StaRProtein: a web server for prediction of stability of repeat proteins

Repeat proteins have become increasingly important due to their capability to bind to almost any proteins and the potential as alternative therapy to monoclonal antibodies. In the past decade repeat proteins have been designed to mediate specific protein-protein interactions. The tetratricopeptide and ankyrin repeat proteins are two classes of helical repeat proteins that form different binding pockets to accommodate various partners. It is important to understand the factors that define folding and stability of repeat proteins in order to prioritize the most stable designed repeat proteins to further explore their potential binding affinities. Here we developed distance-dependant statistical potentials using two classes of alpha-helical repeat proteins, tetratricopeptide and ankyrin repeat proteins respectively, and evaluated their efficiency in predicting the stability of repeat proteins. We demonstrated that the repeat-specific statistical potentials based on these two classes of repeat proteins showed paramount accuracy compared with non-specific statistical potentials in: 1) discriminate correct vs. incorrect models 2) rank the stability of designed repeat proteins. In particular, the statistical scores correlate closely with the equilibrium unfolding free energies of repeat proteins and therefore would serve as a novel tool in quickly prioritizing the designed repeat proteins with high stability. StaRProtein web server was developed for predicting the stability of repeat proteins.

Young, Old, and Weathered Carbon—Part 2: Using Radiocarbon and Stable Isotopes to Identify Terrestrial Carbon Support of the Food Web in an Alkaline, Humic Lake

Carbon (C) and nitrogen (N) stable isotope analysis (SIA) has been used to identify the terrestrial subsidy of freshwater food webs. However, SIA fails to differentiate between the contributions of old and recently fixed terrestrial C and consequently cannot fully determine the source, age, and biochemical quality of terrestrial carbon. Natural abundance radiocarbon (∆14C) was used to examine the age and origin of carbon in Lower Lough Erne, Northern Ireland. 14C and stable isotope values were obtained from invertebrate, algae, and fish samples, and the results indicate that terrestrial organic C is evident at all trophic levels. High winter δ15N values in calanoid zooplankton (δ15N = 24‰) relative to phytoplankton and particulate organic matter (δ15N = 6‰ and 12‰, respectively) may reflect several microbial trophic levels between terrestrial C and calanoid invertebrates. Winter and summer calanoid ∆14C values show a seasonal switch between autochthonous and terrestrial carbon sources. Fish ∆14C values indicate terrestrial support at the highest trophic levels in littoral and pelagic food webs. 14C therefore is useful in attributing the source of carbon in freshwater in addition to tracing the pathway of terrestrial carbon through the food web.

Deflagrations in hybrid CONe white dwarfs: a route to explain the faint Type Iax supernova 2008ha

Stellar evolution models predict the existence of hybrid white dwarfs (WDs) with a carbon-oxygen core surrounded by an oxygen-neon mantle. Being born with masses similar to 1.1 M-aS (TM), hybrid WDs in a binary system may easily approach the Chandrasekhar mass (M-Ch) by accretion and give rise to a thermonuclear explosion. Here, we investigate an off-centre deflagration in a near-M-Ch hybrid WD under the assumption that nuclear burning only occurs in carbon-rich material. Performing hydrodynamics simulations of the explosion and detailed nucleosynthesis post-processing calculations, we find that only 0.014 M-aS (TM) of material is ejected while the remainder of the mass stays bound. The ejecta consist predominantly of iron-group elements, O, C, Si and S. We also calculate synthetic observables for our model and find reasonable agreement with the faint Type Iax SN 2008ha. This shows for the first time that deflagrations in near-M-Ch WDs can in principle explain the observed diversity of Type Iax supernovae. Leaving behind a near-M-Ch bound remnant opens the possibility for recurrent explosions or a subsequent accretion-induced collapse in faint Type Iax SNe, if further accretion episodes occur. From binary population synthesis calculations, we find the rate of hybrid WDs approaching M-Ch to be of the order of 1 per cent of the Galactic SN Ia rate.

Effect of a Web-Based Behavior Change Program on Weight Loss and Cardiovascular Risk Factors in Overweight and Obese Adults at High Risk of Developing Cardiovascular Disease:Randomized Controlled Trial

BACKGROUND: Web-based programs are a potential medium for supporting weight loss because of their accessibility and wide reach. Research is warranted to determine the shorter- and longer-term effects of these programs in relation to weight loss and other health outcomes.

OBJECTIVE: The aim was to evaluate the effects of a Web-based component of a weight loss service (Imperative Health) in an overweight/obese population at risk of cardiovascular disease (CVD) using a randomized controlled design and a true control group.

METHODS: A total of 65 overweight/obese adults at high risk of CVD were randomly allocated to 1 of 2 groups. Group 1 (n=32) was provided with the Web-based program, which supported positive dietary and physical activity changes and assisted in managing weight. Group 2 continued with their usual self-care (n=33). Assessments were conducted face-to-face. The primary outcome was between-group change in weight at 3 months. Secondary outcomes included between-group change in anthropometric measurements, blood pressure, lipid measurements, physical activity, and energy intake at 3, 6, and 12 months. Interviews were conducted to explore participants' views of the Web-based program.

RESULTS: Retention rates for the intervention and control groups at 3 months were 78% (25/32) vs 97% (32/33), at 6 months were 66% (21/32) vs 94% (31/33), and at 12 months were 53% (17/32) vs 88% (29/33). Intention-to-treat analysis, using baseline observation carried forward imputation method, revealed that the intervention group lost more weight relative to the control group at 3 months (mean -3.41, 95% CI -4.70 to -2.13 kg vs mean -0.52, 95% CI -1.55 to 0.52 kg, P<.001), at 6 months (mean -3.47, 95% CI -4.95 to -1.98 kg vs mean -0.81, 95% CI -2.23 to 0.61 kg, P=.02), but not at 12 months (mean -2.38, 95% CI -3.48 to -0.97 kg vs mean -1.80, 95% CI -3.15 to -0.44 kg, P=.77). More intervention group participants lost ≥5% of their baseline body weight at 3 months (34%, 11/32 vs 3%, 1/33, P<.001) and 6 months (41%, 13/32 vs 18%, 6/33, P=.047), but not at 12 months (22%, 7/32 vs 21%, 7/33, P=.95) versus control group. The intervention group showed improvements in total cholesterol, triglycerides, and adopted more positive dietary and physical activity behaviors for up to 3 months verus control; however, these improvements were not sustained.

CONCLUSIONS: Although the intervention group had high attrition levels, this study provides evidence that this Web-based program can be used to initiate clinically relevant weight loss and lower CVD risk up to 3-6 months based on the proportion of intervention group participants losing ≥5% of their body weight versus control group. It also highlights a need for augmenting Web-based programs with further interventions, such as in-person support to enhance engagement and maintain these changes.

Analysing Web-Orchestrations Under Stress Using Uncertainty Profiles

An orchestration is a multi-threaded computation that invokes a number of remote services. In practice, the responsiveness of a web-service fluctuates with demand; during surges in activity service responsiveness may be degraded, perhaps even to the point of failure. An uncertainty profile formalizes a user's perception of the effects of stress on an orchestration of web-services; it describes a strategic situation, modelled by a zero-sum angel–daemon game. Stressed web-service scenarios are analysed, using game theory, in a realistic way, lying between over-optimism (services are entirely reliable) and over-pessimism (all services are broken). The ‘resilience’ of an uncertainty profile can be assessed using the valuation of its associated zero-sum game. In order to demonstrate the validity of the approach, we consider two measures of resilience and a number of different stress models. It is shown how (i) uncertainty profiles can be ordered by risk (as measured by game valuations) and (ii) the structural properties of risk partial orders can be analysed.

14C as a tool to trace terrestrial carbon in a complex lake system: implications for food-web structure and carbon cycling

Globally lakes bury and remineralise significant quantities of terrestrial C, and the associated flux of terrestrial C strongly influences their functioning. Changing deposition chemistry, land use and climate induced impacts on hydrology will affect soil biogeochemistry and terrestrial C export¹ and hence lake ecology with potential feedbacks for regional and global C cycling. C and nitrogen stable isotope analysis (SIA) has identified the terrestrial subsidy of freshwater food webs. The approach relies on different ¹³C fractionation in aquatic and terrestrial primary producers, but also that inorganic C demands of aquatic primary producers are partly met by ¹³C depleted C from respiration of terrestrial C, and ‘old’ C derived from weathering of catchment geology. SIA thus fails to differentiate between the contributions of old and recently fixed terrestrial C. Natural abundance ¹⁴C can be used as an additional biomarker to untangle riverine food webs² where aquatic and terrestrial δ ¹³C overlap, but may also be valuable for examining the age and origin of C in the lake. Primary production in lakes is based on dissolved inorganic C (DIC). DIC in alkaline lakes is partially derived from weathering of carbonaceous bedrock, a proportion of which is¹⁴C-free. The low ¹⁴C activity yields an artificial age offset leading samples to appear hundreds to thousands of years older than their actual age. As such, ¹⁴C can be used to identify the proportion of autochthonous C in the food-web. With terrestrial C inputs likely to increase, the origin and utilisation of ‘fossil’ or ‘recent’ allochthonous C in the food-web can also be determined. Stable isotopes and 14C were measured for biota, particulate organic matter (POM), DIC and dissolved organic carbon (DOC) from Lough Erne, Northern Ireland, a humic alkaline lake. Temporal and spatial variation was evident in DIC, DOC and POM C isotopes with implications for the fluctuation in terrestrial export processes. Ramped pyrolysis of lake surface sediment indicates the burial of two C components. ¹⁴C activity (507 ± 30 BP) of sediment combusted at 400˚C was consistent with algal values and younger than bulk sediment values (1097 ± 30 BP). The sample was subsequently combusted at 850˚C, yielding 14C values (1471 ± 30 BP) older than the bulk sediment age, suggesting that fossil terrestrial carbon is also buried in the sediment. Stable isotopes in the food web indicate that terrestrial organic C is also utilised by lake organisms. High winter δ ¹⁵N values in calanoid zooplankton (δ ¹⁵N = 24%¸) relative to phytoplankton and POM (δ ¹⁵N = 6h and 12h respectively) may reflect several microbial trophic levels between terrestrial C and calanoids. Furthermore winter calanoid 14C ages are consistent with DOC from an inflowing river (75 ± 24 BP), not phytoplankton (367 ± 70 BP). Summer calanoid δ ^13C, δ ¹⁵N and ¹⁴C (345 ± 80 BP) indicate greater reliance on phytoplankton.

¹ Monteith, D.T et al., (2007) Dissolved organic carbon trends resulting from changes in atmospheric deposition chemistry. Nature, 450:537-535

² Caraco, N., et al.,(2010) Millennial-aged organic carbon subsidies to a modern river food web. Ecology,91: 2385-2393.

Potentially harmful excipients in neonatal medicines: A pan-European observational study

Objectives We aimed to describe administration of eight potentially harmful excipients of interest (EOI)-parabens, polysorbate 80, propylene glycol, benzoates, saccharin sodium, sorbitol, ethanol and benzalkonium chloride-to hospitalised neonates in Europe and to identify risk factors for exposure. Methods All medicines administered to neonates during 1 day with individual prescription and demographic data were registered in a web-based point prevalence study. Excipients were identified from the Summaries of Product Characteristics. Determinants of EOI administration (geographical region, gestational age (GA), active pharmaceutical ingredient, unit level and hospital teaching status) were identified using multivariable logistical regression analysis. Results Overall 89 neonatal units from 21 countries participated. Altogether 2095 prescriptions for 530 products administered to 726 neonates were recorded. EOI were found in 638 (31%) prescriptions and were administered to 456 (63%) neonates through a relatively small number of products (n=142; 27%). Parabens, found in 71 (13%) products administered to 313 (43%) neonates, were used most frequently. EOI administration varied by geographical region, GA and route of administration. Geographical region remained a significant determinant of the use of parabens, polysorbate 80, propylene glycol and saccharin sodium after adjustment for the potential covariates including anatomical therapeutic chemical class of the active ingredient. Conclusions European neonates receive a number of potentially harmful pharmaceutical excipients. Regional differences in EOI administration suggest that EOI-free products are available and provide the potential for substitution to avoid side effects of some excipients.

Limitations of a measurement-assisted optomechanical route to quantum macroscopicity of superposition states

Optomechanics is currently believed to provide a promising route towards the achievement of genuine quantum effects at the large, massive-system scale. By using a recently proposed figure of merit that is well suited to address continuous-variable systems, in this paper we analyze the requirements needed for the state of a mechanical mode (embodied by an end-cavity cantilever or a membrane placed within an optical cavity) to be qualified as macroscopic. We show that, according to the phase space-based criterion that we have chosen for our quantitative analysis, the state achieved through strong single-photon radiation-pressure coupling to a quantized field of light and conditioned by measurements operated on the latter might be interpreted as macroscopically quantum. In general, though, genuine macroscopic quantum superpositions appear to be possible only under quite demanding experimental conditions

Preparation of La2NiO4+δ powders as a cathode material for SOFC via a PVP-assisted hydrothermal route

Uniform submicron La₂NiO_4+δ (sm-LNO) powders have been synthesized by a facile polyvinylpyrrolidone (PVP)-assisted hydrothermal route. In the presence of PVP, sm-LNO of pure phase has been obtained by calcination at the relatively low temperature of 900 °C for 8 h. Compared micron-sized LNO (m-LNO) particles obtained at 1,000 °C by hydrothermal synthesis route without PVP assisted, the sm-LNO-PVP displays regularly shaped and well-distributed particles in the range of 0.3–0.5 μm. The scanning electron microscopy (SEM) results showed that the sm-LNO sample is submicronic and that the m-LNO sample shows agglomerates with a broad size distribution. The electrochemical performance of m-LNO and sm-LNO-PVP has been investigated by electrochemical impedance spectroscopy. The polarization resistance of the sm-LNO-PVP cathode reaches a value of 0.40 Ω cm² at 750 °C, which is lower than that of m-LNO (0.62 Ω cm²). This result indicates that a fine electrode microstructure with submicron particles can help to increase the active sites, accelerate oxygen diffusion, and reduce polarization resistance. An anode-supported single cell with sm-LNO cathode has been fabricated and tested over a temperature range from 650 to 800 °C. The maximum power density of the cell has achieved 834 mW cm⁻² at 750 °C. These results therefore show that this PVP-assisted hydrothermal method is an effective approach to construct submicron-structured cathode and enhance the performance of intermediate temperature solid oxide fuel cell.

Optimal Route Search with the Coverage of Users' Preferences

The preferences of users are important in route search and planning. For example, when a user plans a trip within a city, their preferences can be expressed as keywords shopping mall, restaurant, and museum, with weights 0.5, 0.4, and 0.1, respectively. The resulting route should best satisfy their weighted preferences. In this paper, we take into account the weighted user preferences in route search, and present a keyword coverage problem, which finds an optimal route from a source location to a target location such that the keyword coverage is optimized and that the budget score satisfies a specified constraint. We prove that this problem is NP-hard. To solve this complex problem, we pro- pose an optimal route search based on an A* variant for which we have defined an admissible heuristic function. The experiments conducted on real-world datasets demonstrate both the efficiency and accu- racy of our proposed algorithms.