Search results for: Representative Concentration Pathway (RCP)

Authors: Renalda El Samra, Elie Bou-Zeid, Hamza Kunhu Bangalath, Georgiy Stenchikov, Mutasem El Fadel

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The regional-scale impact of climate change over complex terrain was examined through high-resolution dynamic downscaling conducted using the Weather Research and Forecasting (WRF) model, with initial and boundary conditions from a High-Resolution Atmospheric Model (HiRAM). The analysis was conducted over the eastern Mediterranean, with a focus on the country of Lebanon, which is characterized by a challenging complex topography that magnifies the effect of orographic precipitation. Four year-long WRF simulations, selected based on HiRAM time series, were performed to generate future climate projections of extreme temperature and precipitation over the study area under the conditions of the Representative Concentration Pathway (RCP) 4.5. One past WRF simulation year, 2008, was selected as a baseline to capture dry extremes of the system. The results indicate that the study area might be exposed to a temperature increase between 1.0 and 3ºC in summer mean values by 2050, in comparison to 2008. For extreme years, the decrease in average annual precipitation may exceed 50% at certain locations in comparison to 2008.

Keywords: HiRAM, regional climate modeling, WRF, Representative Concentration Pathway (RCP)

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Authors: Ida Bagus Mandhara Brasika, I Dewa Gde Sathya Deva

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Wolbachia is recently developed as the natural enemy of Dengue virus (DENV). It inhibits the replication of DENV in Aedes aegypti. Both DENV and its vector, Aedes aegypty, are sensitive to climate factor especially temperature. The changing of climate has a direct impact on temperature which means changing the vector transmission. Temperature has been known to effect Wolbachia density as it has an ideal temperature to grow. Some scenarios, which are known as Representative Concentration Pathways (RCPs), have been developed by Intergovernmental Panel on Climate Change (IPCC) to predict the future climate based on greenhouse gases concentration. These scenarios are applied to mitigate the future change of Aedes aegypti migration and how Wolbachia could control the virus. The prediction will determine the schemes to release Wolbachia-injected Aedes aegypti to reduce DENV transmission.

Keywords: Aedes aegypti, climate change, dengue virus, Intergovernmental Panel on Climate Change, representative concentration pathways, Wolbachia

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Authors: Deepa Gandhi, Pravin K. Naoghare, Amit Bafana, Krishnamurthi Kannan, Saravanadevi Sivanesana

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Oxidative stress is known to depreciate normal functioning of osteoblast cells. Present study reports oxidative/inflammatory signatures in fluoride exposed human osteosarcoma (HOS) cells and its possible association with the genes involved in bone developmental pathway. Microarray analysis was performed to understand the possible molecular mechanisms of stress-mediated bone lose in HOS cells. Cells were chronically exposed with sub-lethal concentration of fluoride. Global gene expression is profiling revealed 34 up regulated and 2598 down-regulated genes, which were associated with several biological processes including bone development, osteoblast differentiation, stress response, inflammatory response, apoptosis, regulation of cell proliferation. Microarray data were further validated through qRT-PCR and western blot analyses using key representative genes. Based on these findings, it can be proposed that chronic exposure of fluoride may impair bone development via oxidative and inflammatory stress. The present finding also provides important biological clues, which will be helpful for the development of therapeutic targets against diseases related bone.

Keywords: bone, HOS cells, microarray, stress

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Authors: Valentina L. Kouznetsova, Jonathan W. Wang, Igor F. Tsigelny

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Metabolomics has become a rising field of research for various diseases, particularly cancer. Increases or decreases in metabolite concentrations in the human body are indicative of various cancers. Further elucidation of metabolic pathways and their significance in cancer research may greatly spur medicinal discovery. We analyzed the metabolomics profiles of lung cancer. Thirty-three metabolites were selected as significant. These metabolites are involved in 37 metabolic pathways delivered by MetaboAnalyst software. The top pathways are glyoxylate and dicarboxylate pathway (its hubs are formic acid and glyoxylic acid) along with Citrate cycle pathway followed by Taurine and hypotaurine pathway (the hubs in the latter are taurine and sulfoacetaldehyde) and Glycine, serine, and threonine pathway (the hubs are glycine and L-serine). We studied interactions of the metabolites with the proteins involved in cancer-related signaling networks, and developed an approach to metabolomics biomarker use in cancer diagnostics. Our analysis showed that a significant part of lung-cancer-related metabolites interacts with main cancer-related signaling pathways present in this network: PI3K–mTOR–AKT pathway, RAS–RAF–ERK1/2 pathway, and NFKB pathway. These results can be employed for use of metabolomics profiles in elucidation of the related cancer proteins signaling networks.

Keywords: cancer, metabolites, metabolic pathway, signaling pathway

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Authors: Dhruvit S. Berawala, Jann R. Ursin, Obrad Slijepcevic

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Shale gas is one of the most rapidly growing forms of natural gas. Unconventional natural gas deposits are difficult to characterize overall, but in general are often lower in resource concentration and dispersed over large areas. Moreover, gas is densely packed into the matrix through adsorption which accounts for large volume of gas reserves. Gas production from tight shale deposits are made possible by extensive and deep well fracturing which contacts large fractions of the formation. The conventional reservoir modelling and production forecasting methods, which rely on fluid-flow processes dominated by viscous forces, have proved to be very pessimistic and inaccurate. This paper presents a new approach to forecast shale gas production by detailed modeling of gas desorption, diffusion and non-linear flow mechanisms in combination with statistical representation of these processes. The representation of the model involves a cube as a porous media where free gas is present and a sphere (SiC: Sphere in Cube model) inside it where gas is adsorbed on to the kerogen or organic matter. Further, the sphere is considered consisting of many layers of adsorbed gas in an onion-like structure. With pressure decline, the gas desorbs first from the outer most layer of sphere causing decrease in its molecular concentration. The new available surface area and change in concentration triggers the diffusion of gas from kerogen. The process continues until all the gas present internally diffuses out of the kerogen, gets adsorbs onto available surface area and then desorbs into the nanopores and micro-fractures in the cube. Each SiC idealizes a gas pathway and is characterized by sphere diameter and length of the cube. The diameter allows to model gas storage, diffusion and desorption; the cube length takes into account the pathway for flow in nanopores and micro-fractures. Many of these representative but general cells of the reservoir are put together and linked to a well or hydraulic fracture. The paper quantitatively describes these processes as well as clarifies the geological conditions under which a successful shale gas production could be expected. A numerical model has been derived which is then compiled on FORTRAN to develop a simulator for the production of shale gas by considering the spheres as a source term in each of the grid blocks. By applying SiC to field data, we demonstrate that the model provides an effective way to quickly access gas production rates from shale formations. We also examine the effect of model input properties on gas production.

Keywords: adsorption, diffusion, non-linear flow, shale gas production

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Authors: Muhammad Azam, Micheal Olaolu Arowolo, Fei He, Mihail Popescu, Dong Xu

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The number of biological papers is growing quickly, which means that the number of biological pathway figures in those papers is also increasing quickly. Each pathway figure shows extensive biological information, like the names of genes and how the genes are related. However, manually annotating pathway figures takes a lot of time and work. Even though using advanced image understanding models could speed up the process of curation, these models still need to be made more accurate. To improve gene name recognition from pathway figures, we applied a Siamese network to map image segments to a library of pictures containing known genes in a similar way to person recognition from photos in many photo applications. We used a triple loss function and a triplet spatial pyramid pooling network by combining the triplet convolution neural network and the spatial pyramid pooling (TSPP-Net). We compared VGG19 and VGG16 as the Siamese network model. VGG16 achieved better performance with an accuracy of 93%, which is much higher than OCR results.

Keywords: biological pathway, image understanding, gene name recognition, object detection, Siamese network, VGG

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Authors: Chia-Ju Peng, Shih-Jui Chen

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This paper proposes a method to discriminate electroencephalogram (EEG) signals between different concentration states using empirical mode decomposition (EMD). Brain-computer interface (BCI), also called brain-machine interface, is a direct communication pathway between the brain and an external device without the inherent pathway such as the peripheral nervous system or skeletal muscles. Attention level is a common index as a control signal of BCI systems. The EEG signals acquired from people paying attention or in relaxation, respectively, are decomposed into a set of intrinsic mode functions (IMF) by EMD. Fast Fourier transform (FFT) analysis is then applied to each IMF to obtain the frequency spectrums. By observing power spectrums of IMFs, the proposed method has the better identification of EEG attention level than the original EEG signals between different concentration states. The band power of IMF3 is the most obvious especially in β wave, which corresponds to fully awake and generally alert. The signal processing method and results of this experiment paves a new way for BCI robotic system using the attention-level control strategy. The integrated signal processing method reveals appropriate information for discrimination of the attention and relaxation, contributing to a more enhanced BCI performance.

Keywords: biomedical engineering, brain computer interface, electroencephalography, rehabilitation

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Authors: Jiahui Song, Ravindra Joshi

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High-intensity, nanosecond, pulsed electric fields have been shown to be useful non-thermal tools capable of producing a variety of specific cellular responses. While reversible and temporary changes are often desired based on electromanipulation, irreversible effects can also be important objectives. These include elimination of tumor cells and bacterial decontamination. A simple model-based rate-equation treatment of the various cellular biochemical processes was used to qualitatively predict the pulse number-dependent caspase activation and cell survival trends. The model incorporated the caspase-8 associated extrinsic pathway, the delay inherent in its activation, cytochrome c release, and the internal feedback mechanism between caspase-3 and Bid. Results were roughly in keeping with the experimental cell-survival data. A pulse-number threshold was predicted followed by a near-exponential fall-off. The intrinsic pathway was shown to be much weaker as compared to the extrinsic mechanism for electric pulse induced cell apoptosis. Also, delays of about an hour are predicted for detectable molecular concentration increases following electrical pulsing.

Keywords: apoptosis, cell survival, model, pathway

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Authors: Okpor Victor, Selegha Abrakasa

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Oil (Petroleum) spill occur frequently and in this era of a higher degree of awareness, it is pertinent that the trajectory of the spill is properly defined, to make certain of the area of impact by the spill. In this study, biomarkers that are known as the custodians of paleo information in oils are suggested to be used as reliable tools for defining the pathway of a spill. Samples were collected as tills alongside the GPS coordinates of the sample points suspected to have been impacted by a spill. Oils in the samples were extracted and analyzed as whole oil using GC–MS. Some biomarker parametric ratios were derived, and the ratio showed consistency of values along the sample trail from sample 1 to sample 20. The consistency of the values indicates that the oils at each sample point are the same hence the same value. This method can be used to validate the trajectory/pathway of a spill and also to define or establish a suspected pathway for a spill. The Oleanane/C30Hopane ratio showed good consistency and was suggested as a reliable parameter for establishing the trajectory of an oil spill.

Keywords: spill, biomarkers, trajectory, pathway

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Authors: Dani Sukkar, Ali Kanso, Philippe Laval-Gilly, Jairo Falla-Angel

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The honeybees' immune system is challenged by different risk factors that induce various responses. However, complex scenarios where bees are exposed to different pesticides simultaneously with immune activation are not well evaluated. The Toll pathway is one of the main signaling pathways studied in invertebrate immune responses, and it is a good indicator of the effect of such complex interactions in addition to key signaling elements of other pathways like Relish of the immune deficiency (IMD) pathway or Eater, the phagocytosis receptor or vitellogenin levels. Honeybee hemocytes extracted from 5th instar larvae were exposed to imidacloprid and/or amitraz with or without the presence of the zymosan a as an immune activator. The gene expression of multiple immune related genes were studied, including spaetzle, Toll, myD88, relish, eater and vitellogenin, by real-time polymerase chain reaction after RNA extraction. The results demonstrated that the Toll pathway is mainly affected by the pesticides; imidacloprid and amitraz, especially by their different combinations. Furthermore, immune activation by zymosan A, a fungal cell-wall component, acts to mitigate to some extent the effect of pesticides on the different levels of the Toll pathway. In addition, imidacloprid, amitraz, and zymosan A have complex and context-specific interactions depending on the levels of immune activation and the pathway evaluated affecting immune-gene expression differently.

Keywords: toll pathway, immune modulation, β-glucan, imidacloprid, amitraz, honeybees, immune genes

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Authors: Tahsien Okasha

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Transplantation medicine is one of the most challenging and complex areas of modern medicine. Some of the key areas for medical management are the problems of transplant rejection, during which the body has an immune response to the transplanted organ, possibly leading to transplant failure and the need to immediately remove the organ from the recipient. When possible, transplant rejection can be reduced through serotyping to determine the most appropriate donor-recipient match and through the use of immunosuppressant drugs. Postoperative care actually begins before the surgery in terms of education, discharge planning, nutrition, pulmonary rehabilitation, and patient/family education. This also allows for expectations to be managed. A multidisciplinary approach is the key, and collaborative team meetings are essential to ensuring that all team members are "on the same page.". The following clinical pathway map and guidelines with the aim to decrease alteration in clinical practice and are intended for those healthcare professionals who look after organ transplant patients. They are also intended to be useful to both medical and surgical trainees as well as nurse specialists and other associated healthcare professionals involved in the care of organ transplant patients. This pathway is general pathway include the general guidelines that can be applicable for all types of organ transplant with special considerations to each organ.

Keywords: organ transplant, clinical pathway, postoperative care, same page

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Authors: Tahsien Okasha

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Transplantation medicine is one of the most challenging and complex areas of modern medicine. Some of the key areas for medical management are the problems of transplant rejection, during which the body has an immune response to the transplanted organ, possibly leading to transplant failure and the need to immediately remove the organ from the recipient. When possible, transplant rejection can be reduced through serotyping to determine the most appropriate donor-recipient match and through the use of immunosuppressant drugs. Postoperative care actually begins before the surgery in terms of education, discharge planning, nutrition, pulmonary rehabilitation, and patient/family education. This also allows for expectations to be managed. A multidisciplinary approach is the key, and collaborative team meetings are essential to ensuring that all team members are "on the same page." .The following clinical pathway map and guidelines with the aim to decrease alteration in clinical practice and are intended for those healthcare professionals who look after organ transplant patients. They are also intended to be useful to both medical and surgical trainees as well as nurse specialists and other associated healthcare professionals involved in the care of organ transplant patients. This pathway is general pathway include the general guidelines that can be applicable for all types of organ transplant with special considerations to each organ.

Keywords: postoperative care, organ transplant, clinical pathway, patient

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Authors: M. Rajasekar, K. Suresh

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Diosmin is a flavonoid, most abundantly found in many citrus fruits. As a flavonoid, it possesses a multitude of biological activities including anti-hyperglycemic, anti-lipid peroxidative, anti-inflammatory, antioxidant, and anti-mutagenic properties. At this point, we established the anti-proliferative and apoptosis-inducing activities of diosmin in Hep-2 and KB cells. Diosmin has cytotoxic effects through inhibiting cellular proliferation of Hep-2 and KB cells, which leads to the induction of apoptosis, as apparent by an increase in the fraction of cells in the sub-G1phase of the cell cycle. Results exposed that inhibition of cell proliferation is associated with regulation of the Interleukins/STAT pathway. In addition, Diosmin treatment with Hep-2 and KB cells actively stimulated reactive oxygen species (ROS) and mitochondrial membrane depolarization. And also an imbalance in the Bax/Bcl-2 ratio triggered the caspase cascade and shifting the balance in favor of apoptosis. These observations conclude that Diosmin induce apoptosis via Interleukins /STAT-mediated pathway.

Keywords: diosmin, apoptosis, antioxidant, STAT pathway

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Authors: Nahid H. Hajrah, Jamal S. M. Sabir, Neil Hall

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The jasmonic pathway is ubiquitous in plants and is crucial to plant development. It Is involved in fertility, ripening, and sex determination as well as in response to environmental stresses such as herbivory, pathogen drought or temperature shock. Essentially the jasmonic pathway acts to shut down growth in order to induce defence pathways. These pathways include the production of secondary metabolites which have evolved to defend against herbivores and pathogens but are of increasing interest due to their roll in medicine and biotechnology. Here we describe the transcriptional response of Rhazia stricta (a poisonous shrub widely used in traditional medicine) to jasmonic acid, in order to better characterize the genes involved in secondary metabolite production and its response to stress. We observe coordinated upregulation of flavonoid biosynthesis pathway leading to flavonols, flavones and anthocyanins but no similar coordination of the monoterpene indole alkaloid pathway.

Keywords: medicinal plants, Rhazia stricta, jasmonic acid, transcriptional analysis

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Authors: Ankita Shukla, Tiratha Raj Singh

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Colorectal cancer (CRC) imposes serious mortality burden worldwide and it has been increasing for past consecutive years. Continuous efforts have been made so far to diagnose the disease condition and to identify the root cause for it. In this study, we performed the pathway level as well as the differential gene expression studies for CRC. We analyzed the gene expression profile GSE24514 from Gene Expression Omnibus (GEO) along with the gene pathways involved in the CRC. This analysis helps us to understand the behavior of the genes that have shown differential expression through their targeted pathways. Pathway analysis for the targeted genes covers the wider area which therefore decreases the possibility to miss the significant ones. This will prove to be beneficial to expose the ones that have not been given attention so far. Through this analysis, we attempt to understand the various neighboring genes that have close relationship to the targeted one and thus proved to be significantly controlling the CRC. It is anticipated that the identified hub and neighboring genes will provide new directions to look at the pathway level differently and will be crucial for the regulatory processes of the disease.

Keywords: mismatch repair, microsatellite instability, carcinogenesis, morbidity

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Authors: Laras Tursilowati, Bambang Siswanto

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Urban climate change has short- and long-term implications for decision-makers in urban development. The problem for this important metropolitan regional of population and economic value is that there is very little usable information on climate change. Research about urban climate change has been carried out in Bali Indonesia by using Conformal Cubic Atmospheric Model (CCAM) that runs with Representative Concentration Pathway (RCP)4.5. The history data means average data from 1975 to 2005, climate projections with RCP4.5 scenario means average data from 2006 to 2099, and anomaly (urban climate change) is RCP4.5 minus history. The results are the history of temperature between 22.5-27.5 OC, and RCP4.5 between 25.5-29.5 OC. The temperature anomalies can be seen in most of northern Bali that increased by about 1.6 to 2.9 OC. There is a reduced humidity tendency (drier) in most parts of Bali, especially the northern part of Bali, while a small portion in the south increase moisture (wetter). The comfort index of Bali region in history is still relatively comfortable (20-26 OC), but on the condition RCP4.5 there is no comfortable area with index more than 26 OC (hot and dry). This research is expected to be useful to help the government make good urban planning.

Keywords: CCAM, comfort index, IPCC AR5, temperature, urban climate change

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Authors: Sarit Gideoni Cohen

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The aim of the study was to examine possible risk pathway which initiated by the distal risk factors of insecure attachment to the mother, the father and peers and then developed by means of proximal risk factors: stressful life events and emotional distress. 275 participants (aged 13-26) from high-schools, youth groups and university were requited. Twenty-two percent participants reported at least one episode of self-injury. The relationship between paternal and peer attachment were partly mediated by stressful life events and depressive symptoms. Paternal and peer attachment influences during adolescence as contributing to risk pathway for self-injury were acknowledged.

Keywords: self-injury, attachment, depression, stressful life-events, adolescence

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Authors: F. M. El-Domyati, A. Atef, S. Edris, N. O. Gadalla, M. A. Al-Kordy, A. M. Ramadan, Y. M. Saad, H. S. Al-Zahrani, A. Bahieldin

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Transcriptome retrieved from SRA database of different tissues and treatments of C. roseus was assembled in order to detect tissue-specific transcription factors (TFs) and TFs possibly related to terpenoid indole alkaloids (TIA) pathway. A number of 290 TF-like transcripts along with 12 transcripts related to TIA biosynthetic pathway were divided in terms of co-expression in the different tissues, treatments and genotypes. Three transcripts encoding peroxidases 1 and 12 were downregulated in hairy root, while upregulated in mature leaf. Eight different transcripts of the TIA pathway co-expressed with TFs either functioning downstream tryptophan biosynthesis, e.g., tdc, str1 and sgd, or upstream vindoline biosynthesis, e.g., t16h, omt, nmt, d4h and dat. The results showed no differential expression of TF transcripts in hairy roots knocked down for tdc gene (TDCi) as compared to their wild type controls. There were several evidences of tissue-specific expression of TF transcripts in flower, mature leaf, root/hairy root, stem, seedling, hairy root and immature/mature leaves. Regulation included transcription factor families, e.g., bHLH, MYB and WRKY mostly induced by ABA and/or JA (or MeJA) and regulated during abiotic or biotic stress. The information of tissue-specific regulation and co-expression of TFs and genes in the TIA pathway can be utilized in manipulating alkaloid biosynthesis in C. roseus.

Keywords: SRA database, bHLH, MYB, WRKY, co-expression

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Authors: Isaac Mugume

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Since the beginning of the 21st century, climate change has been an issue due to the reported rise in global temperature and changes in the frequency as well as severity of extreme weather and climatic events. The changing climate has been attributed to rising concentrations of greenhouse gases, including environmental changes such as ecosystems and land-uses. Climatic projections have been carried out under the auspices of the intergovernmental panel on climate change where a couple of models have been run to inform us about the likelihood of future climates. Since one of the major forcings informing the changing climate is emission of greenhouse gases, different scenarios have been proposed and future climates for different periods presented. The global climate models project different areas to experience different impacts. While regional modeling is being carried out for high impact studies, bias correction is less documented. Yet, the regional climate models suffer bias which introduces uncertainty. This is addressed in this study by bias correcting the regional models. This study uses the Weather Research and Forecasting model under different representative concentration pathways and correcting the products of these models using observed climatic data. This study notes that bias correction (e.g., the running-mean bias correction; the best easy systematic estimator method; the simple linear regression method, nearest neighborhood, weighted mean) improves the climatic projection skill and therefore reduce the uncertainty inherent in the climatic projections.

Keywords: bias correction, climatic projections, numerical models, representative concentration pathways

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Authors: I-Han Hsiao, Chun-Ping Huang, Ching-Liang Hsieh, Yi-Wen Lin

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Epilepsy is chronic brain disorder that results in the sporadic occurrence of spontaneous seizures in the temporal lobe, cerebral cortex, and hippocampus. Clinical antiepileptic medicines are often ineffective or little benefits in the small amount of patients and usually initiate severe side effects. This inflammation contributes to enhanced neuronal excitability and the onset of epilepsy. Auricular electric-stimulation (AES) can increase parasympathetic activity and stimulate the solitary tract nucleus to induce the cholinergic anti-inflammatory pathway. Furthermore, it may be a therapeutic strategy for the treatment of epilepsy. In the present study, we want to investigate the effects of AES on inflammatory mediators in kainic acid (KA)-induced epileptic seizure rats. Experimental KA injection increased expression of TLR-2 pathway associated inflammatory mediators, were further reduced by either 2Hz or 15 Hz AES in the prefrontal cortex, hippocampus, and somatosensory cortex. We suggest that AES can successfully control the epileptic seizure by down-regulation of inflammation signaling pathway.

Keywords: auricular electric-stimulation, epileptic seizures, anti-inflammation

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Authors: Juan Huang, Nanqu Huang, Jingshan Shi, Yu Qiu

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Objectives: There are pathophysiological connections between type 2 diabetes mellitus (T2DM) and Alzheimer's disease (AD), and research on drugs with hypoglycemic and beta-amyloid (Aβ)-clearing effects have great therapeutic potential for AD. Dendrobium nobile Lindl. Alkaloids (DNLA) as one of the active compounds of Dendrobium nobile Lindl. In this study, we attempted to verify the hypoglycemic effect and investigate the effects of DNLA on the amyloid precursor protein (APP) metabolic pathway of the hippocampus in db/db mice. Methods: 4-weeks-old male C57BL/KsJ mice were the control group. And the same age and sexuality db/db mice were: model, DNLA-L (20 mg/kg), DNLA-M (40 mg/kg), and DNLA-H (80 mg/kg). After, mice were treated with different concentrations of DNLA for 17 weeks. The fasting blood glucose (FBG) was detected by glucose oxidase assay every week from the 4th to last week. The protein expression of β-amyloid 1-42 (Aβ1-42), β-site amyloid precursor protein-cleaving enzyme 1 (BACE1), and APP were examined by Western blotting. Results: The concentration of FBG and the protein expression of Aβ1-42, BACE1, and APP were increased in the hippocampus of the model group. Moreover, DNLA not only significantly decreased the concentration of FBG but also reduced the protein expressions of Aβ1-42, BACE1 and APP in the hippocampus of db/db mice in a dose-dependent manner. Conclusions: DNLA can decrease the protein expressions of Aβ1-42 in the hippocampus of db/db mice, and the mechanism may be involved in the APP metabolic pathway.

Keywords: Alzheimer's disease, type 2 diabetes mellitus, β-site amyloid precursor protein-cleaving enzyme 1, traditional Chinese medicines, beta-amyloid

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Authors: Shohei Maruyama, Yasuo Matsuyama, Sachiyo Aburatani

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The development of the method to annotate unknown gene functions is an important task in bioinformatics. One of the approaches for the annotation is The identification of the metabolic pathway that genes are involved in. Gene expression data have been utilized for the identification, since gene expression data reflect various intracellular phenomena. However, it has been difficult to estimate the gene function with high accuracy. It is considered that the low accuracy of the estimation is caused by the difficulty of accurately measuring a gene expression. Even though they are measured under the same condition, the gene expressions will vary usually. In this study, we proposed a feature extraction method focusing on the variability of gene expressions to estimate the genes' metabolic pathway accurately. First, we estimated the distribution of each gene expression from replicate data. Next, we calculated the similarity between all gene pairs by KL divergence, which is a method for calculating the similarity between distributions. Finally, we utilized the similarity vectors as feature vectors and trained the multiclass SVM for identifying the genes' metabolic pathway. To evaluate our developed method, we applied the method to budding yeast and trained the multiclass SVM for identifying the seven metabolic pathways. As a result, the accuracy that calculated by our developed method was higher than the one that calculated from the raw gene expression data. Thus, our developed method combined with KL divergence is useful for identifying the genes' metabolic pathway.

Keywords: metabolic pathways, gene expression data, microarray, Kullback–Leibler divergence, KL divergence, support vector machines, SVM, machine learning

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Authors: H. Fraga, J. A. Santos

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Vitiviniculture in Portugal is a key socio-economic sector, with a strong connection to local traditions and culture. Despite being a relatively small country, with prevailing Mediterranean environments, Portugal comprises an exceptionally large diversity of growth conditions (Terroirs). The vineyard area in Portugal is over 190 thousand hectares, being the eleventh wine producer and ninth wine exporter worldwide. Owing to the strong impact of weather and climate conditions on grapevine physiological development, grape berry quantity and quality show important inter-annual variability. Grapevines are also susceptible to climate change, as their responses will be unavoidably different under future climates. These impacts may change wine typicity of a given region or even its viticultural suitability. The current study reveals that the projected warming and drying trends for Portugal under the Representative Concentration Pathway (RCP) 4.5 and 8.5, are projected to 1) significantly shift current grapevine growing thermal conditions (e.g., heat and chill accumulation), 2) enhance water stress, 3) anticipate phenological timings and 4) modify yields. Moreover, the present study provides some hints regarding the effectiveness of mulching and irrigation as climate change adaptation measures. Our results show that the effectiveness of these adaptation measures will strongly rest on the strength of the climate change signal at a local scale, thus emphasizing the need for local-to-regional climate change assessments.

Keywords: viticulture, climate change, adaptation measures, Portugal

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Authors: Farideh K. Khosroushahi, Serkan Erdal, Mucip Geni̇şel

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Soil salinity is one of the major abiotic stress factors that restricts arable land and reduces crop productivity worldwide. High salt concentration adversely affects plant growth and development inducing water deficit, ionic toxicity, nutrient imbalance, and lead to oxidative stress. Although the stimulating role of mammalian sex hormones on various biological and biochemical processes under normal and stress condition have been proven, there is no study regarding with these hormone's effect on modulation of the alternative respiration pathway and AOX gene expression. In this study, changes in alternative respiration pathway in leaves of maize seedlings under salinity and the possible modulating effect of estrogen on these changes were investigated. Maize seedlings were grown in a hydroponic media for 11 days and then were exposed to salt stress for 3 days after being sprayed estrogen. The data obtained from oxygen consumption revealed that salt stress elevated cellular respiration value in the leaves. In addition, a marked increase was observed at alternative respiration level in salt-stressed seedlings. Compared to salt application alone, supplementation with estrogen resulted in a significant rise in alternative oxidase (AOX) activities. Similarly, while salt stress caused to rise in expressions of AOX gene compared to control seedlings, estrogen application resulted in further activation of these genes’ expression compared to stressed-seedlings alone. These data revealed that mitigating role of estrogen against the detrimental effects of salt stress is linked to modulation of alternative respiration pathway.

Keywords: alternative oxidase, estrogen, Ssalt stress, AOX, maize

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Authors: Ali Dalirbod, Peyman Ahmadian

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Inclusions are unavoidable part of all steels. Non-metallic inclusions have significant effects on mechanical properties of steel. The effects of inclusion on stress concentration around the matrix/inclusion have been extensively studied. The results relating to single inclusion behavior, describe properly the behavior of stress but not the elongation drop. The raised stress in inclusion/matrix results in crack initiation. The influence of binary inclusions on stress concentration around matrix is a major aim of this work which is representative of the simple pattern distribution of non-metallic inclusions. Stress concentration around inclusions in this case depends on parameters like distance between two inclusions (d), angle between centrally linking line of two inclusions, load axis (φ), and rotational angle of inclusion (θ). FEM analysis was applied to investigate the highest and lowest ductility versus varying parameters above. The simulation results show that there is a critical distance between two cubic inclusions in which bigger than the threshold, the stress, and strain field in matrix/inclusions interface converts into individual fields around each inclusion.

Keywords: nitride inclusion, simulation, tensile properties, inclusion-matrix interface

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Authors: Jiun-Nan Hou, Tien-Huang Chen, Wei-June Chen

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Dengue viruses (DENVs) are naturally transmitted between humans by mosquito vectors. Mosquito cells usually survive DENV infection, allowing infected mosquitoes to retain an active status for virus transmission. In this study, we found that DENV2 virus infection in mosquito cells causes the unfolded protein response (UPR) that activates the protein kinase RNA-like endoplasmic reticulum kinase (PERK) signal pathway, leading to shutdown of global protein translation in infected cells which was apparently regulated by the PERK signal pathway. According to observation in this study, the PERK signal pathway in DENV2-infected C6/36 cells alleviates ER stress, and reduces initiator and effector caspases, as well as the apoptosis rate via shutdown of cellular proteins. In fact, phosphorylation of eukaryotic initiation factor 2ɑ (eIF2ɑ) by the PERK signal pathway may impair recruitment of ribosomes that bind to the mRNA 5’-cap structure, resulting in an inhibitory effect on canonical cap-dependent cellular protein translation. The resultant pro-survival “byproduct” of infected mosquito cells is undoubtedly advantageous for viral replication. This finding provides insights into elucidating the PERK-mediated modulating web that is actively involved in dynamic protein synthesis, cell survival, and viral replication in mosquito cells.

Keywords: cap-dependent protein translation, dengue virus, endoplasmic reticulum stress, mosquito cells, PERK signal pathway

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Authors: Yousuf Al Suleimani, Ahmed Al Mahruqi

Abstract:

A typical cannabinoid O-1602 induces vasorelaxation and activates the orphan G protein-coupled receptor GPR55 in human endothelial cells. The aim of this study is to characterize the mechanisms of endothelium-independent relaxation of O-1602 in the rat small mesenteric artery using wire myograph. In endothelium-denuded vessels, O-1602 partially produced concentration-dependent vasorelaxation. In vessels depleted of intracellular Ca2+ (by EGTA and methoxamine), CaCl2 produced concentration-dependent contraction. Preincubation with O-1602 (at 10 µM and 30 µM) abolished the contractile responses (P<0.01). The putative antagonist at novel “endothelial anandamide receptor” O-1918 (10 µM) significantly reversed the inhibitory effect of O-1602 on CaCl2-induced vasoconstriction. It is likely that the mechanism of endothelium-independent vasorelaxation to O-1602 is mediated by interfering with Ca2+ entry via an O-1918-sensitive pathway.

Keywords: O-1602, endothelium, vasorelaxation, calcium

Procedia PDF Downloads 360

Authors: A. O. Ogunkeyede, D. Amuchi, A. A. Adebayo

Abstract:

Heavy metal contaminations in soil have received great attention. Anthropogenic activities such as vehicular emission, industrial activities and constructions have resulted in elevated concentration of heavy metals in the surface soils. The metal particles can be free from the surface soil when they are disturbed and re-entrained in air, which necessitated the need to investigate surface soil at market environment where adults and children are present on daily basis. This study assesses concentration of heavy metal pollution, ecological and health risk factors in surface soil at Effurun market. 8 samples were collected at household material (EMH), fish (EMFs), fish and commodities (EMF-C), Abattoir (EMA 1 & 2), fruit sections (EMF 1 & 2) and lastly main road (EMMR). The samples were digested and analyzed in triplicate for contents of Lead (Pb), Nickel (Ni), Cadmium (Cd) and Copper (Cu). The mean concentration of the Pb mg/kg (112.27 ± 1.12) and Cu mg/kg (156.14 ± 1.10) were highest in the abattoir section (EMA 1). The mean concentrations of the heavy metal were then used to calculate the ecological and health risk for people within the market. Pb contamination at EMMR, EMF 2, EMFs were moderately while Pb shows considerable contamination at EMH, EMA 1, EMA 2 and EMF-C sections of the Effurun market. The ecological risk factor varies between low to moderate pollution for Pb and EMA 1 has the highest potential ecological risk that falls within moderate pollution. The hazard quotient results show that dermal exposure pathway is the possible means of heavy metal exposure to the traders while ingestion is the least sources of exposure to adult. The ingestion suggested that children around the EMA 1 have the highest possible exposure to children due to hand-to-mouth and object-to-mouth behaviour. The results further show that adults at the EMA1 will have the highest exposure to Pb due to inhalation during burning of cow with tyre that contained Pb and Cu. The carcinogenic risk values of most sections were higher than acceptable values, while Ni at EMMR, EMF 1 & 2, EMFs and EMF-C sections that were below the acceptable values. The cancer risk for inhalation exposure pathway for Pb (1.01E+17) shows a significant level of contamination than all the other sections of the market. It suggested that the people working at the Abattoir were very prone to cancer risk.

Keywords: carcinogenic, ecological, heavy metal, risk

Procedia PDF Downloads 146

Authors: Adriana Martínez-Arias, John Josephraj Selvaraj, Luis Octavio González-Salcedo

Abstract:

In the Colombian Pacific, Dorado fish (Coryphaena hippurus L.) fisheries is of great commercial interest. However, its habitat and fisheries may be affected by climatic change especially by the actual increase in sea surface temperature. Hence, it is of interest to study the dynamics of these species fishing zones. In this study, we developed Artificial Neural Networks (ANN) models to predict Catch per Unit Effort (CPUE) as an indicator of species abundance. The model was based on four oceanographic variables (Chlorophyll a, Sea Surface Temperature, Sea Level Anomaly and Bathymetry) derived from satellite data. CPUE datasets for model training and cross-validation were obtained from logbooks of commercial fishing vessel. Sea surface Temperature for Colombian Pacific were projected under Representative Concentration Pathway (RCP) scenarios 4.5 and 8.5 using Coupled Model Intercomparison Project Phase 5 (CMIP5) and CPUE maps were created. Our results indicated that an increase in sea surface temperature reduces the potential fishing zones of this species in the Colombian Pacific. We conclude that ANN is a reliable tool for simulation of climate change effects on the potential fishing zones. This research opens a future agenda for other species that have been affected by climate change.

Keywords: climatic change, artificial neural networks, dorado fish, CPUE

Procedia PDF Downloads 245

Authors: Md. Jahoor Alam

Abstract:

Recent studies suggest that Glucose controls several lifesaving pathways. Glucose molecule is reported to be responsible for the production of ROS (reactive oxygen species). In the present work, a p53-MDM2-Glucose model is developed in order to study spatiotemporal properties of the p53 pathway. The systematic model is mathematically described. The model is numerically simulated using high computational facility. It is observed that the variation in glucose concentration level triggers the system at different states, namely, oscillation death (stabilized), sustain and damped oscillations which correspond to various cellular states. The transition of these states induced by glucose is phase transition-like behaviour. Further, the amplitude of p53 dynamics with the variation of glucose concentration level follows power law behaviour, As(k) ~ kϒ, where, ϒ is a constant. Further Stochastic approach is needed for understanding of realistic behaviour of the model. The present model predicts the variation of p53 states under the influence of glucose molecule which is also supported by experimental facts reported by various research articles.

Keywords: oscillation, temporal behavior, p53, glucose

Procedia PDF Downloads 304