Search results for: gene frequency

Authors: V. Geza, J. Vencels, G. Zageris, S. Pavlovs

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One of the most perspective methods to produce SoG-Si is refinement via metallurgical route. The most critical part of this route is refinement from boron and phosphorus. Therefore, a new approach could address this problem. We propose an approach of creating surface waves on silicon melt’s surface in order to enlarge its area and accelerate removal of boron via chemical reactions and evaporation of phosphorus. A two dimensional numerical model is created which includes coupling of electromagnetic and fluid dynamic simulations with free surface dynamics. First results show behaviour similar to experimental results from literature.

Keywords: numerical modelling, silicon refinement, surface waves, VOF method

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Authors: R. M. Srivastava, Subbanna A.R.N.S, Md Abbas Ahmad, S. P.More, Shivashankar, B. Kalyanbabu

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The similar morphology associated with high genetic variability poses problems in phylogenetic studies of Helicoverpa armigera (Hubner). To identify genetic variation of North Western Himalayan population’s, partial (Mid to terminal region) cytochrome c oxidase subunit I (COX-1) gene was amplified and sequenced for three populations collected from Pantnagar, Almora, and Chinyalisaur. The alignment of sequences with other two populations, Nagpur representing central India population and Anhui, China representing complete COX-1 sequence revealed unanimity in middle region with eleven single nucleotide polymorphisms (SNPs) in Nagpur populations. However, the consensus is missing when approaching towards terminal region, which is associated with 15 each SNPs and pair base substitutions in Chinyalisaur populations. In minimum evolution tree, all the five populations were majorly separated into two clades, one comprising of only Nagpur population and the other with rest. Amongst, North Western populations, Chinyalisaur one is promising by farming a separate clade. The pairwise genetic distance ranges from 0.025 to 0.192 with the maximum between H. armigera populations of Nagpur and Chinyalisaur. This genetic isolation of populations can be attributed to a key role of topological barriers of weather and mountain ranges and temporal barriers due to cropping patterns.

Keywords: cytochrome c oxidase subunit I, northwestern Himalayan population, Helicoverpa armigera (Noctuidae: Lepidoptera), phylogenetic relationship, genetic variation

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Authors: H. Imad, Y. Cheah, O. Aamera

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The aims of this research are to study the mitochondrial non-coding region by using the Sanger sequencing technique and establish the degree of variation characteristics of a fragment. FTA® Technology (FTA™ paper DNA extraction) utilized to extract DNA. A portion of a non-coding region encompassing positions 37 to 340 amplified in accordance with the Anderson reference sequence. PCR products purified by EZ-10 spin column then sequenced and detected by using the ABI 3730xL DNA Analyzer. New polymorphic positions 57, 63, and 101 are described may in future be suitable sources for identification purpose. The data obtained can be used to identify variable nucleotide positions characterized by frequent occurrence most promising for identification variants.

Keywords: encompassing nucleotide positions 37 to 340, HVII, Iraq, mitochondrial DNA, polymorphism, frequency

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Authors: Shakila N. Senarath, Dinesh Asanka, Janaka Wijayanayake

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The necessity of cosmetic products is arising to fulfill consumer needs of personality appearance and hygiene. A cosmetic product consists of various chemical ingredients which may help to keep the skin healthy or may lead to damages. Every chemical ingredient in a cosmetic product does not perform on every human. The most appropriate way to select a healthy cosmetic product is to identify the texture of the body first and select the most suitable product with safe ingredients. Therefore, the selection process of cosmetic products is complicated. Consumer surveys have shown most of the time, the selection process of cosmetic products is done in an improper way by consumers. From this study, a content-based system is suggested that recommends cosmetic products for the human factors. To such an extent, the skin type, gender and price range will be considered as human factors. The proposed system will be implemented by using Machine Learning. Consumer skin type, gender and price range will be taken as inputs to the system. The skin type of consumer will be derived by using the Baumann Skin Type Questionnaire, which is a value-based approach that includes several numbers of questions to derive the user’s skin type to one of the 16 skin types according to the Bauman Skin Type indicator (BSTI). Two datasets are collected for further research proceedings. The user data set was collected using a questionnaire given to the public. Those are the user dataset and the cosmetic dataset. Product details are included in the cosmetic dataset, which belongs to 5 different kinds of product categories (Moisturizer, Cleanser, Sun protector, Face Mask, Eye Cream). An alternate approach of TF-IDF (Term Frequency – Inverse Document Frequency) is applied to vectorize cosmetic ingredients in the generic cosmetic products dataset and user-preferred dataset. Using the IF-IPF vectors, each user-preferred products dataset and generic cosmetic products dataset can be represented as sparse vectors. The similarity between each user-preferred product and generic cosmetic product will be calculated using the cosine similarity method. For the recommendation process, a similarity matrix can be used. Higher the similarity, higher the match for consumer. Sorting a user column from similarity matrix in a descending order, the recommended products can be retrieved in ascending order. Even though results return a list of similar products, and since the user information has been gathered, such as gender and the price ranges for product purchasing, further optimization can be done by considering and giving weights for those parameters once after a set of recommended products for a user has been retrieved.

Keywords: content-based filtering, cosmetics, machine learning, recommendation system

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Authors: Sana Gul, Sheeba Murad, Aneela Javed

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Introduction: Human Papilloma Virus (HPV) is small DNA virus mostly infecting mucosa and cutaneous keratinocytes. So far, more than 200 Human papillomaviruses are known. HPV have been divided into high- and low-risk on the basis of their oncogenic potential. High risk HPV is considered to be the main etiological cause for cervical cancer. Objective: Current study was designed to screen the local cervical cancer patients from the twin cities of Pakistan for the occurance of high risk HPV. Methodology: A total of 67 formalin fixed paraffin-embedded samples of cervical cancer biopsies were obtained from the government hospitals in Islamabad and Rawalpindi. Cervical cancer biopsies were examined for the presence of HPV DNA. Polymerase chain reaction (PCR) was used for the amplification of a region in the HPV-L1 gene for the general detection of the Papilloma virus and for the genotype specific detection of high risk HPV 16 and 18 using the GP5/GP6 primers and genotype specific primers respectively. Results: HPV DNA was detected in 59 out of 67 samples analyzed. 30 samples showed the presence of HPV16 while 22 samples were positive for HPV 18 . HPV subtype could not be determined in 7 samples. Conclusion: Our results show a strong association between HPV infection and cervical cancer among women in twin cities of Pakistan. One way to minimize the disease burden in relation to HPV infection in Pakistani population is the use of prophylactic vaccines and routine screening. An early diagnosis of HPV infection will allow better health management to reduce the risk of developing cervical cancer.

Keywords: cervical cancer, Pakistan, human papillomavirus, HPV 16

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Authors: Mohd Adil, Rosina Khan, Danishuddin, Asad U. Khan

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The aim of this study was to evaluate the influence of the crude and active solvent fraction of Trachyspermum ammi on S. mutans cariogenicity, effect on expression of genes involved in biofilm formation and caries development in rats. GC–MS was carried out to identify the major components present in the crude and the active fraction of T. ammi. The crude extract and the solvent fraction exhibiting least MIC were selected for further experiments. Scanning electron microscopy was carried out to observe the effect of the extracts on S. mutans biofilm. Comparative gene expression analysis was carried out for nine selected genes. 2-Isopropyl-5-methyl-phenol was found as major compound in crude and the active fraction. Binding site of this compound within the proteins involved in biofilm formation was mapped with the help of docking studies. Real-time RT-PCR analyses revealed significant suppression of the genes involved in biofilm formation. All the test groups showed reduction in caries (smooth surface as well as sulcal surface caries) in rats. Moreover, it also provides new insight to understand the mechanism influencing biofilm formation in S. mutans. Furthermore, the data suggest the putative cariostatic properties of T. Ammi and hence can be used as an alternative medicine to prevent caries infection.

Keywords: bio-film, Streptococcus mutans, dental caries, bio-informatic

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Authors: Marcelo Sanhueza Cartes, Nelson Maureira Carsalade

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This research evaluates the effectiveness of a pallet isolation device for the protection of selective-type industrial storage racks. The device works only in the longitudinal direction of the aisle, and it is made up of a platform installed on the rack beams. At both ends, the platform is connected to the rack structure by means of a spring-damper system working in parallel. A system of wheels is arranged between the isolation platform and the rack beams in order to reduce friction, decoupling of the movement and improve the effectiveness of the device. The latter is evaluated by the reduction of the maximum dynamic responses of basal shear load and story drift in relation to those corresponding to the same rack with the traditional construction system. In the first stage, numerical simulations of industrial storage racks were carried out with and without the pallet isolation device. The numerical results allowed us to identify the archetypes in which it would be more appropriate to carry out experimental tests, thus limiting the number of trials. In the second stage, experimental tests were carried out on a shaking table to a select group of full-scale racks with and without the proposed device. The movement simulated by the shaking table was based on the Mw 8.8 magnitude earthquake of February 27, 2010, in Chile, registered at the San Pedro de la Paz station. The peak ground acceleration (PGA) was scaled in the frequency domain to fit its response spectrum with the design spectrum of NCh433. The experimental setup contemplates the installation of sensors to measure relative displacement and absolute acceleration. The movement of the shaking table with respect to the ground, the inter-story drift of the rack and the pallets with respect to the rack structure were recorded. Accelerometers redundantly measured all of the above in order to corroborate measurements and adequately capture low and high-frequency vibrations, whereas displacement and acceleration sensors are respectively more reliable. The numerical and experimental results allowed us to identify that the pallet isolation period is the variable with the greatest influence on the dynamic responses considered. It was also possible to identify that the proposed device significantly reduces both the basal cut and the maximum inter-story drift by up to one order of magnitude.

Keywords: pallet isolation system, industrial storage racks, basal shear load, interstory drift.

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Authors: Erzen Muharemi, Emmanuel De Jaeger, Jos Knockaert

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The work presented here investigates the modeling of power electronics converters in terms of their harmonic production. Specifically, it addresses high-frequency emissions in the range of 2-150 kHz, referred to as supraharmonics. This paper models a conventional converter, namely the boost converter used as an active power factor corrector (APFC). Furthermore, the modeling is extended to the case of the interleaved boost converter, which offers advantages such as halving the emissions. Finally, a comparison between the theoretical, numerical, and experimental results will be provided.

Keywords: APFC, boost converter, converter modeling, double fourier series, supraharmonics

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Authors: Xin-Yu Shih, Yue-Qu Liu, Hong-Ru Chou

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This paper presents a low-area and fully-reconfigurable Fast Fourier Transform (FFT) hardware design for 3GPP-LTE communication standard. It can fully support 32 different FFT sizes, up to 2048 FFT points. Besides, a special processing element is developed for making reconfigurable computing characteristics possible, while first-in first-out (FIFO) scheduling scheme design technique is proposed for hardware-friendly FIFO resource arranging. In a synthesis chip realization via TSMC 40 nm CMOS technology, the hardware circuit only occupies core area of 0.2325 mm² and dissipates 233.5 mW at maximal operating frequency of 250 MHz.

Keywords: reconfigurable, fast Fourier transform (FFT), single-path delay feedback (SDF), 3GPP-LTE

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Authors: Nazeef, Suleiman, Umar, Danladi Muhammad, Ja'afar Ali, Zaliha Adamu Umar

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The population dynamics of Auchenoglanis occidentalis from the Dadin-Kowa reservoir were studied. Population dynamic parameters such as growth, mortality and recruitment patterns were analyzed using length frequency data over a 12-month period employing FiSAT II software. Findings revealed that LWR (b - constant) = 2.88, K = 0.72 -yr., L∞ = 40.91 cm and Tmax = 3.57 years and Ɵ’ = 3.14. Mortality indices revealed that natural mortality (M = 1.39), fishing mortality (F = 0.22) and exploitation ratio (E = 0.14), Lc/L∞ = 0.48, Emax = 0.64, while Lopt = 26.4 cm. Uni-modal recruitment peak observed with Lm = 27.3 cm. A restocking program is suitable to ensure its continuous existence as it seems to have a low population.

Keywords: fish population dynamics, auchenoglanis occidentalis, FISAT II, natural mortality

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Authors: Negar Riazifar, Nigel G. Stocks

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This paper proposes strategies in level crossing (LC) sampling and reconstruction that provide alias-free high-fidelity signal reconstruction for speech signals without exponentially increasing sample number with increasing bit-depth. We introduce methods in LC sampling that reduce the sampling rate close to the Nyquist frequency even for large bit-depth. The results indicate that larger variation in the sampling intervals leads to an alias-free sampling scheme; this is achieved by either reducing the bit-depth or adding jitter to the system for high bit-depths. In conjunction with windowing, the signal is reconstructed from the LC samples using an efficient Toeplitz reconstruction algorithm.

Keywords: alias-free, level crossing sampling, spectrum, trigonometric polynomial

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Authors: Seolah Lee, Yoohyk Jang, Soyoung Lee, Kon Chu, Sang Kun Lee

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Objective: The International League Against Epilepsy (ILAE) currently suggests a topiramate serum level range of 5-20 mg/L. However, numerous institutions have observed substantial drug response at lower levels. This study aims to investigate the correlation between topiramate serum levels, drug responsiveness, and adverse events to establish a more accurate and tailored therapeutic range. Methods: We retrospectively analyzed topiramate serum samples collected between January 2017 and January 2022 at Seoul National University Hospital. Clinical data, including serum levels, antiseizure regimens, seizure frequency, and adverse events, were collected. Patient responses were categorized as "insufficient" (reduction in seizure frequency <50%) or "sufficient" (reduction ≥ 50%). Within the "sufficient" group, further subdivisions included seizure-free and tolerable seizure subgroups. A population pharmacokinetic model estimated serum levels from spot measurements. ROC curve analysis determined the optimal serum level cut-off. Results: A total of 389 epilepsy patients, with 555 samples, were reviewed, having a mean dose of 178.4±117.9 mg/day and a serum level of 3.9±2.8 mg/L. Out of the samples, only 5.6% (n=31) exhibited insufficient response, with a mean serum level of 3.6±2.5 mg/L. In contrast, 94.4% (n=524) of samples demonstrated sufficient response, with a mean serum level of 4.0±2.8 mg/L. This difference was not statistically significant (p = 0.45). Among the 78 reported adverse events, logistic regression analysis identified a significant association between ataxia and serum concentration (p = 0.04), with an optimal cut-off value of 6.5 mg/L. In the subgroup of patients receiving monotherapy, those in the tolerable seizure group exhibited a significantly higher serum level compared to the seizure-free group (4.8±2.0 mg/L vs 3.4±2.3 mg/L, p < 0.01). Notably, patients in the tolerable seizure group displayed a higher likelihood of progressing into drug-resistant epilepsy during follow-up visits compared to the seizure-free group. Significance: This study proposed an optimal therapeutic concentration for topiramate based on the patient's responsiveness to the drug and the incidence of adverse effects. We employed a population pharmacokinetic model and analyzed topiramate serum levels to recommend a serum level below 6.5 mg/L to mitigate the risk of ataxia-related side effects. Our findings also indicated that topiramate dose elevation is unnecessary for suboptimal responders, as the drug's effectiveness plateaus at minimal doses.

Keywords: topiramate, therapeutic range, low dos, antiseizure effect

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Authors: Juan Jose Filgueira, Daniela Londono-Serna, Liliana Maria Hoyos

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Carnation (Dianthus caryophyllus) is one of the most important products of exportation in the floriculture industry worldwide. Fusariosis is the disease that causes the highest losses on farms, in particular the one produced by Fusarium oxysporum f.sp. dianthi, called vascular wilt. Gene identification and metabolic routes of the genes that participate in the building of the plant response to Fusarium are some of the current targets in the carnation breeding industry. The techniques for the identifying of resistant genes in the plants, is the analysis of the transcriptome obtained during the host-pathogen interaction. In this work, we report the cell transcriptome of different varieties of carnation that present differential response from Fusarium oxysporum f.sp. dianthi attack. The cells of the different hybrids produced in the outbreeding program were cultured in vitro and elicited with the parasite in a dual culture. The isolation and purification of mRNA was achieved by using affinity chromatography Oligo dT columns and the transcriptomes were obtained by using Illumina NGS techniques. A total of 85,669 unigenes were detected in all the transcriptomes analyzed and 31,000 annotations were found in databases, which correspond to 36.2%. The library construction of genic expression techniques used, allowed to recognize the variation in the expression of genes such as Germin-like protein, Glycosyl hydrolase family and Cinnamate 4-hydroxylase. These have been reported in this study for the first time as part of the response mechanism to the presence of Fusarium oxysporum.

Keywords: Carnation, Fusarium, vascular wilt, transcriptome

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Authors: Leila Azadbakht, Maedeh Moradi, Mohammad Reza Merasi, Farzaneh Jahangir

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Maternal dietary intake during lactation might affect the growth rate of an exclusive breastfed infant. The present study was conducted to evaluate the effect of maternal dietary patterns and quality during lactation on the growth of the exclusive breastfed infant. Methods: 484 healthy lactating mothers with their infant were enrolled in this study. Only exclusive breastfed infants were included in this study which was conducted in Iran. Dietary intake of lactating mothers was assessed using a validated and reliable semi-quantitative food frequency questionnaire. Diet quality indices such as alternative Healthy eating index (HEI), Dietary energy density (DED), and adherence to Mediterranean dietary pattern score, Nordic and dietary approaches to stop hypertension (DASH) eating pattern were created. Anthropometric features of infant (weight, height, and head circumference) were recorded at birth, two and four months. Results: Weight, length, weight for height and head circumference of infants at two months and four months age were mostly in the normal range among those that mothers adhered more to the HEI in lactation period (normal weight: 61%; normal height: 59%). The prevalence of stunting at four months of age among those whose mothers adhered more to the HEI was 31% lower than those with the least adherence to HEI. Mothers in the top tertiles of HEI score had the lowest frequency of having underweight infants (18% vs. 33%; P=0.03). Odds ratio of being overweight or obese at four months age was the lowest among those infants whose mothers adhered more to the HEI (OR: 0.67 vs 0.91; Ptrend=0.03). However, there was not any significant association between adherence of mothers to Mediterranean diet as well as DASH diet and Nordic eating pattern and the growth of infants (none of weight, height or head circumference). Infant weight, length, weight for height and head circumference at two months and four months did not show significant differences among different tertile categories of mothers’ DED. Conclusions: Higher diet quality indices and more adherence of lactating mother to HEI (as an indicator of diet quality) may be associated with better growth indices of the breastfed infant. However, it seems that DED of the lactating mother does not affect the growth of the breastfed infant. Adherence to the different dietary patterns such as Mediterranean, DASH or Nordic among mothers had no different effect on the growth indices of the infants. However, higher diet quality indices and more adherence of lactating mother to HEI may be associated with better growth indices of the breastfed infant. Breastfeeding is a complete way that is not affected much by the dietary patterns of the mother. However, better diet quality might be associated with better growth.

Keywords: breastfeeding, growth, infant, maternal diet

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Authors: Sonam Kumari

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Tuberculosis is the deadliest disease worldwide. Millions of people lose their lives every year due to this disease. It has turned lethal due to the erratic nature of its causative organism, Mycobacterium tuberculosis (Mtb). Mtb tends to enter into an inactive, dormant state and emerge to replicating state upon encountering favorable conditions. The mechanism by which Mtb switches from the dormant state to the replicative form is still poorly characterized. Proteome studies have given us an insight into the role of certain proteins in giving stupendous virulence to Mtb, but numerous dotsremain unconnected and unaccounted. The WhiB family of proteins is one such protein that is associated with developmental processes in actinomycetes. Mtb has seven such proteins (WhiB1 to WhiB7). WhiB proteins are transcriptional regulators; they regulate various essential genes of Mtbby binding to their promoter DNA. Biophysical parameters of the effect of DNA binding on WhiB proteins has not yet been appropriately characterized. Interaction with DNA induces conformational changes in the WhiB proteins, confirmed by steady-state fluorescence and circular dichroism spectroscopy. ITC has deduced thermodynamic parameters and the binding affinity of the interaction. Since these transcription factors are highly unstable in vitro, their stability and solubility were enhanced by the co-expression of molecular chaperones. The present study findings help determine the conditions under which the WhiB proteins interact with their interacting partner and the factors that influence their binding affinity. This is crucial in understanding their role in regulating gene expression in Mtbandin targeting WhiB proteins as a drug target to cure TB.

Keywords: mycobacterium tuberculosis, TB, whiB proteins, ITC

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Authors: Arati Inamdar, Siddharth Bhattacharyya, Kester Haye

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Collision tumors are rare entities characterized by neoplasms of two different cell populations with distinct separating boundaries. Such tumors could be benign, malignant, or a combination of both. The exact mechanism of origin for collision tumors is predicted to be tumor heterogeneity or concurrent occurrence of neoplasm in the same organ. We present two cases of plasmacytoma presenting as a collision tumor, one with a tumor of hematological origin and another with a non-hematological origin, namely Chronic Lymphocytic Leukemia and Adenocarcinoma of the colon, respectively. The immunohistochemical stains and flowcytometry analysis performed on the specimens aided incorrect diagnosis. Interestingly, neoplastic cells of plasmacytoma in the first case demonstrated strong cytokeratin along with weak Epithelial Specific Antigen/ Epithelial cell adhesion molecule Monoclonal Antibody (MOC31) positivity, indicating that the tumor may influence the microenvironment of the tumor in the vicinity. Furthermore, the next-generation sequencing studies performed on the specimen with plasmacytoma and chronic lymphocytic lymphoma demonstrated BReast CAncer gene (BRCA2) and Tumor Necrosis Factor Alpha Induced Protein 3 (TNFAIP3) as a disease associated variants suggestive of risk for multiple tumors including collision tumors. Our reports highlight the unique collision tumors involving plasmacytoma, which have never been reported previously, as well as provide necessary insights about the underline genetic aberrations and tumor heterogeneity through sequencing studies and allow clonality assessment for subsequent tumors.

Keywords: BRCA2, collision tumor, chronic lymphocytic leukemia, plasmacytoma

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Authors: A. R. Nezamabadi, M. Veiskarami

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This paper studies free vibration of simply supported functionally graded beams with piezoelectric layers based on the first order shear deformation theory. The Young's modulus of beam is assumed to be graded continuously across the beam thickness. The governing equation is established. Resulting equation is solved using the Euler's equation. The effects of the constituent volume fractions, the influences of applied voltage on the vibration frequency are presented. To investigate the accuracy of the present analysis, a compression study is carried out with a known data.

Keywords: mechanical buckling, functionally graded beam, first order shear deformation theory, free vibration

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Authors: Seyyed Mohammad Amin Mousavi Sagharchi, Alireza Mahmoudi Nasab, Tim Bakker

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Introduction: Mycobacterium tuberculosis (MTB) is the most intelligent bacterium that existed in the world to our best knowledge. This bacterium can cause tuberculosis (TB) which is responsible for its spread speed and murder of millions of people around the world. MTB has the practical function to escape from anti-tuberculosis drugs (AT), for this purpose, it handles some mutations in the main genes and creates new patterns for inhibited genes. Method and materials: Researchers have their best tries to safely isolate MTB from the sputum specimens of 35 patients in some hospitals in the Tehran province and detect MTB by culture on Löwenstein-Jensen (LJ) medium and microscopic examination. DNA was extracted from the established bacterial colony by enzymatic extraction method. It was amplified by the polymerase chain reaction (PCR) method, reverse hybridization, and evaluation for detection of resistance genes; generally, researchers apply GenoType MTBDRplus assay. Results: Investigations of results declare us that 21 of the isolated specimens (about 60%) have mutation in rpoB gene, which resisted to rifampicin (most prevalence), and 8 of them (about 22.8%) have mutation in katG or inhA genes which resisted to isoniazid. Also, 4 of them (about 11.4%) don't have any mutation, and 2 of them (about 5.7%) have mutation in every three genes, which makes them resistant to the two drugs mentioned above. Conclusion: Rifampicin and isoniazid are two essential AT that using in the first line of treatment. Resistance in rpoB, and katG, and inhA genes related to mentioned drugs lead to ineffective treatment.

Keywords: mycobacterium tuberculosis, tuberculosis, drug resistance, isoniazid, rifampicin

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Authors: Zia Ullah, Muhammad Asim, Shi Sujuan, Rayyan Khan, Aaqib Shaheen, LIU Haobao

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The plant-specific auxin efflux proteins PIN-FORMED (PIN) have been well depicted in many plant species for their essential roles in regulating the transport of auxins in several phases of plant growth. Little is known about the various functions of the PIN family genes in the Nicotiana tabacum (N. tabacum) species during plant growth. To define the expression pattern of the NtPIN1a gene under abiotic stresses and hormone treatment, transgenic tobacco with promoterNtPIN1a::GUS construct was employed. Comprehensive computational analyses of the NtPIN1a promoter confirmed the existence of common core promoter elements including CAAT-box, TATA-box, hormone, and abiotic stress-responsive elements such as ABRE, P-box, MYC, MYB, ARE, and GC-motifs. The transgenic plants with the promoter of NtPIN1a displayed a promising expression of β-glucuronidase (GUS) in germinating seeds, root tips, shoot-apex, and developing leaves under optimal conditions. While the differential expression of GUS in moderate salt, drought, low potassium stresses, and externally high auxin level at two different time points, suggested NtPIN1a played a key role in growth processes and the plants’ response to abiotic stresses. This analysis provides a foundation for more in-depth discoveries of the biological functions of NtPIN1a in Nicotiana species and this promoter may be employed in genetic engineering of other crops for enhanced stress tolerance.

Keywords: tobacco, nicotiana tabacum, pin, promoter, GUS, abiotic stresses, auxin

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Authors: Kais Amir Kadhim

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Context: The study focuses on the rhetorical structure of chapters in engineering final year projects, specifically the Introduction chapter, written by UMT (University of Marine Technology) engineering students. Existing research has explored the use of genre-based approaches to analyze the writing of final year projects in various disciplines. Research Aim: The aim of this study is to investigate the rhetorical structure of Introduction chapters in engineering final year projects by UMT students. The study aims to identify the frequency of communicative moves and their constituent steps within the Introduction chapters, as well as understand how students justify their research projects. Methodology: The research design will utilize a mixed method approach, combining both quantitative and qualitative methods. Forty Introduction chapters from two different fields in UMT engineering undergraduate programs will be selected for analysis. Findings: The study intends to identify the types of moves present in the Introduction chapters of engineering final year projects by UMT students. Additionally, it aims to determine if these moves and steps are obligatory, conventional, or optional. Theoretical Importance: The study draws upon Bunton's modified CARS (Creating a Research Space) model, which is a conceptual framework used for analyzing the introduction sections of theses. By applying this model, the study contributes to the understanding of the rhetorical structure of Introduction chapters in engineering final year projects. Data Collection: The study will collect data from forty Introduction chapters of engineering final year projects written by UMT engineering students. These chapters will be selected from two different fields within UMT's engineering undergraduate programs. Analysis Procedures: The analysis will involve identifying and categorizing the communicative moves and their constituent steps within the Introduction chapters. The study will utilize both quantitative and qualitative analysis methods to examine the frequency and nature of these moves. Question Addressed: The study aims to address the question of how UMT engineering students structure and justify their research projects within the Introduction chapters of their final year projects. Conclusion: The study aims to contribute to the knowledge of rhetorical structure in engineering final year projects by investigating the Introduction chapters written by UMT engineering students. By using a mixed method research design and applying the modified CARS model, the study intends to identify the types of moves and steps employed by students and explore their justifications for their research projects. The findings have the potential to enhance the understanding of effective academic writing in engineering disciplines.

Keywords: cohesive markers, learning, meaning, students

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Authors: Burcu Inal, Irfan Kandemir

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Sequences of mitochondrial cytochrome oxidase I (COI) gene of twenty-five Turkish and one Greek Myzus cerasi (Fabricus) (Hemiptera: Aphididae) in populations were collected from Prunus avium and Prunus cerasus. The partial coding region of COI studied is 605 bp for all the populations, from which 565 nucleotides were conserved, 40 were variable, 37 were singleton, and 3 sites were parsimony-informative. Four haplotypes were identified based on nucleotide substitutions, and the mean of intraspecific divergence was calculated to be 0.3%. Phylogenetic trees were constructed using Maximum Likelihood, Minimum Evolution, Neighbor-joining, and Unweighed Pair Group Method of Arithmetic Averages (UPGMA) and Myzus persicae (Sulzer) and Myzus borealis Ossiannilson were included as outgroups. The population of M. cerasi from Isparta diverged from the rest of the groups and formed a clade (Haplotype B) with Myzus borealis. The rest of the haplotype diversity includes Haplotype A and Haplotype C with individuals characterized as Myzus cerasi pruniavium and Haplotype D with Myzus cerasi cerasi. M. cerasi diverge into two subspecies and it must be reevaluated whether this pest is monophagous or oligophagous in terms of plant type dependence. The obligated endosymbiont Buchnera aphidicola was also found during this research, but no facultative symbionts could be found. It is expected further studies will be required for a complete barcoding and diversity of bacterial endosymbionts present.

Keywords: bacterial endosymbionts, barcoding, black cherry aphid, nucleotide diversity

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Authors: Carlos Teodoro, Oscar Bautista

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In this work, we analyze theoretically the mass transport in a time-periodic electroosmotic flow through a parallel flat plate microchannel under different periodic functions of the applied external electric field. The microchannel connects two reservoirs having different constant concentrations of an electro-neutral solute, and the zeta potential of the microchannel walls are assumed to be uniform. The governing equations that allow determining the mass transport in the microchannel are given by the Poisson-Boltzmann equation, the modified Navier-Stokes equations, where the Debye-Hückel approximation is considered (the zeta potential is less than 25 mV), and the species conservation. These equations are nondimensionalized and four dimensionless parameters appear which control the mass transport phenomenon. In this sense, these parameters are an angular Reynolds, the Schmidt and the Péclet numbers, and an electrokinetic parameter representing the ratio of the half-height of the microchannel to the Debye length. To solve the mathematical model, first, the electric potential is determined from the Poisson-Boltzmann equation, which allows determining the electric force for various periodic functions of the external electric field expressed as Fourier series. In particular, three different excitation wave forms of the external electric field are assumed, a) sawteeth, b) step, and c) a periodic irregular functions. The periodic electric forces are substituted in the modified Navier-Stokes equations, and the hydrodynamic field is derived for each case of the electric force. From the obtained velocity fields, the species conservation equation is solved and the concentration fields are found. Numerical calculations were done by considering several binary systems where two dilute species are transported in the presence of a carrier. It is observed that there are different angular frequencies of the imposed external electric signal where the total mass transport of each species is the same, independently of the molecular diffusion coefficient. These frequencies are called crossover frequencies and are obtained graphically at the intersection when the total mass transport is plotted against the imposed frequency. The crossover frequencies are different depending on the Schmidt number, the electrokinetic parameter, the angular Reynolds number, and on the type of signal of the external electric field. It is demonstrated that the mass transport through the microchannel is strongly dependent on the modulation frequency of the applied particular alternating electric field. Possible extensions of the analysis to more complicated pulsation profiles are also outlined.

Keywords: electroosmotic flow, mass transport, oscillatory flow, species separation

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Authors: Hafsa Tahir, Sanaullah Iqbal

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Glactooligosaccharide (GOS) is a type of prebiotic which is mainly found in human milk. GOS belongs to those bacteria which stimulates the growth of beneficial bacteria in human intestines. The aim of the present study was to develop a value-added product by producing prebiotic (GOS) in buttermilk through trans galactosylation. Buttermilk is considered as an industrial waste which is discarded after the production of butter and cream. It contains protein, minerals, vitamins and a smaller amount of fat. Raw milk was pasteurized at 100º C for butter production and then trans galactosylation process was induced in the butter milk thus obtained to produce prebiotic GOS. Results showed that the enzyme (which was obtained from bacterial strain of Esecrshia coli and has a gene of Lactobacillus reuteri L103) concentration between 400-600µl/5ml can produce GOS in 30 minutes. Chemical analysis and sensory evaluation of plain and GOS containing buttermilk showed no remarkable difference in their composition. Furthermore, the shelf-life study showed that there was non-significant (P>0.05) difference in glass and pouch packaging of buttermilk. Buttermilk in pouch packaging maintained its stability for 6 days without the addition of preservatives. Therefore it is recommended that GOS enriched buttermilk which is generally considered as a processing waste in dairy manufacturing can be turned into a cost-effective nutritional functional food product. This will not only enhance the production efficiency of butter processing but also will create a new market opportunity for dairy manufacturers all over the world.

Keywords: buttermilk, galactooligosaccharide, shelf Life, transgalactosylation

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Authors: Navkiran Kaur, Apoorva Mathur, Abhishree Agarwal, Sakshi Gupta, Tuhin Rashmi

Abstract:

Aim: Breast cancer is the most common cancer in women worldwide, and resistance to the current therapeutics, often concurrently, is an increasing clinical challenge. Glycosylation of proteins is one of the most important post-translational modifications. It is widely known that aberrant glycosylation has been implicated in many different diseases due to changes associated with biological function and protein folding. Alterations in cell surface glycosylation, can promote invasive behavior of tumor cells that ultimately lead to the progression of cancer. In breast cancer, there is an increasing evidence pertaining to the role of glycosylation in tumor formation and metastasis. In the present study, an attempt has been made to study the disease associated sialoglycoproteins in breast cancer by using bioinformatics tools. The sequence will be retrieved from UniProt database. A database in the form of a word document was made by a collection of FASTA sequences of breast cancer gene sequence. Glycosylation was studied using yinOyang tool on ExPASy and Differential genes expression and protein analysis was done in context of breast cancer metastasis. The number of residues predicted O-glc NAc threshold containing 50 aberrant glycosylation sites or more was detected and recorded for individual sequence. We found that the there is a significant change in the expression profiling of glycosylation patterns of various proteins associated with breast cancer. Differential aberrant glycosylated proteins in breast cancer cells with respect to non-neoplastic cells are an important factor for the overall progression and development of cancer.

Keywords: breast cancer, bioinformatics, cancer, metastasis, glycosylation

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Authors: Liyana Zahid, Mohd Fareq Abd Malek, Ee Meng Cheng, Wei Wen Liu, Yeng Seng Lee, Muhammad Nadeem Iqbal, Fwen Hoon Wee

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One of the parameters that affect the performance of microwave absorbers is the shape of the absorbers. This paper shows the performance (reflection loss) of truncated pyramidal and truncated wedge microwave absorbers in the range frequency between 8.2 to 12.4 GHz (X-Band) in simulation. The material used is sugarcane bagasse (SCB) which is one of the new materials that used to fabricate the microwave absorber. The complex permittivity was measured using Agilent dielectric probe technique. The designs were simulated using CST Microwave Studio Software. The reflection losses between these two shapes were compared.

Keywords: microwave absorber, reflection loss, sugarcane bagasse (SCB), X-Band

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Authors: Abeer A. Q. Ahmed, Tracey McKay

Abstract:

Biomass can provide a sustainable source for the production of high valued chemicals. Under the uncertain availability of fossil resources biomass could be the only available source for chemicals in future. Cellulose and hemicellulose can be hydrolyzed into their building blocks (hexsoses and pentoses) which can be converted later to the desired high valued chemicals. A cellulase- and xylanase- producing bacterial strain identified as Paenibacillus illinoisensis CX11 by 16S rRNA gene sequencing and phylogenetic analysis was found to have the ability to saccharify different lignocellulosic materials. Cellulase and xylanase activities were evaluated by 3,5-dinitro-salicylic acid (DNS) method using CMC and xylan as substrates. Results showed that P. illinoisensis CX11 have cellulase (2.63± 0.09 mg/ml) and xylanase (3.25 ± 0.2 mg/ml) activities. The ability of P. illinoisensis CX11 to saccharify lignocellulosic materials was tested using wheat straw (WS), wheat bran (WB), saw dust (SD), and corn stover (CS). DNS method was used to determine the amount of reducing sugars that were released from lignocellulosic materials. P. illinoisensis CX11 showed to have the ability to saccharify lignocellulosic materials and producing total reducing sugars as 2.34 ± 0.12, 2.51 ± 0.37, 1.86 ± 0.16, and 3.29 ± 0.20 mg/l from WS, WB, SD, and CS respectively. According to the author's knowledge, current findings are the first to report P. illinoisensis CX11 as a cellulase and xylanase producing species and that it has the ability to saccharify different lignocellulosic materials. This study presents P. illinoisensis CX11 that can be good source for cellulase and xylanase enzymes which could be introduced into lignocellulose bioconversion processes to produce high valued chemicals.

Keywords: cellulase, high valued chemicals, lignocellulosic materials, Paenibacillus illinoisensis CX11, Xylanase

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Authors: Charles Ruffner, Michael Manton, Gintautas Kibirkstis, Gediminas Brazaitas, Vitas Marozas, Ekaterine Makrickiene, Rutile Pukiene, Per Angelstam

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In dynamic boreal forests, fire is an important natural disturbance, which drives regeneration and mortality of living and dead trees, and thus successional trajectories. However, current forest management practices focusing on wood production only have effectively eliminated fire as a stand-level disturbance. While this is generally well studied across much of Europe, in Lithuania, little is known about the historic fire regime and the role fire plays as a management tool towards the sustainable management of future landscapes. Focusing on Scots pine forests, we explore; i) the relevance of fire disturbance regimes on forestlands of Lithuania; ii) fire occurrence in the Dzukija landscape for dry upland and peatland forest sites, and iii) correlate tree-ring data with climate variables to ascertain climatic influences on growth and fire occurrence. We sampled and cross-dated 132 Scots pine samples with fire scars from 4 dry pine forest stands and 4 peatland forest stands, respectively. The fire history of each sample was analyzed using standard dendrochronological methods and presented in FHAES format. Analyses of soil moisture and nutrient conditions revealed a strong probability of finding forests that have a high fire frequency in Scots pine forests (59%), which cover 34.5% of Lithuania’s current forestland. The fire history analysis revealed 455 fire scars and 213 fire events during the period 1742-2019. Within the Dzukija landscape, the mean fire interval was 4.3 years for the dry Scots pine forest and 8.7 years for the peatland Scots pine forest. However, our comparison of fire frequency before and after 1950 shows a marked decrease in mean fire interval. Our data suggest that hemi-boreal forest landscapes of Lithuania provide strong evidence that fire, both human and lightning-ignited fires, has been and should be a natural phenomenon and that the examination of biological archives can be used to guide sustainable forest management into the future. Currently, fire use is prohibited by law as a tool for forest management in Lithuania. We recommend introducing trials that use low-intensity prescribed burning of Scots pine stands as a regeneration tool towards mimicking natural forest disturbance regimes.

Keywords: biodiversity conservation, cultural burning, dendrochronology, forest dynamics, forest management, succession

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Authors: Shantol McIntosh

Abstract:

Due to environmental and underlying health disparities, the COVID-19 pandemic has caused an added set of economic implications worldwide. Black and Hispanic individuals are more susceptible to contract COVID-19, and if they do, they are more likely to have a severe case that necessitates hospitalization or results in death (Altarum et al., 2020). The literature shows that disparities in health and health treatment are nothing new as they have been recorded for decades and indicate systemic and structural imbalances rooted in racism and discrimination. The purpose of this study is to determine the frequency with which these populations have access to healthcare and treatment. The study will also highlight the key drivers of health disparities. Findings and implications for research and policy will be discussed.

Keywords: COVID-19, racial and ethnic disparities, discrimination, policy

Procedia PDF Downloads 191

Authors: Muhammad Sohail Sajid, Qurat-ul-Ain, Zafar Iqbal, Muhammad Nisar Khan, Asma Kausar, Adil Ejaz

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Rickettsiosis, caused by a Spotted Fever Group Rickettsiae (SFGR), is considered as an emerging infectious disease from public and veterinary perspective. The present study reports distribution of SFGR in the host (buffalo and cattle) and vector (ticks) population determined through gene specific amplification through PCR targeting outer membrane protein (ompA). Tick and blood samples were collected using standard protocols through convenient sampling from district Faisalabad. Ticks were dissected to extract salivary glands (SG). Blood and tick SG pools were subjected to DNA extraction and amplification of ompA using PCR. Overall prevalence of SFGR was reported as 21.5% and 33.6 % from blood and ticks, respectively. Hyalomma anatolicum was more prevalent tick associated with SFGR as compared to Rhipicephalus sp. Higher prevalence of SFGR was reported in cattle (25%) population as compared to that of buffalo (17.07%). On seasonal basis, high SFGR prevalence was recorded during spring season (48.1%, 26.32%, 17.76%) as compared to winter (27.9%, 21.43%, 15.38%) in vector and host (cattle and buffalo respectively) population. Sequencing analysis indicated that rickettsial endo-symbionts were associated with ticks of the study area. These results provided baseline information about the prevalence of SFGR in vector and host population.

Keywords: Rickettsia, livestock, polymerase chain reaction, sequencing, ticks, vectors

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Authors: Rudzani Manafe, Ezekiel Green

Abstract:

Brucella, has many different virulence factors that act as a causative agent of brucellosis, depending on the environment and other factors, some factors may play a role more than others during infection and as a result, play a role in becoming a causative agent for pathogenesis. Brucella melitensis and Brucella abortus are considered to be pathogenic to humans. The genetic regularity of nine potential causes of virulence of two Brucella species in Eastern Cape livestock have been examined. A hundred and twenty isolates obtained from Molecular Pathogenesis and Molecular Epidemiology Research Group (MPMERG) were used for this study. All isolates were grown on Brucella agar medium. Nine primer pairs were used for the detection of virB2, virB5, vceC, btpA, btpB, prpA, betB, bpe275, and bspB virulence factors using Polymerase chain reaction (PCR). Approximately 100% was observed for genes BecC and BetB from B. arbotus. While the lowest gene observed was PrpA at 4.6% from B. arbotus. BetB was detected in 34.7%, while virB2 and prpA (0%) were not detected in B. melitensis. The results from this research suggest that most isolates of Brucella have virulence-related genes associated with disease pathogenesis. Finally, our findings showed that Brucella strains in the Eastern Cape Province are extremely virulent as virulence characteristics exist in most strains investigated.

Keywords: putative virulence genes, brucella, polymerase chain reaction, milk

Procedia PDF Downloads 139