Search results for: simple sequence repeat (SSR)

Authors: Mohammad Salem Abdullah Al-Hwaiti

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The stratiform copper mineralization of the Burj-Dolomite shale (BDS) formations of deposits shows that the copper mineralization within the BDS occurs as hydrated copper chlorides and carbonates (mainly paratacamite and malachite, respectively), while copper silicates (mainly chrysocolla and planchette) are the major ore minerals in the BDS. Thus, on the basis of the petrographic and field occurrence, three main stages operated during the development of the copper ore in the sandy and shaly lithofacies. During the first stage, amorphous chrysocolla replaced clays, feldspars, and quartz. This stage was followed by the transition from an amorphous phase to a better-crystallized phase, i.e., the formation of planchette and veins from chrysocolla. The third stage was the formation of chrysocolla along fracture planes. Other secondary minerals are pseudomalachite, dioptase, neoticite together with authigenic fluorapatite. Paratacamite and malachite, which are common in the dolomitic lithofacies, are relatively rare in the sandy and silty lithofacies. The Rare Earth Elements (REEs) patterns for the BDS showed three stages in the evolution of the Precambrian–Cambrian copper mineralization system, involving the following: (A) Epigenetic mobilization of Cu-bearing solution with formation Cu-carbonate in dolomite and limestone mineralization and Cu-silicate mineralization in sandstone; (B) Transgression of Cambrian Sea and SSC deposition of Cu-sulphides during dolomite diagenesis in the BDS Formation; continued diagenesis and oxidation leads to the formation of Cu(II) minerals; (C) Erosion and supergene enrichment of Cu in basement rocks. Detrital copper-bearing sediments accumulate in the lower Cambrian clastic sequence.

Keywords: dolomite shale, copper mineralization, REE, Jordan

Procedia PDF Downloads 66

Authors: Aaron Akinloye

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this research focuses on the impact of jungle justice on the emotional health challenges experienced by residents in the Lagos metropolitan city in Nigeria. Jungle justice refers to the practice of individuals taking the law into their own hands and administering punishment without proper legal procedures. The aim of this study is to investigate the influence of jungle justice on the emotional challenges faced by residents in Lagos. The specific objectives of the study are to examine the effects of jungle justice on trauma, pressure, fear, and depression among residents. The study adopts a descriptive survey research design and uses a questionnaire as the research instrument. The population of the study consisted of residents in the three senatorial districts that make up Lagos State. A simple random sampling technique was used to select two Local Government Areas (Yaba and Shomolu) from each of the three senatorial districts of Lagos State. Also, a simple random sampling technique was used to select fifty (50) residents from each of the chosen Local Government Areas to make three hundred (300) residents that formed the sample of the study. Accidental sampling technique is employed to select a sample of 300 residents. Data on the variables of interest is collected using a self-developed questionnaire. The research instrument undergoes validation through face, content, and construct validation processes. The reliability coefficient of the instrument is found to be 0.84. The study reveals that jungle justice significantly influences trauma, pressure, fear, and depression among residents in Lagos metropolitan city. The statistical analysis shows significant relationships between jungle justice and these emotional health challenges (df (298) t= 2.33, p< 0.05; df (298) t= 2.16, p< 0.05; df (298) t= 2.20, p< 0.05; df (298) t= 2.14, p< 0.05). This study contributes to the literature by highlighting the negative effects of jungle justice on the emotional well-being of residents. It emphasizes the importance of addressing this issue and implementing measures to prevent such vigilante actions. Data is collected through the administration of the self-developed questionnaire to the selected residents. The collected data is then analyzed using inferential statistics, specifically mean analysis, to examine the relationships between jungle justice and the emotional health challenges experienced by the residents. The main question addressed in this study is how jungle justice affects the emotional health challenges faced by residents in Lagos metropolitan city. Conclusion: The study concludes that jungle justice has a significant influence on trauma, pressure, fear, and depression among residents. To address this issue, recommendations are made, including the implementation of comprehensive awareness campaigns, improvement of law enforcement agencies, development of support systems for victims, and revision of the legal framework to effectively address jungle justice. Overall, this research contributes to the understanding of the consequences of jungle justice and provides recommendations for intervention to protect the emotional well-being of residents in Lagos metropolitan city.

Keywords: jungle justice, emotional health, depression, anger

Procedia PDF Downloads 58

Authors: A. Keramaris, T. Sawidis, E. Kasapidou, P. Mitlianga

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Although the gastronomy of the Greeks of Pontus is highly prominent, it has not received the same level of scientific analysis as another local cuisine of Greece, that of Crete. As a result, we intended to focus our research on Greek Pontic cuisine to shed light on its unique recipes, food products, and, ultimately, its features. The Greeks of Pontus, who lived for a long time in the northern part (Black Sea Region) of contemporary Turkey and now widely inhabit northern Greece, have one of Greece's most distinguished local cuisines. Despite their gastronomy being simple, it features several inspiring delicacies. It's been a century since they immigrated to Greece, yet their gastronomic culture remains a critical component of their collective identity. As a first step toward comprehending Greek Pontic cuisine, it was attempted to investigate the production of one of its most renowned traditional products, furniko flour. In this project, we targeted residents of Western Macedonia, a province in northern Greece with a large population of descendants of Greeks of Pontus who are primarily engaged in agricultural activities. In this quest, we approached a descendant of the Greeks of Pontus who is involved in the production of furniko flour and who consented to show us the entire process of its production as we participated in it. The furniko flour is made from non-hybrid heirloom corn. It is harvested by hand when the moisture content of the seeds is low enough to make them suitable for roasting. Manual harvesting entails removing the cob from the plant and detaching the husks. The harvested cobs are then roasted for 24 hours in a traditional wood oven. The roasted cobs are then collected and stored in sacks. The next step is to extract the seeds, which is accomplished by rubbing the cobs. The seeds should ideally be ground in a traditional stone hand mill. We end up with aromatic and dark golden furniko flour, which is used to cook havitz. Accompanied by the preparation of the furnikoflour, we also recorded the cooking process of the havitz (a porridge-like cornflour dish). A savory delicacy that is simple to prepare and one of the most delightful dishes in Greek Pontic cuisine. According to the research participant, havitzis a highly nutritious dish due to the ingredients of furniko flour. In addition, he argues that preparing havitz is a great way to bring families together, share stories, and revisit fond memories. In conclusion, this study illustrates the traditional preparation of furnikoflour and its use in various traditional recipes as an initial effort to highlight the elements of Pontic Greek cuisine. As a continuation of the current study, it could be the analysis of the chemical components of the furniko flour to evaluate its nutritional content.

Keywords: furniko flour, greek pontic cuisine, havitz, traditional foods

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Authors: Paola Millare, Nelinda Catherine Pangilinan

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Background and Aim: Cervical cancer is the most commonly diagnosed gynecological malignancy during pregnancy. Owing to the rarity of the disease, and the complexity of all factors that have to be taken into consideration, standardization of treatment is very difficult. Cervical cancer is the second most common malignancy among women. The treatment of cancer during pregnancy is most challenging in the case of cervical cancer, since the pregnant uterus itself is affected. This report aims to present a case of cervical cancer in a pregnant woman and how to manage this case and several issues accompanied with it. Methods: This is a case of a 28 year-old, Gravida 4 Para 2 (1111), who presented with watery to mucoid, whitish, non-foul smelling and increasing in amount. Internal examination revealed normal external genitalia, parous outlet, cervix was transformed into a fungating mass measuring 5x4 cm, with left parametrial involvement, body of uterus was enlarged to 24 weeks size, no adnexal mass or tenderness. She had cervical punch biopsy, which revealed, adenocarcinoma, well-differentiated cervical tissue. Standard management for cases with stage 2B cervical carcinoma was to start radiation or radical hysterectomy. In the case of patients diagnosed with cervical cancer and currently pregnant, these kind of management will result to fetal loss. The patient still declined the said management and opted to delay the treatment and wait for her baby to reach at least term and proceed to cesarean section as route of delivery. Results: The patient underwent an elective cesarean section at 37th weeks age of gestation, with an outcome of a term, live baby boy APGAR score 7,9 birthweight 2600 grams. One month postpartum, the patient followed up and completed radiotherapy, chemotherapy and brachytherapy. She was advised to go back after 6 months for monitoring. On her last check up, an internal examination was done which revealed normal external genitalia, vagina admits 2 fingers with ease, there is a palpable fungating mass at the cervix measuring 2x2 cm. A repeat gynecologic oncologic ultrasound was done revealing cervical mass, endophytic, grade 1 color score with stromal invasion 35% post radiation reactive lymph nodes with intact paracolpium, pericervical, and parametrial involvement. The patient was then advised to undergo pelvic boost and for close monitoring of the cervical mass. Conclusion: Cervical cancer in pregnancy is rare but is a dilemma for women and their physicians. Treatment should be multidisciplinary and individualized following careful counseling. In this case, the treatment was clearly on the side of preventing the progression of cervical cancer while she is pregnant, however due to ethical reasons, the management deviates on the right of the patient to decide for her own health and her unborn child. The collaborative collection of data relating to treatment and outcome is strongly encouraged.

Keywords: cancer, cervical, ethical, pregnancy

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Authors: Shuo Mu, Guangzhi Jiang, Jinsa Chen

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The analysis of Indel for RNA sequencing of clinical samples is easily affected by sequencing experiment errors and software selection. In order to improve the efficiency and accuracy of analysis, we developed an automatic reporting system for Indel recognition and annotation based on image snapshot of transcriptome reads alignment. This system includes sequence local-assembly and realignment, target point snapshot, and image-based recognition processes. We integrated high-confidence Indel dataset from several known databases as a training set to improve the accuracy of image processing and added a bioinformatical processing module to annotate and filter Indel artifacts. Subsequently, the system will automatically generate data, including data quality levels and images results report. Sanger sequencing verification of the reference Indel mutation of cell line NA12878 showed that the process can achieve 83% sensitivity and 96% specificity. Analysis of the collected clinical samples showed that the interpretation accuracy of the process was equivalent to that of manual inspection, and the processing efficiency showed a significant improvement. This work shows the feasibility of accurate Indel analysis of clinical next-generation sequencing (NGS) transcriptome. This result may be useful for RNA study for clinical samples with microsatellite instability in immunotherapy in the future.

Keywords: automatic reporting, indel, next-generation sequencing, NGS, transcriptome

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Authors: Tahisa M. Pedroso, Hérida R. N. Salgado

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The microbiological turbidimetric assay allows the determination of potency of the drug, by measuring the turbidity (absorbance), caused by inhibition of microorganisms by ertapenem sodium. Ertapenem sodium (ERTM), a synthetic antimicrobial agent of the class of carbapenems, shows action against Gram-negative, Gram-positive, aerobic and anaerobic microorganisms. Turbidimetric assays are described in the literature for some antibiotics, but this method is not described for ertapenem. The objective of the present study was to develop and validate a simple, sensitive, precise and accurate microbiological assay by turbidimetry to quantify ertapenem sodium injectable as an alternative to the physicochemical methods described in the literature. Several preliminary tests were performed to choose the following parameters: Staphylococcus aureus ATCC 25923, IAL 1851, 8 % of inoculum, BHI culture medium, and aqueous solution of ertapenem sodium. 10.0 mL of sterile BHI culture medium were distributed in 20 tubes. 0.2 mL of solutions (standard and test), were added in tube, respectively S1, S2 and S3, and T1, T2 and T3, 0.8 mL of culture medium inoculated were transferred to each tube, according parallel lines 3 x 3 test. The tubes were incubated in shaker Marconi MA 420 at a temperature of 35.0 °C ± 2.0 °C for 4 hours. After this period, the growth of microorganisms was inhibited by addition of 0.5 mL of 12% formaldehyde solution in each tube. The absorbance was determined in Quimis Q-798DRM spectrophotometer at a wavelength of 530 nm. An analytical curve was constructed to obtain the equation of the line by the least-squares method and the linearity and parallelism was detected by ANOVA. The specificity of the method was proven by comparing the response obtained for the standard and the finished product. The precision was checked by testing the determination of ertapenem sodium in three days. The accuracy was determined by recovery test. The robustness was determined by comparing the results obtained by varying wavelength, brand of culture medium and volume of culture medium in the tubes. Statistical analysis showed that there is no deviation from linearity in the analytical curves of standard and test samples. The correlation coefficients were 0.9996 and 0.9998 for the standard and test samples, respectively. The specificity was confirmed by comparing the absorbance of the reference substance and test samples. The values obtained for intraday, interday and between analyst precision were 1.25%; 0.26%, 0.15% respectively. The amount of ertapenem sodium present in the samples analyzed, 99.87%, is consistent. The accuracy was proven by the recovery test, with value of 98.20%. The parameters varied did not affect the analysis of ertapenem sodium, confirming the robustness of this method. The turbidimetric assay is more versatile, faster and easier to apply than agar diffusion assay. The method is simple, rapid and accurate and can be used in routine analysis of quality control of formulations containing ertapenem sodium.

Keywords: ertapenem sodium, turbidimetric assay, quality control, validation

Procedia PDF Downloads 382

Authors: Fuad M. Alkoot

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DNA data have been used in forensics for decades. However, current research looks at using the DNA as a biometric identity verification modality. The goal is to improve the speed of identification. We aim at using gene data that was initially used for autism detection to find if and how accurate is this data for identification applications. Mainly our goal is to find if our data preprocessing technique yields data useful as a biometric identification tool. We experiment with using the nearest neighbor classifier to identify subjects. Results show that optimal classification rate is achieved when the test set is corrupted by normally distributed noise with zero mean and standard deviation of 1. The classification rate is close to optimal at higher noise standard deviation reaching 3. This shows that the data can be used for identity verification with high accuracy using a simple classifier such as the k-nearest neighbor (k-NN). 

Keywords: biometrics, genetic data, identity verification, k nearest neighbor

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Authors: A. A. Hussen, I. N. Jleta

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Micro-electromechanical system (MEMS) accelerometers and gyroscopes are suitable for the inertial navigation system (INS) of many applications due to the low price, small dimensions and light weight. The main disadvantage in a comparison with classic sensors is a worse long term stability. The estimation accuracy is mostly affected by the time-dependent growth of inertial sensor errors, especially the stochastic errors. In order to eliminate negative effect of these random errors, they must be accurately modeled. Where the key is the successful implementation that depends on how well the noise statistics of the inertial sensors is selected. In this paper, the Allan variance technique will be used in modeling the stochastic errors of the inertial sensors. By performing a simple operation on the entire length of data, a characteristic curve is obtained whose inspection provides a systematic characterization of various random errors contained in the inertial-sensor output data.

Keywords: Allan variance, accelerometer, gyroscope, stochastic errors

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Authors: El Asnaoui Khalid, Chawki Youness, Aksasse Brahim, Ouanan Mohammed

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In these recent decades, the important and fast growth in the development and demand of multimedia products is contributing to an insufficient in the bandwidth of device and network storage memory. Consequently, the theory of data compression becomes more significant for reducing the data redundancy in order to save more transfer and storage of data. In this context, this paper addresses the problem of the lossless and the near-lossless compression of images. This proposed method is based on Block SVD Power Method that overcomes the disadvantages of Matlab's SVD function. The experimental results show that the proposed algorithm has a better compression performance compared with the existing compression algorithms that use the Matlab's SVD function. In addition, the proposed approach is simple and can provide different degrees of error resilience, which gives, in a short execution time, a better image compression.

Keywords: image compression, SVD, block SVD power method, lossless compression, near lossless

Procedia PDF Downloads 368

Authors: İsmail İnce

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The aim of this study is to determine index and mechanical properties of pyroclastic rock in a practical way by means of electrical resistivity method. For this purpose, electrical resistivity, uniaxial compressive strength, point load strength, P-wave velocity, density and porosity values of 10 different pyroclastic rocks were measured in the laboratory. A simple regression analysis was made among the index-mechanical properties of the samples compatible with electrical resistivity values. A strong exponentially relation was found between index-mechanical properties and electrical resistivity values. The electrical resistivity method can be used to assess the engineering properties of the rock from which it is difficult to obtain regular shaped samples as a non-destructive method.

Keywords: electrical resistivity, index-mechanical properties, pyroclastic rocks, regression analysis

Procedia PDF Downloads 455

Authors: Niloofar Fariborzi, Hamzeh Alipour, Kourosh Azizi, Neda Eskandarzade, Abozar Ghorbani

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The family Parvoviridae consists of a large diversity of single-stranded DNA viruses, which cause mild to severe diseases in both vertebrates and invertebrates. The Parvoviridae are classified into three subfamilies: Parvovirinae infect vertebrates, Densovirinae infects invertebrates, while Hamaparovirinae infects both vertebrates and invertebrates. Except for the NS1 region, which is the prime criterion for phylogeny analysis, other parts of the parvoviruses genome, such as UTRs, are diverse even among closely related viruses or within the same genus. It is believed that host switching in parvoviruses may be related to genetic changes in regions other than NS1; therefore, whole-genome screening is valuable for studying parvoviruses' host-virus interactions. The aim of this study was to analyze genome organization and phylogeny of the complete genome sequence of the 132 Paroviridae family members, focusing on viruses that infect invertebrates. The maximum and minimum divergence within each subfamily belonged to Densovirinae and Parvovirinae, respectively. The greatest evolutionary divergence was between Hamaparovirinae and Parvovirinae. Unclassified viruses were mostly from Parovirinae and had the highest divergence to densoviruses and the lowest divergence to Parovirinae viruses. In a phylogenetic tree, all hamparoviruses were found in the center of densoviruses, with the exception of Syngnathid Ichthamaparvovirus 1 (NC_055527), which was positioned between two Parvovirinae members (NC _022089 and NC_038544). The proximity of hamparoviruses members to some densoviruses strengthens the possibility that densoviruses may be the ancestors of hamaparoviruses or vice versa. Therefore, examination and phylogeny analysis of the whole genome is necessary to understand Parvoviridae family host selection.

Keywords: densoviruses, parvoviridae, bioinformatics, phylogeny

Procedia PDF Downloads 76

Authors: Feng Ji Mervin Goh, Edmund Chee Jian Pua, Stuart Alexander Cook

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Dilated cardiomyopathy (DCM) is a common cause of heart failure. Genetic mutations account for 50% of DCM cases with TTN mutations being the most common, accounting for up to 25% of DCM cases. However, the genetic architecture underlying Asian DCM patients is unknown. We evaluated 68 patients (female= 17) with DCM who underwent follow-up at the National Heart Centre, Singapore from 2013 through 2014. Clinical data were obtained and analyzed retrospectively. Genomic DNA was subjected to next-generation targeted sequencing. Nextera Rapid Capture Enrichment was used to capture the exons of a panel of 169 cardiac genes. DNA libraries were sequenced as paired-end 150-bp reads on Illumina MiSeq. Raw sequence reads were processed and analysed using standard bioinformatics techniques. The average age of onset of DCM was 46.1±10.21 years old. The average left ventricular ejection fraction (LVEF), left ventricular diastolic internal diameter (LVIDd), left ventricular systolic internal diameter (LVIDs) were 26.1±11.2%, 6.20±0.83cm, and 5.23±0.92cm respectively. The frequencies of mutations in major DCM-associated genes were as follows TTN (5.88% vs published frequency of 20%), LMNA (4.41% vs 6%), MYH7 (5.88% vs 4%), MYH6 (5.88% vs 4%), and SCN5a (4.41% vs 3%). The average callability at 10 times coverage of each major gene were: TTN (99.7%), LMNA (87.1%), MYH7 (94.8%), MYH6 (95.5%), and SCN5a (94.3%). In conclusion, TTN mutations are not common in Singaporean DCM patients. The frequencies of other major DCM-associated genes are comparable to frequencies published in the current literature.

Keywords: heart failure, dilated cardiomyopathy, genetics, next-generation sequencing

Procedia PDF Downloads 233

Authors: Fahad Alamoudi, Yaser Miaji

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The growing popularity of swimming pools and other activities in the water for sport, fitness, therapy or just enjoyable relaxation have led to the increased use of swimming pools and the establishment of a variety of specific-use pools such as spa pools, water slides, and more recently, hydrotherapy and wave pools. In this research, a few simple equipment is used for test, detect and alert for detection of water cleanness and pollution. YSI Photometer Systems, TDSTestr High model, Rio 12HF and Electrode A1. The researchers used electrolysis as a method of separating bonded elements and compounds by passing an electric current through them. The results which use 41 experiments show the higher the salt concentration, the more efficient the electrode and the smaller the gap between the plates, the lower the electrode voltage. Furthermore, it is proved that the larger the surface area, the lower the cell voltage and the higher current used the more chlorine produced.

Keywords: photometer, electrode, electrolysis, swimming pool chlorination

Procedia PDF Downloads 348

Authors: Rodrigo S. Piera, Jailson Sales Ara´ujo, Gabriela B. Lemos, Matthew B. Weiss, John B. DeBrota, Gabriel H. Aguilar, Jacques L. Pienaar

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The Born rule was historically viewed as an independent axiom of quantum mechanics until Gleason derived it in 1957 by assuming the Hilbert space structure of quantum measurements [1]. In subsequent decades there have been diverse proposals to derive the Born rule starting from even more basic assumptions [2]. In this work, we demonstrate that a simple reinforcement-learning algorithm, having no pre-programmed assumptions about quantum theory, will nevertheless converge to a behaviour pattern that accords with the Born rule, when tasked with predicting the output of a quantum optical implementation of a symmetric informationally-complete measurement (SIC). Our findings support a hypothesis due to QBism (the subjective Bayesian approach to quantum theory), which states that the Born rule can be thought of as a normative rule for making decisions in a quantum world [3].

Keywords: quantum Bayesianism, quantum theory, quantum information, quantum measurement

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Authors: Nguyen J. M., Lucas G., Ruan S., Digonnet H., Antonioli D.

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Introduction: Deep Learning (DL) is a very powerful tool for analyzing image data. But for tabular data, it cannot compete with machine learning methods like XGBoost. The research question becomes: can tabular data be transformed into images that can be analyzed by simple CNNs (Convolutional Neuron Networks)? Will DL be the absolute tool for data classification? All current solutions consist in repositioning the variables in a 2x2 matrix using their correlation proximity. In doing so, it obtains an image whose pixels are the variables. We implement a technology, DeepNIC, that offers the possibility of obtaining an image for each variable, which can be analyzed by simple CNNs. Material and method: The 'ROP' (Regression OPtimized) model is a binary and atypical decision tree whose nodes are managed by a new artificial neuron, the Neurop. By positioning an artificial neuron in each node of the decision trees, it is possible to make an adjustment on a theoretically infinite number of variables at each node. From this new decision tree whose nodes are artificial neurons, we created the concept of a 'Random Forest of Perfect Trees' (RFPT), which disobeys Breiman's concepts by assembling very large numbers of small trees with no classification errors. From the results of the RFPT, we developed a family of 10 statistical information criteria, Nguyen Information Criterion (NICs), which evaluates in 3 dimensions the predictive quality of a variable: Performance, Complexity and Multiplicity of solution. A NIC is a probability that can be transformed into a grey level. The value of a NIC depends essentially on 2 super parameters used in Neurops. By varying these 2 super parameters, we obtain a 2x2 matrix of probabilities for each NIC. We can combine these 10 NICs with the functions AND, OR, and XOR. The total number of combinations is greater than 100,000. In total, we obtain for each variable an image of at least 1166x1167 pixels. The intensity of the pixels is proportional to the probability of the associated NIC. The color depends on the associated NIC. This image actually contains considerable information about the ability of the variable to make the prediction of Y, depending on the presence or absence of other variables. A basic CNNs model was trained for supervised classification. Results: The first results are impressive. Using the GSE22513 public data (Omic data set of markers of Taxane Sensitivity in Breast Cancer), DEEPNic outperformed other statistical methods, including XGBoost. We still need to generalize the comparison on several databases. Conclusion: The ability to transform any tabular variable into an image offers the possibility of merging image and tabular information in the same format. This opens up great perspectives in the analysis of metadata.

Keywords: tabular data, CNNs, NICs, DeepNICs, random forest of perfect trees, classification

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Authors: Asma Karim

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Fish taxonomy plays a fundamental role in the study of biodiversity. However, traditional methods of fish taxonomy rely on morphological features, which can lead to confusion due to great similarities between closely related species. To overcome this limitation, modern taxonomy employs DNA barcoding as a species identification method. This involves using a short standardized mitochondrial DNA region as a barcode, specifically a 658 base pair fragment near the 5′ ends of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene, to exploit the diversity in this region for identification of species. To test the effectiveness and reliability of DNA barcoding, 25 fish specimens from nine different fish species found in various rivers of Pakistan were identified morphologically using a dichotomous key at the start of the study. Comprising nine freshwater fish species, including Mystus cavasius, Mystus bleekeri, Osteobrama cotio, Labeo rohita, Labeo culbasu, Labeo gonius, Cyprinus carpio, Catla catla and Cirrhinus mrigala from different rivers of Pakistan were used in the present study. DNA was extracted from one of the pectoral fins and a partial sequence of CO1 gene was amplified using the conventional PCR method. Analysis of the barcodes confirmed that genetically identified fishes were the same as those identified morphologically at the beginning of the study. The sequences were also analyzed for biodiversity and phylogenetic studies. Based on the results of the study, it can be concluded that DNA barcoding is an effective and reliable method for studying biodiversity and conducting phylogenetic analysis of different fish species in Pakistan.

Keywords: DNA barcoding, fresh water fishes, taxonomy, biodiversity, Pakistan

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Authors: Atif Zafar, Fan Haijun

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A sequence of different Reservoir Engineering methods and tools in reservoir characterization and field development are presented in this paper. The real data of Jin Gas Field of L-Basin of Pakistan is used. The basic concept behind this work is to enlighten the importance of well test analysis in a broader way (i.e. reservoir characterization and field development) unlike to just determine the permeability and skin parameters. Normally in the case of reservoir characterization we rely on well test analysis to some extent but for field development plan, the well test analysis has become a forgotten tool specifically for locations of new development wells. This paper describes the successful implementation of well test analysis in Jin Gas Field where the main uncertainties are identified during initial stage of field development when location of new development well was marked only on the basis of G&G (Geologic and Geophysical) data. The seismic interpretation could not encounter one of the boundary (fault, sub-seismic fault, heterogeneity) near the main and only producing well of Jin Gas Field whereas the results of the model from the well test analysis played a very crucial rule in order to propose the location of second well of the newly discovered field. The results from different methods of well test analysis of Jin Gas Field are also integrated with and supported by other tools of Reservoir Engineering i.e. Material Balance Method and Volumetric Method. In this way, a comprehensive way out and algorithm is obtained in order to integrate the well test analyses with Geological and Geophysical analyses for reservoir characterization and field development. On the strong basis of this working and algorithm, it was successfully evaluated that the proposed location of new development well was not justified and it must be somewhere else except South direction.

Keywords: field development plan, reservoir characterization, reservoir engineering, well test analysis

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Authors: Wesley H. Brewer, John C. Sanford

Abstract:

SciPaaS is a prototype development of an execution platform/middleware designed to make it easy for scientists to rapidly deploy their scientific applications (apps) to the cloud. It provides all the necessary infrastructure for running typical IXP (Input-eXecute-Plot) style apps, including: a web interface, post-processing and plotting capabilities, job scheduling, real-time monitoring of running jobs, and even a file/case manager. In this paper, first the system architecture is described and then is demonstrated for a two scientific applications: (1) a simple finite-difference solver of the inviscid Burger’s equation, and (2) Mendel’s Accountant—a forward-time population genetics simulation model. The implications of the prototype are discussed in terms of ease-of-use and deployment options, especially in cloud environments.

Keywords: web-based simulation, cloud computing, Platform-as-a-Service (PaaS), rapid application development (RAD), population genetics

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Authors: Yu-Kuei Hsu, Yan-Gu Lin

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A facile and simple fabrication of copper(II) oxide (CuO) nanosheet on copper foil as nanoelectrode for H2O2 sensing application was proposed in this study. The spontaneous formation of CuO nanosheets by immersing the copper foil into 0.1 M NaOH aqueous solution for 48 hrs was carried out at room temperature. The sheet-like morphology with several ten nanometers in thickness and ~500 nm in width was observed by SEM. Those nanosheets were confirmed the monoclinic-phase CuO by the structural analysis of XRD and Raman spectra. The directly grown CuO nanosheets film is mechanically stable and offers an excellent electrochemical sensing platform. The CuO nanosheets electrode shows excellent electrocatalytic response to H2O2 with significantly lower overpotentials for its oxidation and reduction and also exhibits a fast response and high sensitivity for the amperometric detection of H2O2. The novel spontaneously grown CuO nanosheets electrode is readily applicable to other analytes and has great potential applications in the electrochemical detection.

Keywords: CuO, nanosheets, H2O2 detection, Cu foil

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Authors: Sina Keyhanian, Abbas Ahmadi, Behrooz Karimi

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We present a multi-objective binary programming model which considers surgical cases are scheduling among operating rooms and the configuration of surgical instruments in limited capacity hospital trays, simultaneously. Many mathematical models have been developed previously in the literature addressing different challenges in health-care logistics such as assigning operating rooms, leveling beds, etc. But what happens inside the operating rooms along with the inventory management of required instruments for various operations, and also their integration with surgical scheduling have been poorly discussed. Our model considers the minimization of movements between trays during a surgery which recalls the famous cell formation problem in group technology. This assumption can also provide a major potential contribution to robotic surgeries. The tray configuration problem which consumes surgical instruments requirement plan (SIRP) and sequence of surgical procedures based on required instruments (SIRO) is nested inside the bin packing problem. This modeling approach helps us understand that most of the same-output solutions will not be necessarily identical when it comes to the rearrangement of surgeries among rooms. A numerical example has been dealt with via a proposed nested simulated annealing (SA) optimization approach which provides insights about how various configurations inside a solution can alter the optimal condition.

Keywords: health-care logistics, hospital tray configuration, off-line bin packing, simulated annealing optimization, surgical case scheduling

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Authors: K. Djellabi, M. E. H. Latreche

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The induction heating phenomenon depends on various factors, making the problem highly nonlinear. The mathematical analysis of this problem in most cases is very difficult and it is reduced to simple cases. Another knowledge of induction heating systems is generated in production environments, but these trial-error procedures are long and expensive. The numerical models of induction heating problem are another approach to reduce abovementioned drawbacks. This paper deals with the simulation model of induction heating problem. The simulation model of induction heating system in COMSOL Multiphysics is created. In this work we present results of numerical simulations of induction heating process in pieces of cylindrical shapes, in an inductor with four coils. The modeling of the inducting heating process was made with the software COMSOL Multiphysics Version 4.2a, for the study we present the temperature charts.

Keywords: induction heating, electromagnetic field, inductor, numerical simulation, finite element

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Authors: Chunduru Amareswara Prasad

Abstract:

The main aim of this proposal it to reveal the secrets of the universe by accelerating neutrons. The proposal idea in its abridged version speaks about the possibility of making neutrons accelerate with help of thermal energy and magnetic energy under controlled conditions. Which is helpful in revealing the hidden secrets of the universe namely dark energy and in finding properties of Higgs boson. The paper mainly speaks about accelerating neutrons to near velocity of light in a LINAC, using magnetic energy by magnetic pressurizers. The center of mass energy of two colliding neutron beams is 94 GeV (~0.5c) can be achieved using this method. The conventional ways to accelerate neutrons has some constraints in accelerating them electromagnetically as they need to be separated from the Tritium or Deuterium nuclei. This magnetic gradient method provides efficient and simple way to accelerate neutrons.

Keywords: neutron, acceleration, thermal energy, magnetic energy, Higgs boson

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Authors: Juan Antonio Mondragon Sanchez, Ruben Santamaria

Abstract:

The DNA G-quadruplex is a four-stranded DNA structure conformed by stacked planes of four base paired guanines (G-quartet). The guanine rich DNA sequences are present in many sites of genomic DNA and can potentially lead to the formation of G-quadruplexes, especially at the 3'-terminus of the human telomeric DNA with many TTAGGG repeats. The formation and stabilization of a G-quadruplex by small ligands at the telomeric region can inhibit the telomerase activity. In turn, the ligands can be used to regulate oncogene expression making the G-quadruplex an attractive target for anticancer therapy. Clearly, the G-quadruplex structured in the telomeric DNA is of fundamental importance for rational drug design. In this context, we investigate two G-quadruplex structures, the first follows from the sequence TTAGGG(TTAGGG)3TT (HUT1), and the second from AAAGGG(TTAGGG)3AA (HUT2), both in a K+ solution. We determine the free energy surfaces of the HUT1 and HUT2 structures and investigate their conformations using replica-exchange metadynamics simulations. The carbonyl-carbonyl distances belonging to different guanines residues are selected as the main collective variables to determine the free energy surfaces. The surfaces exhibit two main local minima, compatible with experiments on the conformational transformations of HUT1 and HUT2 under substitution of the K+ ions by the Na+ ions. The conformational transitions are not observed in short MD simulations without the use of the metadynamics approach. The results of this work should be of help to understand the formation and stability of human telomeric G-quadruplex in environments including the presence of K+ and Na+ ions.

Keywords: g-quadruplex, metadynamics, molecular dynamics, replica-exchange

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Authors: Bilal Ahmed

Abstract:

Rehabilitation of congenital and acquired maxillofacial defects is always a challenging clinical scenario. These defects pose major physiological and psychological threat not only to the patient but to the entire family. There has been an enormous scientific development in maxillofacial rehabilitation with the advent of CAD CAM, 3-D scanning, Osseo-integrated implants and improved restorative materials. There are also specialized centers with latest diagnostic and treatment facilities in the developed countries. However, in certain clinical case scenarios, conventional prosthodontic principles are still the gold standards. Similarly in a less developed world, financial and technical constraints are factors affecting treatment planning and final outcomes. However, we can do a lot of benefits to the affected human beings, even with use of simple and cost-effective conventional prosthodontic techniques and materials. These treatment strategies may sometimes be considered as intermediate or temporary options, but with regular follow-up maintenance these can be used on a definitive basis.

Keywords: maxillofacial defects, obturators, prosthodontics, medical and health sciences

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Authors: Arnab Roy, P. S. Anil Kumar

Abstract:

Hall bar magnetic field sensors based on planar hall effect were fabricated from permalloy (Ni¬80Fe20) thin films grown by pulsed laser ablation. As large as 400% planar Hall voltage change was observed for a magnetic field sweep within ±4 Oe, a value comparable with present day TMR sensors at room temperature. A very large planar Hall sensitivity of 1200 Ω/T was measured close to switching fields, which was not obtained so far apart from 2DEG Hall sensors. In summary, a highly sensitive low magnetic field sensor has been constructed which has the added advantage of simple architecture, good signal to noise ratio and robustness.

Keywords: planar hall effect, permalloy, NiFe, pulsed laser ablation, low magnetic field sensor, high sensitivity magnetic field sensor

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Authors: Ashkan Shafee, Ahmad Fahimifar

Abstract:

There is a growing demand for construction of high-rise buildings and infrastructures in large cities, which sometimes require deep excavations in the vicinity of pile foundations. In this study, a two-dimensional finite element analysis is used to gain insight into the response of pile groups adjacent to deep excavations in sand. The numerical code was verified by available experimental works, and a parametric study was performed on different working load combinations, excavation depth and supporting system. The results show that the simple two-dimensional plane strain model can accurately simulate the excavation induced changes on adjacent pile groups. It was found that further excavation than pile toe level and also inclined loading on adjacent pile group can severely affect the serviceability of the foundation.

Keywords: deep excavation, inclined loading, lateral deformation, pile group

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Authors: John Vergara, Giuseppe Palmese

Abstract:

Fundamental studies aimed at elucidating the key contributions to corrosion performance are needed to make progress toward effective and environmentally compliant corrosion control. Epoxy/amine systems are typically employed as barrier coatings for corrosion control. However, the hardening agents used for coating applications can be very complex, making fundamental studies of water and oxygen permeability challenging to carry out. Creating model building blocks for epoxy/amine coatings is the first step in carrying out these studies. We will demonstrate the synthesis and characterization of model amine building blocks from saturated fatty acids and simple amines such as diethylenetriamine (DETA) and Bis(3-aminopropyl)amine. The structure-property relationship of thermosets made from these model amines and Diglycidyl ether of bisphenol A (DGBEA) will be discussed.

Keywords: building block, amine, synthesis, characterization

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Authors: Eileen K. Africa, Karel J. van Deventer

Abstract:

Neuro-typical children develop the motor skills necessary to play, do schoolwork and interact with others. However, this is not observed in children who have learning or behavioural problems. Children with Autism Spectrum Disorder (ASD) are often referred to as clumsy because their body parts do not work well together in a sequence. Physical Activity (PA) has shown to be beneficial to the general population, therefore, providing children with ASD opportunities to take part in PA programmes, could prove to be beneficial in many ways and should be investigated. The purpose of this study was to design a specialised group intervention programme, to attempt to improve gross motor skills of selected children diagnosed with ASD between the ages of eight and 13 years. A government school for ASD learners was recruited to take part in this study, and a sample of convenience (N=7) was selected. Children in the experimental group (n=4) participated in a 12-week group intervention programme twice per week, while the control group continued with their normal daily routine. The Movement Assessment Battery for Children-Second Edition (MABC-2), was administered pre- and post-test to determine the children’s gross motor proficiency and to determine if the group intervention programme had an effect on the gross motor skills of the experimental group. Statistically significant improvements were observed in total motor skill proficiency (p < 0.05), of the experimental group. These results demonstrate the importance of gross motor skills interventions for children diagnosed with ASD. Future research should include more participants to ensure that the results can be generalised.

Keywords: autism spectrum disorder, children, gross motor skills, group intervention programme

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Authors: Yanshuang Zhang, Byungho Jeong

Abstract:

In many cases, there is a time lag between the consumption of inputs and the production of outputs. This time lag effect should be considered in evaluating the performance of organizations. Recently, a couple of DEA models were developed for considering time lag effect in efficiency evaluation of research activities. Multi-periods input(MpI) and Multi-periods output(MpO) models are integrated models to calculate simple efficiency considering time lag effect. However, these models can’t discriminate efficient DMUs because of the nature of basic DEA model in which efficiency scores are limited to ‘1’. That is, efficient DMUs can’t be discriminated because their efficiency scores are same. Thus, this paper suggests a super-efficiency model for efficiency evaluation under the consideration of time lag effect based on the MpO model. A case example using a long-term research project is given to compare the suggested model with the MpO model.

Keywords: DEA, super-efficiency, time lag, multi-periods input

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Authors: Roy B. Clariana, Ryan L. Solnosky

Abstract:

Structural feedback is any form of feedback that aims to improve the quality of students’ domain-normative conceptual interrelationships. Research with structural feedback points to the potential mediating role of network graphs as feedback for tuning students’ conceptual understanding; for example, improved content knowledge and motivation were observed for undergraduate students who accessed the instructor’s networks of course content. This exploratory study uses a one-group pretest-posttest design to examine the effects of instructor-provided network feedback during lectures on students’ knowledge structure measured using a concept sorting task at the pretest and posttest. Undergraduate students in an architectural engineering course (n = 32) completed a lesson module and then an end-of-unit quiz on building with wood and wood framing. Three weeks later, as a review, students completed a sorting task that used 26 terms from that lesson, then a week later, the sorting task data were used to create a group-average network, this network along with the instructor’s expert network were added to that week’s lecture slides and were compared and discussed during class time. A week later, students completed the sorting task again. The pre and post-sorting data were rendered into pathfinder networks, and then these students’ networks were compared to five referent networks, specifically the textbook chapter network, the lecture slides network, a network of the end-of-unit quiz, the actual expert network that served as the feedback intervention, and the group-average network. Inspection of means shows that knowledge structure measures improved for all five measures from pre-to-post, becoming more like the lesson content and like the expert. Repeated measures analysis with follow-up paired samples t-tests showed pre-to-post significant increases for both the end-of-unit quiz and the expert network referents. The findings show that instructor presentation of structural feedback as networks improved or ‘tuned’ students’ knowledge structure of the lesson content. This approach only takes a few extra minutes of class time and is fairly simple to implement in ordinary classrooms, and so it has wide potential to support classroom instruction and student learning. Further research is needed to determine how critical it is to present both the group-average network along with the expert network for comparison in order to highlight group-level misconceptions, or is presenting only the expert network sufficient? If a group-level network is necessary, then a simple clicker-like classroom tool could be developed to collect sorting task data during lectures that could then immediately provide the group-average network for class discussion and reflection.

Keywords: classroom instruction, engineering education, knowledge structure, pathfinder networks, structural feedback

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