Search results for: molecular identification

Authors: Margarita S. Tikhonova, Alireza Baniasad, Anton G. Kalmykov, Georgy A. Kalmykov, Ralf Littke

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There is a high complexity in the pore structure of organic-rich rocks caused by the combination of inter-particle porosity from inorganic mineral matter and ultrafine intra-particle porosity from both organic matter and clay minerals. Fluids are retained in that pore space, but there are major uncertainties in how and where the fluids are stored and to what extent they are accessible or trapped in 'closed' pores. A large degree of tortuosity may lead to fractionation of organic matter so that the lighter and flexible compounds would diffuse to the reservoir whereas more complicated compounds may be locked in place. Additionally, parts of hydrocarbons could be bound to solid organic matter –kerogen– and mineral matrix during expulsion and migration. Larger compounds can occupy thin channels so that clogging or oil and gas entrapment will occur. Sequential extraction of applying different solvents is a powerful tool to provide more information about the characteristics of trapped organic matter distribution. The Upper Jurassic – Lower Cretaceous Bazhenov shale is one of the most petroliferous source rock extended in West Siberia, Russia. Concerning the variable mineral composition, pore space distribution and thermal maturation, there are high uncertainties in distribution and composition of organic matter in this formation. In order to address this issue geological and geochemical properties of 30 samples including mineral composition (XRD and XRF), structure and texture (thin-section microscopy), organic matter contents, type and thermal maturity (Rock-Eval) as well as molecular composition (GC-FID and GC-MS) of different extracted materials during sequential extraction were considered. Sequential extraction was performed by a Soxhlet apparatus using different solvents, i.e., n-hexane, chloroform and ethanol-benzene (1:1 v:v) first on core plugs and later on pulverized materials. The results indicate that the studied samples are mainly composed of type II kerogen with TOC contents varied from 5 to 25%. The thermal maturity ranged from immature to late oil window. Whereas clay contents decreased with increasing maturity, the amount of silica increased in the studied samples. According to molecular geochemistry, stored hydrocarbons in open and closed pore space reveal different geochemical fingerprints. The results improve our understanding of hydrocarbon expulsion and migration in the organic-rich Bazhenov shale and therefore better estimation of hydrocarbon potential for this formation.

Keywords: Bazhenov formation, bitumen, molecular geochemistry, sequential extraction

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Authors: Memoona Ramzan, Bushra Tabassum, Anwar Khan, Muhammad Tariq, Mudassar Fareed Awan, Idrees Ahmad Nasir, Zahida Qamar, Naila Shahid, Tayyab Husnain

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Biological control is a novel approach being used in crop protection nowadays. Bacteria like Bacillus and Pseudomonas are reported for this purpose and few of their products are commercially available too. Rhizosphere and phyllosphere of healthy cotton plants were used as a source to isolate bacteria capable of exhibiting properties worthy for selection as biocontrol agent. For this purpose all isolated strains were screened for the activities like phosphate solubilization, Indole acetic acid (IAA) production and biocontrol against fungi. Two strains S1HL3 and S1HL4 showed phosphate solubilization and IAA production simultaneously while two other JS2HR4 and JS3HR2 were good inhibitors of fungal pathogens. Through biochemical and molecular characterization these bacteria were identified as P. aeruginosa, Burkholderia and Bacillus respectively. In green house trials of these isolates against Cotton leaf curl virus (CLCuV), seven treatments including individual bacterial isolate and consortia were included. Treated plants were healthy as compared to control plants in which upto 74% CLCuV symptomatic plants exist. Maximum inhibition of CLCuV was observed in T7 treated plants where viral load was only 0.4% as compared to control where viral load was upto 74%. This treatment consortium included Bacillus and Pseudomonas isolates; S1HL3, S1HL4, JS2HR4 and JS3HR2. Principal Component Biplot depicted highly significant correlation between percentage viral load and the disease incidence.

Keywords: cotton leaf curl virus, biological control, bacillus, pseudomonas

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Authors: Haixu Yu, Wenhui Cao

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Tailoring Large Language Models (LLMs) to perform legal reasoning has been a popular trend in the study of AI and law. Researchers have mainly employed two methods to unlock the potential of LLMs, namely by finetuning the LLMs to expand their knowledge of law and by restructuring the prompts (In-Context Learning) to optimize the LLMs’ understanding of the legal questions. Although claiming the finetuning and renovated prompting can make LLMs more competent in legal reasoning, most state-of-the-art studies show quite limited improvements of practicability. In this paper, drawing on the study of the complexity and low interpretability of legal texts, we propose a prompting strategy based on the Chain of Thought (CoT) method. Instead of merely instructing the LLM to reason “step by step”, the prompting strategy requires the tested LLM to identify the ambiguity in the questions as the first step and then allows the LLM to generate corresponding answers in line with different understandings of the identified terms as the following step. The proposed prompting strategy attempts to encourage LLMs to "interpret" the given text from various aspects. Experiments that require the LLMs to answer “case analysis” questions of bar examination with general LLMs such as GPT 4 and legal LLMs such as LawGPT show that the prompting strategy can improve LLMs’ ability to better understand complex legal texts.

Keywords: ambiguity-identification, prompt, large language model, legal text understanding

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Authors: Balaji Ganesh Rajagopal, Subramanian Appavu alias Balamurugan, Ayyalraj Midhun Kumar, Krishnan Nallaperumal

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Intelligent Transportation System is an Emerging area to solve multiple transportation problems. Several forms of inputs are needed in order to solve ITS problems. Advanced Traveler Information System (ATIS) is a core and important ITS area of this modern era. This involves travel time forecasting, efficient road map analysis and cost based path selection, Detection of the vehicle in the dynamic conditions and Traffic congestion state forecasting. This Article designs and provides an algorithm for traffic data generation which can be used for the above said ATIS application. By inputting the real world traffic situation in the form of video sequences, the algorithm determines the Traffic density in terms of congestion, number of vehicles in a given path which can be fed for various ATIS applications. The Algorithm deduces the key frame from the video sequences and follows the Blob detection, Identification and Tracking using connected components algorithm to determine the correlation between the vehicles moving in the real road scene.

Keywords: traffic transportation, traffic density estimation, blob identification and tracking, relative velocity of vehicles, correlation between vehicles

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Authors: B. Wang, W. H. Or, S.C. Lee, Y.C. Leung, B. Organ

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This study presents an investigation of diesel vehicle particulate-phase emissions with neat ultralow sulphur diesel (B0, ULSD) and 5% waste cooking oil-based biodiesel blend (B5) in Hong Kong. A Euro VI light duty diesel vehicle was tested under transient (New European Driving Cycle (NEDC)), steady-state and idling on a chassis dynamometer. Chemical analyses including organic carbon (OC), elemental carbon (EC), as well as 30 polycyclic aromatic hydrocarbons (PAHs) and 10 oxygenated PAHs (oxy-PAHs) were conducted. The OC fuel-based emission factors (EFs) for B0 ranged from 2.86 ± 0.33 to 7.19 ± 1.51 mg/kg, and those for B5 ranged from 4.31 ± 0.64 to 15.36 ± 3.77 mg/kg, respectively. The EFs of EC were low for both fuel blends (0.25 mg/kg or below). With B5, the EFs of total PAHs were decreased as compared to B0. Specifically, B5 reduced total PAH emissions by 50.2%, 30.7%, and 15.2% over NEDC, steady-state and idling, respectively. It was found that when B5 was used, PAHs and oxy-PAHs with lower molecular weight (2 to 3 rings) were reduced whereas PAHs/oxy-PAHs with medium or high molecular weight (4 to 7 rings) were increased. Our study suggests the necessity of taking atmospheric and health factors into account for biodiesel application as an alternative motor fuel.

Keywords: biodiesel, OC/EC, PAHs, vehicular emission

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Authors: Recep Kesli, Huseyin Bilgin, Yasar Unlu, Gokhan Gungor

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Aim: The aim of this study was to compare diagnostic values of two different molecular-based tests (GenoType® HelicoDR ve Seeplex® H. pylori-ClaR- ACE Detection) in detection presence of the H. pylori from gastric biopsy specimens. In addition to this also was aimed to determine resistance ratios of H. pylori strains against to clarytromycine and quinolone isolated from gastric biopsy material cultures by using both the genotypic (GenoType® HelicoDR, Seeplex ® H. pylori -ClaR- ACE Detection) and phenotypic (gradient strip, E-test) methods. Material and methods: A total of 266 patients who admitted to Konya Education and Research Hospital Department of Gastroenterology with dyspeptic complaints, between January 2011-June 2013, were included in the study. Microbiological and histopathological examinations of biopsy specimens taken from antrum and corpus regions were performed. The presence of H. pylori in all the biopsy samples was investigated by five differnt dignostic methods together: culture (C) (Portagerm pylori-PORT PYL, Pylori agar-PYL, GENbox microaer, bioMerieux, France), histology (H) (Giemsa, Hematoxylin and Eosin staining), rapid urease test (RUT) (CLOtest, Cimberly-Clark, USA), and two different molecular tests; GenoType® HelicoDR, Hain, Germany, based on DNA strip assay, and Seeplex ® H. pylori -ClaR- ACE Detection, Seegene, South Korea, based on multiplex PCR. Antimicrobial resistance of H. pylori isolates against clarithromycin and levofloxacin was determined by GenoType® HelicoDR, Seeplex ® H. pylori -ClaR- ACE Detection, and gradient strip (E-test, bioMerieux, France) methods. Culture positivity alone or positivities of both histology and RUT together was accepted as the gold standard for H. pylori positivity. Sensitivity and specificity rates of two molecular methods used in the study were calculated by taking the two gold standards previously mentioned. Results: A total of 266 patients between 16-83 years old who 144 (54.1 %) were female, 122 (45.9 %) were male were included in the study. 144 patients were found as culture positive, and 157 were H and RUT were positive together. 179 patients were found as positive with GenoType® HelicoDR and Seeplex ® H. pylori -ClaR- ACE Detection together. Sensitivity and specificity rates of studied five different methods were found as follows: C were 80.9 % and 84.4 %, H + RUT were 88.2 % and 75.4 %, GenoType® HelicoDR were 100 % and 71.3 %, and Seeplex ® H. pylori -ClaR- ACE Detection were, 100 % and 71.3 %. A strong correlation was found between C and H+RUT, C and GenoType® HelicoDR, and C and Seeplex ® H. pylori -ClaR- ACE Detection (r:0.644 and p:0.000, r:0.757 and p:0.000, r:0.757 and p:0.000, respectively). Of all the isolated 144 H. pylori strains 24 (16.6 %) were detected as resistant to claritromycine, and 18 (12.5 %) were levofloxacin. Genotypic claritromycine resistance was detected only in 15 cases with GenoType® HelicoDR, and 6 cases with Seeplex ® H. pylori -ClaR- ACE Detection. Conclusion: In our study, it was concluded that; GenoType® HelicoDR and Seeplex ® H. pylori -ClaR- ACE Detection was found as the most sensitive diagnostic methods when comparing all the investigated other ones (C, H, and RUT).

Keywords: Helicobacter pylori, GenoType® HelicoDR, Seeplex ® H. pylori -ClaR- ACE Detection, antimicrobial resistance

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Authors: Nutnicha Wongpadungkiat, Suwit Siriwatanayotin, Aluck Thipayarat, Punchira Vongsawasdi, Chotika Viriyarattanasak

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Chicken products are major export product of Thailand. With a dramatically increasing consumption of chicken product in the world, there are abundant wastes from chicken meat processing industry. Recently, much research in the development of value-added products from chicken meat industry has focused on the production of protein hydrolysate, utilized as food ingredients for human diet and animal feed. The present study aimed to determine the effect of thermal pre-treatment on functional properties of chicken protein hydrolysate. Chicken breasts were heated at 40, 60, 80 and 100ºC prior to hydrolysis by Alcalase at 60ºC, pH 8 for 4 hr. The hydrolysate was freeze-dried, and subsequently used for assessment of its functional properties molecular weight by gel electrophoresis (SDS-PAGE). The obtained results show that increasing the pre-treatment temperature increased oil holding capacity and emulsion stability while decreasing antioxidant activity and water holding capacity. The SDS-PAGE analysis showed the evidence of protein aggregation in the hydrolysate treated at the higher pre-treatment temperature. These results suggest the connection between molecular weight of the hydrolysate and its functional properties.

Keywords: chicken protein hydrolysate, enzymatic hydrolysis, thermal pretreatment, functional properties

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

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

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

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Authors: Tsega Asresa, Getahun Tigistu, Melaku Bayih

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Computer vision is a subfield of artificial intelligence that allows computers and systems to extract meaning from digital images and video. It is used in a wide range of fields of study, including self-driving cars, video surveillance, medical diagnosis, manufacturing, law, agriculture, quality control, health care, facial recognition, and military applications. Aromatic medicinal plants are botanical raw materials used in cosmetics, medicines, health foods, essential oils, decoration, cleaning, and other natural health products for therapeutic and Aromatic culinary purposes. These plants and their products not only serve as a valuable source of income for farmers and entrepreneurs but also going to export for valuable foreign currency exchange. In Ethiopia, there is a lack of technologies for the classification and identification of Aromatic medicinal plant parts and disease type cured by aromatic medicinal plants. Farmers, industry personnel, academicians, and pharmacists find it difficult to identify plant parts and disease types cured by plants before ingredient extraction in the laboratory. Manual plant identification is a time-consuming, labor-intensive, and lengthy process. To alleviate these challenges, few studies have been conducted in the area to address these issues. One way to overcome these problems is to develop a deep learning model for efficient identification of Aromatic medicinal plant parts with their corresponding disease type. The objective of the proposed study is to identify the aromatic medicinal plant parts and their disease type classification using computer vision technology. Therefore, this research initiated a model for the classification of aromatic medicinal plant parts and their disease type by exploring computer vision technology. Morphological characteristics are still the most important tools for the identification of plants. Leaves are the most widely used parts of plants besides roots, flowers, fruits, and latex. For this study, the researcher used RGB leaf images with a size of 128x128 x3. In this study, the researchers trained five cutting-edge models: convolutional neural network, Inception V3, Residual Neural Network, Mobile Network, and Visual Geometry Group. Those models were chosen after a comprehensive review of the best-performing models. The 80/20 percentage split is used to evaluate the model, and classification metrics are used to compare models. The pre-trained Inception V3 model outperforms well, with training and validation accuracy of 99.8% and 98.7%, respectively.

Keywords: aromatic medicinal plant, computer vision, convolutional neural network, deep learning, plant classification, residual neural network

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Authors: Marianna Maiaru, Gregory M. Odegard, Josh Kemppainen, Ivan Gallegos, Michael Olaya

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Ceramic matrix composites (CMCs) are typically used in applications that require long-term mechanical integrity at elevated temperatures. CMCs are usually fabricated using a polymer precursor that is initially polymerized in situ with fiber reinforcement, followed by a series of cycles of pyrolysis to transform the polymer matrix into a rigid glass or ceramic. The pyrolysis step typically generates volatile gasses, which creates porosity within the polymer matrix phase of the composite. Subsequent cycles of monomer infusion, polymerization, and pyrolysis are often used to reduce the porosity and thus increase the durability of the composite. Because of the significant expense of such iterative processing cycles, new generations of CMCs with improved durability and manufacturability are difficult and expensive to develop using standard Edisonian approaches. The goal of this research is to develop a computational process-modeling-based approach that can be used to design the next generation of CMC materials with optimized material and processing parameters for maximum strength and efficient manufacturing. The process modeling incorporates computational modeling tools, including molecular dynamics (MD), to simulate the material at multiple length scales. Results from MD simulation are used to inform the continuum-level models to link molecular-level characteristics (material structure, temperature) to bulk-level performance (strength, residual stresses). Processing parameters are optimized such that process-induced residual stresses are minimized and laminate strength is maximized. The multiscale process modeling method developed with this research can play a key role in the development of future CMCs for high-temperature and high-strength applications. By combining multiscale computational tools and process modeling, new manufacturing parameters can be established for optimal fabrication and performance of CMCs for a wide range of applications.

Keywords: digital engineering, finite elements, manufacturing, molecular dynamics

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Authors: Muneeba Butt

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One of the most important physical evidence which leaves suspects at the crime scene is footprints. Analysis of footprints, which can provide useful information for personal identification, is helpful in crime scene investigation. For the current study, 200 samples collected (144 male and 56 female) from Pakistani population with a consent form. The footprints were collected by using black ink with an ink pad. The entire samples were photographed, and then the magnifying glass was used for visualization of individual characteristics including detail of toes, humps, phalange mark, and flat foot cracks in footprint patterns. The descriptive results of individualizing characteristics features were presented in tabular form with respective frequency and percentage. In the result in the male population, the prevalence of tibialis type (T-type) is highest. In the female population, the prevalence of midularis type (M-type) is highest. Humps on the first toe are more found in the male population rather than other humps. In the female population, humps on the third toe are more found rather than other humps. In the male population, the prevalence of phalange mark by toe 1 is highest followed by toe 3, toe 5, toe 2, toe 4 and in female population the prevalence of phalange mark by toe 1 is highest followed by toe 5, 4, 3 and 2. Creases marks are found highest in male population as compared to the female population.

Keywords: foot prints, toes, humps, cracks

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Authors: Niki K. Burns, James R. Pearson, Paul G. Stevenson, Xavier A. Conlan

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In Australian state Victoria, synthetic cannabinoids have recently been made illegal under an amendment to the drugs, poisons and controlled substances act 1981. Identification of synthetic cannabinoids in popular brands of ‘incense’ and ‘potpourri’ has been a difficult and challenging task due to the sample complexity and changes observed in the chemical composition of the cannabinoids of interest. This study has developed analytical methodology for the targeted extraction and determination of synthetic cannabinoids available pre-ban. A simple solvent extraction and solid phase extraction methodology was developed that selectively extracted the cannabinoid of interest. High performance liquid chromatography coupled with UV‐visible and chemiluminescence detection (acidic potassium permanganate and tris (2,2‐bipyridine) ruthenium(III)) were used to interrogate the synthetic cannabinoid products. Mass spectrometry and nuclear magnetic resonance spectroscopy were used for structural elucidation of the synthetic cannabinoids. The tris(2,2‐bipyridine)ruthenium(III) detection was found to offer better sensitivity than the permanganate based reagents. In twelve different brands of herbal incense, cannabinoids were extracted and identified including UR‐144, XLR 11, AM2201, 5‐F‐AKB48 and A796‐260.

Keywords: electrospray mass spectrometry, high performance liquid chromatography, solid phase extraction, synthetic cannabinoids

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Authors: Farid Benkaci-Alia, Abdelhamid Neggada, Sophie Laurentb

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A new extraction method of polyphenols from honey using a biodegradable resin was developed and compared with the common commercial resin amberlite XAD2. For this purpose, three honey samples of Algerian origin were selected for the different physico-chemical and biochemical parameters study. After extraction of the target compounds by both resins, the polyphenol content was determined, the antioxidant activity was tested, and LC-MS analyses were performed for identification and quantification. The results showed that physico-chemical and biochemical parameters meet the norms of the International Honey commission, and the H1 sample seemed to be of high quality. The optimal conditions of extraction by biodegradable resin were a pH of 3, an adsorption dose of 40 g/L, a contact time of 50 min, an extraction temperature of 60°C and no stirring. The regeneration and reuse number of both resins was three cycles. The polyphenol contents demonstrated a higher extraction efficiency of biosorbent than of XAD2, especially in H1. LC-MS analyses allowed for the identification and quantification of fifteen compounds in the different honey samples extracted using both resins and the most abundant compound was 3,4,5-trimethoxybenzoic acid. In addition, the biosorbent extracts showed stronger antioxidant activities than the XAD2 extracts.

Keywords: extraction, polyphénols, biosorbent, resin amberlite, HPLC-MS

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Authors: Karim Hamidi Machekposhti, Hossein Sedghi, Abdolrasoul Telvari, Hossein Babazadeh

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Floods have huge environmental and economic impact. Therefore, flood prediction is given a lot of attention due to its importance. This study analysed the annual maximum streamflow (discharge) (AMS or AMD) of Karkheh River in Karkheh River Basin for flood predicting using ARIMA model. For this purpose, we use the Box-Jenkins approach, which contains four-stage method model identification, parameter estimation, diagnostic checking and forecasting (predicting). The main tool used in ARIMA modelling was the SAS and SPSS software. Model identification was done by visual inspection on the ACF and PACF. SAS software computed the model parameters using the ML, CLS and ULS methods. The diagnostic checking tests, AIC criterion, RACF graph and RPACF graphs, were used for selected model verification. In this study, the best ARIMA models for Annual Maximum Discharge (AMD) time series was (4,1,1) with their AIC value of 88.87. The RACF and RPACF showed residuals’ independence. To forecast AMD for 10 future years, this model showed the ability of the model to predict floods of the river under study in the Karkheh River Basin. Model accuracy was checked by comparing the predicted and observation series by using coefficient of determination (R²).

Keywords: time series modelling, stochastic processes, ARIMA model, Karkheh river

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Authors: Bilal Ahmad

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Alzheimer’s disease (AD) is one of the most common neurodegenerative illnesses. However, how Gut-microbiota plays a role in the pathogenesis of AD is not well elucidated. The purpose of this literature review is to summarize and understand the current findings that may elucidate the gut microbiota's role in the development of AD. Methods: A literature review of all the relevant papers known to the author was conducted. Relevant articles, abstracts and research papers were collected from well-accepted web sources like PubMed, PMC, and Google Scholar. Results: Recent studies have shown that Gut-microbiota has an important role in the progression of AD via Gut-Microbiota-Brain Axis. The onset of AD supports the ‘Hygiene Hypothesis’, which shows that AD might begin in the Gut, causing dysbiosis, which interferes with the intestinal barrier by releasing pro-inflammatory cytokines and making its way up to the brain via the blood-brain barrier (BBB). Molecular mechanisms lipopolysaccharides and serotonin kynurenine (tryptophan) pathways have a direct association with inflammation, the immune system, neurodegeneration, and AD. Conclusion: The studies helped to analyze the molecular basis of AD, other neurological conditions like depression, autism, and Parkinson's disease and how they are linked to Gut-microbiota. Further, studies to explore the therapeutic effects of probiotics in AD and cognitive enhancement should be warranted to provide significant clinical and practical value.

Keywords: gut-microbiota, Alzheimer’s disease, second brain aging, lipopolysaccharides, short-chain fatty acids

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Authors: Zuliani Mahmood, Thirumulu Ponnuraj Kannan, Yean Yean Chan, Salahddin A. Al-Hudhairy

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Caries is the most common childhood disease which develops due to disturbances in the physiological equilibrium in the dental plaque resulting in demineralization of tooth structures. Plaque and dentine samples were collected from three different tooth surfaces representing caries progression (intact, over carious lesion and dentine) in children with early childhood caries (ECC, n=36). In caries free (CF) children, plaque samples were collected from sound tooth surfaces at baseline and after one year (n=12). The genomic DNA was extracted from all samples and subjected to 16S rRNA PCR amplification. The end products were cloned into pCR®2.1-TOPO® Vector. Five randomly selected positive clones collected from each surface were sent for sequencing. Identification of the bacterial clones was performed using BLAST against GenBank database. In the ECC group, the frequency of Lactobacillus sp. detected was significantly higher in the dentine surface (p = 0.031) than over the cavitated lesion. The highest frequency of bacteria detected in the intact surfaces was Fusobacterium nucleatum subsp. polymorphum (33.3%) while Streptococcus mutans was detected over the carious lesions and dentine surfaces at a frequency of 33.3% and 52.7% respectively. Fusobacterium nucleatum subsp. polymorphum was also found to be highest in the CF group (41.6%). Follow up at the end of one year showed that the frequency of Corynebacterium matruchotii detected was highest in those who remained caries free (16.6%), while Porphyromonas catoniae was highest in those who developed caries (25%). In conclusion, Streptococcus mutans and Porphyromonas catoniae are strongly associated with caries progression, while Lactobacillus sp. is restricted to deep carious lesions. Fusobacterium nucleatum subsp. polymorphum and Corynebacterium matruchotii may play a role in sustaining the healthy equilibrium in the dental plaque. These identified bacteria show promise as potential biomarkers in diagnosis which could help in the management of dental caries in children.

Keywords: early childhood caries, genotypic identification, oral bacteria, 16S rRNA

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Authors: Tuhina-khatun, Mohamed Hanafi Musa, Mohd Rafii Yosup, Wong Mui Yun, Aktar-uz-Zaman, Mahbod Sahebi

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Suppression subtractive hybridization (SSH) method is valuable tool for identifying differentially regulated genes in disease specific or tissue specific genes important for cellular growth and differentiation. It is a widely used method for separating DNA molecules that distinguish two closely related DNA samples. SSH is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. It is based primarily on a suppression polymerase chain reaction (PCR) technique and combines normalization and subtraction in a solitary procedure. The normalization step equalizes the abundance of DNA fragments within the target population, and the subtraction step excludes sequences that are common to the populations being compared. This dramatically increases the probability of obtaining low-abundance differentially expressed cDNAs or genomic DNA fragments and simplifies analysis of the subtracted library. SSH technique is applicable to many comparative and functional genetic studies for the identification of disease, developmental, tissue specific, or other differentially expressed genes, as well as for the recovery of genomic DNA fragments distinguishing the samples under comparison.

Keywords: suppression subtractive hybridization, differentially expressed genes, disease specific genes, tissue specific genes

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Authors: Mohammed Bakhit Kashoob, Mohammed Salim Al-Maashani, Ahmed Abdullah Al-Marhoon

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The use of Geographic Information System (GIS) tools in the analysis of traffic crash data can help to identify locations or hotspots with high instances or risk of traffic crashes. The identification of traffic crash hotspots can effectively improve road safety measures. Mapping of road traffic crash hotspots can help the concerned authorities to give priority and take targeted measures and improvements to the road structure at these locations to reduce traffic crashes and fatalities. In Oman, there are countless rural roads that have more risks for traveling vehicles compared to urban roads. The likelihood of traffic crashes as well as fatality rate may increase with the presence of risks that are associated with the rural type of community. In this paper, the traffic crash hotspots on rural roads in Oman are specified using spatial analysis methods in GIS and traffic crash data. These hotspots are ranked based on the frequency of traffic crash occurrence (i.e., number of traffic crashes) and the rate of fatalities. The result of this study presents a map visualization of locations on rural roads with high traffic crashes and high fatalities rates.

Keywords: road safety, rural roads, traffic crash, GIS tools

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Authors: Ferdinando Montemari, Antonio Vitale, Nicola Genito, Giovanni Cuciniello

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The introduction of tilt-rotor aircraft into the existing civilian air transportation system will provide beneficial effects due to tilt-rotor capability to combine the characteristics of a helicopter and a fixed-wing aircraft into one vehicle. The disposability of reliable tilt-rotor simulation models supports the development of such vehicle. Indeed, simulation models are required to design automatic control systems that increase safety, reduce pilot's workload and stress, and ensure the optimal aircraft configuration with respect to flight envelope limits, especially during the most critical flight phases such as conversion from helicopter to aircraft mode and vice versa. This article presents a process to build a simplified tilt-rotor simulation model, derived from the analysis of flight data. The model aims to reproduce the complex dynamics of tilt-rotor during the in-flight conversion phase. It uses a set of scheduled linear transfer functions to relate the autopilot reference inputs to the most relevant rigid body state variables. The model also computes information about the rotor flapping dynamics, which are useful to evaluate the aircraft control margin in terms of rotor collective and cyclic commands. The rotor flapping model is derived through a mixed theoretical-empirical approach, which includes physical analytical equations (applicable to helicopter configuration) and parametric corrective functions. The latter are introduced to best fit the actual rotor behavior and balance the differences existing between helicopter and tilt-rotor during flight. Time-domain system identification from flight data is exploited to optimize the model structure and to estimate the model parameters. The presented model-building process was applied to simulated flight data of the ERICA Tilt-Rotor, generated by using a high fidelity simulation model implemented in FlightLab environment. The validation of the obtained model was very satisfying, confirming the validity of the proposed approach.

Keywords: flapping dynamics, flight dynamics, system identification, tilt-rotor modeling and simulation

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Authors: Laura G. Caixeta, Maico R. Severino

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One of the biggest challenges that the industries find nowadays is to incorporate sustainability practices into its operations. The Green Supply Chain Management (GSCM) concept assists industries in such incorporation. For the full application of this concept is important that enterprises of a same supply chain have the GSCM practices coordinated among themselves. Note that this type of analyses occurs on the context of developed countries and sectors considered big impactors (as automotive, mineral, among others). The propose of this paper is to analyze as the GSCM concepts are applied on the Brazilian animal nutrition industries. The method used was the Case Study. For this, it was selected a supply chain relationship composed by animal nutrition products manufacturer (Enterprise A) and its supplier of animal waste, such as blood, viscera, among others (Enterprise B). First, a literature review was carried out to identify the main GSCM practices. Second, it was done an individual analysis of each one selected enterprise of the application of GSCM concept. For the observed practices, the coordination of each practice in this supply chain was studied. And, it was developed propose of GSCM applications for the practices no observed. The findings of this research were: a) the systematization of main GSCM practices, as: Internal Environment Management, Green Consumption, Green Design, Green Manufacturing, Green Marketing, Green Packaging, Green Procurement, Green Recycling, Life Cycle Analysis, Consultation Selection Method, Environmental Risk Sharing, Investment Recovery, and Reduced Transportation Time; b) the identification of GSCM practices on Enterprise A (7 full application, 3 partial application and 3 no application); c) the identification of GSCM practices on Enterprise B (2 full application, 2 partial application and 9 no application); d) the identification of how is the incentive and the coordination of the GSCM practices on this relationship by Enterprise A; e) proposals of application and coordination of the others GSCM practices on this supply chain relationship. Based on the study, it can be concluded that its possible apply GSCM on animal nutrition industries, and when occurs the motivation on the application of GSCM concepts by a supply chain echelon, these concepts are deployed for the others supply chain echelons by the coordination (orchestration) of the first echelon.

Keywords: animal nutrition industries, coordination, green supply chain management, supply chain management, sustainability

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Authors: Harminder Kaur, Manpreet Kaur, Akanksha Kapila, Reenu

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Schiff base with general formula H₂L was derived from condensation of o-vanillin and 3-nitro-o-phenylenediamine. This Schiff base was used for the synthesis of organotin(IV) complexes with general formula R₂SnL [R=Phenyl or n-octyl] using equimolar quantities. Elemental analysis UV-Vis, FTIR, and multinuclear spectroscopic techniques (¹H, ¹³C, and ¹¹⁹Sn) NMR were carried out for the characterization of the synthesized complexes. These complexes were coloured and soluble in polar solvents. Computational studies have been performed to obtain the details of the geometry and electronic structures of ligand as well as complexes. Geometry of the ligands and complexes have been optimized at the level of Density Functional Theory with B3LYP/6-311G (d,p) and B3LYP/MPW1PW91 respectively followed by vibrational frequency analysis using Gaussian 09. Observed ¹¹⁹Sn NMR chemical shifts of one of the synthesized complexes showed tetrahedral geometry around Tin atom which is also confirmed by DFT. HOMO-LUMO energy distribution was calculated. FTIR, ¹HNMR and ¹³CNMR spectra were also obtained theoretically using DFT. Further IRC calculations were employed to determine the transition state for the reaction and to get the theoretical information about the reaction pathway. Moreover, molecular docking studies can be explored to ensure the anticancer activity of the newly synthesized organotin(IV) complexes.

Keywords: DFT, molecular docking, organotin(IV) complexes, o-vanillin, 3-nitro-o-phenylenediamine

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Authors: R. F. B. Gonçalves, E. N. Iwama, J. A. F. F. Rocco, K. Iha

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Propellants based on Hydroxyl Terminated Polybutadiene/Ammonium Perchlorate (HTPB/AP) are the most commonly used in most of the rocket engines used by the Brazilian Armed Forces. This work aimed at the possibility of extending its useful life (currently in 10 years) by performing kinetic-chemical analyzes of its energetic material via Differential Scanning Calorimetry (DSC) and also performing computer simulation of aging process using the software Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). Thermal analysis via DSC was performed in triplicates and in three heating ratios (5 ºC, 10 ºC, and 15 ºC) of rocket motor with 11 years shelf-life, using the Arrhenius equation to obtain its activation energy, using Ozawa and Kissinger kinetic methods, allowing comparison with manufacturing period data (standard motor). In addition, the kinetic parameters of internal pressure of the combustion chamber in 08 rocket engines with 11 years of shelf-life were also acquired, for comparison purposes with the engine start-up data.

Keywords: shelf-life, thermal analysis, Ozawa method, Kissinger method, LAMMPS software, thrust

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Authors: Marisol Rodriguez-Duarte, Aide Saenz-Galindo, Carolina Flores-Gallegos, Raul Rodriguez-Herrera, Juan Ascacio-Valdes

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The plant known as tarbush (Fluorensia cernua) is a plant originating in northern Mexico, mainly in the states of Coahuila, Durango, San Luis Potosí, Zacatecas and Chihuahua. It is a branched shrub that belongs to the family Asteraceae, has oval leaves of 6 to 11 cm in length and also has small yellow flowers. In Mexico, the tarbush is a very appreciated plant because it has been used as a traditional medicinal agent, for the treatment of gastrointestinal diseases, skin infections and as a healing agent. This plant has been used mainly as an infusion. Due to its traditional use, the content and type of phytochemicals present in the plant are currently unknown and are responsible for its biological properties, so its recovery and identification is very important because the compounds that it contains have relevant applications in the field of food, pharmaceuticals and medicine. The objective of this work was to determine the best extraction condition of phytochemical compounds (mainly polyphenolic compounds) from the leaf using ultrasound/microwave assisted extraction (U/M-AE). To reach the objective, U/M-AE extractions were performed evaluating three mass/volume ratios (1:8, 1:12, 1:16), three ethanol/water solvent concentrations (0%, 30% and 70%), ultrasound extraction time of 20 min and 5 min at 70°C of microwave treatment. All experiments were performed using a fractional factorial experimental design. Once the best extraction condition was defined, the compounds were recovered by liquid column chromatography using Amberlite XAD-16, the polyphenolic fraction was recovered with ethanol and then evaporated. The recovered polyphenolic compounds were quantified by spectrophotometric techniques and identified by HPLC/ESI/MS. The results obtained showed that the best extraction condition of the compounds was using a mass/volume ratio of 1:8 and solvent ethanol/water concentration of 70%. The concentration obtained from polyphenolic compounds using this condition was 22.74 mg/g and finally, 16 compounds of polyphenolic origin were identified. The results obtained in this work allow us to postulate the Mexican plant known as tarbush as a relevant source of bioactive polyphenolic compounds of food, pharmaceutical and medicinal interest.

Keywords: U/M-AE, tarbush, polyphenols, identification

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Authors: Barsha Saha, Shouvik Chakravarty, Sukanta Ray, Kshaunish Das, Nidhan K. Biswas, Srikanta Goswami

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Pancreatic Ductal Adenocarcinoma is a well-recognised cause of cancer death with a five-year survival rate of about 9%, and its incidence in India has been found to be increased manifold in recent years. Due to delayed detection, this highly metastatic disease has a poor prognosis. Several molecular alterations happen during the progression of the disease from pre-cancerous conditions, and many such alterations could be investigated for their biomarker potential. MicroRNAs have been shown to be prognostic for PDAC patients in a variety of studies. We hereby used NGS technologies to evaluate the role of small RNA changes during pancreatic cancer development from chronic pancreatitis. Plasma samples were collected from pancreatic cancer patients (n=16), chronic pancreatitis patients (n=8), and also from normal individuals (n=16). Pancreatic tumour tissue (n=5) and adjacent normal tissue samples (n=5) were also collected. Sequencing of small RNAs was carried out after small RNAs were isolated from plasma samples and tissue samples. We find that certain microRNAs are highly deregulated in pancreatic cancer patients in comparison to normal samples. A combinatorial analysis of plasma and tissue microRNAs and subsequent exploration of their targets and altered molecular pathways could not only identify potential biomarkers for disease diagnosis but also help to understand the underlying mechanism.

Keywords: small RNA sequencing, pancreatic cancer, biomarkers, tissue sample

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Authors: Lynda Golea, Rachid Chebaki

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Schiff bases contain heterocyclic structural units with N and O donor atoms which plays an important role in coordination chemistry. Azomethine groups are a broad class of widely used compounds with applications in many fields, including analytical, inorganic chemistry and biological. Schiff's base is of promising research interest due to the widespread antibacterial resistance in medical science. In addition, the research is essential to generate Schiff base metal complexes with various applications. Schiff complexes have been used as drugs and have antibacterial, antifungal, antiviral, and anti-inflammatory properties. The various donor atoms they contain offer a special ability for metal binding. In this research on the physicochemical properties of azomethine groups, we synthesized and studied the Schiff base compounds by a condensation reaction of tryptamines and acetophenone in ethanol. The structure of the prepared compound was interpreted using 1H NMR, 13C NMR, UV-vis and FT-IR. A computational analysis at the level of DFT with functional B3LYP in conjunction with the base 6-311+G (d, p) was conducted to study its electronic and molecular structure. The biological study was performed on three bacterial strains usually causing infection, including Gram-positive and Gram-negative, for antibacterial activity. Results showed moderate biological activity and proportional activity with increasing concentration.

Keywords: azomethine, HOMO, LUMO, RMN, molecular docking

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Authors: Ajibade T., Omotesho O. A., Ayinde O. E, Ajibade E. T., Muhammad-Lawal A.

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This study was carried out to examine the extent and magnitude of food security amongst farming rural households in Nigeria. Data used for this study was collected from a total of two hundred and forty rural farming households using a two-stage random sampling technique. The main tools of analysis for this study include descriptive statistics and a constructed food security index using the identification and aggregation procedure. The headcount ratio in this study reveals that 71% of individuals in the study area were food secure with an average per capita calorie and protein availability of 4,213.92kcal and 99.98g respectively. The aggregated household daily calorie availability and daily protein availability per capita were 3,634.57kcal and 84.08g respectively which happens to be above the food security line of 2,470kcal and 65g used in this study. The food insecure households fell short of the minimum daily per capita calorie and protein requirement by 2.1% and 24.9%. The study revealed that the area is food insecure due to unequal distribution of the available food amongst the sampled population. The study recommends that the households should empower themselves financially in order to enhance their ability to afford the food during both on and off seasons. Also, processing and storage of farm produce should be enhanced in order to improve on availability throughout the year.

Keywords: farming household, food security, identification and aggregation, food security index

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Authors: Jessica C. Bannon, Cleso M. Jordao Jr., Mohammad Melebari, Carlos Leon-Velarde, Roger Johnson, Keith Warriner

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There has been an increased incidence of non-O157 Shiga Toxin Escherichia coli (STEC) with six serotypes (Top 6) being implicated in causing haemolytic uremic syndrome (HUS). Beef has been suggested to be a significant vehicle for non-O157 STEC although conclusive evidence has yet to be obtained. The following aimed to determine the prevalence of the Top 6 non-O157 STEC in beef processing using three different diagnostic platforms then characterize the recovered isolates. Hide, carcass and environmental swab samples (n = 60) were collected from a beef processing facility over a 12 month period. Enriched samples were screened using Biocontrol GDS, BAX or PALLgene molecular diagnostic tests. Presumptive non-O157 STEC positive samples were confirmed using conventional PCR and serology. STEC was detected by GDS (55% positive), BAX (85% positive), and PALLgene (93%). However, during confirmation testing only 8 of the 60 samples (13%) were found to harbour STEC. Interestingly, the presence of virulence factors in the recovered isolates was unstable and readily lost during subsequent sub-culturing. There is a low prevalence of Top 6 non-O157 STEC associated with beef although other serotypes are encountered. Yet, the instability of the virulence factors in recovered strains would question their clinical relevance.

Keywords: beef, food microbiology, shiga toxin, STEC

Procedia PDF Downloads 445

Authors: Mukul Sharma, Madhusmita Das, Sundeep Chaitanya Vedithi

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Leprosy is a chronic human disease caused by Mycobacterium leprae, that cannot be cultured in vitro. Though treatable with multidrug therapy (MDT), recently, bacteria reported resistance to multiple antibiotics. Targeting DNA replication and repair pathways can serve as the foundation of developing new anti-leprosy drugs. Due to the absence of an axenic culture medium for the propagation of M. leprae, studying cellular processes, especially those belonging to DNA repair pathways, is challenging. Genomic understanding of M. Leprae harbors several protein-coding genes with no previously assigned function known as 'hypothetical proteins'. Here, we report identification and expression of known and hypothetical DNA repair genes from a human skin biopsy and mouse footpads that are involved in base excision repair, direct reversal repair, and SOS response. Initially, a bioinformatics approach was employed based on sequence similarity, identification of known protein domains to screen the hypothetical proteins in the genome of M. leprae, that are potentially related to DNA repair mechanisms. Before testing on clinical samples, pure stocks of bacterial reference DNA of M. leprae (NHDP63 strain) was used to construct standard graphs to validate and identify lower detection limit in the qPCR experiments. Primers were designed to amplify the respective transcripts, and PCR products of the predicted size were obtained. Later, excisional skin biopsies of newly diagnosed untreated, treated, and drug resistance leprosy cases from SIHR & LC hospital, Vellore, India were taken for the extraction of RNA. To determine the presence of the predicted transcripts, cDNA was generated from M. leprae mRNA isolated from clinically confirmed leprosy skin biopsy specimen across all the study groups. Melting curve analysis was performed to determine the integrity of the amplification and to rule out primer‑dimer formation. The Ct values obtained from qPCR were fitted to standard curve to determine transcript copy number. Same procedure was applied for M. leprae extracted after processing a footpad of nude mice of drug sensitive and drug resistant strains. 16S rRNA was used as positive control. Of all the 16 genes involved in BER, DR, and SOS, differential expression pattern of the genes was observed in terms of Ct values when compared to human samples; this was because of the different host and its immune response. However, no drastic variation in gene expression levels was observed in human samples except the nth gene. The higher expression of nth gene could be because of the mutations that may be associated with sequence diversity and drug resistance which suggests an important role in the repair mechanism and remains to be explored. In both human and mouse samples, SOS system – lexA and RecA, and BER genes AlkB and Ogt were expressing efficiently to deal with possible DNA damage. Together, the results of the present study suggest that DNA repair genes are constitutively expressed and may provide a reference for molecular diagnosis, therapeutic target selection, determination of treatment and prognostic judgment in M. leprae pathogenesis.

Keywords: DNA repair, human biopsy, hypothetical proteins, mouse footpads, Mycobacterium leprae, qPCR

Procedia PDF Downloads 88

Authors: Maria Bercea, Bernhard A. Wolf

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The thermodynamic behavior for solutions of poly (methyl methacrylate-ran-t-butyl methacrylate) of variable composition as compared with the corresponding homopolymers was investigated by light scattering measurements carried out for dilute solutions and vapor pressure measurements of concentrated solutions. The complex dependencies of the Flory Huggins interaction parameter on concentration and copolymer composition in solvents of different polarity (toluene and chloroform) can be understood by taking into account the ability of the polymers to rearrange in a response to changes in their molecular surrounding. A recent unified thermodynamic approach was used for modeling the experimental data, being able to describe the behavior of the different solutions by means of two adjustable parameters, one representing the effective number of solvent segments and another one accounting for the interactions between the components. Thus, it was investigated how the solvent quality changes with the composition of the copolymers through the Gibbs energy of mixing as a function of polymer concentration. The largest reduction of the Gibbs energy at a given composition of the system was observed for the best solvent. The present investigation proves that the new unified thermodynamic approach is a general concept applicable to homo- and copolymers, independent of the chain conformation or shape, molecular and chemical architecture of the components and of other dissimilarities, such as electrical charges.

Keywords: random copolymers, Flory Huggins interaction parameter, Gibbs energy of mixing, chemical architecture

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Authors: Hediyeh Talebi, Shokoofeh Ghiam, Changiz Eslahchi

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Traditionally, Alzheimer’s disease research has focused on genes with significant fold changes, potentially neglecting subtle but biologically important alterations. Our study introduces an integrative approach that highlights genes crucial to underlying biological processes, regardless of their fold change magnitude. Alzheimer's Single-cell RNA-seq data related to the peripheral blood mononuclear cells (PBMC) was extracted from the Gene Expression Omnibus (GEO). After quality control, normalization, scaling, batch effect correction, and clustering, differentially expressed genes (DEGs) were identified with adjusted p-values less than 0.05. These DEGs were categorized based on cell-type, resulting in four datasets, each corresponding to a distinct cell type. To distinguish between cells from healthy individuals and those with Alzheimer's, an adversarial autoencoder with a classifier was employed. This allowed for the separation of healthy and diseased samples. To identify the most influential genes in this classification, the weight matrices in the network, which includes the encoder and classifier components, were multiplied, and focused on the top 20 genes. The analysis revealed that while some of these genes exhibit a high fold change, others do not. These genes, which may be overlooked by previous methods due to their low fold change, were shown to be significant in our study. The findings highlight the critical role of genes with subtle alterations in diagnosing Alzheimer's disease, a facet frequently overlooked by conventional methods. These genes demonstrate remarkable discriminatory power, underscoring the need to integrate biological relevance with statistical measures in gene prioritization. This integrative approach enhances our understanding of the molecular mechanisms in Alzheimer’s disease and provides a promising direction for identifying potential therapeutic targets.

Keywords: alzheimer's disease, single-cell RNA-seq, neural networks, blood biomarkers

Procedia PDF Downloads 47