Production and quality assessment of a smoked tuna (Euthynnus affinis) product

The sensory, instrumental, and chemical profile of a smoked tuna product comparable and competitive to smoked turkey and pork was studied, based on four experimental factors. Despite their different brining times, all brined, sliced portions of tuna were assessed by panelists as quite acceptable products in terms of firmness, juiciness, color, and saltiness. Protein denaturation seemed to be affected by the brining time. Lipid oxidation seemed quite extensive; the ratio of C22:6n-3/C16:0 was decreased at 15% and 20%. Histamine content was between 3.7 mg/ 100 g and 7.5 mg/100 g. After 3 mo in refrigeration, the aerobic bacteria was 19.10^5 to 250.10^6 in contrast to the unprocessed samples at 28.10^5.

Automated tertiary structure prediction with accurate local model quality assessment using the IntFOLD-TS method

The IntFOLD-TS method was developed according to the guiding principle that the model quality assessment would be the most critical stage for our template based modelling pipeline. Thus, the IntFOLD-TS method firstly generates numerous alternative models, using in-house versions of several different sequence-structure alignment methods, which are then ranked in terms of global quality using our top performing quality assessment method – ModFOLDclust2. In addition to the predicted global quality scores, the predictions of local errors are also provided in the resulting coordinate files, using scores that represent the predicted deviation of each residue in the model from the equivalent residue in the native structure. The IntFOLD-TS method was found to generate high quality 3D models for many of the CASP9 targets, whilst also providing highly accurate predictions of their per-residue errors. This important information may help to make the 3D models that are produced by the IntFOLD-TS method more useful for guiding future experimental work

Nutritional biomarkers for objective dietary assessment

The accurate assessment of dietary exposure is important in investigating associations between diet and disease. Research in nutritional epidemiology, which has resulted in a large amount of information on associations between diet and chronic diseases in the last decade, relies on accurate assessment methods to identify these associations. However, most dietary assessment instruments rely to some extent on self-reporting, which is prone to systematic bias affected by factors such as age, gender, social desirability and approval. Nutritional biomarkers are not affected by these and therefore provide an additional, alternative method to estimate intake. However, there are also some limitations in their application: they are affected by inter-individual variations in metabolism and other physiological factors, and they are often limited to estimating intake of specific compounds and not entire foods. It is therefore important to validate nutritional biomarkers to determine specific strengths and limitations. In this perspective paper, criteria for the validation of nutritional markers and future developments are discussed.

Improving sequence-based fold recognition by using 3D model quality assessment

Motivation: The ability of a simple method (MODCHECK) to determine the sequence–structure compatibility of a set of structural models generated by fold recognition is tested in a thorough benchmark analysis. Four Model Quality Assessment Programs (MQAPs) were tested on 188 targets from the latest LiveBench-9 automated structure evaluation experiment. We systematically test and evaluate whether the MQAP methods can successfully detect native-likemodels. Results: We show that compared with the other three methods tested MODCHECK is the most reliable method for consistently performing the best top model selection and for ranking the models. In addition, we show that the choice of model similarity score used to assess a model's similarity to the experimental structure can influence the overall performance of these tools. Although these MQAP methods fail to improve the model selection performance for methods that already incorporate protein three dimension (3D) structural information, an improvement is observed for methods that are purely sequence-based, including the best profile–profile methods. This suggests that even the best sequence-based fold recognition methods can still be improved by taking into account the 3D structural information.

Improvement of 3D protein models using multiple templates guided by single-template model quality assessment

Motivation: Modelling the 3D structures of proteins can often be enhanced if more than one fold template is used during the modelling process. However, in many cases, this may also result in poorer model quality for a given target or alignment method. There is a need for modelling protocols that can both consistently and significantly improve 3D models and provide an indication of when models might not benefit from the use of multiple target-template alignments. Here, we investigate the use of both global and local model quality prediction scores produced by ModFOLDclust2, to improve the selection of target-template alignments for the construction of multiple-template models. Additionally, we evaluate clustering the resulting population of multi- and single-template models for the improvement of our IntFOLD-TS tertiary structure prediction method. Results: We find that using accurate local model quality scores to guide alignment selection is the most consistent way to significantly improve models for each of the sequence to structure alignment methods tested. In addition, using accurate global model quality for re-ranking alignments, prior to selection, further improves the majority of multi-template modelling methods tested. Furthermore, subsequent clustering of the resulting population of multiple-template models significantly improves the quality of selected models compared with the previous version of our tertiary structure prediction method, IntFOLD-TS.

FunFOLDQA: a quality assessment tool for protein-ligand binding site residue predictions

The estimation of prediction quality is important because without quality measures, it is difficult to determine the usefulness of a prediction. Currently, methods for ligand binding site residue predictions are assessed in the function prediction category of the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment, utilizing the Matthews Correlation Coefficient (MCC) and Binding-site Distance Test (BDT) metrics. However, the assessment of ligand binding site predictions using such metrics requires the availability of solved structures with bound ligands. Thus, we have developed a ligand binding site quality assessment tool, FunFOLDQA, which utilizes protein feature analysis to predict ligand binding site quality prior to the experimental solution of the protein structures and their ligand interactions. The FunFOLDQA feature scores were combined using: simple linear combinations, multiple linear regression and a neural network. The neural network produced significantly better results for correlations to both the MCC and BDT scores, according to Kendall’s τ, Spearman’s ρ and Pearson’s r correlation coefficients, when tested on both the CASP8 and CASP9 datasets. The neural network also produced the largest Area Under the Curve score (AUC) when Receiver Operator Characteristic (ROC) analysis was undertaken for the CASP8 dataset. Furthermore, the FunFOLDQA algorithm incorporating the neural network, is shown to add value to FunFOLD, when both methods are employed in combination. This results in a statistically significant improvement over all of the best server methods, the FunFOLD method (6.43%), and one of the top manual groups (FN293) tested on the CASP8 dataset. The FunFOLDQA method was also found to be competitive with the top server methods when tested on the CASP9 dataset. To the best of our knowledge, FunFOLDQA is the first attempt to develop a method that can be used to assess ligand binding site prediction quality, in the absence of experimental data.

The ModFOLD4 server for the quality assessment of 3D protein models

Once you have generated a 3D model of a protein, how do you know whether it bears any resemblance to the actual structure? To determine the usefulness of 3D models of proteins, they must be assessed in terms of their quality by methods that predict their similarity to the native structure. The ModFOLD4 server is the latest version of our leading independent server for the estimation of both the global and local (per-residue) quality of 3D protein models. The server produces both machine readable and graphical output, providing users with intuitive visual reports on the quality of predicted protein tertiary structures. The ModFOLD4 server is freely available to all at: http://www.reading.ac.uk/bioinf/ModFOLD/.

Soil quality assessment based on carbon stratification index in different olive grove management practices in Mediterranean areas

In Mediterranean areas, conventional tillage increases soil organic matter losses, reduces soil quality, and contributes to climate change due to increased CO2 emissions. CO2 sequestration rates in soil may be enhanced by appropriate agricultural soil management and increasing soil organic matter content. This study analyzes the stratification ratio (SR) index of soil organic carbon (SOC), nitrogen (N) and C:N ratio under different management practices in an olive grove (OG) in Mediterranean areas (Andalusia, southern Spain). Management practices considered in this study are conventional tillage (CT) and no tillage (NT). In the first case, CT treatments included addition of alperujo (A) and olive leaves (L). A control plot with no addition of olive mill waste was considered (CP). In the second case, NT treatments included addition of chipped pruned branches (NT1) and chipped pruned branches and weeds (NT2). The SRs of SOC increased with depth for all treatments. The SR of SOC was always higher in NT compared to CT treatments, with the highest SR of SOC observed under NT2. The SR of N increased with depth in all cases, ranging between 0.89 (L-SR1) and 39.11 (L-SR3 and L-SR4).The SR of C:N ratio was characterized by low values, ranging from 0.08 (L-SR3) to 1.58 (NT1-SR2) and generally showing higher values in SR1 and SR2 compared to those obtained in SR3 and SR4. This study has evaluated several limitations to the SR index such as the fact that it is descriptive but does not analyze the behavior of the variable over time. In addition, basing the assessment of soil quality on a single variable could lead to an oversimplification of the assessment. Some of these limitations were experienced in the assessment of L, where SR1 of SOC was the lowest of the studied soils. In this case, the higher content in the second depth interval compared to the first was caused by the intrinsic characteristics of this soil's formation process rather than by degradation. Despite the limitations obtained SRs demonstrate that NT with the addition of organic material improves soil quality.

Water quality assessment of Toledo River and determination of metal concentrations by using SR-TXRF technique

The region of Toledo River, Parana, Brazil is characterized by intense anthropogenic activities. Hence, metal concentrations and physical-chemical parameters of Toledo River water were determined in order to complete an environmental evaluation catalog. Samples were collected monthly during one year period at seven different sites from the source down the river mouth, physical-chemical variables were analyzed, and major metallic ions were measured. Metal analysis was performed by using the synchrotron radiation total reflection X-ray fluorescence technique. A statistical analysis was applied to evaluate the reliability of experimental data. The analysis of obtained results have shown that a strong correlation between physical-chemical parameters existed among sites 1 and 7, suggesting that organic pollutants were mainly responsible for decreasing the Toledo River water quality.

Road network and GPS tracking with data processing and quality assessment

GPS technology has been embedded into portable, low-cost electronic devices nowadays to track the movements of mobile objects. This implication has greatly impacted the transportation field by creating a novel and rich source of traffic data on the road network. Although the promise offered by GPS devices to overcome problems like underreporting, respondent fatigue, inaccuracies and other human errors in data collection is significant; the technology is still relatively new that it raises many issues for potential users. These issues tend to revolve around the following areas: reliability, data processing and the related application. This thesis aims to study the GPS tracking form the methodological, technical and practical aspects. It first evaluates the reliability of GPS based traffic data based on data from an experiment containing three different traffic modes (car, bike and bus) traveling along the road network. It then outline the general procedure for processing GPS tracking data and discuss related issues that are uncovered by using real-world GPS tracking data of 316 cars. Thirdly, it investigates the influence of road network density in finding optimal location for enhancing travel efficiency and decreasing travel cost. The results show that the geographical positioning is reliable. Velocity is slightly underestimated, whereas altitude measurements are unreliable.Post processing techniques with auxiliary information is found necessary and important when solving the inaccuracy of GPS data. The densities of the road network influence the finding of optimal locations. The influence will stabilize at a certain level and do not deteriorate when the node density is higher.

Faculty Instructional Quality Assessment Practices Incorporating Teaching Portfolios and Peer Review with Student Course Evaluations

Program directors and department chairs require different means of assessing faculty quality due to the unreliability of student course evaluation data. This report outlines alternative strategies for review committees to assess faculty instructional quality. This report also details incorporation of annual performance reviews for tenure-track faculty into tenure decisions.

Integrated sediment quality assessment in Paranagua Estuarine System, Southern Brazil

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Comparative sediment quality assessment in different littoral ecosystems from Spain (Gulf of Cadiz) and Brazil (Santos and Sao Vicente estuarine system)

The goal of this work was to establish comparisons among environmental degradation in different areas from Southern Spain (Gulf of Cadiz) and Brazil (Santos and Sao Vicente estuary), by using principal component analyses (PCA) to integrate sediment toxicity (amphipods mortality) and chemical-physical data (Zn, Cd, Pb; Cu, Ni, Co, V, PCBs, PAHs concentrations, OC and fines contents). The results of PCA extraction of Spanish data showed that Bay of Cadiz, CA-1 did not present contamination or degradation; CA-2 exhibited contamination by PCBs, however it was not related to the amphipods mortality. Ria of Huelva was the most impacted site, showing contamination caused principally by hydrocarbons, in HV-1 and HV-2, but heavy metals were also important contaminants at HV-1, HV-2 and HV-3. Algeciras Bay was considered as not degraded in GR-3 and -4, but in GR-3' high contamination by PAHs was found. In the Brazilian area, the most degraded sediments were found in the stations situated at the inner parts of the estuary (SSV-2, SSV-3, and SSV-4), followed by SSV-6, which is close to the Submarine Sewage Outfall of Santos - SSOS. Sediments from SSV-1 and SSV-5 did not present chemical contamination, organic contamination or significant amphipod mortality. The results, of this investigation showed that both countries present environmental degradation related to PAHs: in Spain, at Ria of Huelva and Gudarranque river's estuary areas; and in Brasil, in the internal portion of the Santos and Sao Vicente estuary. The same situation is found for heavy metals, since all of the identified metals are related to toxicity in the studied areas, with few exceptions (V for both Brazil and Spain, and Cd and Co for Brazilian areas). The contamination by PCBs is more serious for Santos and Sao Vicente estuary than for the investigated areas in Gulf of Cadiz, where such compound did not relate to the toxicity. (c) 2006 Elsevier Ltd. All rights reserved.

Indoor air quality assessment of elementary schools in Curitiba, Brazil

The promotion of good indoor air quality in schools is of particular public concern for two main reasons: (1) school-age children spend at least 30% of their time inside classrooms and (2) indoor air quality in urban areas is substantially influenced by the outdoor pollutants, exposing tenants to potentially toxic substances. Two schools in Curitiba, Brazil, were selected to characterize the gaseous compounds indoor and outdoor of the classrooms. The concentrations of benzene, toluene, ethylbenzene, and the isomers xylenes (BTEX); NO2; SO2; O3; acetic acid (HAc); and formic acid (HFor) were assessed using passive diffusion tubes. BTEX were analyzed by gas chromatography-ion trap mass spectrometry and other collected gasses by ion chromatography. The concentration of NO2 varied between 9.5 and 23 μg m-3, whereas SO2 showed an interval from 0.1 to 4.8 μg m-3. Within the schools, BTEX concentrations were predominant. Formic and acetic acids inside the classrooms revealed intermediate concentrations of 1.5 μg m-3 and 1.2 μg m-3, respectively. © Springer Science + Business Media B.V. 2009.