Physicochemical Methods for Prediction of Functional Information for Proteins

Structural genomics initiatives are determining thousands of new protein structures. Many of these structures are of unknown function, and computational methods for the rapid determination of functional information from protein structure are needed. We present details of how functional information is obtained from the structure using THEMATICS (Theoretical Microscopic Titration Curves). THEMATICS is a computational procedure that gives information about chemical reactivity, based on solution of the Poisson-Boltzmann equations for the electrical potential function. We show how anomalies in predicted titration curves are established. We show further that when residues with anomalous predicted titration curves form a cluster in physical space, these residues tend to be very highly conserved across species and such clusters are reliable predictors of the active site. Results are given for ten enzymes; detailed results are shown for the enzymes triosephosphate isomerase (from chicken), 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (from E. coli), and papain (from papaya).     

L'échelle de développement pubertaire: équivalence en langue fran?aise du <>.

The Pubertal Development Scale from A. C. Petersen and L. J. Crockett (1985) is a self-report instrument that measures levels of pubertal maturation in adolescence. The main goal of this study was to validate the French version of the instrument on a high school population. The latter was administered on 3 occasions to 255 students during their 1st and 2nd high school years. The measure's internal consistency and the sequence of bodily changes of boys and girls allowed the authors to establish the reliability of the students' perception of their pubertal development. Like J. M. Tanner (1962) and Petersen et al. (1985, 1988), 5 categories identifying different pubertal status were labeled. Results show satisfactory reliability from such a pubertal classification system. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Health status recovery at one year in children injured in a road accident: A cohort study

Despite the frequency of traumatic injuries due to road accidents and potential importance of identifying children at risk of impaired recovery one year after a road accident, there is a lack of data on long-term recovery of health status, except in children with severe traumatic brain injury. The aim of the present study was to evaluate predictive factors of recovery in children one year after road traffic injuries. The prospective cohort study was composed of children aged <16 years, admitted to public or private sector hospitals in the Rhône administrative area of France following a road accident. Recovery of health status one year after the accident and information concerning quality of life and the consequences of the accident for the child or family 1 year after the accident were collected by questionnaire, usually completed by the parents. Victims were in majority male (64.6%) and had mild or moderate injuries (81.9% with Maximum Abbreviated Injury Scale (M-AIS) <3). One year after the accident, 75.0% of the mild-to-moderate and 34.8% of the severe cases estimated health status as fully recovered. After adjustment, severity score (M-AIS ≥ 3) and lower limb injury (AIS > 1) were associated with incomplete recovery of health status: weighted odds ratio (OR_w), 4.3 [95% confidence interval (95% CI), 1.3–14.6] and OR_w, 6.5 [95% CI, 1.9–21.7], respectively. Recovery status correlated significantly with quality of life physical scores (r = 0.46), especially body pain (r = 0.48) and role/social–physical (r = 0.50) and, to a lesser extent, quality of life psychosocial scores (r = 0.21). In a cohort of children injured in a road accident, those with high injury severity score and those with lower limb injuries are less likely to recover full health status by 1 year. Impaired health status was associated with a lower physical quality of life score at 1 year.     

Predictive factors of chronic post-traumatic stress disorder 6 months after a road traffic accident

Background

This study sets out to identify risk factors for post-traumatic stress disorder (PTSD) after a road traffic accident with a view to improving prevention.

Methods

The study used a prospective cohort of road traffic accident casualties. All subjects over 15 years of age were recruited in the course of an interview conducted while they were receiving care in a hospital of the Rhône area administrative département. Six months after their accident, they answered a self-administered postal questionnaire that included the Post-traumatic Check-List Scale (PCLS) in order to evaluate PTSD. Multivariate logistic regression analysis was conducted to compare those subjects with a PCLS score of 44 or over with those with a lower score, in order to identify factors that might be associated with PTSD.

Results

592 subjects (out of 1168) returned the 6-month questionnaire and 541 completed the PCLS test. One hundred subjects had a PCLS score ≥44, suggesting PTSD, and 441 subjects did not. The factors associated with PTSD were initial injury severity, post-traumatic amnesia, the feeling of not being responsible for their accident and persistent pain 6 months after it. A lower odds-ratio was associated with users of two-wheel than four-wheel motor vehicles (OR = 0.4; 0.2–0.9).

Conclusion

Besides predictive factors for PTSD (injury severity, post-traumatic amnesia and the feeling of not being responsible for their accident), our study suggested a reduced risk of PTSD among two-wheel motor vehicle users.     

At home in inner-city immigrant community gardens

This paper extends the definition of the domestic sphere to include urban community gardens, which I argue serve as critical “home-like” places that marginalized Latina/o immigrants use to sustain themselves and to re-create homeland in urban Los Angeles. Based on over 1 year of ethnographic and interview research at the gardens, I argue that the immigrant community gardeners are creating new homes, attachments and means of livelihood that link their past with the present, restoring them during this historical moment of the US immigration crisis in deportations and detentions. A range of social reproductive and restorative activities normally associated with the private domestic sphere unfold at these community gardens, allowing us to see these sites as shared open-air domiciles, hybrid-domestic places, set among plant nature. I suggest that focusing on the everyday practices, the materiality and meanings of place may productively shift our theoretical gaze from understanding migration experiences only through the lens of assimilation or transnationalism, and toward one that acknowledges active assertions organized around the right to home-making.     

Resolving the long-term trends of polycyclic aromatic hydrocarbons in the Canadian Arctic atmosphere

Polycyclic aromatic hydrocarbon (PAH) air concentrations measured over the period 1992-2000 at the Canadian High Arctic station of Alert were subject to time-series analysis using dynamic harmonic regression (DHR). For most of the PAHs, the DHR model fit to the observed data was good, with DHR capable of interpolating over missing data points during periods when air concentrations were below detection limits. As expected, DHR identified seasonal increases in PAH air concentrations. However, it has also identified additional, subtler "seasonal" patterns as a series of harmonics with varying periodicity. For example, a regular summer high in air concentrations was apparent for many PAHs, particularly the lower molecular weight (two- to three-ringed) compounds, which may be attributed to summertime regional combustion events such as forestfires and/or revolatilization from surfaces (e.g., soil and oceans, as well as arctic surfaces). Comparison of wintertime PAH concentrations (where sigmaPAH ranged from 260 to 516 pg m(-3)) with an earlier arctic study did not reveal a reduction in PAH levels. However, removal of the seasonal components by DHR revealed a declining trend in PAH concentrations over the 1992-2000 period. For many lighter PAHs, this was typified by a linear decrease over the whole time series, although, for the higher molecular weight PAHs, a marked reduction was apparent in the first few years of sampling followed by a leveling off in concentrations by the mid/late-1990s. This behavior is similar to reported trends of other air pollutants in the Arctic, may be attributed to the decline in Soviet industry during the early 1990s, and has implications regarding the major PAH sources affecting the Arctic.     

Infrared measurement of total fatty acids in blood serum

Quantitative determination of total fatty acids in rabbit blood serum is achieved using the infrared absorption band, associated with the C = O stretching vibration at 1713 cm^?1 (5.84 μm). Different tests are described to show the validity of this method for a wide range of variation in total concentration and in individual percentages of any one fatty acid. The results are treated by statistical methods, and it is found that infrared analysis is five times more sensitive than methods described previously. This accurate technique, which can be applied to other serums has, for example, been applied to disclose a systematic error in the preparation of total fatty acid samples when nitrogen flushing is not used.     

How do climate fluctuations affect persistent organic pollutant distribution in North America? Evidence from a decade of air monitoring

Interannual variations of persistent organic pollutant (POP) air concentrations from the Great Lakes region and the Arctic during the 1990s are strongly associated with atmospheric low-frequency fluctuations, notably the North Atlantic Oscillation (NAO), the El Ni?o-Southern Oscillation (ENSO), and the Pacific North American (PNA) pattern. This suggests interactions between climate variation and the global distribution of POPs. Atmospheric concentrations of hexachlorocyclohexanes (HCHs), hexachlorobenzene (HCB), and several lighter polychlorinated biphenyls (PCBs) measured around the Great Lakes basin increased during the positive phases of NAO and ENSO in the spring. This implies that anomalous high air temperatures associated with NAO and ENSO enhance volatilization of POPs from reservoirs on the Earth's surface accumulated in the past. These compounds are then available for transport from source regions to more pristine regions such as the Arctic under favorable flow patterns associated with global climate variations.     

Temporal and spatial trends of atmospheric polychlorinated biphenyl concentrations near the Great Lakes

Polychlorinated biphenyl (PCB) concentrations were measured in the atmosphere at six regionally representative sites near the five Great Lakes from 1990 to 2003 as part of the Integrated Atmospheric Deposition Network (IADN). Concentration data for several individual PCB congeners and for total PCBs were analyzed for temporal and spatial trends after correcting for the temperature dependency of the partial pressures. Atmospheric PCB concentrations are decreasing relatively slowly for tetra- and pentachlorinated congeners, an observation that is in agreement with primary emissions modeling. Relatively rapid decreases in PCB concentrations at the sites near Lakes Michigan and Ontario may reflect successful reduction efforts in Chicago and Toronto, respectively. Atmospheric PCB concentrations near Lakes Superior and Huron are now so low that the air and water concentrations may be close to equilibrium. Atmospheric PCB concentrations at sites near Lakes Michigan, Erie, and Ontario are relatively higher than those measured at sites near Lakes Superior and Huron. The highest PCB level was observed at the site near Lake Erie, most likely due to nearby urban activity. However, this relatively higher concentration is still 6-10 times lower than that previously reported at the Chicago site. A correlation between average gas-phase PCB concentration with local population indicates a strong urban source of PCBs. The temperature dependence of gas-phase PCB concentrations is similar at most sites except at Burnt Island on Lake Huron, where very low concentrations, approaching virtual elimination, prevent reliable temperature correlation calculations.