Improving the description of interactions between Ca2+ and protein carboxylate groups, including γ-carboxyglutamic acid: revised CHARMM22∗ parameters

A reliable description of ion pair interactions for biological systems, particularly those involving polyatomic ions such as carboxylate and divalent ions such as Ca²⁺, using biomolecular force-fields is essential for making useful predictions for a range of protein functions. In particular, the interaction of divalent ions with the double carboxylate group present in γ-carboxyglutamic acid (Gla), relevant to the function of many proteins, is relatively understudied using biomolecular force-fields. Using force-field based metadynamics simulations to predict the free energy of binding between Ca²⁺ and the carboxylate group in liquid water, we show that a widely-used biomolecular force-field, CHARMM22∗, substantially over-estimates the binding strength between Ca²⁺ and the side-chains of both glutamic acid (Glu) and Gla, compared with experimental data obtained for the analogous systems of aqueous calcium-acetate and calcium-malonate. To correct for this, we propose and test a range of modifications to the σ value of the heteroatomic Lennard-Jones interaction between Ca²⁺ and the oxygen of the carboxylate group. Our revised parameter set can recover the same three association modes of this aqueous ion pair as the standard parameter set, and yields free energies of binding for the carboxylate-Ca²⁺ interaction in good agreement with experimental data. The revised parameter set recovers other structural properties of the ion pair in agreement with the standard CHARMM22∗ parameter set.

Rapid effects of essential fatty acid deficiency on growth and development parameters and transcription of key fatty acid metabolism genes in juvenile barramundi (Lates calcarifer)

Barramundi (Lates calcarifer), a catadromous teleost of significant and growing commercial importance, are reported to have limited fatty acid bioconversion capability and therefore require preformed long-chain PUFA (LC-PUFA) as dietary essential fatty acid (EFA). In this study, the response of juvenile barramundi (47·0 g/fish initial weight) fed isolipidic and isoenergetic diets with 8·2 % added oil was tested. The experimental test diets were either devoid of fish oil (FO), and thus with no n-3 LC-PUFA (FO FREE diet), or with a low inclusion of FO (FO LOW diet). These were compared against a control diet containing only FO (FO CTRL diet) as the added lipid source, over an 8-week period. Interim samples and measurements were taken fortnightly during the trial in order to define the aetiology of the onset and progression of EFA deficiency. After 2 weeks, the fish fed the FO FREE and FO LOW diets had significantly lower live-weights, and after 8 weeks significant differences were detected for all performance parameters. The fish fed the FO FREE diet also had a significantly higher incidence of external abnormalities. The transcription of several genes involved in fatty acid metabolism was affected after 2 weeks of feeding, showing a rapid nutritional regulation. This experiment documents the aetiology of the onset and the progression of EFA deficiency in juvenile barramundi and demonstrates that such deficiencies can be detected within 2 weeks in juvenile fish.

Sensitivity of the final properties of tailored hot stamping components to the process and material parameters

The final mechanical properties of hot stamped components are affected by many process and material parameters due to the multidisciplinary nature of this thermal-mechanical-metallurgical process. The phase transformation, which depends on the temperature field and history, determines the final microstructure and consequently the final mechanical properties. Tailored hot stamping parts - where the cooling rates are locally chosen to achieve structures with graded properties - has been increasingly adopted in the automotive industry. In this case, the robustness of final part properties is more critical than in the conventional hot stamping parts, where the part is fully quenched. In this study, a wide range of input parameters in a generalized hot stamping model have been investigated, examining the effect on the temperature history and resulting final material properties. A generic thermo-mechanical finite element model of hot stamping was created and a modified phase transformation model, based on Scheil's additive principle, has been applied. The comparison between modeling and experiments shows that the modified phase transformation model coupled with the incubation time provides higher accuracy on the simulation of transformation kinetics history. The robustness of four conditions relevant to tailored hot stamping was investigated: heated tooling (with low and high tool conductance), air cooling, and conventional hot stamping. The results show the high robustness of the conventional hot stamping compared to tailored hot stamping, with respect to the stamped component's final material properties (i.e. phase fraction and hardness). Furthermore, tailored hot stamping showed higher robustness when low conductivity tools are used relative to high conductivity tools.

Research on the influence of yarn parameters on the ultraviolet protection of yarns

Considering both the yarn parameters and the light interaction (reflectance and transmittance) between two adjacent yarns, an optical model was presented to understand the ultraviolet (UV) light penetrating a single undyed yarn and a lot of yarns. The optical model was verified with results of diffuse reflectance spectra measurement on wool yarn samples. This optical model was used to predict the factors influencing UV protection, including fibre diameter, yarn linear density, yarn twist, transmittance index and refractive index. The statistical predictive model was also set up to show the relationship between the yarn parameters and the UV protection (UPF values) of the yarns. Yarns with the fine diameter, large yarn linear density and low yarn twist had the high UV protection.

Determination of Kamlet–Taft parameters for selected solvate ionic liquids

The normalised polarity E and Kamlet-Taft parameters of recently described solvate ionic liquids, composed of lithium bis(trifluoromethyl)sulfonimide (LiTFSI) in tri- () or tetraglyme () have been determined and compared to the parent glyme ( and ). We show that these solvate ionic liquids have a high polarity (, (E) = 1.03; , (E) = 1.03) and display very high electron pair accepting characteristics (, α = 1.32; , α = 1.35). Molecular dynamics simulations suggest that the chelated lithium cation is responsible for this observation. The relatively small hydrogen bond acceptor (β) values for these systems (, β = 0.41; , β = 0.37) are thought to be due primarily to the TFSI anion, which is supplemented slightly by the glyme oxygen atom. In addition, these solvate ionic liquids are found to have a high polarisability (, π* = 0.94; , π* = 0.90).

The influence of various seat design parameters: a computational analysis

Nowadays, low back pain becomes a common healthcare problem. Poor or unsuitable seat design is related to the discomfort and other healthcare problems of users. The aim of this study is to investigate the influence of seat design variables on the compressive loadings of lumbar joints. A basis that includes a musculoskeletal human body model and a chair model has been developed using LifeMOD Biomechanics Modeller. Inverse and forward dynamic simulations have been performed for various seat design parameters. The results show that the inclination of backrest and seat pan may or may not decrease the compressive spinal joint forces, depending on other conditions. The medium-level height and depth of seat pan and the medium-level and high-level height of backrest are found to cause the minimum compressive loads on lumbar joints. This work contributes to a better understanding of sitting biomechanics and provides some useful guidelines for seat design.

Performance Evaluation Of SMOS Soil Moisture Retrieval Parameters For Hydrological Application

Microwave remote sensing has high potential for soil moisture retrieval. However, the efficient retrieval of soil moisture depends on optimally choosing the soil moisture retrieval parameters. In this study first the initial evaluation of SMOS L2 product is performed and then four approaches regarding soil moisture retrieval from SMOS brightness temperature are reported. The radiative transfer equation based tau-omega rationale is used in this study for the soil moisture retrievals. The single channel algorithms (SCA) using H polarisation is implemented with modifications, which includes the effective temperatures simulated from ECMWF (downscaled using WRF-NOAH Land Surface Model (LSM)) and MODIS. The retrieved soil moisture is then utilized for soil moisture deficit (SMD) estimation using empirical relationships with Probability Distributed Model based SMD as a benchmark. The square of correlation during the calibration indicates a value of R2 =0.359 for approach 4 (WRF-NOAH LSM based LST with optimized roughness parameters) followed by the approach 2 (optimized roughness parameters and MODIS based LST) (R2 =0.293), approach 3 (WRF-NOAH LSM based LST with no optimization) (R2 =0.267) and approach 1(MODIS based LST with no optimization) (R2 =0.163). Similarly, during the validation a highest performance is reported by approach 4. The other approaches are also following a similar trend as calibration. All the performances are depicted through Taylor diagram which indicates that the H polarisation using ECMWF based LST is giving a better performance for SMD estimation than the original SMOS L2 products at a catchment scale.

Bounds on policy relevant parameters with discrete policy variation

When estimating policy parameters, also known as treatment effects, the assignment to treatment mechanism almost always causes endogeneity and thus bias many of these policy parameters estimates. Additionally, heterogeneity in program impacts is more likely to be the norm than the exception for most social programs. In situations where these issues are present, the Marginal Treatment Effect (MTE) parameter estimation makes use of an instrument to avoid assignment bias and simultaneously to account for heterogeneous effects throughout individuals. Although this parameter is point identified in the literature, the assumptions required for identification may be strong. Given that, we use weaker assumptions in order to partially identify the MTE, i.e. to stablish a methodology for MTE bounds estimation, implementing it computationally and showing results from Monte Carlo simulations. The partial identification we perfom requires the MTE to be a monotone function over the propensity score, which is a reasonable assumption on several economics' examples, and the simulation results shows it is possible to get informative even in restricted cases where point identification is lost. Additionally, in situations where estimated bounds are not informative and the traditional point identification is lost, we suggest a more generic method to point estimate MTE using the Moore-Penrose Pseudo-Invese Matrix, achieving better results than traditional methods.

Estimates of genetic parameters for visual scores and their correlation with production and reproductive traits in Brahman cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Source populations in coastal crabs: parameters affecting egg production

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Profile of cortisol, glycaemia, and blood parameters of American Bullfrog tadpoles Lithobates catesbeianus exposed to density and hypoxia stressors

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Haematological characteristics of Brazilian Teleosts: III. Parameters of the hybrid tambacu (Piaractus mesopotamicus Holmberg x Colossoma macropomum Cuvier) (Osteichthyes, Characidae)

Fifty six specimens of the hybrid tambacu (Piaractus mesopotamicus Holmberg, 1887 male x Colossoma macropomum Cuvier, 1818 female) were collected from fishfarm of Guariba, São Paulo, to evaluate their haematology. Fishes presented 400.0 to 3,100.0 g total weight and 20.0 to 52.0 cm total length. Haemoglobin, haematocrit, mean corpuscular haemoglobin content (MCHC) and percentage of defense blood cells including leucocytes and thrombocytes, were studied. Statistical analysis showed positive correlation (P<0.01) between haematocrit, MCHC and haemoglobin rate. Nevertheless, thrombocytes and lymphocytes showed negative correlation (P<0.01).

Estimates of genetic parameters for visual scores and daily weight gain in Brangus animals

(Co) variance components were estimated for visual scores of conformation (CY), early finishing (PY) and muscling (MY) at 550 days of age (yearling), average daily gain from weaning to yearling (GWY), conformation (CW), early finishing (PW) and muscling (MW) scores at weaning, and average daily gain from birth to weaning (GBW) in animals forming the Brazilian Brangus breed born between 1986 and 2002 from the livestock files of GenSys Consultants Associados S/C Ltda. The data set contained 53 683; 45 136; 52 937; 56 471; 24 531; 21 166; 24 006 and 25 419 records for CW, PW, MW, GBW, CY, PY, MY and GWY, respectively. Data were analyzed by the restricted maximum likelihood method using single-and two-trait animal models. Direct heritability estimates obtained by single-trait analysis were 0.12, 0.14, 0.13 and 0.14 for CY, PY and MY scores and GWY, respectively. A positive association was observed between the same visual scores at weaning and yearling, with correlations ranging from 0.64 to 0.94. Estimated correlations between GBW and weaning and yearling scores ranged from 0.60 to 0.77. The genetic correlation between GBW and GWY was low (0.10), whereas correlations of 0.55, 0.37 and 0.47 were observed between GWY and CY, PY and MY, respectively. Moreover, GWY showed a weak correlation with CW (0.10), PW (-0.08) and MW (-0.03) scores. These results indicate that selection of the traits that was studied would result in a small response. In addition, selection based on average daily gain may have an indirect effect on visual scores as the correlations between GWY and visual scores were generally strong.

Effect of crude protein levels and organic selenium supplementation in the diets fed during the breeding season on reproductive parameters of red-winged tinamous (Rhynchotus rufescens)

There is little information on the nutrition of red-winged tinamous (Rhynchotus rufescens) reared in captivity, and their nutritional requirements still need to be determined. This study aimed at determining dietary crude protein requirements and testing four organic selenium supplementation levels in the diet of red-winged tinamous during the breeding season. Birds were housed in a conventional broiler house divided in 16 boxes with one male and three females each. Iso-energy (2800kcal ME/kg) pelleted feeds, based on corn and soybean meal, were supplied in tube feeders. In the first experiment, treatments consisted of four different diets containing different crude protein (CP) contents (15, 18, 21, or 24%) and in the second experiment, the four diets contained equal protein level (22.5%) and four different organic selenium levels (0, 0.2, 0.4, or 0.8ppm). Data were analyzed by the least square method. The best egg weight and eggshell thickness were obtained with 22.5% dietary CP. Organic selenium did not influence the studied reproductive traits of red-winged tinamous (Rhynchotus rufescens) males or females.