Search results for: genome scale metabolic reconstruction

Authors: Safwat Mohamed, Rasha Metawi, Hadeel Khalil, Hussein Kamal

Abstract:

This paper discusses and reveals the manufacturing techniques of the leather scale armour of Tutankhamun. This armour was in critical condition and went under many conservation procedures as it suffered from some serious deterioration aspects including fragmentation. In addition, its original shape was lost, the leather scales were found scattered in the box and separated from the linen basis, and hence its outlines were blurred and incomprehensible. In view of this, the leather scale armour of Tutankhamun was desperate for urgent conservation and reconstruction interventions. Documentation measures were done before conservation. Several re-treatable conservation procedures were applied seeking for stabilizing the armour and reaching sustainable condition. The conservation treatments included many investigations and analyses that helped in revealing materials and techniques of making the armour. The leather scale armour of Tutankhamun consisted of leather scales attached to a linen support. This linen support consisted of several layers. Howard Carter assumed that the linen support consisted of 6 layers. The undertaken conservation treatments helped in revealing the actual number of layers of the linen support as well as in reaching the most sustainable condition. This paper views the importance of the conservation procedures, which were recently carried out on Tutankhamun’s leather scale armour, in identifying and revealing all materials and techniques used in its manufacturing. The collected data about manufacturing techniques were used in making a replica of the leather scale armour with the same methods and materials.

Keywords: leather scales armours, conservation, manufacturing techniques, Tutankhamun, producing a replica

Procedia PDF Downloads 67

Authors: Borys Stegniy, Anton Gerilovych, Oleksii Solodiankin, Vitaliy Bolotin, Anton Stegniy, Denys Muzyka, Claudio Afonso

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New APMV was isolated from white fronted goose in Ukraine. This isolate was tested serologically using monoclonal antibodies in haemagglutination-inhibition tests against APMV1-9. As the results obtained isolate showed cross reactions with APMV7. Following investigations were provided for the full genome sequencing using random primers and cloning into pCRII-TOPO. Analysis of 100 transformed colonies of E.coli using traditional sequencing gave us possibilities to find only 3 regions, which could identify by BLAST. The first region with the length of 367 bp had 70 % nucleotide sequence identity to the APMV 12 isolate Wigeon/Italy/3920_1/2005 at genome position 2419-2784. Next region (344 bp) had 66 % identity to the same APMV 12 isolate at position 4760-5103. The last region (365 bp) showed 71 % identity to Newcastle disease virus strain M4 at position 12569-12928.

Keywords: APMV, Newcastle disease virus, Ukraine, full genome sequencing

Procedia PDF Downloads 422

Authors: Manendra Singh Parihar, Sandip Ghosh Chowdhury

Abstract:

Austenitic stainless steels are widely used and give a good combination of properties. When this steel is plastically deformed, a phase transformation of the metastable Face Centred Cubic Austenite to the stable Body Centred Cubic (α’) or to the Hexagonal close packed (ԑ) martensite may occur, leading to the enhancement in the mechanical properties like strength. The work was based on variant selection and corresponding texture analysis for the strain induced martensitic transformation during deformation of the parent austenite FCC phase to form the product HCP and the BCC martensite phases separately, obeying their respective orientation relationships. The automated method for reconstruction of the parent phase orientation using the EBSD data of the product phase orientation is done using the MATLAB and TSL-OIM software. The method of triplets was used which involves the formation of a triplet of neighboring product grains having a common variant and linking them using a misorientation-based criterion. This led to the proper reconstruction of the pre-transformation phase orientation data and thus to its microstructure and texture. The computational speed of current method is better compared to the previously used methods of reconstruction. The reconstruction of austenite from ԑ and α’ martensite was carried out for multiple samples and their IPF images, pole figures, inverse pole figures and ODFs were compared. Similar type of results was observed for all samples. The comparison gives the idea for estimating the correct sequence of the transformation i.e. γ → ε → α’ or γ → α’, during deformation of AISI 304 austenitic stainless steel.

Keywords: variant selection, reconstruction, EBSD, austenitic stainless steel, martensitic transformation

Procedia PDF Downloads 475

Authors: Ayca Bilginoglu, Belma Turan

Abstract:

Metabolic syndrome, is associated impaired blood glucose level, insulin resistance, dyslipidemia caused by abdominal obesity. Also, it is related with cardiovascular risk accumulation and cardiomyopathy. The hypothesis of this study was to examine the effect of thiazolidinediones such as pioglitazone which is widely used insulin-sensitizing agents that improve glycemic control, on intracellular Na+ homeostasis in metabolic syndrome-induced cardiomyopathy in male rats. Male Wistar-Albino rats were randomly divided into three groups, namely control (Con, n=7), metabolic syndrome (MetS, n=7) and pioglitazone treated metabolic syndrome group (MetS+PGZ, n=7). Metabolic syndrome was induced by providing drinking water that was 32% sucrose, for 18 weeks. All of the animals were exposed to a 12 h light – 12 h dark cycle. Abdominal obesity and glucose intolerance had measured as a marker of metabolic syndrome. Intracellular Na+ ([Na+]i) is an important modulator of excitation–contraction coupling in heart. [Na+]i at rest and [Na+]i during pacing with electrical field stimulation in 0.2 Hz, 0.8 Hz, 2.0 Hz stimulation frequency were recorded in cardiomyocytes. Also, Na+ channel current (INa) density and I-V curve were measured to understand [Na+]i homeostasis. In results, high sucrose intake, as well as the normal daily diet, significantly increased body mass and blood glucose level of the rats in the metabolic syndrome group as compared with the non-treated control group. In MetS+PZG group, the blood glucose level and body inclined to decrease to the Con group. There was a decrease in INa density and there was a shift both activation and inactivation curve of INa. Pioglitazone reversed the shift to the control side. Basal [Na+]i either MetS and Con group were not significantly different, but there was a significantly increase in [Na+]i in stimulated cardiomyocytes in MetS group. Furthermore, pioglitazone had not effect on basal [Na+]i but it reversed the increase in [Na+]i in stimulated cardiomyocytes to the that of Con group. Results of the present study suggest that pioglitazone has a significant effect on the Na+ homeostasis in the metabolic syndrome induced cardiomyopathy in rats. All animal procedures and experiments were approved by the Animal Ethics Committee of Ankara University Faculty of Medicine (2015-2-37).

Keywords: insulin resistance, intracellular sodium, metabolic syndrome, sodium current

Procedia PDF Downloads 268

Authors: Bilal Wajid, Erchin Serpedin

Abstract:

The health industry is aiming towards personalized medicine. If the patient’s genome needs to be sequenced it is important that the entire analysis be completed quickly. This paper explores use of parallel computing to analyze very large sequences. Two cases have been considered. In the first case, the sequence is kept constant and the effect of increasing the number of MPI-based processes is evaluated in terms of execution time, speed and efficiency. In the second case the number of MPI-based processes have been kept constant whereas, the length of the sequence was increased.

Keywords: parallel computing, alignment, genome assembly, alignment

Procedia PDF Downloads 249

Authors: Hazel Ann Gianelli Cu, Stephanie Co, Radcliff Cobankiat

Abstract:

Objectives: TRC101/Veverimer is an orally administered, non absorbed, sodium- and counterion-free hydrochloric acid binder for the treatment of metabolic acidosis associated with chronic kidney disease. The main objective of this study is to determine the efficacy of TRC 101/ Veverimer 6g/day in increasing serum bicarbonate levels of chronic kidney disease patients with metabolic acidosis. In this meta analysis, we also aim to look at safety outcomes, adverse effects and if the level of serum bicarbonate reached metabolic alkalosis when given TRC101/Veverimer. Methodology: Pubmed, Cochrane, Google Scholar and Science direct were used to search for randomized controlled trials about TRC101/Veverimer use in Chronic kidney disease patients with metabolic acidosis. Search strategy according to the Prisma checklist was done with evaluation of biases and synthesis of results using the Cochrane Review Manager software 5.4. Results: Two randomized controlled trials involving 371 chronic kidney disease patients were included in this study. Results show there was a significant increase in the serum bicarbonate level when given TRC101/Veverimer compared to the placebo. Both studies had a significant number of participants who completed the studies until the end. P value of <0.00001 was used in both studies with a confidence interval of 95%. Conclusion: TRC101/Veverimer 6g/day was shown to effectively and safely increase serum bicarbonate or achieve normalization in chronic kidney disease patients with metabolic acidosis as compared with a placebo. This was associated with delayed progression of kidney disease with improvement of physical functioning, however longer duration of future studies is ideal in order to assess further the long advantages and consequences of TRC 101/Veverimer.

Keywords: chronic kidney disease, metabolic acidosis, Veverimer, TRC101

Procedia PDF Downloads 174

Authors: Vyacheslav Furtak, Merja Roivainen, Olga Mirochnichenko, Majid Laassri, Bella Bidzhieva, Tatiana Zagorodnyaya, Vladimir Chizhikov, Konstantin Chumakov

Abstract:

Molecular epidemiology and environmental surveillance are parts of a rational strategy to control infectious diseases. They have been widely used in the worldwide campaign to eradicate poliomyelitis, which otherwise would be complicated by the inability to rapidly respond to outbreaks and determine sources of the infection. The conventional scheme involves isolation of viruses from patients and the environment, followed by their identification by nucleotide sequences analysis to determine phylogenetic relationships. This is a tedious and time-consuming process that yields definitive results when it may be too late to implement countermeasures. Because of the difficulty of high-throughput full-genome sequencing, most such studies are conducted by sequencing only capsid genes or their parts. Therefore the important information about the contribution of other parts of the genome and inter- and intra-species recombination to viral evolution is not captured. Here we propose a new approach based on the rapid concentration of sewage samples with tangential flow filtration followed by deep sequencing and reconstruction of nucleotide sequences of viruses present in the samples. The entire nucleic acids content of each sample is sequenced, thus preserving in digital format the complete spectrum of viruses. A set of rapid algorithms was developed to separate deep sequence reads into discrete populations corresponding to each virus and assemble them into full-length consensus contigs, as well as to generate a complete profile of sequence heterogeneities in each of them. This provides an effective approach to study molecular epidemiology and evolution of natural viral populations.

Keywords: poliovirus, eradication, environmental surveillance, laboratory diagnosis

Procedia PDF Downloads 254

Authors: William Kelly, Sorelle Veigne, Xianhua Li, Zuyi Huang, Shyamsundar Subramanian, Eugene Schaefer

Abstract:

The ambr15™ bioreactor is a single-use microbioreactor for cell line development and process optimization. The ambr system offers fully automatic liquid handling with the possibility of fed-batch operation and automatic control of pH and oxygen delivery. With operating conditions for large scale biopharmaceutical production properly scaled down, micro bioreactors such as the ambr15™ can potentially be used to predict the effect of process changes such as modified media or different cell lines. In this study, gassing rates and dilution rates were varied for a semi-continuous cell culture system in the ambr15™ bioreactor. The corresponding changes to metabolite production and consumption, as well as cell growth rate and therapeutic protein production were measured. Conditions were identified in the ambr15™ bioreactor that produced metabolic shifts and specific metabolic and protein production rates also seen in the corresponding larger (5 liter) scale perfusion process. A Dynamic Flux Balance model was employed to understand and predict the metabolic changes observed. The DFB model-predicted trends observed experimentally, including lower specific glucose consumption when CO₂ was maintained at higher levels (i.e. 100 mm Hg) in the broth. A Computational Fluid Dynamic (CFD) model of the ambr15™ was also developed, to understand transfer of O₂ and CO₂ to the liquid. This CFD model predicted gas-liquid flow in the bioreactor using the ANSYS software. The two-phase flow equations were solved via an Eulerian method, with population balance equations tracking the size of the gas bubbles resulting from breakage and coalescence. Reasonable results were obtained in that the Carbon Dioxide mass transfer coefficient (kLa) and the air hold up increased with higher gas flow rate. Volume-averaged kLa values at 500 RPM increased as the gas flow rate was doubled and matched experimentally determined values. These results form a solid basis for optimizing the ambr15™, using both CFD and FBA modelling approaches together, for use in microscale simulations of larger scale cell culture processes.

Keywords: cell culture, computational fluid dynamics, dynamic flux balance analysis, microbioreactor

Procedia PDF Downloads 257

Authors: Zahra Bahadoran, Parvin Mirmiran, Fereidoun Azizi

Abstract:

Background: Higher consumption of white rice has been suggested as a risk factor for development of metabolic abnormalities. In this study we investigated the association between consumption of white rice and the 3-year occurrence of metabolic syndrome (MetS) in adults with and without abdominal obesity. Methods: This longitudinal study was conducted within the framework of the Tehran Lipid and Glucose Study on 1476 adults, aged 19-70 years. Dietary intakes were measured, using a 168-food items validated semi-quantitative food frequency questionnaire at baseline. Biochemical and anthropometric measurements were evaluated at both baseline (2006-2008) and after 3-year follow-up (2009-2011). MetS and its components were defined according to the diagnostic criteria proposed by NCEP ATP III, and the new cutoff points of waist circumference for Iranian adults. Multiple logistic regression models were used to estimate the occurrence of the MetS in each quartile of white rice consumption. Results: The mean age of participants was 37.8±12.3 y, and mean BMI was 26.0±4.5 kg/m2 at baseline. The prevalence of MetS in subjects with abdominal obesity was significantly higher (40.9 vs. 16.2%, P<0.01). There was no significant difference in white rice consumption between the two groups. Mean daily intake of white rice was 93±59, 209±58, 262±60 and 432±224 g/d, in the first to fourth quartiles of white rice, respectively. Stratified analysis by categories of waist circumference showed that higher consumption of white rice was more strongly related to the risk of metabolic syndrome in participants who had abdominal obesity (OR: 2.34, 95% CI:1.14-4.41 vs. OR:0.99, 95% CI:0.60-1.65) Conclusion: We demonstrated that higher consumption of white rice may be a risk for development of metabolic syndrome in adults with abdominal obesity.

Keywords: white rice, abdominal obesity, metabolic syndrome, food science, triglycerides

Procedia PDF Downloads 424

Authors: Manendra Singh Parihar, Sandip Ghosh Chowdhury

Abstract:

Austenitic stainless steels are widely used and give a good combination of properties. When this steel is plastically deformed, a phase transformation of the metastable Face Centred Cubic Austenite to the stable Body Centred Cubic (α’) or to the Hexagonal close packed (ԑ) martensite may occur, leading to the enhancement in the mechanical properties like strength. The work was based on variant selection and corresponding texture analysis for the strain induced martensitic transformation during deformation of the parent austenite FCC phase to form the product HCP and the BCC martensite phases separately, obeying their respective orientation relationships. The automated method for reconstruction of the parent phase orientation using the EBSD data of the product phase orientation is done using the MATLAB and TSL-OIM software. The method of triplets was used which involves the formation of a triplet of neighboring product grains having a common variant and linking them using a misorientation-based criterion. This led to the proper reconstruction of the pre-transformation phase orientation data and thus to its micro structure and texture. The computational speed of current method is better compared to the previously used methods of reconstruction. The reconstruction of austenite from ԑ and α’ martensite was carried out for multiple samples and their IPF images, pole figures, inverse pole figures and ODFs were compared. Similar type of results was observed for all samples. The comparison gives the idea for estimating the correct sequence of the transformation i.e. γ → ε → α’ or γ → α’, during deformation of AISI 304 austenitic stainless steel.

Keywords: variant selection, reconstruction, EBSD, austenitic stainless steel, martensitic transformation

Procedia PDF Downloads 471

Authors: A. Almohammedi, A. J. Hudson, N. M. Storey

Abstract:

Following ischaemia/reperfusion injury, as in a myocardial infraction, cardiac myocytes undergo oxidative stress which leads to several potential outcomes including; necrotic or apoptotic cell death or dysregulated calcium homeostasis or disruption of the electron transport chain. Several studies have shown that nitric oxide donors protect cardiomyocytes against ischemia and reperfusion. However until present, the mechanism of cardioprotective effect of nitric oxide donor in isolated ventricular cardiomyocytes is not fully understood and has not been investigated before using Raman spectroscopy. For these reasons, the aim of this study was to develop a novel technique, pre-resonance Raman spectroscopy, to investigate the mechanism of cardioprotective effect of nitric oxide donor in isolated ventricular cardiomyocytes exposed to metabolic inhibition and re-energisation. The results demonstrated the first time that Raman microspectroscopy technique has the capability to monitor the metabolic inhibition of cardiomyocytes and to monitor the effectiveness of cardioprotection by nitric oxide donor prior to metabolic inhibition of cardiomyocytes. Metabolic inhibition and reenergisation were used in this study to mimic the low and high oxygen levels experienced by cells during ischaemic and reperfusion treatments. A laser wavelength of 488 nm used in this study has been found to provide the most sensitive means of observe the cellular mechanisms of myoglobin during nitric oxide donor preconditioning, metabolic inhibition and re-energisation and did not cause any damage to the cells. The data also highlight the considerably different cellular responses to metabolic inhibition to ischaemia. Moreover, the data has been shown the relationship between the release of myoglobin and chemical ischemia where that the release of myoglobin from the cell only occurred if a cell did not recover contractility.

Keywords: ex vivo biospectroscopy, Raman spectroscopy, biophotonics, cardiomyocytes, ischaemia / reperfusion injury, cardioprotection, nitric oxide donor

Procedia PDF Downloads 332

Authors: Amany Ragab, Nashwa Khairat Abousamra, Omayma Saleh, Asmaa Higazy

Abstract:

Insulin resistance syndrome has been shown to be associated with many coagulation and fibrinolytic proteins and these associations suggest that some coagulation and fibrinolytic proteins have a role in atherothrombotic disorders. This study was conducted to determine the levels of some of the haemostatic parameters in subjects having metabolic syndrome and to correlate these values with the anthropometric and metabolic variables associated with this syndrome. The study included 46 obese non diabetic subjects of whom 28 subjects(group1) fulfilled the ATP III criteria of the metabolic syndrome and 18 subjects (group2) did not have metabolic syndrome as well as 14 lean subjects (group 3) of matched age and sex as a control group. Clinical and laboratory evaluation of the study groups stressed on anthropometric measurements (weight, height, body mass index, waist circumference, and sagittal abdominal diameter), blood pressure, and laboratory measurements of fasting plasma glucose, fasting insulin, serum lipids, tissue plasminogen activator (t-PA), antithrombin III activity (ATIII), protein C and von Willebrand factor (vWf) antigen. There was significant increase in the concentrations of t-PA and vWf antigens in subjects having metabolic syndrome (group 1) in comparison to the other groups while there were non-significant changes in the levels of protein C antigen and AT III activity. Both t-PA and vWf showed significant correlation with HOMA-IR as a measure of insulin sensitivity. The t-PA showed also significant correlation with most of the variables of metabolic syndrome including waist circumference, BMI, systolic blood pressure, fasting plasma glucose, fasting insulin, and HDL cholesterol. On the other hand, vWf showed significant correlations with fasting plasma glucose, fasting insulin and sagital abdominal diameter, with non-significant correlations with the other variables. Haemostatic and fibrinolytic parameters should be included in the features and characterization of the insulin resistance syndrome. t-PA and vWf antigens concentrations were increased in subjects with metabolic syndrome and correlated with the HOMA-IR measure of insulin sensitivity. Taking into consideration that both t-PA and vWf are mainly released from vascular endothelium, these findings could be an indicator of endothelial dysfunction in that group of subjects.

Keywords: insulin resistance, obesity, metabolic syndrome, coagulation

Procedia PDF Downloads 119

Authors: Shu-Yen Wang, Shyh-Huei Hwang

Abstract:

Designated as an important architectural complex of settlement by the Ministry of Culture, Hua-Zhai Settlement located in Wang-An Township, Peng-Hu County, of Taiwan has been progressively restored year by year and is now at the revitalization and reutilization stage. Over the last 5 years, YunTech has participated in the restoration project while being in compliance with the Bureau of Cultural Heritage’s spirit of 'Living Heritage Conservation'. In this study, reflections have been made to evaluate the contemporariness of traditional settlement development from the aspects of revitalization and reutilization. On the one hand, the connection between settlers’ experiences and emotions have been clarified through the living nodes, collective memory, and social-cultural connotation. On the other hand, activity design has promoted the reconstruction of living nodes and facilitated the reconnection of collective memory, enabling us to explore the contemporariness of living nodes after the reconstruction. With the adoption of literature review, participant observation, and interview analysis methods, this study concludes the following results: 1) The node reconstruction brings back the memories and makes emotional connections: the spatial collective memory is composed of different components. During the reconstruction of node space, villagers participated not only in the narration of the history but also in the restoration of the space. This process enables villagers to bring back their memories and make emotional connections thereto. 2) Villagers’ understanding towards revitalization has been facilitated through node reconstruction: as a medium of this project, activity design has facilitated node reconstruction by offering villagers a natural environment to build up emotional connections to the settlement. This also enables us to better understand the meaning of settlement activation for the local community. 3) New connections are established in life between villagers and the university through the construction of living nodes: through the local implementation of node reconstruction, new connections have been established in life between villagers who participated in the project and the university. In the meantime, the university’s entrance to the community has also been revalued.

Keywords: collective memory, local sense of belonging, reconstruction of living nodes, the important architectural complex of Wang-An Hua-Zhai settlement

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Authors: N. Noroozian, M. Halim, B. Holloway

Abstract:

Computed Tomography (CT) has become the largest source of radiation exposure in modern countries however, recent technological advances have created new methods to reduce dose without negatively affecting image quality. SAFIRE has emerged as a new software package which utilizes full raw data projections for iterative reconstruction, thereby allowing for lower CT dose to be used. this audit was performed to compare CT doses in certain examinations before and after the introduction of SAFIRE at our Radiology department which showed CT doses were significantly lower using SAFIRE compared with pre-SAFIRE software at SAFIRE 3 setting for the following studies:CSKUH Unenhanced brain scans (-20.9%), CABPEC Abdomen and pelvis with contrast (-21.5%), CCHAPC Chest with contrast (-24.4%), CCHAPC Abdomen and pelvis with contrast (-16.1%), CCHAPC Total chest, abdomen and pelvis (-18.7%).

Keywords: dose reduction, iterative reconstruction, low dose CT techniques, SAFIRE

Procedia PDF Downloads 264

Authors: Mi Kyeong Yu, Seon Jeong Lee, So Young Kim, Bora Choi, Young Mi Lee, Su-Jung Cho, Je Tae Woo, Myung-Sook Choi

Abstract:

A high-fat diet (HFD) induces excessive fat accumulation in white adipose tissue (WAT), which increases metabolic disorders such as obesity, dyslipidemia and type 2 diabetes. Many plants are known to have effects that improve metabolic disorders. Therefore, the aim of this present study is to investigate the effect of nepodin-enrich plant extract on dyslipidemia, hyperglycemia in high fat diet-induced C57BL/6J mice. Male C57BL/6J mice were randomly divided into two groups, and fed HFD (20% fat, w/w) or HFD supplemented with nepodin-enrich plant extract (NPE 0.005%, w/w) for 16 weeks. Body weight and food intake were measured every week. And we also analysed metabolic rates (respiratory quotient), blood glucose level, and plasma high-density lipoprotein (HDL)-cholesterol, free fatty acid, apolipoprotein (apo) A-1 and apo B levels. Food intakes and body weights were not different between NPE group and HFD group, while plasma apo B, free fatty acid levels, and blood glucose concentration were significantly decreased in NPE group than in HFD group. Furthermore, plasma apo A and HDL-cholesterol levels in NPE group were remarkably increased than in HFD group. Metabolic rates (respiratory quotient) were significantly increased in NPE group than in HFD group. These results indicate that NPE can alleviate dyslipidemia, hyperglycemia. Further studies are required to identify the effects of NPE on metabolic disorders.

Keywords: dyslipidemia, hyperglycemia, metabolic disorders, nepodin enrich plant extract

Procedia PDF Downloads 350

Authors: Aprilia, Wei Liang Keith Nguyen, Shu Beng Tor, Gerald Gim Lee Seet, Chee Kai Chua

Abstract:

Automated remanufacturing process is of great interest in today’s marine and offshore industry. Most of the current remanufacturing processes are carried out manually and hence they are error prone, labour-intensive and costly. In this paper, a conceptual framework for automated remanufacturing is presented. This framework involves the integration of 3D non-contact digitization, adaptive surface reconstruction, additive manufacturing and machining operation. Each operation is operated and interconnected automatically as one system. The feasibility of adaptive surface reconstruction on marine and offshore engineering components is also discussed. Several engineering components were evaluated and the results showed that this proposed system is feasible. Conclusions are drawn and further research work is discussed.

Keywords: adaptive surface reconstruction, automated remanufacturing, automatic repair, reverse engineering

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Authors: Igor V. Grigoriev

Abstract:

Understanding of biological processes encoded in fungi is instrumental in addressing future food, feed, and energy demands of the growing human population. Genomics is a powerful and quickly evolving tool to understand these processes. The Fungal Genomics Program of the US Department of Energy Joint Genome Institute (JGI) partners with researchers around the world to explore fungi in several large scale genomics projects, changing the fungal genomics landscape. The key trends of these changes include: (i) rapidly increasing scale of sequencing and analysis, (ii) developing approaches to go beyond culturable fungi and explore fungal ‘dark matter,’ or unculturables, and (iii) functional genomics and multi-omics data integration. Power of comparative genomics has been recently demonstrated in several JGI projects targeting mycorrhizae, plant pathogens, wood decay fungi, and sugar fermenting yeasts. The largest JGI project ‘1000 Fungal Genomes’ aims at exploring the diversity across the Fungal Tree of Life in order to better understand fungal evolution and to build a catalogue of genes, enzymes, and pathways for biotechnological applications. At this point, at least 65% of over 700 known families have one or more reference genomes sequenced, enabling metagenomics studies of microbial communities and their interactions with plants. For many of the remaining families no representative species are available from culture collections. To sequence genomes of unculturable fungi two approaches have been developed: (a) sequencing DNA from fruiting bodies of ‘macro’ and (b) single cell genomics using fungal spores. The latter has been tested using zoospores from the early diverging fungi and resulted in several near-complete genomes from underexplored branches of the Fungal Tree, including the first genomes of Zoopagomycotina. Genome sequence serves as a reference for transcriptomics studies, the first step towards functional genomics. In the JGI fungal mini-ENCODE project transcriptomes of the model fungus Neurospora crassa grown on a spectrum of carbon sources have been collected to build regulatory gene networks. Epigenomics is another tool to understand gene regulation and recently introduced single molecule sequencing platforms not only provide better genome assemblies but can also detect DNA modifications. For example, 6mC methylome was surveyed across many diverse fungi and the highest among Eukaryota levels of 6mC methylation has been reported. Finally, data production at such scale requires data integration to enable efficient data analysis. Over 700 fungal genomes and other -omes have been integrated in JGI MycoCosm portal and equipped with comparative genomics tools to enable researchers addressing a broad spectrum of biological questions and applications for bioenergy and biotechnology.

Keywords: fungal genomics, single cell genomics, DNA methylation, comparative genomics

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Authors: N. H. Adenan, M. S. M. Noorani

Abstract:

River flow prediction is an essential to ensure proper management of water resources can be optimally distribute water to consumers. This study presents an analysis and prediction by using nonlinear prediction method involving monthly river flow data in Tanjung Tualang from 1976 to 2006. Nonlinear prediction method involves the reconstruction of phase space and local linear approximation approach. The phase space reconstruction involves the reconstruction of one-dimensional (the observed 287 months of data) in a multidimensional phase space to reveal the dynamics of the system. Revenue of phase space reconstruction is used to predict the next 72 months. A comparison of prediction performance based on correlation coefficient (CC) and root mean square error (RMSE) have been employed to compare prediction performance for nonlinear prediction method, ARIMA and SVM. Prediction performance comparisons show the prediction results using nonlinear prediction method is better than ARIMA and SVM. Therefore, the result of this study could be used to developed an efficient water management system to optimize the allocation water resources.

Keywords: river flow, nonlinear prediction method, phase space, local linear approximation

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Authors: Aishik Deb, Rituparna Sinha

Abstract:

We have developed an algorithm to detect the abnormal segment/"structural variation in the genome across a number of samples. We have worked on simulated as well as real data from the BAM Files and have designed a segmentation algorithm where abnormal segments are detected. This algorithm aims to improve the accuracy and performance of the existing CNV-CH algorithm. The next-generation sequencing (NGS) approach is very fast and can generate large sequences in a reasonable time. So the huge volume of sequence information gives rise to the need for Big Data and parallel approaches of segmentation. Therefore, we have designed a map-reduce approach for the existing CNV-CH algorithm where a large amount of sequence data can be segmented and structural variations in the human genome can be detected. We have compared the efficiency of the traditional and map-reduce algorithms with respect to precision, sensitivity, and F-Score. The advantages of using our algorithm are that it is fast and has better accuracy. This algorithm can be applied to detect structural variations within a genome, which in turn can be used to detect various genetic disorders such as cancer, etc. The defects may be caused by new mutations or changes to the DNA and generally result in abnormally high or low base coverage and quantification values.

Keywords: cancer detection, convex hull segmentation, map reduce, next generation sequencing

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Authors: N. K. Gupta, R. C. Bhattacharjee

Abstract:

In the aftermath of the tsunami in 2004 and terrible humanitarian disaster affecting thousands of kilometers of coastal south, the immediate priority is to begin the process of reconstruction of livelihoods including basic services. It is likely that many coastal wetlands would have been affected by the large inflow of salt-water and littoral sediments during the tsunami, with longer-term effects including changes in their hydrogeology caused by changes to coastlines and damage to sea-defenses. The reconstruction process is likely to provide opportunities to better integrate environmental protection and management with economic development in the region, including the opportunity to conserve and restore coastal habitats. Presented herein is a study pertaining to salinity problems encountered in coastal south during tsunami in 2004 and the consequent loss of fertility of agricultural land including remedial measures to revitalize economic growth in the region.

Keywords: tsunami, salinity, costal area, reconstruction

Procedia PDF Downloads 355

Authors: Farahnaz Sadat Golestan Hashemi, Mohd Razi Ismail, Mohd Y. Rafii

Abstract:

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) system can facilitate targeted genome editing in organisms. Dual or single guide RNA (gRNA) can program the Cas9 nuclease to cut target DNA in particular areas; thus, introducing concise mutations either via error-prone non-homologous end-joining repairing or via incorporating foreign DNAs by homologous recombination between donor DNA and target area. In spite of high demand of such promising technology, developing a well-organized procedure in order for reliable mining of potential target sites for gRNAs in large genomic data is still challenging. Hence, we aimed to perform high-throughput detection of target sites by specific PAMs for not only common Streptococcus pyogenes (SpCas9) but also for Neisseria meningitides (NmCas9) CRISPR-Cas systems. Previous research confirmed the successful application of such RNA-guided Cas9 orthologs for effective gene targeting and subsequently genome manipulation. However, Cas9 orthologs need their particular PAM sequence for DNA cleavage activity. Activity levels are based on the sequence of the protospacer and specific combinations of favorable PAM bases. Therefore, based on the specific length and sequence of PAM followed by a constant length of the target site for the two orthogonals of Cas9 protein, we created a reliable procedure to explore possible gRNA sequences. To mine CRISPR target sites, four different searching modes of sgRNA binding to target DNA strand were applied. These searching modes are as follows i) coding strand searching, ii) anti-coding strand searching, iii) both strand searching, and iv) paired-gRNA searching. Finally, a complete list of all potential gRNAs along with their locations, strands, and PAMs sequence orientation can be provided for both SpCas9 as well as another potential Cas9 ortholog (NmCas9). The artificial design of potential gRNAs in a genome of interest can accelerate functional genomic studies. Consequently, the application of such novel genome editing tool (CRISPR/Cas technology) will enhance by presenting increased versatility and efficiency.

Keywords: CRISPR/Cas9 genome editing, gRNA mining, SpCas9, NmCas9

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Authors: Kartik Thakore, Anna-Roza Tamas, Adam Cole

Abstract:

The world health organization (WHO) reports that by 2030 more than 23.7 million deaths annually will be caused by Cardiovascular Diseases (CVDs); with a 2008 economic impact of $3.76 T. Metabolic syndrome is a disorder of multiple metabolic risk factors strongly indicated in the development of cardiovascular diseases. Guided lifestyle intervention driven by live coaching has been shown to have a positive impact on metabolic risk factors. Individuals’ path to improved (decreased) metabolic risk factors are driven by personal motivation and personalized messages delivered by coaches and augmented by technology. Using interactions captured between 400 individuals and 3 coaches over a program period of 500 days, a preliminary model was designed. A novel real time event tracking system was created to track and classify clients based on their genetic profile, baseline questionnaires and usage of a mobile application with live coaching sessions. Classification of clients and coaches was done using a support vector machines application build on Apache Spark, Stanford Natural Language Processing Library (SNLPL) and decision-modeling.

Keywords: guided lifestyle intervention, metabolic risk factors, personal coaching, support vector machines application, Apache Spark, natural language processing

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Authors: Andrey Kashcheev, Victor Sytnikov, Mikhail Dubinin, Elena Filipeva, Dmitriy Sorokin

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Various variants of technical solutions aimed at improving the reliability of power supply to consumers of 110 kV substation are considered. For each technical solution, the results of calculation and analysis of electrical modes and short-circuit currents in the electrical network are presented. The estimation of electric energy consumption for losses within the boundaries of substation reconstruction was carried out in accordance with the methodology for determining the standards of technological losses of electricity during its transmission through electric networks. The assessment of the technical and economic feasibility of the use of HTS CL compared with the complex reconstruction of the 110 kV substation was carried out. It is shown that the use of high-temperature superconducting AC cable lines is a possible alternative to traditional technical solutions used in the reconstruction of substations.

Keywords: superconductivity, cable lines, superconducting cable, AC cable, feasibility

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Authors: Blanca Fatela Cantillo, Silvia Iglesias Cerrato, Guadalupe Garrido Ceca

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Purpose: Bleb dysfunction is a late complication following glaucoma filtration surgery. We describe our surgical technique for excision and reconstruction of a hypertrophic bleb complication using bovine pericardium patch graft (Tutopatch®) and amniotic membrane. Material and methods: The case report presents a hypertrophic bleb over the cornea with good intraocular pressure control. The hanging bleb without leak caused dysesthesia and high irregular astigmatism. Bleb reconstruction involved the excision of corneal fibrous material and avascular conjunctiva, preserving the original scleral and tennon. Bovine pericardium patch graft (Tutopatch®) was sited over these with fixed sutures, reinforcing the underlying scleral, and the conjunctiva advanced. The superior epithelium corneal defect was covered using an amniotic membrane. Conclusion: Repair of bleb dysfunction with varied techniques has been reported, including conjunctival advancement, use of scleral patch graft, dural patch graft, or pericardium. Additional use of amniotic membrane promotes epithelialization and exhibits anti-fibrotic and anti-inflammatory features. Reconstruction with bovine pericardium patch graft and amniotic membrane resulted in pain relief, visual rehabilitation, and good aesthetic results, with preservation of bleb function.

Keywords: reconstruction, hypertrophic bleb, bovine pericardium, amniotic membrane, dysesthesia of the bleb

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Authors: Omer Cahana, Maya Herman, Ofer Levi

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Magnetic resonance imaging (MRI) is a long medical scan that stems from a long acquisition time. This length is mainly due to the traditional sampling theorem, which defines a lower boundary for sampling. However, it is still possible to accelerate the scan by using a different approach, such as compress sensing (CS) or parallel imaging (PI). These two complementary methods can be combined to achieve a faster scan with high-fidelity imaging. In order to achieve that, two properties have to exist: i) the signal must be sparse under a known transform domain, ii) the sampling method must be incoherent. In addition, a nonlinear reconstruction algorithm needs to be applied to recover the signal. While the rapid advance in the deep learning (DL) field, which has demonstrated tremendous successes in various computer vision task’s, the field of MRI reconstruction is still in an early stage. In this paper, we present an extension of the state-of-the-art model in MRI reconstruction -VarNet. We utilize VarNet by using dilated convolution in different scales, which extends the receptive field to capture more contextual information. Moreover, we simplified the sensitivity map estimation (SME), for it holds many unnecessary layers for this task. Those improvements have shown significant decreases in computation costs as well as higher accuracy.

Keywords: MRI, deep learning, variational network, computer vision, compress sensing

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Authors: Michelle Jennett, Jana Dengler, Maytal Perlman

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Background: Cervical spinal cord injury (SCI) is a devastating event that results in upper limb paralysis, loss of independence, and disability. People living with cervical SCI have identified improvement of upper limb function as a top priority. Nerve and tendon transfer surgery has successfully restored upper limb function in cervical SCI but is not universally used or available to all eligible individuals. This exploratory mixed-methods study used an implementation science approach to better understand these factors that influence access to upper limb reconstruction in the Canadian context and design an intervention to increase access to care. Methods: Data from the Canadian Institute for Health Information’s Discharge Abstracts Database (CIHI-DAD) and the National Ambulatory Care Reporting System (NACRS) were used to determine the annual rate of nerve transfer and tendon transfer surgeries performed in cervical SCI in Canada over the last 15 years. Semi-structured interviews informed by the consolidated framework for implementation research (CFIR) were used to explore Ontario healthcare provider knowledge and practices around upper limb reconstruction. An inductive, iterative constant comparative process involving descriptive and interpretive analyses was used to identify themes that emerged from the data. Results: Healthcare providers (n = 10 upper extremity surgeons, n = 10 SCI physiatrists, n = 12 physical and occupational therapists working with individuals with SCI) were interviewed about their knowledge and perceptions of upper limb reconstruction and their current practices and discussions around upper limb reconstruction. Data analysis is currently underway and will be presented. Regional variation in rates of upper limb reconstruction and trends over time are also currently being analyzed. Conclusions: Utilization of nerve and tendon transfer surgery to improve upper limb reconstruction in Canada remains low. There are a complex array of interrelated individual-, provider- and system-level barriers that prevent individuals with cervical SCI from accessing upper limb reconstruction. In order to offer equitable access to care, a multi-modal approach addressing current barriers is required.

Keywords: cervical spinal cord injury, nerve and tendon transfer surgery, spinal cord injury, upper extremity reconstruction

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Authors: Lisa Tragbar

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In post-war scenarios, reconstruction is a principle towards creating a Just Peace in order to restore a stable post-war society. Just peace theorists explore normative behaviour after war, including the duties and responsibilities of different actors and peacebuilding strategies to achieve a lasting, positive peace. Environmental peace ethicists have argued for including the role of nature in the Ethics of War and Peace. This text explores the question of why and how to rethink the value of nature in post-war scenarios. The aim is to include the rights of nature within a maximalist account of reconstruction by highlighting sumak kawsay in the post-war period. Destruction of nature is usually considered collateral damage in war scenarios. Common universal standards for post-war reconstruction are restitution, compensation and reparation programmes, which is mostly anthropocentric approach. The problem of reconstruction in the aftermath of war is the instrumental value of nature. The responsibility to rebuild needs to be revisited within a non-anthropocentric context. There is an ongoing debate about a minimalist or maximalist approach to post-war reconstruction. While Michael Walzer argues for minimalist in-and-out interventions, Alex Bellamy argues for maximalist strategies such as the responsibility to protect, a UN-concept on how face mass atrocity crimes and how to reconstruct peace. While supporting the tradition of maximalist responsibility to rebuild, these normative post-Bellum concepts do not yet sufficiently consider the rights of nature in the aftermath of war. While reconstruction of infrastructures seems important and necessary, concepts that strengthen the intrinsic value of nature in post-bellum measures must also be included. Peace is not Just Peace without a thriving nature that provides the conditions and resources to live and guarantee human rights. Ecuador's indigenous philosophy of life can contribute to the restoration of nature after war by changing the perspective on the value of nature. The sumak kawsay includes the de-hierarchisation of humans and nature and the principle of reciprocity towards nature. Transferring this idea of life and interconnectedness to post-war reconstruction practices, post bellum perpetrators have restorative obligations not only to people but also to nature. This maximalist approach would include both a restitutive principle, by restoring the balance between humans and nature, and a retributive principle, by punishing the perpetrators through compensatory duties to nature. A maximalist approach to post-war reconstruction that takes into account the rights of nature expands the normative post-war questions to include a more complex field of responsibilities. After a war, Just Peace is restored once not only human rights but also the rights of nature are secured. A minimalist post-bellum approach to reconstruction does not locate future problems at their source and does not offer a solution for the inclusion of obligations to nature. There is a lack of obligations towards nature after a war, which can be changed through a different perspective: The indigenous philosophy of life provides the necessary principles for a comprehensive reconstruction of Just Peace.

Keywords: normative ethics, peace, post-war, sumak kawsay, applied ethics

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Authors: Ghulam Muhammad Ali

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Unveiling of genes involved in drought and root architecture using transcriptomic analyses remained fragmented for further improvement of wheat through genome editing. The purpose of this research endeavor was to unveil the variations in different genes implicated in drought tolerance and root architecture in wheat through RNA-seq data analysis. In this study seedlings of 8 days old, 6 cultivars of wheat namely, Batis, Blue Silver, Local White, UZ888, Chakwal 50 and Synthetic wheat S22 were subjected to transcriptomic analysis for root and shoot genes. Total of 12 RNA samples was sequenced by Illumina. Using updated wheat transcripts from Ensembl and IWGC references with 54,175 gene models, we found that 49,621 out of 54,175 (91.5%) genes are expressed at an RPKM of 0.1 or more (in at least 1 sample). The number of genes expressed was higher in Local White than Batis. Differentially expressed genes (DEG) were higher in Chakwal 50. Expression-based clustering indicated conserved function of DRO1and RPK1 between Arabidopsis and wheat. Dendrogram showed that Local White is sister to Chakwal 50 while Batis is closely related to Blue Silver. This study flaunts transcriptomic sequence variations in different cultivars that showed mutations in genes associated with drought that may directly contribute to drought tolerance. DRO1 and RPK1 genes were fetched/isolated for genome editing. These genes are being edited in wheat through CRISPR-Cas9 for yield enhancement.

Keywords: transcriptomic, wheat, genome editing, drought, CRISPR-Cas9, yield enhancement

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Authors: Vladyslav Povoroznyuk, Larysa Martynyuk, Iryna Syzonenko, Liliya Martynyuk

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Medical, social, and economic relevance of osteoporosis is caused by reducing quality of life, increasing disability and mortality of the patients as a result of fractures due to the low-energy trauma. This study is aimed to examine the associations of metabolic syndrome components, bone mineral density (BMD) and trabecular bone score (TBS) in menopausal women with non-vertebral fractures. 1161 menopausal women aged 50-79 year-old were examined and divided into three groups: A included 419 women with increased body weight (BMI - 25.0-29.9 kg/m²), B – 442 females with obesity (BMI >29.9 kg/m²)i and C – 300 women with metabolic syndrome (diagnosis according to IDF criteria, 2005). BMD of lumbar spine (L1-L4), femoral neck, total body and forearm was investigated with usage of dual-energy X-ray absorptiometry. The bone quality indexes were measured according to Med-Imaps installation. All analyses were performed using Statistical Package 6.0. BMD of lumbar spine (L1-L4), femoral neck, total body, and ultradistal radius was significant higher in women with obesity and metabolic syndrome compared to the pre-obese ones (p<0.001). TBS was significantly higher in women with increased body weight compared to obese and metabolic syndrome patients. Analysis showed significant positive correlation between waist circumference, triglycerides level and BMD of lumbar spine and femur. Significant negative association between serum HDL level and BMD of investigated sites was established. The TBS (L1-L4) indexes positively correlated with HDL (high-density lipoprotein) level. Despite the fact that BMD indexes were better in women with metabolic syndrome, the frequency of non-vertebral fractures was significantly higher in this group of patients.

Keywords: bone mineral density, trabecular bone score, metabolic syndrome, fracture

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Authors: Janis Zarins, Kristaps Blums, Oskars Radzins, Renars Deksnis, Atis Svare, Santa Salaka

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Wide tumor resection remains the first choice method for tumors of the oral cavity. Nevertheless, remained tissue defect impacts patients functional and aesthetical outcome, which could be improved using microvascular tissue transfers. Mandibular reconstruction is challenging due to the complexity of composite tissue defects and occlusal relationships for normal eating, chewing, and pain free jaw motions. Individual 3-D virtual planning would provide better symmetry and functional outcome. The main goal of preoperative planning is to develop a customized surgical approach with patient specific cutting guides of the mandible, osteotomy guides of the fibula, pre-bended osteosynthesis plates to perform more precise reconstruction, to decrease the surgery time and reach the best outcome. Our study is based on the analysis of 32 patients operated on between 2019 to 2021. All patients underwent mandible reconstruction with vascularized fibula flaps. Patients characteristics, surgery profile, survival, functional outcome, and quality of life was evaluated. Preoperative planning provided a significant decrease of surgery time and the best arrangement of bone closely similar as before the surgery. In cases of bone asymmetry, deformity and malposition, a new mandible was created using 3D planning to restore the appearance of lower jaw anatomy and functionality.

Keywords: mandibular, 3D planning, cutting guides, fibula flap, reconstruction

Procedia PDF Downloads 105