Grazing incidence fast atom diffraction: general considerations, semiclassical perturbation theory and experimental implications.

Using semiclassical methods, an analytical approach to describe grazing incidence scattering of fast atoms (GIFAD) from surfaces is described. First, we consider a model with a surface corrugated in the scattering plane, which includes the surface normal and the incidence direction. The treatment uses a realistic, Morse potential, within a perturbation approach, and correctly reproduces the basic GIFAD phenomenology, whereby the scattering is directed primarily in the specular direction. Second, we treat the more general case of scattering from a surface corrugated in two-dimensions. Using time averaging along the direction of fast motion in the incidence direction, we derive a time dependent potential for the GIFAD scattering away from a low index direction. The results correctly describe the observation that diffraction is seen only when the scattering plane is aligned close to a low-index direction in the surface plane. For the case of helium scattering from LiF(001) we demonstrate that the resulting theoretical predictions agree well with experiment and show that the analysis provides new information on the scattering time and the length scale of the interaction. The analysis also gives insights into the validity of the axial surface channeling approximation (ASCA) and shows that within first order perturbation theory, along a low-index direction, the full 3-dimensional problem can be represented accurately by an equivalent 2-dimensional problem with a potential averaged along the third dimension. In contrast, away from low-index directions, the effective 2-dimensional potential in the projectile frame is time-dependent.

Reply to the 'Comment on "Perturbation theory of scattering for grazing-incidence fast-atom diffraction"' by G. A. Bocan, H. Breiss, S. Szilasi, A. Momeni, E. M. S. Casagrande, E. A. Sánchez, M. S. Gravielle and H. Khemliche, Phys. Chem. Chem. Phys., 2023, 25, DOI: 10.1039/D3CP02486E.

In this Reply, we show that criticisms of perturbation theory for grazing-incidence fast-atom diffraction (GIFAD) are ill-founded. We show explicitly that our formulation (W. Allison, S. Miret-Artés and E. Pollak, Phys. Chem. Chem. Phys., 2022, 24, 15851) provides a similar precision in describing the observed phenomena as ab initio potentials. Since that is the main criterion to distinguish between methods, it seems reasonable to conclude that the perturbation approach using a Morse-type potential reproduces the essential aspects of the dynamics correctly. In addition we expand on the historical context and summarize the physical insights provided by our methods.

Comparison of Bayesian models to estimate direct genomic values in multi-breed commercial beef cattle.

BACKGROUND: While several studies have examined the accuracy of direct genomic breeding values (DGV) within and across purebred cattle populations, the accuracy of DGV in crossbred or multi-breed cattle populations has been less well examined. Interest in the use of genomic tools for both selection and management has increased within the hybrid seedstock and commercial cattle sectors and research is needed to determine their efficacy. We predicted DGV for six traits using training populations of various sizes and alternative Bayesian models for a population of 3240 crossbred animals. Our objective was to compare alternate models with different assumptions regarding the distributions of single nucleotide polymorphism (SNP) effects to determine the optimal model for enhancing feasibility of multi-breed DGV prediction for the commercial beef industry. RESULTS: Realized accuracies ranged from 0.40 to 0.78. Randomly assigning 60 to 70% of animals to training (n ≈ 2000 records) yielded DGV accuracies with the smallest coefficients of variation. Mixture models (BayesB95, BayesCπ) and models that allow SNP effects to be sampled from distributions with unequal variances (BayesA, BayesB95) were advantageous for traits that appear or are known to be influenced by large-effect genes. For other traits, models differed little in prediction accuracy (~0.3 to 0.6%), suggesting that they are mainly controlled by small-effect loci. CONCLUSIONS: The proportion (60 to 70%) of data allocated to training that optimized DGV accuracy and minimized the coefficient of variation of accuracy was similar to large dairy populations. Larger effects were estimated for some SNPs using BayesA and BayesB95 models because they allow unequal SNP variances. This substantially increased DGV accuracy for Warner-Bratzler Shear Force, for which large-effect quantitative trait loci (QTL) are known, while no loss in accuracy was observed for traits that appear to follow the infinitesimal model. Large decreases in accuracy (up to 0.07) occurred when SNPs that presumably tag large-effect QTL were over-regressed towards the mean in BayesC0 analyses. The DGV accuracies achieved here indicate that genomic selection has predictive utility in the commercial beef industry and that using models that reflect the genomic architecture of the trait can have predictive advantages in multi-breed populations.

QTLs associated with dry matter intake, metabolic mid-test weight, growth and feed efficiency have little overlap across 4 beef cattle studies.

BACKGROUND: The identification of genetic markers associated with complex traits that are expensive to record such as feed intake or feed efficiency would allow these traits to be included in selection programs. To identify large-effect QTL, we performed a series of genome-wide association studies and functional analyses using 50 K and 770 K SNP genotypes scored in 5,133 animals from 4 independent beef cattle populations (Cycle VII, Angus, Hereford and Simmental×Angus) with phenotypes for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake. RESULTS: A total of 5, 6, 11 and 10 significant QTL (defined as 1-Mb genome windows with Bonferroni-corrected P-value<0.05) were identified for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake, respectively. The identified QTL were population-specific and had little overlap across the 4 populations. The pleiotropic or closely linked QTL on BTA 7 at 23 Mb identified in the Angus population harbours a promising candidate gene ACSL6 (acyl-CoA synthetase long-chain family member 6), and was the largest effect QTL associated with dry matter intake and mid-test body weight explaining 10.39% and 14.25% of the additive genetic variance, respectively. Pleiotropic or closely linked QTL associated with average daily gain and mid-test body weight were detected on BTA 6 at 38 Mb and BTA 7 at 93 Mb confirming previous reports. No QTL for residual feed intake explained more than 2.5% of the additive genetic variance in any population. Marker-based estimates of heritability ranged from 0.21 to 0.49 for residual feed intake across the 4 populations. CONCLUSIONS: This GWAS study, which is the largest performed for feed efficiency and its component traits in beef cattle to date, identified several large-effect QTL that cumulatively explained a significant percentage of additive genetic variance within each population. Differences in the QTL identified among the different populations may be due to differences in power to detect QTL, environmental variation, or differences in the genetic architecture of trait variation among breeds. These results enhance our understanding of the biology of growth, feed intake and utilisation in beef cattle.

Beef cattle body temperature during climatic stress: a genome-wide association study.

Cattle are reared in diverse environments and collecting phenotypic body temperature (BT) measurements to characterize BT variation across diverse environments is difficult and expensive. To better understand the genetic basis of BT regulation, a genome-wide association study was conducted utilizing crossbred steers and heifers totaling 239 animals of unknown pedigree and breed fraction. During predicted extreme heat and cold stress events, hourly tympanic and vaginal BT devices were placed in steers and heifers, respectively. Individuals were genotyped with the BovineSNP50K_v2 assay and data analyzed using Bayesian models for area under the curve (AUC), a measure of BT over time, using hourly BT observations summed across 5-days (AUC summer 5-day (AUCS5D) and AUC winter 5-day (AUCW5D)). Posterior heritability estimates were moderate to high and were estimated to be 0.68 and 0.21 for AUCS5D and AUCW5D, respectively. Moderately positive correlations between direct genomic values for AUCS5D and AUCW5D (0.40) were found, although a small percentage of the top 5% 1-Mb windows were in common. Different sets of genes were associated with BT during winter and summer, thus simultaneous selection for animals tolerant to both heat and cold appears possible.

Use of robust multivariate linear mixed models for estimation of genetic parameters for carcass traits in beef cattle.

Assumptions of normality of residuals for carcass evaluation may make inferences vulnerable to the presence of outliers, but heavy-tail densities are viable alternatives to normal distributions and provide robustness against unusual or outlying observations when used to model the densities of residual effects. We compare estimates of genetic parameters by fitting multivariate Normal (MN) or heavy-tail distributions (multivariate Student's t and multivariate Slash, MSt and MS) for residuals in data of hot carcass weight (HCW), longissimus muscle area (REA) and 12th to 13th rib fat (FAT) traits in beef cattle using 2475 records from 2007 to 2008 from a large commercial operation in Nebraska. Model comparisons using deviance information criteria (DIC) favoured MSt over MS and MN models, respectively. The posterior means (and 95% posterior probability intervals, PPI) of v for the MSt and MS models were 5.89 ± 0.90 (4.35, 7.86) and 2.04 ± 0.18 (1.70, 2.41), respectively. Smaller values of posterior densities of v for MSt and MS models confirm that the assumption of normally distributed residuals is not adequate for the analysis of the data set. Posterior mean (PM) and posterior median (PD) estimates of direct genetic variances were variable with MSt having the highest mean value followed by MS and MN, respectively. Posterior inferences on genetic variance were, however, comparable among the models for FAT. Posterior inference on additive heritabilities for HCW, REA and FAT using MN, MSt and MS models indicated similar and moderate heritability comparable with the literature. Posterior means of genetic correlations for carcass traits were variable but positive except for between REA and FAT, which showed an antagonistic relationship. We have demonstrated that genetic evaluation and selection strategies will be sensitive to the assumed model for residuals.

Comparison of molecular breeding values based on within- and across-breed training in beef cattle.

BACKGROUND: Although the efficacy of genomic predictors based on within-breed training looks promising, it is necessary to develop and evaluate across-breed predictors for the technology to be fully applied in the beef industry. The efficacies of genomic predictors trained in one breed and utilized to predict genetic merit in differing breeds based on simulation studies have been reported, as have the efficacies of predictors trained using data from multiple breeds to predict the genetic merit of purebreds. However, comparable studies using beef cattle field data have not been reported. METHODS: Molecular breeding values for weaning and yearling weight were derived and evaluated using a database containing BovineSNP50 genotypes for 7294 animals from 13 breeds in the training set and 2277 animals from seven breeds (Angus, Red Angus, Hereford, Charolais, Gelbvieh, Limousin, and Simmental) in the evaluation set. Six single-breed and four across-breed genomic predictors were trained using pooled data from purebred animals. Molecular breeding values were evaluated using field data, including genotypes for 2227 animals and phenotypic records of animals born in 2008 or later. Accuracies of molecular breeding values were estimated based on the genetic correlation between the molecular breeding value and trait phenotype. RESULTS: With one exception, the estimated genetic correlations of within-breed molecular breeding values with trait phenotype were greater than 0.28 when evaluated in the breed used for training. Most estimated genetic correlations for the across-breed trained molecular breeding values were moderate (> 0.30). When molecular breeding values were evaluated in breeds that were not in the training set, estimated genetic correlations clustered around zero. CONCLUSIONS: Even for closely related breeds, within- or across-breed trained molecular breeding values have limited prediction accuracy for breeds that were not in the training set. For breeds in the training set, across- and within-breed trained molecular breeding values had similar accuracies. The benefit of adding data from other breeds to a within-breed training population is the ability to produce molecular breeding values that are more robust across breeds and these can be utilized until enough training data has been accumulated to allow for a within-breed training set.

Communication: Optical cooling of trans-stilbene.

Trans-stilbene in n-hexane is excited with excess vibrational energy in the range 0-7000 cm(-1). In the excited electronic state, the Raman linewidth of the ethylenic C=C stretching mode at 1570 cm(-1) is followed with ~100 fs time resolution. Upon excitation with substantial excess energy, the width of the peak is initially broad and then narrows within a few picoseconds, as observed previously by Iwata and Hamaguchi [Chem. Phys. Lett. 196, 462 (1992)]. This narrowing is understood as being caused by cooling of the initially hot molecule, by the surrounding solvent. In this Communication, we report that upon excitation without excess energy, the width is initially relatively narrow and then broadens on a picosecond time scale. The broadening is attributed to heating of the molecule by solvent collisions. It follows that the nascent population in the excited electronic state is cold as compared with the solvent. Such reduction of the initial vibrational energy may affect the rate for the subsequent photoreaction, especially in the absence of the solvent.

Genetic parameter estimates for bull prolificacy and its relationship with scrotal circumference in a commercial beef cattle population.

The commercial beef cattle industry relies heavily on the use of natural service sires. When artificial insemination is deemed difficult to implement, multisire breeding pastures are used to increase reproductive rates in large breeding herds or to safe-guard against bull injury during the breeding season. Although each bull might be given an equal opportunity to produce offspring, evidence suggest that there is substantial variation in the number of calves sired by each bull in a breeding pasture. With the use of DNA-based paternity testing, correctly assigning calves to their respective sires in multisire pastures is possible and presents an opportunity to investigate the degree to which this trait complex is under genetic control. Field data from a large commercial ranch was used to estimate genetic parameters for calf count (CC; 574 records from 443 sires) and yearling scrotal circumference (SC; n = 1961) using univariate and bivariate animal models. Calf counts averaged 12.2 ± 10.7 and SC averaged 35.4 ± 2.30 cm. Bulls had an average of 1.30 records and there were 23.9 ± 11.1 bulls per contemporary group. The model for CC included fixed effects of age during the breeding season (in years) and contemporary group (concatenation of breeding pasture and year). Random effects included additive genetic and permanent environmental effects, and a residual. The model for SC included fixed effects of age (in days) and contemporary group (concatenation of month and year of measurement). Random effects included an additive genetic effect and a residual. Univariate model heritability estimates for CC and SC were 0.178 ± 0.142 and 0.455 ± 0.072, respectively. Similarly, the bivariate model resulted in heritability estimates for CC and SC of 0.184 ± 0.142 and 0.457 ± 0.072, respectively. Repeatability estimates for CC from univariate and bivariate models were 0.315 ± 0.080 and 0.317 ± 0.080, respectively. The estimate of genetic correlation between CC and SC was 0.268 ± 0.274. Heritability estimates suggest that both CC and SC would respond favorably to selection. Moreover, CC is lowly repeatable and although favorably correlated, SC appears to be weakly associated with CC.

Determination of the quantum contribution to the activated motion of hydrogen on a metal surface: H/Pt(111).

Measurements of the atomic-scale motion of H and D atoms on the Pt(111) surface, above the crossover temperature to deep tunneling, are presented. The results indicate that quantum effects are significant up to the highest temperature studied (250 K). The motion is shown to correspond to nearest neighbor hopping diffusion on a well defined fcc (111) lattice. The measurements provide information on the adiabatic potential of both the adsorption site and the transition state and give strong empirical support for a dissipative transition-state theory description of the quantum contribution to the motion.

Sexual behavior: normal male patterning in androgenized female rats.

Female rats treated with testosterone as neonates and as adults exhibited a temporal patterning of male copulatory behavior identical to that of normal males, although such females displayed few intromission reflexes and almost no ejaculatory patterns. With prenatal, postnatal, and adult testosterone treatment, female rats displayed all the characteristic masculine responses and intervals, including the ultrasonic postejaculatory vocalization.

PAC1 receptor localization in a model nervous system: light and electron microscopic immunocytochemistry on the earthworm ventral nerve cord ganglia.

The presence and pattern of pituitary adenylate cyclase activating polypeptide (PACAP) type I (PAC1) receptors were identified by means of pre- and post-embedding immunocytochemical methods in the ventral nerve cord ganglia (VNC) of the earthworm Eisenia fetida. Light and electron microscopic observations revealed the exact anatomical positions of labeled structures suggesting that PACAP mediates the activity of some interneurons, a few small motoneurons and certain sensory fibers that are located in ventrolateral, ventromedial and intermediomedial sensory longitudinal axon bundles of the VNC ganglia. No labeling was located on large interneuronal systems such as dorsal medial and lateral giant axon systems and ventral giant axons. At the ultrastructural level labeling was mainly restricted to endo- and plasma membranes showing characteristic unequal distribution in various neuron parts. An increasing abundance of PAC1 receptors located on both rough endoplasmic reticulum and plasma membranes was seen from perikarya to neural processes, indicating that intracellular membrane traffic might play a crucial role in the transportation of PAC1 receptors. High number of PAC1 receptors was found in both pre- and postsynaptic membranes in addition to extrasynaptic sites suggesting that PACAP acts as neurotransmitter and neuromodulator in the earthworm nervous system.

Increased ADAMTS-13 proteolytic activity in rat hepatic stellate cells upon activation in vitro and in vivo.

INTRODUCTION: ADAMTS-13 is a member of A Disintegrin And Metalloprotease with ThromboSpondin type 1 repeats (ADAMTS) family, primarily synthesized in hepatic stellate cells (HSCs), one of the major cell types transdifferentiating into myofibroblasts during liver fibrosis. However, the association between ADAMTS-13 expression and HSC activation or liver fibrosis is not known. METHODS: In this study, we determined the ADAMTS-13 mRNA, protein, and activity in isolated primary HSCs upon activation on a plastic dish and in liver after administration of carbon tetrachloride (CCl(4)) in rats. RESULTS: We showed that ADAMTS-13 antigen and proteolytic activity in the activated rat HSCs were dramatically increased, whereas ADAMTS-13 mRNA in these cells was only minimally altered. Similarly, the ADAMTS-13 antigen and proteolytic activity in rat liver after CCl(4) injury were also significantly increased, whereas the ADAMTS-13 mRNAs in these liver tissues were only slightly increased compared with normal. Surprisingly, despite the dramatic up-regulation of ADAMTS-13 protein synthesis in the activated HSCs after CCl(4) administration, the plasma levels of ADAMTS-13 protease in rats did not increase concordantly. CONCLUSION: We conclude that the up-regulation of ADAMTS-13 protein expression in rat HSCs during activation in vitro and in vivo suggests the possibility of ADAMTS-13 proteolysis, an important part of function of the activated HSCs, perhaps through modulation of liver regeneration or formation of liver fibrosis after various injuries. The data also suggest the minimal contribution of the activated HSCs in regulation of plasma levels of ADAMTS-13 protease.

A novel missense mutation responsible for factor VII deficiency in research Beagle colonies.

BACKGROUND: Canine factor VII (cFVII) deficiency, an autosomal recessive trait originally identified in research Beagles, is associated with a mild to moderate bleeding tendency. OBJECTIVE: Our aim was to identify and characterize the mutation causing cFVII deficiency. METHODS: In order to sequence the coding regions of the cFVII gene, we cloned the cFVII cDNA. Genomic DNA and plasma from FVII-deficient Beagles and obligate carriers were utilized. RESULTS: In all FVII-deficient dogs, we identified a single causative G to A missense mutation in exon 5, encoding the second epidermal growth factor-like domain, resulting in substitution of glycine 96 by glutamic acid, with plasma FVII coagulant activity of

A new method for estimating the effective population size from allele frequency changes.

A new procedure is proposed for estimating the effective population size, given that information is available on changes in frequencies of the alleles at one or more independently segregating loci and the population is observed at two or more separate times. Approximate expressions are obtained for the variances of the new statistic, as well as others, also based on allele frequency changes, that have been discussed in the literature. This analysis indicates that the new statistic will generally have a smaller variance than the others. Estimates of effective population sizes and of the standard errors of the estimates are computed for data on two fly populations that have been discussed in earlier papers. In both cases, there is evidence that the effective population size is very much smaller than the minimum census size of the population.

On the theory of partially inbreeding finite populations. I. Partial selfing.

Some stochastic theory is developed for monoecious populations of size N in which there are probabilities beta and 1 - beta of reproduction by selfing and by random mating. It is assumed that beta much greater than N-1. Expressions are derived for the inbreeding coefficient of one random individual and the coefficient of kinship of two random separate individuals at time t. The mean and between-lines variance of the fraction of copies of a locus that are identical in two random separate individuals in an equilibrium population are obtained under the assumption that there is an infinite number of possible alleles. It is found that the theory for random mating populations holds if the effective population number is Ne = N'/(1 + FIS), where FIS is the inbreeding coefficient at equilibrium when N is infinite and N' is the reciprocal of the probability that two gametes contributing to random separate adults come from the same parent. When there is a binomial distribution of successful gametes emanating from each adult, N' = N. An approximation to the probability that an allele A survives if it is originally present in one AA heterozygote is found to be 2(N'/N)(FISS1 + (1 - FIS)S2), where S1 and S2 are the selective advantages of AA and AA in comparison with AA. In the last section it is shown that if there is partial full sib mating and binomial offspring distributions Ne = N/(1 + 3FIS).

With selection for fecundity the mean fitness does not necessarily increase.

A population with two alleles at one locus is considered. It is assumed that there is random mating of adults and that matings in which a particular pair of genotypes is involved may have a different mean number of offspring, or fecundity, than other types of matings. There is assumed to be no other selection. It is shown that the genotypic frequencies that maximize the mean fecundity of the population are not necessarily the same as the stable equilibrium frequencies. Thus, examples can be found for which the mean fecundity decreases from one generation to the next, and one such example is presented. An example in which there is no stable equilibrium, and the mean fecundity oscillates, is also given.

On the theory of partially inbreeding finite populations. II. Partial sib mating.

It is assumed that a population has M males in every generation, each of which is permanently mated with c-1 females, and that a proportion beta of matings are between males and their full sisters or half-sisters. Recurrence equations are derived for the inbreeding coefficient of one random individual, coefficients of kinship of random pairs of mates and probabilities of allelic identity when the infinite alleles model holds. If Ft is the inbreeding coefficient at time t and M is large, (1-Ft)/(1-Ft-1)----1-1/(2Ne) as t increases. The effective population number Ne = aM/[1 + (2a-1)FIS], where FIS is the inbreeding coefficient at equilibrium when M is infinite and the constant a depends upon the conditional probabilities of matings between full sibs and the two possible types of half-sibs. When there are M permanent couples, an approximation to the probability that an allele A survives if it is originally present in one AA heterozygote is proportional to FISs1 + (1-FIS)s2, where s1 and s2 are the selective advantages of AA and AA in comparison with AA. The paper concludes with a comparison between the results when there is partial selfing, partial full sib mating (c = 2) and partial sib mating when c is large.

Some effects of selection when there is partial full-sib mating.

If there is selection only for viability between zygote formation and adulthood, the frequency of a particular allele changes between these two stages of life. With complete mating this is all that happens, but if there is a positive probability that full sibs mate, there is an extra change between adulthood and the appearance of zygotes in the next generation. This occurs because there are then correlated frequencies of the alleles carried by the mates. An expression for the change in the frequency of an allele, which incorporates these two effects, is derived, and the result is found to be consistent with earlier work by the author on the probability of survival of a rare allele in a large population. The result is inconsistent with the usual expression for the change in frequency of an allele when there is partial inbreeding because that expression does not incorporate the second change in frequency within one generation.

On the theory of partially inbreeding finite populations. III. Fixation probabilities under partial selfing when heterozygotes are intermediate in viability.

In a previous paper by the senior author, an approximation to the probability of survival was given for a mutant, which is originally present in a single heterozygote, in a population that reproduces partly by selfing and partly by random mating. The population was assumed to be very large, but the result obtained is general with regard to the level of dominance in viability. In this paper two errors which were made in that earlier work are corrected. A general approximate expression is then derived for the probability that an allele A is fixed in a partially self fertilizing population of size N, if its initial frequency is p, selection is weak and heterozygotes with the allele are exactly intermediate in viability compared with genotypes AA and AA. A rigorous proof is given for a special case that is a generalization of the classical binomial sampling model. In this case, but not in general, the approximate fixation probability is independent of the probability of reproduction by selfing. Some implications are discussed.