Funneling and frustration in the energy landscapes of some designed and simplified proteins

We explore the similarities and differences between the energy landscapes of proteins that have been selected by nature and those of some proteins designed by humans. Natural proteins have evolved to function as well as fold, and this is a source of energetic frustration. The sequence of Top7, on the other hand, was designed with architecture alone in mind using only native state stability as the optimization criterion. Its topology had not previously been observed in nature. Experimental studies show that the folding kinetics of Top7 is more complex than the kinetics of folding of otherwise comparable naturally occurring proteins. In this paper, we use structure prediction tools, frustration analysis, and free energy profiles to illustrate the folding landscapes of Top7 and two other proteins designed by Takada. We use both perfectly funneled (structure-based) and predictive (transferable) models to gain insight into the role of topological versus energetic frustration in these systems and show how they differ from those found for natural proteins. We also study how robust the folding of these designs would be to the simplification of the sequences using fewer amino acid types. Simplification using a five amino acid type code results in comparable quality of structure prediction to the full sequence in some cases, while the two-letter simplification scheme dramatically reduces the quality of structure prediction

Context-driven Policies Enforcement for Edge-based IoT Data Sharing-as-a-Service

Sharing real-time data originating from connected devices is crucial to real-world intelligent Internet of Things (IoT) applications, i.e., based on artificial intelligence/machine learning (AI/ML). Such IoT data sharing involves multiple parties for different purposes and is usually based on data contracts that might depend on the dynamic change of IoT data variety and velocity. It is still an open challenge to support multiple parties (aka tenants) with these dynamic contracts based on the data value for their specific contextual purposes.This work addresses these challenges by introducing a novel dynamic context-based policy enforcement framework to support IoT data sharing (on-Edge) based on dynamic contracts. Our enforcement framework allows IoT Data Hub owners to define extensible rules and metrics to govern the tenants in accessing the shared data on the Edge based on policies defined with static and dynamic contexts. We have developed a proof-of-concept prototype for sharing sensitive data such as surveillance camera videos to illustrate our proposed framework. The experimental results demonstrated that our framework could soundly and timely enforce context-based policies at runtime with moderate overhead. Moreover, the context and policy changes are correctly reflected in the system in nearly real-time.acceptedVersio

Determining the Importance of Macro and Trace Dietary Minerals on Growth and Nutrient Retention in Juvenile Penaeus monodon

Twelve minerals were screened to identify key dietary minerals important for Penaeus monodon growth. The minerals selected included boron, calcium plus phosphorus (assessed in tandem at a 1:1 ratio), cobalt, copper, magnesium, manganese, potassium, selenium, sodium, strontium and zinc. Twelve purified casein/gelatin-based diets were formulated and contained minerals at two levels: below expected requirements, as attributed by the basal formulation (-) and above expected requirements by adding inorganic minerals (+). The two levels were allocated to dietary treatments in juvenile prawns in accordance with the PB design. A two-level screening analysis was employed where effect of each mineral at level - or + across twelve diets were compared to identify the minerals of importance for culture performance of juvenile prawns. Calcium plus phosphorus (at a 1:1 ratio), magnesium, boron, manganese, selenium and zinc produced the greatest positive effects on weight gain, feed conversion efficiency, biomass gain and nutrient/energy retention. Particularly, boron and manganese significantly increased retention of key macronutrients and energy including gross energy, crude protein and crude lipid. Our study demonstrates the importance of several macro and trace minerals in prawn diets and the pressing need to refine their requirements for P. monodon

Effects of phytase inclusions in diets containing ground wheat or 12.5% whole wheat (pre- and post-pellet) and phytase and protease additions, individually and in combination, to diets containing 12.5% pre-pellet whole wheat on the performance of broiler chickens

Each of eight dietary treatments was offered to seven replicates (six birds per cage) of male Ross 308 chicks from 7 to 28 days post-hatch. The diets contained 741 g/kg wheat incorporated as ground (3.2 mm hammer-mill screen) wheat or 125 g/kg whole wheat included in diets, either pre- or post-pelleting. In Experiment 1 of the study, ground grain, pre-pellet and post-pellet whole grain diets were offered with and without phytase as a 3 × 2 factorial array of treatments. The effects of dietary treatments on gizzard and pancreas weights, bone mineralisation, excreta dry matter, growth performance, nutrient utilisation, digestibility coefficients and disappearance rates of starch and protein (N) in four small intestinal segments were determined. Post-pellet whole grain addition significantly increased gizzard weight by 12.5% (18.17 versus 16.15 g/kg;

The interactions of exogenous phytase with whole grain feeding and effects of barley as the whole grain component in broiler diets based on wheat, sorghum and wheat-sorghum blends

The objectives of this experiment were two-fold; the first was to evaluate exogenous phytase in either conventional or whole grain diets as a 2 × 2 factorial treatment array. Wheat-sorghum blended rations containing 12.5% ground or whole barley were offered without and with 1000 FTU/kg exogenous phytase. The second objective was to evaluate barley as the whole grain component in diets based on wheat, sorghum and equal wheat-sorghum blends as a 3 × 2 factorial treatment array. Rations based on wheat, sorghum and wheat-sorghum blends were offered as an intact pellet containing 12.5% ground barley or offered as a mix of 12.5% whole barley and a pelleted concentrate. Each of the dietary treatments was offered to 7 replicates (6 birds per cage) of male Ross 308 chicks from 7 to 28 days post-hatch. Treatment effects on growth performance, gizzard and pancreas weights, gizzard pH, bone mineralisation, nutrient utilisation, digestibility coefficients of starch and protein (N) and starch:protein disappearance rate ratios in four small intestinal segments (proximal and distal jejunum, proximal and distal ileum), excreta dry matter and incidence of dilated proventriculi were determined. In the 2 × 2 analysis there was a significant (

Mineral nutrition in penaeid shrimp

This review summarises the current knowledge of mineral nutrition for penaeid shrimp. It investigates how the aquatic environment and the lifecycle of shrimp affect requirements and the role that minerals play in shrimp health. Methods of supplying minerals via either water or to feed, and novel ways of supplementing minerals within feed, are discussed. The requirements for individual minerals are summarised with recommendations for minimum levels of dietary inclusion for semi-intensive and intensive commercial shrimp culture presented where data permits. Estimates of dietary requirement remain broad for most minerals for the main shrimp production species (Penaeus vannamei, Penaeus monodon and Penaeus japonicus), with some essential minerals remaining unstudied (Table 2 in Section 5.10). Mineral nutrition will become more important as intensification and diversification of production systems provide new challenges to shrimp aquaculture.</p

Grain Sorghum: A Conundrum for Chicken-Meat Production

The inclusion of grain sorghum in diets for broiler chickens is quite common; however, under Australian conditions, the utilisation of starch/energy by birds offered sorghum-based diets appears inadequate. Various factors inherent in sorghum, including kafirin, phenolic compounds and phytate, may limit energy utilisation. The recent quantification of kafirin, the dominant protein fraction in sorghum, has allowed its nutritional significance to be assessed. This is important as indirect evidence suggests that kafirin concentrations in local sorghums are increasing as an unintended consequence of breeding programs. Presently, Australian sorghums do not contain condensed tannin but, from analyses and assessments of other polyphenolic compounds and phenolic acids, “non-tannin” phenols appear to be negative influences. Anecdotally, white sorghums are considered to be superior to red varieties thus the fact that polyphenolic pigments are responsible for the “redness” of sorghum assumes relevance. Inclusions of sulphite reducing agents in broiler diets have generated promising responses but seem dependent on sorghum properties. Preliminary studies have shown the possibilities of using rapid visco-analyser (RVA) starch pasting profiles, promatest protein solubilities and grain textures to indicate sorghum quality and further studies are required to confirm these hypotheses. These assessments may indicate which sorghums will best respond to reducing agents such as sodium metabisulphite. Finally, the usually modest responses of broilers to exogenous feed enzyme inclusions in sorghum-based are considered in this review

Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam

Background: Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. Results: The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. Conclusions: Some of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development

A Randomised Controlled Trial Assessing the Effect of Oral Diazepam on F-18-FDG Uptake in the Neck and Upper Chest Region

A distinctive pattern of physiological symmetrical uptake of F-18-fluorodeoxyglucose (F-18-FDG) in the neck and upper chest region is a phenomenon that is sometimes observed on positron emission tomography (PET) scans of some oncologic patients. Initially, it was assumed to be muscle uptake secondary to patient anxiety or tension, which could be prevented by diazepam treatment. However, PET-computed tomography data have shown that F-18-FDG uptake is not restricted to the musculature but is also localised within the non-muscular soft tissue, such as brown adipose tissue. The efficacy of benzodiazepine treatment to reduce this uptake has not been well established. Therefore, a randomised controlled trial was conducted to decide whether diazepam would decrease physiological F-18-FDG uptake in the neck and upper chest region (FDG-NUC). A randomised, double-blind, placebo-controlled trial was conducted to assess the effect on FDG-NUC of 5 mg diazepam, given orally 1 h before F-18-FDG injection. Patients younger than 40 years, having or suspected to have a malignancy, were eligible for inclusion. The primary endpoint was FDG-NUC, as assessed by visual analysis of whole-body PET scans by two independent observers. The secondary endpoint was clinical relevance of FDG-NUC. Fifty-two patients were included between September 2003 and January 2005. Twenty-eight patients (54%) received placebo; 24 (46%) received diazepam. FDG-NUC was seen in 25% of the patients in the diazepam group versus 29% in the placebo group. This difference was not statistically significant. No beneficial effect of administration of diazepam could be established. Pre-medication with benzodiazepines to diminish physiological uptake of F-18-FDG in the neck and upper chest region is not indicate

Functional outcome and muscle wasting in adults with tetanus.

BACKGROUND: In many countries, in-hospital survival from tetanus is increasing, but long-term outcome is unknown. In high-income settings, critical illness is associated with muscle wasting and poor functional outcome, but there are few data from resource-limited settings. In this study we aimed to assess muscle wasting and long-term functional outcome in adults with tetanus. METHODS: In a prospective observational study involving 80 adults with tetanus, sequential rectus femoris ultrasound measurements were made at admission, 7 days, 14 days and hospital discharge. Functional outcome was assessed at hospital discharge using the Timed Up and Go test, Clinical Frailty Score, Barthel Index and RAND 36-item Short Form Health Survey (SF-36) and 3 and 6 months after discharge using the SF-36 and Barthel Index. RESULTS: Significant muscle wasting occurred between hospital admission and discharge (p70 y of age, functional recovery at 6 months was reduced compared with younger patients. Hospital-acquired infection and age were risk factors for muscle wasting. CONCLUSIONS: Significant muscle wasting during hospitalization occurred in patients with tetanus, the extent of which correlates with functional outcome