FastContact: a free energy scoring tool for protein–protein complex structures

‘FastContact’ is a server that estimates the direct electrostatic and desolvation interaction free energy between two proteins in units of kcal/mol. Users submit two proteins in PDB format, and the output is emailed back to the user in three files: one output file, and the two processed proteins. Besides the electrostatic and desolvation free energy, the server reports residue contact free energies that rapidly highlight the hotspots of the interaction and evaluates the van der Waals interaction using CHARMm. Response time is ∼1 min. The server has been successfully tested and validated, scoring refined complex structures and blind sets of docking decoys, as well as proven useful predicting protein interactions. ‘FastContact’ offers unique capabilities from biophysical insights to scoring and identifying important contacts

Dietary fibre in Europe: current state of knowledge on definitions, sources, recommendations, intakes and relationships to health

Research into the analysis, physical properties and health effects of dietary fibre has continued steadily over the last 40-50 years. From the knowledge gained, countries have developed guidelines for their populations on the optimal amount of fibre to be consumed each day. Food composition tables from many countries now contain values for the dietary fibre content of foods, and, from these, combined with dietary surveys, population intakes have been determined. The present review assessed the uniformity of the analytical methods used, health claims permitted, recommendations and intakes, particularly from national surveys across Europe and around the world. It also assessed current knowledge on health effects of dietary fibre and related the impact of different fibre types on health. The overall intent was to be able to provide more detailed guidance on the types of fibre which should be consumed for good health, rather than simply a total intake figure, the current situation. Analysis of data indicated a fair degree of uniformity in the definition of dietary fibre, the method used for analysis, the recommended amount to be consumed and a growing literature on effects on digestive health and disease risk. However, national dietary survey data showed that intakes do not reach recommendations and very few countries provide guidance on the types of fibre that are preferable to achieve recommended intakes. Research gaps were identified and ideas suggested to provide information for more detailed advice to the public about specific food sources that should be consumed to achieve health benefits

Development of a Web-Based Human Resource Sourcing System for Labour Only Contracts

Nowadays in some areas of Nigeria, it has been noticed that the search for a satisfactory team of labourers (skilled and unskilled) or even the right amount of people to undertake the job has become a laborious activity. Therefore, there is need to build a two-way partnership system linking construction firms with the required skilled labour and vice versa. The aim of this research is to develop a web-based human resource sourcing system for labour only contracts. The study made use of a questionnaire instrument and developed a web-based interface for skilled labour sourcing. The questionnaire was distributed to fifty (50) construction professionals who were selected through a convenience sampling technique. The data collected was analyzed using SPSS v.21. The design of the system was done using hypertext markup language (HTML) for authoring web pages. The study revealed that contractors’ sourcing techniques for skilled labour on construction projects were mostly by referral from colleagues and workers from past projects. The study identified the major barriers in sourcing for skilled labour on construction projects as the unavailability of trained skilled labour. The study revealed that years of experience, wages charged and behavior of the worker were major criteria considered while sourcing for skilled labour on construction projects. In conclusion, the study developed a web based human resource sourcing system for labour only contracts that incorporated the needs of the skilled labour and requirement of construction firms. It was recommended that construction professionals and contractors need to harness the benefits of web-based technologies. In addition, there is need to increase the information and communication technology (ICT) trainings of workers in the construction industry so has to have a successful integration of ICT and the construction industry

FDG-PET staging and importance of lymph node SUV in head and neck cancer

OBJECTIVES: The role of positron emission tomography (PET) with fluoro-deoxy-glucose (FDG) in the staging of head and neck cancer (HNC) is unclear. The NCCN guidelines do not recommend FDG-PET as a part of standard workup. The purpose of this report is to examine the role of FDG-PET imaging in altering management and providing prognostic information for HNC. METHODS: Retrospective review of HNC patients who had a staging FDG-PET scan performed at either Thomas Jefferson University or University of Kansas Medical Center between the years 2001 and 2007. A total of 212 PET scans were performed in patients who went on to receive radiotherapy. RESULTS: The median follow-up time for all patients was 469 days. The PPV and NPV of PET imaging to correctly identify lymph node status was 94% and 89% respectively. Lymph nodes with extracapsular extension (ECE) had higher SUVs than nodes without ECE, 11.0 vs. 5.0 (p \u3c 0.0007). Maximum SUV for the primary tumor \u3e 8.0 was predictive of worse overall survival (p \u3c 0.045), while the SUV of the lymph nodes was predictive for distant recurrence at one year--with a mean SUV value of 10.4 for patients with distant failure vs. 7.0 without (p \u3c 0.05). CONCLUSIONS: FDG-PET staging in head and neck cancer has good positive and negative predictive values in determining lymph node status. The maximum SUV of the primary tumor is predictive of overall survival. This is the first report to find that the SUV of a lymph node is predictive for ECE and also for distant recurrence

The Impact of Serum Glucose, Anti-Diabetic Agents, and Statin Usage in Non-Small Cell Lung Cancer Patients Treated With Definitive Chemoradiation

Introduction: Epidemiologic data indicate diabetes confers an augmented risk of lung cancer development, yet the relationship between hyperglycemia, metabolic agents, and prognosis is unclear. We analyzed the impact of hyperglycemia, anti-diabetic agents, and statins on outcomes in non-small cell lung cancer (NSCLC) patients undergoing chemoradiation. Method and Materials: In total, data from 170 patients with stage III NSCLC treated at the University of Pittsburgh Medical Center between 2001 and 2014 were obtained for analysis. Kaplan-Meier survival analysis was used to estimate time-to-event for overall survival (OS), disease-free survival, distant metastasis (DM), and loco-regional control (LRC). Blood glucose values (n = 2870), statins, and diabetic medications were assessed both continuously and categorically in univariable and multivariable Cox proportional hazard regression models to estimate hazard ratios and identify prognostic factors. Results: Tumor volume was a negative prognostic factor for OS, disease-free survival, DM, and LRC (p = 0.001). Tumor stage and treatment time were associated with increased all-cause mortality. Any glucose measurement ≥ 130 mg/dl during treatment (2-year estimate 49.9 vs. 65.8%, p = 0.095) was borderline significant for decreased LRC, with similar trends on multivariable analysis (HR 1.636, p = 0.126) and for OS (HR 1.476, p = 0.130). Statin usage was associated with improved 2-year LRC (53.4 vs. 62.4%, p = 0.088) but not with improvements in survival. Other glycemic parameters, comorbid diabetes diagnosis, or anti-diabetic medications were not significantly associated with outcomes. Conclusions: There were trends for blood glucose value over 130 mg/dl and statin nonuse being associated with inferior prognosis for LRC in stage III NSCLC patients; glycemic state, statin usage, and glucose-modulating medications were not associated with survival outcomes in multivariable analysis in this retrospective database

Relating Spatial Patterns of Stream Metabolism to Distributions of Juveniles Salmonids at the River Network Scale

Understanding the factors that drive spatial patterns in stream ecosystem processes and the distribution of aquatic biota is important to effective management of these systems and the conservation of biota at the network scale. In this study, we conducted field surveys throughout an extensive river network in NE Oregon that supports diminishing populations of wild salmonids. We collected data on physical habitat, nutrient concentrations, biofilm standing stocks, stream metabolism (gross primary production [GPP] and ecosystem respiration [ER]), and ESA‐listed juvenile salmonid density from approximately 50 sites across two sub‐basins. Our goals were to (1) to evaluate network patterns in these metrics, and (2) determine network‐scale linkages among these metrics, thus providing inference of processes driving observed patterns. Ambient nitrate‐N and phosphate‐P concentrations were low across both sub‐basins (\u3c40 μg/L). Nitrate‐N decreased with watershed area in both sub‐basins, but phosphate‐P only decreased in one sub‐basin. These spatial patterns suggest co‐limitation in one sub‐basin but N limitation in the other; experimental results using nutrient diffusing substrates across both sub‐basins supported these predictions. Solar exposure, temperature, GPP, ER, and GPP:ER increased with watershed area, but biofilm Chl a and ash‐free dry mass (AFDM) did not. Spatial statistical network (SSN) models explained between 70% and 75% of the total variation in biofilm Chl a, AFDM, and GPP, but only 21% of the variation in ER. Temperature and nutrient concentrations were the most supported predictors of Chl aand AFDM standing stocks, but these variables explained little of the total variation compared to spatial autocorrelation. In contrast, solar exposure and temperature were the most supported variables explaining GPP, and these variables explained far more variation than autocorrelation. Solar exposure, temperature, and nutrient concentrations explained almost none of the variation in ER. Juvenile salmonids—a key management focus in these sub‐basins—were most abundant in cool stream sections where rates of GPP were low, suggesting temperature constraints on these species restrict their distribution to oligotrophic areas where energy production at the base of the food web may be limited

Transport of <i>Sporosarcina pasteurii</i> in sandstone and its significance for subsurface engineering technologies

The development of microbially mediated technologies for subsurface remediation and rock engineering is steadily increasing; however, we are lacking experimental data and models to predict bacterial movement through rock matrices. Here, breakthrough curves (BTCs) were obtained to quantify the transport of the ureolytic bacterium, Sporosarcina pasteurii, through sandstone cores, as a function of core length (1.8–7.5 cm), bacterial density (4 × 10&lt;sup&gt;6&lt;/sup&gt; to 9 × 10&lt;sup&gt;7&lt;/sup&gt; cells/ml) and flow rate (5.8–17.5 m/s). &lt;i&gt;S. pasteurii&lt;/i&gt; was easily immobilised within the homogeneous sandstone matrix (&gt;80%) in comparison to a packed sand column (&lt;20%; under similar experimental conditions), and percentage recovery decreased almost linearly with increasing rock core length. Moreover, a decrease in bacterial density or flow rate enhanced bacterial retention. A numerical model based on 1D advection dispersion models used for unconsolidated sand was fitted to the BTC data obtained here for sandstone. Good agreement between data and model was obtained at shorter rock core lengths (&lt;4 cm), suggesting that physicochemical filtration processes are similar in homogeneous packed sand and sandstones at these lengths. Discrepancies were, however observed at longer core lengths and with varying flow rates, indicating that the attributes of consolidated rock might impact bacterial transport progressively more with increasing core length. Implications of these results on microbial mineralisation technologies currently being developed for sealing fluid paths in subsurface environment is discussed