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.

Multimodel assessment of the upper troposphere and lower stratosphere: Extratropics

A multimodel assessment of the performance of chemistry-climate models (CCMs) in the extratropical upper troposphere/lower stratosphere (UTLS) is conducted for the first time. Process-oriented diagnostics are used to validate dynamical and transport characteristics of 18 CCMs using meteorological analyses and aircraft and satellite observations. The main dynamical and chemical climatological characteristics of the extratropical UTLS are generally well represented by the models, despite the limited horizontal and vertical resolution. The seasonal cycle of lowermost stratospheric mass is realistic, however with a wide spread in its mean value. A tropopause inversion layer is present in most models, although the maximum in static stability is located too high above the tropopause and is somewhat too weak, as expected from limited model resolution. Similar comments apply to the extratropical tropopause transition layer. The seasonality in lower stratospheric chemical tracers is consistent with the seasonality in the Brewer-Dobson circulation. Both vertical and meridional tracer gradients are of similar strength to those found in observations. Models that perform less well tend to use a semi-Lagrangian transport scheme and/or have a very low resolution. Two models, and the multimodel mean, score consistently well on all diagnostics, while seven other models score well on all diagnostics except the seasonal cycle of water vapor. Only four of the models are consistently below average. The lack of tropospheric chemistry in most models limits their evaluation in the upper troposphere. Finally, the UTLS is relatively sparsely sampled by observations, limiting our ability to quantitatively evaluate many aspects of model performance.

Assessing L2 task performance: understanding effects of task design

The overarching aim of the research reported here was to investigate the effects of task structure and storyline complexity of oral narrative tasks on second language task performance. Participants were 60 Iranian language learners of English who performed six narrative tasks of varying degree of structure and storyline complexity in an assessment setting. A number of analytic detailed measures were employed to examine whether there were any differences in the participants’ performances elicited by the different tasks in terms of their accuracy, fluency, syntactic complexity and lexical diversity. Results of the data analysis showed that performance in the more structured tasks was more accurate and to a great extent more fluent than that in the less structured tasks. The results further revealed that syntactic complexity of L2 performance was related to the storyline complexity, i.e. more syntactic complexity was associated with narratives that had both foreground and background storylines. These findings strongly suggest that there is some unsystematic variance in the participants’ performance triggered by the different aspects of task design.

Multimodel assessment of the upper troposphere and lower stratosphere: tropics and global trends

The performance of 18 coupled Chemistry Climate Models (CCMs) in the Tropical Tropopause Layer (TTL) is evaluated using qualitative and quantitative diagnostics. Trends in tropopause quantities in the tropics and the extratropical Upper Troposphere and Lower Stratosphere (UTLS) are analyzed. A quantitative grading methodology for evaluating CCMs is extended to include variability and used to develop four different grades for tropical tropopause temperature and pressure, water vapor and ozone. Four of the 18 models and the multi-model mean meet quantitative and qualitative standards for reproducing key processes in the TTL. Several diagnostics are performed on a subset of the models analyzing the Tropopause Inversion Layer (TIL), Lagrangian cold point and TTL transit time. Historical decreases in tropical tropopause pressure and decreases in water vapor are simulated, lending confidence to future projections. The models simulate continued decreases in tropopause pressure in the 21st century, along with ∼1K increases per century in cold point tropopause temperature and 0.5–1 ppmv per century increases in water vapor above the tropical tropopause. TTL water vapor increases below the cold point. In two models, these trends are associated with 35% increases in TTL cloud fraction. These changes indicate significant perturbations to TTL processes, specifically to deep convective heating and humidity transport. Ozone in the extratropical lowermost stratosphere has significant and hemispheric asymmetric trends. O3 is projected to increase by nearly 30% due to ozone recovery in the Southern Hemisphere (SH) and due to enhancements in the stratospheric circulation. These UTLS ozone trends may have significant effects in the TTL and the troposphere.

Assessment of the Wind Gust Estimate Method in mesoscale modelling of storm events over West Germany

A physically based gust parameterisation is added to the atmospheric mesoscale model FOOT3DK to estimate wind gusts associated with storms over West Germany. The gust parameterisation follows the Wind Gust Estimate (WGE) method and its functionality is verified in this study. The method assumes that gusts occurring at the surface are induced by turbulent eddies in the planetary boundary layer, deflecting air parcels from higher levels down to the surface under suitable conditions. Model simulations are performed with horizontal resolutions of 20 km and 5 km. Ten historical storm events of different characteristics and intensities are chosen in order to include a wide range of typical storms affecting Central Europe. All simulated storms occurred between 1990 and 1998. The accuracy of the method is assessed objectively by validating the simulated wind gusts against data from 16 synoptic stations by means of “quality parameters”. Concerning these parameters, the temporal and spatial evolution of the simulated gusts is well reproduced. Simulated values for low altitude stations agree particularly well with the measured gusts. For orographically exposed locations, the gust speeds are partly underestimated. The absolute maximum gusts lie in most cases within the bounding interval given by the WGE method. Focussing on individual storms, the performance of the method is better for intense and large storms than for weaker ones. Particularly for weaker storms, the gusts are typically overestimated. The results for the sample of ten storms document that the method is generally applicable with the mesoscale model FOOT3DK for mid-latitude winter storms, even in areas with complex orography.

An assessment of the prebiotic potential of single and blended substrates in anaerobic in vitro batch culture fermentations using canine faecal samples as inocula

Previously, using an in vitro static batch culture system, it was found that rice bran (RB), inulin, fibersol, mannanoligosaccharides (MOS), larch arabinogalactan and citrus pectin elicited prebiotic effects (in terms of increased numbers of bifidobacteria and lactic acid bacteria) on the faecal microbiota of a dog. The aim of the present study was to confirm the prebiotic potential of each individual substrate using multiple faecal donors, as well as assessing the prebiotic potential of 15 substrate blends made from them. Anaerobic static and stirred, pH-controlled batch culture systems inoculated with faecal samples from healthy dogs were used for this purpose. Fluorescence in situ hybridization (FISH) analysis using seven oligonucleotide probes targeting selected bacterial groups and DAPI (total bacteria) was used to monitor bacterial populations during fermentation runs. High-performance liquid chromatography was used to measure butyrate produced as a result of bacterial fermentation of the substrates. RB and a MOS/RB blend (1:1, w/w) were shown to elicit prebiotic and butyrogenic effects on the canine microbiota in static batch culture fermentations. Further testing of these substrates in stirred, pH-controlled batch culture fermentation systems confirmed the prebiotic and butyrogenic effects of MOS/RB, with no enhancement of Clostridium clusters I and II and Escherichia coli populations.

The effects of corporate social performance on the cost of corporate debt and credit ratings

This study investigates the differential impact that various dimensions of corporate social performance have on the pricing of corporate debt as well as the assessment of the credit quality of specific bond issues. The empirical analysis, based on an extensive longitudinal data set, suggests that overall, good performance is rewarded and corporate social transgressions are penalized through lower and higher corporate bond yield spreads, respectively. Similar conclusions can be drawn when focusing on either the bond rating assigned to a specific debt issue or the probability of it being considered to be an asset of speculative grade.

Importance of initial state and atmospheric conditions for urban land surface models' performance

Urban land surface models (LSM) are commonly evaluated for short periods (a few weeks to months) because of limited observational data. This makes it difficult to distinguish the impact of initial conditions on model performance or to consider the response of a model to a range of possible atmospheric conditions. Drawing on results from the first urban LSM comparison, these two issues are considered. Assessment shows that the initial soil moisture has a substantial impact on the performance. Models initialised with soils that are too dry are not able to adjust their surface sensible and latent heat fluxes to realistic values until there is sufficient rainfall. Models initialised with too wet soils are not able to restrict their evaporation appropriately for periods in excess of a year. This has implications for short term evaluation studies and implies the need for soil moisture measurements to improve data assimilation and model initialisation. In contrast, initial conditions influencing the thermal storage have a much shorter adjustment timescale compared to soil moisture. Most models partition too much of the radiative energy at the surface into the sensible heat flux at the probable expense of the net storage heat flux.

Effects of hydration status on cognitive performance and mood

Although it is well known that water is essential for human homeostasis and survival, only recently have we begun to understand its role in the maintenance of brain function. Herein, we integrate emerging evidence regarding the effects of both dehydration and additional acute water consumption on cognition and mood. Current findings in the field suggest that particular cognitive abilities and mood states are positively influenced by water consumption. The impact of dehydration on cognition and mood is particularly relevant for those with poor fluid regulation, such as the elderly and children. We critically review the most recent advances in both behavioural and neuroimaging studies of dehydration and link the findings to the known effects of water on hormonal, neurochemical and vascular functions in an attempt to suggest plausible mechanisms of action. We identify some methodological weaknesses, including inconsistent measurements in cognitive assessment and the lack of objective hydration state measurements as well as gaps in knowledge concerning mediating factors that may influence water intervention effects. Finally, we discuss how future research can best elucidate the role of water in the optimal maintenance of brain health and function.

A review of the performance of different ventilation and airflow distribution systems in buildings

The objective of this article is to review the scientific literature on airflow distribution systems and ventilation effectiveness to identify and assess the most suitable room air distribution methods for various spaces. In this study, different ventilation systems are classified according to specific requirements and assessment procedures. This study shows that eight ventilation methods have been employed in the built environment for different purposes and tasks. The investigation shows that numerous studies have been carried out on ventilation effectiveness but few studies have been done regarding other aspects of air distribution. Amongst existing types of ventilation systems, the performance of each ventilation methods varies from one case to another due to different usages of the ventilation system in a room and the different assessment indices used. This review shows that the assessment of ventilation effectiveness or efficiency should be determined according to each task of the ventilation system, such as removal of heat, removal of pollutant, supply fresh air to the breathing zone or protecting the occupant from cross infection. The analysis results form a basic framework regarding the application of airflow distribution for the benefit of designers, architects, engineers, installers and building owners.

The effects of flavonoid and other polyphenol consumption on cognitive performance: A systematic research review of human experimental and epidemiological studies

Literature reviews suggest flavonoids, a sub-class of polyphenols, are beneficial for cognition. This is the first review examining the effect of consumption of all polyphenol groups on cognitive function. Inclusion criteria were polyphenol vs. control interventions and epidemiological studies with an objective measure of cognitive function. Participants were healthy or mildly cognitively impaired adults. Studies were excluded if clinical assessment or diagnosis of Alzheimer’s disease, dementia, or cognitive impairment was the sole measure of cognitive function, or if the polyphenol was present with potentially confounding compounds such as caffeine (e.g. tea studies) or Ginkgo Biloba. 28 studies were identified; 4 berry juice studies, 4 cocoa studies, 13 isoflavone supplement studies, 3 other supplement studies, and 4 epidemiological surveys. Overall, 16 studies reported cognitive benefits following polyphenol consumption. Evidence suggests that consuming additional polyphenols in the diet can lead to cognitive benefits, however, the observed effects were small. Declarative memory and particularly spatial memory appear most sensitive to polyphenol consumption and effects may differ depending on polyphenol source. Polyphenol berry fruit juice consumption was most beneficial for immediate verbal memory, whereas isoflavone based interventions were associated with significant improvements for delayed spatial memory and executive function. Comparison between studies was hampered by methodological inconsistencies. Hence, there was no clear evidence for an association between cognitive outcomes and polyphenol dose response, duration of intervention, or population studied. In conclusion, however, the findings do imply that polyphenol consumption has potential to benefit cognition both acutely and chronically.

Assessment of plant uptake models used in exposure assessment tools for soils contaminated with organic pollutants

The aim of this study was to evaluate and improve the accuracy of plant uptake models for neutral hydrophobic organic pollutants (1 < logKOW < 9, −8 < logKAW < 0) used in regulatory exposure assessment tools, using uncertainty and sensitivity analyses. The models considered were RAIDAR, EUSES, CSOIL, CLEA, and CalTOX. In this research, CSOIL demonstrated the best performance of all five exposure assessment tools for root uptake from polluted soil in comparison with observed data, but no model predicted shoot uptake well. Recalibration of the transpiration and volatilisation parameters improved the performance of CSOIL and CLEA. The dominant pathway for shoot uptake simulated differed according to the properties of the chemical under consideration; those with a higher air–water partition coefficient were transported into shoots via the soil-air-plant pathway, while chemicals with a lower octanol–water partition coefficient and air–water partition coefficient were transported via the root. The soil organic carbon content was a particularly sensitive parameter in each model and using a site specific value improved model performance.

The STEP scale: a measure of short-term export performance improvement

This article is a direct response to a recent observation in the literature that managers appear to be short-term oriented in their assessment of the performance of an export venture (Madsen 1998). On the basis of a cross-national survey of exporting firms, the authors present a three-dimensional scale for assessing managerial judgment of short-term export performance (i.e., the STEP scale). The three dimensions are (1) satisfaction with short-term performance improvement, (2) short-term exporting intensity improvement, and (3) expected short-term performance improvement. The scale presents evidence of reliability as well as convergent, discriminant, and nomological validity, and it reveals factorial similarity and factorial equivalence across both samples. The authors outline managerial and public policy implications that stem from the scale and identify avenues for further export marketing research.

An AeroCom assessment of black carbon in Arctic snow and sea ice

Though many global aerosols models prognose surface deposition, only a few models have been used to directly simulate the radiative effect from black carbon (BC) deposition to snow and sea ice. Here, we apply aerosol deposition fields from 25 models contributing to two phases of the Aerosol Comparisons between Observations and Models (AeroCom) project to simulate and evaluate within-snow BC concentrations and radiative effect in the Arctic. We accomplish this by driving the offline land and sea ice components of the Community Earth System Model with different deposition fields and meteorological conditions from 2004 to 2009, during which an extensive field campaign of BC measurements in Arctic snow occurred. We find that models generally underestimate BC concentrations in snow in northern Russia and Norway, while overestimating BC amounts elsewhere in the Arctic. Although simulated BC distributions in snow are poorly correlated with measurements, mean values are reasonable. The multi-model mean (range) bias in BC concentrations, sampled over the same grid cells, snow depths, and months of measurements, are −4.4 (−13.2 to +10.7) ng g−1 for an earlier phase of AeroCom models (phase I), and +4.1 (−13.0 to +21.4) ng g−1 for a more recent phase of AeroCom models (phase II), compared to the observational mean of 19.2 ng g−1. Factors determining model BC concentrations in Arctic snow include Arctic BC emissions, transport of extra-Arctic aerosols, precipitation, deposition efficiency of aerosols within the Arctic, and meltwater removal of particles in snow. Sensitivity studies show that the model–measurement evaluation is only weakly affected by meltwater scavenging efficiency because most measurements were conducted in non-melting snow. The Arctic (60–90° N) atmospheric residence time for BC in phase II models ranges from 3.7 to 23.2 days, implying large inter-model variation in local BC deposition efficiency. Combined with the fact that most Arctic BC deposition originates from extra-Arctic emissions, these results suggest that aerosol removal processes are a leading source of variation in model performance. The multi-model mean (full range) of Arctic radiative effect from BC in snow is 0.15 (0.07–0.25) W m−2 and 0.18 (0.06–0.28) W m−2 in phase I and phase II models, respectively. After correcting for model biases relative to observed BC concentrations in different regions of the Arctic, we obtain a multi-model mean Arctic radiative effect of 0.17 W m−2 for the combined AeroCom ensembles. Finally, there is a high correlation between modeled BC concentrations sampled over the observational sites and the Arctic as a whole, indicating that the field campaign provided a reasonable sample of the Arctic.

The importance of accurate wind resource assessment for evaluating the economic viability of small wind turbines

The techno-economic performance of a small wind turbine is very sensitive to the available wind resource. However, due to financial and practical constraints installers rely on low resolution wind speed databases to assess a potential site. This study investigates whether the two site assessment tools currently used in the UK, NOABL or the Energy Saving Trust wind speed estimator, are accurate enough to estimate the techno-economic performance of a small wind turbine. Both the tools tend to overestimate the wind speed, with a mean error of 23% and 18% for the NOABL and Energy Saving Trust tool respectively. A techno-economic assessment of 33 small wind turbines at each site has shown that these errors can have a significant impact on the estimated load factor of an installation. Consequently, site/turbine combinations which are not economically viable can be predicted to be viable. Furthermore, both models tend to underestimate the wind resource at relatively high wind speed sites, this can lead to missed opportunities as economically viable turbine/site combinations are predicted to be non-viable. These results show that a better understanding of the local wind resource is a required to make small wind turbines a viable technology in the UK.