On the hydrophobicity of peptides:comparing empirical predictions of peptide log P values

Peptides are of great therapeutic potential as vaccines and drugs. Knowledge of physicochemical descriptors, including the partition coefficient logP, is useful for the development of predictive Quantitative Structure-Activity Relationships (QSARs). We have investigated the accuracy of available programs for the prediction of logP values for peptides with known experimental values obtained from the literature. Eight prediction programs were tested, of which seven programs were fragment-based methods: XLogP, LogKow, PLogP, ACDLogP, AlogP, Interactive Analysis's LogP and MlogP; and one program used a whole molecule approach: QikProp. The predictive accuracy of the programs was assessed using r(2) values, with ALogP being the most effective (r( 2) = 0.822) and MLogP the least (r(2) = 0.090). We also examined three distinct types of peptide structure: blocked, unblocked, and cyclic. For each study (all peptides, blocked, unblocked and cyclic peptides) the performance of programs rated from best to worse is as follows: all peptides - ALogP, QikProp, PLogP, XLogP, IALogP, LogKow, ACDLogP, and MlogP; blocked peptides - PLogP, XLogP, ACDLogP, IALogP, LogKow, QikProp, ALogP, and MLogP; unblocked peptides - QikProp, IALogP, ALogP, ACDLogP, MLogP, XLogP, LogKow and PLogP; cyclic peptides - LogKow, ALogP, XLogP, MLogP, QikProp, ACDLogP, IALogP. In summary, all programs gave better predictions for blocked peptides, while, in general, logP values for cyclic peptides were under-predicted and those of unblocked peptides were over-predicted.

Bidding For Parking: The Impact of University Affiliation on Predicting Bid Values in Dutch Auctions of On-Campus Parking Permits

Parking is often underpriced and expanding its capacity is expensive; universities need a better way of reducing congestion outside of building costly parking garages. Demand based pricing mechanisms, such as auctions, offer a possible solution to the problem by promising to reduce parking at peak times. However, faculty, students, and staff at universities have systematically different parking needs, leading to different parking valuations. In this study, I determine the impact university affiliation has on predicting bid values cast in three Dutch Auctions of on-campus parking permits sold at Chapman University in Fall 2010. Using clustering techniques crosschecked with university demographic information to detect affiliation groups, I ran a log-linear regression, finding that university affiliation had a larger effect on bid amount than on lot location and fraction of auction duration. Generally, faculty were predicted to have higher bids whereas students were predicted to have lower bids.

Geochemical analyses and Delta47 values in shallow water corals

Geochemical variations in shallow water corals provide a valuable archive of paleoclimatic information. However, biological effects can complicate the interpretation of these proxies, forcing their application to rely on empirical calibrations. Carbonate clumped isotope thermometry (Delta47) is a novel paleotemperature proxy based on the temperature dependent "clumping" of 13C-18O bonds. Similar ?47-temperature relationships in inorganically precipitated calcite and a suite of biogenic carbonates provide evidence that carbonate clumped isotope variability may record absolute temperature without a biological influence. However, large departures from expected values in the winter growth of a hermatypic coral provided early evidence for possible Delta47 vital effects. Here, we present the first systematic survey of Delta47 in shallow water corals. Sub-annual Red Sea Delta47 in two Porites corals shows a temperature dependence similar to inorganic precipitation experiments, but with a systematic offset toward higher Delta47 values that consistently underestimate temperature by ~8 °C. Additional analyses of Porites, Siderastrea, Astrangia and Caryophyllia corals argue against a number of potential mechanisms as the leading cause for this apparent Delta47 vital effect including: salinity, organic matter contamination, alteration during sampling, the presence or absence of symbionts, and interlaboratory differences in analytical protocols. However, intra- and inter-coral comparisons suggest that the deviation from expected Delta47 increases with calcification rate. Theoretical calculations suggest this apparent link with calcification rate is inconsistent with pH-dependent changes in dissolved inorganic carbon speciation and with kinetic effects associated with CO2 diffusion into the calcifying space. However, the link with calcification rate may be related to fractionation during the hydration/hydroxylation of CO2 within the calcifying space. Although the vital effects we describe will complicate the interpretation of Delta47 as a paleothermometer in shallow water corals, it may still be a valuable paleoclimate proxy, particularly when applied as part of a multi-proxy approach.

Friendships of High-Achieving African American Adolescents: Relation to Ethnic Identity and Achievement Values

The academic achievement of African American adolescents is a national concern for educators and researchers especially since current reports depict the underachievement of African American students as continuing to lag behind their European American peers. Determining what factors within the school environment that contributes to the achievement gap and how it can be reduced remains an important issue in alleviating disparities seen in educational achievement and attainment. This study examined the relation between characteristics of the close friendships of high-achieving African American adolescents and students’ identity development and motivation in school. Data were collected from 217 high-achieving African American students within 10th to 12th grade from 5 public and private high schools. Each student self-reported on their ethnicity, gender, parents’ education level, grade, FARMs, GPA, perceived teacher support (emotional, academic, and instrumental support), their perception of their ethnic identity, and their perception of their achievement values. Through the use of nomination procedures, students also identified their close friends and responded to questions concerning how supportive (emotional, academic, and instrumental support) they each were. Results from multiple regression analyses showed that the provision of instrumental support from close friends related to the exploration process of the high-achieving students’ ethnic identity. In addition, there was a strong relation between the ethnic identity of close friends and that of the individual. Furthermore, although friend support was not a significant predictor of achievement values, demographic (mother’s education level, grade, and FARMS) and control (teacher support) variables predicted students’ importance and utility of school respectively. These findings add to the literature on age and socioeconomic status as they relate to student’s motivation to achieve. Overall, this study provides some evidence highlighting ways in which close friendships might relate to the self-development of high-achieving African American adolescents. This study provides a starting point for additional ways in which to explore how peer processes relate to the academic behaviors of high-achieving African American adolescents.

Predicted residual activity of rilpivirine in HIV-1 infected patients failing therapy including NNRTIs efavirenz or nevirapine

This is an open access article under the CC BY-NC-ND license - http://creativecommons.org/licenses/by-nc-nd/4.0/

Cultural Values Change in the Rehabilitation of Historic Schools in Portugal

Despite the importance of the preservation of the historic built environment for the benefit of present and future generations, there is a lack of knowledge of the effects of architectural rehabilitation decisions on the cultural significance of historic buildings. Architectural heritage conservation literature has focused almost exclusively on providing principles and guidelines, describing intervention methodologies, and discussing predicted impacts of design on material values. This thesis argues that a focus on the actual effects is needed if the sociocultural sustainability of historic buildings significance is to be achieved. Supported by an extensive literature review and informed by personal insights from the researcher’s everyday practice, an adapted model of the Theory of Change based on Weiss (1995) was designed, providing a tool to evaluate the effects of rehabilitation on cultural significance [ERECS]. Using a selection of six recently rehabilitated historic secondary schools in Portugal (liceus), this research investigated architectural decisions and their effects on the cultural values of this building typology for education, focusing on three objectives, corresponding to three stages of interventions: understanding the existing cultural significance, identifying the design strategies applied and assessing the short-term effects of design decisions on the cultural values. Stressing the role of stakeholders in rehabilitation processes, data were collected from the buildings and architectural projects, the decision makers in the conservation process, and the school community. Although confirming that the evaluation of the effects of architectural decisions on cultural values is a complex task, the findings demonstrate that the historic liceus have historical, architectural and sociocultural values, and whilst strategies did not value social values, material cultural values were generally considered and preserved, contributing to the enhancement of intangible values. The implications of this theory-based and evidence-based research highlight the importance of evaluating actual effects for cultural heritage theory, architectural conservation practice and heritage management policy.