Search results for: sequence dependent setup times

Authors: Fern Baedyananda, Arkom Chaiwongkot, Somchai Niruthisard, Nakarin Kitkumthorn, Parvapan Bhattarakosol

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High-risk human papillomavirus (HPV) infections cause transformation of the host cells by down-regulating and inhibiting host regulatory proteins such as p53 and pRb by overexpressing the viral oncoproteins E6 and E7. However, the E1 protein which is the only enzyme encoded by HPV has also been shown to cause DNA instability leading to the integration of the virus into the host genome and triggering carcinogenic events. A 63bp duplication in the E1 helicase region has been detected in European patients. However, the clinical prognosis of these patients is still controversial. This study was performed to determine the presence of the HPV-16 E1 63bp duplication in patient cervical samples in Thai women and determine the sequence of the variant in the Thai population. Detection of the HPV-16 E1 duplication in the helicase region was performed in 90 patient cell samples across normal, cervical intraepithelial neoplasia I-III, and squamous cervical carcinoma stages by PCR. The PCR products were purified and sequenced to determine the presence of duplication variants.The variant form was found in 10% of all CIN 1 patients. In this study, the presence of the 63 bp duplication variant in the Thai population was found to be present and was further characterized. Interestingly, all samples that exhibited the variant form of HPV-16 E1 were classified as CIN I. Presence of the variant, constricted to mild dysplasia signifies the importance of HPV-16 E1 in carcinogenesis.

Keywords: carcinogenesis, cervical cancer, human papillomavirus, HPV-16 E1

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Authors: Dolly Kumari, H. Lhungdim

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Maternal health is one of the crucial health indicators for any country. 5th goal of Millennium Development Goals is also emphasising on improvement of maternal health. Soon after Independence government of India realizing the importance of maternal and child health care services, and took steps to strengthen in 1st and 2nd five year plans. In past decade the other health indicator which is life expectancy at birth has been observed remarkable improvement. But still maternal mortality is high in India and in some states it is observe much higher than national average. Government of India pour lots of fund and initiate National Rural Health Mission (NRHM) in 2005 to improve maternal health in country by providing affordable and accessible health care services. Accredited Social Heath Activist (ASHA) is one of the key components of the NRHM. Mainly ASHAs are selected female aged 25-45 years from village itself and accountable for the monitoring of maternal health care for the same village. ASHA are trained to works as an interface between the community and public health system. This study tries to assess the role of ASHA in utilizing maternal health care services and to see the level of awareness about benefits given under JSY scheme and utilization of those benefits by eligible women. For the study concurrent evaluation data from National Rural health Mission (NRHM), initiated by government of India in 2005 has been used. This study is based on 78205 currently married women from 70 different districts of India. Descriptive statistics, chi2 test and binary logistic regression have been used for analysis. The probability of institutional delivery increases by 2.03 times (p<0.001) while if ASHA arranged or helped in arranging transport facility the probability of institutional delivery is increased by 1.67 times (p<0.01) than if she is not arranging transport facility. Further if ASHA facilitated to get JSY card to the pregnant women probability of going for full ANC is increases by 1.36 times (p<0.05) than reference. However if ASHA discuses about institutional delivery and approaches to get register than probability of getting TT injection is 1.88 and 1.64 times (p<0.01) higher than that if she did not discus. Further, Probability of benefits from JSY schemes is 1.25 times (p<0.001) higher among women who get married after 18 years. The probability of benefits from JSY schemes is 1.25 times (p<0.001) higher among women who get married after 18 year of age than before 18 years, it is also 1.28 times (p<0.001) and 1.32 times (p<0.001) higher among women have 1 to 8 year of schooling and with 9 and above years of schooling respectively than the women who never attended school. Those women who are working have 1.13 times (p<0.001) higher probability of getting benefits from JSY scheme than not working women. Surprisingly women belongs to wealthiest quintile are .53times (P<0.001) less aware about JSY scheme. Results conclude that work done by ASHA has great influence on maternal health care utilization in India. But results also show that still substantial numbers of needed population are far from utilization of these services. Place of delivery is significantly influenced by referral and transport facility arranged by ASHA.

Keywords: institutional delivery, JSY beneficiaries, referral faculty, public health

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Authors: Kashif Nadeem, W. Zhang, X. G. Qiu

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Role of Co spins in CaCo2As2 single crystal is systematically studied by using dc magnetization and magnetic torque measurements. A spin-flop transition in the antiferromagnetism (AFM) CaCo2As2 single crystal is studied by using dc magnetization and magnetic torque. Field dependent and angle dependent torque magnetometry confirmed the existence of spin-flop transition in this compound which is in agreement with the dc magnetization studies. A comparison of dc magnetization and torque magnetometry measurements for CaCo2As2 single crystal is done in detail. In conclusion, torque magnetometry can be a useful tool to study the spin flop transition in low anisotropic compounds analogous to dc magnetization studies.

Keywords: spin flop transition, torque magnetometry, magnetization, anisotropic

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Authors: Manoj Kumar Gupta, Jayashree Bijwe

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Additives in lubricating oils are the focus of research attention since the further reduction in friction and wear properties of oils would lead to the further saving of tribo-materials and energy apart from improving their efficiency. Remarkable tribo-performance enhancement is reported in the literature due to addition of particles of solid lubricants in lubricating oils; especially that of nano-sizes. In the present work graphite nano-particles (NPs) in various amounts (1, 2, 3 and 4 wt. %) were used to explore the possible anti-wear (AW) performance enhancement in Group III oil. Polyisobutylene succinimide (PIBSI- 1 wt. %) was used as a dispersant for dispersing these NPs and to enhance the stability of these nano-suspensions. It was observed that PIBSI inclusion enhanced the stability of oil almost by eight times. NPs in all amounts enhanced the AW performance of oil considerably. The optimum amount was three wt. %, which led to the highest enhancement under all loads. The extent of benefits, however, were dependent on load. At the lowest (392 N) and highest loads (784 N), the benefits were not profound. At moderate load (588 N), highest improvement (around 60 %) was recorded. The SEM and AFM studies were done on the worn ball surfaces to reveal the detailed features of films transferred and proved useful to correlate the wear performance of oils.

Keywords: dispersant, graphite, nano-lubricant, anti-wear additive

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Authors: Jin-Hyeong Park, Hong-Seok Kim, Jin-Hyeok Yim, Young-Ji Kim, Dong-Hyeon Kim, Jung-Whan Chon, Kun-Ho Seo

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Salmonella contamination in chicken samples can cause major health problems in humans. However, not only the effects of antibiotic treatment during growth but also the impacts of poultry slaughter line on the prevalence of Salmonella in final chicken meat sold to consumers are unknown. In this study, we compared the isolation rates and antimicrobial resistance of Salmonella between antibiotic-free, conventional, conventional Korean native retail chicken meat samples and clonal divergence of Salmonella isolates by multilocus sequence typing. In addition, the distribution of extended-spectrum β-lactamase (ESBL) genes in ESBL-producing Salmonella isolates was analyzed. A total of 72 retail chicken meat samples (n = 24 antibiotic-free broiler [AFB] chickens, n = 24 conventional broiler [CB] chickens, and n = 24 conventional Korean native [CK] chickens) were collected from local retail markets in Seoul, South Korea. The isolation rates of Salmonella were 66.6% in AFB chickens, 45.8% in CB chickens, and 25% in CK chickens. By analyzing the minimum inhibitory concentrations of β -lactam antibiotics with the disc-diffusion test, we found that 81.2% of Salmonella isolates from AFB chickens, 63.6% of isolates from CB chickens, and 50% of isolates from CK chickens were ESBL producers; all ESBL-positive isolates had the CTX-M-15 genotype. Interestingly, all ESBL-producing Salmonella were revealed as ST16 by multilocus sequence typing. In addition, all CTX-M-15-positive isolates had the genetic platform of blaCTX-M gene (IS26-ISEcp1-blaCTX-M-15-IS903), to the best of our knowledge, this is the first report in Salmonella around the world. The Salmonella ST33 strain (S. Hadar) isolated in this study has never been reported in South Korea. In conclusion, our findings showed that antibiotic-free retail chicken meat products were also largely contaminated with ESBL-producing Salmonella and that their ESBL genes and genetic platforms were the same as those isolated from conventional retail chicken meat products.

Keywords: antibiotic-free poultry, conventional poultry, multilocus sequence typing, extended-spectrum β-lactamase, antimicrobial resistance

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Authors: Surajit Chakrabarty, Piyush Chauhan, Subhasis Panda, Sujoy Bhattacharya

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A large proportion of roads in India are not well maintained as per the laid down public safety guidelines leading to loss of direction control and fatal accidents. We propose a technique to detect speed breakers and potholes using mobile sensor data captured from multiple vehicles and provide a profile of the road. This would, in turn, help in monitoring roads and revolutionize digital maps. Incorporating randomness in the model formulation for detection of speed breakers and potholes is crucial due to substantial heterogeneity observed in data obtained using a mobile application from multiple vehicles driven by different drivers. This is accomplished with Hidden Markov Models, whose hidden state sequence is found for each time step given the observables sequence, and are then fed as input to LSTM network with peephole connections. A precision score of 0.96 and 0.63 is obtained for classifying bumps and potholes, respectively, a significant improvement from the machine learning based models. Further visualization of bumps/potholes is done by converting time series to images using Markov Transition Fields where a significant demarcation among bump/potholes is observed.

Keywords: deep learning, hidden Markov model, pothole, speed breaker

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Authors: Adriana C. Panayi, Riaz A. Agha, Brady A. Sieber, Dennis P. Orgill

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Background: Increased rates of both breast cancer and obesity have resulted in more women seeking breast reconstruction. These women may be at increased risk for perioperative complications. A systematic review was conducted to assess the outcomes in obese women who have undergone breast reconstruction following mastectomy. Methods: Cochrane, PUBMED and EMBASE electronic databases were screened and data was extracted from included studies. The clinical outcomes assessed were surgical complications, medical complications, length of postoperative hospital stay, reoperation rate and patient satisfaction. Results: 33 studies met the inclusion criteria for the review and 29 provided enough data to be included in the meta-analysis (71368 patients, 20061 of which were obese). Obese women were 2.3 times more likely to experience surgical complications (95 percent CI 2.19 to 2.39; P < 0.00001), 2.8 times more likely to have medical complications (95 percent CI 2.41 to 3.26; P < 0.00001) and had a 1.9 times higher risk of reoperation (95 percent CI 1.75 to 2.07; P < 0.00001). The most common complication, wound dehiscence, was 2.5 times more likely in obese women (95 percent CI 1.80 to 3.52; P < 0.00001). Sensitivity analysis confirmed that obese women were more likely to experience surgical complications (RR 2.36, 95% CI 2.22–2.52; P < 0.00001). Conclusions: This study provides evidence that obesity increases the risk of complications in both implant and autologous reconstruction. Additional prospective and observational studies are needed to determine if weight reduction prior to reconstruction reduces the perioperative risks associated with obesity.

Keywords: autologous reconstruction, breast cancer, breast reconstruction, literature review, obesity, oncology, prosthetic reconstruction

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Authors: R. Pääkkönen, L. Korpinen, F. Gobba

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The objective of our study is to investigate UV exposure in Finland through sample measurements as a typical case study in summer and winter. We measured UV-BC weighted radiation and calculated a daily dose, which is about 100–150 times the Finnish exposure limit value in summer and 1–6 times in winter. The measured ultraviolet indices varied from 0 to 7 (scale 0–18), which is less than the values obtained in countries that are located farther south from Tampere latitude of 61 degrees. In wintertime, the UV exposure was modest compared to summertime, 50–150 mW/m² and about 1–5 mW/m² in summer and winter, respectively. However, technical means to manage UV exposure in Scandinavia are also needed in summer- and springtime.

Keywords: ultraviolet radiation, measurement, winter, summer

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Authors: J. Adeppa, S. Samanta, O. K. Raina

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Fasciolosis is a widespread economically important parasitic infection throughout the world caused by Fasciola hepatica and F. gigantica. In order to identify novel immunogen conferring significant protection against fasciolosis, currently, research has been focused on the defined antigens viz. glutathione S-transferase, fatty acid binding protein, cathepsin-L, fluke hemoglobin, paramyosin, myosin and F. hepatica- Kunitz Type Molecule. Among various antigens, GST which plays a crucial role in detoxification processes, i.e. phase II defense mechanism of this parasite, has a unique position as a novel vaccine candidate and a drug target in the control of this disease. For producing the antigens in large quantities and their purification to complete homogeneity, the recombinant DNA technology has become an important tool to achieve this milestone. RT- PCR was carried out using F. gigantica total RNA as template, and an amplicon of 657 bp GST gene was obtained. TA cloning vector was used for cloning of this gene, and the presence of insert was confirmed by blue-white selection for recombinant colonies. Sequence analysis of the present isolate showed 99.1% sequence homology with the published sequence of the F. gigantica GST gene of cattle origin (accession no. AF112657), with six nucleotide changes at 72, 74, 423, 513, 549 and 627th bp found in the present isolate, causing an overall change of 4 amino acids. The 657 bp GST gene was cloned at BamH1 and HindIII restriction sites of the prokaryotic expression vector pPROEXHTb in frame with six histidine residues and expressed in E. coli DH5α. Recombinant protein was purified from the bacterial lysate under non-denaturing conditions by the process of sonication after lysozyme treatment and subjecting the soluble fraction of the bacterial lysate to Ni-NTA affinity chromatography. Western blotting with rabbit hyper-immune serum showed immuno-reactivity with 25 kDa recombinant GST. Recombinant protein detected F. gigantica experimental as well as field infection in buffaloes by dot-ELISA. However, cross-reactivity studies on Fasciola gigantica GST antigen are needed to evaluate the utility of this protein in the serodiagnosis of fasciolosis.

Keywords: fasciola gigantic, fasciola hepatica, GST, RT- PCR

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Authors: Evangelos Kaisar, Anika Tabassum, Taraneh Ardalan, Majed Al-Ghandour

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The economy of any country is dependent on its ability to accommodate the movement and delivery of goods. The demand for goods movement and services increases truck traffic on highways and inside the cities. The livability of most cities is directly affected by the congestion and environmental impacts of trucks, which are the backbone of the urban freight system. Better operation of heavy vehicles on highways and arterials could lead to the network’s efficiency and reliability. In many cases, roundabouts can respond better than at-level intersections to enable traffic operations with increased safety for both cars and heavy vehicles. Recently emerged, the concept of turbo-roundabout is a viable alternative to the two-lane roundabout aiming to improve traffic efficiency. The primary objective of this study is to evaluate the operation and performance level of an at-grade intersection, a conventional two-lane roundabout, and a basic turbo roundabout for freight movements. To analyze and evaluate the performances of the signalized intersections and the roundabouts, micro simulation models were developed PTV VISSIM. The networks chosen for this analysis in this study are to experiment and evaluate changes in the performance of the movement of vehicles with different geometric and flow scenarios. There are several scenarios that were examined when attempting to assess the impacts of various geometric designs on vehicle movements. The overall traffic efficiency depends on the geometric layout of the intersections, which consists of traffic congestion rate, hourly volume, frequency of heavy vehicles, type of road, and the ratio of major-street versus side-street traffic. The traffic performance was determined by evaluating the delay time, number of stops, and queue length of each intersection for varying truck percentages. The results indicate that turbo-roundabouts can replace signalized intersections and two-lane roundabouts only when the traffic demand is low, even with high truck volume. More specifically, it is clear that two-lane roundabouts are seen to have shorter queue lengths compared to signalized intersections and turbo-roundabouts. For instance, considering the scenario where the volume is highest, and the truck movement and left turn movement are maximum, the signalized intersection has 3 times, and the turbo-roundabout has 5 times longer queue length than a two-lane roundabout in major roads. Similarly, on minor roads, signalized intersections and turbo-roundabouts have 11 times longer queue lengths than two-lane roundabouts for the same scenario. As explained from all the developed scenarios, while the traffic demand lowers, the queue lengths of turbo-roundabouts shorten. This proves that turbo roundabouts perform well for low and medium traffic demand. The results indicate that turbo-roundabouts can replace signalized intersections and two-lane roundabouts only when the traffic demand is low, even with high truck volume. Finally, this study provides recommendations on the conditions under which different intersections perform better than each other.

Keywords: At-grade intersection, simulation, turbo-roundabout, two-lane roundabout

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Authors: Jessica Lopez Espejel, Mahaman Sanoussi Yahaya Alassan, Walid Dahhane, El Hassane Ettifouri

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Pretrained transformer-based models have shown high performance in natural language generation tasks. However, a new wave of interest has surged: automatic programming language code generation. This task consists of translating natural language instructions to a source code. Despite the fact that well-known pre-trained models on language generation have achieved good performance in learning programming languages, effort is still needed in automatic code generation. In this paper, we introduce JaCoText, a model based on Transformer neural network. It aims to generate java source code from natural language text. JaCoText leverages the advantages of both natural language and code generation models. More specifically, we study some findings from state of the art and use them to (1) initialize our model from powerful pre-trained models, (2) explore additional pretraining on our java dataset, (3) lead experiments combining the unimodal and bimodal data in training, and (4) scale the input and output length during the fine-tuning of the model. Conducted experiments on CONCODE dataset show that JaCoText achieves new state-of-the-art results.

Keywords: java code generation, natural language processing, sequence-to-sequence models, transformer neural networks

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Authors: Marcel Ciesla, Victoria Oberascher, Sven Eder, Stefan Kirchweger, Wolfgang E. Baaske, Gerald Ostermayer

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The omnipresent trend towards sustainable mobility is a major challenge, especially for commuters in rural areas. The use of micro public transport systems is expected to significantly reduce pollutant emissions, as several commuters travel the first mile together with a single pick-up bus instead of their own car. In this paper, different aspects of such a micro public transport system are analyzed. The main findings of the investigations should be how the travel times of commuters change and how many CO₂ emissions can be saved if some of the commuters use public transport instead of their own vehicle.

Keywords: micro public transport, green transportation, sustainable mobility, low-emission commuting

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Authors: Joseph Zernik

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The mechanics of rip currents are complex, involving interactions between waves, currents, water levels and the bathymetry, that present particular challenges for numerical models. Here, the effects of a grid-spacing dependent horizontal mixing on the wave-current interactions are studied. Near the shore, wave rays diverge from channels towards bar crests because of refraction by topography and currents, in a way that depends on the rip current intensity which is itself modulated by the horizontal mixing. At low resolution with the grid-spacing dependent horizontal mixing, the wave motion is the same for both coupling modes because the wave deviation by the currents is weak. In high-resolution case, however, classical results are found with the stabilizing effect of the flow by feedback of waves on currents. Lastly, wave-current interactions and the horizontal mixing strongly affect the intensity of the three-dimensional rip velocity.

Keywords: e-justice, federal courts, human rights, banking regulation, United States

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Authors: Cynthia E. Nwobodo, A. E. Agwu

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The study was carried out in Benue State, Nigeria. Multi-stage sampling technique was used to select 120 respondents from two agricultural zones in the State. Data was collected using interview schedule. Descriptive statistics was used in data analysis. Findings showed that youth farmers in the area had positive attitude to climate change adaptation and mitigation as shown by their response to a set of positive and negative statement including: the youth are very important stakeholders in climate change issues (M= 2.91), youths should be encouraged to be climate change conscious (2.90), everybody should be involved in planting trees not just the government (M= 2.89), I will be glad to participate in climate change seminars (M= 2.89) among others. Findings on information seeking behavior indicate that majority (80.8 %) of the respondents sought climate change information from radio at an average of 19.78 times per month, 53.3 % sought from friends and neighbours at an average of 12.55 times per month and 42.5 % sought from family members at an average of 12.55 times per month among others. It was recommended that Youth farmers should be made important stakeholders in climate change policies and programmes since they have a very positive attitude to climate change adaptation and mitigation.

Keywords: adaptation, mitigation, attitude, climate change, youth farmers

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Authors: A. C. Bennis, F. Dumas, F. Ardhuin, B. Blanke

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The mechanics of rip currents are complex, involving interactions between waves, currents, water levels and the bathymetry, that present particular challenges for numerical models. Here, the effects of a grid-spacing dependent horizontal mixing on the wave-current interactions are studied. Near the shore, wave rays diverge from channels towards bar crests because of refraction by topography and currents, in a way that depends on the rip current intensity which is itself modulated by the horizontal mixing. At low resolution with the grid-spacing dependent horizontal mixing, the wave motion is the same for both coupling modes because the wave deviation by the currents is weak. In high-resolution case, however, classical results are found with the stabilizing effect of the flow by feedback of waves on currents. Lastly, wave-current interactions and the horizontal mixing strongly affect the intensity of the three-dimensional rip velocity.

Keywords: numerical modeling, wave-current interactions, turbulence modeling, rip currents

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Authors: Yousuf Al Suleimani, Ahmed Al Mahruqi

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A typical cannabinoid O-1602 induces vasorelaxation and activates the orphan G protein-coupled receptor GPR55 in human endothelial cells. The aim of this study is to characterize the mechanisms of endothelium-independent relaxation of O-1602 in the rat small mesenteric artery using wire myograph. In endothelium-denuded vessels, O-1602 partially produced concentration-dependent vasorelaxation. In vessels depleted of intracellular Ca2+ (by EGTA and methoxamine), CaCl2 produced concentration-dependent contraction. Preincubation with O-1602 (at 10 µM and 30 µM) abolished the contractile responses (P<0.01). The putative antagonist at novel “endothelial anandamide receptor” O-1918 (10 µM) significantly reversed the inhibitory effect of O-1602 on CaCl2-induced vasoconstriction. It is likely that the mechanism of endothelium-independent vasorelaxation to O-1602 is mediated by interfering with Ca2+ entry via an O-1918-sensitive pathway.

Keywords: O-1602, endothelium, vasorelaxation, calcium

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Authors: Zineb Benouahmane, Zhang Lifeng

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Experimental oxidation tests at high temperature (1300°C-1500°C) on α-SiC samples have been performed with different holding times and atmosphere (air, argon). Oxidized samples were then analyzed using X-ray photoelectron spectroscopy coupled to SEM and DAKTEK surface profiler verification. The oxidation rate and the mas gain were found to increase with temperature and holding times, corresponding to a passive oxidation regime which lead to the formation of SiO2 layer. The sessile drop method is employed in order to measure the wetting angles between Si/SiC system at high temperature (1430°C-1550°C). Contact angle can be varied between 44 °C to 85°C, by controlling the oxygen content in α-SiC. Increasing the temperature occurred the infiltration of liquid silicon and deoxidation of the coating.

Keywords: oxidation, wettability, silicon, SiC

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Authors: Wen-Yang Hu, Ranli Lu, Mark Maienschein-Cline, Danping Hu, Larisa Nonn, Toshi Shioda, Gail S. Prins

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Background: Genetic mutations are highly associated with increased prostate cancer risk. In addition to whole genome sequencing, somatic mutations can be identified by aligning transcriptome sequences to the human genome. Here we analyzed bulk RNAseq and single cell RNAseq data of human prostate cancer cells and their matched non-cancer cells in benign regions from 4 individual patients. Methods: Sequencing raw reads were aligned to the reference genome hg38 using STAR. Variants were annotated using Annovar with respect to overlap gene annotation information, effect on gene and protein sequence, and SIFT annotation of nonsynonymous variant effect. We determined cancer-specific novel alleles by comparing variant calls in cancer cells to matched benign cells from the same individual by selecting unique alleles that were only detected in the cancer samples. Results: In bulk RNAseq data from 3 patients, the most common variants were the noncoding mutations at UTR3/UTR5, and the major variant types were single-nucleotide polymorphisms (SNP) including frameshift mutations. C>T transversion is the most frequently presented substitution of SNP. A total of 222 genes carrying unique exonic or UTR variants were revealed in cancer cells across 3 patients but not in benign cells. Among them, transcriptome levels of 7 genes (CITED2, YOD1, MCM4, HNRNPA2B1, KIF20B, DPYSL2, NR4A1) were significantly up or down regulated in cancer stem cells. Out of the 222 commonly mutated genes in cancer, 19 have nonsynonymous variants and 11 are damaged genes with variants including SIFT, frameshifts, stop gain/loss, and insertions/deletions (indels). Two damaged genes, activating transcription factor 6 (ATF6) and histone demethylase KDM3A are of particular interest; the former is a survival factor for certain cancer cells while the later positively activates androgen receptor target genes in prostate cancer. Further, single cell RNAseq data of cancer cells and their matched non-cancer benign cells from both primary 2D and 3D tumoroid cultures were analyzed. Similar to the bulk RNAseq data, single cell RNAseq in cancer demonstrated that the exonic mutations are less common than noncoding variants, with SNPs including frameshift mutations the most frequently presented types in cancer. Compared to cancer stem cell enriched-3D tumoroids, 2D cancer cells carried 3-times higher variants, 8-times more coding mutations and 10-times more nonsynonymous SNP. Finally, in both 2D primary and 3D tumoroid cultures, cancer stem cells exhibited fewer coding mutations and noncoding SNP or insertions/deletions than non-stem cancer cells. Summary: Our study demonstrates the usefulness of bulk and single cell RNAseaq data in identifying somatic mutations in prostate cancer, providing an alternative method in screening candidate genes for prostate cancer diagnosis and potential therapeutic targets. Cancer stem cells carry fewer somatic mutations than non-stem cancer cells due to their inherited immortal stand DNA from parental stem cells that explains their long-lived characteristics.

Keywords: prostate cancer, stem cell, genomic mutation, RNAseq

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Authors: Lian Liu

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By analyzing the content of the New York Times' China-related energy reports, this study aims to explore the construction of China's national image by the mainstream media in the United States. The study analyzes three aspects of the coverage: topics, reporting tendencies, and countries involved. The results of the study show that economic issues are the main focus of the New York Times’ China-related energy coverage, followed by political issues and environmental issues. Overall, the coverage tendency was mainly negative, but positive coverage was dominated by science and technology issues. In addition, the study found that U.S.-China relations and Sino-Russian relations were important contexts for the construction of China's national image in the NYT's China-related energy coverage. These stories highlight China's interstate interactions with the United States, Japan, and Russia, which serve as important links in the coverage. The findings of this study reveal some characteristics and trends of the U.S. mainstream media's country image of China, which are important for a deeper understanding of the U.S.-China relationship and the media's influence on the construction of the country's image.

Keywords: media coverage, China, content analysis, visualization technology

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Authors: Wan Liu, Haibo Wang, Cathy Huang, Zhiwu Tan, Zhiwei Chen

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The tremendous diversity of HIV-1 has been a major challenge for an effective AIDS vaccine development. Mosaic approach presents the potential for vaccine design aiming for global protection. The mosaic antigen of HIV-1 Gag allows antigenic breadth for vaccine-elicited immune response against a wider spectrum of viral strains. However, the enhancement of immune response using vaccines is dependent on the strategy used. Heterologous prime/boost regimen has been shown to elicit high levels of immune responses. Here, we investigated whether priming using plasmid DNA with electroporation followed by boosting with the live replication-competent modified vaccinia virus vector TianTan (MVTT) combined with the mosaic antigenic sequence could elicit a greater and broader antigen-specific response against HIV-1 Gag in mice. When compared to DNA or MVTT alone, or MVTT/MVTT group, DNA/MVTT group resulted in coincidentally high frequencies of broadly reactive, Gag-specific, polyfunctional, long-lived, and cytotoxic CD8+ T cells and increased anti-Gag antibody titer. Meanwhile, the vaccination could upregulate PD-1+, and Tim-3+ CD8+ T cell, myeloid-derived suppressive cells and Treg cells to balance the stronger immune response induced. Importantly, the prime/boost vaccination could help control the EcoHIV and mesothelioma AB1-gag challenge. The stronger protective Gag-specific immunity induced by a Mosaic DNA/MVTT vaccine corroborate the promise of the mosaic approach, and the potential of two acceptably safe vectors to enhance anti-HIV immunity and cancer prevention.

Keywords: DNA/MVTT vaccine, EcoHIV, mosaic antigen, mesothelioma AB1-gag

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Authors: Remi Safi, Aline Hamade, Najat Bteich, Jamal El Saghir, Mona Diab Assaf, Marwan El-Sabban, Fadia Najjar

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Estrogen is considered a risk factor for breast cancer since it promotes breast-cell proliferation. The jaesckeanadiol-3-p-hydroxyphenylpropanoate, a hemi-synthetic analogue of the natural phytoestrogen ferutinin (jaesckeanadiol-p-hydroxybenzoate), is designed to be devoid of estrogenic activity. This analogue induces a cytotoxic effect 30 times higher than that of ferutinin towards MCF-7 breast cancer cell line. We compared these two compounds with respect to their effect on proliferation, cell cycle distribution and cancer stem-like cells in the MCF-7 cell line. Treatment with ferutinin (30 μM) and its analogue (1 μM) produced a significant accumulation of cells at the pre G0/G1 cell cycle phase and triggered apoptosis. Importantly, this compound retains its anti-proliferative activity against breast cancer stem/progenitor cells that are naturally insensitive to ferutinin at the same dose. These results position ferutinin analogue as an effective compound inhibiting the proliferation of estrogen-dependent breast cancer cells and consistently targeting their stem-like cells.

Keywords: ferutinin, hemi-synthetic analogue, breast cancer, estrogen, stem/progenitor cells

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Authors: Sulaiman A. Alrumman, Abd El-Latif Hesham

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Despite medical progress worldwide, dental caries are still widespread. Miswak is derived from the plant arak (Salvadora persica). It is used by Muslim people as a natural product for the cleansing of teeth, to ensure oral and dental hygiene. This study was designed to evaluate the antimicrobial effects of ethanol, methanol, and ethanol/methanol extracts of miswak against three bacterial pathogens of the oral cavity. The pathogens were isolated from the oral cavity of volunteers/patients and were identified on the basis of 16S rRNA gene amplification data. Sequence comparisons were made with 16S rRNA gene sequences available in the GenBank database. The results of sequence alignment and phylogenetic analysis identified the three pathogens as being Staphylococcus aureus strain KKU-020, Enterococcus faecalis strain KKU-021 and Klebsiella pneumoniae strain KKU-022. All miswak extracts showed powerful antimicrobial activity against the three pathogens. The maximum zone of inhibition (40.67±0.88 mm) was observed against E. faecalis with ethanolic extracts whilst methanolic extracts showed the minimum zone of inhibition (10.33±0.88 mm) against K. pneumonia KKU-022. Based on the significant effects of the miswak extracts against the oral cavity pathogens in our study, we recommend that miswak is to be used as a dental hygiene method to prevent tooth caries.

Keywords: antibacterial, miswak, Salvadora persica, oral cavity pathogens

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Authors: Sonal Budhiraja, Biswabrata Pradhan

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This work considers statistical inference based on progressive Type-I interval censored data with random removal. The scheme of progressive Type-I interval censoring with random removal can be described as follows. Suppose n identical items are placed on a test at time T0 = 0 under k pre-fixed inspection times at pre-specified times T1 < T2 < . . . < Tk, where Tk is the scheduled termination time of the experiment. At inspection time Ti, Ri of the remaining surviving units Si, are randomly removed from the experiment. The removal follows a binomial distribution with parameters Si and pi for i = 1, . . . , k, with pk = 1. In this censoring scheme, the number of failures in different inspection intervals and the number of randomly removed items at pre-specified inspection times are observed. Asymptotic properties of the maximum likelihood estimators (MLEs) are established under some regularity conditions. A β-content γ-level tolerance interval (TI) is determined for two parameters Weibull lifetime model using the asymptotic properties of MLEs. The minimum sample size required to achieve the desired β-content γ-level TI is determined. The performance of the MLEs and TI is studied via simulation.

Keywords: asymptotic normality, consistency, regularity conditions, simulation study, tolerance interval

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Authors: Sarah Holdren, Laura Crook, Anne Drapkin Lyerly

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Objective: The COVID-19 Pandemic has drawn new attention to long-existing bioethical questions around pregnancy, childbirth, and parenthood. Due to the increased risk of severe COVID-19, pregnant individuals may experience anxiety regarding medical decision-making. Especially in the case of hospital births, questions around the ethics of bringing healthy pregnant individuals into a high-risk environment for viral transmission illuminate gaps in the American maternal and child healthcare system. Limited research has sought to understand the experiences of those who gave birth outside hospitals during this time. This study aims to understand pregnant individuals’ conceptualization of risk during the COVID-19 pandemic. Methods: Individuals who gave birth after March 2020 were recruited through advertisements on social media. Participants completed a 1-hour semi-structured interview and a demographic questionnaire. Interviews were transcribed and coded by members of the research team using thematic narrative analysis. Results: A total of 18 participants were interviewed and completed the demographic questionnaire. The language of risk was utilized in birth narratives in three different ways, which highlighted the multileveled and nuanced ways in which risk is understood and mitigated by pregnant and birthing individuals. These included: 1. The risk of contracting COVID-19 before, during, and after birth, 2. The risk of birth complications requiring medical interventions dependent on selected birthing space (home, birthing center, hospital), and 3. The overall risk of creating life in the middle of a pandemic. The risk of contracting COVID-19 and risk of birth complications were often weighed in paradoxical ways throughout each individual’s pregnancy, while phrases such as “pandemic baby” and “apocalypse” appeared throughout narratives and highlighted the broader implications of pregnancy and childbirth during this momentous time. Conclusions: Healthcare professionals should consider the variety of ways that pregnant and birthing individuals understand the risk when counseling patients on healthcare decisions, especially during times of healthcare crisis such as COVID-19. Future work should look to understand how the language of risk fits into a broader understanding of the human experience of growing life in times of crisis.

Keywords: maternal and child health, thematic narrative analysis, COVID-19, risk mitigation

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Authors: Arif İsmailov, Naila Hasanova, Gunay Orujalieva

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Homocysteine (HCY) is an indicator of prognostic value in monitoring regenerative processes in osteoporosis and osteoporotic fractures. The osteoporosis is known to be a serious health and economic problem, especially for women in the postmenopausal period. The study was carried out on patients 45-83 years old divided into 3 groups: group I – 14 patients with osteoporosis , group II – 15 patients with non-osteoporotic fractures, group III – 25 patients with osteoporotic fractures. The control group consisted of practically healthy 14 people. A blood sample was taken at 3 stages to monitor the dynamics of HCY level: on the 1st day before treatment, on the 10th day of treatment and 1 month after it. Blood levels of Hcy were determined at a wavelength of 450 nm by the ELİSA(Cloud Clone Corp.Elisa kits,USA). The statistical evaluation was performed by using SPSS 26.0 program (IBM SPSS Inc., USA).The results showed that on the 1st day before the treatment HCY concentration was statistically increased 2.7 times(PU = 0.108) in group I, 5.6 times (PU <0.001) in group II and 6.5 times (PU <0.001) in group III compared to the control group. Thus, the average value of HCY in group I was 1.76 ± 0.56 μg/ml; in group II – 3.57 ± 0.62 μg/ml; in group III – 4.2 ± 0.50 μg/ml. HCY level increases more sharply after fractures,especially in osteoporotic patients. In treatment period Vitamin D plays an important role in synthesis of the Cystathionine β‐synthase enzyme, which regulates HCY metabolism. Increased Hcy levels could lead to an increase in the risk of fracture through the interference in collagen cross-linking.

Keywords: homocysteine, osteoporosis, osteoporotic fractures, Vitamin D

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Authors: Bin Liu

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MicroRNAs (miRNAs) are small non-coding RNA molecules, functioning in transcriptional and post-transcriptional regulation of gene expression. The discrimination of the real pre-miRNAs from the false ones (such as hairpin sequences with similar stem-loops) is necessary for the understanding of miRNAs’ role in the control of cell life and death. Since both their small size and sequence specificity, it cannot be based on sequence information alone but requires structure information about the miRNA precursor to get satisfactory performance. Kmers are convenient and widely used features for modeling the properties of miRNAs and other biological sequences. However, Kmers suffer from the inherent limitation that if the parameter K is increased to incorporate long range effects, some certain Kmer will appear rarely or even not appear, as a consequence, most Kmers absent and a few present once. Thus, the statistical learning approaches using Kmers as features become susceptible to noisy data once K becomes large. In this study, we proposed a Gapped k-mer approach to overcome the disadvantages of Kmers, and applied this method to the field of miRNA prediction. Combined with the structure status composition, a classifier called imiRNA-GSSC was proposed. We show that compared to the original imiRNA-kmer and alternative approaches. Trained on human miRNA precursors, this predictor can achieve an accuracy of 82.34 for predicting 4022 pre-miRNA precursors from eleven species.

Keywords: gapped k-mer, imiRNA-GSSC, microRNA precursor, support vector machine

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Authors: Ruziana Masiran, Hamidin Awang, Cheah Y. T. Jun, Nor Fauziah Hashim, Archana Premkumar, Mohd. Feizel Aisiddiq, Mohd. Fakharuddin

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Risk behaviours among secondary school students are common and show an increasing trend over the years. Existing attachment styles between the students and their parents influence the psychosocial development of this group of population hence contributing to the adoption of risk behaviours. The aim of this study was to determine the associations between three risk behaviours; smoking, bullying and being bullied among secondary school students and their styles of attachment to parents in a district in Malaysia. Using multistage simple random sampling, a cross-sectional study was designed with the level of significance, α set at 0.05. The validated self-administered Inventory of Parent and Peer Attachment (IPPA) and Youth Risk Behaviours Surveillance Questionnaire focusing on smoking and bullying were utilized. Secondary school students aged 13 to 17 years old from ten schools in the district of Hulu Langat, Malaysia were sampled. Prevalence of smoking was 15.8%, bullying 8.5% and being bully victims 19.0%. It was found that male gender was a significant risk factor for smoking (p < 0.001), while being Chinese (OR=0.156, 95%CI=0.029-0.837, p=0.030) and having married parents (OR=0.490, 95%CI=0.302-0.796, p=0.490) are protective against smoking. Students with insecure attachment to mothers (OR=1.650, 95%CI=1.018-2.675, p=0.042) and fathers (OR=2.039, 95%CI=1.285-3.234, p=0.002) are at 1.6 and 2 times risk respectively to smoke compared to those with secure attachment. The odds of male students bullying is almost twice than that for female students (OR=2.017, 95%CI=1.416-2.873, p < 0.001), and the odds of being bullied is 1.5 times higher for male students (OR=1.519, 95%CI=1.183-1.950, p=0.001). Those who are insecurely attached to fathers are at 1.8 times higher risk to be bullies (OR=1.867, 95%CI=1.272-2.740, p < 0.001) and 1.5 times higher risk to be bullied (OR=1.546, 95%CI=1.026-2.329, p=0.037). In conclusion, insecure attachment shows a strong association with smoking, bullying and being bullied among secondary school students in Malaysia.

Keywords: attachment styles, bullied, bullying, insecure attachment, risk behaviours, smoking and attachment

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Authors: Shiva Emami, Jenny Persson, Bengt Johansson Lindbom

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Group A streptococcus (GAS) is a prevalent human pathogen, causing a wide range of infections and diseases. One of the most well-known virulence factors in GAS is M protein, a surface protein that facilitates bacterial invasion. In this study, we used a recombinant GAS strain (GAS-2W) expressing M protein containing a hyper immunogenic peptide (2W). Mice were immunized three times with heat-killed-GAS subcutaneously at three weeks intervals. Three weeks post last immunization, mice were challenged intraperitoneally with a lethal dose of live GAS. In order to investigate the impact of IFN-ƴ and antibodies in protection against GAS infection, we used a mouse model knock-out for IFN-ƴ (IFN-ƴ KO). We observed immunization with GAS-2W strain can increase protection against GAS infection in mice compared with the original GAS strain. Higher levels of antibodies against M1 protein were measured in GAS-2W-immunized mice. There was also a significant increase in IgG2c response in mice immunized with GAS2W. By using IFN-ƴ KO mice, we showed that not a high level of total IgG, but IgG2c was correlated with protection through the i.p challenge. It also emphasizes the importance of IFN-ƴ cytokine to combat GAS by isotype switching to IgG2c (which is opsonic for phagocytosis). Our data indicate the crucial role of IFN-ƴ in the protective immune response that, together with IgG2c, can induce protection against GAS.

Keywords: Group A streptococcus, IgG2c, IFN-γ, protection

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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

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Authors: Bundit Pungnirund

Abstract:

The purposes of this research were to develop and to monitor the antecedent factors which directly affected the success rate of new product development. This was a case study of the leather industry in Bangkok, Thailand. A total of 350 leather factories were used as a sample group. The findings revealed that the new product development model was harmonized with the empirical data at the acceptable level, the statistic values are: x^2=6.45, df= 7, p-value = .48856; RMSEA = .000; RMR = .0029; AGFI = .98; GFI = 1.00. The independent variable that directly influenced the dependent variable at the highest level was marketing outcome which had a influence coefficient at 0.32 and the independent variables that indirectly influenced the dependent variables at the highest level was a clear organization policy which had a influence coefficient at 0.17, whereas, all independent variables can predict the model at 48 percent.

Keywords: antecedent, new product development, leather industry, Thailand

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