Search results for: biomarker quantification

Authors: Morten Stigaard Laursen, Rasmus Nyholm Jørgensen, Henrik Skov Midtiby, Anders Krogh Mortensen, Sanmohan Baby

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This work contributes a statistical model and simulation framework yielding the best estimate possible for the potential herbicide reduction when using the MoDiCoVi algorithm all the while requiring a efficacy comparable to conventional spraying. In June 2013 a maize field located in Denmark were seeded. The field was divided into parcels which was assigned to one of two main groups: 1) Control, consisting of subgroups of no spray and full dose spraty; 2) MoDiCoVi algorithm subdivided into five different leaf cover thresholds for spray activation. In addition approximately 25% of the parcels were seeded with additional weeds perpendicular to the maize rows. In total 299 parcels were randomly assigned with the 28 different treatment combinations. In the statistical analysis, bootstrapping was used for balancing the number of replicates. The achieved potential herbicide savings was found to be 70% to 95% depending on the initial weed coverage. However additional field trials covering more seasons and locations are needed to verify the generalisation of these results. There is a potential for further herbicide savings as the time interval between the first and second spraying session was not long enough for the weeds to turn yellow, instead they only stagnated in growth.

Keywords: herbicide reduction, macrosprayer, weed crop discrimination, site-specific, sprayer boom

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Authors: Pijush Roy, Vinay Kumar Rai

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The present study highlights the estimation of soil loss and identification of critical area for implementation of best management practice is central to the success of soil conservation programme. The quantification of morphometric and Universal Soil Loss Equation (USLE) factors using remote sensing and GIS for prioritization of micro-watersheds in Asan River catchment, western Doon valley at foothills of Siwalik ranges in the Dehradun districts of Uttarakhand, India. The watershed has classified as a dendritic pattern with sixth order stream. The area is classified into very high, high, moderately high, medium and low susceptibility zones. High to very high erosion zone exists in the urban area and agricultural land. Average annual soil loss of 64 tons/ha/year has been estimated for the watershed. The optimum management practices proposed for micro-watersheds of Asan River basin are; afforestation, contour bunding suitable sites for water harvesting structure as check dam and soil conservation, agronomical measure and bench terrace.

Keywords: erosion susceptibility zones, morphometric characteristics, prioritization, remote sensing and GIS, universal soil loss equation

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Authors: Eirini Konstanta, Cedric Gouedard, Aggeliki Delimitsou, Stefania Patera, Samuel Murray

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Introduction: Quality reference DNA standards (QRS) for molecular testing by next-generation sequencing (NGS) are essential for accurate quantitation of copy number variations (CNV) for germline and variant allelic frequencies (VAF) for somatic analyses. Objectives: Presently, several molecular analytics for oncology patients are reliant upon quantitative metrics. Test validation and standardisation are also reliant upon the availability of surrogate control materials allowing for understanding test LOD (limit of detection), sensitivity, specificity. We have developed a dual calibration platform allowing for QRS pairs to be included in analysed DNA samples, allowing for accurate quantitation of CNV and VAF metrics within and between patient samples. Methods: QRS™ blocks up to 500nt were designed for common NGS panel targets incorporating ≥ 2 identification tags (IDTDNA.com). These were analysed upon spiking into gDNA, somatic, and ctDNA using a proprietary CalSuite™ platform adaptable to common LIMS. Results: We demonstrate QRS™ calibration reproducibility spiked to 5–25% at ± 2.5% in gDNA and ctDNA. Furthermore, we demonstrate CNV and VAF within and between samples (gDNA and ctDNA) with the same reproducibility (± 2.5%) in a clinical sample of lung cancer and HBOC (EGFR and BRCA1, respectively). CNV analytics was performed with similar accuracy using a single pair of QRS calibrators when using multiple single targeted sequencing controls. Conclusion: Dual paired QRS™ calibrators allow for accurate and reproducible quantitative analyses of CNV, VAF, intrinsic sample allele measurement, inter and intra-sample measure not only simplifying NGS analytics but allowing for monitoring clinically relevant biomarker VAF across patient ctDNA samples with improved accuracy.

Keywords: calibrator, CNV, gene copy number, VAF

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Authors: Jeong Woo Kang, MiYoung Baek, Ki-Suk Kim, Kwang-Jick Lee, ByungJae So

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Introduction: A fast, easy and sensitive detection method was developed and validated by liquid chromatography tandem mass spectrometry for the determination of marbofloxacin in pig plasma which was further applied to study the pharmacokinetics of marbofloxacin. Materials and Methods: The plasma sample (500 μL) was mixed with 1.5 ml of 0.1% formic acid in MeCN to precipitate plasma proteins. After shaking for 20 min, The mixture was centrifuged at 5,000 × g for 30 min. It was dried under a nitrogen flow at 50℃. 500 μL aliquot of the sample was injected into the LC-MS/MS system. Chromatographic analysis was carried out mobile phase gradient consisting 0.1% formic acid in D.W. (A) and 0.1% formic acid in MeCN (B) with C18 reverse phase column. Mass spectrometry was performed using the positive ion mode and the selected ion monitoring (MRM). Results and Conclusions: The method validation was performed in the sample matrix. Good linearities (R2>0.999) were observed and the quantified average recoveries of marbofloxacin were 87 - 92% at level of 10 ng g-1 -100 ng g-1. The percent of coefficient of variation (CV) for the described method was less than 10 % over the range of concentrations studied. The limits of detection (LOD) and quantification (LOQ) were 2 and 5 ng g-1, respectively. This method has also been applied successfully to pharmacokinetic analysis of marbofloxacin after intravenous (IV), intramuscular (IM) and oral administration (PO). The mean peak plasma concentration (Cmax) was 2,597 ng g-1at 0.25 h, 2,587 ng g-1at 0.44 h and 2,355 ng g-1at 1.58 h for IV, IM and PO, respectively. The area under the plasma concentration-time curve (AUC0–t) was 24.8, 29.0 and 25.2 h μg/mL for IV, IM and PO, respectively. The elimination half-life (T1/2) was 8.6, 13.1 and 9.5 for IV, IM and PO, respectively. Bioavailability (F) of the marbofloxacin in pig was 117 and 101 % for IM and PO, respectively. Based on these result, marbofloxacin does not have any obstacles as therapeutics to develop the oral formulations such as tablets and capsules.

Keywords: marbofloxacin, LC-MS/MS, pharmacokinetics, chromatographic

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Authors: Amar Ranjan, Julieana Durai, Pranay Tanwar

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Background &Introduction: Ovarian cancer is one of the most common malignant tumor in the female. 70% of the cases of ovarian cancer are diagnosed at an advanced stage. The five-year survival rate associated with ovarian cancer is less than 30%. The early diagnosis of ovarian cancer becomes a key factor in improving the survival rate of patients. Presently, CAl25 (carbohydrate antigen125) is used for the diagnosis and therapeutic monitoring of ovarian cancer, but its sensitivity and specificity is not ideal. The introduction of HE4, human epididymis protein 4 has attracted much attention. HE4 has a sensitivity and specificity of 72.9% and 95% for differentiating between benign and malignant adnexal masses, which is better than CA125 detection.  Methods: Serum HE4 and CA -125 were estimated using the chemiluminescence method. Our cases were 40 epithelial ovarian cancer, 9 benign ovarian tumor, 29 benign gynaecological diseases and 13 healthy individuals. This group include healthy woman those who have undergoing family planning and menopause-related medical consultations and they are negative for ovarian mass. Optimal cut off values for HE4 and CA125 were 55.89pmol/L and 40.25U/L respectively (determined by statistical analysis). Results: The level of HE4 was raised in all ovarian cancer patients (n=40) whereas CA125 levels were normal in 6/40 ovarian cancer patients, which were the cases of OC confirmed by histopathology. There is a significant decrease in the level of HE4 with comparison to CA125 in benign ovarian tumor cases. Both the levels of HE4 and CA125 were raised in the nonovarian cancer group, which includes cancer of endometrium and cervix. In the healthy group, HE4 was normal in all patients except in one case of the rudimentary horn, and the reason for this raised HE4 level is due to the incomplete development of uterus whereas CA125 was raised in 3 cases. Conclusions: Findings showed that the serum level of HE4 is an important indicator in the diagnosis of ovarian cancer, and it also distinguishes between benign and malignant pelvic masses. However, a combination of HE4 and CA125 panel will be extremely valuable in improving the diagnostic efficiency of ovarian cancer. These findings of our study need to be validated in the larger cohort of patients.

Keywords: human epididymis protein 4, ovarian cancer, diagnosis, benign lesions

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Authors: H. M. Zakir Hossain

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Cenozoic mudstone samples, obtained from drilled cored and outcrop in northeastern Bengal Basin of Bangladesh were organic geochemically analyzed to identify vertical variations of organic facies, thermal maturity, hydrocarbon potential and depositional environments. Total organic carbon (TOC) content ranges from 0.11 to 1.56 wt% with an average of 0.43 wt%, indicating a good source rock potential. Total sulphur content is variable with values ranging from ~0.001 to 1.75 wt% with an average of 0.065 wt%. Rock-Eval S1 and S2 yields range from 0.03 to 0.14 mg HC/g rock and 0.01 to 0.66 mg HC/g rock, respectively. The hydrogen index values range from 2.71 to 56.09 mg HC/g TOC. These results revealed that the samples are dominated by type III kerogene. Tmax values of 426 to 453 °C and vitrinite reflectance of 0.51 to 0.66% indicate the organic matter is immature to mature. Saturated hydrocarbon ratios such as pristane, phytane, steranes, and hopanes, indicate mostly terrigenous organic matter with small influence of marine organic matter. Organic matter in the succession was accumulated in three different environmental conditions based on the integration of biomarker proxies. First phase (late Eocene to early Miocene): Deposition occurred entirely in seawater-dominated oxic conditions, with high inputs of land plants organic matter including angiosperms. Second phase (middle to late Miocene): Deposition occurred in freshwater-dominated anoxic conditions, with phytoplanktonic organic matter and a small influence of land plants. Third phase (late Miocene to Pleistocene): Deposition occurred in oxygen-poor freshwater conditions, with abundant input of planktonic organic matter and high influx of angiosperms. The lower part (middle Eocene to early Miocene) of the succession with moderate TOC contents and primarily terrestrial organic matter could have generated some condensates and oils in and around the study area.

Keywords: Bangladesh, geochemistry, hydrocarbon potential, mudstone

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Authors: Daniel F. Bohorquez, Luis M. Agudelo, Henry H. León

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Heart rate variability (HRV) is defined as the temporary variation between heartbeats or RR intervals (distance between R waves in an electrocardiographic signal). This distance is currently a recognized biomarker. With the analysis of the distance, it is possible to assess the sympathetic and parasympathetic nervous systems. These systems are responsible for the regulation of the cardiac muscle. The analysis allows health specialists and researchers to diagnose various pathologies based on this variation. For the acquisition and analysis of HRV taken from a cardiac electrical signal, electronic equipment and analysis software that work independently are currently used. This complicates and delays the process of interpretation and diagnosis. With this delay, the health condition of patients can be put at greater risk. This can lead to an untimely treatment. This document presents a single portable device capable of acquiring electrocardiographic signals and calculating a total of 19 HRV metrics. This reduces the time required, resulting in a timelier intervention. The device has an electrocardiographic signal acquisition card attached to a microcontroller capable of transmitting the cardiac signal wirelessly to a mobile device. In addition, a mobile application was designed to analyze the cardiac waveform. The device calculates the RR and different metrics. The application allows a user to visualize in real-time the cardiac signal and the 19 metrics. The information is exported to a cloud database for remote analysis. The study was performed under controlled conditions in the simulated hospital of the Universidad de la Sabana, Colombia. A total of 60 signals were acquired and analyzed. The device was compared against two reference systems. The results show a strong level of correlation (r > 0.95, p < 0.05) between the 19 metrics compared. Therefore, the use of the portable system evaluated in clinical scenarios controlled by medical specialists and researchers is recommended for the evaluation of the condition of the cardiac system.

Keywords: biological signal análisis, heart rate variability (HRV), HRV metrics, mobile app, portable device.

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Authors: Wen-Ting Wang, Wei-An Tsai, Rong-Hong Hsieh

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Long term taking high fat diet can lead to over production of energy, result in accumulation of body fat, dyslipidemia and increased lipid metabolism in the body. Over metabolism of lipid results in excessive reactive oxygen species and oxidative stress, may also cause mitochondrial dysfunction and cell death. Krill oil, fish oil and linseed oil are good sources of n-3 polyunsaturated fatty acids (PUFA). The present study investigated the effect of high fat diet and various oil rich of n-3 fatty acids on mitochondrial function and cell membrane composition. Six-weeks old male Spraque-Dawley rats were randomly divided into 8 groups including: control group, high fat diet group, low dosage and high dosage krill oil group, low dosage and high dosage fish oil group, and low dosage and high dosage linseed oil group. After 12 weeks of experimental period, the low dosage krill oil, fish oil group and linseed oil group with different dosage prevented mitochondrial dysfunction caused by high fat diet. The supplementation of different oils increased plasma, erythrocyte and mitochondrial n-3/n-6 ratio and further increased the proportion of PUFA in erythrocyte and mitochondrial membrane. It also decreased serum triglyceride (TG) and low density lipoprotein cholesterol (LDL-C) concentration. However, there was no significant change in serum total cholesterol (TC), high density lipoprotein cholesterol (HDL-C), biomarker of liver function, glucose, insulin, homeostasis model assessment-insulin resistance (HOMA-IR) and plasma malonadialdehyde (MDA) concentration when compared with high fat diet group. The supplementation of different sources of n-3 PUFA can maintain mitochondrial function and modulate cell membrane fatty acid composition in high fat diet conditions, and there is a positive relationship between mitochondrial function and mitochondrial membrane composition.

Keywords: fish oil, linseed oil, mitochondria, n-3 PUFA

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Authors: S. Jain, R. Savalia, V. Saini

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A simple, accurate, precise, sensitive and specific RP-HPLC method was developed and validated for simultaneous estimation of Metoprolol Succinate and Olmesartan Medoxomil in bulk and tablet dosage form. The RP-HPLC method has shown adequate separation for Metoprolol Succinate and Olmesartan Medoxomil from its degradation products. The separation was achieved on a Phenomenex luna ODS C18 (250mm X 4.6mm i.d., 5μm particle size) with an isocratic mixture of acetonitrile: 50mM phosphate buffer pH 4.0 adjusted with glacial acetic acid in the ratio of 55:45 v/v. The mobile phase at a flow rate of 1.0ml/min, Injection volume 20μl and wavelength of detection was kept at 225nm. The retention time for Metoprolol Succinate and Olmesartan Medoxomil was 2.451±0.1min and 6.167±0.1min, respectively. The linearity of the proposed method was investigated in the range of 5-50μg/ml and 2-20μg/ml for Metoprolol Succinate and Olmesartan Medoxomil, respectively. Correlation coefficient was 0.999 and 0.9996 for Metoprolol Succinate and Olmesartan Medoxomil, respectively. The limit of detection was 0.2847μg/ml and 0.1251μg/ml for Metoprolol Succinate and Olmesartan Medoxomil, respectively and the limit of quantification was 0.8630μg/ml and 0.3793μg/ml for Metoprolol and Olmesartan, respectively. Proposed methods were validated as per ICH guidelines for linearity, accuracy, precision, specificity and robustness for estimation of Metoprolol Succinate and Olmesartan Medoxomil in commercially available tablet dosage form and results were found to be satisfactory. Thus the developed and validated stability indicating method can be used successfully for marketed formulations.

Keywords: metoprolol succinate, olmesartan medoxomil, RP-HPLC method, validation, ICH

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Authors: Philip Edinger, Christian Ludwig

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The formation and control of tars remain one of the major challenges in the implementation of biomass gasification technologies. Robust, on-line analytical methods are needed to investigate the fate of tar compounds when different measures for their reduction are applied. This work establishes an on-line UV-Vis method, based on a liquid quench sampling system, to monitor tar compounds in biomass gasification processes. Recorded spectra from the liquid phase were analyzed for their tar composition by means of a classical least squares (CLS) and partial least squares (PLS) approach. This allowed for the detection of UV-Vis active tar compounds with detection limits in the low part per million by volume (ppmV) region. The developed method was then applied to two case studies. The first involved a lab-scale reactor, intended to investigate the decomposition of a limited number of tar compounds across a catalyst. The second study involved a gas scrubber as part of a pilot scale wood gasification plant. Tar compound quantification results showed good agreement with off-line based reference methods (GC-FID) when the complexity of tar composition was limited. The two case studies show that the developed method can provide rapid, qualitative information on the tar composition for the purpose of process monitoring. In cases with a limited number of tar species, quantitative information about the individual tar compound concentrations provides an additional benefit of the analytical method.

Keywords: biomass gasification, on-line, tar, UV-Vis

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Authors: Ajai Singh

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Simulation of hydrological processes at the watershed outlet through modelling approach is essential for proper planning and implementation of appropriate soil conservation measures in Damodar Barakar catchment, Hazaribagh, India where soil erosion is a dominant problem. This study quantifies the parametric uncertainty involved in simulation of stream flow using Soil and Water Assessment Tool (SWAT), a watershed scale model and Radial Basis Neural Network (RBNN), an artificial neural network model. Both the models were calibrated and validated based on measured stream flow and quantification of the uncertainty in SWAT model output was assessed using ‘‘Sequential Uncertainty Fitting Algorithm’’ (SUFI-2). Though both the model predicted satisfactorily, but RBNN model performed better than SWAT with R2 and NSE values of 0.92 and 0.92 during training, and 0.71 and 0.70 during validation period, respectively. Comparison of the results of the two models also indicates a wider prediction interval for the results of the SWAT model. The values of P-factor related to each model shows that the percentage of observed stream flow values bracketed by the 95PPU in the RBNN model as 91% is higher than the P-factor in SWAT as 87%. In other words the RBNN model estimates the stream flow values more accurately and with less uncertainty. It could be stated that RBNN model based on simple input could be used for estimation of monthly stream flow, missing data, and testing the accuracy and performance of other models.

Keywords: SWAT, RBNN, SUFI 2, bootstrap technique, stream flow, simulation

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Authors: Liang-Jen Wang, Sung-Chou Li, Yuan-Ming Yeh, Sheng-Yu Lee, Ho-Chang Kuo, Chia-Yu Yang

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Background: Dysbiosis in the gut microbial community might be involved in the pathophysiology of attention deficit/hyperactivity disorder (ADHD). The fungal component of the gut microbiome, namely the mycobiota, is a hyperdiverse group of multicellular eukaryotes that can influence host intestinal permeability. This study therefore aimed to investigate the impact of fungal mycobiome dysbiosis and intestinal permeability on ADHD. Methods: Faecal samples were collected from 35 children with ADHD and from 35 healthy controls. Total DNA was extracted from the faecal samples, and the internal transcribed spacer (ITS) regions were sequenced using high-throughput next-generation sequencing (NGS). The fungal taxonomic classification was analysed using bioinformatics tools, and the differentially expressed fungal species between the ADHD and healthy control groups were identified. An in vitro permeability assay (Caco-2 cell layer) was used to evaluate the biological effects of fungal dysbiosis on intestinal epithelial barrier function. Results: The β-diversity (the species diversity between two communities), but not α-diversity (the species diversity within a community), reflected the differences in fungal community composition between ADHD and control groups. At the phylum level, the ADHD group displayed a significantly higher abundance of Ascomycota and significantly lower abundance of Basidiomycota than the healthy control group. At the genus level, the abundance of Candida (especially Candida albicans) was significantly increased in ADHD patients compared to the healthy controls. In addition, the in vitro cell assay revealed that C. albicans secretions significantly enhanced the permeability of Caco-2 cells. Conclusions: The current study is the first to explore altered gut mycobiome dysbiosis using the NGS platform in ADHD. The findings from this study indicated that dysbiosis of the fungal mycobiome and intestinal permeability might be associated with susceptibility to ADHD.

Keywords: ADHD, fungus, gut–brain axis, biomarker, child psychiatry

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Authors: Akhigbe Mark, Abang Roger, Mwoltu Nanaribet, Edet Blessing

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Introduction.: The introduction of pre- exposure prophylaxis (PrEP) as a biomedical prevention method for HIV/AIDS has been around for more than a decade since the first confirmed evidence of its effectiveness when used daily as an oral pill. It is now a very valuable addition for people who are at higher risk of contracting HIV. Although globalacceptanceof PrEP hasincreased, PrEP is still highly concentrated in a small number of countries and within a small sub-population, with Kenya and South Africa accounting for only 19% of people who have received PrEP in Africa region, there is still a significant regionGap in PrEP availability and use, with only 28% of the target of 3 million in low-and middle countries currently using PrEP. Description: The purpose of this study is to find out if serum creatinine could be used as an incentive to improve PrEP uptake among Key population.Numerous approaches to increasing the uptake ofPrEP as a prevention mechanism for HIV in KPs has beenemployed, and one of them is serum creatinine. This approach is a biomarker of renal function, which was used in study as an incentive to increase PrEP uptake among key population groups (female sex workers, men who have sex with men, persons who inject drugs, transgender) in 3 states from South-South Nigeria. Whole blood samples are collected from clients, analysis of the samples is done using the clinical chemistry analyzer before they are initiated onto PrEP. Lessons learned and Recommendations: Secondary data was extracted from 3 states of HALG Implementing facilities in Southern part of Nigeria, PrEP uptake before and afterthe introduction of serum creatinine between March 2020 and August 2020 among key populationsin Nigeria. A total of 5664 patients were initiated on PrEP before, and after the introduction of serum creatinine, the PrEP uptake rate before (March 2020 to May 2020) introduction of serum creatinine accounted for only 5% of the total onset, and after (June 2020 to August 2020) introduction of serum creatinine, the uptake rate accounted for 95% of the total onset. These finding shows that increased uptake of PrEP before/after serum creatineindicates that serum creatine may be an effective stimulus for promoting PrEP in key populations.

Keywords: serum creatinine, incentives, PrEP, key populations, Nigeria

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Authors: Marcela Jelicova, Anna Lierova, Zuzana Sinkorova, Radovan Metelka

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At present, electrochemical methods are used in various research fields, especially for analysis of biological molecules. The fact offers the possibility of using the detection of oxidative damage induced indirectly by γ rays in DNA in biodosimentry. The main goal of our study is to optimize the detection of 8-hydroxyguanine by differential pulse voltammetry. The level of this stable and specific indicator of DNA damage could be determined in DNA isolated from peripheral blood lymphocytes, plasma or urine of irradiated individuals. Screen-printed carbon electrodes modified with carboxy-functionalized multi-walled carbon nanotubes were utilized for highly sensitive electrochemical detection of 8-hydroxyguanine. Electrochemical oxidation of 8-hydroxoguanine monitored by differential pulse voltammetry was found pH-dependent and the most intensive signal was recorded at pH 7. After recalculating the current density, several times higher sensitivity was attained in comparison with already published results, which were obtained using screen-printed carbon electrodes with unmodified carbon ink. Subsequently, the modified electrochemical technique was used for the detection of 8-hydroxoguanine in calf thymus DNA samples irradiated by 60Co gamma source in the dose range from 0.5 to 20 Gy using by various types of sample pretreatment and measurement conditions. This method could serve for fast retrospective quantification of absorbed dose in cases of accidental exposure to ionizing radiation and may play an important role in biodosimetry.

Keywords: biodosimetry, electrochemical detection, voltametry, 8-hydroxyguanine

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Authors: Isabella Jabbour

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The world's population is expected to reach over 10 billion by 2050, creating a significant demand for food production, particularly in the agricultural industry. Cellular agriculture presents a solution to this challenge by producing meat that resembles traditionally produced meat, but with significantly less land use. Decellularized plant scaffolds, such as spinach leaves, have been shown to be a suitable edible scaffold for growing animal muscle, enabling cultured cells to grow and organize into three-dimensional structures that mimic the texture and flavor of conventionally produced meat. However, the use of freshwater to remove the intact extracellular material from these plants remains a concern, particularly when considering scaling up the production process. In this study, two protocols were used, 1X SDS and Boom Sauce, to decellularize spinach leaves with both distilled water and ocean water. The decellularization process was confirmed by histology, which showed an absence of cell nuclei, DNA and protein quantification. Results showed that spinach decellularized with ocean water contained 9.9 ± 1.4 ng DNA/mg tissue, which is comparable to the 9.2 ± 1.1 ng DNA/mg tissue obtained with DI water. These findings suggest that decellularized spinach leaves using ocean water hold promise as an eco-friendly and cost-effective scaffold for laboratory-grown meat production, which could ultimately transform the meat industry by providing a sustainable alternative to traditional animal farming practices while reducing freshwater use.

Keywords: cellular agriculture, plant scaffold, decellularization, ocean water usage

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Authors: Suveen Kumar

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Oral cancer (OC) is the sixth most death causing cancer in world which includes tumour of lips, floor of the mouth, tongue, palate, cheeks, sinuses, throat, etc. Conventionally, the techniques used for OC detection are toluidine blue staining, biopsy, liquid-based cytology, visual attachments, etc., however these are limited by their highly invasive nature, low sensitivity, time consumption, sophisticated instrument handling, sample processing and high cost. Therefore, we developed biosensing chips for non-invasive detection of OC via CYFRA-21-1 biomarker. CYFRA-21-1 (molecular weight: 40 kDa) is secreted in saliva of OC patients which is a non-invasive biological fluid with a cut-off value of 3.8 ng mL-1, above which the subjects will be suffering from oral cancer. Therefore, in first work, 3-aminopropyl triethoxy silane (APTES) functionalized zirconia (ZrO2) nanoparticles (APTES/nZrO2) were used to successfully detect CYFRA-21-1 in a linear detection range (LDR) of 2-16 ng mL-1 with sensitivity of 2.2 µA mL ng-1. Successively, APTES/nZrO2-RGO was employed to prevent agglomeration of ZrO2 by providing high surface area reduced graphene oxide (RGO) support and much wider LDR (2-22 ng mL-1) was obtained with remarkable limit of detection (LOD) as 0.12 ng mL-1. Further, APTES/nY2O3/ITO platform was used for oral cancer bioseneor development. The developed biosensor (BSA/anti-CYFRA-21-1/APTES/nY2O3/ITO) have wider LDR (0.01-50 ng mL-1) with remarkable limit of detection (LOD) as 0.01 ng mL-1. To improve the sensitivity of the biosensing platform, nanocomposite of yattria stabilized nanostructured zirconia-reduced graphene oxide (nYZR) based biosensor has been developed. The developed biosensing chip having ability to detect CYFRA-21-1 biomolecules in the range of 0.01-50 ng mL-1, LOD of 7.2 pg mL-1 with sensitivity of 200 µA mL ng-1. Further, the applicability of the fabricated biosensing chips were also checked through real sample (saliva) analysis of OC patients and the obtained results showed good correlation with the standard protein detection enzyme linked immunosorbent assay (ELISA) technique.

Keywords: non-invasive, oral cancer, nanomaterials, biosensor, biochip

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Authors: Moiseenko F. V., Volkov N. M., Zhabina A. S., Stepanova E. O., Kirillov A. V., Myslik A. V., Artemieva E. V., Agranov I. R., Oganesyan A. P., Egorenkov V. V., Abduloeva N. H., Aleksakhina S. Yu., Ivantsov A. O., Kuligina E. S., Imyanitov E. N., Moiseyenko V. M.

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Analysis of ctDNA in patients with NSCLC is an emerging biomarker. Multiple research efforts of quantitative or at least qualitative analysis before and during the first periods of treatment with TKI showed the prognostic value of ctDNA clearance. Still, these important results are not incorporated in clinical standards. We evaluated the role of ctDNA in EGFR-mutated NSCLC receiving first-line TKI. Firstly, we analyzed sequential plasma samples from 30 patients that were collected before intake of the first tablet (at baseline) and at 6, 12, 24, 36, and 48 hours after the “starting point.” EGFR-M+ allele was measured by ddPCR. Afterward, we included sequential qualitative analysis of ctDNA with cobas® EGFR Mutation Test v2 from 99 NSCLC patients before the first dose, after 2 and 4 months of treatment, and on progression. Early response analysis showed the decline of EGFR-M+ level in plasma within the first 48 hours of treatment in 11 subjects. All these patients showed objective tumor response. 10 patients showed either elevation of EGFR-M+ plasma concentration (n = 5) or stable content of circulating EGFR-M+ after the start of the therapy (n = 5); only 3 of these patients achieved an objective response (p = 0.026) when compared to the former group). The rapid decline of plasma EGFR-M+ DNA concentration also predicted for longer PFS (13.7 vs. 11.4 months, p = 0.030). Long-term ctDNA monitoring showed clinically significant heterogeneity of EGFR-mutated NSCLC treated with 1st line TKIs in terms of progression-free and overall survival. Patients without detectable ctDNA at baseline (N = 32) possess the best prognosis on the duration of treatment (PFS: 24.07 [16.8-31.3] and OS: 56.2 [21.8-90.7] months). Those who achieve clearance after two months of TKI (N = 42) have indistinguishably good PFS (19.0 [13.7 – 24.2]). Individuals who retain ctDNA after 2 months (N = 25) have the worst prognosis (PFS: 10.3 [7.0 – 13.5], p = 0.000). 9/25 patients did not develop ctDNA clearance at 4 months with no statistical difference in PFS from those without clearance at 2 months. Prognostic heterogeneity of EGFR-mutated NSCLC should be taken into consideration in planning further clinical trials and optimizing the outcomes of patients.

Keywords: NSCLC, EGFR, targeted therapy, ctDNA, prognosis

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Authors: Lakshmana Ravi Raj Gali, K. Sridhar Reddy, M. Amaranatha Reddy

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Load transfer between adjacent slabs of the jointed plain concrete pavement (JPCP) system is inevitable for long-lasting performance. Dowel bars are generally used to ensure sufficient degree of load transfer, in addition to the load transferred by aggregate interlock mechanism at the joints. Joint efficiency is the measure of joint quality, a major concern and therefore the dowel bar system should be designed and constructed well. The interaction between dowel bars and concrete that includes various parameters of dowel bar and concrete will explain the degree of joint efficiency. The present study focuses on the methodology of selecting contact stiffness, which quantifies dowel-concrete interaction. In addition, a parametric study which focuses on the effect of dowel diameter, dowel shape, the spacing between dowel bars, joint opening, the thickness of the slab, the elastic modulus of concrete, and concrete cover on contact stiffness was also performed. The results indicated that the thickness of the slab is most critical among various parameters to explain the joint efficiency. Further displacement equivalency method was proposed to find out the contact stiffness. The proposed methodology was validated with the available field surface deflection data collected by falling weight deflectometer (FWD).

Keywords: contact stiffness, displacement equivalency method, Dowel-concrete interaction, joint behavior, 3D numerical simulation

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Authors: Marek Kuźniewski, Magdalena B. Kaziuk , Danuta Fedak, Paulina Dumnicka, Ewa Stępień, Beata Kuśnierz-Cabala, Władysław Sułowicz

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Background: The high prevalence of cardiovascular morbidity and mortality among patients with chronic kidney disease (CKD) is observed especially in those undergoing dialysis. Osteoprotegerin (OPG) and its ligands, receptor activator of nuclear factor kappa-B ligand (RANKL) and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) have been associated with cardiovascular complications. Our aim was to study their role as cardiovascular risk factors in stage 5 CKD patients. Methods: OPG, RANKL and TRAIL concentrations were measured in 69 hemodialyzed CKD patients and 35 healthy volunteers. In CKD patients, cardiovascular dysfunction was assessed with aortic pulse wave velocity (AoPWV), carotid artery intima-media thickness (CCA-IMT), coronary artery calcium score (CaSc) and N-terminal pro-B-type natriuretic peptide (NT-proBNP) serum concentration. Cardiovascular and overall mortality data were collected during a 7-years follow-up. Results: OPG plasma concentrations were higher in CKD patients comparing to controls. Total soluble RANKL was lower and OPG/RANKL ratio higher in patients. Soluble TRAIL concentrations did not differ between the groups and OPG/TRAIL ratio was higher in CKD patients. OPG and OPG/TRAIL positively predicted long-term mortality (all-cause and cardiovascular) in CKD patients. OPG positively correlated with AoPWV, CCA-IMT and NT-proBNP whereas OPG/TRAIL with AoPWV and NT-proBNP. Described relationships were independent of classical and non-classical cardiovascular risk factors, with exception of age. Conclusions: Our study confirmed the role of OPG as a biomarker of cardiovascular dysfunction and a predictor of mortality in stage 5 CKD. OPG/TRAIL ratio can be proposed as a predictor of cardiovascular dysfunction and mortality.

Keywords: osteoprotegerin, tumor necrosis factor-related apoptosis-inducing ligand, receptor activator of nuclear factor kappa-B ligand, hemodialysis, chronic kidney disease, cardiovascular disease

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Authors: M. Nadeem, Y. K. Chang, C. Diallo, U. Venkatadri, P. Havard, T. Nguyen-Quang

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Uniform distribution of agro-chemicals is highly important because there is a significant loss of agro-chemicals, for example from pesticide, during spraying due to non-uniformity of droplet and off-target drift. Improving the efficiency of spray pattern for different cropping systems would reduce energy, costs and to minimize environmental pollution. In this paper, we examine the water jet patterns in order to study the performance and uniformity of water distribution during the spraying process. We present a method to quantify the water amount from a sprayer jet by using the Particle Image Velocimetry (PIV) system. The results of the study will be used to optimize sprayer or nozzles design for chemical application. For this study, ten sets of images were acquired by using the following PIV system settings: double frame mode, trigger rate is 4 Hz, and time between pulsed signals is 500 µs. Each set of images contained different numbers of double-framed images: 10, 20, 30, 40, 50, 60, 70, 80, 90 and 100 at eight different pressures 25, 50, 75, 100, 125, 150, 175 and 200 kPa. The PIV images obtained were analysed using custom-made image processing software for droplets and volume calculations. The results showed good agreement of both manual and PIV measurements and suggested that the PIV technique coupled with image processing can be used for a precise quantification of flow through nozzles. The results also revealed that the method of measuring fluid flow through PIV is reliable and accurate for sprayer patterns.

Keywords: image processing, PIV, quantifying the water volume from nozzle, spraying pattern

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Authors: Xinwen Zhu, Xingguang Li, Sun Yi

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Crack is one of the most common damages in buildings, bridges, roads and so on, which may pose safety hazards. However, cracks frequently happen in structures of various materials. Traditional methods of manual detection and measurement, which are known as subjective, time-consuming, and labor-intensive, are gradually unable to meet the needs of modern development. In addition, crack detection and measurement need be safe considering space limitations and danger. Intelligent crack detection has become necessary research. In this paper, an efficient method for crack detection and quantification using a 3D sensor, LiDAR, and depth camera is proposed. This method works even in a dark environment, which is usual in real-world applications. The LiDAR rapidly spins to scan the surrounding environment and discover cracks through lasers thousands of times per second, providing a rich, 3D point cloud in real-time. The LiDAR provides quite accurate depth information. The precision of the distance of each point can be determined within around  ±3 cm accuracy, and not only it is good for getting a precise distance, but it also allows us to see far of over 100m going with the top range models. But the accuracy is still large for some high precision structures of material. To make the depth of crack is much more accurate, the depth camera is in need. The cracks are scanned by the depth camera at the same time. Finally, all data from LiDAR and Depth cameras are analyzed, and the size of the cracks can be quantified successfully. The comparison shows that the minimum and mean absolute percentage error between measured and calculated width are about 2.22% and 6.27%, respectively. The experiments and results are presented in this paper.

Keywords: LiDAR, depth camera, real-time, detection and measurement

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Authors: Arredondo Valdés Roberto, Hernández Castillo Francisco Daniel, Laredo Alcalá Elan Iñaky, Gonzalez Gallegos Esmeralda, Castro Del Angel Epifanio

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The common bean or Phaseolus vulgaris L. is the most important food legume for direct consumption in the world. Fusarium dry rot in the major fungus disease affects Phaseolus vulgaris L, after planting. In another hand, Rhizoctonia can be found on all underground parts of the plant and various times during the growing season. In recent years, the world has conducted studies about the use of natural products as substitutes for herbicides and pesticides, because of possible ecological and economic benefits. Plants respond to fungal invasion by activating defense responses associated with accumulation of several enzymes and inhibitors, which prevent pathogen infection. This study focused on the role of proteins, peroxidase (POD), phenylalanine ammonia lyase (PAL), in imparting resistance to soft rot pathogens by applied different bacterial consortium, formulated and provided by Biofertilizantes de Méxicanos industries, analyzing the enzyme activity at different times of application (6 h, 12 h and 24 h). The resistance of these treatments was correlated with high POD and PAL enzyme activity as well as increased concentrations of proteins. These findings show that PAL, POD and synthesis of proteins play a role in imparting resistance to Phaseolus vulgaris L. soft rot infection by Fusarium and Rhizoctonia.

Keywords: fusarium, peroxidase, phenylalanine ammonia lyase, rhizoctonia

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Authors: Nabil Ghedadba, Abdessemed Samira, Leila Hambaba, Sidi Mohamed Ould Mokhtar, Nassima Fercha, Houas Bousselsela

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The overall objective of this study was to evaluate in vitro the hemostatic activity of secondary metabolites (polyphenols, flavonoids, and tannins) of Marrubium vulgare leaves, aromatic plant widely used in traditional medicine for the treatment of asthma, cough, diabetes (by its effect on the pancreas to secrete insulin), heart disease, fever has a high efficiency as against inflammation. Qualitative analysis of the aqueous extract (AQE) by thin layer chromatography revealed the presence of quercetin, kaempferol and rutin. Quantification of total phenols by Folin Ciocalteu method and flavonoids by AlCl3 method gave high values with AQE: 175±0.80 mg GAE per 100g of the dry matter, 23.86±0.36 mg QE per 100g of dry matter. Moreover, the assay of condensed tannins by the vanillin method showed that AQE contains the highest value: 16.55±0.03 mg e-catechin per 100 g of dry matter. Assessment of hemostatic activity by the plasma recalcification method (time of Howell) has allowed us to discover the surprising dose dependent anticoagulant effect of AQE lyophilized from leaves of M. vulgare. A positive linear correlation between the two parameters studied: the content of condensed tannins and hemostatic activity (r=0.96) were used to highlight a possible role of these compounds that are potent vasoconstrictor activity in hemostatic. From these results we can see that Marrubium vulgre could be used for the treatment of health.

Keywords: Marrubium vulgare L., aqueous extract, phenolic compounds dosing, hemostatic activity, condensed tannins

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Authors: Abhishek Mukherjee, Juan C. Cajas, Jenny Suckale, Guillaume Houzeaux, Oriol Lehmkuhl, Simone Marras

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The investigation of tsunami flow characteristics and the quantification of tsunami energy reduction through the coastal vegetation is important to understand the protective benefits of nature-based mitigation parks. In the present study, a three-dimensional non-hydrostatic incompressible Computational Fluid Dynamics model with a two-way coupling enabled fluid-structure interaction approach (FSI) is used. After validating the numerical model against experimental data, tsunami flow characteristics have been investigated by varying vegetation density, modulus of elasticity, the gap between stems, and arrangement or distribution of vegetation patches. Streamwise depth average velocity profiles, turbulent kinetic energy, energy flux reflection, and dissipation extracted by the numerical study will be presented in this study. These diagnostics are essential to assess the importance of different parameters to design the proper coastal defense systems. When a tsunami wave reaches the shore, it transforms into undular bores, which induce scour around offshore structures and sediment transport. The bed shear stress, instantaneous turbulent kinetic energy, and the vorticity near-bed will be presented to estimate the importance of vegetation to prevent tsunami-induced scour and sediment transport.

Keywords: coastal defense, energy flux, fluid-structure interaction, natural hazards, sediment transport, tsunami mitigation

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Authors: Nahida Sultana

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Globally, an estimated 58 million people have chronic hepatitis C virus infection, with about 1.5 million new infections occurring per year. The hepatitis C virus is a blood-borne virus, and most infections occur through exposure to blood from unsafe injection practices, unsafe health care, unscreened blood transfusion, injection drug use, and sexual practices that lead to exposure to blood. Hepatitis C virus (HCV) causes chronic infections that mainly affect the liver leading to liver diseases. This study aimed to determine whether there is any significant association between HCV transmission risk factors in relation to genotypes in HCV-infected Bangladeshi patients. After quantification of HCV viral load, 36 samples were randomly selected for HCV genotyping and risk factor measurement. A greater proportion of genotype 1 (p > 0.05) patients (40%) underwent blood transfusion compared to patients (22.6%) with genotype 3 infections. More genotype 1 patient underwent surgery and invasive procedures (20%), and rather than those with genotype 3 patients (16.1%). The history of IDUs (25.8%) and sexual exposure (3.2%) are only prevalent in genotype 3 patients and absent in patients with genotype 1 (p >0.05). There was no significant statistical difference found in HCV transmission risk factors (blood transfusion, IDUs, Surgery& interventions, sexual transmission) between patients infected with genotypes 1 and 3. In HCV infection, genotype may have no relation to transmission risk factors among Bangladeshi patients.

Keywords: HCV genotype, alanine aminotransferase (ALT), HCV viral load, IDUs

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Authors: S. Mohamed, D. Gonzalez, C. Sayada, P. Halfon

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Drug resistance mutations are routinely detected using standard Sanger sequencing, which does not detect minor variants with a frequency below 20%. The impact of detecting minor variants generated by ultra-deep sequencing (UDS) on HIV drug-resistance (DR) interpretations has not yet been studied. Fifty HIV-1 patients who experienced virological failure were included in this retrospective study. The HIV-1 UDS protocol allowed the detection and quantification of HIV-1 protease and reverse transcriptase variants related to genotypes A, B, C, E, F, and G. DeepChek®-HIV simplified DR interpretation software was used to compare Sanger sequencing and UDS. The total time required for the UDS protocol was found to be approximately three times longer than Sanger sequencing with equivalent reagent costs. UDS detected all of the mutations found by population sequencing and identified additional resistance variants in all patients. An analysis of DR revealed a total of 643 and 224 clinically relevant mutations by UDS and Sanger sequencing, respectively. Three resistance mutations with > 20% prevalence were detected solely by UDS: A98S (23%), E138A (21%) and V179I (25%). A significant difference in the DR interpretations for 19 antiretroviral drugs was observed between the UDS and Sanger sequencing methods. Y181C and T215Y were the most frequent mutations associated with interpretation differences. A combination of UDS and DeepChek® software for the interpretation of DR results would help clinicians provide suitable treatments. A cut-off of 1% allowed a better characterisation of the viral population by identifying additional resistance mutations and improving the DR interpretation.

Keywords: HIV-1, ultra-deep sequencing, Sanger sequencing, drug resistance

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Authors: Eric Dede, Marcus Tindall, John W. Cherrie, Steve Hankin, Christopher Collins

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Current exposure models used in contaminated land risk assessment are highly conservative. Use of these models may lead to over-estimation of actual exposures, possibly resulting in negative financial implications due to un-necessary remediation. Thus, we are carrying out a study seeking to improve our understanding of human exposure to selected toxic elements in soil: arsenic (As), cadmium (Cd), chromium (Cr), nickel (Ni), and lead (Pb) resulting from allotment land-use. The study employs biomonitoring and physiologically-based pharmacokinetic (PBPK) modelling to quantify human exposure to these elements. We recruited 37 allotment users (adults > 18 years old) in Scotland, UK, to participate in the study. Concentrations of the elements (and their bioaccessibility) were measured in allotment samples (soil and allotment produce). Amount of produce consumed by the participants and participants’ biological samples (urine and blood) were collected for up to 12 consecutive months. Ethical approval was granted by the University of Reading Research Ethics Committee. PBPK models (coded in MATLAB) were used to estimate the distribution and accumulation of the elements in key body compartments, thus indicating the internal body burden. Simulating low element intake (based on estimated ‘doses’ from produce consumption records), predictive models suggested that detection of these elements in urine and blood was possible within a given period of time following exposure. This information was used in planning biomonitoring, and is currently being used in the interpretation of test results from biological samples. Evaluation of the models is being carried out using biomonitoring data, by comparing model predicted concentrations and measured biomarker concentrations. The PBPK models will be used to generate bioavailability values, which could be incorporated in contaminated land exposure models. Thus, the findings from this study will promote a more sustainable approach to contaminated land management.

Keywords: biomonitoring, exposure, PBPK modelling, toxic elements

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Authors: Parvin Samadi Pakchin, Reza Saber, Hossein Ghanbari, Yadollah Omidi

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Ovarian cancer is one of the leading cause of mortality among the gynecological malignancies, and it remains the one of the most prevalent cancer in females worldwide. Tumor markers are biochemical molecules in blood or tissues which can indicates cancers occurrence in the human body. So, the sensitive and specific detection of cancer markers typically recruited for diagnosing and evaluating cancers. Recently extensive research efforts are underway to achieve a simple, inexpensive and accurate device for detection of cancer biomarkers. Compared with conventional immunoassay techniques, electrochemical immunosensors are of great interest, because they are specific, simple, inexpensive, easy to handling and miniaturization. Moreover, in the past decade nanotechnology has played a crucial role in the development of biosensors. In this study, a signal-off electrochemical immunosensor for the detection of CA125 antigen has been developed using chitosan-gold nanoparticles (CS-AuNP) and multi-wall carbon nanotubes (MWCNT) composites. Toluidine blue (TB) is used as redox probe which is immobilized on the electrode surface. CS-AuNP is synthesized by a simple one step method that HAuCl4 is reduced by NH2 groups of chitosan. The CS-AuNP-MWCNT modified electrode has shown excellent electrochemical performance compared with bare Au electrode. MWCNTs and AuNPs increased electrochemical conductivity and accelerate electrons transfer between solution and electrode surface while excessive amine groups on chitosan lead to the effective loading of the biological material (CA125 antibody) and TB on the electrode surface. The electrochemical, immobilization and sensing properties CS-AuNP-MWCNT-TB modified electrodes are characterized by cyclic voltammetry, electrochemical impedance spectroscopy, differential pulse voltammetry and square wave voltammetry with Fe(CN)63−/4−as an electrochemical redox indicator.

Keywords: signal-off electrochemical biosensor, CA125, ovarian cancer, chitosan-gold nanoparticles

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Authors: Parul Grover, K. A. Suri, Raj Kumar, Gulshan Bansal

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Background: Nyctanthes arbortristis Linn is traditionally used as anticancer herb in Indian system of medicine, but its introduction into modern system of medicine is still awaited due to lack of systematic scientific studies. Objective: The objective of the present study was to isolate and characterize anticancer phytoconstituents from N. arbortristis L. leaves based on bioactivity guided fractionation. Method: Different extracts of the leaves of the plant were prepared by Soxhlet extractor. Each extract was evaluated for anticancer activity against HL-60 cell lines. Chloroform and HA extract showed potent anticancer activity and hence were selected for fractionation. Fraction C1 from chloroform extract was found to be most potent amongst all when tested against three cell lines (HL-60, A-549, and HCT-116) and thus was selected for further fractionation and a pure compound CP-01 was isolated. RP-HPLC method has been developed for quantification of isolated compound by using Kinetex C-18 column with gradient elution at 0.7 mL/min using mobile phase containing potassium dihydrogen phosphate (0.01 M, pH 3.0) with acetonitrile. The wavelength of maximum absorption (λₘₐₓ) selected was 210 nm. Results: The structure of potent anticancer CP-01 was determined on the basis spectroscopic methods like IR, 1H-NMR, ¹³C-NMR and Mass Spectrometry and it was characterized as 1,1,2-tris(2’,4’-di-tert-butylbenzene)-4,4-dimethyl-pent-1-ene. The content of CP-01 was found to be 0.88 %w/w of chloroform extract and 0.08 %w/w of N.arbortristis leaves. Conclusion: The study supports the traditional use of N. arbortristis as anticancer herb & the identified compound CP-01 can serve as an excellent lead to develop potent and safe anticancer drugs.

Keywords: anticancer, HL-60 cell lines, Nyctanthes arbor-tristis, RP-HPLC

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Authors: Sagar Shiwakoti, Narendra Man Shakya

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The lumped conceptual hydrological model HBV is applied to the Karnali River Basin to estimate runoff at several gauging stations and to analyze the changes in catchment hydrology and future flood magnitude due to climate change. The performance of the model is analyzed to assess its suitability to simulate streamflow in snow fed mountainous catchments. Due to the structural complexity, the model shows difficulties in modeling low and high flows accurately at the same time. It is observed that the low flows were generally underestimated and the peaks were correctly estimated except for some sharp peaks due to isolated precipitation events. In this study, attempt has been made to evaluate the importance of snow melt discharge in the runoff regime of the basin. Quantification of contribution of snowmelt to annual, summer and winter runoff has been done. The contribution is highest at the beginning of the hot months as the accumulated snow begins to melt. Examination of this contribution under conditions of increased temperatures indicate that global warming leading to increase in average basin temperature will significantly lead to higher contributions to runoff from snowmelt. Forcing the model with the output of HadCM3 GCM and the A1B scenario downscaled to the station level show significant changes to catchment hydrology in the 2040s. It is observed that the increase in runoff is most extreme in June - July. A shift in the hydrological regime is also observed.

Keywords: hydrological modeling, HBV light, rainfall runoff modeling, snow melt, climate change

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