Search results for: molecular marker

Authors: Wisam H. Benamer, Ehab A. Elfallah, Mohamed A. Elshaari, Farag A. Elshaari

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A challenge for laboratories is to provide bacterial identification and antibiotic sensitivity results within a short time. Hence, advancement in the required technology is desirable to improve timing, accuracy and quality. Even with the current advances in methods used for both phenotypic and genotypic identification of bacteria the need is there to develop method(s) that enhance the outcome of bacteriology laboratories in accuracy and time. The hypothesis introduced here is based on the assumption that the chromosome of any bacteria contains unique sequences that can be used for its identification and typing. The outcome of a pilot study designed to test this hypothesis is reported in this manuscript. Methods: The complete chromosome sequences of several bacterial species were downloaded to use as search targets for unique sequences. Visual basic and SQL server (2014) were used to generate a complete set of 18-base long primers, a process started with reverse translation of randomly chosen 6 amino acids to limit the number of the generated primers. In addition, the software used to scan the downloaded chromosomes using the generated primers for similarities was designed, and the resulting hits were classified according to the number of similar chromosomal sequences, i.e., unique or otherwise. Results: All primers that had identical/similar sequences in the selected genome sequence(s) were classified according to the number of hits in the chromosomes search. Those that were identical to a single site on a single bacterial chromosome were referred to as unique. On the other hand, most generated primers sequences were identical to multiple sites on a single or multiple chromosomes. Following scanning, the generated primers were classified based on ability to differentiate between medically important bacterial and the initial results looks promising. Conclusion: A simple strategy that started by generating primers was introduced; the primers were used to screen bacterial genomes for match. Primer(s) that were uniquely identical to specific DNA sequence on a specific bacterial chromosome were selected. The identified unique sequence can be used in different molecular diagnostic techniques, possibly to identify bacteria. In addition, a single primer that can identify multiple sites in a single chromosome can be exploited for region or genome identification. Although genomes sequences draft of isolates of organism DNA enable high throughput primer design using alignment strategy, and this enhances diagnostic performance in comparison to traditional molecular assays. In this method the generated primers can be used to identify an organism before the draft sequence is completed. In addition, the generated primers can be used to build a bank for easy access of the primers that can be used to identify bacteria.

Keywords: bacteria chromosome, bacterial identification, sequence, primer generation

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Authors: Sonia Mahajan Dinesh, Anant Dinesh, Madhavi Tripathi, Vinod Kumar Ramteke, Rajnish Sharma, Anupam Mondal

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Background: Neo-adjuvant chemotherapy plays an important role in treatment of breast cancer by decreasing the tumour load and it offers an opportunity to evaluate response of primary tumour to chemotherapy. Standard anatomical imaging modalities are unable to accurately reflect the response to chemotherapy until several cycles of drug treatment have been completed. Metabolic imaging using tracers like 18F-fluorodeoxyglucose (FDG) as a marker of glucose metabolism or amino acid tracers like L-methyl-11C methionine (MET) have potential role for the measurement of treatment response. In this study, our objective was to compare these two PET tracers for assessment of response to neoadjuvant chemotherapy, in locally advanced breast carcinoma. Methods: In our prospective study, 20 female patients with histology proven locally advanced breast carcinoma underwent PET-CT imaging using FDG and MET before and after three cycles of neoadjuvant chemotherapy (CAF regimen). Thereafter, all patients were taken for MRM and the resected specimen was sent for histo-pathological analysis. Tumour response to the neoadjuvant chemotherapy was evaluated by PET-CT imaging using PERCIST criteria and correlated with histological results. Responses calculated were compared for statistical significance using paired t- test. Results: Mean SUVmax for primary lesion in FDG PET and MET PET was 15.88±11.12 and 5.01±2.14 respectively (p<0.001) and for axillary lymph nodes was 7.61±7.31 and 2.75±2.27 respectively (p=0.001). Statistically significant response in primary tumour and axilla was noted on both FDG and MET PET after three cycles of NAC. Complete response in primary tumour was seen in only 1 patient in FDG and 7 patients in MET PET (p=0.001) whereas there was no histological complete resolution of tumor in any patient. Response to therapy in axillary nodes noted on both PET scans were similar (p=0.45) and correlated well with histological findings. Conclusions: For the primary breast tumour, FDG PET has a higher sensitivity and accuracy than MET PET and for axilla both have comparable sensitivity and specificity. FDG PET shows higher target to background ratios so response is better predicted for primary breast tumour and axilla. Also, FDG-PET is widely available and has the advantage of a whole body evaluation in one study.

Keywords: 11C-methionine, 18F-FDG, breast carcinoma, neoadjuvant chemotherapy

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Authors: Amal M. Nassar, Nehal S. Ahmed, Rasha S. Kamal

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Some lube oil additives improve the base oil performance such as viscosity index improvers and pour point depressants which are the most important type of additives. In the present work, some homopolymeric additives were prepared by esterification of acrylic acid with different alcohols (1-dodecyl, 1-hexadecyl, and 1-octadecyl )and then homopolymerization of the prepared esters with different ratio of benzoyl peroxide catalyst (0.25%& 0.5 % and 1%). Structure of the prepared esters was confirmed by Infra-Red Spectroscopy. The molecular weights of the prepared homopolymers were determined by using Gel Permeation Chromatograph. The efficiency of the prepared homopolymers as viscosity index improvers and pour point depressants for lube oil was the investigation. It was found that all the prepared homopolymers are effective as viscosity index improvers and pour point depressants.

Keywords: lube oil additives, homopolymerization, viscosity index improver, pour point depressant

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Authors: Lubna Azmi, Ila Shukla, Shyam Sundar Gupta, Padam Kant, C. V. Rao

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To investigate the chemoprotective potential of NBRIQU16 chemotype isolated from Argyreia speciosa (Family: Convolvulaceae) on N-methyl-N-nitro-N-nitrosoguanidine (MNNG) and NaCl-induced gastric carcinomas in Wistar rats. Forty-six male 6-week-old Wistar rats were divided into two groups. Thirty rats in group A were fed with a diet supplemented with 8 % NaCl for 20 weeks and simultaneously given N-methyl-N’-nitro-N-nitrosoguanidine (MNNG) in drinking water at a concentration of 100 ug/ml for the first 17 weeks. After administration of the carcinogen, 200 and 400 mg/kg of NBRIQU16 were administered orally once a day throughout the study. From week 18, these rats were given normal water. From week 21, these rats were fed with a normal diet for 15 weeks. Group B containing 16 rats was fed standard diet for thirty-five days. It served as control. Ten rats from group A were sacrificed after 20 weeks. Scarification of remaining animals was conducted after 35 weeks. Entire stomach and some part of the duodenum were incised parallel to the greater curvature, and the samples were collected. After opening the stomach location and size of tumors were recorded. The number of tumors with their locations and sizes were recorded. Expression of survivin was examined by recording the Immunohistochemistry of the specimens. The treatment with NBRIQU16 significantly reduced the nodule incidence and nodule multiplicity in the rats after MNNG administration. Surviving expression in glandular stomachs of normal rats, of rats in middle induction period, in adenocarcinomas and NBRIQU16 treated tissues adjacent to tumor were 0, 42.0 %, 79.3%, and 36.4 %, respectively. Expression of survivin was significantly different as compared to the normal rats. Histological observations of stomach tissues too correlated with the biochemical observations.These finding powerfully supports that NBRIQU16 chemopreventive effect by suppressing the tumor burden and restoring the activities of gastric cancer marker enzymes on MNNG and NaCl-induced gastric carcinomas in Wistar rats.

Keywords: Argyreia speciosa, gastric carcinoma, immunochemistry, NBRIQU16

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Authors: Jyoti Singh, Ranju Bansal

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Fighting pain and inflammation is a common problem faced by physicians while dealing with a wide variety of diseases. Since ancient time nonsteroidal anti-inflammatory agents (NSAIDs) and opioids have been the cornerstone of treatment therapy, however, the usefulness of both these classes is limited due to severe side effects. NSAIDs, which are mainly used to treat mild to moderate inflammatory pain, induce gastric irritation and nephrotoxicity whereas opioids show an array of adverse reactions such as respiratory depression, sedation, and constipation. Moreover, repeated administration of these drugs induces tolerance to the analgesic effects and physical dependence. Further discovery of selective COX-2 inhibitors (coxibs) suggested safety without any ulcerogenic side effects; however, long-term use of these drugs resulted in kidney and hepatic toxicity along with an increased risk of secondary cardiovascular effects. The basic approaches towards inflammation and pain treatment are constantly changing, and researchers are continuously trying to develop safer and effective anti-inflammatory drug candidates for the treatment of different inflammatory conditions such as osteoarthritis, rheumatoid arthritis, ankylosing spondylitis, psoriasis and multiple sclerosis. Synthetic 3(2H)-pyridazinones constitute an important scaffold for drug discovery. Structure-activity relationship studies on pyridazinones have shown that attachment of a lactam at N-2 of the pyridazinone ring through a methylene spacer results in significantly increased anti-inflammatory and analgesic properties of the derivatives. Further introduction of the heterocyclic ring at lactam nitrogen results in improvement of biological activities. Keeping in mind these SAR studies, a new series of compounds were synthesized as shown in scheme 1 and investigated for anti-inflammatory, analgesic, anti-platelet activities and docking studies. The structures of newly synthesized compounds have been established by various spectroscopic techniques. All the synthesized pyridazinone derivatives exhibited potent anti-inflammatory and analgesic activity. Homoveratryl substituted derivative was found to possess highest anti-inflammatory and analgesic activity displaying 73.60 % inhibition of edema at 40 mg/kg with no ulcerogenic activity when compared to standard drugs indomethacin. Moreover, 2-substituted-4-benzo[d][1,3]dioxole-6-phenylpyridazin-3(2H)-ones derivatives did not produce significant changes in bleeding time and emerged as safe agents. Molecular docking studies also illustrated good binding interactions at the active site of the cyclooxygenase-2 (hCox-2) enzyme.

Keywords: anti-inflammatory, analgesic, pyridazin-3(2H)-one, selective COX-2 inhibitors

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Authors: F. Varga, Z. Liber, J. Jakše, A. Turudić, Z. Šatović, I. Radosavljević, N. Jeran, M. Grdiša

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Dalmatian pyrethrum (Tanacetum cinerariifolium (Trevir.) Sch. Bip.; Asteraceae), a source of the commercially dominant plant insecticide pyrethrin, is a species endemic to the eastern Adriatic. Genetic diversity of T. cinerariifolium was previously studied using amplified fragment length polymorphism (AFLP) markers. However, microsatellite markers (single sequence repeats - SSRs) are more informative because they are codominant, highly polymorphic, locus-specific, and more reproducible, and thus are most often used to assess the genetic diversity of plant species. Dalmatian pyrethrum is an outcrossing diploid (2n = 18) whose large genome size and high repeatability have prevented the success of the traditional approach to SSR markers development. The advent of next-generation sequencing combined with the specifically developed method recently enabled the development of, to the author's best knowledge, the first set of SSRs for genomic characterization of Dalmatian pyrethrum, which is essential from the perspective of plant genetic resources conservation. To evaluate the effectiveness of the developed SSR markers in genetic differentiation of Dalmatian pyrethrum populations, a preliminary genetic diversity study was conducted on 30 individuals from three geographically distinct natural populations in Croatia (northern Adriatic island of Mali Lošinj, southern Adriatic island of Čiovo, and Mount Biokovo) based on 12 SSR loci. Analysis of molecular variance (AMOVA) by randomization test with 10,000 permutations was performed in Arlequin 3.5. The average number of alleles per locus, observed and expected heterozygosity, probability of deviations from Hardy-Weinberg equilibrium, and inbreeding coefficient was calculated using GENEPOP 4.4. Genetic distance based on the proportion of common alleles (DPSA) was calculated using MICROSAT. Cluster analysis using the neighbor-joining method with 1,000 bootstraps was performed with PHYLIP to generate a dendrogram. The results of the AMOVA analysis showed that the total SSR diversity was 23% within and 77% between the three populations. A slight deviation from Hardy-Weinberg equilibrium was observed in the Mali Lošinj population. Allele richness ranged from 2.92 to 3.92, with the highest number of private alleles observed in the Mali Lošinj population (17). The average observed DPSA between 30 individuals was 0.557. The highest DPSA (0.875) was observed between several pairs of Dalmatian pyrethrum individuals from the Mali Lošinj and Mt. Biokovo populations, and the lowest between two individuals from the Čiovo population. Neighbor-joining trees, based on DPSA, grouped individuals into clusters according to their population affiliation. The separation of Mt. Biokovo clade was supported (bootstrap value 58%), which is consistent with the previous study on AFLP markers, where isolated populations from Mt. Biokovo differed from the rest of the populations. The developed SSR markers are an effective tool for assessing the genetic diversity and structure of natural Dalmatian pyrethrum populations. These preliminary results are encouraging for a future comprehensive study with a larger sample size across the species' range. Combined with the biochemical data, these highly informative markers could help identify potential genotypes of interest for future development of breeding lines and cultivars that are both resistant to environmental stress and high in pyrethrins. Acknowledgment: This work has been supported by the Croatian Science Foundation under the project ‘Genetic background of Dalmatian pyrethrum (Tanacetum cinerariifolium /Trevir./ Sch. Bip.) insecticidal potential’- (PyrDiv) (IP-06-2016-9034) and by project KK.01.1.1.01.0005, Biodiversity and Molecular Plant Breeding, at the Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Zagreb, Croatia.

Keywords: Asteraceae, genetic diversity, genomic SSRs, NGS, pyrethrum, Tanacetum cinerariifolium

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Authors: Deniz Guven, Wil Ward, Jinming Duan, Li Bai

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Over the past two decades or so, Optical Coherence Tomography (OCT) has been used to diagnose retina and optic nerve diseases. The retinal nerve fibre layer, for example, is a powerful diagnostic marker for detecting and staging glaucoma. With the advances in optical imaging hardware, the adoption of OCT is now commonplace in clinics. More and more OCT images are being generated, and for these OCT images to have clinical applicability, accurate automated OCT image segmentation software is needed. Oct image segmentation is still an active research area, as OCT images are inherently noisy, with the multiplicative speckling noise. Simple edge detection algorithms are unsuitable for detecting retinal layer boundaries in OCT images. Intensity fluctuation, motion artefact, and the presence of blood vessels also decrease further OCT image quality. In this paper, we introduce a new method for segmenting three-dimensional (3D) OCT images. This involves the use of a Kalman filter, which is commonly used in computer vision for object tracking. The Kalman filter is applied to the 3D OCT image volume to track the retinal layer boundaries through the slices within the volume and thus segmenting the 3D image. Specifically, after some pre-processing of the OCT images, points on the retinal layer boundaries in the first image are identified, and curve fitting is applied to them such that the layer boundaries can be represented by the coefficients of the curve equations. These coefficients then form the state space for the Kalman Filter. The filter then produces an optimal estimate of the current state of the system by updating its previous state using the measurements available in the form of a feedback control loop. The results show that the algorithm can be used to segment the retinal layers in OCT images. One of the limitations of the current algorithm is that the curve representation of the retinal layer boundary does not work well when the layer boundary is split into two, e.g., at the optic nerve, the layer boundary split into two. This maybe resolved by using a different approach to representing the boundaries, such as b-splines or level sets. The use of a Kalman filter shows promise to developing accurate and effective 3D OCT segmentation methods.

Keywords: optical coherence tomography, image segmentation, Kalman filter, object tracking

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Authors: Hayrettin Eroglu, Oguz Aksakal

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In this study, it is analysed that which decontamination products are more effective and how decontamination process should be performed in the case of contamination of radioactive 99mTc which is the most common radioactive element used in nuclear applications dealing with the human body or the environment. Based on the study, it is observed that existing radioactive washers are less effective than expected, alcohol has no effect on the decontamination of 99mTc, and temperature and pH are the most important factors. In the light of the analysis, it is concluded that the most effective decontamination product is DM-D (Decontamination Material-D). When the effect of DM-D on surfaces is analysed, it is observed that decontamination is very fast on scrubs and formica with both DM-D and water, and although DM-D is very effective on skin, it is not effective on f ceramic tiles and plastic floor covering material. Also in this study, the effectiveness of different molecular groups in the decontaminant was investigated. As a result, the acetate group has been observed as the most effective component of the decontaminant.

Keywords: contamination, radioactive, technetium, decontamination

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Authors: Eric Beyegue, Boris Azantza, Judith Laure Ngondi, Julius E. Oben

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Background: Insulin resistance (IR) and oxidative stress are associated with obesity, diabetes mellitus, and other cardio metabolic disorders. The aim of this study was to investigate the effect of Coula edulis extracts (CEE) on insulin resistance and oxidative stress markers in high-fat/high sucrose diet-induced insulin resistance in rats. Materials and Methods: Thirty male rats were divided into 6 groups of 5 rats each fed, received daily oral administration of CE extracts for 8 weeks as follows: Group 1 or negative control group, fed with standard diet (SD); Group 2 fed with high-fat/high sucrose diet (HFHS) only; Group3 fed with HFHS + CEAq 200; Group 4 fed with HFHS + CEAq 400; Group 5 fed with HFHS + CEEt 200; Group 6 fed with HFHS + CEEt 400. At the end of the experiment (8 weeks), animals were sacrificed plasma lipid profile, glucose, insulin, oxidative marker and digestive enzyme activities were measured. The homeostasis model assessment for insulin resistance (HOMA-IR) was determined. Results: Feedings with HFHS significantly (p < 0.01) induced plasma hyperglycaemia, hyperinsulinaemia, increased triglyceride, total cholesterol, and low-density lipoprotein levels, decreased high-density lipoprotein levels, alterations of α amylase, and glucose-6-phosphatase activities, and oxidative stress. Daily oral administration with CEE for eight weeks after insulin resistance induction had a hypolipidaemic action, antioxidative activities and modulated metabolic markers. Ethanolic extract at the higher dose had the best effect on body weight gain and insulin resistance, whereas aqueous extract showed the better activity on hyperlipidemia. Conclusion: These results suggest that CEAq and CEEt at 400mg/kg are promising complementary supplements that can be used to protect better from metabolic disorders associated with HFHS.

Keywords: Coula edulis Baill, high-fat / high sucrose diet, insulin resistance, oxidative stress

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Authors: Chueh Chang, Chia-jung Hsieh, Fu-yu Yu, Yu-Hwa Lin

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Background:The majority of women diagnosed with breast cancer undergo treatment involving surgery and radiotherapy or chemotherapy, or both. With these major advances in breast cancer management, many patients still have to deal with short or long-term side effects and psychological distress related to the disease and treatment, which have a substantial impact on their quality of life. The Laughing Qigong Program (LQP) is an interactive laughter program that combines the physical and physiological benefits of laughter with the mental benefits of Chinese qigong. Purpose: In order to improve the quality of life for breast cancer women in the community as well as echoing the WHO 2004 “Promoting Mental Health” for every one. This study focused on how to promote the positive mental health for women of breast cancer through the “laughter program” in Taiwan. During the presentation, how to practice Laughing Qigong will be demonstrated. Method: Using nonequivalent pretest-posttest design, ix-one breast cancer patients were volunteered to enroll in this study from the Taiwan Breast Cancer Alliance (TBCA). Thirty patients were assigned to the experimental group and the other 31 patients were assigned to the control group. The women who were assigned to the experimental group received laughter program one hour per session, once a week, totally 12 sessions. All subjects were tested before and after the intervention on the following: Self-Esteem scale (RSE), Face Scale (FS), Anxiety and pain experience were measured as psychological markers; saliva cortisol (CS) as an immunological marker; blood pressure (BP), heart rate (HR),and heart rate variability (HRV) as physiological markers of the body’s response to stress. Results: After comparing the experimental and control groups, the results revealed that those breast cancer women with “laughing program” their sense of humor were improved, less uncomfortable on self report physical conditions, more positive attitudes toward stress management by using laughter, and had emotional improvement according to the face scale.

Keywords: mental health promotion, breast cancer, laughing Qigong, women

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Authors: Asim Cengiz, Dede Basturk, Hakan Ozalp

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Practicing recurring resistance workout such as may cause changes in human muscle. These changes may be because combination if several factors determining physical fitness. Thus, it is important to identify these changes. Several studies were reviewed to investigate these changes. As a result, the changes included positive modifications in amplified citrate synthase (CS) maximal activity, increased capacity for pyruvate oxidation, improvement on molecular signaling on human performance, amplified resting muscle glycogen and whole GLUT4 protein content, better health outcomes such as enhancement in cardiorespiratory fitness. Sprint training also have numerous long long-term changes inhuman body such as better enzyme action, changes in muscle fiber and oxidative ability. This is important because SV is the critical factor influencing maximal cardiac output and therefore oxygen delivery and maximal aerobic power.

Keywords: sprint, training, performance, exercise

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Authors: Souad Mouzaoui, Bahia Djerdjouri

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Oxidative stress is one of the main factors involved in the onset and chronicity of inflammatory bowel disease (IBD). In this study, we investigated the beneficial effects of a potent natural antioxidant, curcumin (Cur) on colitis and mitochondrial dysfunction in trinitrobenzene sulfonic acid (TNBS)-induced colitis in mice. Rectal instillation of the chemical irritant TNBS (30 mg kg-1) induced the disruption of distal colonic architecture and a massive inflammatory cells influx to the mucosa and submucosa layers. Under these conditions, daily administration of Cur (25 mg kg-1) efficiently decreased colitis scores in the inflamed distal colon by reducing leukocyte infiltrate as attested by reduced myeloperoxidase (MPO) activity. Moreover, the levels of nitrite, an end product of inducible NO synthase activity (iNOS) and malonyl dialdehyde (MDA), a marker of lipid peroxidation increased in a time depending manner in response to TNBS challenge. Conversely, the markers of the antioxidant pool, reduced glutathione (GSH) and catalase activity (CAT) were drastically reduced. Cur attenuated oxidative stress markers and partially restored CAT and GSH levels. Moreover, our results expanded the effect of Cur on TNBS-induced colonic mitochondrial dysfunction. In fact, TNBS induced mitochondrial swelling and lipids peroxidation. These events reflected in the opening of mitochondrial transition pore and could be an initial indication in the cascade process leading to cell death. TNBS inhibited also mitochondrial respiratory activity, caused overproduction of mitochondrial superoxide anion (O2-.) and reduced level of mitochondrial GSH. Nevertheless, Cur reduced the extent of mitochondrial oxidative stress induced by TNBS and restored colonic mitochondrial function. In conclusion, our results showed the critical role of oxidative stress in TNBS-induced colitis. They highlight the role of colonic mitochondrial dysfunction induced by TNBS, as a potential source of oxidative damages. Due to its potent antioxidant properties, Cur opens a promising therapeutic approach against oxidative inflammation in IBD.

Keywords: colitis, curcumin, mitochondria, oxidative stress, TNBS

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Authors: Pasquale Porcu, Mireille Vonlanthen, Gerardo Zaragoza-Galán, Ernesto Rivera

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In this work, we report the synthesis of a novel series of dendritic molecules bearing donor-acceptor groups (pyrene-bodipy) with potential applications in energy transfer. Initially, first and second generation Fréchet type dendrons (Py2-G1OH and Py4-G2OH) were prepared from 1-pyrenylbutanol and 3,5-dihydroxybenzylic alcohol. These compounds were further linked to a bodipy unit via an esterification reaction in order to obtain the desired products (Bodipy-G1Py2) and Bodipy-G2Py4). These compounds were fully characterized by FTIR and 1H and 13C NMR spectroscopy and their molecular weights were determined by MALDITOF. The optical and photophysical properties of these molecules were evaluated by absorbance and fluorescence spectroscopy, in order to compare their behaviour with other analogue molecules.

Keywords: bodipy, dendritic molecules, optical properties, pyrene

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Authors: Zita Šereš, Dragana Šoronja Simović, Ljubica Dokić, Lidietta Giorno, Biljana Pajin, Cecilia Hodur, Nikola Maravić

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Membrane technology is convenient for separation of suspended solids, colloids and high molecular weight materials that are present. The idea is that the waste stream from edible oil industry, after the separation of oil by using skimmers is subjected to microfiltration and the obtained permeate can be used again in the production process. The wastewater from edible oil industry was used for the microfiltration. For the microfiltration of this effluent a tubular membrane was used with a pore size of 200 nm at transmembrane pressure in range up to 3 bar and in range of flow rate up to 300 L/h. Box–Behnken design was selected for the experimental work and the responses considered were permeate flux and chemical oxygen demand (COD) reduction. The reduction of the permeate COD was in the range 40-60% according to the feed. The highest permeate flux achieved during the process of microfiltration was 160 L/m²h.

Keywords: ceramic membrane, edible oil, microfiltration, wastewater

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Authors: Sadeem Aljamaan, Reem Hariri, Rahaf Alghamdi, Batool Alotaibi, Batool Alsenan, Lama Althunayyan, Areej Alnemer

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The aim of this study is to correlate between radiological findings and histopathological results in regard to the breast imaging-reporting and data system scores, size of breast masses, molecular subtypes and suspicious radiological features, as well as to assess the concordance rate in histological grade between core biopsy and surgical excision among breast cancer patients, followed by analyzing the change of concordance rate in relation to neoadjuvant chemotherapy in a Saudi population. A retrospective review was conducted over 6-year period (2017-2022) on all breast core biopsies of women preceded by radiological investigation. Chi-squared test (χ2) was performed on qualitative data, the Mann-Whitney test for quantitative non-parametric variables, and the Kappa test for grade agreement. A total of 641 cases were included. Ultrasound, mammography, and magnetic resonance imaging demonstrated diagnostic accuracies of 85%, 77.9% and 86.9%; respectively. magnetic resonance imaging manifested the highest sensitivity (72.2%), and the lowest was for ultrasound (61%). Concordance in tumor size with final excisions was best in magnetic resonance imaging, while mammography demonstrated a higher tendency of overestimation (41.9%), and ultrasound showed the highest underestimation (67.7%). The association between basal-like molecular subtypes and the breast imaging-reporting and data system score 5 classifications was statistically significant only for magnetic resonance imaging (p=0.04). Luminal subtypes demonstrated a significantly higher percentage of speculation in mammography. Breast imaging-reporting and data system score 4 manifested a substantial number of benign pathologies in all the 3 modalities. A fair concordance rate (k= 0.212 & 0.379) was demonstrated between excision and the preceding core biopsy grading with and without neoadjuvant therapy, respectively. The results demonstrated a down-grading in cases post-neoadjuvant therapy. In cases who did not receive neoadjuvant therapy, underestimation of tumor grade in biopsy was evident. In summary, magnetic resonance imaging had the highest sensitivity, specificity, positive predictive value and accuracy of both diagnosis and estimation of tumor size. Mammography demonstrated better sensitivity than ultrasound and had the highest negative predictive value, but ultrasound had better specificity, positive predictive value and accuracy. Therefore, the combination of different modalities is advantageous. The concordance rate of core biopsy grading with excision was not impacted by neoadjuvant therapy.

Keywords: breast cancer, mammography, MRI, neoadjuvant, pathology, US

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Authors: Gilbert O. Osayemwenre, Meyer L. Edson

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Ethylene vinyl acetate (EVA) encapsulation degradation affects the performance of photovoltaic (PV) module. Hotspot formation causes the EVA encapsulation to undergo photothermal deterioration and molecular breakdown by UV radiation. This leads to diffusion of chemical particles into other layers. During outdoor deployment, the EVA encapsulation in the affect region loses its adhesive strength, when this happen the affected region layer undergoes rapid delamination. The presence of photo-thermal degradation is detrimental to PV modules as it causes both optical and thermal degradation. Also, it enables the encapsulant to be more susceptible to chemicals substance and moisture. Our findings show a high concentration of Sodium, Phosphorus and Aluminium which originate from the glass substrate, cell emitter and back contact respectively.

Keywords: ethylene vinyl acetate (EVA), encapsulation, photo-thermal degradation, thermogravimetric analysis (TGA), scanning probe microscope (SPM)

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Authors: Shadia Al-Bahlani, Ruqaya Al-Rashdi, Shadia Al-Sinawi, Maya Al-Bahri

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Background: Breast cancer is the most common cancer in women worldwide. Triple-negative breast cancer (TNBC) is an aggressive type of breast cancer, which is defined by the absence of Estrogen (ER), Progesterone (PR) and Human epidermal growth factor (Her-2) receptors. The calpain system plays an important role in many cellular processes including apoptosis, necrosis, cell signaling and proliferation. The role of clapins in pathogenesis and tumor progression has been studied in certain cancer types; however, its definite role is not yet established in breast cancer especially in the TNBC subtype. Objectives: This study aims to measure calpain-1 expression and correlate this measurement with the proliferating/apoptotic index as well with the prognostic factors in TNBC patients’ tissue. Materials and Methods: Thirty nine paraffin blocks from patients diagnosed with TNBC were used to measure the expression of calpain-1 and Ki-67 (proliferating marker) proteins using immunohistochemistry. Apoptosis was assessed morphological and biochemically using conventional Haematoxylin and Eosin (H&E) staining method and terminal deoxynucleotidyl transferase-mediate dUTP nick and labeling (TUNEL) assay respectively. Data was statistically analyzed using Pearson X2 test of association. Results: Calpain-1 content was visualized in the nucleus of the TNBC cells and its expression varied from low to high among the patients tissue. Calpain expression showed no significant correlation with the proliferating/apoptotic index as well with the clinicopathological variables. Apoptotic counts quantified by H&E staining showed significant association with the apoptotic TUNEL assay, validating both approaches. Conclusion: Although calpain-1 expression showed no significant association with the clinical outcome, its variable level of expression might indicate a hidden role in breast cancer tissue. Larger number of samples and different mode of assessments are needed to fully investigate such role. Exploring the involvement of calpain-1 in cancer progression might help in considering it as a biomarker of breast cancer.

Keywords: breast cancer, calpain, apoptosis, prognosis

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Authors: Rajlakshmi Banerjee, Sujoy Banerjee

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The prevalence of malnutrition, as the most common cause of morbidity and mortality increases with old age, especially in developing countries like India, because of many factors out of which dentate status is one. It affects diet, nutritional status and general health due to reduced chewing ability and poor food choices. Aim and Objective: This study aimed to evaluate the effect of nutritional status, dietary intake on the Oral Health-related Quality of life (OHRQoL) of elderly edentulous complete denture wearing patients and to know whether they are at a higher risk of malnutrition. The objective was to assess the need to include dietary and nutritional counselling during Prosthodontic rehabilitation of elderly edentulous patients. Materials and method: A cross-sectional study was conducted among 200 elderly denture wearing patients above 60 yrs of age from Nagpur, Maharashtra. The majority of study subjects (60%) were between the age group 60 and 75 years. Mini-Nutritional Assessment (MNA) Questionnaire was used to assess nutritional status and General Oral Health Assessment Index (GOHAI) questionnaire was used to determine the Oral health related Quality of life of these patients.Descriptive statistics was used to analyze data using SPSS version 21. Results: Among the assessed subjects, nearly 80% of them had total scores of GOHAI between 12 and 57 which require ‘needed dental care.’ As per MNA, 10.5% had adequate nutrition, 70 % were at risk of malnutrition, and remaining 19.5 % of subjects were malnourished. There was a significant correlation between GOHAI and MNA scores. A strong association was found between mean GOHAI and MNA scores and thereby nutritional status and OHRQOL.Conclusion: The use of conventional dentures increases the risk of malnutrition in the elderly due to inability to eat and chew food properly and therefore severely affecting the quality of life. Dietary analysis and counselling should be strictly incorporated into geriatric treatment planning during Prosthetic rehabilitation.

Keywords: general oral health assessment index, General Oral Health Assessment Index (GOHAI), nutritional assessment, mini-nutritional assessment, Mini-Nutritional Assessment (MNA), quality of life

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Authors: Angana Bhattacharya, Rakesh Sarkar, Gagan Kumar

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Toroidal resonances, a new class of electromagnetic excitations, demonstrate exceptional properties as compared to electric and magnetic dipolar resonances. The advantage of narrow linewidth in toroidal resonance is utilized in this proposed work, where a bilayer metamaterial (MM) sensor has been designed in the terahertz frequency regime (THz). A toroidal MM geometry in a single layer is first studied. A second identical MM geometry placed on top of the first layer results in the coupling of toroidal excitations, leading to an increase in the quality factor (Q) of the resonance. The sensing capability of the resonance is studied. Further, the dynamic switching from an 'off' stage to an 'on' stage in the bilayer configuration is explored. The ardent study of such toroidal bilayer MMs could provide significant potential in the development of bio-molecular and chemical sensors, switches, and modulators.

Keywords: toroidal resonance, bilayer, metamaterial, terahertz, sensing, switching

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Authors: Alessandra Pardu, Elena Curti, Marco Caredda, Alessio Dedola, Margherita Addis, Massimo Pes, Antonio Pirisi, Tonina Roggio, Sergio Uzzau, Roberto Anedda

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Some of the artisanal cheeses products of European Countries certificated as PDO (Protected Designation of Origin) are made from raw milk. To recognise potential frauds (e.g. pasteurisation or thermisation of milk aimed at raw milk cheese production), the alkaline phosphatase (ALP) assay is currently applied only for pasteurisation, although it is known to have notable limitations for the validation of ALP enzymatic state in nonbovine milk. It is known that frauds considerably impact on customers and certificating institutions, sometimes resulting in a damage of the product image and potential economic losses for cheesemaking producers. Robust, validated, and univocal analytical methods are therefore needed to allow Food Control and Security Organisms, to recognise a potential fraud. In an attempt to develop a new reliable method to overcome this issue, Time-Domain Nuclear Magnetic Resonance (TD-NMR) spectroscopy has been applied in the described work. Daily fresh milk was analysed raw (680.00 µL in each 10-mm NMR glass tube) at least in triplicate. Thermally treated samples were also produced, by putting each NMR tube of fresh raw milk in water pre-heated at temperatures from 68°C up to 72°C and for up to 3 min, with continuous agitation, and quench-cooled to 25°C in a water and ice solution. Raw and thermally treated samples were analysed in terms of 1H T2 transverse relaxation times with a CPMG sequence (Recycle Delay: 6 s, interpulse spacing: 0.05 ms, 8000 data points) and quasi-continuous distributions of T2 relaxation times were obtained by CONTIN analysis. In line with previous data collected by high field NMR techniques, a decrease in the spin-spin relaxation constant T2 of the predominant 1H population was detected in heat-treated milk as compared to raw milk. The decrease of T2 parameter is consistent with changes in chemical exchange and diffusive phenomena, likely associated to changes in milk protein (i.e. whey proteins and casein) arrangement promoted by heat treatment. Furthermore, experimental data suggest that molecular alterations are strictly dependent on the specific heat treatment conditions (temperature/time). Such molecular variations in milk, which are likely transferred to cheese during cheesemaking, highlight the possibility to extend the TD-NMR technique directly on cheese to develop a method for assessing a fraud related to the use of a milk thermal treatment in PDO raw milk cheese. Results suggest that TDNMR assays might pave a new way to the detailed characterisation of heat treatments of milk.

Keywords: cheese fraud, milk, pasteurisation, TD-NMR

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Authors: Moon Jung Kim, Guil Rhim

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The clinical sensitivity of the “VEUPLEXTM TBI assay”, a clinical trial medical device, in mild traumatic brain injury was 28.6% (95% CI, 19.7%-37.5%), and the clinical specificity was 94.0% (95% CI, 89.3%). -98.7%). In addition, when the results analyzed by marker were put together, the sensitivity was higher when interpreting the two tests together than the two tests, UCHL1 and GFAP alone. Additionally, when sensitivity and specificity were analyzed based on CT results for the mild traumatic brain injury patient group, the clinical sensitivity for 2 CT-positive cases was 50.0% (95% CI: 1.3%-98.7%), and 19 CT-negative cases. The clinical specificity for cases was 68.4% (95% CI: 43.5% - 87.4%). Since the low clinical sensitivity for the two CT-positive cases was not statistically significant due to the small number of samples analyzed, it was judged necessary to secure and analyze more samples in the future. Regarding the clinical specificity analysis results for 19 CT-negative cases, there were a large number of patients who were actually clinically diagnosed with mild traumatic brain injury but actually received a CT-negative result, and about 31.6% of them showed abnormal results on VEUPLEXTM TBI assay. Although traumatic brain injury could not be detected in 31.6% of the CT scans, the possibility of actually suffering a mild brain injury could not be ruled out, so it was judged that this could be confirmed through follow-up observation of the patient. In addition, among patients with mild traumatic brain injury, CT examinations were not performed in many cases because the symptoms were very mild, but among these patients, about 25% or more showed abnormal results in the VEUPLEXTM TBI assay. In fact, no damage is observed with the naked eye immediately after traumatic brain injury, and traumatic brain injury is not observed even on CT. But in some cases, brain hemorrhage may occur (delayed cerebral hemorrhage) after a certain period of time, so the patients who did show abnormal results on VEUPLEXTM TBI assay should be followed up for the delayed cerebral hemorrhage. In conclusion, it was judged that it was difficult to judge mild traumatic brain injury with the VEUPLEXTM TBI assay only through clinical findings without CT results, that is, based on the GCS value. Even in the case of CT, it does not detect all mild traumatic brain injury, so it is difficult to necessarily judge that there is no traumatic brain injury, even if there is no evidence of traumatic brain injury in CT. And in the long term, more patients should be included to evaluate the usefulness of the VEUPLEXTM TBI assay in the detection of microscopic traumatic brain injuries without using CT.

Keywords: brain injury, traumatic brain injury, GFAP, UCHL1

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Authors: C. N. Okafor, M. Maaza, T. A. E. Mokrani

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A proton exchange membrane has been developed for Direct Methanol Fuel Cell (DMFC). The nanofiber network composite membranes were prepared by interconnected network of Nafion (perfuorosulfonic acid) nanofibers that have been embedded in an uncharged and inert polymer matrix, by electro-spinning. The spinning solution of Nafion with a low concentration (1 wt. % compared to Nafion) of high molecular weight poly(ethylene oxide), as a carrier polymer. The interconnected network of Nafion nanofibers with average fiber diameter in the range of 160-700nm, were used to make the membranes, with the nanofiber occupying up to 85% of the membrane volume. The matrix polymer was cross-linked with Norland Optical Adhesive 63 under UV. The resulting membranes showed proton conductivity of 0.10 S/cm at 25°C and 80% RH; and methanol permeability of 3.6 x 10-6 cm2/s.

Keywords: composite membrane, electrospinning, fuel cell, nanofibers

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Authors: Ekpekpo Arthur

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Thin films can either be conductive or dielectric (non-conductive). It is formed through atom/molecules state or formed after decomposing the materials into atomic/molecular scale by physical or chemical processes. In this study, thin films of Lead Sulphide were deposited on glass substrate prepared from lead acetate and thiourea solution using chemical bath deposition (CBD). The glass slides were subjected to the pretreatment by soaking them in a solution of 50% sulphuric acid and 50% nitric acid. Lead sulphide was deposited at different parameters such as deposition time and temperature. The optical properties of the thin films were determined from spectroscopy measurements of absorbance and reflectance. Optical studies show that the band gap of lead sulphide ranges between 0.41 eV to 300K.

Keywords: lead sulphide, spectroscopy, absorbance, reflectance

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Authors: Zelalem Fantahun

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Part-of-speech tagging is the process of assigning a part-of-speech or other lexical class marker to each word into naturally occurring text. Part-of-speech tagging is the most fundamental and basic task almost in all natural language processing. In natural language processing, the problem of providing large amount of manually annotated data is a knowledge acquisition bottleneck. Since, Amharic is one of under-resourced language, the availability of tagged corpus is the bottleneck problem for natural language processing especially for POS tagging. A promising direction to tackle this problem is to provide a system that does not require manually tagged data. In unsupervised learning, the learner is not provided with classifications. Unsupervised algorithms seek out similarity between pieces of data in order to determine whether they can be characterized as forming a group. This paper explicates the development of unsupervised part-of-speech tagger using K-Means clustering for Amharic language since large amount of data is produced in day-to-day activities. In the development of the tagger, the following procedures are followed. First, the unlabeled data (raw text) is divided into 10 folds and tokenization phase takes place; at this level, the raw text is chunked at sentence level and then into words. The second phase is feature extraction which includes word frequency, syntactic and morphological features of a word. The third phase is clustering. Among different clustering algorithms, K-means is selected and implemented in this study that brings group of similar words together. The fourth phase is mapping, which deals with looking at each cluster carefully and the most common tag is assigned to a group. This study finds out two features that are capable of distinguishing one part-of-speech from others these are morphological feature and positional information and show that it is possible to use unsupervised learning for Amharic POS tagging. In order to increase performance of the unsupervised part-of-speech tagger, there is a need to incorporate other features that are not included in this study, such as semantic related information. Finally, based on experimental result, the performance of the system achieves a maximum of 81% accuracy.

Keywords: POS tagging, Amharic, unsupervised learning, k-means

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Authors: Ouafae Baida, Najma Hamzaoui, Maha Akbib, Abdelfettah Sedqui, Abdelouahid Lyhyaoui

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Numerous scientific works present various methods to analyze the data for several domains, specially the comparison of classifications. In our recent work, we presented a new approach to help the user choose the best classification method from the results obtained by every method, by basing itself on the distances between the trees of classification. The result of our approach was in the form of a dendrogram contains methods as a succession of connections. This approach is much needed in phylogeny analysis. This discipline is intended to analyze the sequences of biological macro molecules for information on the evolutionary history of living beings, including their relationship. The product of phylogeny analysis is a phylogenetic tree. In this paper, we recommend the use of a new method of construction the phylogenetic tree based on comparison of different classifications obtained by different molecular genes.

Keywords: hierarchical classification, classification methods, structure of tree, genes, phylogenetic analysis

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Authors: Ma. Roxanne Fernandez, Josie Athens, Balsalobre-Fernandez, Masayoshi Kubo, Kim Hébert-Losier

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Objectives: The calf raise test (CRT) is used in rehabilitation and sports medicine to evaluate calf muscle function. For testing, individuals stand on one leg and go up on their toes and back down to volitional fatigue. The newly developed Calf Raise application (CRapp) for iOS uses computer-vision algorithms enabling objective measurement of CRT outcomes. We aimed to validate the CRapp by examining its concurrent validity and agreement levels against laboratory-based equipment and establishing its intra- and inter-rater reliability. Methods: CRT outcomes (i.e., repetitions, positive work, total height, peak height, fatigue index, and peak power) were assessed in thirteen healthy individuals (6 males, 7 females) on three occasions and both legs using the CRapp, 3D motion capture, and force plate technologies simultaneously. Data were extracted from two markers: one placed immediately below the lateral malleolus and another on the heel. Concurrent validity and agreement measures were determined using intraclass correlation coefficients (ICC₃,ₖ), typical errors expressed as coefficient of variations (CV), and Bland-Altman methods to assess biases and precision. Reliability was assessed using ICC3,1 and CV values. Results: Validity of CRapp outcomes was good to excellent across measures for both markers (mean ICC ≥0.878), with precision plots showing good agreement and precision. CV ranged from 0% (repetitions) to 33.3% (fatigue index) and were, on average better for the lateral malleolus marker. Additionally, inter- and intra-rater reliability were excellent (mean ICC ≥0.949, CV ≤5.6%). Conclusion: These results confirm the CRapp is valid and reliable within and between users for measuring CRT outcomes in healthy adults. The CRapp provides a tool to objectivise CRT outcomes in research and practice, aligning with recent advances in mobile technologies and their increased use in healthcare.

Keywords: calf raise test, mobile application, validity, reliability

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Authors: Mona Alwhibi, Najat Bukhary

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Heliotropium digynum, a member of Boraginaceae family, the growth of the plant, as well as its size, length of inflorescence, and speed of development depends on the amount of rain in its habitat. In this study, we studied the applicability of inter-simple sequence repeat (ISSR) polymorphism in Heliotropium digynum in a different region of Saudi Arabia. We found that. ISSR analysis using 15 primers were used for ISSR-PCR optimization trials, five primers (UBC810, UBC811, UBC818, UBC834, and UBC849) which gave the best amplification results produced a total of 43 polymorphic bands. The number of polymorphic loci was 20 and the percentage of polymorphism was 90.47%. The similarity result indicates the presence of a high-level genetic diversity between populations and a dendrogram constructed by UPGMA method.

Keywords: genetic differentiation, genetic diversity, Heliotropium digynum, ISSR

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Authors: Katarzyna Palus, Jarosław Całka

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Gastrointestinal disorders, especially acid-related diseases, including peptic and duodenal ulcers, gastroesophageal reflux disease, upper GI bleeding or stress-related mucosal disease, are currently serious health issues encountered very frequently in patients worldwide. However, to date, the response of sympathetic neurons to gastric mucosal injury and local inflammation following hyperacidity is unknown. Thus, the present study was designed to determine possible changes in expression of galanin (GAL) in the CSMG neurons supplying the prepyloric area of the porcine stomach in a physiological state and following experimentally-induced hyperacidity by using combined retrograde tracing and double-labelling immunohistochemistry. The choice of the domestic pig as an experimental model in the present study is not accidental and is justified by the high degree of physiological and anatomical similarity to human digestive system functions. In this experiment ten juvenile female pigs of the Large White Polish breed were used. The animals were divided into two groups: control and animals with hydrochloric acid infusion (HCl). The neuronal retrograde marker Fast Blue (FB) was injected into the anterior prepyloric wall of the stomach of all animals. After 23 days, animals of the HCl-group were reintroduced into a state of general anesthesia and intragastrically given 5 ml/kg of body weight of 0.25 M aqueous solution of hydrochloric acid. On the 28th day, all animals were euthanized. The CSMG complexes were then collected and the CSMG cryostat sections were stained immunocytochemically for GAL and TH (tyrosine hydroxylase). Immunohistochemistry revealed that in the control group 8.40 ± 0.53 % out of 200 FB-positive CSMG neurons contained GAL. In HCl group upregulation of the GAL-IR neurons to 22.52 ± 1.18 % were observed. All GAL-IR neurons in both groups showed the simultaneously TH immunoreactivity. Increase in the expression of GAL in FB-positive neurons of the HCL group may suggest its participation in the protective mechanisms of neurons in different pathological processes, such as gastric hyperacidity.

Keywords: coeliac-superior mesenteric ganglion complex, gastric innervation, hyperacidity, immunohistochemistry

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Authors: Mehdi Mohebodini, Iman Khalili-Baseri, Mehdi Behnamian, Sara Dezhsetan

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Diversity analysis at the molecular level using PCR-based markers is the efficient and rapid method of identifying the relationships and differences among the genotypes. In the present study, genetic diversity and relationships among 20 collected purslane accessions were evaluated using ISSR markers. The genotyping data were used to understand the relationships among the collected accessions and identify genetically diverse purslane accessions. The 25 primers gave a total of 92 bands, of which 62 were polymorphic (67.4%). The genetic diversity as estimated by Shannon’s information index was 0.55, revealing a quite high level of genetic diversity in the germplasm. The average number of an observed allele, effective allele, polymorphic information content (PIC) and Nei’s index were 2, 1.65, 0.37 and 0.37, respectively.

Keywords: Portulaca oleracea L., genetic diversity, ISSR, germplasm

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Authors: Mousaab Alrhmoun, Magali Casellas, Michel Baudu, Christophe Dagot

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The aim of the study is to improve removal of trace organic contaminants dissolved in activated sludge by the process of filtration with membrane bioreactor combined with modified activated carbon, for a maximum removal of organic compounds characterized by low molecular weight. Special treatment was conducted in laboratory on activated carbon. Tow reaction parameters: The pH of aqueous middle and the type of granular activated carbon were very important to improve the removal and to motivate the electrostatic Interactions of organic compounds with modified activated carbon in addition to physical adsorption, ligand exchange or complexation on the surface activated carbon. The results indicate that modified activated carbon has a strong impact in removal 21 of organic contaminants and in percentage of 100% of the process.

Keywords: activated carbon, organic micropolluants, membrane bioreactor, carbon

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