Search results for: biomarker of autism

Authors: Rozhgar A. Khailany, Mehri Igci, Emine Bayraktar, Sakip Erturhan, Metin Karakok, Ahmet Arslan

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Kidney cancer is the most lethal urological cancer accounting for 3% of adult malignancies. VHL, a tumor-suppressor gene, is best known to be associated with renal cell carcinoma (RCC). The VHL functions as negative regulator of hypoxia inducible factors. Recent sequencing efforts have identified several novel frequent mutations of histone modifying and chromatin remodeling genes in ccRCC (clear cell RCC) including PBRM1 and SETD2. The PBRM1 gene encodes the BAF180 protein, which involved in transcriptional activation and repression of selected genes. SETD2 encodes a histone methyltransferase, which may play a role in suppressing tumor development. In this study, RNAs of 30 paired tumor and normal samples that were grouped according to the types of kidney cancer and clinical characteristics of patients, including gender and average age were examined by RT-PCR, SSCP and sequencing techniques. VHL, PBRM1 and SETD2 expressions were relatively down-regulated. However, statistically no significance was found (Wilcoxon signed rank test, p>0.05). Interestingly, no mutation was observed on the contrary of previous studies. Understanding the molecular mechanisms involved in the pathogenesis of RCC has aided the development of molecular-targeted drugs for kidney cancer. Further analysis is required to identify the responsible genes rather than VHL, PBRM1 and SETD2 in kidney cancer.

Keywords: Kidney cancer, molecular biomarker, expression analysis, mutation screening.

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Authors: Aref Aasi, Sahar Ebrahimi Bajgani, Erfan Aasi

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Breast cancer (BC) continues to be the most frequent cancer in females and causes the highest number of cancer-related deaths in women worldwide. Inspired by recent advances in studying the relationship between different patient attributes and features and the disease, in this paper, we have tried to investigate the different classification methods for better diagnosis of BC in the early stages. In this regard, datasets from the University Hospital Centre of Coimbra were chosen, and different machine learning (ML)-based and neural network (NN) classifiers have been studied. For this purpose, we have selected favorable features among the nine provided attributes from the clinical dataset by using a random forest algorithm. This dataset consists of both healthy controls and BC patients, and it was noted that glucose, BMI, resistin, and age have the most importance, respectively. Moreover, we have analyzed these features with various ML-based classifier methods, including Decision Tree (DT), K-Nearest Neighbors (KNN), eXtreme Gradient Boosting (XGBoost), Logistic Regression (LR), Naive Bayes (NB), and Support Vector Machine (SVM) along with NN-based Multi-Layer Perceptron (MLP) classifier. The results revealed that among different techniques, the SVM and MLP classifiers have the most accuracy, with amounts of 96% and 92%, respectively. These results divulged that the adopted procedure could be used effectively for the classification of cancer cells, and also it encourages further experimental investigations with more collected data for other types of cancers.

Keywords: Breast cancer, health diagnosis, Machine Learning, biomarker classification, Neural Network.

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Authors: S. Mahmoudi, A. Belhaj Mohamed, M. Saidi, F. Rezgui

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Depositional environment and source potential of the different organic-rich levels of Devonian age (up to 990m thick) from the onshore EC-1 well (Southern Tunisia) were investigated based on the analysis of more than 130 cutting samples by different geochemical techniques (Rock-Eval pyrolysis, GC-MS). The obtained results including Rock Eval Pyrolysis data and biomarker distribution (terpanes, steranes and aromatics) have been used to describe the depositional environment and to assess the thermal maturity of the Devonian organic matter. These results show that the Emsian deposits exhibit poor to fair TOC contents. The associated organic matter is composed of mixed kerogen (type II/III), as indicated by the predominance of C29 steranes over C27 and C28 homologous, that was deposited in a slightly reduced environment favoring organic matter preservation. Thermal maturity assessed from Tmax, TNR and MPI-1 values shows a mature stage of organic matter. The Middle Devonian (Eifelian) shales are rich in type II organic matter that was deposited in an open marine depositional environment. The TOC values are high and vary between 2 and 7% indicating good to excellent source rock. The relatively high HI values (reaching 547 mg HC/g TOC) and the low values of t19/t23 tricyclic terpane ratio (< 0.2) confirm the marine origin of the organic matter (type II). During the Upper Devonian, the organic matter was deposited under variable redox conditions, oxic to suboxic which is clearly indicated by the low C35/C34 hopanes ratio, immature to marginally mature with the vitrinite reflectance ranging from 0.5 to 0.7 Ro and Tmax value of 426°C-436 °C and the TOC values range between 0.8% to 4%.

Keywords: Depositional environment, Devonian, Source rock.

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Authors: Huong M. T. Nguyen, Hoa A. P. Nguyen, Mai P. T. Nguyen, Ngoc D. Ngo, Van T. Ta, Hai T. Le, Chi V. Phan

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Wilson’s disease (WD) is an autosomal recessive disorder of the copper metabolism, which is caused by a mutation in the copper-transporting P-type ATPase (ATP7B). The mechanism of this disease is the failure of hepatic excretion of copper to bile, and leads to copper deposits in the liver and other organs. The ATP7B gene is located on the long arm of chromosome 13 (13q14.3). This study aimed to investigate the gene mutation in the Vietnamese patients with WD, and make a presymptomatic diagnosis for their familial members. Forty-three WD patients and their 65 siblings were identified as having ATP7B gene mutations. Genomic DNA was extracted from peripheral blood samples; 21 exons and exon-intron boundaries of the ATP7B gene were analyzed by direct sequencing. We recognized four mutations ([R723=; H724Tfs*34], V1042Cfs*79, D1027H, and IVS6+3A>G) in the sum of 20 detectable mutations, accounting for 87.2% of the total. Mutation S105* was determined to have a high rate (32.6%) in this study. The hotspot regions of ATP7B were found at exons 2, 16, and 8, and intron 14, in 39.6 %, 11.6 %, 9.3%, and 7 % of patients, respectively. Among nine homozygote/compound heterozygote siblings of the patients with WD, three individuals were determined as asymptomatic by screening mutations of the probands. They would begin treatment after diagnosis. In conclusion, 20 different mutations were detected in 43 WD patients. Of this number, four novel mutations were explored, including [R723=; H724Tfs*34], V1042Cfs*79, D1027H, and IVS6+3A>G. The mutation S105* is the most prevalent and has been considered as a biomarker that can be used in a rapid detection assay for diagnosis of WD patients. Exons 2, 8, and 16, and intron 14 should be screened initially for WD patients in Vietnam. Based on risk profile for WD, genetic testing for presymptomatic patients is also useful in diagnosis and treatment.

Keywords: ATP7B gene, mutation detection, presymptomatic diagnosis, Vietnamese Wilson’s disease.

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Authors: Ebtehal Alawi Alsaggaf, Shehab A. Gamalel-Din

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Exploring an autistic child in Elementary school is a difficult task that must be fully thought out and the teachers should be aware of the many challenges they face raising their child especially the behavioral problems of autistic children. Hence there arises a need for developing Artificial intelligence (AI) Contemporary Techniques to help diagnosis to discover autistic people. In this research, we suggest designing architecture of expert system that combine Cognitive Maps (CM) with Case Based Reasoning technique (CBR) in order to reduce time and costs of traditional diagnosis process for the early detection to discover autistic children. The teacher is supposed to enter child's information for analyzing by CM module. Then, the reasoning processor would translate the output into a case to be solved a current problem by CBR module. We will implement a prototype for the model as a proof of concept using java and MYSQL. This will be provided a new hybrid approach that will achieve new synergies and improve problem solving capabilities in AI. And we will predict that will reduce time, costs, the number of human errors and make expertise available to more people who want who want to serve autistic children and their families.

Keywords: Autism, Cognitive Maps (CM), Case Based Reasoning technique (CBR).

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Authors: Mustafa M. Donma, Sule G. Kacmaz, Ahsen Yilmaz, Savas Guzel, Orkide Donma

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Obesity, as excessive fat accumulation in the body, is a global health problem. The prevalence of obesity and its complications increase due to easy access to high-energy food and decreased physical activity. Cardiovascular diseases (CVDs) constitute a significant part of obesity-related morbidity and mortality. Since the effects of obesity on cardiovascular system may start during childhood without clinical findings, elucidating the mechanisms of cardiovascular changes associated with childhood obesity became more important. In this study, we aimed to investigate some biochemical parameters which may be involved in obesity-related pathologic processes of CVDs. One hundred and seventy-seven children were included in the study, and they were divided into four groups based upon WHO criteria and presence of the metabolic syndrome (MetS): children with normal-BMI, obesity, morbid obesity, and MetS. High-sensitive cardiac troponin T (hs-cTnT), cardiac myosin binding protein C (cMyBP-C), trimethylamine N-oxide (TMAO), soluble tumor necrosis factor-like weak inducer (sTWEAK), chromogranin A (CgA), multimerin-2 levels, and other biochemical parameters were measured in serum samples. Anthropometric measurements and clinical findings of the children were recorded. Statistical analyses were performed. Children with normal-BMI had significantly higher CgA levels than children with obesity, morbid obesity, and MetS (p < 0.05). Cardiac MyBP-C levels of children with MetS were significantly higher than of children with normal-BMI and OB children (p < 0.05). There was no significant difference in hs-cTnT, sTWEAK, TMAO and multimerin-2 between the groups (p>0.05). These results suggested that cMyBP-C and CgA molecules may be involved in the pathogenesis of obesity-related CVDs.

Keywords: biomarker, cardiovascular diseases, children, obesity

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Authors: I. M. Yusuff, A. M. Arogunjo, S. B. Ibikunle, O. M. Oni, P. O. Osho

Abstract:

Generally, water contamination is a serious health concern, affecting millions of people worldwide every year. Among the water contaminants, radon is a radioactive contaminant understudied and under-regulated. It produces many adverse health effects, including cancer. It is a natural gas that cannot be seen, tasted, or smelled. It develops from the radioactive decay of radium found in the rock of soil and has been considered a health hazard due to its radioactivity in nature. To examine its effects and physicochemical characteristics on the blood biomarkers due to its ingestion in drinking water, its concentrations were monitored and measured in treated and untreated water using Electronic Radon Active Detector (RAD7), while human blood samples were collected using the required laboratory tools. The blood samples were collected and examined physicochemically using semi-automated chemistry analyzer to evaluate the chemistry parameters of the blood. Statistically, results obtained were analyzed using T-test of variables at 95% confidence interval. The outcome of results revealed 112.03 Bq/m3, 561.67 Bq/m3 and 2,753.00 Bq/m3 of radon-222 concentrations in the three water samples used respectively. Demographically, chemistry parameters biomarkers of the blood determined displayed some levels of variations due to radon-222 contaminants ingested from untreated water. Also, analyzed results of blood revealed the associations between the physicochemical parameters of the blood biomarkers and volunteers’ health consequences. The consequences observed were more severed with group B volunteers than group A, due to high level of radon contaminants in borehole water consumed by group B than in well water consumed by group A. The percentages of elevated and depressed biomarkers observed differ from initial reference values and, were the dysfunction indicators. They are directly or indirectly associated to human’s state of health. Most significant biomarkers affected were; HCO3, Cl, K, Cr and Na, they are relevant biomarkers in medicine to determine human’s state of health at any point in time.

Keywords: Radioactive, radon, biomarker, ingestion, dysfunction.

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Authors: Ratnakar Tripathi, Rajnikant Mishra

Abstract:

The PAX6, a transcription factor, is essential for the morphogenesis of the eyes, brain, pituitary and pancreatic islets. In rodents, the loss of Pax6 function leads to central nervous system defects, anophthalmia, and nasal hypoplasia. The haplo-insufficiency of Pax6 causes microphthalmia, aggression and other behavioral abnormalities. It is also required in brain patterning and neuronal plasticity. In human, heterozygous mutation of Pax6 causes loss of iris [aniridia], mental retardation and glucose intolerance. The 3- deletion in Pax6 leads to autism and aniridia. The phenotypes are variable in peneterance and expressivity. However, mechanism of function and interaction of PAX6 with other proteins during development and associated disease are not clear. It is intended to explore interactors of PAX6 to elucidated biology of PAX6 function in the tissues where it is expressed and also in the central regulatory pathway. This report describes In-silico approaches to explore interacting proteins of PAX6. The models show several possible proteins interacting with PAX6 like MITF, SIX3, SOX2, SOX3, IPO13, TRIM, and OGT. Since the Pax6 is a critical transcriptional regulator and master control gene of eye and brain development it might be interacting with other protein involved in morphogenesis [TGIF, TGF, Ras etc]. It is also presumed that matricelluar proteins [SPARC, thrombospondin-1 and osteonectin etc] are likely to interact during transport and processing of PAX6 and are somewhere its cascade. The proteins involved in cell survival and cell proliferation can also not be ignored.

Keywords: Interacting Proteins, Pax6, PIP, STRING

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Authors: Mustafa M. Donma, Orkide Donma

Abstract:

Zinc (Zn) is a vital element required for growth and development particularly in children. It exhibits some protective effects against cardiovascular diseases (CVDs). Zn may be a potential biomarker of cardiovascular health. High sensitive cardiac troponin T (hs-cTnT) and cardiac myosin binding protein C (cMyBP-C) are new generation markers used for prediagnosis, diagnosis and prognosis of CVDs. The aim of this study is to determine Zn as well as new generation cardiac markers’ profiles in children with normal body mass index (N-BMI), obese (OB), morbid obese (MO) children and children with metabolic syndrome (MetS) findings. The association among them will also be investigated. Four study groups were constituted. The study protocol was approved by the institutional Ethics Committee of Tekirdag Namik Kemal University. Parents of the participants filled informed consent forms to participate in the study. Group 1 is composed of 44 children with N-BMI. Group 2 and Group 3 comprised 43 OB and 45 MO children, respectively. 45 MO children with MetS findings were included in Group 4. World Health Organization age- and sex-adjusted BMI percentile tables were used to constitute groups. These values were 15-85, 95-99 and above 99 for N-BMI, OB and MO, respectively. Criteria for MetS findings were determined. Routine biochemical analyses including Zn were performed. hs-cTnT and cMyBP-C concentrations were measured by enzyme-linked immunosorbent assay. Data were analyzed by using SPSS software. p < 0.05 was accepted as significant. Four groups were matched for age and gender. Decreased Zn concentrations were measured in Groups 2, 3 and 4 compared to Group 1. Groups did not differ from one another in terms of hs-cTnT. There were statistically significant differences between cMyBP-C levels of MetS group and N-BMI as well as OB groups. There was an increasing trend going from N-BMI group to MetS group. There were statistically significant negative correlations between Zn and hs-cTnT as well as cMyBP-C concentrations in MetS group. In conclusion, inverse correlations detected between Zn and new generation cardiac markers (hs-TnT and cMyBP-C) have pointed out that decreased levels of Zn accompany increased levels of hs-cTnT as well as cMyBP-C in children with MetS. This finding emphasizes that both Zn and these new generation cardiac markers may be evaluated as biomarkers of cardiovascular health during severe childhood obesity precipitated with MetS findings and also suggested as the messengers of the future risk in the adulthood periods of children with MetS.

Keywords: Cardiac myosin binding protein-C, cardiovascular diseases, children, high sensitive cardiac troponin T, obesity.

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Authors: A. Belhaj Mohamed, M. Saidi, N. Boucherb, N. Ourtani, A. Soltani, I. Bouazizi, M. Ben Jrad

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Natural hydrocarbon seepage has helped petroleum exploration as a direct indicator of gas and/or oil subsurface accumulations. Surface macro-seeps are generally an indication of a fault in an active Petroleum Seepage System belonging to a Total Petroleum System. This paper describes a case study in which multiple analytical techniques were used to identify and characterize trace petroleum-related hydrocarbons and other volatile organic compounds in groundwater samples collected from Sousse aquifer (Central Tunisia). The analytical techniques used for analyses of water samples included gas chromatography-mass spectrometry (GCMS), capillary GC with flame-ionization detection, Compound Specific Isotope Analysis, Rock Eval Pyrolysis. The objective of the study was to confirm the presence of gasoline and other petroleum products or other volatile organic pollutants in those samples in order to assess the respective implication of each of the potentially responsible parties to the contamination of the aquifer. In addition, the degree of contamination at different depths in the aquifer was also of interest. The oil and gas seeps have been investigated using biomarker and stable carbon isotope analyses to perform oil-oil and oil-source rock correlations. The seepage gases are characterized by high CH4 content, very low δ13CCH4 values (-71,9 ‰) and high C1/C1–5 ratios (0.95–1.0), light deuterium–hydrogen isotope ratios (- 198 ‰) and light δ13CC2 and δ13CCO2 values (-23,8‰ and-23,8‰ respectively) indicating a thermogenic origin with the contribution of the biogenic gas. An organic geochemistry study was carried out on the more ten oil seep samples. This study includes light hydrocarbon and biomarkers analyses (hopanes, steranes, n-alkanes, acyclic isoprenoids, and aromatic steroids) using GC and GC-MS. The studied samples show at least two distinct families, suggesting two different types of crude oil origins: the first oil seeps appears to be highly mature, showing evidence of chemical and/or biological degradation and was derived from a clay-rich source rock deposited in suboxic conditions. It has been sourced mainly by the lower Fahdene (Albian) source rocks. The second oil seeps was derived from a carbonate-rich source rock deposited in anoxic conditions, well correlated with the Bahloul (Cenomanian-Turonian) source rock.

Keywords: Biomarkers, oil and gas seeps, organic geochemistry, source rock.

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