental protein structure for all these proteins in Bubalus bubalis is not known till date. Therefore computational approach was explored to identify three-dimensional structure analysis of all these proteins. In this study, an extensive in silico analysis has been performed including sequence comparison among species to comparative modeling of Bubalus bubalis HSP60, HSP70 and HSF-1 protein. The stereochemical properties of proteins were assessed by utilizing several scrutiny bioinformatics tools to ensure model accuracy. Further docking approach was used to study interactions between Heat shock proteins and HSF-1.

Keywords: Bubalus bubalis, comparative modelling, docking, heat shock protein

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Authors: A. Bahieldin, A. Atef, S. Edris, N. O. Gadalla, S. M. Hassan, M. A. Al-Kordy, A. M. Ramadan, A. S. M. Al- Hajar, F. M. El-Domyati

Abstract:

The idea of this work is based on a natural exciting phenomenon suggesting that suppression of genes related to the program cell death (or PCD) mechanism might help the plant cells to efficiently tolerate abiotic stresses. The scope of this work was the detection of PCD-related transcription factors (TFs) that might also be related to salt stress tolerance in plant. Two model plants, e.g., tobacco and Arabidopsis, were utilized in order to investigate this phenomenon. Occurrence of PCD was first proven by Evans blue staining and DNA laddering after tobacco leaf discs were treated with oxalic acid (OA) treatment (20 mM) for 24 h. A number of 31 TFs up regulated after 2 h and co-expressed with genes harboring PCD-related domains were detected via RNA-Seq analysis and annotation. These TFs were knocked down via virus induced gene silencing (VIGS), an RNA interference (RNAi) approach, and tested for their influence on triggering PCD machinery. Then, Arabidopsis SALK knocked out T-DNA insertion mutants in selected TFs analogs to those in tobacco were tested under salt stress (up to 250 mM NaCl) in order to detect the influence of different TFs on conferring salt tolerance in Arabidopsis. Involvement of a number of candidate abiotic-stress related TFs was investigated.

Keywords: VIGS, PCD, RNA-Seq, transcription factors

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Authors: Sarah Reker

Abstract:

The Convention on the Rights of Persons with Disabilities (CRPD) provides the basis of this study. For all countries which have ratified the convention since its entry into force in 2007, the effective implementation of the requirements often leads to considerable challenges. Furthermore, missing indicators make it difficult to measure progress. Therefore, the aim of the research project is to contribute to analyze the consequences of the implementation process on the inclusion and exclusion conditions for people with disabilities in Germany. Disabled People’s Organisations and other associations consider the social space to be relevant for the successful implementation of the CRPD. Against this background, the research project wants to focus on the relationship between a barrier-free access to the social space and the “full and effective participation and inclusion” (Art. 3) of persons with disabilities. The theoretical basis of the study is the sociological theory of social space (“Sozialraumtheorie”).

Keywords: decentralisation, qualitative research, residential facilities, social space

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Authors: Alice Petzold, Alexandre Hassanin

Abstract:

The number of giraffe species has been in focus of interest since the exploration of sub-Saharan Africa by European naturalists during the 18th and 19th centuries, as previous taxonomists, like Geoffroy Saint-Hilaire, Richard Owen or William Edward de Winton, recognized two or three species of Giraffa. For the last decades, giraffes were commonly considered as a single species subdivided into nine subspecies. In this study, we have re-examined available nuclear and mitochondrial data. Our genetic admixture analyses of seven introns support three species: G. camelopardalis (i.e., northern giraffes including reticulated giraffes), G. giraffa (southern giraffe) and G. tippelskirchi (Masai giraffe). However, the nuclear alignments show small variation and our phylogenetic analyses provide high support only for the monophyly of G. camelopardalis. Comparisons with the mitochondrial tree revealed a robust conflict for the position and monophyly of G. giraffa and G. tippelskirchi, which is explained firstly by a mitochondrial introgression from Masai giraffe to southeastern giraffe, and secondly, by gene flow mediated by male dispersal between southern populations (subspecies angolensis and giraffa). We conclude that current data gives only moderate support for three giraffe species and point out that additional nuclear data need to be studied to revise giraffe taxonomy.

Keywords: autosomal markers, Giraffidae, mitochondrial introgression, taxonomy

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Authors: Mary Fargher

Abstract:

This paper examines the opportunities of using a more hierarchical approach to geospatial enquiry in using GIS in school geography. A case is made that it is not just the lack of teacher technological knowledge that is stopping some teachers from using GIS in the classroom but that there is a gap in their understanding of how to link GIS use more specifically to the pedagogy of teaching geography with GIS. Using a hierarchical approach to geospatial enquiry as a theoretical framework, the analysis shows clearly how concepts of spatial distribution, interaction, relation, comparison, and temporal relationships can be used by teachers more explicitly to capitalise on the analytical power of GIS and to construct what can be interpreted as powerful geographical knowledge. An exemplar illustrating this approach on the topic of geo-hazards is then presented for critical analysis and discussion. Recommendations are then made for a model of progression for geography teacher education with GIS through hierarchical geospatial enquiry that takes into account beginner, intermediate, and more advanced users.

Keywords: digital geography, GIS, education, hierarchical geospatial enquiry, powerful geographical knowledge

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Authors: Sheng-Hui Lan, Shan-Ying Wu, Shu-Ching Lin, Wei-Chen Wang, Hsiao-Sheng Liu

Abstract:

Autophagy is an essential mechanism to maintain cellular homeostasis through its degradation function, and the autophagy deficiency is related various diseases including tumorigenesis in several cancers. MicroRNAs (miRNAs) are small none coding RNAs, which regulate gene expression through degradation of mRNA or inhibition of translation. However, the relationship between autophagy deficiency and dysregulated miRNAs is still unclear. We revealed a mechanism that autophagy up-regulates miR-449a expression at the transcriptional level through activation of forkhead transcription factor family member FoxO1 and then suppresses tumorigenesis in CRC. Our data showed that the autophagic activity and miR-449a expression were lower in colorectal cancer (CRC) and has a positive correlation. We further reveal that autophagy degrades p300 expression and then suppresses acetylation of FoxO1. Under autophagic induction conditions, FoxO1 is transported from the cytoplasm to the nucleus and binds to the miR-449a promoter and then promotes miR-449a expression. In addition, either miR-449a overexpression or amiodarone-induced autophagy inhibits cell cycle progression, proliferation, colony formation migration, invasion, and tumor formation of SW480 cells. Our findings indicate that autophagy inducers may have the potential to be used for prevention and treatment of CRC through upregulation of miR-449a expression.

Keywords: autophagy, MiR-449a, FoxO1, colorectal cancer

Procedia PDF Downloads 320