Optical control of an atomic inner-shell x-ray laser

X-ray free-electron lasers have had an enormous impact on x-ray science by achieving femtosecond pulses with unprecedented intensities. However, present-day facilities operating by the self-amplified spontaneous emission (SASE) principle have a number of shortcomings, namely, their radiation has a chaotic pulse profile and short coherence times. We put forward a scheme for a neon-based atomic inner-shell x-ray laser (XRL) which produces temporally and spatially coherent subfemtosecond pulses that are controlled by and synchronized to an optical laser with femtosecond precision. We envision that such an XRL will allow for numerous applications such as nuclear quantum optics and the study of ultrafast quantum dynamics of atoms, molecules, and condensed matter.Comment: 8 pages, 5 figures, RevTeX4.1, revise

Mapping Mendelian traits in asexual progeny using changes in marker allele frequency

Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny of a cross between two inbred lines. This strategy is usually employed when pooling is used to reduce genotyping costs. When the cross progeny are asexual, the extreme progeny may be selected by multiple generations of asexual reproduction and selection. We analyse this method of measuring phenotype in asexual progeny and examine the changes in marker allele frequency due to selection over many generations. Stochasticity in marker frequency in the selected population arises due to the finite initial population size. We derive the distribution of marker frequency as a result of selection at a single major locus, and show that in order to avoid spurious changes in marker allele frequency in the selected population, the initial population size should be in the low to mid hundreds

The variance of identity-by-descent sharing in the Wright-Fisher model

Widespread sharing of long, identical-by-descent (IBD) genetic segments is a hallmark of populations that have experienced recent genetic drift. Detection of these IBD segments has recently become feasible, enabling a wide range of applications from phasing and imputation to demographic inference. Here, we study the distribution of IBD sharing in the Wright-Fisher model. Specifically, using coalescent theory, we calculate the variance of the total sharing between random pairs of individuals. We then investigate the cohort-averaged sharing: the average total sharing between one individual and the rest of the cohort. We find that for large cohorts, the cohort-averaged sharing is distributed approximately normally. Surprisingly, the variance of this distribution does not vanish even for large cohorts, implying the existence of "hyper-sharing" individuals. The presence of such individuals has consequences for the design of sequencing studies, since, if they are selected for whole-genome sequencing, a larger fraction of the cohort can be subsequently imputed. We calculate the expected gain in power of imputation by IBD, and subsequently, in power to detect an association, when individuals are either randomly selected or specifically chosen to be the hyper-sharing individuals. Using our framework, we also compute the variance of an estimator of the population size that is based on the mean IBD sharing and the variance in the sharing between inbred siblings. Finally, we study IBD sharing in an admixture pulse model, and show that in the Ashkenazi Jewish population the admixture fraction is correlated with the cohort-averaged sharing.Comment: Includes Supplementary Materia

Genetic Influences on Brain Gene Expression in Rats Selected for Tameness and Aggression

Inter-individual differences in many behaviors are partly due to genetic differences, but the identification of the genes and variants that influence behavior remains challenging. Here, we studied an F2 intercross of two outbred lines of rats selected for tame and aggressive behavior towards humans for more than 64 generations. By using a mapping approach that is able to identify genetic loci segregating within the lines, we identified four times more loci influencing tameness and aggression than by an approach that assumes fixation of causative alleles, suggesting that many causative loci were not driven to fixation by the selection. We used RNA sequencing in 150 F2 animals to identify hundreds of loci that influence brain gene expression. Several of these loci colocalize with tameness loci and may reflect the same genetic variants. Through analyses of correlations between allele effects on behavior and gene expression, differential expression between the tame and aggressive rat selection lines, and correlations between gene expression and tameness in F2 animals, we identify the genes Gltscr2, Lgi4, Zfp40 and Slc17a7 as candidate contributors to the strikingly different behavior of the tame and aggressive animals

Homework : exploring teachers’ beliefs and practices in relation with pupils’ self-regulation

Homework is commonly assigned to primary school children, yet homework completion has not been associated with academic achievement in this age group. Nevertheless, homework has the potential to help children develop self-regulated learning strategies and adaptive beliefs. Previous studies focused on the tasks assigned only when discussing the guidelines for supporting self-regulation during homework. However, homework is a complex phenomenon including both the classroom and home environment; and several participants: teachers, parents and pupils. All these elements have the potential of affecting the homework process and its beneficial effects. Having a social-cognitive theoretical background, this thesis set out to explore the ways teachers support pupils’ self-regulation through homework. The research focuses on the different ways teachers could possible influence their students’ self-regulatory development: teacher beliefs, homework assignments and classroom environment. Data was collected from 13 fourth grade students (age 11) and two of their teachers from an urban school in Romania. The data consisted of open-ended interviews, which were analyzed using qualitative research methods. The main coding categories are: homework beliefs, homework assignments, classroom environment, home environment and learning strategies and self-motivation beliefs. Students’ and teachers’ views are compared in the results section. Results show that students’ and teachers’ beliefs about homework were similar, and they both recognized personal development as the main purpose of homework. The task types were diverse and most of them supported the use of self-regulation strategies, with projects and creative writing tasks standing out. Repetitive exercises were not seen by students as useful, while challenging exercises were seen as improving self-efficacy beliefs and self-confidence. The consequences of homework not done were related to focusing on grades and tests, while assessment of projects and writing tasks through feedback had positive associations. The results demonstrate that other elements than just the task influence students’ self-regulatory processes and beliefs while doing homework. This research contributed to both research on homework and the wider research of promoting self-regulation in the classroom. Practical recommendations are given to teachers on how to help children develop self-regulated learning skills through homework

Under the Hood: An (Auto) Ethnographic Study of How White Adolescent Males Critically Engage with Race in Grand Theft Auto V

Grand Theft Auto V (GTA V) is emblematic of the public controversies that associate video games with violence, misogyny, and damaging depictions of race and gender. However, it is also a layered referential and self-reflexive text that roundly critiques US culture, including the pernicious complicity of media on issues of identity. GTA V is the third best selling video game in history, and primarily targets white adolescent males, but its effects on the attitudes and behaviors of its chief consumers are virtually unstudied. Furthermore, the tendency for schools to keep controversial games at a distance may neglect a need to better equip adolescent boys with the tools to critically consume the complex media in which they are immersed. This doctoral dissertation employs a postcolonial lens and documents a month-long qualitative study where a high school class of ten white adolescent boys played GTA V while in a formal instructional context that encouraged them to critically reflect on their gameplay. Although they viewed the game through the lenses of gender, masculinities, violence, and hegemony, my research specifically reports on how they engaged with representations of race and racialized places in the elaborate urban simulation. The participants were positioned as co-researchers and trained in basic ethnographic methods, and the fieldnotes and filmed videos of their play were synthesized in autoethnographic accounts of their experiences. Data was also gathered from pre- and post-surveys, filmed classroom sessions, a private Facebook group, the counter-hegemonic media they produced, and their notes and videos. The investigation revealed that participants naturalized racial stereotypes and problematic connections of race and place. And, the instructional approach was found to provoke a greater awareness about discriminatory depictions of race in the game and, in some cases, media at large. Some also become aware of their own tendencies to appropriate commodified forms of blackness. Finally, their discourse and views were found to be largely shaped by media, highlighting the need for a greater emphasis on media literacy in schools

Mapping genetic determinants of host susceptibility to Pseudomonas aeruginosa lung infection in mice.

Background: P. aeruginosa is one of the top three causes of opportunistic human bacterial infections. The remarkable variability in the clinical outcomes of this infection is thought to be associated with genetic predisposition. However, the genes underlying host susceptibility to P. aeruginosa infection are still largely unknown. Results: As a step towards mapping these genes, we applied a genome wide linkage analysis approach to a mouse model. A large F2 intercross population, obtained by mating P. aeruginosa-resistant C3H/HeOuJ, and susceptible A/J mice, was used for quantitative trait locus (QTL) mapping. The F2 progenies were challenged with a P. aeruginosa clinical strain and monitored for the survival time up to 7 days post-infection, as a disease phenotype associated trait. Selected phenotypic extremes of the F2 distribution were genotyped with high-density single nucleotide polymorphic (SNP) markers, and subsequently QTL analysis was performed. A significant locus was mapped on chromosome 6 and was named P. aeruginosa infection resistance locus 1 (Pairl1). The most promising candidate genes, including Dok1, Tacr1, Cd207, Clec4f, Gp9, Gata2, Foxp1, are related to pathogen sensing, neutrophils and macrophages recruitment and inflammatory processes. Conclusions: We propose a set of genes involved in the pathogenesis of P. aeruginosa infection that may be explored to complement human studie

Comparing linkage and association analyses in sheep points to a better way of doing GWAS

Genome wide association studies (GWAS) have largely succeeded family-based linkage studies in livestock and human populations as the preferred method to map loci for complex or quantitative traits. However, the type of results produced by the two analyses contrast sharply due to differences in linkage disequilibrium (LD) imposed by the design of studies. In this paper, we demonstrate that association and linkage studies are in agreement provided that (i) the effects from both studies are estimated appropriately as random effects, (ii) all markers are fitted simultaneously and (iii) appropriate adjustments are made for the differences in LD between the study designs. We demonstrate with real data that linkage results can be predicted by the sum of association effects. Our association study captured most of the linkage information because we could predict the linkage results with moderate accuracy. We suggest that the ability of common single nucleotide polymorphism (SNP) to capture the genetic variance in a population will depend on the effective population size of the study organism. The results provide further evidence for many loci of small effect underlying complex traits. The analysis suggests a more informed method for GWAS is to fit statistical models where all SNPs are analysed simultaneously and as random effects

Haplotype Probabilities in Advanced Intercross Populations

Advanced intercross populations, in which multiple inbred strains are mated at random for many generations, have the advantage of greater precision of genetic mapping because of the accumulation of recombination events across the multiple generations. Related designs include heterogeneous stock and the diversity outcross population. In this article, I derive the two-locus haplotype probabilities on the autosome and X chromosome with these designs. These haplotype probabilities provide the key quantities for developing hidden Markov models for the treatment of missing genotype information. I further derive the map expansion in these populations, which is the frequency of recombination breakpoints on a random chromosome