The Lactamase Engineering Database: a critical survey of TEM sequences in public databases

<p>Abstract</p> <p>Background</p> <p>TEM β-lactamases are the main cause for resistance against β-lactam antibiotics. Sequence information about TEM β-lactamases is mainly found in the NCBI peptide database and TEM mutation table at <url>http://www.lahey.org/Studies/temtable.asp</url>. While the TEM mutation table is manually curated by experts in the lactamase field, who guarantee reliable and consistent information, the rapidly growing sequence and annotation information from the NCBI peptide database is sometimes inconsistent. Therefore, the Lactamase Engineering Database has been developed to collect the TEM β-lactamase sequences from the NCBI peptide database and the TEM mutation table, systematically compare sequence information and naming, identify inconsistencies, and thus provide a versatile tool for reconciliation of data and for an investigation of the sequence-function relationship.</p> <p>Description</p> <p>The LacED currently provides 2399 sequence entries and 37 structure entries. Sequence information on 150 different TEM β-lactamases was derived from the TEM mutation table which provides a unique number to each protein classified as TEM β-lactamase. 293 TEM-like proteins were found in the NCBI protein database, but only 113 TEM β-lactamase were common to both data sets. The 180 TEM β-lactamases from the NCBI protein database which have not yet been assigned to a TEM number fall in three classes: (1) 89 proteins from microbial organisms and 35 proteins from cloning or expression vectors had a new mutation profile; (2) 55 proteins had inconsistent annotation in terms of TEM assignment or reported mutation profile; (3) 39 proteins are fragments. The LacED is web accessible at <url>http://www.LacED.uni-stuttgart.de</url> and contains multisequence alignments, structure information and reconciled annotation of TEM β-lactamases. The LacED is weekly updated and supplies all data for download.</p> <p>Conclusion</p> <p>The Lactamase Engineering Database enables a systematic analysis of TEM β-lactamase sequence and annotation data from different data sources, and thus provides a valuable tool to identify inconsistencies in sequences from the NCBI peptide database, to detect TEM β-lactamases with a novel mutation profile, and to identify new amino acid positions at which mutations can occur.</p

Evaluation of genetic diversity of Vietnamese dogs based on mitochondrial DNA hypervariable-1 region

Haplogroup E were detected with high frequency in the population of Phu Quoc ridgeback dogs suggesting that this Vietnamese valuable dog breed originated from domestic dogs harbouring haplogroup E from Vietnam’s mainland or from East Asia where the presence of haplogroup E was reported. Evaluation of the genetic diversity of the Vietnam’s mainland dogs and haplogroup Escreening would support us in tracking out the origin of Phu Quoc ridgeback dog

A size-dependent functionally graded sinusoidal plate model based on a modified couple stress theory

A size-dependent model for bending and free vibration of functionally graded plate is developed based on the modified couple stress theory and sinusoidal shear deformation theory. In the former theory, the small scale effect is taken into consideration, while the effect of shear deformation is accounted for in the latter theory. The equations of motion and boundary conditions are derived from Hamilton’s principle. Analytical solutions for the bending and vibration problems of simply supported plates are obtained. Numerical examples are presented to illustrate the influences of small scale on the responses of functionally graded microplates. The results indicate that the inclusion of small scale effects results in an increase in plate stiffness, and consequently, leads to a reduction of deflection and an increase in frequency. Such small scale effects are significant when the plate thickness is small, but become negligible with increasing plate thickness

Examining the effects of lead on the life of larval zebrafish (1-7 days old)

Lead (Pb) is a toxic metal and and can cause variety of disorders and effect on neu-ronal function and neurodevelopment. Using zebrafish as a model, the aim of this study was to evaluate the effects of concentrations of Pb2+ on the life of zebrafish larvae (from 1 to 7 days old)yesBelgorod State Universit

Developing a Novel Image Marker to Predict the Responses of Neoadjuvant Chemotherapy (NACT) for Ovarian Cancer Patients

Objective: Neoadjuvant chemotherapy (NACT) is one kind of treatment for advanced stage ovarian cancer patients. However, due to the nature of tumor heterogeneity, the patients' responses to NACT varies significantly among different subgroups. To address this clinical challenge, the purpose of this study is to develop a novel image marker to achieve high accuracy response prediction of the NACT at an early stage. Methods: For this purpose, we first computed a total of 1373 radiomics features to quantify the tumor characteristics, which can be grouped into three categories: geometric, intensity, and texture features. Second, all these features were optimized by principal component analysis algorithm to generate a compact and informative feature cluster. Using this cluster as the input, an SVM based classifier was developed and optimized to create a final marker, indicating the likelihood of the patient being responsive to the NACT treatment. To validate this scheme, a total of 42 ovarian cancer patients were retrospectively collected. A nested leave-one-out cross-validation was adopted for model performance assessment. Results: The results demonstrate that the new method yielded an AUC (area under the ROC [receiver characteristic operation] curve) of 0.745. Meanwhile, the model achieved overall accuracy of 76.2%, positive predictive value of 70%, and negative predictive value of 78.1%. Conclusion: This study provides meaningful information for the development of radiomics based image markers in NACT response prediction

Evaluating the Effectiveness of 2D and 3D Features for Predicting Tumor Response to Chemotherapy

2D and 3D tumor features are widely used in a variety of medical image analysis tasks. However, for chemotherapy response prediction, the effectiveness between different kinds of 2D and 3D features are not comprehensively assessed, especially in ovarian cancer-related applications. This investigation aims to accomplish such a comprehensive evaluation. For this purpose, CT images were collected retrospectively from 188 advanced-stage ovarian cancer patients. All the metastatic tumors that occurred in each patient were segmented and then processed by a set of six filters. Next, three categories of features, namely geometric, density, and texture features, were calculated from both the filtered results and the original segmented tumors, generating a total of 1595 and 1403 features for the 3D and 2D tumors, respectively. In addition to the conventional single-slice 2D and full-volume 3D tumor features, we also computed the incomplete-3D tumor features, which were achieved by sequentially adding one individual CT slice and calculating the corresponding features. Support vector machine (SVM) based prediction models were developed and optimized for each feature set. 5-fold cross-validation was used to assess the performance of each individual model. The results show that the 2D feature-based model achieved an AUC (area under the ROC curve [receiver operating characteristic]) of 0.84+-0.02. When adding more slices, the AUC first increased to reach the maximum and then gradually decreased to 0.86+-0.02. The maximum AUC was yielded when adding two adjacent slices, with a value of 0.91+-0.01. This initial result provides meaningful information for optimizing machine learning-based decision-making support tools in the future

HIGH PROTECTION PERFORMANCE OF COATING SYSTEMS BASED ON ZINC RICH PRIMER AND FLUOROPOLYMER COATING

Coating systems based on zinc rich primer and fluoropolymer top coat were exposed for 8 years at different atmospheric stations in Vietnam: Hanoi, Ha Long and Nha Trang. For comparison the coating system with zinc rich primer and polyurethane topcoat was also tested. The degradations of coating systems were evaluated by gloss measurement and electrochemical impedance spectroscopy. The obtained results show that coating systems with zinc rich primer and top coatings based on fluoropolymer  and polyurethane topcoats show very high weather resistance and corrosion protection performance, but the systems with fluoropolymer are better than coating system with polyurethane topcoat

Effect of time and temperature on the survival rate of mouse sperm (Mus musculus var. Albino) in short-term preservation without cryoprotectant agents

In this study, we studied the use of physiological saline solution (NaCl 0,9%) or dulbecco’s phosphatebuffered saline (D-PBS) for mature sperms short-term preservation. After being collected from epididymides, sperms were adjusted to desired concentration (2x106 sperms/ml) with NaCl 0.9% solution or D-PBS solution (the dishes containing sperms were covered by mineral oil) and stored at 4oC, iooC and room temperature (RT/26oC