Aminoterminal amphipathic α-helix AH1 of hepatitis C virus nonstructural protein 4B possesses a dual role in RNA replication and virus production.

Nonstructural protein 4B (NS4B) is a key organizer of hepatitis C virus (HCV) replication complex formation. In concert with other nonstructural proteins, it induces a specific membrane rearrangement, designated as membranous web, which serves as a scaffold for the HCV replicase. The N-terminal part of NS4B comprises a predicted and a structurally resolved amphipathic α-helix, designated as AH1 and AH2, respectively. Here, we report a detailed structure-function analysis of NS4B AH1. Circular dichroism and nuclear magnetic resonance structural analyses revealed that AH1 folds into an amphipathic α-helix extending from NS4B amino acid 4 to 32, with positively charged residues flanking the helix. These residues are conserved among hepaciviruses. Mutagenesis and selection of pseudorevertants revealed an important role of these residues in RNA replication by affecting the biogenesis of double-membrane vesicles making up the membranous web. Moreover, alanine substitution of conserved acidic residues on the hydrophilic side of the helix reduced infectivity without significantly affecting RNA replication, indicating that AH1 is also involved in virus production. Selective membrane permeabilization and immunofluorescence microscopy analyses of a functional replicon harboring an epitope tag between NS4B AH1 and AH2 revealed a dual membrane topology of the N-terminal part of NS4B during HCV RNA replication. Luminal translocation was unaffected by the mutations introduced into AH1, but was abrogated by mutations introduced into AH2. In conclusion, our study reports the three-dimensional structure of AH1 from HCV NS4B, and highlights the importance of positively charged amino acid residues flanking this amphipathic α-helix in membranous web formation and RNA replication. In addition, we demonstrate that AH1 possesses a dual role in RNA replication and virus production, potentially governed by different topologies of the N-terminal part of NS4B.

Circadian glomerular function: from physiology to molecular and therapeutical aspects.

Life on earth is rhythmic by essence due to day/night alternation, and many biological processes are also cyclic. The kidney has a special role in the organism, controlling electrolytes and water balance, blood pressure, elimination of metabolic waste and xenobiotics and the production of several hormones. The kidney is submitted to changes throughout 24 h with periods of intense activity followed by calmer periods. Filtration, reabsorption and secretion are the three components determining renal function. Here, we review circadian changes related to glomerular function and proteinuria and emphasize the role of the clock in these processes.

A gain-of-function allele of TPC1 activates oxylipin biogenesis after leaf wounding in Arabidopsis.

Jasmonates, potent lipid mediators of defense gene expression in plants, are rapidly synthesized in response to wounding. These lipid mediators also stimulate their own production via a positive feedback circuit, which depends on both JA synthesis and JA signaling. To date, molecular components regulating the activation of jasmonate biogenesis and its feedback loop have been poorly characterized. We employed a genetic screen capable of detecting the misregulated activity of 13-lipoxygenase, which operates at the entry point of the jasmonate biosynthesis pathway. Leaf extracts from the Arabidopsis fou2 (fatty acid oxygenation upregulated 2) mutant displayed an increased capacity to catalyze the synthesis of lipoxygenase (LOX) metabolites. Quantitative oxylipin analysis identified less than twofold increased jasmonate levels in healthy fou2 leaves compared to wild-type; however, wounded fou2 leaves strongly increased jasmonate biogenesis compared to wounded wild-type. Furthermore, the plants displayed enhanced resistance to the fungus Botrytis cinerea. Higher than wild-type LOX activity and enhanced resistance in the fou2 mutant depend fully on a functional jasmonate response pathway. The fou2 mutant carries a missense mutation in the putative voltage sensor of the Two Pore Channel 1 gene (TPC1), which encodes a Ca(2+)-permeant non-selective cation channel. Patch-clamp analysis of fou2 vacuolar membranes showed faster time-dependent conductivity and activation of the mutated channel at lower membrane potentials than wild-type. The results indicate that cation fluxes exert strong control over the positive feedback loop whereby JA stimulates its own synthesis.

Pasture characteristics of Italian ryegrass and milk production under different management strategies

The objective of this work was to assess the effects of the sward structure of Italian ryegrass (Lolium multiflorum), during the first grazing cycle, on its morphological and bromatological characteristics throughout the growing season, and on the performance of dairy cows. The treatments consisted of two structures obtained as a function of canopy-light interception: high-light interception (HLI) and low-light interception (LLI), with different pre-grazing heights in the first grazing cycle. Pasture was managed under rotational grazing with a herbage allowance not below 30 kg dry matter (DM) per cow per day. Three grazing cycles, with a grazing interval of 30 days, were evaluated. Pre-grazing herbage mass was greater (2,240 vs. 1,656 kg ha-1 DM), but the proportion of leaf blades was smaller (0.35 vs. 0.43) for HLI swards. Neutral detergent fiber (NDF) content and organic matter digestibility (OMD) were similar between treatments in the first grazing cycle, but in the second and third ones NDF was greater, and OMD lower, for the HLI swards. Milk yields were greater for cows grazing LLI swards (19.4 vs. 21.1 kg per day). Initial grazing with 90% of light interception promotes greater nutritional value in the subsequent cycles.

Local optima networks of hard combinatorial landscapes

Combinatorial optimization involves finding an optimal solution in a finite set of options; many everyday life problems are of this kind. However, the number of options grows exponentially with the size of the problem, such that an exhaustive search for the best solution is practically infeasible beyond a certain problem size. When efficient algorithms are not available, a practical approach to obtain an approximate solution to the problem at hand, is to start with an educated guess and gradually refine it until we have a good-enough solution. Roughly speaking, this is how local search heuristics work. These stochastic algorithms navigate the problem search space by iteratively turning the current solution into new candidate solutions, guiding the search towards better solutions. The search performance, therefore, depends on structural aspects of the search space, which in turn depend on the move operator being used to modify solutions. A common way to characterize the search space of a problem is through the study of its fitness landscape, a mathematical object comprising the space of all possible solutions, their value with respect to the optimization objective, and a relationship of neighborhood defined by the move operator. The landscape metaphor is used to explain the search dynamics as a sort of potential function. The concept is indeed similar to that of potential energy surfaces in physical chemistry. Borrowing ideas from that field, we propose to extend to combinatorial landscapes the notion of the inherent network formed by energy minima in energy landscapes. In our case, energy minima are the local optima of the combinatorial problem, and we explore several definitions for the network edges. At first, we perform an exhaustive sampling of local optima basins of attraction, and define weighted transitions between basins by accounting for all the possible ways of crossing the basins frontier via one random move. Then, we reduce the computational burden by only counting the chances of escaping a given basin via random kick moves that start at the local optimum. Finally, we approximate network edges from the search trajectory of simple search heuristics, mining the frequency and inter-arrival time with which the heuristic visits local optima. Through these methodologies, we build a weighted directed graph that provides a synthetic view of the whole landscape, and that we can characterize using the tools of complex networks science. We argue that the network characterization can advance our understanding of the structural and dynamical properties of hard combinatorial landscapes. We apply our approach to prototypical problems such as the Quadratic Assignment Problem, the NK model of rugged landscapes, and the Permutation Flow-shop Scheduling Problem. We show that some network metrics can differentiate problem classes, correlate with problem non-linearity, and predict problem hardness as measured from the performances of trajectory-based local search heuristics.

Random regression models to estimate genetic parameters for milk production of Guzerat cows using orthogonal Legendre polynomials

The objective of this work was to compare random regression models for the estimation of genetic parameters for Guzerat milk production, using orthogonal Legendre polynomials. Records (20,524) of test-day milk yield (TDMY) from 2,816 first-lactation Guzerat cows were used. TDMY grouped into 10-monthly classes were analyzed for additive genetic effect and for environmental and residual permanent effects (random effects), whereas the contemporary group, calving age (linear and quadratic effects) and mean lactation curve were analized as fixed effects. Trajectories for the additive genetic and permanent environmental effects were modeled by means of a covariance function employing orthogonal Legendre polynomials ranging from the second to the fifth order. Residual variances were considered in one, four, six, or ten variance classes. The best model had six residual variance classes. The heritability estimates for the TDMY records varied from 0.19 to 0.32. The random regression model that used a second-order Legendre polynomial for the additive genetic effect, and a fifth-order polynomial for the permanent environmental effect is adequate for comparison by the main employed criteria. The model with a second-order Legendre polynomial for the additive genetic effect, and that with a fourth-order for the permanent environmental effect could also be employed in these analyses.

TSLP promotes influenza-specific CD8+ T-cell responses by augmenting local inflammatory dendritic cell function.

Thymic stromal lymphopoietin (TSLP) is a mucosal tissue-associated cytokine that has been widely studied in the context of T helper type 2 (Th2)-driven inflammatory disorders. Although TSLP is also produced upon viral infection in vitro, the role of TSLP in antiviral immunity is unknown. In this study we report a novel role for TSLP in promoting viral clearance and virus-specific CD8+ T-cell responses during influenza A infection. Comparing the immune responses of wild-type and TSLP receptor (TSLPR)-deficient mice, we show that TSLP was required for the expansion and activation of virus-specific effector CD8+ T cells in the lung, but not the lymph node. The mechanism involved TSLPR signaling on newly recruited CD11b+ inflammatory dendritic cells (DCs) that acted to enhance interleukin-15 production and expression of the costimulatory molecule CD70. Taken together, these data highlight the pleiotropic activities of TSLP and provide evidence for its beneficial role in antiviral immunity.

In conditions of limited chromophore supply rods entrap 11-cis-retinal leading to loss of cone function and cell death.

RPE65 is a retinoid isomerase required for the production of 11-cis-retinal, the chromophore of both cone and rod visual pigments. We recently established an R91W knock-in mouse strain as homologous animal model for patients afflicted by this mutation in RPE65. These mice have impaired vision and can only synthesize minute amounts of 11-cis-retinal. Here, we investigated the consequences of this chromophore insufficiency on cone function and pathophysiology. We found that the R91W mutation caused cone opsin mislocalization and progressive geographic cone atrophy. Remnant visual function was mostly mediated by rods. Ablation of rod opsin corrected the localization of cone opsin and improved cone retinal function. Thus, our analyses indicate that under conditions of limited chromophore supply rods and cones compete for 11-cis-retinal that derives from regeneration pathway(s) which are reliant on RPE65. Due to their higher number and the instability of cone opsin, rods are privileged under this condition while cones suffer chromophore deficiency and degenerate. These findings reinforce the notion that in patients any effective gene therapy with RPE65 needs to target the cone-rich macula directly to locally restore the cones' chromophore supply outside the reach of rods.

Origins of production errors and significance of employee empowerment in reducing production error amount in sheet metal fabricating industry

The market place of the twenty-first century will demand that manufacturing assumes a crucial role in a new competitive field. Two potential resources in the area of manufacturing are advanced manufacturing technology (AMT) and empowered employees. Surveys in Finland have shown the need to invest in the new AMT in the Finnish sheet metal industry in the 1990's. In this run the focus has been on hard technology and less attention is paid to the utilization of human resources. In manymanufacturing companies an appreciable portion of the profit within reach is wasted due to poor quality of planning and workmanship. The production flow production error distribution of the sheet metal part based constructions is inspectedin this thesis. The objective of the thesis is to analyze the origins of production errors in the production flow of sheet metal based constructions. Also the employee empowerment is investigated in theory and the meaning of the employee empowerment in reducing the overall production error amount is discussed in this thesis. This study is most relevant to the sheet metal part fabricating industrywhich produces sheet metal part based constructions for electronics and telecommunication industry. This study concentrates on the manufacturing function of a company and is based on a field study carried out in five Finnish case factories. In each studied case factory the most delicate work phases for production errors were detected. It can be assumed that most of the production errors are caused in manually operated work phases and in mass production work phases. However, no common theme in collected production error data for production error distribution in the production flow can be found. Most important finding was still that most of the production errors in each case factory studied belong to the 'human activity based errors-category'. This result indicates that most of the problemsin the production flow are related to employees or work organization. Development activities must therefore be focused to the development of employee skills orto the development of work organization. Employee empowerment gives the right tools and methods to achieve this.

V0 production in p+A collisions at √s = 41.6 GeV

Inclusive doubly differential cross sections d 2 σ pA /dx F   dp T 2 as a function of Feynman-x (x F ) and transverse momentum (p T ) for the production of K S 0 , Λ and Λ¯ in proton-nucleus interactions at 920 GeV are presented. The measurements were performed by HERA-B in the negative x F range (−0.12production cross sections are presented and discussed. The Cronin effect is clearly observed for all three V 0 species. The atomic number dependence is parameterized as σ pA =σ pN ⋅A α where σ pN is the proton-nucleon cross section. The measured values of α are all near one. The results are compared with EPOS 1.67 and PYTHIA 6.3. EPOS reproduces the data to within ≈20% except at very low transverse momentum.

Using time and stochastic models for software reliability forecasting and analysis

Tämä työ luo katsauksen ajallisiin ja stokastisiin ohjelmien luotettavuus malleihin sekä tutkii muutamia malleja käytännössä. Työn teoriaosuus sisältää ohjelmien luotettavuuden kuvauksessa ja arvioinnissa käytetyt keskeiset määritelmät ja metriikan sekä varsinaiset mallien kuvaukset. Työssä esitellään kaksi ohjelmien luotettavuusryhmää. Ensimmäinen ryhmä ovat riskiin perustuvat mallit. Toinen ryhmä käsittää virheiden ”kylvöön” ja merkitsevyyteen perustuvat mallit. Työn empiirinen osa sisältää kokeiden kuvaukset ja tulokset. Kokeet suoritettiin käyttämällä kolmea ensimmäiseen ryhmään kuuluvaa mallia: Jelinski-Moranda mallia, ensimmäistä geometrista mallia sekä yksinkertaista eksponenttimallia. Kokeiden tarkoituksena oli tutkia, kuinka syötetyn datan distribuutio vaikuttaa mallien toimivuuteen sekä kuinka herkkiä mallit ovat syötetyn datan määrän muutoksille. Jelinski-Moranda malli osoittautui herkimmäksi distribuutiolle konvergaatio-ongelmien vuoksi, ensimmäinen geometrinen malli herkimmäksi datan määrän muutoksille.

INCLUDING RISK IN ECONOMIC FEASIBILITY ANALYSIS:A STOCHASTIC SIMULATION MODEL FOR BLUEBERRY INVESTMENT DECISIONS IN CHILE

ABSTRACT The traditional method of net present value (NPV) to analyze the economic profitability of an investment (based on a deterministic approach) does not adequately represent the implicit risk associated with different but correlated input variables. Using a stochastic simulation approach for evaluating the profitability of blueberry (Vaccinium corymbosum L.) production in Chile, the objective of this study is to illustrate the complexity of including risk in economic feasibility analysis when the project is subject to several but correlated risks. The results of the simulation analysis suggest that the non-inclusion of the intratemporal correlation between input variables underestimate the risk associated with investment decisions. The methodological contribution of this study illustrates the complexity of the interrelationships between uncertain variables and their impact on the convenience of carrying out this type of business in Chile. The steps for the analysis of economic viability were: First, adjusted probability distributions for stochastic input variables (SIV) were simulated and validated. Second, the random values of SIV were used to calculate random values of variables such as production, revenues, costs, depreciation, taxes and net cash flows. Third, the complete stochastic model was simulated with 10,000 iterations using random values for SIV. This result gave information to estimate the probability distributions of the stochastic output variables (SOV) such as the net present value, internal rate of return, value at risk, average cost of production, contribution margin and return on capital. Fourth, the complete stochastic model simulation results were used to analyze alternative scenarios and provide the results to decision makers in the form of probabilities, probability distributions, and for the SOV probabilistic forecasts. The main conclusion shown that this project is a profitable alternative investment in fruit trees in Chile.

Monotonic continuous-time random walks with drift and stochastic reset events

In this paper we consider a stochastic process that may experience random reset events which suddenly bring the system to the starting value and analyze the relevant statistical magnitudes. We focus our attention on monotonic continuous-time random walks with a constant drift: The process increases between the reset events, either by the effect of the random jumps, or by the action of the deterministic drift. As a result of all these combined factors interesting properties emerge, like the existence (for any drift strength) of a stationary transition probability density function, or the faculty of the model to reproduce power-law-like behavior. General formulas for two extreme statistics, the survival probability, and the mean exit time, are also derived. To corroborate in an independent way the results of the paper, Monte Carlo methods were used. These numerical estimations are in full agreement with the analytical predictions.

Skeletal Muscle Mitochondrial Function and Fatigability in Older Adults.

BACKGROUND: Fatigability increases while the capacity for mitochondrial energy production tends to decrease significantly with age. Thus, diminished mitochondrial function may contribute to higher levels of fatigability in older adults. METHODS: The relationship between fatigability and skeletal muscle mitochondrial function was examined in 30 participants aged 78.5 ± 5.0 years (47% female, 93% white), with a body mass index of 25.9 ± 2.7 kg/m(2) and usual gait-speed of 1.2 ± 0.2 m/s. Fatigability was defined using rating of perceived exertion (6-20 point Borg scale) after a 5-minute treadmill walk at 0.72 m/s. Phosphocreatine recovery in the quadriceps was measured using (31)P magnetic resonance spectroscopy and images of the quadriceps were captured to calculate quadriceps volume. ATPmax (mM ATP/s) and oxidative capacity of the quadriceps (ATPmax·Quadriceps volume) were calculated. Peak aerobic capacity (VO2peak) was measured using a modified Balke protocol. RESULTS: ATPmax·Quadriceps volume was associated with VO2peak and was 162.61mM ATP·mL/s lower (p = .03) in those with high (rating of perceived exertion ≥10) versus low (rating of perceived exertion ≤9) fatigability. Participants with high fatigability required a significantly higher proportion of VO2peak to walk at 0.72 m/s compared with those with low fatigability (58.7 ± 19.4% vs 44.9 ± 13.2%, p < .05). After adjustment for age and sex, higher ATPmax was associated with lower odds of having high fatigability (odds ratio: 0.34, 95% CI: 0.11-1.01, p = .05). CONCLUSIONS: Lower capacity for oxidative phosphorylation in the quadriceps, perhaps by contributing to lower VO2peak, is associated with higher fatigability in older adults.

Neck Muscle Function and Adolescent Headache

Muscular function of the neck region may be of importance for the etiology of headache, especially of tension-type headache. However, very few data exist on the association of neck muscle function with different types of headache in adolescents. The main aim of the study was to examine the association of neck muscle function with adolescent headache. The associations between leisure time activities, endurance strength of the upper extremities (UE endurance) and mobility of the neck-shoulder region and adolescent headache were studied. In addition, the associations of force production, EMG/force ratio, co-activation and fatigue characteristics, and cross-sectional area (CSA) of neck muscles with adolescent headache were studied. The study is part of a population-based cohort study of 12-year-old children with and without headache. The study had five phases (years 1998-2003). At the age of 13 years, a sample of 183 adolescents (183/311) participated in endurance strength and mobility measurements of the neck-shoulder region. In addition, the type and level of physical and other leisure activity were elicited with open and structured questions. At the age of 17 years, a random sample of 89 adolescents (89/202) participated in force and EMG measurements of the neck-shoulder muscles. In addition, at the age of 17 years, a sample of 65 adolescents (65/89) participated in CSA measurements of the neck muscles. At the age of 13 years, intensive participation in overall sports activity was associated with migraine. Frequent computer use was associated both with migraine and tension-type headache. The type of sports or other leisure activity classified them on the basis of body loading was not associated with headache type. In girls, low UE endurance of both sides, and low cervical rotation of the dominant side, were associated with tension-type headache, and low UE endurance of non-dominant side with migraine. In boys, no associations occurred between UE endurance and mobility variables and headache types. At the age of 17 years, in girls, high EMG/force ratios between the EMG of the left agonist sternocleidomastoid muscle (SCM) and maximal neck flexion and neck rotation force to the right side as well as high co-activation of right antagonist cervical erector spinae (CES) muscles during maximal neck flexion force were associated with migraine-type headache. In girls, neck force production was not associated with headache types but low left shoulder flexion force was associated with tension-type headache. In boys, no associations were found between EMG and force variables and headache. Increased SCM muscles fatigue of both sides was associated with tension-type headache. In boys, the small CSA of the right SCM muscle and, in girls, of combined right SCM and scalenus muscles was associated with tension-type headache. Similarly, in boys, the large CSA of the right SCM muscle, of the combined right SCM and scalenus muscles, of the left semispinalis capitis muscle, of the combined left semispinalis and splenius muscles was associated with migraine. No other differences in the CSA of neck flexion or extension muscles were found. Differences in the neuromucular function of the neck-shoulder muscles were associated with adolescent headache, especially in girls. Differences in the cross-sectional area of unilateral neck muscles were associated with headache, especially in boys. Differences in the neuromuscular function and in the cross-sectional area of the neck muscles also occurred between different types of headache. It remains to be established whether the findings are primary or secondary to adolescent migraine and tension headache. Keywords: adolescent, cross-sectional area, electromyography, endurance strength, fatigue, force, headache, leisure time activity, migraine, mobility, neck muscles, tension-type headache