Search results for: genome sequence alignment

Authors: Narjes Ebrahimi, Soheila Alyasin, Navid Nezafat, Hossein Esmailzadeh, Younes Ghasemi, Seyed Hesamodin Nabavizadeh

Abstract:

Immunotherapy with allergy vaccines is of great importance in allergen-specific immunotherapy. In recent years, B-cell epitope-based vaccines have attracted considerable attention and the prediction of epitopes is crucial to design these types of allergy vaccines. B-cell epitopes might be linear or conformational. The prerequisite for the identification of conformational epitopes is the information about allergens' tertiary structures. Bioinformatics approaches have paved the way towards the design of epitope-based allergy vaccines through the prediction of tertiary structures and epitopes. Mite allergens are one of the major allergy contributors. Several mite allergens can elicit allergic reactions; however, their structures and epitopes are not well established. So, B-cell epitopes of various groups of mite allergens (24 allergens in 6 allergen groups) were predicted in the present work. Tertiary structures of 17 allergens with unknown structure were predicted and refined with RaptorX and GalaxyRefine servers, respectively. The predicted structures were further evaluated by Rampage, ProSA-web, ERRAT and Verify 3D servers. Linear and conformational B-cell epitopes were identified with Ellipro, Bcepred, and DiscoTope 2 servers. To improve the accuracy level, consensus epitopes were selected. Fifty-four conformational and 133 linear consensus epitopes were predicted. Furthermore, overlapping epitopes in each allergen group were defined, following the sequence alignment of the allergens in each group. The predicted epitopes were also compared with the experimentally identified epitopes. The presented results provide valuable information for further studies about allergy vaccine design.

Keywords: B-cell epitope, Immunotherapy, In silico prediction, Mite allergens, Tertiary structure

Procedia PDF Downloads 132

Authors: Olga Blagova, Yuliya Osipova, Evgeniya Kogan, Alexander Nedostup

Abstract:

Purpose: to quantify the value of various clinical, laboratory and instrumental signs in the diagnosis of myocarditis in comparison with morphological studies of the myocardium. Methods: in 100 patients (65 men, 44.7±12.5 years) with «idiopathic» arrhythmias (n = 20) and dilated cardiomyopathy (DCM, n = 80) were performed 71 endomyocardial biopsy (EMB), 13 intraoperative biopsy, 5 study of explanted hearts, 11 autopsy with virus investigation (real-time PCR) of the blood and myocardium. Anti-heart antibodies (AHA) were also measured as well as cardiac CT (n = 45), MRI (n = 25), coronary angiography (n = 47). The comparison group included of 50 patients (25 men, 53.7±11.7 years) with non-inflammatory heart diseases who underwent open heart surgery. Results. Active/borderline myocarditis was diagnosed in 76.0% of the study group and in 21.6% of patients of the comparison group (p < 0.001). The myocardial viral genome was observed more frequently in patients of comparison group than in study group (group (65.0% and 40.2%; p < 0.01. Evaluated the diagnostic value of noninvasive markers of myocarditis. The panel of anti-heart antibodies had the greatest importance to identify myocarditis: sensitivity was 81.5%, positive and negative predictive value was 75.0 and 60.5%. It is defined diagnostic value of non-invasive markers of myocarditis and diagnostic algorithm providing an individual assessment of the likelihood of myocarditis is developed. Conclusion. The greatest significance in the diagnosis of latent myocarditis in patients with 'idiopathic' arrhythmias and DCM have AHA. The use of complex of noninvasive criteria allows estimate the probability of myocarditis and determine the indications for EMB.

Keywords: myocarditis, "idiopathic" arrhythmias, dilated cardiomyopathy, endomyocardial biopsy, viral genome, anti-heart antibodies

Procedia PDF Downloads 149

Authors: Stephan Printz, Kristina Lahl, René Vossen, Sabina Jeschke

Abstract:

Strategic investment decisions are characterized by high innovation potential and long-term effects on the competitiveness of enterprises. Due to the uncertainty and risks involved in this complex decision making process, the need arises for well-structured support activities. A method that considers cost and the long-term added value is the cost-benefit effectiveness estimation. One of those methods is the “profitability estimation focused on benefits – PEFB”-method developed at the Institute of Management Cybernetics at RWTH Aachen University. The method copes with the challenges associated with strategic investment decisions by integrating long-term non-monetary aspects whilst also mapping the chronological sequence of an investment within the organization’s target system. Thus, this method is characterized as a holistic approach for the evaluation of costs and benefits of an investment. This participation-oriented method was applied to business environments in many workshops. The results of the workshops are a library of more than 96 cost aspects, as well as 122 benefit aspects. These aspects are preprocessed and comparatively analyzed with regards to their alignment to a series of risk levels. For the first time, an accumulation and a distribution of cost and benefit aspects regarding their impact and probability of occurrence are given. The results give evidence that the PEFB-method combines precise measures of financial accounting with the incorporation of benefits. Finally, the results constitute the basics for using information technology and data science for decision support when applying within the PEFB-method.

Keywords: cost-benefit analysis, multi-criteria decision, profitability estimation focused on benefits, risk and uncertainty analysis

Procedia PDF Downloads 416

Authors: Binder Hans

Abstract:

Cancer is no longer seen as solely a genetic disease where genetic defects such as mutations and copy number variations affect gene regulation and eventually lead to aberrant cell functioning which can be monitored by transcriptome analysis. It has become obvious that epigenetic alterations represent a further important layer of (de-)regulation of gene activity. For example, aberrant DNA methylation is a hallmark of many cancer types, and methylation patterns were successfully used to subtype cancer heterogeneity. Hence, unraveling the interplay between different omics levels such as genome, transcriptome and epigenome is inevitable for a mechanistic understanding of molecular deregulation causing complex diseases such as cancer. This objective requires powerful downstream integrative bioinformatics methods as an essential prerequisite to discover the whole genome mutational, transcriptome and epigenome landscapes of cancer specimen and to discover cancer genesis, progression and heterogeneity. Basic challenges and tasks arise ‘beyond sequencing’ because of the big size of the data, their complexity, the need to search for hidden structures in the data, for knowledge mining to discover biological function and also systems biology conceptual models to deduce developmental interrelations between different cancer states. These tasks are tightly related to cancer biology as an (epi-)genetic disease giving rise to aberrant genomic regulation under micro-environmental control and clonal evolution which leads to heterogeneous cellular states. Machine learning algorithms such as self organizing maps (SOM) represent one interesting option to tackle these bioinformatics tasks. The SOMmethod enables recognizing complex patterns in large-scale data generated by highthroughput omics technologies. It portrays molecular phenotypes by generating individualized, easy to interpret images of the data landscape in combination with comprehensive analysis options. Our image-based, reductionist machine learning methods provide one interesting perspective how to deal with massive data in the discovery of complex diseases, gliomas, melanomas and colon cancer on molecular level. As an important new challenge, we address the combined portrayal of different omics data such as genome-wide genomic, transcriptomic and methylomic ones. The integrative-omics portrayal approach is based on the joint training of the data and it provides separate personalized data portraits for each patient and data type which can be analyzed by visual inspection as one option. The new method enables an integrative genome-wide view on the omics data types and the underlying regulatory modes. It is applied to high and low-grade gliomas and to melanomas where it disentangles transversal and longitudinal molecular heterogeneity in terms of distinct molecular subtypes and progression paths with prognostic impact.

Keywords: integrative bioinformatics, machine learning, molecular mechanisms of cancer, gliomas and melanomas

Procedia PDF Downloads 122

Authors: Zainul A. Khan, Malik Z. Abdin, Jawaid A. Khan

Abstract:

Begomoviruses belonging to the family Geminiviridae, have single-stranded circular DNA genomes that are monopartite or bipartite. The large intergenic region (LIR) of the monopartite and common region (CR) of bipartite begomoviruses possess promoter activity in their genomes. In this study, we have characterized novel bidirectional promoters from Cotton leaf curl Burewala virus (CLCuBuV) genome using high-throughput software and analyzed with PlantCARE, PLACE, Cister and PlantPAN databases. The promoters (Rep and CP promoters) were assayed both in stable and transient expression systems in tobacco as well as cotton plants. Rep and CP-based promoters from the LIR sequence of CLCuBuV and 35S promoter of Cauliflower mosaic virus (CaMV) were tagged with β-glucuronidase (GUS) and green fluorescent protein (GFP) reporter genes to check the efficacy of the promoters. Histochemical staining of GUS in transformed tobacco (Nicotiana tabacum cv. Xanthi) leaves showed higher GUS expression driven by CLCuBuV Rep (complimentary sense) promoter as compared to conventional CaMV 35S promoter and CLCuBuV CP (virion sense) promoter, respectively. GUS activity in individual plant cells driven by CLCuBuV Rep, CLCuBuV CP, and CaMV 35S promoter were quantified through fluorometric GUS assay and reverse transcription quantitative real-time PCR (RT-qPCR). The expression level of GUS tagged with CLCuBuV Rep promoter in the transformed tobacco plants was obtained 2 to 4 fold higher than CaMV 35S promoter. When CLCuBuV CP promoter was used, lower expression level was monitored than that by CaMV 35S promoter. The expression of GFP-tagged with CLCuBuV promoters was also investigated through agroinfiltration. The CLCuBuV Rep promoters showed stronger consistent transient expression in the leaves of N. benthamiana, N. tabacum and Gossypium hirsutum plants when compared with CaMV 35S and CLCuBuV CP promoter.

Keywords: Begmovirus, bidirectional promoter, CaMV 35S promoter, GFP, GUS, qPCR

Procedia PDF Downloads 312

Authors: Gurjit Kaur, Neena Gupta

Abstract:

In this paper, we have analyzed and compared the performance of various coding schemes. The basic ID prime sequence codes are unique in only dimension, i.e. time slots, whereas 2D coding techniques are not unique by their time slots but with their wavelengths also. In this research, we have evaluated and compared the performance of 1D and 2D coding techniques constructed using prime sequence coding pattern for Optical Code Division Multiple Access (OCDMA) system on a single platform. Analysis shows that 2D prime code supports lesser number of active users than 1D codes, but they are having large code family and are the most secure codes compared to other codes. The performance of all these codes is analyzed on basis of number of active users supported at a Bit Error Rate (BER) of 10-9.

Keywords: CDMA, OCDMA, BER, OOC, PC, EPC, MPC, 2-D PC/PC, λc, λa

Procedia PDF Downloads 314

Authors: Jose A. Aznar-Moreno, Xi Jiang, Stefan Burén, Luis M. Rubio

Abstract:

Integration of prokaryotic nitrogen fixation (nif) genes into the plastid genome for expression of functional nitrogenase components could render plants capable of assimilating atmospheric N2 making their crops less dependent of nitrogen fertilizers. The nitrogenase Fe protein component (NifH) has been used as proxy for expression and targeting of Nif proteins within plant and yeast cells. Here we use tobacco plants with the Azotobacter vinelandii nifH and nifM genes integrated into the plastid genome. NifH and its maturase NifM were constitutively produced in leaves, but not roots, during light and dark periods. Nif protein expression in transplastomic plants was stable throughout development. Chloroplast NifH was soluble, but it only showed in vitro activity when isolated from leaves collected at the end of the dark period. Exposing the plant extracts to elevated temperatures precipitated NifM and apo-NifH protein devoid of [Fe4S4] clusters, dramatically increasing the specific activity of remaining NifH protein. Our data indicate that the chloroplast endogenous [Fe-S] cluster biosynthesis was insufficient for complete NifH maturation, albeit a negative effect on NifH maturation due to excess NifM in the chloroplast cannot be excluded. NifH and NifM constitutive expression in transplastomic plants did not affect any of the following traits: seed size, germination time, germination ratio, seedling growth, emergence of the cotyledon and first leaves, chlorophyll content and plant height throughout development.

Keywords: NifH, chloroplast, nitrogen fixation, crop improvement, transplastomic plants, fertilizer, biotechnology

Procedia PDF Downloads 136

Authors: Jialin Ma, Jia Meng

Abstract:

Genomic features, the genome-based coordinates, are commonly used for the representation of biological features such as genes, RNA transcripts and transcription factor binding sites. For the analysis of RNA-related genomic features, such as RNA modification sites, a common task is to correlate these features with transcript components (5'UTR, CDS, 3'UTR) to explore their distribution characteristics in terms of transcriptomic coordinates, e.g., to examine whether a specific type of biological feature is enriched near transcription start sites. Existing approaches for performing these tasks involve the manipulation of a gene database, conversion from genome-based coordinate to transcript-based coordinate, and visualization methods that are capable of showing RNA transcript components and distribution of the features. These steps are complicated and time consuming, and this is especially true for researchers who are not familiar with relevant tools. To overcome this obstacle, we develop a dedicated web app TARF, which represents web toolkit for annotating RNA-related genomic features. TARF web tool intends to provide a web-based way to easily annotate and visualize RNA-related genomic features. Once a user has uploaded the features with BED format and specified a built-in transcript database or uploaded a customized gene database with GTF format, the tool could fulfill its three main functions. First, it adds annotation on gene and RNA transcript components. For every features provided by the user, the overlapping with RNA transcript components are identified, and the information is combined in one table which is available for copy and download. Summary statistics about ambiguous belongings are also carried out. Second, the tool provides a convenient visualization method of the features on single gene/transcript level. For the selected gene, the tool shows the features with gene model on genome-based view, and also maps the features to transcript-based coordinate and show the distribution against one single spliced RNA transcript. Third, a global transcriptomic view of the genomic features is generated utilizing the Guitar R/Bioconductor package. The distribution of features on RNA transcripts are normalized with respect to RNA transcript landmarks and the enrichment of the features on different RNA transcript components is demonstrated. We tested the newly developed TARF toolkit with 3 different types of genomics features related to chromatin H3K4me3, RNA N6-methyladenosine (m6A) and RNA 5-methylcytosine (m5C), which are obtained from ChIP-Seq, MeRIP-Seq and RNA BS-Seq data, respectively. TARF successfully revealed their respective distribution characteristics, i.e. H3K4me3, m6A and m5C are enriched near transcription starting sites, stop codons and 5’UTRs, respectively. Overall, TARF is a useful web toolkit for annotation and visualization of RNA-related genomic features, and should help simplify the analysis of various RNA-related genomic features, especially those related RNA modifications.

Keywords: RNA-related genomic features, annotation, visualization, web server

Procedia PDF Downloads 184

Authors: Anoop T. R., Otman Basir, Robert F. Hess, Eileen E. Birch, Brooke A. Koritala, Reed M. Jost, Becky Luu, David Stager, Ben Thompson

Abstract:

Strabismus refers to a misalignment of the eyes. Early detection and treatment of strabismus in childhood can prevent the development of permanent vision loss due to abnormal development of visual brain areas. We developed a two-stage method for strabismus detection and classification based on photographs of the face. The first stage detects the presence or absence of strabismus, and the second stage classifies the type of strabismus. The first stage comprises face detection using Haar cascade, facial landmark estimation, face alignment, aligned face landmark detection, segmentation of the eye region, and detection of strabismus using VGG 16 convolution neural networks. Face alignment transforms the face to a canonical pose to ensure consistency in subsequent analysis. Using facial landmarks, the eye region is segmented from the aligned face and fed into a VGG 16 CNN model, which has been trained to classify strabismus. The CNN determines whether strabismus is present and classifies the type of strabismus (exotropia, esotropia, and vertical deviation). If stage 1 detects strabismus, the eye region image is fed into stage 2, which starts with the estimation of pupil center coordinates using mask R-CNN deep neural networks. Then, the distance between the pupil coordinates and eye landmarks is calculated along with the angle that the pupil coordinates make with the horizontal and vertical axis. The distance and angle information is used to characterize the degree and direction of the strabismic eye misalignment. This model was tested on 100 clinically labeled images of children with (n = 50) and without (n = 50) strabismus. The True Positive Rate (TPR) and False Positive Rate (FPR) of the first stage were 94% and 6% respectively. The classification stage has produced a TPR of 94.73%, 94.44%, and 100% for esotropia, exotropia, and vertical deviations, respectively. This method also had an FPR of 5.26%, 5.55%, and 0% for esotropia, exotropia, and vertical deviation, respectively. The addition of one more feature related to the location of corneal light reflections may reduce the FPR, which was primarily due to children with pseudo-strabismus (the appearance of strabismus due to a wide nasal bridge or skin folds on the nasal side of the eyes).

Keywords: strabismus, deep neural networks, face detection, facial landmarks, face alignment, segmentation, VGG 16, mask R-CNN, pupil coordinates, angle deviation, horizontal and vertical deviation

Procedia PDF Downloads 59

Authors: Siddhant Sethi, Yasuharu Takashima, Shigetaka Nakamura, Kenzo Fujimoto

Abstract:

Site-directed mutagenesis is a renowned technique to introduce specific mutations in the genome. To achieve site-directed mutagenesis, many chemical and enzymatic approaches have been reported in the past like disulphite induced genome editing, CRISPR-Cas9, TALEN etc. The chemical methods are invasive whereas the enzymatic approaches are time-consuming and expensive. Most of these techniques are unusable in the cellular application due to their toxicity and other limitations. Photo-chemical cytosine deamination, introduced in 2010, is one of the major technique for enzyme-free single-point mutation of cytosine to uracil in DNA and RNA, wherein, 3-cyanovinylcarbazole nucleoside (CNVK) containing oligodeoxyribonucleotide (ODN) having CNVK at -1 position to that of target cytosine is reversibly crosslinked to target DNA strand using 366 nm and then incubated at 90ºC to accommodate deamination. This technique is superior to enzymatic methods of site-directed mutagenesis but has a disadvantage that it requires the use of high temperature for the deamination step which restricts its applicability in the in vivo applications. This study has been focused on improving the technique by reducing the temperature required for deamination. Firstly, the photo-cross-linker, CNVK has been modified by replacing cyano group attached to vinyl group with methyl ester (OMeVK), amide (NH2VK), and carboxylic acid (OHVK) to observe the acceleration in the deamination of target cytosine cross-linked to vinylcarbazole derivative. Among the derivatives, OHVK has shown 2 times acceleration in deamination reaction as compared to CNVK, while the other two derivatives have shown deceleration towards deamination reaction. The trend of rate of deamination reaction follows the same order as that of hydrophilicity of the vinylcarbazole derivatives. OHVK being most hydrophilic has shown highest acceleration while OMeVK is least hydrophilic has proven to be least active for deamination. Secondly, in the related study, the counter-base of the target cytosine, guanine has been replaced by inosine, 2-aminopurine, nebularine, and 5-nitroindole having distinct hydrogen bonding patterns with target cytosine. Among the ODNs with these counter bases, ODN with inosine has shown 12 fold acceleration towards deamination of cytosine cross-linked to CNVK at physiological conditions as compared to guanosine. Whereas, when 2-aminopurine, nebularine, and 5-nitroindole were used, no deamination reaction took place. It can be concluded that inosine has potential to be used as the counter base of target cytosine for the CNVK mediated photo-cross-linking induced deamination of cytosine. The increase in rate of deamination reaction has been attributed to pattern and number of hydrogen bonding between the cytosine and counter base. One of the important factor is presence of hydrogen bond between exo-cyclic amino group of cytosine and the counter base. These results will be useful for development of more efficient technique for site-directed mutagenesis for C → U transformations in the DNA/RNA which might be used in the living system for treatment of various genetic disorders and genome engineering for making designer and non-native proteins.

Keywords: C to U transformation, DNA editing, genome engineering, ultra-fast photo-cross-linking

Procedia PDF Downloads 211

Authors: Sa’ed Abed, Mohammad H. Al Shayeji, Ovais Ahmed, Sahel Alouneh

Abstract:

Session Initiation Protocol (SIP) is a signaling layer protocol for building, adjusting and ending sessions among participants including Internet conferences, telephone calls and multimedia distribution. SIP facilitates user movement by proxying and forwarding requests to the present location of the user. In this paper, we provide a formal Specification and Description Language (SDL) and Message Sequence Chart (MSC) to model and define the Internet Engineering Task Force (IETF) SIP protocol and its sample services resulted from informal SIP specification. We create an “Abstract User Interface” using case analysis so that can be applied to identify SIP services more explicitly. The issued sample SIP features are then used as case scenarios; they are revised in MSCs format and validated to their corresponding SDL models.

Keywords: modeling, MSC, SDL, SIP, validating

Procedia PDF Downloads 185

Authors: Sikiru Ademola Adewale, Joe Thomas, Bolanle Hafiz Matti, Tosin Ige

Abstract:

This project demonstrates the implementation and use of an encoder-decoder model to perform a many-to-many mapping of video data to text captions. The many-to-many mapping occurs via an input temporal sequence of video frames to an output sequence of words to form a caption sentence. Data preprocessing, model construction, and model training are discussed. Caption correctness is evaluated using 2-gram BLEU scores across the different splits of the dataset. Specific examples of output captions were shown to demonstrate model generality over the video temporal dimension. Predicted captions were shown to generalize over video action, even in instances where the video scene changed dramatically. Model architecture changes are discussed to improve sentence grammar and correctness.

Keywords: decoder, encoder, many-to-many mapping, video captioning, 2-gram BLEU

Procedia PDF Downloads 70

Authors: Maria Korman, Carmit Gal, Ella Gabitov, Avi Karni

Abstract:

The main question addressed in this study was whether the time-of-day wherein training is afforded is a significant factor for motor skill ('how-to', procedural knowledge) acquisition and consolidation into long term memory in the healthy elderly population. Twenty-nine older adults (60-75 years) practiced an explicitly instructed 5-element key-press sequence by repeatedly generating the sequence ‘as fast and accurately as possible’. Contribution of three parameters to acquisition, 24h post-training consolidation, and 1-week retention gains in motor sequence speed was assessed: (a) time of training (morning vs. evening group) (b) sleep quality (actigraphy) and (c) chronotype. All study participants were moderately morning type, according to the Morningness-Eveningness Questionnaire score. All participants had sleep patterns typical of age, with average sleep efficiency of ~ 82%, and approximately 6 hours of sleep. Speed of motor sequence performance in both groups improved to a similar extent during training session. Nevertheless, evening group expressed small but significant overnight consolidation phase gains, while morning group showed only maintenance of performance level attained at the end of training. By 1-week retention test, both groups showed similar performance levels with no significant gains or losses with respect to 24h test. Changes in the tapping patterns at 24h and 1-week post-training were assessed based on normalized Pearson correlation coefficients using the Fisher’s z-transformation in reference to the tapping pattern attained at the end of the training. Significant differences between the groups were found: the evening group showed larger changes in tapping patterns across the consolidation and retention windows. Our results show that morning-oriented older adults effectively acquired, consolidated, and maintained a new sequence of finger movements, following both morning and evening practice sessions. However, time-of-training affected the time-course of skill evolution in terms of performance speed, as well as the re-organization of tapping patterns during the consolidation period. These results are in line with the notion that motor training preceding a sleep interval may be beneficial for the long-term memory in the elderly. Evening training should be considered an appropriate time window for motor skill learning in older adults, even in individuals with morning chronotype.

Keywords: time-of-day, elderly, motor learning, memory consolidation, chronotype

Procedia PDF Downloads 112

Authors: Mozhgan Chaichi, Farhad Sharif, Saeede Mazinani

Abstract:

Polymer nanocomposites are a new class of materials for fabricating future multifunctional and lightweight structures. To obtain good mechanical, thermal and electrical properties, it is essential to achieve uniform dispersion of nanoparticles in polymer matrix. Alignment of nanoparticles in matrix can enhance mechanical, thermal, electrical and barrier properties of nanocomposites in oriented direction. Fe3O4 nanoparticles have generated huge activity in many areas of science and engineering due to its magnetic properties. Magnetic nanoparticles have been investigated for a wide range of applications in sensors, magnetic energy storage, environmental remediation, heterogeneous catalysts and drug delivery. The magnetic response from the Fe3O4 nanoparticles can facilitate with the alignment of nanofillers in a polymer matrix under magnetic field, aiming at fabricating composites with directional properties and functions. Here we report oriented nanocomposites based on Fe3O4 nanoparticles and poly (vinyl alcohol) (PVA), which prepared via a facile aqueous solution by applying a low external magnetic field (750 G). A significant enhancement of mechanical properties, and especially toughness of nanofilms, of oriented PVA/ Fe3O4 nanocomposites is obtained at low nanoparticles loading. Orientation of nanoparticles can align polymer chains and enhance mechanical properties. For example, orientation of 0.1 wt. % Fe3O4 nanoparticles increase 31% toughness and 23% modulus of oriented nanocomposite in compare of pure films, which indicate good dispersion of nanoparticles and efficient load transfer between nanoparticles and matrix.

Keywords: magnetic nanoparticles, nanocomposites, toughness, orientation

Procedia PDF Downloads 301

Authors: Bin Liu

Abstract:

Protein remote homology detection and fold recognition are two most important tasks in protein sequence analysis, which is critical for protein structure and function studies. In this study, we combined the profile-based features with various string kernels, and constructed several computational predictors for protein remote homology detection and fold recognition. Experimental results on two widely used benchmark datasets showed that these methods outperformed the competing methods, indicating that these predictors are useful computational tools for protein sequence analysis. By analyzing the discriminative features of the training models, some interesting patterns were discovered, reflecting the characteristics of protein superfamilies and folds, which are important for the researchers who are interested in finding the patterns of protein folds.

Keywords: protein remote homology detection, protein fold recognition, profile-based features, Support Vector Machines (SVMs)

Procedia PDF Downloads 136

Authors: Chul Lee, Seoae Cho, Erich D. Jarvis, Heebal Kim

Abstract:

Vocal learning, the ability to imitate vocalizations based on auditory experience, is a homoplastic character state observed in different independent lineages of animals such as songbirds, parrots, hummingbirds and human. It has now become possible to perform genome-wide molecular analyses across vocal learners and vocal non-learners with the recent expansion of avian genome data. It was analyzed the whole genomes of human and 48 avian species including those belonging to the three avian vocal learning lineages, to determine if behavior and neural convergence are associated with molecular convergence in divergent species of vocal learners. Analyses of 8295 orthologous genes across bird species revealed 141 genes with amino acid substitutions specific to vocal learners. Out of these, 25 genes have vocal learner specific genetic homoplasies, and their functions were enriched for learning. Several sites in these genes are estimated under convergent evolution and positive selection. A potential role for a subset of these genes in vocal learning was supported by associations with gene expression profiles in vocal learning brain regions of songbirds and human disease that cause language dysfunctions. The key candidate gene with multiple independent lines of the evidences specific to vocal learners was DRD5. Our findings suggest cAMP-based learning pathway in avian vocal learners, indicating molecular homoplastic changes associated with a complex behavioral trait, vocal learning.

Keywords: amino acid substitutions, convergent evolution, positive selection, vocal learning

Procedia PDF Downloads 312

Authors: Micheale Yifter Weldemichael, Stefaan Werbrouck, Hailay Mehari Gebremedhn

Abstract:

Sesame (Sesamum indicum L.) is among the most important oilseed crops for its high edible oil quality and quantity. Sesame is grown for food, medicinal, pharmaceutical, and industrial uses. Sesame is also cultivated as a main cash crop in Asia and Africa by smallholder farmers. Despite the global exponential increase in sesame cultivation area, its production and productivity remain low, mainly due to biotic and abiotic constraints. Notwithstanding the efforts to solve these problems, a low level of genetic variation and inadequate genomic resources hinder the progress of sesame improvement. The objective of this paper is, therefore, to review recent advances in the area of molecular breeding and transformation to overcome major production constraints and could result in enhanced and sustained sesame production. This paper reviews various researches conducted to date on molecular breeding and genetic transformation in sesame focusing on molecular markers used in assessing the available online database resources, genes responsible for key agronomic traits as well as transgenic technology and genome editing. The review concentrates on quantitative and semi-quantitative studies on molecular breeding for key agronomic traits such as improvement of yield components, oil and oil-related traits, disease and insect/pest resistance, and drought, waterlogging and salt tolerance, as well as sesame genetic transformation and genome editing techniques. Pitfalls and limitations of existing studies and methodologies used so far are identified and some priorities for future research directions in sesame genetic improvement are identified in this review.

Keywords: molecular breeding, oil, sesame, shattering

Procedia PDF Downloads 47

Authors: Yi-Lin Chen, Sheng-Jou Hung, Tsunglin Liu

Abstract:

Adaptive immune system recognizes a wide range of antigens via expressing a large number of structurally distinct T cell and B cell receptor genes. The distinct receptor genes arise from complex rearrangements called V(D)J recombination, and constitute the immune repertoire. A common method of profiling immune repertoire is via amplifying recombined receptor genes using multiple primers and high-throughput sequencing. This multiplex-PCR approach is efficient; however, the resulting repertoire can be distorted because of primer bias. To eliminate primer bias, 5’ RACE is an alternative amplification approach. However, the application of RACE approach is limited by its low efficiency (i.e., the majority of data are non-regular receptor sequences, e.g., containing intronic segments) and lack of the convenient tool for analysis. We propose a computational tool that can correctly identify non-regular receptor sequences in RACE data via aligning receptor sequences against the whole gene instead of only the exon regions as done in all other tools. Using our tool, the remaining regular data allow for an accurate profiling of immune repertoire. In addition, a RACE approach is improved to yield a higher fraction of regular T-cell receptor sequences. Finally, we quantify the degree of primer bias of a multiplex-PCR approach via comparing it to the RACE approach. The results reveal significant differences in frequency of VJ combination by the two approaches. Together, we provide a new experimental and computation pipeline for an unbiased profiling of immune repertoire. As immune repertoire profiling has many applications, e.g., tracing bacterial and viral infection, detection of T cell lymphoma and minimal residual disease, monitoring cancer immunotherapy, etc., our work should benefit scientists who are interested in the applications.

Keywords: immune repertoire, T-cell receptor, 5' RACE, high-throughput sequencing, sequence alignment

Procedia PDF Downloads 166

Authors: Rubin Dan, Xingcai Wang, Ziyang Chen

Abstract:

A chaotic time series noise reduction method based on the fusion of the local projection method, wavelet transform, and particle swarm algorithm (referred to as the LW-PSO method) is proposed to address the problem of false recognition due to noise in the recognition process of chaotic time series containing noise. The method first uses phase space reconstruction to recover the original dynamical system characteristics and removes the noise subspace by selecting the neighborhood radius; then it uses wavelet transform to remove D1-D3 high-frequency components to maximize the retention of signal information while least-squares optimization is performed by the particle swarm algorithm. The Lorenz system containing 30% Gaussian white noise is simulated and verified, and the phase space, SNR value, RMSE value, and K value of the 0-1 test method before and after noise reduction of the Schreiber method, local projection method, wavelet transform method, and LW-PSO method are compared and analyzed, which proves that the LW-PSO method has a better noise reduction effect compared with the other three common methods. The method is also applied to the classical system to evaluate the noise reduction effect of the four methods and the original system identification effect, which further verifies the superiority of the LW-PSO method. Finally, it is applied to the Chengdu rainfall chaotic sequence for research, and the results prove that the LW-PSO method can effectively reduce the noise and improve the chaos recognition rate.

Keywords: Schreiber noise reduction, wavelet transform, particle swarm optimization, 0-1 test method, chaotic sequence denoising

Procedia PDF Downloads 165

Authors: Rohan Bhasin

Abstract:

Agrammatism in non-fluent Aphasia Cases can be defined as a language disorder wherein a patient can only use content words ( nouns, verbs and adjectives ) for communication and their speech is devoid of functional word types like conjunctions and articles, generating speech of with extremely rudimentary grammar . Past approaches involve Speech Therapy of some order with conversation analysis used to analyse pre-therapy speech patterns and qualitative changes in conversational behaviour after therapy. We describe this approach as a novel method to generate functional words (prepositions, articles, ) around content words ( nouns, verbs and adjectives ) using a combination of Natural Language Processing and Deep Learning algorithms. The applications of this approach can be used to assist communication. The approach the paper investigates is : LSTMs or Seq2Seq: A sequence2sequence approach (seq2seq) or LSTM would take in a sequence of inputs and output sequence. This approach needs a significant amount of training data, with each training data containing pairs such as (content words, complete sentence). We generate such data by starting with complete sentences from a text source, removing functional words to get just the content words. However, this approach would require a lot of training data to get a coherent input. The assumptions of this approach is that the content words received in the inputs of both text models are to be preserved, i.e, won't alter after the functional grammar is slotted in. This is a potential limit to cases of severe Agrammatism where such order might not be inherently correct. The applications of this approach can be used to assist communication mild Agrammatism in non-fluent Aphasia Cases. Thus by generating these function words around the content words, we can provide meaningful sentence options to the patient for articulate conversations. Thus our project translates the use case of generating sentences from content-specific words into an assistive technology for non-Fluent Aphasia Patients.

Keywords: aphasia, expressive aphasia, assistive algorithms, neurology, machine learning, natural language processing, language disorder, behaviour disorder, sequence to sequence, LSTM

Procedia PDF Downloads 142

Authors: Elena Carcano, Mirzi Betasolo

Abstract:

This study helps Public Water Bureaus in giving reliable answers to water concession requests. Rapidly increasing water requests can be supported provided that further uses of a river course are not totally compromised, and environmental features are protected as well. Strictly speaking, a water concession can be considered a continuous drawing from the source and causes a mean annual streamflow reduction. Therefore, deciding if a water concession is appropriate or inappropriate seems to be easily solved by comparing the generic demand to the mean annual streamflow value at disposal. Still, the immediate shortcoming for such a comparison is that streamflow data are information available only for few catchments and, most often, limited to specific sites. Subsequently, comparing the generic water demand to mean daily discharge is indeed far from being completely satisfactory since the mean daily streamflow is greater than the water withdrawal for a long period of a year. Consequently, such a comparison appears to be of little significance in order to preserve the quality and the quantity of the river. In order to overcome such a limit, this study aims to complete the information provided by flow duration curves introducing a link between Flow Duration Curves (FDCs) and recession curves and aims to show the chronological sequence of flows with a particular focus on low flow data. The analysis is carried out on 25 catchments located in North-Eastern Italy for which daily data are provided. The results identify groups of catchments as hydrologically homogeneous, having the lower part of the FDCs (corresponding streamflow interval is streamflow Q between 300 and 335, namely: Q(300), Q(335)) smoothly reproduced by a common recession curve. In conclusion, the results are useful to provide more reliable answers to water request, especially for those catchments which show similar hydrological response and can be used for a focused regionalization approach on low flow data. A mathematical link between streamflow duration curves and recession curves is herein provided, thus furnishing streamflow duration curves information upon a temporal sequence of data. In such a way, by introducing assumptions on recession curves, the chronological sequence upon low flow data can also be attributed to FDCs, which are known to lack this information by nature.

Keywords: chronological sequence of discharges, recession curves, streamflow duration curves, water concession

Procedia PDF Downloads 155

Authors: Tahira Hussain, Ilhom Rahamkulov, Muhammad Aasim, Ugur Pirlak, Emre Aksoy, Mehmet Emin Caliskan, Allah Bakhsh

Abstract:

RNA interference (RNAi) has proved its usefulness in functional genomic research on insects recently and is considered potential strategy in crop improvement for the control of insect pests. The different insect pests incur significant losses to potato yield worldwide, Colorado Potato Beetle (CPB) being most notorious one. The present study focuses to knock down highly specific 20-hydroxyecdysone hormone-receptor complex interaction by using RNAi approach to silence Ecdysone receptor (EcR) gene of CPB in transgenic potato plants expressing dsRNA of EcR gene. The partial cDNA of Ecdysone receptor gene of CPB was amplified using specific primers in sense and anti-sense orientation and cloned in pRNAi-GG vector flanked by an intronic sequence (pdk). Leaf and internodal explants of Lady Olympia, Agria and Granola cultivars of potato were infected with Agrobacterium strain LBA4404 harboring plasmid pRNAi-CPB, pRNAi-GFP (used as control). Neomycin phosphotransferase (nptII) gene was used as a plant selectable marker at a concentration of 100 mg L⁻¹. The primary transformants obtained have shown proper integration of T-DNA in plant genome by standard molecular analysis like polymerase chain reaction (PCR), real-time PCR, Sothern blot. The transgenic plants developed out of these cultivars are being evaluated for their efficacy against larvae as well adults of CPB. The transgenic lines are expected to inhibit expression of EcR protein gene, hindering their molting process, hence leading to increased potato yield.

Keywords: plant mediated RNAi, molecular strategy, ecdysone receptor, insect metamorphosis

Procedia PDF Downloads 145

Authors: Antonela Matana, Dubravka Brdar, Vesela Torlak, Marijana Popovic, Ivana Gunjaca, Ozren Polasek, Vesna Boraska Perica, Maja Barbalic, Ante Punda, Caroline Hayward, Tatijana Zemunik

Abstract:

Parathyroid hormone (PTH) plays a critical role in the regulation of bone mineral metabolism and calcium homeostasis. Higher PTH levels are associated with heart failure, hypertension, coronary artery disease, cardiovascular mortality and poorer bone health. A twin study estimated that 60% of the variation in PTH concentrations is genetically determined. Only one GWAS of PTH concentration has been reported to date. Identified loci explained 4.5% of the variance in circulating PTH, suggesting that additional genetic variants remain undiscovered. Therefore, the aim of this study was to identify novel genetic variants associated with PTH levels in a general population. We have performed a GWAS meta-analysis on 2596 individuals originating from three Croatian cohorts: City of Split and the Islands of Korčula and Vis, within a large-scale project of “10,001 Dalmatians”. A total of 7 411 206 variants, imputed using the 1000 Genomes reference panel, with minor allele frequency ≥ 1% and Rsq ≥ 0.5 were analyzed for the association. GWAS within each data set was performed under an additive model, controlling for age, gender and relatedness. Meta-analysis was conducted using the inverse-variance fixed-effects method. Furthermore, to identify sex-specific effects, we have conducted GWAS meta-analyses analyzing males and females separately. In addition, we have performed biological pathway analysis. Four SNPs, representing one locus, reached genome-wide significance. The most significant SNP was rs11099476 on chromosome 4 (P=1.15x10-8), which explained 1.14 % of the variance in PTH. The SNP is located near the protein-coding gene RASGEF1B. Additionally, we detected suggestive association with SNPs, rs77178854 located on chromosome 2 in the DPP10 gene (P=2.46x10-7) and rs481121 located on chromosome 1 (P=3.58x10-7) near the GRIK1 gene. One of the top hits detected in the main meta-analysis, intron variant rs77178854 located within DPP10 gene, reached genome-wide significance in females (P=2.21x10-9). No single locus was identified in the meta-analysis in males. Fifteen biological pathways were functionally enriched at a P<0.01, including muscle contraction, ion homeostasis and cardiac conduction as the most significant pathways. RASGEF1B is the guanine nucleotide exchange factor, known to be associated with height, bone density, and hip. DPP10 encodes a membrane protein that is a member of the serine proteases family, which binds specific voltage-gated potassium channels and alters their expression and biophysical properties. In conclusion, we identified 2 novel loci associated with PTH levels in a general population, providing us with further insights into the genetics of this complex trait.

Keywords: general population, genome-wide association analysis, parathyroid hormone, single nucleotide polymorphisms.

Procedia PDF Downloads 203

Authors: David Levy

Abstract:

The newly released Distributed System Interface 3 (DSI3) Bus Standard specification defines 3 modulation levels from which 16 valid symbols are coded. This structure creates power consumption variations depending on the transmitted data of a factor of more than 2 between minimum and maximum. The power generation unit has to consider therefore the worst case maximum consumption all the time and be built accordingly. This paper proposes a method to reduce both the average current consumption and worst case current consumption. The transmitter randomizes the data using several pseudo-random sequences. It then estimates the energy consumption of the generated frames and selects to transmit the one which consumes the least. The transmitter also prepends the index of the pseudo-random sequence, which is not randomized, to allow the receiver to recover the original data using the correct sequence. We show that in the case that the frame occupies most of the DSI3 synchronization period, we achieve average power consumption reduction by up to 13% and the worst case power consumption is reduced by 17.7%.

Keywords: DSI3, energy, power consumption, randomization

Procedia PDF Downloads 509

Authors: Maharani Yulisti, Amin Mugera, James Fogarty

Abstract:

Food safety standards have received significant attention in the fisheries global market due to health issues, free trade agreements, and increasing aquaculture production. Vertical coordination throughout the supply chain of fish producing and exporting countries is needed to meet food safety demands imposed by importing countries. However, the complexities of the supply chain governance structures and difficulties in standard implementation can generate safety uncertainty and high transaction costs. Using a Transaction Cost Economics framework, this paper examines the alignment between food safety standards and the governance structures in the shrimp supply chain in Indonesia. We find the supply chain is organized closer to the hierarchy-like governance structure where private standard (organic standard) are implemented and more towards a market-like governance structure where public standard (IndoGAP certification) are more prevalent. To verify the statements, two cases are examined from Sidoarjo district as a centre of shrimp production in Indonesia. The results show that public baseline FSS (Food Safety Standards) need additional mechanism to achieve a coordinated chain-wide response because uncertainty, asset specificity, and performance measurement problems are high in this chain. Organic standard as private chain-wide FSS is more efficient because it has been achieved by hierarchical-like type of governance structure.

Keywords: governance structure, shrimp value chain, food safety standards, transaction costs economics

Procedia PDF Downloads 350

Authors: Rajkumar Ghosh

Abstract:

The Sutlej River Valley in Himachal Pradesh, India, is home to four Out-of-Sequence Thrusts (OOST) in the Higher Himalaya. These OOSTs include Jhakri Thrust (JT), Sarahan Thrust (ST), Chaura Thrust (CT), and Jeori Dislocation (JD). The study focuses on the rock types of these OOSTs, including ductile sheared gneisses and upper greenschist-amphibolite facies metamorphosed schists. Microstructural tests reveal a progressive increase in strain approaching the Jakhri thrust zone, with temperatures increasing from 400 to 750°C. The Chaura Thrust is assumed to be folded with this anticlinorium, with various branches that make up the thrust system. Fieldwork and microstructural research have revealed the following: (a) initial top-to-SW sense of ductile shearing (Chaura thrust); (b) brittle-ductile extension (Jeori Dislocation); and (c) uniform top-to-SW sense of brittle shearing (Jhakri thrust). Samples of Rampur Quartzite from the Rampur Group of Lesser Himalayan Crystalline and schistose rock from the Jutogh Group of Greater Himalayan Crystalline were examined.The study emphasizes the value of microscopic research in detecting different types of crenulated schistosity and documenting mylonitized zones. The paper explains the field evidence for the OOST and comes to the conclusion that the Chaura Thrust is not a blind thrust. The paper describes the box fold and its characteristics in the Himachal Himalayan regional geology.

Keywords: Out-of-sequence thrust (OOST), jakhri thrust (JT), sarahan thrust (ST), chaura thrust (CT), jeori dislocation (JD)

Procedia PDF Downloads 54

Authors: Wanatchapong Kongkaew

Abstract:

This paper proposes an application of probabilistic technique, namely Gaussian process regression, for estimating an optimal sequence of the single machine with total weighted tardiness (SMTWT) scheduling problem. In this work, the Gaussian process regression (GPR) model is utilized to predict an optimal sequence of the SMTWT problem, and its solution is improved by using an iterated local search based on simulated annealing scheme, called GPRISA algorithm. The results show that the proposed GPRISA method achieves a very good performance and a reasonable trade-off between solution quality and time consumption. Moreover, in the comparison of deviation from the best-known solution, the proposed mechanism noticeably outperforms the recently existing approaches.

Keywords: Gaussian process regression, iterated local search, simulated annealing, single machine total weighted tardiness

Procedia PDF Downloads 282

Authors: Monika Szymańska-Czerwińska, Agnieszka Jodełko, Krzysztof Niemczuk

Abstract:

Q fever (coxiellosis) is an infectious disease of animals and humans causes by C. burnetii and widely distributed throughout the world. Cattle and small ruminants are commonly known as shedders of C. burnetii. The aims of this study were the evaluation of seroprevalence and shedding of C. burnetii in cattle. Genotypes of the pathogen present in the tested specimens were also identified using MLVA (Multiple Locus Variable-Number Tandem Repeat Analysis) and MST (multispacer sequence typing) methods. Sampling was conducted in different regions of Poland in 2018-2021. In total, 2180 bovine serum samples from 801 cattle herds were tested by ELISA (enzyme-linked immunosorbent assay). 489 specimens from 157 cattle herds such as: individual milk samples (n=407), bulk tank milk (n=58), vaginal swabs (n=20), placenta (n=3) and feces (n=1) were subjected to C. burnetii specific qPCR. The qPCR (IS1111 transposon-like repetitive region) was performed using Adiavet COX RealTime PCR kit. Genotypic characterization of the strains was conducted utilizing MLVA and MST methods. MLVA was performed using 6 variable loci. The overall herd-level seroprevalence of C. burnetii infection was 36.74% (801/2180). Shedders were detected in 29.3% (46/157) cattle herds in all tested regions. ST 61 sequence type was identified in 10 out of 18 genotyped strains. Interestingly one strain represents sequence type which has never been recorded previously. MLVA method identified three previously known genotypes: most common was J but also I and BE were recognized. Moreover, a one genotype has never been described previously. Seroprevalence and shedding of C. burnetii in cattle is common and strains are genetically diverse.

Keywords: Coxiella burnetii, cattle, MST, MLVA, Q fever

Procedia PDF Downloads 53

Authors: Afsheen Aman, Shah Ali Ul Qader

Abstract:

Dextransucrase [EC 2.4.1.5] is a glucosyltransferase that catalysis the biosynthesis of a natural biopolymer called dextran. It can catalyze the transfer of D-glucopyranosyl residues from sucrose to the main chain of dextran. This unique biopolymer has multiple applications in several industries and the key utilization of dextran lies on its molecular weight and the type of branching. Extracellular dextransucrase from Leuconostoc mesenteroides is most extensively studied and characterized. Limited data is available regarding cell-bound or intracellular dextransucrase and on the characterization of dextran produced by in-vitro reaction of intracellular dextransucrase. L. mesenteroides AA1 is reported to produce extracellular dextransucrase that catalyzes biosynthesis of a high molecular weight dextran with only α-(1→6) linkage. Current study deals with the characterization of an intracellular dextransucrase and in vitro biosynthesis of low molecular weight dextran from L. mesenteroides AA1. Intracellular dextransucrase was extracted from cytoplasm and purified to homogeneity for characterization. Kinetic constants, molecular weight and N-terminal sequence analysis of intracellular dextransucrase reveal unique variation with previously reported extracellular dextransucrase from the same strain. In vitro synthesized biopolymer was characterized using NMR spectroscopic techniques. Intracellular dextransucrase exhibited Vmax and Km values of 130.8 DSU ml-1 hr-1 and 221.3 mM, respectively. Optimum catalytic activity was detected at 35°C in 0.15 M citrate phosphate buffer (pH-5.5) in 05 minutes. Molecular mass of purified intracellular dextransucrase is approximately 220.0 kDa on SDS-PAGE. N-terminal sequence of the intracellular enzyme is: GLPGYFGVN that showed no homology with previously reported sequence for the extracellular dextransucrase. This intracellular dextransucrase is capable of in vitro synthesis of dextran under specific conditions. This intracellular dextransucrase is capable of in vitro synthesis of dextran under specific conditions and this biopolymer can be hydrolyzed into different molecular weight fractions for various applications.

Keywords: characterization, dextran, dextransucrase, leuconostoc mesenteroides

Procedia PDF Downloads 369

Authors: David L. Knott, Robert Kingsland, Alistair Hitchon

Abstract:

The proposed Newcastle Light Rail is a key part of the revitalisation of Newcastle, NSW and will provide a frequent and reliable travel option throughout the city centre, running from Newcastle Interchange at Wickham to Pacific Park in Newcastle East, a total of 2.7 kilometers in length. Approximately one-third of the route, along Hunter and Scott Streets, is subject to potential shallow underground mine workings. The extent of mining and seams mined is unclear. Convicts mined the Yard Seam and overlying Dudley (Dirty) Seam in Newcastle sometime between 1800 and 1830. The Australian Agricultural Company mined the Yard Seam from about 1831 to the 1860s in the alignment area. The Yard Seam was about 3 feet (0.9m) thick, and therefore, known as the Yard Seam. Mine maps do not exist for the workings in the area of interest and it was unclear if both or just one seam was mined. Information from 1830s geological mapping and other data showing shaft locations were used along Scott Street and information from the 1908 Royal Commission was used along Hunter Street to develop an investigation program. In addition, mining was encountered for several sites to the south of the alignment at depths of about 7 m to 25 m. Based on the anticipated depths of mining, it was considered prudent to assess the potential for sinkhole development on the proposed alignment and realigned underground utilities and to obtain approval for the work from Subsidence Advisory NSW (SA NSW). The assessment consisted of a desktop study, followed by a subsurface investigation. Four boreholes were drilled along Scott Street and three boreholes were drilled along Hunter Street using HQ coring techniques in the rock. The placement of boreholes was complicated by the presence of utilities in the roadway and traffic constraints. All the boreholes encountered the Yard Seam, with conditions varying from unmined coal to an open void, indicating the presence of mining. The geotechnical information obtained from the boreholes was expanded by using various downhole techniques including; borehole camera, borehole sonar, and downhole geophysical logging. The camera provided views of the rock and helped to explain zones of no recovery. In addition, timber props within the void were observed. Borehole sonar was performed in the void and provided an indication of room size as well as the presence of timber props within the room. Downhole geophysical logging was performed in the boreholes to measure density, natural gamma, and borehole deviation. The data helped confirm that all the mining was in the Yard Seam and that the overlying Dudley Seam had been eroded in the past over much of the alignment. In summary, the assessment allowed the potential for sinkhole subsidence to be assessed and a mitigation approach developed to allow conditional approval by SA NSW. It also confirmed the presence of mining in the Yard Seam, the depth to the seam and mining conditions, and indicated that subsidence did not appear to have occurred in the past.

Keywords: downhole investigation techniques, drilling, mine subsidence, yard seam

Procedia PDF Downloads 289