Search results for: ensemble genetic programming

Authors: Sadaf Moeez, Madiha Khalid, Zoya Khalid, Sania Shaheen, Sumbul Khalid

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Background: Inter-individual variation in response to metformin, which has been considered as a first line therapy for T2DM treatment is considerable. In the current study, it was aimed to investigate the impact of two genetic variants Leu125Phe (rs77474263) and Gly64Asp (rs77630697) in gene SLC47A1 on the clinical efficacy of metformin in T2DM Pakistani patients. Methods: The study included 800 T2DM patients (400 metformin responders and 400 metformin non-responders) along with 400 ethnically matched healthy individuals. The genotypes were determined by allele-specific polymerase chain reaction. In-silico analysis was done to confirm the effect of the two SNPs on the structure of genes. Association was statistically determined using SPSS software. Results: Minor allele frequency for rs77474263 and rs77630697 was 0.13 and 0.12. For SLC47A1 rs77474263 the homozygotes of one mutant allele ‘T’ (CT) of rs77474263 variant were fewer in metformin responders than metformin non-responders (29.2% vs. 35.5 %). Likewise, the efficacy was further reduced (7.2% vs. 4.0 %) in homozygotes of two copies of ‘T’ allele (TT). Remarkably, T2DM cases with two copies of allele ‘C’ (CC) had 2.11 times more probability to respond towards metformin monotherapy. For SLC47A1 rs77630697 the homozygotes of one mutant allele ‘A’ (GA) of rs77630697 variant were fewer in metformin responders than metformin non-responders (33.5% vs. 43.0 %). Likewise, the efficacy was further reduced (8.5% vs. 4.5%) in homozygotes of two copies of ‘A’ allele (AA). Remarkably, T2DM cases with two copies of allele ‘G’ (GG) had 2.41 times more probability to respond towards metformin monotherapy. In-silico analysis revealed that these two variants affect the structure and stability of their corresponding proteins. Conclusion: The present data suggest that SLC47A1 Leu125Phe (rs77474263) and Gly64Asp (rs77630697) polymorphisms were associated with the therapeutic response of metformin in T2DM patients of Pakistan.

Keywords: diabetes, T2DM, SLC47A1, Pakistan, polymorphism

Procedia PDF Downloads 157

Authors: Elcin Timur Cakmak, Ayse Oguzlar

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This study presents the results of the tweets sent by Twitter users on social media about the Russia-Ukraine war by bigram and trigram methods. On February 24, 2022, Russian President Vladimir Putin declared a military operation against Ukraine, and all eyes were turned to this war. Many people living in Russia and Ukraine reacted to this war and protested and also expressed their deep concern about this war as they felt the safety of their families and their futures were at stake. Most people, especially those living in Russia and Ukraine, express their views on the war in different ways. The most popular way to do this is through social media. Many people prefer to convey their feelings using Twitter, one of the most frequently used social media tools. Since the beginning of the war, it is seen that there have been thousands of tweets about the war from many countries of the world on Twitter. These tweets accumulated in data sources are extracted using various codes for analysis through Twitter API and analysed by Python programming language. The aim of the study is to find the word sequences in these tweets by the n-gram method, which is known for its widespread use in computational linguistics and natural language processing. The tweet language used in the study is English. The data set consists of the data obtained from Twitter between February 24, 2022, and April 24, 2022. The tweets obtained from Twitter using the #ukraine, #russia, #war, #putin, #zelensky hashtags together were captured as raw data, and the remaining tweets were included in the analysis stage after they were cleaned through the preprocessing stage. In the data analysis part, the sentiments are found to present what people send as a message about the war on Twitter. Regarding this, negative messages make up the majority of all the tweets as a ratio of %63,6. Furthermore, the most frequently used bigram and trigram word groups are found. Regarding the results, the most frequently used word groups are “he, is”, “I, do”, “I, am” for bigrams. Also, the most frequently used word groups are “I, do, not”, “I, am, not”, “I, can, not” for trigrams. In the machine learning phase, the accuracy of classifications is measured by Classification and Regression Trees (CART) and Naïve Bayes (NB) algorithms. The algorithms are used separately for bigrams and trigrams. We gained the highest accuracy and F-measure values by the NB algorithm and the highest precision and recall values by the CART algorithm for bigrams. On the other hand, the highest values for accuracy, precision, and F-measure values are achieved by the CART algorithm, and the highest value for the recall is gained by NB for trigrams.

Keywords: classification algorithms, machine learning, sentiment analysis, Twitter

Procedia PDF Downloads 73

Authors: Martín Pratto Burgos

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The Engineering School of the University of the Republic in Uruguay offers an Introductory Mathematical Course from the second semester of 2019. This course has been designed to assist students in preparing themselves for math courses that are essential for Engineering Degrees, namely Math1, Math2, and Math3 in this research. The research proposes to build a model that can accurately predict the student's activity and academic progress based on their performance in the three essential Mathematical courses. Additionally, there is a need for a model that can forecast the incidence of the Introductory Mathematical Course in the three essential courses approval during the first academic year. The techniques used are Principal Component Analysis and predictive modelling using the Generalised Linear Model. The dataset includes information from 5135 engineering students and 12 different characteristics based on activity and course performance. Two models are created for a type of data that follows a binomial distribution using the R programming language. Model 1 is based on a variable's p-value being less than 0.05, and Model 2 uses the stepAIC function to remove variables and get the lowest AIC score. After using Principal Component Analysis, the main components represented in the y-axis are the approval of the Introductory Mathematical Course, and the x-axis is the approval of Math1 and Math2 courses as well as student activity three years after taking the Introductory Mathematical Course. Model 2, which considered student’s activity, performed the best with an AUC of 0.81 and an accuracy of 84%. According to Model 2, the student's engagement in school activities will continue for three years after the approval of the Introductory Mathematical Course. This is because they have successfully completed the Math1 and Math2 courses. Passing the Math3 course does not have any effect on the student’s activity. Concerning academic progress, the best fit is Model 1. It has an AUC of 0.56 and an accuracy rate of 91%. The model says that if the student passes the three first-year courses, they will progress according to the timeline set by the curriculum. Both models show that the Introductory Mathematical Course does not directly affect the student’s activity and academic progress. The best model to explain the impact of the Introductory Mathematical Course on the three first-year courses was Model 1. It has an AUC of 0.76 and 98% accuracy. The model shows that if students pass the Introductory Mathematical Course, it will help them to pass Math1 and Math2 courses without affecting their performance on the Math3 course. Matching the three predictive models, if students pass Math1 and Math2 courses, they will stay active for three years after taking the Introductory Mathematical Course, and also, they will continue following the recommended engineering curriculum. Additionally, the Introductory Mathematical Course helps students to pass Math1 and Math2 when they start Engineering School. Models obtained in the research don't consider the time students took to pass the three Math courses, but they can successfully assess courses in the university curriculum.

Keywords: machine-learning, engineering, university, education, computational models

Procedia PDF Downloads 93

Authors: Rida Pervaiz, Bushra Allah Rakha, Muhammad Sajjad Ansari, Shamim Akhter, Kainat Waseem, Sumiyyah Zuha, Tooba Javed

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Ring-necked pheasant (Phasianus colchicus) belongs to order Galliformes and family Phasianidae. It has been recognized as the most hunted bird due to its attractive colorful appearance and meat. Loss of habitat and hunting pressure has caused population fluctuations in the native range. Under these circumstances, this species can be conserved by employing ex-situ in vitro conservation techniques. Captive breeding, in combination with semen cryobanking is the most appropriate option to conserve/propagate this species without deteriorating the genetic diversity. Cryopreservation protocols of adequate efficiency are necessary to establish semen cryobanking for a species. Therefore, present study was designed to devise an efficient extender for cryopreservation of ring-necked pheasant semen. For this purpose, a range of extenders (Beltsville Poultry, red fowl, Lake, EK, Tselutin Poultry and Chicken semen extenders) were evaluated for cryopreservation of ring-necked pheasant semen. Semen collected from 10 cocks, diluted in the Beltsville Poultry (BPSE), Red Fowl (RFE), Lake (LE), EK (EKE), Tselutin Poultry (TPE) and Chicken Semen (CSE) extenders and cryopreserved. Glycerol (10%) was added to semen at 4°C, equilibrated for 10 min, filled in 0.5 mL French straws, kept over liquid nitrogen vapors for 10 min, cryopreserved in LN2 and stored. Sperm motility (%), viability (%), live/dead ratio (%), plasma membrane (%) and DNA Integrity (%) were evaluated at post-dilution, post-cooling, post-equilibration and post-thawing stage of cryopreservation. Sperm motility (83.8 ± 3.1; 81.3 ± 3.8; 73.8 ± 2.4; 62.5 ± 1.4), viability (79.0 ± 1.7; 75.5 ± 1.6; 69.5 ± 2.3; 65.5 ± 2.4), live/dead ratio (80.5 ± 5.7; 77.3 ± 4.9; 76.0 ± 2.7; 68.3 ± 2.3), plasma membrane (74.5 ± 2.9; 73.8 ± 3.4; 71.3 ± 2.3; 75.0 ± 3.4) and DNA integrity (78.3 ± 1.7; 73.0 ± 1.2; 68.0 ± 2.0; 63.0 ± 2.5) at all four stages of cryopreservation were recorded higher (P < 0.05) in red fowl extender compared to all experimental extenders. It is concluded that red fowl extender is the best extender for cryopreservation of ring-necked pheasant semen and can be used in establishing cryobank for ex situ conservation.

Keywords: ring-necked pheasant; extenders; cryopreservation; semen quality; DNA integrity

Procedia PDF Downloads 139

Authors: Victor V. Ribeiro, Thais C. Lopes, Rafael A. A. Monteiro

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The Albatroz, Baleia Jubarte, Coral Vivo, Golfinho Rotador and Tamar projects make up the Young Sea Network (YSN), part of the BIOMAR Network, which aims to integrate the environmental youths of the Brazilian coast. For this, three editions of the Young Sea Meeting (YSM) were performed. Seeking to stimulate belonging, self-knowledge, participation, autonomy and youth protagonism, the Albatroz Project hosted the III YSM, in Bertioga (SP), in April 2019 and aimed to collectively plan the meeting. Five pillars of Environmental Education were used: identity, community, dialogue, power to act and happiness, the OCA Method and the Young Educates Young; Young Chooses Young; and One Generation Learns from the Other principals. In December 2018, still in the II YSM, the participatory planning of the III YSM began. Two "representatives" of each group were voluntarily elected to facilitate joint decisions, propose, receive and communicate demands from their groups and coordinators. The Young Albatroz Collective (YAC) facilitated the organization process as a whole. The purpose of the meeting was collectively constructed, answering the following question: "What is the YSM for?". Only two of the five pairs of representatives responded. There was difficulty gathering the young people in each group, because it was the end of the year, with people traveling. Thus, due to the short planning time, the YAC built a pre-programming to be validated by the other groups, defining as the objective of the meeting the strengthening of youth protagonism within the YSN. In the planning process, the YAC held 20 meetings, with 60 hours of face-to-face work, in three months, and two technical visits to the headquarters of the III YSM. The participatory dynamics of consultation, when it occurred, required up to two weeks, evidencing the limits of participation. The project coordinations stated that they were not being included in the process by their young people. There is a need to work more to be able to aloud the participation, developing skills and understanding about its principles. This training must take place in an articulated way between the network, implying the important role of the five projects in jointly developing and implementing educator processes with this objective in a national dimension, but without forgetting the specificities of each young group. Finally, it is worth highlighting the great potential of the III YSM by stimulating the exercise of leading environmental youth in more than 50 young people from Brazilian coast, linked to the YSN, stimulating the learning and mobilization of young people in favor of coastal and marine conservation.

Keywords: Marine Conservation, Environmental Education, Youth, Participation, Planning

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Authors: Rohini Das, Subhasish Das, Smruti Rekha Sahoo, Shagupta Yesmin

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The Paleoproterozoic Kolhan Group (Purana) ensemble constitutes the youngest lithostratigraphic 'outlier' in the Singhbhum Archaean craton. The Kolhan unconformably overlies both the Singhbhum granite and the Iron Ore Group (IOG). Representing a typical sandstone-shale ( +/- carbonates) sequence, the Kolhan is characterized by the development of thin and discontinuous patches of basal conglomerates draped by sandstone beds. The IOG-fault limits the western 'distal' margin of the Kolhan basin showing evidence of passive subsidence subsequent to the initial rifting stage. The basin evolved as a half-graben under the influence of an extensional stress regime. The assumption of a tectonic setting for the NE-SW trending Kolhan basin possibly relates to the basin opening to the E-W extensional stress system that prevailed during the development of the Newer Dolerite dyke. The Paleoproterozoic age of the Kolhan basin is based on the consideration of the conformable stress pattern responsible both for the basin opening and the development of the conjugate fracture system along which the Newer Dolerite dykes intruded the Singhbhum Archaean craton. The Kolhan sandstones show progressive change towards greater textural and mineralogical maturity in its upbuilding. The trend of variations in different mineralogical and textural attributes, however, exhibits inflections at different lithological levels. Petrological studies collectively indicate that the sandstones were dominantly derived from a weathered granitic crust under a humid climatic condition. Provenance-derived variations in sandstone compositions are therefore a key in unraveling regional tectonic histories. The basin axis controlled the progradation direction which was likely driven by climatically induced sediment influx, a eustatic fall, or both. In the case of the incongruent shift, increased sediment supply permitted the rivers to cross the basinal deep. Temporal association of the Kolhan with tectonic structures in the belt indicates that syn-tectonic thrust uplift, not isostatic uplift or climate, caused the influx of quartz. The sedimentation pattern in the Kolhan reflects a change from braided fluvial-ephemeral pattern to a fan-delta-lacustrine type. The channel geometries and the climate exerted a major control on the processes of sediment transfer. Repeated fault controlled uplift of the source followed by subsidence and forced regression, generated multiple sediment cyclicity that led to the fluvial-fan delta sedimentation pattern. Intermittent uplift of the faulted blocks exposed fresh bedrock to mechanical weathering that generated a large amount of detritus and resulted to forced regressions, repeatedly disrupting the cycles which may reflect a stratigraphic response of connected rift basins at the early stage of extension. The marked variations in the thickness of the fan delta succession and the stacking pattern in different measured profiles reflect the overriding tectonic controls on fan delta evolution. The accumulated fault displacement created higher accommodation and thicker delta sequences. Intermittent uplift of fault blocks exposed fresh bedrock to mechanical weathering, generated a large amount of detritus, and resulted in forced closure of the land-locked basin, repeatedly disrupting the fining upward pattern. The control of source rock lithology or climate was of secondary importance to tectonic effects. Such a retrograding fan delta could be a stratigraphic response of connected rift basins at the early stage of extension.

Keywords: Kolhan basin, petrology, sandstone, tectonics

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Authors: Sher Mohammed, Purushottam Lal, Pawan K. Kasera

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The Thar Desert of Rajasthan covers a wide geographical area spreading between 23.3° to 30.12°, North latitude and 69.3◦ to 76◦ Eastern latitudes; having a unique spectrum of arid zone vegetation. This desert is spreading over 12 districts having a rich source of economically important/threatened plant diversity interacting and growing with adverse climatic conditions of the area. Due to variable geological, physiographic, climatic, edaphic and biotic factors, the arid zone medicinal flora exhibit a wide collection of angiosperm families. The herbal diversity of this arid region is medicinally important in household remedies among tribal communities as well as in traditional systems. The on-going increasing disturbances in natural ecosystems are due to climatic and biological, including anthropogenic factors. The unique flora and subsequently dependent faunal diversity of the desert ecosystem is losing its biotic potential. A large number of plants have no future unless immediate steps are taken to arrest the causes, leading to their biological improvement. At present the potential loss in ecological amplitude of various genera and species is making several plant species as red listed plants of arid zone vegetation such as Commmiphora wightii, Tribulus rajasthanensis, Calligonum polygonoides, Ephedra foliata, Leptadenia reticulata, Tecomella undulata, Blepharis sindica, Peganum harmala, Sarcostoma vinimale, etc. Mostly arid zone species are under serious pressure against prevailing ecosystem factors to continuation their life cycles. Genetic, molecular, cytological, biochemical, metabolic, reproductive, germination etc. are the several points where the floral diversity of the arid zone area is facing severe ecological influences. So, there is an urgent need to conserve them. There are several opportunities in the field to carry out remarkable work at particular levels to protect the native plants in their natural habitat instead of only their in vitro multiplication.

Keywords: ecology, evaluation, xerophytes, economically, threatened plants, conservation

Procedia PDF Downloads 266

Authors: Lorico D. S. Lapitan Jr., Yihan Xu, Yuan Guo, Dejian Zhou

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The ability of ultrasensitive detection of specific genes and discrimination of single nucleotide polymorphisms is important for clinical diagnosis and biomedical research. Herein, we report the development of a new ultrasensitive approach for label-free DNA detection using magnetic nanoparticle (MNP) assisted rapid target capture/separation in combination with signal amplification using poly-enzyme tagged polymer nanobead. The sensor uses an MNP linked capture DNA and a biotin modified signal DNA to sandwich bind the target followed by ligation to provide high single-nucleotide polymorphism discrimination. Only the presence of a perfect match target DNA yields a covalent linkage between the capture and signal DNAs for subsequent conjugation of a neutravidin-modified horseradish peroxidase (HRP) enzyme through the strong biotin-nuetravidin interaction. This converts each captured DNA target into an HRP which can convert millions of copies of a non-fluorescent substrate (amplex red) to a highly fluorescent product (resorufin), for great signal amplification. The use of polymer nanobead each tagged with thousands of copies of HRPs as the signal amplifier greatly improves the signal amplification power, leading to greatly improved sensitivity. We show our biosensing approach can specifically detect an unlabeled DNA target down to 10 aM with a wide dynamic range of 5 orders of magnitude (from 0.001 fM to 100.0 fM). Furthermore, our approach has a high discrimination between a perfectly matched gene and its cancer-related single-base mismatch targets (SNPs): It can positively detect the perfect match DNA target even in the presence of 100 fold excess of co-existing SNPs. This sensing approach also works robustly in clinical relevant media (e.g. 10% human serum) and gives almost the same SNP discrimination ratio as that in clean buffers. Therefore, this ultrasensitive SNP biosensor appears to be well-suited for potential diagnostic applications of genetic diseases.

Keywords: DNA detection, polymer beads, signal amplification, single nucleotide polymorphisms

Procedia PDF Downloads 248

Authors: Samrawit Tamrat Gebretsadik

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Recurrent wheezing is a common respiratory symptom among children, often indicative of underlying airway inflammation and hyperreactivity. Understanding the prevalence and associated factors of recurrent wheezing in specific age groups is crucial for targeted interventions and improved respiratory health outcomes. This study aimed to investigate the prevalence and associated factors of recurrent wheezing among 6-year-old children attending Adama Comprehensive Specialized Hospital Medical College in Ethiopia. A cross-sectional study design was employed, involving structured interviews with parents/guardians, medical records review, and clinical examination of children. Data on demographic characteristics, environmental exposures, family history of respiratory diseases, and socioeconomic status were collected. Logistic regression analysis was used to identify factors associated with recurrent wheezing. The study included X 6-year-old children, with a prevalence of recurrent wheezing found to be Y%. Environmental exposures, including tobacco smoke exposure (OR = Z, 95% CI: X-Y), indoor air pollution (OR = Z, 95% CI: X-Y), and presence of pets at home (OR = Z, 95% CI: X-Y), were identified as significant risk factors for recurrent wheezing. Additionally, a family history of asthma or allergies (OR = Z, 95% CI: X-Y) and low socioeconomic status (OR = Z, 95% CI: X-Y) were associated with an increased likelihood of recurrent wheezing. The impact of recurrent wheezing on the quality of life of affected children and their families was also assessed. Children with recurrent wheezing experienced a higher frequency of respiratory symptoms, increased healthcare utilization, and decreased physical activity compared to their non-wheezing counterparts. In conclusion, recurrent wheezing among 6-year-old children attending Adama Comprehensive Specialized Hospital Medical College is associated with various environmental, genetic, and socioeconomic factors. These findings underscore the importance of targeted interventions aimed at reducing exposure to known triggers and improving respiratory health outcomes in this population. Future research should focus on longitudinal studies to further elucidate the causal relationships between risk factors and recurrent wheezing and evaluate the effectiveness of preventive strategies.

Keywords: wheezing, inflammation, respiratory, crucial

Procedia PDF Downloads 51

Authors: Abraham Castellanos, Christophe Durville, Sophie Echenim

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In this article, a portfolio optimization problem is performed in a Solvency II context: it illustrates how advanced optimization techniques can help to tackle complex operational pain points around the monitoring, control, and stability of Solvency Capital Requirement (SCR). The market SCR of a portfolio is calculated as a combination of SCR sub-modules. These sub-modules are the results of stress-tests on interest rate, equity, property, credit and FX factors, as well as concentration on counter-parties. The market SCR is non convex and non differentiable, which does not make it a natural optimization criteria candidate. In the SCR formulation, correlations between sub-modules are fixed, whereas risk-driven portfolio allocation is usually driven by the dynamics of the actual correlations. Implementing a portfolio construction approach that is efficient on both a regulatory and economic standpoint is not straightforward. Moreover, the challenge for insurance portfolio managers is not only to achieve a minimal SCR to reduce non-invested capital but also to ensure stability of the SCR. Some optimizations have already been performed in the literature, simplifying the standard formula into a quadratic function. But to our knowledge, it is the first time that the standard formula of the market SCR is used in an optimization problem. Two solvers are combined: a bundle algorithm for convex non- differentiable problems, and a BFGS (Broyden-Fletcher-Goldfarb- Shanno)-SQP (Sequential Quadratic Programming) algorithm, to cope with non-convex cases. A market SCR minimization is then performed with historical data. This approach results in significant reduction of the capital requirement, compared to a classical Markowitz approach based on the historical volatility. A comparative analysis of different optimization models (equi-risk-contribution portfolio, minimizing volatility portfolio and minimizing value-at-risk portfolio) is performed and the impact of these strategies on risk measures including market SCR and its sub-modules is evaluated. A lack of diversification of market SCR is observed, specially for equities. This was expected since the market SCR strongly penalizes this type of financial instrument. It was shown that this direct effect of the regulation can be attenuated by implementing constraints in the optimization process or minimizing the market SCR together with the historical volatility, proving the interest of having a portfolio construction approach that can incorporate such features. The present results are further explained by the Market SCR modelling.

Keywords: financial risk, numerical optimization, portfolio management, solvency capital requirement

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Authors: C. Flynn, Q. Yuan, C. Reinhardt

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Alzheimer’s Disease (AD) is a progressive neurodegenerative disorder affecting broad areas of the cerebral cortex and hippocampus. More than 95% of AD cases are representative of sporadic AD, where both genetic and environmental risk factors play a role. The main pathological features of AD include the widespread deposition of amyloid-beta and neurofibrillary tau tangles in the brain. The earliest brain pathology related to AD has been defined as hyperphosphorylated soluble tau in the noradrenergic locus coeruleus (LC) neurons, characterized by Braak. However, the cause of this pathology and the ultimate progression of AD is not understood. Increasing research points to a connection between the gut microbiota and the brain, and mounting evidence has shown that there is a bidirectional interaction between the two, known as the gut-brain axis. This axis can allow for bidirectional movement of neuroinflammatory cytokines and pathogenic misfolded proteins, as seen in AD. Prebiotics and probiotics have been shown to have a beneficial effect on gut health and can strengthen the gut-barrier as well as the blood-brain barrier, preventing the spread of these pathogens across the gut-brain axis. Our laboratory has recently established a pretangle tau rat model, in which we selectively express pseudo-phosphorylated human tau (htauE14) in the LC neurons of TH-Cre rats. LC htauE14 produced pathological changes in rats resembling those of the preclinical AD pathology (reduced olfactory discrimination and LC degeneration). In this work, we will investigate the effects of pre/probiotic ingestion on AD behavioral deficits, blood inflammation/cytokines, and various brain markers in our experimental rat model of AD. Rats will be infused with an adeno-associated viral vector containing a human tau gene pseudophosphorylated at 14 sites (common in LC pretangles) into 2-3 month TH-Cre rats. Fecal and blood samples will be taken at pre-surgery, and various post-surgery time points. A collection of behavioral tests will be performed, and immunohistochemistry/western blotting techniques will be used to observe various biomarkers. This work aims to elucidate the relationship between gut health and AD progression by strengthening gut-brain relationship and aims to observe the overall effect on tau formation and tau pathology in AD brains.

Keywords: alzheimer’s disease, aging, gut microbiome, neurodegeneration

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Authors: Sundus Mona, Atif Adnan, Babar Ali, Fareeha Arshad, Allah Rakha

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Molecular diversity is the variation in the abundance of species. Forensic entomology is a neglected field in Pakistan. Insects collected from the crime scene should be handled by forensic entomologists who are currently virtually non-existent in Pakistan. Correct identification of insect specimen along with knowledge of their biodiversity can aid in solving many problems related to complicated forensic cases. Inadequate morphological identification and insufficient thermal biological studies limit the entomological utility in Forensic Medicine. Recently molecular identification of entomological evidence has gained attention globally. DNA barcoding is the latest and established method for species identification. Only proper identification can provide a precise estimation of postmortem intervals. Arthropods are known to be the first tourists scavenging on decomposing dead matter. The objective of the proposed study was to identify species by molecular techniques and analyze their phylogenetic importance with barcoded necrophagous insect species of early succession on human cadavers. Based upon this identification, the study outcomes will be the utilization of established DNA bar codes to identify carrion feeding insect species for concordant estimation of post mortem interval. A molecular identification method involving sequencing of a 658bp ‘barcode’ fragment of the mitochondrial cytochrome oxidase subunit 1 (CO1) gene from collected specimens of unknown dipteral species from cadavers of Lahore was evaluated. Nucleotide sequence divergences were calculated using MEGA 7 and Arlequin, and a neighbor-joining phylogenetic tree was generated. Three species were identified, Chrysomya megacephala, Chrysomya saffranea, and Chrysomya rufifacies with low genetic diversity. The fixation index was 0.83992 that suggests a need for further studies to identify and classify forensically relevant insects in Pakistan. There is an exigency demand for further research especially when immature forms of arthropods are recovered from the crime scene.

Keywords: molecular diversity, DNA barcoding, species identification, forensically relevant

Procedia PDF Downloads 147

Authors: Oluwaseun Adeleke, Samuel O. Ikani, Fidelis Edet, Anthony Nwala, Mopelola Raji, Simeon Christian Chukwu

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Introduction: Digital innovations have been useful in supporting a client’s contraceptive user journey from awareness to method initiation. The concept of contraceptive self-care is being promoted globally as a means for achieving universal access to quality contraceptive care; however, information about this approach is limited. An important determinant of the scale of awareness is the message construct, choice of information channel, and an understanding of the socio-epidemiological dynamics within the target audience. Significant gains have been made recently in expanding the awareness base of DMPA-SC -a relatively new entrant into the family planning method mix. The cornerstone of this success is a multichannel promotion campaign themed Discover your Power (DYP). The DYP campaign combines content marketing across select social media platforms, chatbots, Cyber-IPC, Interactive Voice Response (IVR), and radio campaigns. Methodology: During implementation, the project monitored predefined metrics of awareness and intent, such as the number of persons reached with the messages, the number of impressions, and meaningful engagement (link-clicks). Metrics/indicators are extracted through native insight/analytics tools across the various platforms. The project also enlists community mobilizers (CMs) who go door-to-door and engage WRA to advertise DISC’s online presence and support them to engage with IVR, digital companion (chatbot), Facebook page, and DiscoverYourPower website. Results: The result showed that the digital platforms recorded 242 million impressions and reached 82 million users with key DMPA-SC self-injection messaging in the three countries. As many as 3.4 million persons engaged (liked, clicked, shared, or reposted) digital posts -an indication of intention. Conclusion: Digital solutions and innovations are gradually becoming the archetype for the advancement of the self-care agenda. Digital innovations can also be used to increase awareness and normalize contraceptive self-care behavior amongst women of reproductive age if they are made an integral part of reproductive health programming.

Keywords: digital transformation, health systems, DMPA-SC, family planning, self-care

Procedia PDF Downloads 81

Authors: Lydia Foucan, Laurent Larifla, Emmanuelle Durand, Christine Rambhojan, Veronique Dhennin, Jean-Marc Lacorte, Philippe Froguel, Amelie Bonnefond

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In the population of Guadeloupe Island (472,124 inhabitants and 80% of subjects of African descent), overweight and obesity were estimated at 23% and 9% respectively among children. High prevalence of diabetes has been reported (~10%) in the adult population. Nevertheless, no study has investigated the contribution of gene mutations to childhood obesity in this population. We aimed to investigate rare genetic mutations in genes involved in monogenic obesity or diabetes in obese Afro-Caribbean children from Guadeloupe Island using next-generation sequencing. The present investigation included unrelated obese children, from a previous study on overweight conducted in Guadeloupe Island in 2013. We sequenced coding regions of 59 genes involved in monogenic obesity or diabetes. A total of 25 obese schoolchildren (with Z-score of body mass index [BMI]: 2.0 to 2.8) were screened for rare mutations (non-synonymous, splice-site, or insertion/deletion) in 59 genes. Mean age of the study population was 12.4 ± 1.1 years. Seventeen children (68%) had insulin-resistance (HOMA-IR > 3.16). A family history of obesity (mother or father) was observed in eight children and three of the accompanying parent presented with type 2 diabetes. None of the children had gonadotrophic abnormality or mental retardation. We detected five rare heterozygous mutations, in four genes involved in monogenic obesity, in five different obese children: MC4R p.Ile301Thr and SIM1 p.Val326Thrfs*43 mutations which were pathogenic; SIM1 p.Ser343Pro and SH2B1 p.Pro90His mutations which were likely pathogenic; and NTRK2 p.Leu140Phe that was of uncertain significance. In parallel, we identified seven carriers of mutation in ABCC8 or KCNJ11 (involved in monogenic diabetes), which were of uncertain significance (KCNJ11 p.Val13Met, KCNJ11 p.Val151Met, ABCC8 p.Lys1521Asn and ABCC8 p.Ala625Val). Rare pathogenic or likely pathogenic mutations, linked to severe obesity were detected in more than 15% of this Afro-Caribbean population at high risk of obesity and type 2 diabetes.

Keywords: childhood obesity, MC4R, monogenic obesity, SIM1

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Authors: Ian Campbell, Gillian Mitchell, Paul James, Na Li, Ella Thompson

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The genetic cause of the majority of multiple-case breast cancer families remains unresolved. Next generation sequencing has emerged as an efficient strategy for identifying predisposing mutations in individuals with inherited cancer. We are conducting whole exome sequence analysis of germ line DNA from multiple affected relatives from breast cancer families, with the aim of identifying rare protein truncating and non-synonymous variants that are likely to include novel cancer predisposing mutations. Data from more than 200 exomes show that on average each individual carries 30-50 protein truncating mutations and 300-400 rare non-synonymous variants. Heterogeneity among our exome data strongly suggest that numerous moderate penetrance genes remain to be discovered, with each gene individually accounting for only a small fraction of families (~0.5%). This scenario marks validation of candidate breast cancer predisposing genes in large case-control studies as the rate-limiting step in resolving the missing heritability of breast cancer. The aim of this study is to screen genes that are recurrently mutated among our exome data in a larger cohort of cases and controls to assess the prevalence of inactivating mutations that may be associated with breast cancer risk. We are using the Agilent HaloPlex Target Enrichment System to screen the coding regions of 168 genes in 1,000 BRCA1/2 mutation-negative familial breast cancer cases and 1,000 cancer-naive controls. To date, our interim analysis has identified 21 genes which carry an excess of truncating mutations in multiple breast cancer families versus controls. Established breast cancer susceptibility gene PALB2 is the most frequently mutated gene (13/998 cases versus 0/1009 controls), but other interesting candidates include NPSR1, GSN, POLD2, and TOX3. These and other genes are being validated in a second cohort of 1,000 cases and controls. Our experience demonstrates that beyond PALB2, the prevalence of mutations in the remaining breast cancer predisposition genes is likely to be very low making definitive validation exceptionally challenging.

Keywords: predisposition, familial, exome sequencing, breast cancer

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Authors: Xianming Chen, Yu Lei, Meinan Wang

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The dikaryotic basidiomycete fungus, Puccinia striiformis, causes stripe rust, one of the most important diseases of wheat and barley worldwide. The pathogen is largely reproduced asexually, and asexual recombination has been hypothesized to be one of the mechanisms for the pathogen variations. To test the hypothesis and understand the genetic process of asexual recombination, somatic recombinant isolates were obtained under controlled conditions by inoculating susceptible host plants with a mixture of equal quantity of urediniospores of isolates with different virulence patterns and selecting through a series of inoculation on host plants with different genes for resistance to one of the parental isolates. The potential recombinant isolates were phenotypically characterized by virulence testing on the set of 18 wheat lines used to differentiate races of the wheat stripe rust pathogen, P. striiformis f. sp. tritici (Pst), for the combinations of Pst isolates; or on both sets of the wheat differentials and 12 barley differentials for identifying races of the barley stripe rust pathogen, P. striiformis f. sp. hordei (Psh) for combinations of a Pst isolate and a Psh isolate. The progeny and parental isolates were also genotypically characterized with 51 simple sequence repeat and 90 single-nucleotide polymorphism markers. From nine combinations of parental isolates, 68 potential recombinant isolates were obtained, of which 33 (48.5%) had similar virulence patterns to one of the parental isolates, and 35 (51.5%) had virulence patterns distinct from either of the parental isolates. Of the 35 isolates of distinct virulence patterns, 11 were identified as races that had been previously detected from natural collections and 24 were identified as new races. The molecular marker data confirmed 66 of the 68 isolates as recombinants. The percentages of parental marker alleles ranged from 0.9% to 98.9% and were significantly different from equal proportions in the recombinant isolates. Except for a couple of combinations, the greater or less contribution was not specific to any particular parental isolates as the same parental isolates contributed more to some of the progeny isolates but less to the other progeny isolates in the same combination. The unequal contributions by parental isolates appear to be a general role in somatic recombination for the stripe rust fungus, which may be used to distinguish asexual recombination from sexual recombination in studying the evolutionary mechanisms of the highly variable fungal pathogen.

Keywords: molecular markers, Puccinia striiformis, somatic recombination, stripe rust

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Authors: Ngoc-Hieu Vu

Abstract:

Although dairy production in Vietnam is a relatively new agricultural activity, milk production increased remarkably in recent years. Smallholders are still the main drivers for this development, especially in the southern part of the country. However, information on the farming practices is very limited. Therefore, this study aimed to characterize husbandry practices, educational experiences, decision-making practices, constraints, income and expenses of smallholder dairy farms in Southern Vietnam. A total of 200 farms, located in the regions Ho Chi Minh (HCM, N=80 farms), Lam Dong (N=40 farms), Binh Duong (N=40 farms) and Long An (N=40 farms) were included. Between October 2013 and December 2014 farmers were interviewed twice. On average, farms owned 3.200m2, 2.000m2, and 193m2 of pasture, cropping and housing area, respectively. The number of total, milking and dry cows, heifers, and calves were 20.4, 11.6, 4.7, 3.3, and 2.9 head. The number of lactating dairy cows was higher (p<0.001) in HCM (15.5) and Lam Dong (14.7) than in Binh Duong (6.7) and Long An (10.7). Animals were mainly crossbred Holstein-Friesian (HF) cows with at least 75% HF origin (84%), whereas a higher (P<0.001) percentage of purebred HF was found in HCM and Lam Dong and crossbreds in Binh Duong and Long An. Animals were mainly raised in tie-stalls (94%) and machine-milked (80%). Farmers used their own replacement animals (76%), and both genetic and phenotypic information (67%) for selecting sires. Farmers were predominantly educated at primary school level (53%). Major constraints for dairy farming were the lack of capital (43%), diseases (17%), marketing (22%), lack of knowledge (8%) and feed (7%). Monthly profit per lactating cow was superior in Lam Dong (2,817 thousand VND) and HCM (2,798 thousand VND) compared to other regions in Long An (2,597 thousand VND), and Binh Duong (1,775 thousand VND). Regional differences may be mainly attributed to environmental factors, urbanization, and particularly governmental support and the availability of extension and financial institutions. Results from this study provide important information on farming practices of smallholders in Southern Vietnam that are useful in determining regions that need to be addressed by authorities in order to improve dairy production.

Keywords: dairy farms, milk yield, Southern Vietnam, socio-economics

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Authors: Diwei Lin, Amanda Tan, Rajinder Singh-Rai

Abstract:

We present the first reported case of a concomitant Leydig cell tumor (LCT) and paratesticular leiomyoma in an adult male with a known history of bilateral cryptorchidism. An 80-year-old male presented with a 2-month history of a left testicular lump associated with mild discomfort and a gradual increase in size on a background of bilateral cryptorchidism requiring multiple orchidopexy procedures as a child. Ultrasound confirmed a lesion suspicious for malignancy and he proceeded to a left radical orchidectomy. Histopathological assessment of the left testis revealed a concomitant testicular LCT with malignant features and paratesticular leiomyoma. Leydig cell tumors (LCTs) are the most common pure testicular sex cord-stromal tumors, accounting for up to 3% of all testicular tumors. They can occur at almost any age, but are noted to have a bi-modal distribution, with a peak incidence at 6 to 10 and at 20 to 50 years of age. LCT’s are often hormonally active and can lead to feminizing or virilizing syndromes. LCT’s are usually regarded as benign but can rarely exhibit malignant traits. Paratesticular tumours are uncommon and their reported prevalence varies between 3% and 16%. They occur in a complex anatomical area which includes the contents of the spermatic cord, testicular tunics, epididymis and vestigial remnants. Up to 90% of paratesticular tumours are believed to originate from the spermatic cord, though it is often difficult to definitively ascertain the exact site of origin. Although any type of soft-tissue neoplasm can be found in the paratesticular region, the most common benign tumors reported are lipomas of the spermatic cord, adenomatoid tumours of the epididymis and leiomyomas of the testis. Genetic studies have identified potential mutations that could potentially cause LCTs, but there are no known associations between concomitant LCTs and paratesticular tumors. The presence of cryptorchidism in adults with both LCTs and paratesticular neoplasms individually has been previously reported and it appears intuitive that cryptorchidism is likely to be associated with the concomitant presentation in this case report. This report represents the first documented case in the literature of a unilateral concomitant LCT and paratesticular leiomyoma on a background of bilateral cryptorchidism.

Keywords: testicular cancer, leydig cell tumour, leiomyoma, paratesticular neoplasms

Procedia PDF Downloads 359

Authors: Omar Shafqat, Jaime Arias, Cristian Bogdan, Björn Palm

Abstract:

Heating constitutes a major part of the overall energy consumption in Sweden. In 2013 heating and hot water accounted for about 55% of the total energy use in the housing sector. Historically, the end users have not been able to make a significant impact on their consumption on account of traditional control systems that do not facilitate interaction and control of the heating systems. However, in recent years internet connected home energy management systems have become increasingly available which allow users to visualize the indoor temperatures as well as control the heating system. However, the adoption of these systems is still in its nascent stages. This paper presents the outcome of a study carried out in a community of single-family houses in Stockholm. Heating in the area is provided through district heating, and the neighbourhood is connected through a local micro thermal grid, which is owned and operated by the local community. Heating in the houses is accomplished through a hydronic system equipped with radiators. The system installed offers the households to control the indoor temperature through a mobile application as well as through a physical thermostat. It was also possible to program the system to, for instance, lower the temperatures during night time and when the users were away. The users could also monitor the indoor temperatures through the application. It was additionally possible to create different zones in the house with their own individual programming. The historical heating data (in the form of billing data) was available for several previous years and has been used to perform quantitative analysis for the study after necessary normalization for weather variations. The experiment involved 30 households out of a community of 178 houses. The area was selected due to uniform construction profile in the area. It was observed that despite similar design and construction period there was a large variation in the heating energy consumption in the area which can for a large part be attributed to user behaviour. The paper also presents qualitative analysis done through survey questions as well as a focus group carried out with the participants. Overall, considerable energy savings were accomplished during the trial, however, there was a considerable variation between the participating households. The paper additionally presents recommendations to improve the impact of home energy management systems for heating in terms of improving user engagement and hence the energy impact.

Keywords: energy efficiency in buildings, energy behavior, heating control system, home energy management system

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Authors: Rolivhuwa Bishop Ramagoma1*, Lynn Cairncross1, , Saartjie Roux1

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According to the world health organisation, colon cancer is among the most common cancers diagnosed in both men and women. Specifically, it is the second leading cause of cancer related deaths accounting for over 860 000 deaths worldwide in 2018. Currently, chemotherapy has become an essential component of most cancer treatments. Despite progress in cancer drug development over the previous years, traditional chemotherapeutic drugs still have low selectivity for targeting tumour tissues and are frequently constrained by dose-limiting toxicity. The creation of nanoscale delivery vehicles capable of directly directing treatment into cancer cells has recently caught the interest of researchers. Herein, the development of peptide-functionalized polyethylene glycol gold nanoparticles (Peptide-PEG-AuNPs) as a cellular probe and delivery agent is described, with the higher aim to develop a specific diagnostic prototype and assess their specificity not only against cell lines but primary human cells as well. Gold nanoparticles (AuNPs) were synthesized and stabilized through chemical conjugation. The synthesized AuNPs were characterized, stability in physiological solutions was assessed, their cytotoxicity against colon carcinoma and non-carcinoma skin fibroblasts was also studied. Furthermore, genetic effect through real-time polymerase chain reaction (RT-PCR), localization and uptake, peptide specificity were also determined. In this study, different peptide-AuNPs were found to have preferential toxicity at higher concentrations, as revealed by cell viability assays, however, all AuNPs presented immaculate stability for over 3 months following the method of synthesis. The final obtained peptide-PEG-AuNP conjugates showed good biocompatibility in the presence of high ionic solutions and biological media and good cellular uptake. Formulation of colon cancer specific targeting peptide was successful, additionally, the genes/pathways affected by the treatments were determined through RT-PCR. Primary cells study is still on going with promising results thus far.

Keywords: nanotechnology, cancer, diagnosis, therapeutics, gold nanoparticles.

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Authors: Ahlem Bouziri, Chiraz Latiri, Eric Gaussier

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The steady growth in the size of textual document collections is a key progress-driver for modern information retrieval techniques whose effectiveness and efficiency are constantly challenged. Given a user query, the number of retrieved documents can be overwhelmingly large, hampering their efficient exploitation by the user. In addition, retaining only relevant documents in a query answer is of paramount importance for an effective meeting of the user needs. In this situation, the query expansion technique offers an interesting solution for obtaining a complete answer while preserving the quality of retained documents. This mainly relies on an accurate choice of the added terms to an initial query. Interestingly enough, query expansion takes advantage of large text volumes by extracting statistical information about index terms co-occurrences and using it to make user queries better fit the real information needs. In this respect, a promising track consists in the application of data mining methods to extract dependencies between terms, namely a generic basis of association rules between terms. The key feature of our approach is a better trade off between the size of the mining result and the conveyed knowledge. Thus, face to the huge number of derived association rules and in order to select the optimal combination of query terms from the generic basis, we propose to model the problem as a classification problem and solve it using a supervised learning algorithm such as SVM or k-means. For this purpose, we first generate a training set using a genetic algorithm based approach that explores the association rules space in order to find an optimal set of expansion terms, improving the MAP of the search results. The experiments were performed on SDA 95 collection, a data collection for information retrieval. It was found that the results were better in both terms of MAP and NDCG. The main observation is that the hybridization of text mining techniques and query expansion in an intelligent way allows us to incorporate the good features of all of them. As this is a preliminary attempt in this direction, there is a large scope for enhancing the proposed method.

Keywords: supervised leaning, classification, query expansion, association rules

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Authors: Nadia Naseem, Farwa Batool, Nasir Mehmood, AbdulHannan Nagi

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Background: The incidence and mortality of breast cancer vary significantly in geographically distinct populations. In Pakistan, breast cancer has shown an increase in incidence in young females and is characterized by more aggressive behavior. The tumor suppressor TP53 gene is a crucial genetic factor that plays a significant role in breast carcinogenesis. This study investigated the TP53 mutations in molecular subtypes of both nodes negative and positive breast cancer in young Pakistani patients. Material and Methods: p53, Estrogen Receptor (ER), Progesterone Receptor (PR), Her-2 neu and Ki 67 expressions were analyzed immunohistochemically in a series of 75 node negative (A) and 75 node positive (B) young (aged: 19-40 years) breast cancer patients diagnosed between 2014 to 2017 at two leading hospitals of Punjab, Pakistan. Tumor tissue specimens and peripheral blood samples were examined for TP53 mutations by direct sequencing of the gene (exons 4-9). The relation of TP53 mutations to these markers and clinicopathological data was investigated. Results: Mean age of the patients was 32.4 + 9.1 SD. Invasive breast carcinoma was the most frequent histological variant (A=92%, B=94.6%). Grade 3 carcinoma was the commonest grade (A=72%, B=81.3%). Triple negative cases (ER-, PR-, Her-2) formed most of the molecular subtypes (A=44%, B=50.6%). A total of 17.2% (A: 6.6%, B: 10.6%) patients showed TP53 mutations. Mutations were significantly more frequent in triple negative cases (A: 74.8%, B: 62.2%) compared to HER2-positive patients (P < 0.0001). In the multivariate analysis of the whole patient group, the independent prognosticator were triple negative cases (P=0.021), TP53 overexpression by IHC (P=0.001) and advanced-stage disease (P=0.007). No statistically significant correlation between TP53 mutations and clinicopathological parameters was found (P < 0.05). Conclusions: It is concluded that TP53 mutations are infrequently present in breast carcinoma of young Pakistani population and there was no significant correlation between p53 mutation and early onset disease. Immunohistochemically detected TP53 expression in our resource-constrained to set up can be beneficial in predicting mutations at the younger age in our population.

Keywords: immunohistochemistry (IHC), invasive breast carcinoma (IBC), Pakistan, TP53

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Authors: Kinza Qadeer, Muhammad Abdul Qyyum, Moonyong Lee

Abstract:

Natural gas has become an attractive energy source in comparison with other fossil fuels because of its lower CO₂ and other air pollutant emissions. Therefore, compared to the demand for coal and oil, that for natural gas is increasing rapidly world-wide. The transportation of natural gas over long distances as a liquid (LNG) preferable for several reasons, including economic, technical, political, and safety factors. However, LNG production is an energy-intensive process due to the tremendous amount of power requirements for compression of refrigerants, which provide sufficient cold energy to liquefy natural gas. Therefore, one of the major issues in the LNG industry is to improve the energy efficiency of existing LNG processes through a cost-effective approach that is 'optimization'. In this context, a bio-inspired Krill-herd (KH) step-up approach was examined to enhance the energy efficiency of a single mixed refrigerant (SMR) natural gas liquefaction (LNG) process, which is considered as a most promising candidate for offshore LNG production (FPSO). The optimal design of a natural gas liquefaction processes involves multivariable non-linear thermodynamic interactions, which lead to exergy destruction and contribute to process irreversibility. As key decision variables, the optimal values of mixed refrigerant flow rates and process operating pressures were determined based on the herding behavior of krill individuals corresponding to the minimum energy consumption for LNG production. To perform the rigorous process analysis, the SMR process was simulated in Aspen Hysys® software and the resulting model was connected with the Krill-herd approach coded in MATLAB. The optimal operating conditions found by the proposed approach significantly reduced the overall energy consumption of the SMR process by ≤ 22.5% and also improved the coefficient of performance in comparison with the base case. The proposed approach was also compared with other well-proven optimization algorithms, such as genetic and particle swarm optimization algorithms, and was found to exhibit a superior performance over these existing approaches.

Keywords: energy efficiency, Krill-herd, LNG, optimization, single mixed refrigerant

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Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

Procedia PDF Downloads 158

Authors: Shivankar Agrawal, Sunil Kumar Deshmukh, Colin Barrow, Alok Adholeya

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A variety of genetic and environmental factors cause various cosmetics and dermatological problems. There are already claimed drugs available in market for treating these problems. However, the challenge remains in finding more potent, environmental friendly, causing minimal side effects and economical cosmeceuticals. This leads to an increased demand for natural cosmeceutical products in the last few decades. Plant derived ingredients are limited because plants either contain toxic metabolites, grow too slow or seasonal harvesting is a problem. To identify new bioactive cosmetics ingredients of marine microbial bioresource, we screened 35 marine fungi isolated from marine samples collected from Andaman Island and west coast of India. Fungal crude extracts were investigated for their antityrosinase, antioxidant and antibacterial activities for the purpose of identifying anti-aging, skin-whitening and anti-acne biomolecule with the potential in cosmetics. In the tyrosinase inhibition and 2, 2-Diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging assays, two fungal extracts, including “P2”, Talaromyces stipitatus and “D4”, Aspergillus terreus showed high inhibitory activity at 1mg/mL for tyrosinase inhibition and 0.5mg/mL for DPPH scavenging. The in vitro antimicrobial activity was investigated by the agar well diffusion method. In the tyrosinase inhibition assay, 8 extracts showed significant antibacterial activity against bacteria causing skin and wound infection in humans. In the course of systematic screening program for bioactive marine fungi, strain “D5” was found to be most potent strain with MIC value of 1mg/mL, which was morphologically identified as Simplicillium lamellicola. The effects of the most active crude extracts against their susceptible test microorganisms were also investigated by SEM analysis. Further investigations will focus on purification and characterization major active components responsible for these activities.

Keywords: antioxidant, antimicrobial activity, tyrosinase, cosmeceuticals, marine fungi

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Authors: Vaishali Sharma

Abstract:

The research is an attempt to hunt a scientific and objective method to transform Ajmer's traditional walled city into a living cultural heritage space, exploring urban management methods to elevate local economy and social space in relation to specific cultural-based initiatives. Ajmer is among the oldest and religiously diverse settlements in Rajasthan, that has seen superimposed developments through the eras. With numerous agencies operating towards the development of the town core of Ajmer, it becomes essential to structure development changes in tune with the transformations and the existing heritage. The study was radio-controlled by the subsequent analysis question: What is the way to overcome the genetic social and economic stress inside the communities and revive public life? In order to create necessary interventions at the neighbourhood level, fifteen neighbourhoods were identified. Each of those was analyzed relatively on three major dimensions: Heritage, Social and Local Economy. Each dimension was further broken down into multiple sub-aspects for an overall and exhaustive understanding. The average median values of the responses were used to develop a color-coded matrix to represent the scores in an exceedingly structured quantified manner, moreover, linking it to the spatial structure. Respondent perceptions on numerous dimensions were additionally recorded, so that the proposals are inclusive in nature. The goals are targeted at Ajmer's traditional walled towns, which will make it easier for the community to regulate the rapid transformations and commercialization occurring within the space. The study recommends the necessity for accrued support in methods and policies from the non-public sector, businesses as well as local stakeholders. An expansion, revitalization and maintenance of the major business and heritage corridors, for an increased local and visitor experience, can produce an impetus for promotion of the intangible heritage, to spur the local economic processes, conservation of heritage precincts and upward development.

Keywords: cultural heritage, economic revitalization, neighbourhoods in walled cities, social space, tangible and intangible heritage

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Authors: Hossein Rassi, Marjan Moradi Fard, Masoud Houshmand

Abstract:

Background: Cervical cancer is multistep disease that is thought to result from an interaction between genetic background and environmental factors. Human papillomavirus (HPV) infection is the leading risk factor for cervical intraepithelial neoplasia(CIN)and cervical cancer. In other hand, some of p53 and miRNA polymorphism may plays an important role in carcinogenesis. This study attempts to clarify the relation of p53 genotypes and miR-146a rs2910164 polymorphism in cervical lesions. Method: Forty two archival samples with cervical lesion retired from Khatam hospital and 40 sample from healthy persons used as control group. A simple and rapid method was used to detect the simultaneous amplification of the HPV consensus L1 region and HPV-16,-18, -11, -31, 33 and -35 along with the b-globin gene as an internal control. We use Multiplex PCR for detection of P53 and miR-146a rs2910164 genotypes in our lab. Finally, data analysis was performed using the 7 version of the Epi Info(TM) 2012 software and test chi-square(x2) for trend. Results: Cervix lesions were collected from 42 patients with Squamous metaplasia, cervical intraepithelial neoplasia, and cervical carcinoma. Successful DNA extraction was assessed by PCR amplification of b-actin gene (99bp). According to the results, p53 GG genotype and miR-146a rs2910164 CC genotype was significantly associated with increased risk of cervical lesions in the study population. In this study, we detected 13 HPV 18 from 42 cervical cancer. Conclusion: The connection between several SNP polymorphism and human virus papilloma in rare researches were seen. The reason of these differences in researches' findings can result in different kinds of races and geographic situations and also differences in life grooves in every region. The present study provided preliminary evidence that a p53 GG genotype and miR-146a rs2910164 CC genotype may effect cervical cancer risk in the study population, interacting synergistically with HPV 18 genotype. Our results demonstrate that the testing of p53 codon 72 polymorphism genotypes and miR-146a rs2910164 polymorphism genotypes in combination with HPV18 can serve as major risk factors in the early identification of cervical cancers. Furthermore, the results indicate the possibility of primary prevention of cervical cancer by vaccination against HPV18 in Iran.

Keywords: cervical cancer, p53, miR-146a, rs2910164, polymorphism

Procedia PDF Downloads 467

Authors: Hossein Rassi, Marjan Moradi fard, Masoud Houshmand

Abstract:

Background: Cervical cancer is multistep disease that is thought to result from an interaction between genetic background and environmental factors. Human Papillomavirus (HPV) infection is the leading risk factor for Cervical Intraepithelial Neoplasia (CIN) and cervical cancer. In other hand, some of p53 and miRNA polymorphism may plays an important role in carcinogenesis. This study attempts to clarify the relation of p53 genotypes and miR-146a rs2910164 polymorphism in cervical lesions. Method: Forty two archival samples with cervical lesion retired from Khatam hospital and 40 sample from healthy persons used as control group. A simple and rapid method was used to detect the simultaneous amplification of the HPV consensus L1 region and HPV-16,-18, -11, -31, 33, and -35 along with the b-globin gene as an internal control. We use Multiplex PCR for detection of P53 and miR-146a rs2910164 genotypes in our lab. Finally, data analysis was performed using the 7 version of the Epi Info(TM) 2012 software and test chi-square(x2) for trend. Results: Cervix lesions were collected from 42 patients with Squamous metaplasia, cervical intraepithelial neoplasia, and cervical carcinoma. Successful DNA extraction was assessed by PCR amplification of b-actin gene (99 bp). According to the results, p53 GG genotype and miR-146a rs2910164 CC genotype was significantly associated with increased risk of cervical lesions in the study population. In this study, we detected 13 HPV 18 from 42 cervical cancer. Conclusion: The connection between several SNP polymorphism and human virus papilloma in rare researches were seen. The reason of these differences in researches' findings can result in different kinds of races and geographic situations and also differences in life grooves in every region. The present study provided preliminary evidence that a p53 GG genotype and miR-146a rs2910164 CC genotype may effect cervical cancer risk in the study population, interacting synergistically with HPV 18 genotype. Our results demonstrate that the testing of p53 codon 72 polymorphism genotypes and miR-146a rs2910164 polymorphism genotypes in combination with HPV18 can serve as major risk factors in the early identification of cervical cancers. Furthermore, the results indicate the possibility of primary prevention of cervical cancer by vaccination against HPV18 in Iran.

Keywords: cervical cancer, miR-146a rs2910164 polymorphism, p53 polymorphism, intraepithelial, neoplasia, HPV

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Authors: A. Schuchter, M. Promegger

Abstract:

The outbreak of the COVID-19 pandemic has shown us that online education is so much more than just a cool feature for teachers – it is an essential part of modern teaching. In online math teaching, it is common to use tools to share screens, compute and calculate mathematical examples, while the students can watch the process. On the other hand, flipped classroom models are on the rise, with their focus on how students can gather knowledge by watching videos and on the teacher’s use of technological tools for information transfer. This paper proposes a co-educational teaching approach for coding and engineering subjects with the help of drone-building to spark interest in technology and create a platform for knowledge transfer. The project combines aspects from mathematics (matrices, vectors, shaders, trigonometry), physics (force, pressure and rotation) and coding (computational thinking, block-based programming, JavaScript and Python) and makes use of collaborative-shared 3D Modeling with clara.io, where students create mathematics knowhow. The instructor follows a problem-based learning approach and encourages their students to find solutions in their own time and in their own way, which will help them develop new skills intuitively and boost logically structured thinking. The collaborative aspect of working in groups will help the students develop communication skills as well as structural and computational thinking. Students are not just listeners as in traditional classroom settings, but play an active part in creating content together by compiling a Handbook of Knowledge (called “open book”) with examples and solutions. Before students start calculating, they have to write down all their ideas and working steps in full sentences so other students can easily follow their train of thought. Therefore, students will learn to formulate goals, solve problems, and create a ready-to use product with the help of “reverse engineering”, cross-referencing and creative thinking. The work on drones gives the students the opportunity to create a real-life application with a practical purpose, while going through all stages of product development.

Keywords: flipped classroom, co-creational education, coding, making, drones, co-education, ARCS-model, problem-based learning

Procedia PDF Downloads 118