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Histologic and histomorphometric evaluation of osteogenesis induced by octacalcium phosphate (OCP) combined with bone matrix gelatin (BMG) in rat skull defects
Sargolzaei F.,Sobhani Ag.,Nik-Nafs B.,Sarani ShA.
Journal of Dental Medicine , 2005,
Abstract: Statement of Problem: Several methods are used to enhance bone repair and new bone formation, and bone matrix gelatin (BMG) is recently introduced. Purpose: The purpose of this histologic and histomorphometric study was to assess the osteogenic potential and the quantity of new trabecular bone formation after implantation of OCP and BMG alone and in combination into the cranial defects in rat. Materials and Methods: In this experimental study, 100 young male Sprague Dawley rats (5-6 weeks age and 120-150gr weight) were divided into four groups randomly. A full thickness standard trephine defect 5mm in diameter was made in the rat’s parietal bone, and 5mg of OCP, BMG alone and in combination were implanted into the defects. No OCP and BMG particles were implanted in control group which was otherwise treated identically. On the 5th, 7th, 14th, 21st and 56th days after implantation, the rats were killed and bone samples collected. After processing the samples by routine histological procedures, 5μm thick sections of bone were cut and stained with Haematoxyline & Eosin (H&E) and Alcian Blue and studied histologically and histomorphometrically using light microscope and eyepiece graticule. The amount of newly formed bone was quantitatively measured by the use of histomorphometric methods. Data were analyzed with SAS statistical package using ANOVA and Duncan tests. Results: In the experimental groups, the new bone formation was initiated from the margin of defects during 5-14 days after implantation. During 14-21 days after implantation, bone marrow cavities and bone marrow tissues in newly formed bone were seen. By the end of the study, the newly formed bone increased and was relatively matured and almost all of the implanted materials were absorbed. In control group, at the end of the study, a few clusters of new bone were seen near to the defect margins and host bone. The histomorphometric analysis indicated statistical significant differences in the amount of newly formed bone between the experimental and control groups (P<0.05). Conclusion: Implants of OCP/BMG appear to stimulate bone induction and new bone growth in bone defects greater than the other groups and these biomaterials could be used in the repair of cranial bone defects in clinical situations.
Profiling Animal Toxicants by Automatically Mining Public Bioassay Data: A Big Data Approach for Computational Toxicology  [PDF]
Jun Zhang, Jui-Hua Hsieh, Hao Zhu
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0099863
Abstract: In vitro bioassays have been developed and are currently being evaluated as potential alternatives to traditional animal toxicity models. Already, the progress of high throughput screening techniques has resulted in an enormous amount of publicly available bioassay data having been generated for a large collection of compounds. When a compound is tested using a collection of various bioassays, all the testing results can be considered as providing a unique bio-profile for this compound, which records the responses induced when the compound interacts with different cellular systems or biological targets. Profiling compounds of environmental or pharmaceutical interest using useful toxicity bioassay data is a promising method to study complex animal toxicity. In this study, we developed an automatic virtual profiling tool to evaluate potential animal toxicants. First, we automatically acquired all PubChem bioassay data for a set of 4,841 compounds with publicly available rat acute toxicity results. Next, we developed a scoring system to evaluate the relevance between these extracted bioassays and animal acute toxicity. Finally, the top ranked bioassays were selected to profile the compounds of interest. The resulting response profiles proved to be useful to prioritize untested compounds for their animal toxicity potentials and form a potential in vitro toxicity testing panel. The protocol developed in this study could be combined with structure-activity approaches and used to explore additional publicly available bioassay datasets for modeling a broader range of animal toxicities.
Effects of Combined Elicitors on Tanshinone Metabolic Profiling and SmCPS Expression in Salvia miltiorrhiza Hairy Root Cultures  [PDF]
Qiqing Cheng,Yunfei He,Geng Li,Yujia Liu,Wei Gao,Luqi Huang
Molecules , 2013, DOI: 10.3390/molecules18077473
Abstract: Tanshinones are abietane-type norditerpenoid quinone natural products found in a well-known traditional Chinese medicinal herb, Salvia miltiorrhiza Bunge. The copalyl diphosphate synthase of S. miltiorrhiza (SmCPS) is the key enzyme in the first step for transformation of geranylgeranyl diphosphate (GGPP) into miltiradiene, which has recently been identified as the precursor of tanshinones. Based on previous gene-to-metabolite network, this study examined the influences of various combined elicitors on the expression of SmCPS and production of tanshinones in S. miltiorrhiza hairy root cultures. Combined elicitors were composed of three classes of elicitors, a heavy metal ion (Ag +), a polysaccharide (yeast extract, YE), and a plant response-signalling compound (methyl jasmonate, MJ). YE + Ag +, Ag + + MJ, YE + MJ, and YE + Ag + + MJ were the combinations we tested. The effect of elicitors on the SmCPS expression level was detected by quantitative real-time PCR (qRT-PCR), and the tanshinones accumulation responses to elicitation were analysed by Ultra Performance Liquid Chromatography (UPLC) metabolite profiling. Of these combined elicitors, the expression of SmCPS was significantly enhanced by elicitation, especially at 24 h and 36 h. Of four tanshinones detected, the contents of cryptotanshinone and dihydrotanshinone I were enhanced by treatment with YE + Ag +, Ag + + MJ, and YE + Ag + + MJ. Our results indicate that appropriate combined elicitors can enhance tanshinones production in hairy root cultures.
Promoter addresses: revelations from oligonucleotide profiling applied to the Escherichia coli genome
Karthikeyan Sivaraman, Aswin Sai Narain Seshasayee, Krishnakumar Swaminathan, Geetha Muthukumaran, Gautam Pennathur
Theoretical Biology and Medical Modelling , 2005, DOI: 10.1186/1742-4682-2-20
Abstract: We have used oligonucleotide profiling to predict regulatory regions in a bacterial genome. The method has been applied to the Escherichia coli K12 genome and the results analyzed. The information content of the putative regulatory oligonucleotides so predicted is validated through intra-genomic analyses, correlations with experimental data and inter-genome comparisons. Based on the results we have proposed a model for the bacterial promoter. The results show that the method is capable of identifying, in the E.coli genome, cis-acting elements such as TATAAT (sigma70 binding site), CCCTAT (1 base relative of sigma32 binding site), CTATNN (LexA binding site), AGGA-containing hexanucleotides (Shine Dalgarno consensus) and CTAG-containing hexanucleotides (core binding sites for Trp and Met repressors).The method adopted is simple yet effective in predicting upstream regulatory elements in bacteria. It does not need any prior experimental data except the sequence itself. This method should be applicable to most known genomes. Profiling, as applied to the E.coli genome, picks up known cis-acting and regulatory elements. Based on the profile results, we propose a model for the bacterial promoter that is extensible even to eukaryotes. The model is that the core promoter lies within a plateau of bent AT-rich DNA. This bent DNA acts as a homing segment for the sigma factor to recognize the promoter. The model thus suggests an important role for local landscapes in prokaryotic and eukaryotic gene regulation.Transcription, the first step of information flow from DNA, is regulated by sequence specific DNA-protein interactions. The regulation depends on the presence of cis-acting elements. The best examples of cis-acting elements are promoters. Other well-known examples in bacteria include the Shine Dalgarno (SD) sequence, sigma 32 binding site, LexA binding site, etc.In bacteria, promoters recognized by sigma factors initiate transcription. The responses of an organism to variou
Theory of Combined Seepage Applied to Dewatering Systems  [PDF]
Magdy M. Aboelela
Journal of Water Resource and Protection (JWARP) , 2016, DOI: 10.4236/jwarp.2016.87060
Abstract: In the present study, an analytical solution is presented to solve the problem of combined seepage, under a sheet piling cofferdam, applied to dewatering systems. Existence of the sheet pile creates a confined seepage followed by an unconfined seepage in the same field, which presents a combined seepage problem. Two equations were developed to analyze the combined seepage underneath a sheet piling wall. Using such equations, both the maximum height of the free surface just behind the sheet piling cofferdam (Ho) and the quantity of seepage discharge to be pumped out from the construction site (q) can be determined. The main parameters affecting the combined seepage characteristics underneath a sheet piling wall are: The depth of permeable foundation layer (T), the horizontal distance behind the sheet pile (X), the depth of excavation in the construction site (D), the embedded depth of sheet pile (S), the retained water head (H1), the accumulated seepage water depth (H2), and the side slope factor of excavation line (M). Study showed that, the above parameters have a great effect on the combined seepage, but with different extents.
On the combined gravity gradient modeling for applied geophysics  [PDF]
Alexey Veryaskin,Wayne McRae
Physics , 2007, DOI: 10.1088/1742-2132/5/3/010
Abstract: Gravity gradiometry research and development has intensified in recent years to the extent that technologies providing a resolution of about 1 Eotvos per 1 sec average shall likely soon be available for multiple critical applications such as natural resources exploration, oil reservoir monitoring and defence establishment. Much of the content of this paper was composed a decade ago, and only minor modifications were required for the conclusions to be just as applicable today. In this paper we demonstrate how gravity gradient data can be modeled, and show some examples of how gravity gradient data can be combined in order to extract valuable information. In particular, this study demonstrates the importance of two gravity gradient components, Txz and Tyz which, when processed together, can provide more information on subsurface density contrasts than that derived solely from the vertical gravity gradient (Tzz).
Occupational medicine and toxicology
David A Groneberg, Axel Fischer
Journal of Occupational Medicine and Toxicology , 2006, DOI: 10.1186/1745-6673-1-1
Abstract: The Journal of Occupational Medicine and Toxicology is an Open Access, online journal that publishes research articles, short reports and reviews related to the field of occupational/environmental medicine and toxicology. The first published articles focus on respiratory medicine and infectious diseases [1-5].Occupational medicine and toxicology belongs to the most wide ranging disciplines of all medical specialties. The field is devoted to the diagnosis, prevention, management and scientific analysis of occupational diseases, injuries and disability. It also covers the promotion of health of workers, their families, and communities. In the era of heavy industries occupational medicine was known as "industrial medicine" with a focus on acute medical care for injured employees. The complexity of modern industrial processes changed the field and today's areas covered by occupational medicine include effects of atmospheric pollution, carcinogenesis, biological monitoring, ergonomics, epidemiology, product safety and health promotion.The field of occupational medicine and toxicology is not static and the demand for studies addressing the large variety of current issues continues to grow. In view of this demand and the fact that numerous occupational medicine and toxicology studies are published by journals of related fields such as pulmonary medicine, oncology or allergy, there is a need for a new online journal that also aims to improve communication between basic and clinical science. These features will be combined by an "Open Access model " and a rapid publication process without major space limitations.The Journal of Occupational Medicine and Toxicology's Open Access policy changes the way in which articles are published. First, all articles become freely and universally accessible online, and so an author's work can be read by anyone at no cost. Second, the authors hold copyright for their work and grant anyone the right to reproduce and disseminate the article, p
Application of PCR techniques in toxicology  [PDF]
Maja Kazubek,Anna D?ugosz,Krzysztof Pawlik
Post?py Higieny i Medycyny Do?wiadczalnej , 2010,
Abstract: Molecular biology techniques have become widely used in toxicology, leading to the creation of a new science – molecular toxicology. The goal of molecular toxicology is to detect and study the changes induced by xenobiotics at the molecular level. The research scope of molecular toxicology includes examination of mutations in genomic DNA, differences in mRNA expression and study of genotype indicating individual sensitivity.The processes of activation and detoxification of xenobiotics, drugs and environmental carcinogens involve several enzymes (xenobiotic-metabolizing enzymes – XMEs). Most of the chemicals entering our bodies, regardless of whether they have medical, pathogenic or carcinogenic properties, require metabolic activation by phase I enzymes (cytochrome P-450). In the next process the phase I products are usually detoxified by phase II enzymes, mainly by epoxide hydrolase, glutathione transferase, N-acetyltransferase or sulfotransferase. PCR techniques allow precise study of the effects of xenobiotics on cells and tissues by examining the level of activation of genes coding for phase I and II enzymes, or by testing the activity of other elements of the transcriptome. Studies of sensitivity of individual cells or tissues based on examination of mutation or gene polymorphism presence are also relevant.This paper presents the possibility of using various PCR techniques in toxicology and especially in the study of genetically determined sensitivity to xenobiotics. It also covers the possibilities of applying qPCR and qRT-PCR methods in the search for exposure biomarkers with particular emphasis on individual cytochrome P450 isoforms. Furthermore, it provides information about the possibility of implementing the differential display technique in the identification of new genes activated by toxic agents.
A prognostic model for the combined analysis of gene expression profiling in hepatocellular carcinoma  [cached]
Zee Chung Ying Benny,Lee Jock Wai Jack,Wong Nathalie,Yeo Winnie
Bioinformation , 2008,
Abstract: Microarray techniques using cDNA array and comparative genomic hybridization (CGH) have been developed for several discovery applications. They are frequently applied for the prediction and diagnosis of cancer in recent years. Many studies have shown that integrating genomic data from different sources may increase the reliability of gene expression analysis results in understanding cancer progression. Therefore, developing a good prognostic model dealing simultaneously with different types of dataset is important. The challenge with these types of data is high background noise. We describe an analytical two-stage framework with a multi-parallel data analysis method named wavelet-based generalized singular value decomposition and shaving method (WGSVD-shaving). This method is proposed for de-noising and dimension-reduction during early stage prognosis modeling. We also applied a supervised gene clustering technique with penalized logistic regression with Cox-model on an integrated data. We show the accuracy of the method using a simulated dataset with a case study on Hepatocelluar Carcinoma (HCC) cDNA and CGH data. The method shows improved results from GSVD-shaving and has application in the discovery of candidate genes associated with cancer.
Gene Expression Profiling Combined with Bioinformatics Analysis Identify Biomarkers for Parkinson Disease  [PDF]
Hongyu Diao, Xinxing Li, Sheng Hu, Yunhui Liu
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0052319
Abstract: Parkinson disease (PD) progresses relentlessly and affects approximately 4% of the population aged over 80 years old. It is difficult to diagnose in its early stages. The purpose of our study is to identify molecular biomarkers for PD initiation using a computational bioinformatics analysis of gene expression. We downloaded the gene expression profile of PD from Gene Expression Omnibus and identified differentially coexpressed genes (DCGs) and dysfunctional pathways in PD patients compared to controls. Besides, we built a regulatory network by mapping the DCGs to known regulatory data between transcription factors (TFs) and target genes and calculated the regulatory impact factor of each transcription factor. As the results, a total of 1004 genes associated with PD initiation were identified. Pathway enrichment of these genes suggests that biological processes of protein turnover were impaired in PD. In the regulatory network, HLF, E2F1 and STAT4 were found have altered expression levels in PD patients. The expression levels of other transcription factors, NKX3-1, TAL1, RFX1 and EGR3, were not found altered. However, they regulated differentially expressed genes. In conclusion, we suggest that HLF, E2F1 and STAT4 may be used as molecular biomarkers for PD; however, more work is needed to validate our result.
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