Predict collagen hydroxyproline sites using support vector machines.

addresses: School of Biosciences, University of Exeter, Exeter, United Kingdom. [email protected]: Journal ArticleThis is a copy of an article published in the Journal of Computational Biology © 2009 copyright Mary Ann Liebert, Inc.; Journal of Computational Biology is available online at: http://online.liebertpub.com.Collagen hydroxyproline is an important posttranslational modification activity because of its close relationship with various diseases and signaling activities. However, there is no study to date for constructing models for predicting collagen hydroxyproline sites. Support vector machines with two kernel functions (the identity kernel function and the bio-kernel function) have been used for constructing models for predicting collagen hydroxyproline sites in this study. The models are constructed based on 37 sequences collected from NCBI. Peptide data are generated using a sliding window with various sizes to scan the sequences. Fivefold cross-validation is used for model evaluation. The best model has specificity of 70% and sensitivity of 90%

Stromal regulatory T-cells are associated with a favourable prognosis in gastric cancer of the cardia

<p>Abstract</p> <p>Background</p> <p>Recent evidence suggests that CD4⁺CD25⁺FoxP3⁺regulatory T-cells (Treg) may be responsible for the failure of host anti-tumour immunity by suppressing cytotoxic T- cells. We assessed the prognostic significance of tumour infiltrating lymphocytes (TIL) in intestinal-type gastric cardiac cancer.</p> <p>Methods</p> <p>Tumour infiltrating lymphocyte (TIL) subsets and tumour infiltrating macrophages (TIM) were investigated in 52 cases using tissue microarrays. The interrelationship between the cell populations (CD3+, CD8+, CD20+, CD68+, GranzymeB+, FoxP3+) in different compartments and NED-survival was investigated (median follow-up time: 61 months).</p> <p>Results</p> <p>Intraepithelial infiltration with TIL and TIM including Treg was generally low and not related to NED-survival. However, patients with large numbers of FoxP3⁺Treg in the tumour stroma (>125.9 FoxP3⁺TILs/mm²) had a median survival time of 58 months while those with low FoxP3⁺TIL counts (<125.9 FoxP3⁺TILs/mm²) had a median survival time of 32 months (p = 0.006). Patients with high versus low stromal CD68⁺/FoxP3⁺cell ratios in primary tumour displayed median survivals of 32 and 55 months, respectively (p = 0.008).</p> <p>Conclusion</p> <p>Our results suggest that inflammatory processes within the tumour stroma of gastric intestinal-type adenocarcinomas located at the gastric cardia may affect outcome in two ways. Tumour-infiltrating macrophages are likely to promote carcinogenesis while large numbers of Treg are associated with improved outcome probably by inhibiting local inflammatory processes promoting carcinogenesis. Thus, inhibition of Treg may not be a feasible treatment option in gastric adenocarcinoma.</p

Phytopharmacological evaluation of Byesukar for hypoglycaemic activity and its effect on lipid profile and hepatic enzymes of glucose metabolism in diabetic rats

Many anti-diabetic herbal preparations have been recommended in alternative systems of medicine for the treatment of diabetes. No systematic study has been done on the anti-diabetic efficacy of Byesukar, a polyherbal formulation to treat diabetes. The anti-diabetic efficacy of byesukar ethanol extract was evaluated in an animal model of diabetes induced by alloxan. Male Wistar rats were divided in to four groups. Group 1 was normal control group; group 2 and 3 received alloxan. After inducing experimental diabetes group 2 served as diabetic control; group 3 received byesukar (500 mg/kg body weight) orally for 30 consecutive days. Group 4 were normal rats which received byesukar extract alone. The effect of byesukar on glucose level in diabetic rats was studied and the level of glucose metabolizing enzymes (Hexokinase, glucose-6-phosphatase and fructose 1, 6-bisphosphatase) in the liver and kidney were estimated. The effect of byesukar on the serum and tissue lipid profile (Cholesterol, triglycerides, phospholipids and free fatty acids) were also estimated in diabetic rats. Our results indicate that treatment with byesukar resulted in significant reduction of blood glucose, tissue glucose-6-phosphatase and fructose 1, 6-bisphosphatase activity. The decreased tissue hexokinase activity in diabetes state was found to be significantly increased by byesukar treatment. Also the byesukar treated diabetic rats showed a significant decrease in the tissue lipid profile compared to the diabetic rats. In conclusion the decreased blood glucose accompanied with decreased lipid profile and changes in the activities of the glucose metabolizing enzymes shows the antidiabetic effect of byesukar

Biophytum sensitivum : Ancient medicine, modern targets

Research on medicinal plants began to focus on discovery of natural products as potential active principles against various diseases. Medicinal plants are very interesting, have the ability to produce remarkable chemical structures with diverse biological activities. Biophytum sensitivum is used as traditional medicine to cure variety of diseases. During the last few decades, extensive research has been carried out to elucidate the chemistry, biological activities, and medicinal applications of B. sensitivum. Phytochemical analysis have shown that the plant parts are rich in various beneficial compounds which include amentoflavone, cupressuflavone, and isoorientin. Extracts and its bioactive compounds have been known to possess antibacterial, anti-inflammatory, antioxidant, antitumor, radioprotective, chemoprotective, antimetastatic, antiangiogenesis, wound-healing, immunomodulation, anti-diabetic, and cardioprotective activity. The present review has been carried out to shed light on the diverse role of this plant in the management of various ailments facing us

Ocean surface warming in Krossfjorden, Svalbard, during the last 60 years

A high-resolution marine sediment core NP16-Kro1-MCB from Krossfjorden, Western Svalbard is studied to investigate changes in sea surface conditions in the fjord during the last 60 years (1953–2014). The diatom-based reconstruction of August sea surface temperature (aSST) demonstrates a clear warming trend of 0.6 °C through the record. As inferred from Marginal Ice Zone (MIZ) diatoms, surface warming occurs in parallel with a decline in sea ice extent (SIE) during recent decades. Factor analysis identified variations in diatom assemblages representing different water masses, showing a dominance of Arctic water diatoms throughout the period and decadal variations in the sea ice assemblage during periods of peak sea ice extent. The strong dominance of Arctic water diatoms along with increasing aSST suggest prolonged open-water conditions and increased sea ice melting in the region throughout the observed period. The reconstructed ocean surface changes are in line with the background warming occurring over the Arctic region. A comparison with instrumental records from neighboring regions supports the quality of the reconstructions, including the average reconstructed aSST and the magnitude of the warming trend. We suggest that increased CO2 forcing together with ocean–atmospheric interaction have caused the increasing SST trend and decreasing sea ice presence in Krossfjorden rather than an increasing influence from Atlantic Water, which has amplified changes in many regions of Svalbard