We present an analysis of the MUSIC-2 /V-body/hydrodynamical simulations aimed at estimating the expected concentration-mass relation for the CLASH (Cluster Lensing and Supernova Survey with Hubble) ...cluster sample. We study nearly 1,400 halos simulated at high spatial and mass resolution. We study the shape of both their density and surface-density profiles and fit them with a variety of radial functions, including the Navarro-Frenk-White (NEW), the generalized NEW, and the Einasto density profiles. We derive concentrations and masses from these fits. We produce simulated Chandra observations of the halos, and we use them to identify objects resembling the X-ray morphologies and masses of the clusters in the CLASH X-ray-selected sample. We also derive a concentration-mass relation for strong-lensing clusters. We find that the sample of simulated halos that resembles the X-ray morphology of the CLASH clusters is composed mainly of relaxed halos, but it also contains a significant fraction of unrelaxed systems. For such a heterogeneous sample we measure an average two-dimensional concentration that is ~11% higher than is found for the full sample of simulated halos. After accounting for projection and selection effects, the average NEW concentrations of CLASH clusters are expected to be intermediate between those predicted in three dimensions for relaxed and super-relaxed halos. Matching the simulations to the individual CLASH clusters on the basis of the X-ray morphology, we expect that the NEW concentrations recovered from the lensing analysis of the CLASH clusters are in the range 3-6, with an average value of 3.87 and a standard deviation of 0.61.
Several approaches for miRNA expression analysis have been developed in recent years. In this article, we provide an updated and comprehensive review of available qPCR-based methods for miRNA ...expression analysis and discuss their advantages and disadvantages. Existing techniques involve the use of stem–loop reverse transcriptase–PCR, polyadenylation of RNAs, ligation of adapters or RT with complex primers, using universal or miRNA-specific qPCR primers and/or probes. Many of these methods are oriented towards the expression analysis of mature miRNAs and few are designed for the study of pre-miRNAs and pri-miRNAs. We also discuss findings from articles that compare results from existing methods. Finally, we suggest key points for the improvement of available techniques and for the future development of additional methods.
LTE V2X is the response of the 3GPP standardization body to the high market expectations related to vehicular communications for safety and infotainment services. To fulfill the stringent ...requirements in terms of reliability associated with safety applications, geolocation-based access (GLOC) has been proposed for direct vehicle-to-vehicle (V2V) communication. Such a scheme aims at maximizing the distance of co-channel transmitters (i.e., transmitter that use the same resources) while preserving a low latency when accessing the resources and a low overhead. In this paper, we analyze, with the aid of stochastic geometry, the delivery of periodic and nonperiodic broadcast messages with GLOC, taking into account path loss and fading as well as the random locations of transmitting vehicles. Analytical results include the average interference, average binary rate, capture probability, i.e., the probability of successful message transmission, and energy efficiency (EE). Mathematical analysis reveals interesting insights about the system performance, which are validated through extensive Monte Carlo simulations. In particular, it is shown that the capture probability is an increasing function with exponential dependence with respect to the transmit power and it is demonstrated that an arbitrary high capture probability can be achieved, as long as the number of access resources is high enough. Finally, to facilitate the system-level design of GLOC, it is obtained the optimum transmit power, which fulfill a given minimum capture probability constraint while maximizing the EE of the system.
Life-history theory predicts that populations experiencing different levels of extrinsic mortality will evolve divergent reproductive strategies. Previous work in the live-bearing fish Brachyrhaphis ...rhabdophora shows that individuals from populations that occur with piscivorous fish mature earlier and at smaller sizes and have more and smaller offspring than fish from populations without predators. However, until now, there have been no data to demonstrate that differences in mortality rates actually exist between predator and predator-free sites. Here we present the results of a serial mark-recapture field study designed to estimate mortality rates in natural populations of B. rhabodophora from Costa Rica. We found that fish from predator environments experience higher overall mortality rates and proportionally higher adult mortality rates than fish from predator-free environments. We then ask what impact differences in mortality rates have on B. rhabdophora population dynamics. Using a population matrix modeling approach, we found that B. rhabdophora that co-occur with predator have population growth rates similar to those without predators and both have confidence intervals that span λ = 1.0. However, elasticity analysis revealed that the most important life-history stages for population growth in predator environments are found early in life and include growth through early ontogenetic stages and survival as small adults; in contrast, the most important life-history stages for population growth in predator-free environments occur late in life, including survival once large juvenile and adult stages are reached. Hence, we demonstrate two important links between predation and population demography, one ecological due to the direct impacts of predator-induced mortality and the other expressed through predator-mediated reproductive adaptation.
Two experiments were conducted to determine the effects of phytate, phytase, fiber, and soybean oil on apparent total tract digestibility (ATTD) and standardized total tract digestibility (STTD) of ...Ca and on ATTD of P in fish meal fed to growing pigs. In Exp. 1, 40 growing pigs (initial average BW: 19.16 ± 2.04 kg) were randomly allotted to 1 of 5 diets with 8 pigs per treatment and placed in metabolism crates. Four diets were used in a 2 ´ 2 factorial design with 2 levels of phytate (0 or 0.7%) and 2 levels of microbial phytase (0 or 500 phytase units/kg). The diet containing no phytate was based on sucrose, cornstarch, fish meal, casein, and soybean oil, and the diet containing 0.7% phytate was based on corn, corn germ, fish meal, casein, and soybean oil. A Ca-free diet was used to determine basal endogenous losses of Ca. Feces were collected from d 6 to 13 after a 5-d adaptation period. Results indicated that the ATTD and STTD of Ca in fish meal and the ATTD of P increased ( < 0.001) if phytase was used and were greater ( < 0.05) in the diets based on corn and corn germ. Experiment 2 was conducted to determine the effects of fiber and soybean oil on the ATTD and STTD of Ca and the ATTD of P in fish meal. Fifty growing pigs (initial average BW: 19.36 ± 0.99 kg) were randomly allotted to 1 of 5 diets with 10 pigs per treatment. Two diets contained sucrose, cornstarch, fish meal, casein, and either 0 or 8% of a synthetic source of fiber. Two additional diets contained fish meal, casein, corn, and either 1 or 7% soybean oil. A Ca-free diet was also used. Pigs were housed individually in metabolism crates and fecal samples were collected. Results indicated that fiber increased ( < 0.001) the ATTD and STTD of Ca and the ATTD of P, but the ATTD and STTD of Ca or the ATTD of P were not affected by soybean oil. In agreement with the results of Exp. 1, the ATTD and STTD of Ca and the ATTD of P in the corn-based diet were greater ( < 0.05) than those in the cornstarch-based diet. In conclusion, phytase and fiber increased the ATTD and STTD of Ca and the ATTD of P in fish meal, but inclusion of soybean oil did not affect digestibility of Ca or P. The observation that values for the ATTD and STTD of Ca and ATTD of P are greater in corn-based diets than in cornstarch-based diets indicates that values for the digestibility of Ca and P obtained in cornstarch-based diets may not always be representative for the digestibility in practical corn-based diets.
Ufmylation is the post-translational modification of proteins through the addition of UFM1. Nahorksi et al. identify mutations in UFM1 and in UFC1, which encodes an enzyme required for ufmylation, in ...individuals with severe early-onset encephalopathy with progressive microcephaly. The findings suggest an essential role for ufmylation in human brain development.
Abstract
The post-translational modification of proteins through the addition of UFM1, also known as ufmylation, plays a critical developmental role as revealed by studies in animal models. The recent finding that biallelic mutations in UBA5 (the E1-like enzyme for ufmylation) cause severe early-onset encephalopathy with progressive microcephaly implicates ufmylation in human brain development. More recently, a homozygous UFM1 variant was proposed as a candidate aetiology of severe early-onset encephalopathy with progressive microcephaly. Here, we establish a locus for severe early-onset encephalopathy with progressive microcephaly based on two families, and map the phenotype to a novel homozygous UFM1 mutation. This mutation has a significantly diminished capacity to form thioester intermediates with UBA5 and with UFC1 (the E2-like enzyme for ufmylation), with resulting impaired ufmylation of cellular proteins. Remarkably, in four additional families where eight children have severe early-onset encephalopathy with progressive microcephaly, we identified two biallelic UFC1 mutations, which impair UFM1-UFC1 intermediate formation with resulting widespread reduction of cellular ufmylation, a pattern similar to that observed with UFM1 mutation. The striking resemblance between UFM1- and UFC1-related clinical phenotype and biochemical derangements strongly argues for an essential role for ufmylation in human brain development. The hypomorphic nature of UFM1 and UFC1 mutations and the conspicuous depletion of biallelic null mutations in the components of this pathway in human genome databases suggest that it is necessary for embryonic survival, which is consistent with the embryonic lethal nature of knockout models for the orthologous genes.
In recent years, advances in technology have led to increasingly high-dimensional datasets. This increase of dimensionality along with the presence of irrelevant and redundant features make the ...feature selection process challenging with respect to efficiency and effectiveness. In this context, approximate algorithms are typically applied since they provide good solutions in a reasonable time. On the other hand, feature grouping has arisen as a powerful approach to reduce dimensionality in high-dimensional data. Recently, some authors have focused their attention on developing methods that combine feature grouping and feature selection to improve the model. In this paper, we propose a feature selection strategy that utilizes feature grouping to increase the effectiveness of the search. As feature selection strategy, we propose a Variable Neighborhood Search (VNS) metaheuristic. Then, we propose to group the input space into subsets of features by using the concept of Markov blankets. To the best of our knowledge, this is the first time in which the Markov blanket is used for grouping features. We test the performance of VNS by conducting experiments on several high-dimensional datasets from two different domains: microarray and text mining. We compare VNS with popular and competitive techniques. Results show that VNS is a competitive strategy capable of finding a small size of features with similar predictive power than that obtained with other algorithms used in this study.
Two experiments were conducted to determine the requirement for standardized total tract digestible (STTD) Ca by 11- to 25-kg pigs based on growth performance, bone ash, or Ca and P retention and to ...determine the effect of dietary Ca on expression of genes related to Ca transport in the jejunum and kidneys. Six diets were formulated to contain 0.36% STTD P and 0.32, 0.40, 0.48, 0.56, 0.64, or 0.72% STTD Ca by including increasing quantities of calcium carbonate in the diets at the expense of cornstarch. Two additional diets contained 0.72% STTD Ca and 0.33% or 0.40% STTD P to determine if 0.36% STTD P had negative effects on the Ca requirement. The same batch of all diets was used in both experiments. In Exp. 1, 256 pigs (11.39 ± 1.21 kg initial BW) were randomly allotted to the 8 diets with 4 pigs per pen and 8 replicate pens per diet in a randomized complete block design. On the last day of the experiment, 1 pig from each pen was euthanized and the right femur and intestine and kidney samples were collected. Results indicated that ADG and G:F started to decline (linear and quadratic, < 0.05) at 0.54 and 0.50% STTD Ca, respectively. In contrast, bone ash increased (quadratic, < 0.05) as dietary Ca increased and reached a plateau indicating that the requirement for STTD Ca to maximize bone ash was 0.48%. Bone ash, but not ADG or G:F, increased (linear, < 0.01) as STTD increased in the diets. The mRNA expression of genes related to transcellular Ca transport decreased (linear, < 0.01) in the jejunum and in kidneys (linear and quadratic, < 0.01) as dietary Ca increased. In Exp. 2, 80 pigs (13.12 ± 1.79 kg initial BW) were placed in metabolism crates and randomly allotted to the 8 diets with 10 replicate pigs per diet in a randomized complete block design. Fecal and urine samples were collected using the marker-to-marker approach. Results indicated that the requirement for STTD Ca to maximize Ca and P retention (g/d) was 0.60 and 0.49%, respectively. In conclusion, the STTD Ca requirement by 11- to 25-kg pigs to maximize bone ash was 0.48%; however, ADG and G:F declined if more than 0.54 or 0.50% STTD Ca, respectively, was fed, and the minimum concentration of Ca needed to maximize ADG and G:F could not be determined under the conditions of this experiment. Increasing dietary Ca decreased the mRNA expression of several genes related to transcellular Ca transport in the jejunum and the kidneys.
There are clear differences in embryo development between angiosperm and gymnosperm species. Most of the current knowledge on gene expression and regulation during plant embryo development has ...derived from studies on angiosperms species, in particular from the model plant Arabidopsis thaliana. The few published studies on transcript profiling of conifer embryogenesis show the existence of many putative embryo-specific transcripts without an assigned function. In order to extend the knowledge on the transcriptomic expression during conifer embryogenesis, we sequenced the transcriptome of zygotic embryos for several developmental stages that cover most of Pinus pinaster (maritime pine) embryogenesis.
Total RNA samples collected from five zygotic embryo developmental stages were sequenced with Illumina technology. A de novo transcriptome was assembled as no genome sequence is yet published for Pinus pinaster. The transcriptome of reference for the period of zygotic embryogenesis in maritime pine contains 67,429 transcripts, which likely encode 58,527 proteins. The annotation shows a significant percentage, 31%, of predicted proteins exclusively present in pine embryogenesis. Functional categories and enrichment analysis of the differentially expressed transcripts evidenced carbohydrate transport and metabolism over-representation in early embryo stages, as highlighted by the identification of many putative glycoside hydrolases, possibly associated with cell wall modification, and carbohydrate transport transcripts. Moreover, the predominance of chromatin remodelling events was detected in early to middle embryogenesis, associated with an active synthesis of histones and their post-translational modifiers related to increased transcription, as well as silencing of transposons.
Our results extend the understanding of gene expression and regulation during zygotic embryogenesis in conifers and are a valuable resource to support further improvements in somatic embryogenesis for vegetative propagation of conifer species. Specific transcripts associated with carbohydrate metabolism, monosaccharide transport and epigenetic regulation seem to play an important role in pine early embryogenesis and may be a source of reliable molecular markers for early embryogenesis.
Wildfire occurrence is expected to increase in future climate and Land Use Land Cover (LULC) change scenarios, especially in vulnerable areas as the European Mediterranean Basin. In this study future ...probability of wildfire occurrence was estimated for a 20-year time period (2041–2060, centered on 2050) by applying a statistically-based regression model using LULC-derived contact areas with the forest cover (interfaces) as proxy for the human-related factor and a combination of Live Fuel Moisture Content and seasonal climate-related variables as predictors. Future wildfire occurrence was mapped under RCP 8.5 high emissions scenario in four Spanish regions with heterogeneous socioeconomic, LULC and natural fire-related characteristics at 1 km2 target spatial resolution. Results showed increased wildfire probability in ∼19–73% of 1 km2 cells, observing regional differences in the variable effects. This approach could be applied to other spatial scales offering tools for planning and management actions and to obtain different possible future scenarios.
•A modelling framework for estimating future wildfire occurrence in LULC and climate change scenarios is described.•LULC-derived interfaces and a combination of LFMC and seasonal climate-related variables were used as predictors.•Expected changes will mainly increase wildfire occurrence with varied effects by analyzed region.•Future regional wildfire predictions are useful to establish mitigation measures and for planning fire prevention actions.
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