Search results for: evolutionary genetics

Authors: Virupakshi Hiremata, Ratnakar M. Shet, Raghavendra Gunnaiah, Prashantha A.

Abstract:

Muskmelon is a health-beneficial and refreshing dessert vegetable with a low shelf life. Mangalore melon, a genetic homeologue of muskmelon, has a shelf life of more than six months and is mostly used for culinary purposes. Understanding the genetics of shelf life, yield and yield-related traits and identification of markers linked to such traits is helpful in transfer of extended shelf life from Mangalore melon to the muskmelon through intra-specific hybridization. For QTL mapping, 276 F2 mapping population derived from the cross Arka Siri × SS-17 was genotyped with 40 polymorphic markers distributed across 12 chromosomes. The same population was also phenotyped for yield, shelf life and fruit quality traits. One major QTL (R2 >10) and fourteen minor QTLs (R2 <10) localized on four linkage groups, governing different traits were mapped in F2 mapping population developed from the intraspecific cross with a LOD > 5.5. The phenotypic varience explained by each locus varied from 3.63 to 10.97 %. One QTL was linked to shelf-life (qSHL-3-1), five QTLs were linked to TSS (qTSS-1-1, qTSS-3-3, qTSS-3-1, qTSS-3-2 and qTSS-1-2), two QTLs for flesh thickness (qFT-3-1, and qFT-3-2) and seven QTLs for fruit yield per vine (qFYV-3-1, qFYV-1-1, qFYV-3-1, qFYV1-1, qFYV-1-3, qFYV2-1 and qFYV6-1). QTL flanking markers may be used for marker assisted introgression of shelf life into muskmelon. Important QTL will be further fine-mapped for identifying candidate genes by QTLseq and RNAseq analysis. Fine-mapping of Important Quantitative Trait Loci (QTL) holds immense promise in elucidating the genetic basis of complex traits. Leveraging advanced techniques like QTLseq and RNA sequencing (RNA seq) is crucial for this endeavor. QTLseq combines next-generation sequencing with traditional QTL mapping, enabling precise identification of genomic regions associated with traits of interest. Through high-throughput sequencing, QTLseq provides a detailed map of genetic variations linked to phenotypic variations, facilitating targeted investigations. Moreover, RNA seq analysis offers a comprehensive view of gene expression patterns in response to specific traits or conditions. By comparing transcriptomes between contrasting phenotypes, RNA seq aids in pinpointing candidate genes underlying QTL regions. Integrating QTLseq with RNA seq allows for a multi-dimensional approach, coupling genetic variation with gene expression dynamics.

Keywords: QTL, shelf life, TSS, muskmelon and Mangalore melon

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Authors: N. D'Amico, E. Grossi, B. Colombo, F. Rigiroli, M. Buscema, D. Fazzini, G. Cornalba, S. Papa

Abstract:

Purpose: To characterize, through a radiomic approach, the nature of nodules considered non-specific by expert radiologists, recognized in magnetic resonance mammography (MRm) with T1-weighted (T1w) sequences with paramagnetic contrast. Material and Methods: 47 cases out of 1200 undergoing MRm, in which the MRm assessment gave uncertain classification (non-specific nodules), were admitted to the study. The clinical outcome of the non-specific nodules was later found through follow-up or further exams (biopsy), finding 35 benign and 12 malignant. All MR Images were acquired at 1.5T, a first basal T1w sequence and then four T1w acquisitions after the paramagnetic contrast injection. After a manual segmentation of the lesions, done by a radiologist, and the extraction of 150 radiomic features (30 features per 5 subsequent times) a machine learning (ML) approach was used. An evolutionary algorithm (TWIST system based on KNN algorithm) was used to subdivide the dataset into training and validation test and to select features yielding the maximal amount of information. After this pre-processing, different machine learning systems were applied to develop a predictive model based on a training-testing crossover procedure. 10 cases with a benign nodule (follow-up older than 5 years) and 18 with an evident malignant tumor (clear malignant histological exam) were added to the dataset in order to allow the ML system to better learn from data. Results: NaiveBayes algorithm working on 79 features selected by a TWIST system, resulted to be the best performing ML system with a sensitivity of 96% and a specificity of 78% and a global accuracy of 87% (average values of two training-testing procedures ab-ba). The results showed that in the subset of 47 non-specific nodules, the algorithm predicted the outcome of 45 nodules which an expert radiologist could not identify. Conclusion: In this pilot study we identified a radiomic approach allowing ML systems to perform well in the diagnosis of a non-specific nodule at MR mammography. This algorithm could be a great support for the early diagnosis of malignant breast tumor, in the event the radiologist is not able to identify the kind of lesion and reduces the necessity for long follow-up. Clinical Relevance: This machine learning algorithm could be essential to support the radiologist in early diagnosis of non-specific nodules, in order to avoid strenuous follow-up and painful biopsy for the patient.

Keywords: breast, machine learning, MRI, radiomics

Procedia PDF Downloads 257

Authors: Avent Grange, Frederic Bertrand, Jean-Baptiste Droin, Amandine Marrel, Jean-Henry Ferrasse, Olivier Boutin

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CEA and its industrial partners are designing a gas Power Conversion System (PCS) based on a Brayton cycle for the ASTRID Sodium-cooled Fast Reactor. Investigations of control and regulation requirements to operate this PCS during operating, incidental and accidental transients are necessary to adapt core heat removal. To this aim, we developed a methodology to optimize the thermal-hydraulic behavior of the reactor during normal operations, incidents and accidents. This methodology consists of a multi-objective optimization for a specific sequence, whose aim is to increase component lifetime by reducing simultaneously several thermal stresses and to bring the reactor into a stable state. Furthermore, the multi-objective optimization complies with safety and operating constraints. Operating, incidental and accidental sequences use specific regulations to control the thermal-hydraulic reactor behavior, each of them is defined by a setpoint, a controller and an actuator. In the multi-objective problem, the parameters used to solve the optimization are the setpoints and the settings of the controllers associated with the regulations included in the sequence. In this way, the methodology allows designers to define an optimized and specific control strategy of the plant for the studied sequence and hence to adapt PCS piloting at its best. The multi-objective optimization is performed by evolutionary algorithms coupled to surrogate models built on variables computed by the thermal-hydraulic system code, CATHARE2. The methodology is applied to a loss of off-site power sequence. Three variables are controlled: the sodium outlet temperature of the sodium-gas heat exchanger, turbomachine rotational speed and water flow through the heat sink. These regulations are chosen in order to minimize thermal stresses on the gas-gas heat exchanger, on the sodium-gas heat exchanger and on the vessel. The main results of this work are optimal setpoints for the three regulations. Moreover, Proportional-Integral-Derivative (PID) control setting is considered and efficient actuators used in controls are chosen through sensitivity analysis results. Finally, the optimized regulation system and the reactor control procedure, provided by the optimization process, are verified through a direct CATHARE2 calculation.

Keywords: gas power conversion system, loss of off-site power, multi-objective optimization, regulation, sodium fast reactor, surrogate model

Procedia PDF Downloads 293

Authors: Abiodun Olayinka, Daniel Dzidzienyo, Pangirayi Tongoona, Samuel Offei, Edwige Gaby Nkouaya Mbanjo, Chiedozie Egesi, Ismail Yusuf Rabbi

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Cassava (Manihot esculenta Crantz) is a major source of starch for various industrial applications. However, the traditional cultivation and harvesting methods of cassava are labour-intensive and inefficient, limiting the supply of fresh cassava roots for industrial starch production. To achieve improved productivity and quality of fresh cassava roots through mechanized cultivation, cassava cultivars with compact plant architecture and moderate plant height are needed. Plant architecture-related traits, such as plant height, harvest index, stem diameter, branching angle, and lodging tolerance, are critical for crop productivity and suitability for mechanized cultivation. However, the genetics of cassava plant architecture remain poorly understood. This study aimed to identify the genetic bases of the relationships between plant architecture traits and productivity-related traits, particularly starch content. A panel of 453 clones developed at the International Institute of Tropical Agriculture, Nigeria, was genotyped and phenotyped for 18 plant architecture and productivity-related traits at four locations in Nigeria. A genome-wide association study (GWAS) was conducted using the phenotypic data from a panel of 453 clones and 61,238 high-quality Diversity Arrays Technology sequencing (DArTseq) derived Single Nucleotide Polymorphism (SNP) markers that are evenly distributed across the cassava genome. Five significant associations between ten SNPs and three plant architecture component traits were identified through GWAS. We found five SNPs on chromosomes 6 and 16 that were significantly associated with shoot weight, harvest index, and total yield through genome-wide association mapping. We also discovered an essential candidate gene that is co-located with peak SNPs linked to these traits in M. esculenta. A review of the cassava reference genome v7.1 revealed that the SNP on chromosome 6 is in proximity to Manes.06G101600.1, a gene that regulates endodermal differentiation and root development in plants. The findings of this study provide insights into the genetic basis of plant architecture and yield in cassava. Cassava breeders could leverage this knowledge to optimize plant architecture and yield in cassava through marker-assisted selection and targeted manipulation of the candidate gene.

Keywords: Manihot esculenta Crantz, plant architecture, DArtseq, SNP markers, genome-wide association study

Procedia PDF Downloads 55

Authors: Girija Madhavanprabhakaran, Frincy Franacis, Sheeba Elizabeth John

Abstract:

Introduction: A wide range of prenatal genetic screening is introduced with increasing incidences of congenital anomalies even in low-risk pregnancies and is an emerging standard of care. Being frontline caretakers, the role and responsibilities of nurses and midwives are critical as they are working along with couples to provide evidence-based supportive educative care. The increasing genetic disorders and advances in prenatal genetic screening with limited genetic counselling facilities urge nurses and midwifery nurses with essential competencies to help couples to take informed decision. Objective: This integrative literature review aimed to explore nurse midwives’ knowledge and role in prenatal screening and genetic counselling competency and the challenges faced by them to cater to all pregnant women to empower their autonomy in decision making and ensuring psychological comfort. Method: An electronic search using keywords prenatal screening, genetic counselling, prenatal counselling, nurse midwife, nursing education, genetics, and genomics were done in the PUBMED, SCOPUS and Medline, Google Scholar. Finally, based on inclusion criteria, 8 relevant articles were included. Results: The main review results suggest that nurses and midwives lack essential support, knowledge, or confidence to be able to provide genetic counselling and help the couples ethically to ensure client autonomy and decision making. The majority of nurses and midwives reported inadequate levels of knowledge on genetic screening and their roles in obtaining family history, pedigrees, and providing genetic information for an affected client or high-risk families. The deficiency of well-recognized and influential clinical academic midwives in midwifery practice is also reported. Evidence recommended to update and provide sound educational training to improve nurse-midwife competence and confidence. Conclusion: Overcoming the challenges to achieving informed choices about fetal anomaly screening globally is a major concern. Lack of adequate knowledge and counselling competency, communication insufficiency, need for education and policy are major areas to address. Prenatal nurses' and midwives’ knowledge on prenatal genetic screening and essential counselling competencies can ensure services to the majority of pregnant women around the globe to be better-informed decision-makers and enhances their autonomy, and reduces ethical dilemmas.

Keywords: challenges, genetic counselling, prenatal screening, prenatal counselling

Procedia PDF Downloads 184

Authors: Elif Gencturk, Ekin Yurdakul, Ahmet Y. Celik, Senol Mutlu, Kutlu O. Ulgen

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Yeast cells are generally used as a model system of eukaryotes due to their complex genetic structure, rapid growth ability in optimum conditions, easy replication and well-defined genetic system properties. Thus, yeast cells increased the knowledge of the principal pathways in humans. During fermentation, carbohydrates (hexoses and pentoses) degrade into some toxic by-products such as 5-hydroxymethylfurfural (5-HMF or HMF) and furfural. HMF influences the ethanol yield, and ethanol productivity; it interferes with microbial growth and is considered as a potent inhibitor of bioethanol production. In this study, yeast single cell behavior under HMF application was monitored by using a continuous flow single phase microfluidic platform. Microfluidic device in operation is fabricated by hot embossing and thermo-compression techniques from cyclo-olefin polymer (COP). COP is biocompatible, transparent and rigid material and it is suitable for observing fluorescence of cells considering its low auto-fluorescence characteristic. The response of yeast cells was recorded through Red Fluorescent Protein (RFP) tagged Nop56 gene product, which is an essential evolutionary-conserved nucleolar protein, and also a member of the box C/D snoRNP complexes. With the application of HMF, yeast cell proliferation continued but HMF slowed down the cell growth, and after HMF treatment the cell proliferation stopped. By the addition of fresh nutrient medium, the yeast cells recovered after 6 hours of HMF exposure. Thus, HMF application suppresses normal functioning of cell cycle but it does not cause cells to die. The monitoring of Nop56 expression phases of the individual cells shed light on the protein and ribosome synthesis cycles along with their link to growth. Further computational study revealed that the mechanisms underlying the inhibitory or inductive effects of HMF on growth are enriched in functional categories of protein degradation, protein processing, DNA repair and multidrug resistance. The present microfluidic device can successfully be used for studying the effects of inhibitory agents on growth by single cell tracking, thus capturing cell to cell variations. By metabolic engineering techniques, engineered strains can be developed, and the metabolic network of the microorganism can thus be manipulated such that chemical overproduction of target metabolite is achieved along with the maximum growth/biomass yield.  

Keywords: COP, HMF, ribosome biogenesis, thermoplastic microbioreactor, yeast

Procedia PDF Downloads 154

Authors: Farahnaz Amini, Woo Yun Kin, Lazwani Kolandaiveloo

Abstract:

Availability of different genetic tests after completion of Human Genome Project increases the physicians’ responsibility to keep themselves update on the potential implementation of these genetic tests in their daily practice. However, due to numbers of barriers, still many of physicians are not either aware of these tests or are not willing to offer or refer their patients for genetic tests. This study was conducted an anonymous, cross-sectional, mailed-based survey to develop a primary data of Malaysian physicians’ level of knowledge and perception of gene profiling. Questionnaire had 29 questions. Total scores on selected questions were used to assess the level of knowledge. The highest possible score was 11. Descriptive statistics, one way ANOVA and chi-squared test was used for statistical analysis. Sixty three completed questionnaires was returned by 27 general practitioners (GPs) and 36 medical specialists. Responders’ age range from 24 to 55 years old (mean 30.2 ± 6.4). About 40% of the participants rated themselves as having poor level of knowledge in genetics in general whilst 60% believed that they have fair level of knowledge. However, almost half (46%) of the respondents felt that they were not knowledgeable about available genetic tests. A majority (94%) of the responders were not aware of any lab or company which is offering gene profiling services in Malaysia. Only 4% of participants were aware of using gene profiling for detection of dosage of some drugs. Respondents perceived greater utility of gene profiling for breast cancer (38%) compared to the colorectal familial cancer (3%). The score of knowledge ranged from 2 to 8 (mean 4.38 ± 1.67). Non-significant differences between score of knowledge of GPs and specialists were observed, with score of 4.19 and 4.58 respectively. There was no significant association between any demographic factors and level of knowledge. However, those who graduated between years 2001 to 2005 had higher level of knowledge. Overall, 83% of participants showed relatively high level of perception on value of gene profiling to detect patient’s risk of disease. However, low perception was observed for both statements of using gene profiling for general population in order to alter their lifestyle (25%) as well as having the full sequence of a patient genome for the purpose of determining a patient’s best match for treatment (18%). The lack of clinical guidelines, limited provider knowledge and awareness, lack of time and resources to educate patients, lack of evidence-based clinical information and cost of tests were the most barriers of ordering gene profiling mentioned by physicians. In conclusion Malaysian physicians who participate in this study had mediocre level of knowledge and awareness in gene profiling. The low exposure to the genetic questions and problems might be a key predictor of lack of awareness and knowledge on available genetic tests. Educational and training workshop might be useful in helping Malaysian physicians incorporate genetic profiling into practice for eligible patients.

Keywords: gene profiling, knowledge, Malaysia, physician

Procedia PDF Downloads 318

Authors: Ahmed O. Apampa, Yinusa A. Jimoh

Abstract:

The potential economic viability and environmental benefits of using a biomass waste, such as corn cob ash (CCA) as pozzolan in stabilizing soils for road pavement construction in a sub-tropical region was investigated. Corn cob was obtained from Maya in South West Nigeria and processed to ash of characteristics similar to Class C Fly Ash pozzolan as specified in ASTM C618-12. This was then blended with ordinary Portland cement in the CCA:OPC ratios of 1:1, 1:2 and 2:1. Each of these blends was then mixed with lateritic soil of ASHTO classification A-2-6(3) in varying percentages from 0 – 7.5% at 1.5% intervals. The soil-CCA-Cement mixtures were thereafter tested for geotechnical index properties including the BS Proctor Compaction, California Bearing Ratio (CBR) and the Unconfined Compression Strength Test. The tests were repeated for soil-cement mix without any CCA blending. The cost of the binder inputs and optimal blends of CCA:OPC in the stabilized soil were thereafter analyzed by developing algorithms that relate the experimental data on strength parameters (Unconfined Compression Strength, UCS and California Bearing Ratio, CBR) with the bivariate independent variables CCA and OPC content, using Matlab R2011b. An optimization problem was then set up minimizing the cost of chemical stabilization of laterite with CCA and OPC, subject to the constraints of minimum strength specifications. The Evolutionary Engine as well as the Generalized Reduced Gradient option of the Solver of MS Excel 2010 were used separately on the cells to obtain the optimal blend of CCA:OPC. The optimal blend attaining the required strength of 1800 kN/m2 was determined for the 1:2 CCA:OPC as 5.4% mix (OPC content 3.6%) compared with 4.2% for the OPC only option; and as 6.2% mix for the 1:1 blend (OPC content 3%). The 2:1 blend did not attain the required strength, though over a 100% gain in UCS value was obtained over the control sample with 0% binder. Upon the fact that 0.97 tonne of CO2 is released for every tonne of cement used (OEE, 2001), the reduced OPC requirement to attain the same result indicates the possibility of reducing the net CO2 contribution of the construction industry to the environment ranging from 14 – 28.5% if CCA:OPC blends are widely used in soil stabilization, going by the results of this study. The paper concludes by recommending that Nigeria and other developing countries in the sub-tropics with abundant stock of biomass waste should look in the direction of intensifying the use of biomass waste as fuel and the derived ash for the production of pozzolans for road-works, thereby reducing overall green house gas emissions and in compliance with the objectives of the United Nations Framework on Climate Change.

Keywords: corn cob ash, biomass waste, lateritic soil, unconfined compression strength, CO2 emission

Procedia PDF Downloads 366

Authors: Abiodun Olayinka, Daniel Dzidzienyo, Pangirayi Tongoona, Samuel Offei, Edwige Gaby Nkouaya Mbanjo, Chiedozie Egesi, Ismail Yusuf Rabbi

Abstract:

Cassava (Manihot esculenta Crantz) is a major source of starch for various industrial applications. However, the traditional cultivation and harvesting methods of cassava are labour-intensive and inefficient, limiting the supply of fresh cassava roots for industrial starch production. To achieve improved productivity and quality of fresh cassava roots through mechanized cultivation, cassava cultivars with compact plant architecture and moderate plant height are needed. Plant architecture-related traits, such as plant height, harvest index, stem diameter, branching angle, and lodging tolerance, are critical for crop productivity and suitability for mechanized cultivation. However, the genetics of cassava plant architecture remain poorly understood. This study aimed to identify the genetic bases of the relationships between plant architecture traits and productivity-related traits, particularly starch content. A panel of 453 clones developed at the International Institute of Tropical Agriculture, Nigeria, was genotyped and phenotyped for 18 plant architecture and productivity-related traits at four locations in Nigeria. A genome-wide association study (GWAS) was conducted using the phenotypic data from a panel of 453 clones and 61,238 high-quality Diversity Arrays Technology sequencing (DArTseq) derived Single Nucleotide Polymorphism (SNP) markers that are evenly distributed across the cassava genome. Five significant associations between ten SNPs and three plant architecture component traits were identified through GWAS. We found five SNPs on chromosomes 6 and 16 that were significantly associated with shoot weight, harvest index, and total yield through genome-wide association mapping. We also discovered an essential candidate gene that is co-located with peak SNPs linked to these traits in M. esculenta. A review of the cassava reference genome v7.1 revealed that the SNP on chromosome 6 is in proximity to Manes.06G101600.1, a gene that regulates endodermal differentiation and root development in plants. The findings of this study provide insights into the genetic basis of plant architecture and yield in cassava. Cassava breeders could leverage this knowledge to optimize plant architecture and yield in cassava through marker-assisted selection and targeted manipulation of the candidate gene.

Keywords: manihot esculenta crantz, plant architecture, dartseq, snp markers, genome-wide association study

Procedia PDF Downloads 78

Authors: S. Cheng, C. Catallo

Abstract:

Introduction: Canada's healthcare and social services systems are failing high risk, vulnerable older adults. Care for vulnerable older Canadians (65 and older) is not optimal in Canada. It does not address the care needs of vulnerable, high risk adults using a holistic approach. Given the growing aging population, and the care needs for seniors with complex conditions is one of the highest in Canada's health care system, there is a sense of urgency to optimize care. Integration of health and social services is an emerging trend in Canada when compared to European countries. There is no common and universal understanding of healthcare and social services integration within the country. Consequently, a clear understanding and definition of integrated health and social services are absent in Canada. Objectives: A study was undertaken to develop a case definition for integrated health and social care initiatives that serve older adults, which was then tested against three Canadian integrated initiatives. Methodology: A limited literature review was undertaken to identify common characteristics of integrated health and social care initiatives that serve older adults, and comprised both scientific and grey literature, in order to develop a case definition. Three Canadian integrated initiatives that are located in the province of Ontario, were identified using an online search and a screening process. They were surveyed to determine if the literature-based integration definition applied to them. Results: The literature showed that there were 24 common healthcare and social services integration characteristics that could be categorized into ten themes: 1) patient-care approach; 2) program goals; 3) measurement; 4) service and care quality; 5) accountability and responsibility; 6) information sharing; 7) Decision-making and problem-solving; 8) culture; 9) leadership; and 10) staff and professional interaction. The three initiatives showed agreement on all the integration characteristics except for those characteristics associated with healthcare and social care professional interaction, collaborative leadership and shared culture. This disagreement may be due to several reasons, including the existing governance divide between the healthcare and social services sectors within the province of Ontario that has created a ripple effect in how professions in the two different sectors interact. In addition, the three initiatives may be at maturing levels of integration, which may explain disagreement on the characteristics associated with leadership and culture. Conclusions: The development of a case definition for healthcare and social services integration that incorporates common integration characteristics can act as a useful instrument in identifying integrated healthcare and social services, particularly given the emerging and evolutionary state of this phenomenon within Canada.

Keywords: Canada, case definition, healthcare and social services integration, integration, seniors health, services delivery

Procedia PDF Downloads 143

Authors: Boutheina Ben Abdelmoumen Mardassi, Salim Chibani, Safa Boujemaa, Amaury Vaysse, Julien Guglielmini, Elhem Yacoub

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Background and aim: Mycoplasma hominis (MH) is a pathogenic bacterium belonging to the Mollicutes class. It causes a wide range of gynecological infections and infertility among adults. Recently, we have explored for the first time the phylodistribution of Tunisian M. hominis clinical strains using an expanded MLST. We have demonstrated their distinction into two pure lineages, which each corresponding to a specific pathotype: genital infections and infertility. The aim of this project is to gain further insight into the evolutionary dynamics and the specific genetic factors that distinguish MH pathotypes Methods: Whole genome sequencing of Mycoplasma hominis clinical strains was performed using illumina Miseq. Denovo assembly was performed using a publicly available in-house pipeline. We used prokka to annotate the genomes, panaroo to generate the gene presence matrix and Jolytree to establish the phylogenetic tree. We used treeWAS to identify genetic loci associated with the pathothype of interest from the presence matrix and phylogenetic tree. Results: Our results revealed a clear categorization of the 62 MH clinical strains into two distinct genetic lineages, with each corresponding to a specific pathotype.; gynecological infections and infertility[AV1] . Genome annotation showed that GC content is ranging between 26 and 27%, which is a known characteristic of Mycoplasma genome. Housekeeping genes belonging to the core genome are highly conserved among our strains. TreeWas identified 4 virulence genes associated with the pathotype gynecological infection. encoding for asparagine--tRNA ligase, restriction endonuclease subunit S, Eco47II restriction endonuclease, and transcription regulator XRE (involved in tolerance to oxidative stress). Five genes have been identified that have a statistical association with infertility, tow lipoprotein, one hypothetical protein, a glycosyl transferase involved in capsule synthesis, and pyruvate kinase involved in biofilm formation. All strains harbored an efflux pomp that belongs to the family of multidrug resistance ABC transporter, which confers resistance to a wide range of antibiotics. Indeed many adhesion factors and lipoproteins (p120, p120', p60, p80, Vaa) have been checked and confirmed in our strains with a relatively 99 % to 96 % conserved domain and hypervariable domain that represent 1 to 4 % of the reference sequence extracted from gene bank. Conclusion: In summary, this study led to the identification of specific genetic loci associated with distinct pathotypes in M hominis.

Keywords: mycoplasma hominis, infertility, gynecological infections, virulence genes, antibiotic resistance

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Authors: Cristina Felipeto, Catherine Bore, Eduardo Calil

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This work aims to analyze and compare the punctuation marks (PM) in school texts of Brazilian and French students and the comments on these PM made spontaneously by the students during the ongoing text. Assuming textual genetics as an investigative field within a dialogical and enunciative approach, we defined a common methodological design in two 1st year classrooms (7 years old) of the primary school, one classroom in Brazil (Maceio) and the other one in France (Paris). Through a multimodal capture system of writing processes in real time and space (Ramos System), we recorded the collaborative writing proposal in dyads in each of the classrooms. This system preserves the classroom’s ecological characteristics and provides a video recording synchronized with dialogues, gestures and facial expressions of the students, the stroke of the pen’s ink on the sheet of paper and the movement of the teacher and students in the classroom. The multimodal register of the writing process allowed access to the text in progress and the comments made by the students on what was being written. In each proposed text production, teachers organized their students in dyads and requested that they should talk, combine and write a fictional narrative. We selected a Dyad of Brazilian students (BD) and another Dyad of French students (FD) and we have filmed 6 proposals for each of the dyads. The proposals were collected during the 2nd Term of 2013 (Brazil) and 2014 (France). In 6 texts written by the BD there were identified 39 PMs and 825 written words (on average, a PM every 23 words): Of these 39 PMs, 27 were highlighted orally and commented by either student. In the texts written by the FD there were identified 48 PMs and 258 written words (on average, 1 PM every 5 words): Of these 48 PM, 39 were commented by the French students. Unlike what the studies on punctuation acquisition point out, the PM that occurred the most were hyphens (BD) and commas (FD). Despite the significant difference between the types and quantities of PM in the written texts, the recognition of the need for writing PM in the text in progress and the comments have some common characteristics: i) the writing of the PM was not anticipated in relation to the text in progress, then they were added after the end of a sentence or after the finished text itself; ii) the need to add punctuation marks in the text came after one of the students had ‘remembered’ that a particular sign was needed; iii) most of the PM inscribed were not related to their linguistic functions, but the graphic-visual feature of the text; iv) the comments justify or explain the PM, indicating metalinguistic reflections made by the students. Our results indicate how the comments of the BD and FD express the dialogic and subjective nature of knowledge acquisition. Our study suggests that the initial learning of PM depends more on its graphic features and interactional conditions than on its linguistic functions.

Keywords: collaborative writing, erasure, graphic marks, learning, metalinguistic awareness, textual genesis

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Authors: Stefan Papastefanou

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Artificial intelligence (AI) is an interdisciplinary field of computer science with the aim of creating intelligent machine behavior. Early approaches to AI have been configured to operate in very constrained environments where the behavior of the AI system was previously determined by formal rules. Knowledge was presented as a set of rules that allowed the AI system to determine the results for specific problems; as a structure of if-else rules that could be traversed to find a solution to a particular problem or question. However, such rule-based systems typically have not been able to generalize beyond the knowledge provided. All over the world and especially in IT-heavy industries such as the United States, the European Union, Singapore, and China, machine learning has developed to be an immense asset, and its applications are becoming more and more significant. It has to be examined how such products of machine learning models can and should be protected by IP law and for the purpose of this paper patent law specifically, since it is the IP law regime closest to technical inventions and computing methods in technical applications. Genetic breeding models are currently less popular than recursive neural network method and deep learning, but this approach can be more easily described by referring to the evolution of natural organisms, and with increasing computational power; the genetic breeding method as a subset of the evolutionary algorithms models is expected to be regaining popularity. The research method focuses on patentability (according to the world’s most significant patent law regimes such as China, Singapore, the European Union, and the United States) of AI inventions and machine learning. Questions of the technical nature of the problem to be solved, the inventive step as such, and the question of the state of the art and the associated obviousness of the solution arise in the current patenting processes. Most importantly, and the key focus of this paper is the problem of patenting inventions that themselves are developed through machine learning. The inventor of a patent application must be a natural person or a group of persons according to the current legal situation in most patent law regimes. In order to be considered an 'inventor', a person must actually have developed part of the inventive concept. The mere application of machine learning or an AI algorithm to a particular problem should not be construed as the algorithm that contributes to a part of the inventive concept. However, when machine learning or the AI algorithm has contributed to a part of the inventive concept, there is currently a lack of clarity regarding the ownership of artificially created inventions. Since not only all European patent law regimes but also the Chinese and Singaporean patent law approaches include identical terms, this paper ultimately offers a comparative analysis of the most relevant patent law regimes.

Keywords: algorithms, inventor, genetic breeding models, machine learning, patentability

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Authors: Dina Dahood Dabash

Abstract:

Refugee camps are habitually defined as receptive sites, transient spaces of exile and nondescript depoliticized places of exception. However, such arguments form partial sides of reality, especially in countries that are geopolitically challenged and rely immensely on international aid. In Jordan, the dynamics brought with the floating population of refugees (Palestinian amongst others) have resulted in spatial after-effects that cannot be easily overlooked. For instance, Palestine refugee camps have turned by time into socioeconomic centers of gravity and cores of spatial evolution. Yet, such a position is not instantaneous. Amongst various reasons, it can be related, according to this paper, to a distinctive institutional climate that has been co-produced by the refugees, host community and the state. This paper aims to investigate the evolution of urban and spatial regulations in Jordan between 1948 and 1995, more specifically, state regulations, community regulations and refugee-self-regulation that all dynamically interacted that period. The paper aims to unpack the relations between refugee camps and their environs to further explore the agency of such floating populations in establishing rooted networks that extended the time and place boundaries. The paper’s argument stems from the fact that the spatial configuration of urban systems is not only an outcome of a historical evolutionary process but is also a result of interactions between the actors. The research operationalizes Marka camp in Jordan as a case study. Marka Camp is one of the six "emergency" camps erected in 1968 to shelter 15,000 Palestine refugees and displaced persons who left the West Bank and Gaza Strip. Nowadays, camp shelters more than 50,000 refugees in the same area of land. The camp is located in Russeifa, a city in Zarqa Governorate in Jordan. Together with Amman and Zarqa, Russeifa is part of a larger metropolitan area that acts as a home to more than half of Jordan’s businesses. The paper aspires to further understand the post-conflict strategies which were historically applied in Jordan and can be employed to handle more recent geopolitical challenges such as the Syrian refugee crisis. Methodological framework: The paper traces the evolution of the refugee-camp regulating norms in Jordan, parallel with the horizontal and vertical evolution of the Marka camp and its surroundings. Consequently, the main methods employed are historical and mental tracing, Interviews, in addition to using available Aerial and archival photos of the Marka camp and its surrounding.

Keywords: forced migration, Palestine refugee camps, spatial agency, urban regulations

Procedia PDF Downloads 174

Authors: Alsu F. Saifitdinova, Alexey S. Komissarov, Svetlana A. Galkina, Elena I. Koshel, Maria M. Kulak, Stephen J. O'Brien, Elena R. Gaginskaya

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The mystery of sex determination is one of the most ancient and still not solved until the end so far. In many species, sex determination is genetic and often accompanied by the presence of dimorphic sex chromosomes in the karyotype. Genomic sequencing gave the information about the gene content of sex chromosomes which allowed to reveal their origin from ordinary autosomes and to trace their evolutionary history. Female-specific W chromosome in birds as well as mammalian male-specific Y chromosome is characterized by the degeneration of gene content and the accumulation of repetitive DNA. Tandem repeats complicate the analysis of genomic data. Despite the best efforts chicken W chromosome assembly includes only 1.2 Mb from expected 55 Mb. Supplementing the information on the sex chromosome composition not only helps to complete the assembly of genomes but also moves us in the direction of understanding of the sex-determination systems evolution. A whole-genome survey to the assembly Gallus_gallus WASHUC 2.60 was applied for repeats search in assembled genome and performed search and assembly of high copy number repeats in unassembled reads of SRR867748 short reads datasets. For cytogenetic analysis conventional methods of fluorescent in situ hybridization was used for previously cloned W specific satellites and specifically designed directly labeled synthetic oligonucleotide DNA probe was used for bioinformatically identified repetitive sequence. Hybridization was performed with mitotic chicken chromosomes and manually isolated giant meiotic lampbrush chromosomes from growing oocytes. A novel chicken W specific satellite (GGAAA)n which is not co-localizes with any previously described classes of W specific repeats was identified and mapped with high resolution. In the composition of autosomes this repeat units was found as a part of upstream regions of gonad specific protein coding sequences. These findings may contribute to the understanding of the role of tandem repeats in sex specific differentiation regulation in birds and sex chromosome evolution. This work was supported by the postdoctoral fellowships from St. Petersburg State University (#1.50.1623.2013 and #1.50.1043.2014), the grant for Leading Scientific Schools (#3553.2014.4) and the grant from Russian foundation for basic researches (#15-04-05684). The equipment and software of Research Resource Center “Chromas” and Theodosius Dobzhansky Center for Genome Bioinformatics of Saint Petersburg State University were used.

Keywords: birds, lampbrush chromosomes, sex chromosomes, tandem repeats

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Authors: Loris Franchi, Daniele Calvi, Sabrina Corpino

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This paper presents a design methodology in which stakeholders are assisted with the exploration of a so-called negotiation space, aiming to the maximization of both group social welfare and single stakeholder’s perceived utility. The outcome results in less design iterations needed for design convergence while obtaining a higher solution effectiveness. During the early stage of a space project, not only the knowledge about the system but also the decision outcomes often are unknown. The scenario is exacerbated by the fact that decisions taken in this stage imply delayed costs associated with them. Hence, it is necessary to have a clear definition of the problem under analysis, especially in the initial definition. This can be obtained thanks to a robust generation and exploration of design alternatives. This process must consider that design usually involves various individuals, who take decisions affecting one another. An effective coordination among these decision-makers is critical. Finding mutual agreement solution will reduce the iterations involved in the design process. To handle this scenario, the paper proposes a design methodology which, aims to speed-up the process of pushing the mission’s concept maturity level. This push up is obtained thanks to a guided negotiation space exploration, which involves autonomously exploration and optimization of trade opportunities among stakeholders via Artificial Intelligence algorithms. The negotiation space is generated via a multidisciplinary collaborative optimization method, infused by game theory and multi-attribute utility theory. In particular, game theory is able to model the negotiation process to reach the equilibria among stakeholder needs. Because of the huge dimension of the negotiation space, a collaborative optimization framework with evolutionary algorithm has been integrated in order to guide the game process to efficiently and rapidly searching for the Pareto equilibria among stakeholders. At last, the concept of utility constituted the mechanism to bridge the language barrier between experts of different backgrounds and differing needs, using the elicited and modeled needs to evaluate a multitude of alternatives. To highlight the benefits of the proposed methodology, the paper presents the design of a CubeSat mission for the observation of lunar radiation environment. The derived solution results able to balance all stakeholders needs and guaranteeing the effectiveness of the selection mission concept thanks to its robustness in valuable changeability. The benefits provided by the proposed design methodology are highlighted, and further development proposed.

Keywords: concurrent engineering, artificial intelligence, negotiation in engineering design, multidisciplinary optimization

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Authors: Marcelo T. Okano, Oduvaldo Vendrametto, Osmildo S. Santos, Marcelo E. Fernandes, Heide Landi

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Teaching of entrepreneurship and innovation in Brazilian universities has increased in recent years due to several factors such as the emergence of disciplines like biotechnology increased globalization reduced basic funding and new perspectives on the role of the university in the system of knowledge production Innovation is increasingly seen as an evolutionary process that involves different institutional spheres or sectors in society Entrepreneurship is a milestone on the road towards economic progress, and makes a huge contribution towards the quality and future hopes of a sector, economy or even a country. Entrepreneurship is as important in small and medium-sized enterprises (SMEs) and local markets as in large companies, and national and international markets, and is just as key a consideration for public companies as or private organizations. Entrepreneurship helps to encourage the competition in the current environment that leads to the effects of globalization. There is an increasing tendency for government policy to promote entrepreneurship for its apparent economic benefit. Accordingly, governments seek to employ entrepreneurship education as a means to stimulate increased levels of economic activity. Entrepreneurship education and training (EET) is growing rapidly in universities and colleges throughout the world, and governments are supporting it both directly and through funding major investments in advice-provision to would-be entrepreneurs and existing small businesses. The Triple Helix of university–industry–government relations is compared with alternative models for explaining the current research system in its social contexts. Communications and negotiations between institutional partners generate an overlay that increasingly reorganizes the underlying arrangements. To achieve the objective of this research was a survey of the literature on the entrepreneurship and innovation and then a field research with 100 students of Fatec. To collect the data needed for analysis, we used the exploratory research of a qualitative nature. We asked to respondents what degree of knowledge over ten related to entrepreneurship and innovation topics, responses were answered in a Likert scale with 4 levels, none, small, medium and large. We can conclude that the terms such as entrepreneurship and innovation are known by most students because the university propagates them across disciplines, lectures, and institutes innovation. The more specific items such as canvas and Design thinking model are unknown by most respondents. The importance of the University in teaching innovation and entrepreneurship in the transmission of this knowledge to the students in order to equalize the knowledge. As a future project, these items will be re-evaluated to create indicators for measuring the knowledge level.

Keywords: Brazilian universities, entrepreneurship, innovation, entrepreneurship, globalization

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Authors: Kristina Amaleviciute, Ieva Jokubauskaite, Alvyra Slepetiene, Jonas Volungevicius, Inga Liaudanskiene

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The main task of this research was to investigate the chemical composition of the differently used soil in profiles. To identify the differences in the soil were investigated organic carbon (SOC) and its fractional composition: dissolved organic carbon (DOC), mobile humic acids (MHA) and C to N ratio of natural and anthropogenically affected Luvisols. Research object: natural and anthropogenically affected Luvisol, Akademija, Kedainiai, distr. Lithuania. Chemical analyses were carried out at the Chemical Research Laboratory of Institute of Agriculture, LAMMC. Soil samples for chemical analyses were taken from the genetics soil horizons. SOC was determined by the Tyurin method modified by Nikitin, measuring with spectrometer Cary 50 (VARIAN) in 590 nm wavelength using glucose standards. For mobile humic acids (MHA) determination the extraction procedure was carried out using 0.1 M NaOH solution. Dissolved organic carbon (DOC) was analyzed using an ion chromatograph SKALAR. pH was measured in 1M H2O. N total was determined by Kjeldahl method. Results: Based on the obtained results, it can be stated that transformation of chemical composition is going through the genetic soil horizons. Morphology of the upper layers of soil profile which is formed under natural conditions was changed by anthropomorphic (agrogenic, urbogenic, technogenic and others) structure. Anthropogenic activities, mechanical and biochemical disturbances destroy the natural characteristics of soil formation and complicates the interpretation of soil development. Due to the intensive cultivation, the pH values of the curve equals (disappears acidification characteristic for E horizon) with natural Luvisol. Luvisols affected by agricultural activities was characterized by a decrease in the absolute amount of humic substances in separate horizons. But there was observed more sustainable, higher carbon sequestration and thicker storage of humic horizon compared with forest Luvisol. However, the average content of humic substances in the soil profile was lower. Soil organic carbon content in anthropogenic Luvisols was lower compared with the natural forest soil, but there was more evenly spread over in the wider thickness of accumulative horizon. These data suggest that the organization of geo-ecological declines and agroecological increases in Luvisols. Acknowledgement: This work was supported by the National Science Program ‘The effect of long-term, different-intensity management of resources on the soils of different genesis and on other components of the agro-ecosystems’ [grant number SIT-9/2015] funded by the Research Council of Lithuania.

Keywords: agrogenization, dissolved organic carbon, luvisol, mobile humic acids, soil organic carbon

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Authors: Ismaila Haruna

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The global downfall in fossil energy prices and dwindling oil reserves in Nigeria has ignited interest in the search for alternative sources of foreign income for the country. Solid minerals, particularly Uranium and other base metals like Lead and Zinc have been considered as potentially good options. Several occurrences of this mineral have been discovered in both the sedimentary and granitic rocks of the Hawal and Adamawa Massifs as well as in the adjoining Benue Trough in northeastern Nigeria. However, the paucity of geochemical data and consequent poor petrogenetic knowledge of the granitoids in this region has made exploration works difficult. Song, a small area within the Hawal Massif, was mapped and the collected samples chemically determined in Activation Laboratory, Canada through fusion dissolution technique of Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Field mapping results show that the area is underlain by Granites, diorites with pockets of gneisses and pegmatites and that these rocks consists of microcline, quartz, plagioclase, biotite, hornblende, pyroxene and accessory apatite, zircon, sphene, magnetite and opaques in various proportions. Geochemical data show continous compositional variation from diorite to granites within silica range of 52.69 to 76.04 wt %. Plot of the data on various Harker variation diagrams show distinct evolutionary trends from diorites to granites indicated by decreasing CaO, Fe2O3, MnO, MgO, Ti2O, and increasing K2O with increasing silica. This pattern is reflected in trace elements data which, in general, decrease from diorite to the granites with rising Rb and K. Tectonic, triangular and other diagrams, indicate high-K calc-alkaline trends, syn-collisional granite signatures, I-type characteristics, with CNK/A of less than 1.1 (minimum of 0.58 and maximum of 0.94) and strong potassic character (K2O/Na2O˃1). However, only the granites are slightly peraluminous containing high silica percentage (68.46 to 76.04), K2O (2.71 to 6.16 wt %) with low CaO (1.88 on the average). Chondrite normalised rare earth elements trends indicate strongly fractionated REEs and enriched LREEs with slightly increasing negative Eu anomaly from the diorite to the granite. On the basis of field and geochemical data, the granitoids are interpreted to be high-K calc-alkaline, I-type, formed as a result of hybridization between mantle-derived magma and continental source materials (probably older meta-sediments) in a syn-collisional tectonic setting.

Keywords: geochemistry, granite, Hawal Massif, Nigeria, petrogenesis, song

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Authors: Mustafa Malki, Ewan R. Pearson

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Tools utilized by health care practitioners to flag potential adverse drug reactions secondary to drug-drug interactions ignore individual genetic variation, which has the potential to markedly alter the severity of these interactions. To our best knowledge, there have been limited published studies on the impact of genetic variation on drug-drug interactions. Therefore, our aim in this project is the discovery of previously unrecognized, clinically important drug-drug-gene interactions (DDGIs) within the list of most commonly used drug combinations in the UK. The UKBB database was utilized to identify the top most frequently prescribed drug combinations in the UK with at least one route of interaction (over than 200 combinations were identified). We have recognised 37 common and unique interacting genes considering all of our drug combinations. Out of around 600 potential genetic variants found in these 37 genes, 100 variants have met the selection criteria (common variant with minor allele frequency ≥ 5%, independence, and has passed HWE test). The association between these variants and the use of each of our top drug combinations has been tested with a case-control analysis under the log-additive model. As the data is cross-sectional, drug intolerance has been identified from the genotype distribution as presented by the lower percentage of patients carrying the risky allele and on the drug combination compared to those free of these risk factors and vice versa with drug tolerance. In GoDARTs database, the same list of common drug combinations identified by the UKBB was utilized here with the same list of candidate genetic variants but with the addition of 14 new SNPs so that we have a total of 114 variants which have met the selection criteria in GoDARTs. From the list of the top 200 drug combinations, we have selected 28 combinations where the two drugs in each combination are known to be used chronically. For each of our 28 combinations, three drug response phenotypes have been identified (drug stop/switch, dose decrease, or dose increase of any of the two drugs during their interaction). The association between each of the three phenotypes belonging to each of our 28 drug combinations has been tested against our 114 candidate genetic variants. The results show replication of four findings between both databases : (1) Omeprazole +Amitriptyline +rs2246709 (A > G) variant in CYP3A4 gene (p-values and ORs with the UKBB and GoDARTs respectively = 0.048,0.037,0.92,and 0.52 (dose increase phenotype)) (2) Simvastatin + Ranitidine + rs9332197 (T > C) variant in CYP2C9 gene (0.024,0.032,0.81, and 5.75 (drug stop/switch phenotype)) (3) Atorvastatin + Doxazosin + rs9282564 (T > C) variant in ABCB1 gene (0.0015,0.0095,1.58,and 3.14 (drug stop/switch phenotype)) (4) Simvastatin + Nifedipine + rs2257401 (C > G) variant in CYP3A7 gene (0.025,0.019,0.77,and 0.30 (drug stop/switch phenotype)). In addition, some other non-replicated, but interesting, significant findings were detected. Our work also provides a great source of information for researchers interested in DD, DG, or DDG interactions studies as it has highlighted the top common drug combinations in the UK with recognizing 114 significant genetic variants related to drugs' pharmacokinetic.

Keywords: adverse drug reactions, common drug combinations, drug-drug-gene interactions, pharmacogenomics

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Authors: Elsher Lawson-Boyd

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In the wake of the Human Genome Project, the life sciences have undergone some fascinating changes. In particular, conventional beliefs relating to gene expression are being challenged by advances in postgenomic sciences, especially by the field of epigenetics. Epigenetics is the modification of gene expression without changes in the DNA sequence. In other words, epigenetics dictates that gene expression, the process by which the instructions in DNA are converted into products like proteins, is not solely controlled by DNA itself. Unlike gene-centric theories of heredity that characterized much of the 20th Century (where the genes were considered as having almost god-like power to create life), gene expression in epigenetics insists on environmental ‘signals’ or ‘exposures’, a point that radically deviates from gene-centric thinking. Science and Technology Studies (STS) scholars have shown that epigenetic research is having vast implications for the ways in which chronic, non-communicable diseases are conceptualized, treated, and governed. However, to the author’s knowledge, there have not yet been any in-depth sociological engagements with neuroepigenetics that examine how the field is affecting mental health and trauma discourse. In this paper, the author discusses preliminary findings from a doctoral ethnographic study on neuroepigenetics, trauma, and embodiment. Specifically, this study investigates the kinds of causal relations neuroepigenetic researchers are making between experiences of trauma and the development of mental illnesses like complex post-traumatic stress disorder (PTSD), both throughout a human’s lifetime and across generations. Using qualitative interviews and nonparticipant observation, the author focuses on two public-facing research centers based in Melbourne: Florey Institute of Neuroscience and Mental Health (FNMH), and Murdoch Children’s Research Institute (MCRI). Preliminary findings indicate that a great deal of ambiguity characterizes this infant field, particularly when animal-model experiments are employed and the results are translated into human frameworks. Nevertheless, researchers at the FNMH and MCRI strongly suggest that adverse and traumatic life events have a significant effect on gene expression, especially when experienced during early development. Furthermore, they predict that neuroepigenetic research will have substantial implications for the ways in which mental illnesses like complex PTSD are diagnosed and treated. These preliminary findings shed light on why medical and health sociologists have good reason to be chiming in, engaging with and de-black-boxing ideations emerging from postgenomic sciences, as they may indeed have significant effects for vulnerable populations not only in Australia but other developing countries in the Global South.

Keywords: genetics, mental illness, neuroepigenetics, trauma

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Authors: Sharmeen Rahman, Daniel Schmidt, Jane Hughes

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Paratya australiensis Kemp (Decapoda: Atyidae) is a widely distributed indigenous freshwater shrimp, highly abundant in eastern Australia. This species has been considered as a model stream organism to study genetics, dispersal, biology, behaviour and evolution in Atyids. Paratya has a filter feeding and scavenging habit which plays a significant role in the formation of lotic community structure. It has been shown to reduce periphyton and sediment from hard substrates of coastal streams and hence acts as a strongly-interacting ecosystem macroconsumer. Besides, Paratya is one of the major food sources for stream dwelling fishes. Paratya australiensis is a cryptic species complex consisting of 9 highly divergent mitochondrial DNA lineages. Among them, one lineage has been observed to favour upstream sites at higher altitudes, with cooler water temperatures. This study aims to identify local adaptation in upstream and downstream populations of this lineage in three streams in the Conondale Range, North-eastern Brisbane, Queensland, Australia. Two populations (up and down stream) from each stream have been chosen to test for local adaptation, and a parallel pattern of adaptation is expected across all streams. Six populations each consisting of 24 individuals were sequenced using the Restriction Site Associated DNA-seq (RAD-seq) technique. Genetic markers (SNPs) were developed using double digest RAD sequencing (ddRAD-seq). These were used for de novo assembly of Paratya genome. De novo assembly was done using the STACKs program and produced 56, 344 loci for 47 individuals from one stream. Among these individuals, 39 individuals shared 5819 loci, and these markers are being used to test for local adaptation using Fst outlier tests (Arlequin) and Bayesian analysis (BayeScan) between up and downstream populations. Fst outlier test detected 27 loci likely to be under selection and the Bayesian analysis also detected 27 loci as under selection. Among these 27 loci, 3 loci showed evidence of selection at a significance level using BayeScan program. On the other hand, up and downstream populations are strongly diverged at neutral loci with a Fst =0.37. Similar analysis will be done with all six populations to determine if there is a parallel pattern of adaptation across all streams. Furthermore, multi-locus among population covariance analysis will be done to identify potential markers under selection as well as to compare single locus versus multi-locus approaches for detecting local adaptation. Adaptive genes identified in this study can be used for future studies to design primers and test for adaptation in related crustacean species.

Keywords: Paratya australiensis, rainforest streams, selection, single nucleotide polymorphism (SNPs)

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Authors: Otuwose E. Agyeno, Adeniyi A. Jayeola, Bashir A. Ajala

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P. esculentus is indigenous to Nigeria yet no wild relation has been encountered or reported. This has made it difficult to establish proper lineages between the varieties and landraces under cultivation. The present work is the first to determine the apormophy of 135 morphoanatomical characters in organs of 46 accessions drawn from 23 populations of this species based on dicta. The character states were coded in accession x character-state matrices and only 83 were informative and utilised for neighbour joining clustering based on euclidean values, and heuristic search in parsimony analysis using PAST ver. 3.15 software. Compatibility and evolutionary trends between accessions were then explored from values and diagrams produced. The low consistency indices (CI) recorded support monophyly and low homoplasy in this taxon. Agglomerative schedules based on character type and source data sets divided the accessions into mainly 3 clades, each of complexes of accessions. Solenostemon rotundifolius (Poir) J.K Morton was the outgroup (OG) used, and it occurred within the largest clades except when the characters were combined in a data set. The OG showed better compatibility with accessions of populations of landrace Isci, and varieties Riyum and Long’at. Otherwise, its aerial parts are more consistent with those of accessions of variety Bebot. The highly polytomous clades produced due to anatomical data set may be an indication of how stable such characters are in this species. Strict consensus trees with more than 60 nodes outputted showed that the basal nodes were strongly supported by 3 to 17 characters across the data sets, suggesting that populations of this species are more alike. The OG was clearly the first diverging lineage and closely related to accessions of landrace Gwe and variety Bebot morphologically, but different from them anatomically. It was also distantly related to landrace Fina and variety Long’at in terms of root, stem and leaf structural attributes. There were at least 5 other clades with each comprising of complexes of accessions from different localities and terrains within the study area. Spherical stem in cross section, size of vascular bundles at the stem corners as well as the alternate and whorl phyllotaxy are attributes which may have facilitated each other’s evolution in all accessions of the landrace Gwe, and they may be innovative since such states are not characteristic of the larger Lamiaceae, and Plectranthus L’Her in particular. In conclusion, this study has provided valuable information about infraspecific diversity in this taxon. It supports recognition of the varietal statuses accorded to populations of P. esculentus, as well as the hypothesis that the wild gene might have been distributed on the Jos Plateau. However, molecular characterisation of accessions of populations of this species would resolve this problem better.

Keywords: clustering, lineage, morphoanatomical characters, Nigeria, phylogenetics, Plectranthus esculentus, population

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Authors: Preetinder Kaur Randhawa

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The rural areas can be differentiated from urban areas in terms of their economic activities as rural areas are primarily involved in agricultural sector and provide natural resources whereas, urban areas are primarily involved in infrastructure sector and provide manufacturing services. Census of India defines a Census Town as an area which satisfies the following three criteria i.e. population exceeds 5000, at least 75 percent of male population engaged in non-agricultural sector and minimum population density of 400 persons per square kilometers. Urban areas can be attributed to the improvement of transport facilities, the massive decline in agricultural, especially male workers and workers shift to non-agricultural activities. This study examines the pattern, process of rural areas transformed into urban areas/ census town. The study has analyzed the various factors which are responsible for land transformation as well as the socio-economic transformation of the village population. Nilpur (CT) which belongs to Rajpura Tehsil in Patiala district, Punjab has been selected for the present study. The methodology adopted includes qualitative and quantitative research design, methods based on secondary data. Secondary data has been collected from unpublished revenue record office of Rajpura Tehsil and Primary Census Abstract of Patiala district, Census of India 2011. The results have showed that rate of transformation of a village to census town in Rajpura Tehsil has been one of highest among other villages. The census town has evolved through the evolutionary process of human settlement which grows in size, population and physical development. There must be a complete economic transformation and attainment of high level of technological development. Urban design and construction of buildings and infrastructure can be carried out better and faster and can be used to aid human habitation with the enhancement of quality of life. The study has concluded that in the selected area i.e Nilpur (CT) literacy rate has increased to 72.1 percent in year 2011 from 67.6 percent in year 2001. Similarly non-agricultural work force has increased to 95.2 percent in year 2011 from 81.1 percent in year 2001. It is very much clear that the increased literacy rate has put a positive impact on the involvement of non-agricultural workers have enhanced. The study has concluded that rural-urban linkages are important tools for understanding complexities of people livelihood and their strategies which involve mobility migration and the diversification of income sources and occupations.

Keywords: Census Town, India, Nilpur, Punjab

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Authors: Tatjana Stefanovic Stanojevic, Milica Tosic Radev, Aleksandra Bogdanovic

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Depression is considered to be a leading cause of death and disability in the female population, and that is the reason why understanding the dynamics of the onset of depressive symptomatology is important. A review of the literature indicates the relationship between depressive symptoms and insecure attachment patterns, but very few studies have examined the mechanism underlying this relation. The aim of the study was to examine the pathway from the preoccupied attachment pattern to depressive symptomatology, as well as to test the mediation effect of mentalization, social anxiety and rumination in this relationship using a serial mediation model. The research was carried out on a geographical cluster sample from the general population of Serbia included within the project ‘Indicators and models of family and work roles harmonization’ funded by the Ministry of Education, Science and Technological Development of the Republic of Serbia. This research was carried out on a subsample of 791 working-age female adults from 37 urban and rural locations distributed through 20 administrative districts of Serbia. The respondents filled in a battery of instruments, including Relationship Questionnaire - Clinical Version (RQ - CV), The Mentalization Scale (MentS), Scale of Social Anxiety (SA), Patient Ruminative Thought Style Questionnaire (RTSQ), Health Questionnaire (PHQ-9). The results confirm our assumption that the total indirect effect of the preoccupied attachment pattern to depressive symptoms is significant across all mediators separately. More importantly, this effect is still present in a model with a sequential mediator relationship, where social anxiety, rumination, and mentalization were perceived as serial mediators of a relationship between preoccupied attachment and depressive symptoms (estimated indirect effect=0.004, boot-strapped 95% CI=0.002 to 0.007). Our findings suggest that there is a significant specific indirect effect of the preoccupied attachment pattern to depressive symptoms, occurring through mentalization, social anxiety and rumination, indicating that preoccupied attachment cause decrease of a self related mentalization, which in turn causes increasing of social anxiety and rumination, concluding in depressive symptoms as a final consequence. The finding that the path from the preoccupied attachment pattern to depressive symptoms is typical in women is understandable from the perspective of both evolutionary and culturally conditioned gender differences. The practical implications of the study are reflected in the recommendations for the prevention and forehand psychotherapy response among preoccupied women with depressive symptomatology. Treatment of this specific group of depressed patients should be focused on strengthening mentalization, learning to accept and to understand herself better, reducing anxiety in situations where mistakes are visible to others, and replacing the rumination strategy with more constructive coping strategies.

Keywords: preoccupied attachment, depression, serial mediation model, mentalization, rumination

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Authors: Mohamed Fawzy Elzarei, Yousef Mohammed Al-Dakheel, Ali Mohamed Alseaf

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Modern molecular techniques, like single marker analysis for linked traits to these markers, can provide us with rapid and accurate genetic results. In the last two decades of the last century, the applications of molecular techniques were reached a faraway point in cattle, sheep, and pig. In goats, especially in our region, the application of molecular techniques is still far from other species. As reported by many researchers, microsatellites marker is one of the suitable markers for lie studies. The single marker linked to traits of interest is one technique allowed us to early select animals without the necessity for mapping the entire genome. Simplicity, applicability, and low cost of this technique gave this technique a wide range of applications in many areas of genetics and molecular biology. Also, this technique provides a useful approach for evaluating genetic differentiation, particularly in populations that are poorly known genetically. The expected breeding value (EBV) and yield deviation (YD) are considered as the most parameters used for studying the linkage between quantitative characteristics and molecular markers, since these values are raw data corrected for the non-genetic factors. A total of 17 microsatellites markers (from chromosomes 6, 14, 18, 20 and 23) were used in this study to search for areas that could be responsible for genetic variability for some milk traits and search of chromosomal regions that explain part of the phenotypic variance. Results of single-marker analyses were used to identify the linkage between microsatellite markers and variation in EBVs of these traits, Milk yield, Protein percentage, Fat percentage, Litter size and weight at birth, and litter size and weight at weaning. The estimates of the parameters from forward and backward solutions using stepwise regression procedure on milk yield trait, only two markers, OARCP9 and AGLA29, showed a highly significant effect (p≤0.01) in backward and forward solutions. The forward solution for different equations conducted that R2 of these equations were highly depending on only two partials regressions coefficient (βi,) for these markers. For the milk protein trait, four marker showed significant effect BMS2361, CSSM66 (p≤0.01), BMS2626, and OARCP9 (p≤0.05). By the other way, four markers (MCM147, BM1225, INRA006, andINRA133) showed highly significant effect (p≤0.01) in both backward and forward solutions in association with milk fat trait. For both litter size at birth and at weaning traits, only one marker (BM143(p≤0.01) and RJH1 (p≤0.05), respectively) showed a significant effect in backward and forward solutions. The estimates of the parameters from forward and backward solution using stepwise regression procedure on litter weight at birth (LWB) trait only one marker (MCM147) showed highly significant effect (p≤0.01) and two marker (ILSTS011, CSSM66) showed a significant effect (p≤0.05) in backward and forward solutions.

Keywords: microsatellites marker, estimated breeding value, stepwise regression, milk traits

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Authors: Debjit Ray

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Horizontal gene transfer (HGT) and recombination leads to the emergence of bacterial antibiotic resistance and pathogenic traits. HGT events can be identified by comparing a large number of fully sequenced genomes across a species or genus, define the phylogenetic range of HGT, and find potential sources of new resistance genes. In-depth comparative phylogenomics can also identify subtle genome or plasmid structural changes or mutations associated with phenotypic changes. Comparative phylogenomics requires that accurately sequenced, complete and properly annotated genomes of the organism. Assembling closed genomes requires additional mate-pair reads or “long read” sequencing data to accompany short-read paired-end data. To bring down the cost and time required of producing assembled genomes and annotating genome features that inform drug resistance and pathogenicity, we are analyzing the performance for genome assembly of data from the Illumina NextSeq, which has faster throughput than the Illumina HiSeq (~1-2 days versus ~1 week), and shorter reads (150bp paired-end versus 300bp paired end) but higher capacity (150-400M reads per run versus ~5-15M) compared to the Illumina MiSeq. Bioinformatics improvements are also needed to make rapid, routine production of complete genomes a reality. Modern assemblers such as SPAdes 3.6.0 running on a standard Linux blade are capable in a few hours of converting mixes of reads from different library preps into high-quality assemblies with only a few gaps. Remaining breaks in scaffolds are generally due to repeats (e.g., rRNA genes) are addressed by our software for gap closure techniques, that avoid custom PCR or targeted sequencing. Our goal is to improve the understanding of emergence of pathogenesis using sequencing, comparative genomics, and machine learning analysis of ~1000 pathogen genomes. Machine learning algorithms will be used to digest the diverse features (change in virulence genes, recombination, horizontal gene transfer, patient diagnostics). Temporal data and evolutionary models can thus determine whether the origin of a particular isolate is likely to have been from the environment (could it have evolved from previous isolates). It can be useful for comparing differences in virulence along or across the tree. More intriguing, it can test whether there is a direction to virulence strength. This would open new avenues in the prediction of uncharacterized clinical bugs and multidrug resistance evolution and pathogen emergence.

Keywords: genomics, pathogens, genome assembly, superbugs

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Authors: E. Calil, L. A. Pereira

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The acquisition of orthography is a complex process, involving both lexical and grammatical questions. This learning occurs simultaneously with the domain of multiple textual aspects (e.g.: graphs, punctuation, etc.). However, most of the research on orthographic acquisition focus on this acquisition from an autonomous point of view, separated from the process of textual production. This means that their object of analysis is the production of words selected by the researcher or the requested sentences in an experimental and controlled setting. In addition, the analysis of the Spelling Problems (SP) are identified by the researcher on the sheet of paper. Considering the perspective of Textual Genetics, from an enunciative approach, this study will discuss the SPs recognized by dyads of newly literate students, while they are writing a text collaboratively. Six proposals of textual production were registered, requested by a 2nd year teacher of a Portuguese Primary School between January and March 2015. In our case study we discuss the SPs recognized by the dyad B and L (7 years old). We adopted as a methodological tool the Ramos System audiovisual record. This system allows real-time capture of the text in process and of the face-to-face dialogue between both students and their teacher, and also captures the body movements and facial expressions of the participants during textual production proposals in the classroom. In these ecological conditions of multimodal registration of collaborative writing, we could identify the emergence of SP in two dimensions: i. In the product (finished text): SP identification without recursive graphic marks (without erasures) and the identification of SPs with erasures, indicating the recognition of SP by the student; ii. In the process (text in progress): identification of comments made by students about recognized SPs. Given this, we’ve analyzed the comments on identified SPs during the text in progress. These comments characterize a type of reformulation referred to as Commented Oral Erasure (COE). The COE has two enunciative forms: Simple Comment (SC) such as ' 'X' is written with 'Y' '; or Unfolded Comment (UC), such as ' 'X' is written with 'Y' because...'. The spelling COE may also occur before or during the SP (Early Spelling Recognition - ESR) or after the SP has been entered (Later Spelling Recognition - LSR). There were 631 words entered in the 6 stories written by the B-L dyad, 145 of them containing some type of SP. During the text in progress, the students recognized orally 174 SP, 46 of which were identified in advance (ESRs) and 128 were identified later (LSPs). If we consider that the 88 erasure SPs in the product indicate some form of SP recognition, we can observe that there were twice as many SPs recognized orally. The ESR was characterized by SC when students asked their colleague or teacher how to spell a given word. The LSR presented predominantly UC, verbalizing meta-orthographic arguments, mostly made by L. These results indicate that writing in dyad is an important didactic strategy for the promotion of metalinguistic reflection, favoring the learning of spelling.

Keywords: collaborative writing, erasure, learning, metalinguistic awareness, spelling, text production

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Authors: Miguel Angel Calvo Salve

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This qualitative and quantitative study will identify the impact of tourism pressure on the intangible cultural heritage of the pilgrim route of El Camino de Santiago (Saint James Way) and propose an approach to a sustainable touristic model for these Cultural Routes. Since 1993, the Spanish Section of the Pilgrim Route of El Camino de Santiago has been on the World Heritage List. In 1994, the International Committee on Cultural Routes (CIIC-ICOMOS) initiated its work with the goal of studying, preserving, and promoting the cultural routes and their significance as a whole. Another ICOMOS group, the Charter on Cultural Routes, pointed out in 2008 the importance of both tangible and intangible heritage and the need for a holistic vision in preserving these important cultural assets. Tangible elements provide a physical confirmation of the existence of these cultural routes, while the intangible elements serve to give sense and meaning to it as a whole. Intangible assets of a Cultural Route are key to understanding the route's significance and its associated heritage values. Like many pilgrim routes, the Route to Santiago, as the result of a long evolutionary process, exhibits and is supported by intangible assets, including hospitality, cultural and religious expressions, music, literature, and artisanal trade, among others. A large increase in pilgrims walking the route, with very different aims and tourism pressure, has shown how the dynamic links between the intangible cultural heritage and the local inhabitants along El Camino are fragile and vulnerable. Economic benefits for the communities and population along the cultural routes are commonly fundamental for the micro-economies of the people living there, substituting traditional productive activities, which, in fact, modifies and has an impact on the surrounding environment and the route itself. Consumption of heritage is one of the major issues of sustainable preservation promoted with the intention of revitalizing those sites and places. The adaptation of local communities to new conditions aimed at preserving and protecting existing heritage has had a significant impact on immaterial inheritance. Based on questionnaires to pilgrims, tourists and local communities along El Camino during the peak season of the year, and using official statistics from the Galician Pilgrim’s Office, this study will identify the risk and threats to El Camino de Santiago as a Cultural Route. The threats visible nowadays due to the impact of mass tourism include transformations of tangible heritage, consumerism of the intangible, changes of local activities, loss in the authenticity of symbols and spiritual significance, and pilgrimage transformed into a tourism ‘product’, among others. The study will also approach some measures and solutions to mitigate those impacts and better preserve this type of cultural heritage. Therefore, this study will help the Route services providers and policymakers to better preserve the Cultural Route as a whole to ultimately improve the satisfying experience of pilgrims.

Keywords: cultural routes, El Camino de Santiago, impact of tourism, intangible heritage

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Authors: K. H. Reeta, Bhavana Prasher, Mitali Mukerji, Dhwani Dholakia, Sangeeta Khanna, Archana Vats, Shivam Pandey, Sandeep Seth, Subir Kumar Maulik

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Introduction Research has demonstrated a connection between coronary artery disease (CAD) and genetics. We did a deep literature mining using both bioinformatics and manual efforts to identify the susceptible polymorphisms in coronary artery disease. Further, the study sought to validate these findings in an Asian population. Methodology In first phase, we used an automated pipeline which organizes and presents structured information on SNPs, Population and Diseases. The information was obtained by applying Natural Language Processing (NLP) techniques to approximately 28 million PubMed abstracts. To accomplish this, we utilized Python scripts to extract and curate disease-related data, filter out false positives, and categorize them into 24 hierarchical groups using named Entity Recognition (NER) algorithms. From the extensive research conducted, a total of 466 unique PubMed Identifiers (PMIDs) and 694 Single Nucleotide Polymorphisms (SNPs) related to coronary artery disease (CAD) were identified. To refine the selection process, a thorough manual examination of all the studies was carried out. Specifically, SNPs that demonstrated susceptibility to CAD and exhibited a positive Odds Ratio (OR) were selected, and a final pool of 324 SNPs was compiled. The next phase involved validating the identified SNPs in DNA samples of 96 CAD patients and 37 healthy controls from Indian population using Global Screening Array. ResultsThe results exhibited out of 324, only 108 SNPs were expressed, further 4 SNPs showed significant difference of minor allele frequency in cases and controls. These were rs187238 of IL-18 gene, rs731236 of VDR gene, rs11556218 of IL16 gene and rs5882 of CETP gene. Prior researches have reported association of these SNPs with various pathways like endothelial damage, susceptibility of vitamin D receptor (VDR) polymorphisms, and reduction of HDL-cholesterol levels, ultimately leading to the development of CAD. Among these, only rs731236 had been studied in Indian population and that too in diabetes and vitamin D deficiency. For the first time, these SNPs were reported to be associated with CAD in Indian population. Conclusion: This pool of 324 SNP s is a unique kind of resource that can help to uncover risk associations in CAD. Here, we validated in Indian population. Further, validation in different populations may offer valuable insights and contribute to the development of a screening tool and may help in enabling the implementation of primary prevention strategies targeted at the vulnerable population.

Keywords: coronary artery disease, single nucleotide polymorphism, susceptible SNP, bioinformatics

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