4,127 research outputs found
RADpainter and fineRADstructure:Population inference from RADseq data
No full textPowerful approaches to inferring recent or current population structure based on nearest neighbor haplotype “coancestry” have so far been inaccessible to users without high quality genome-wide haplotype data. With a boom in nonmodel organism genomics, there is a pressing need to bring these methods to communities without access to such data. Here, we present RADpainter, a new program designed to infer the coancestry matrix from restriction-site-associated DNA sequencing (RADseq) data. We combine this program together with a previously published MCMC clustering algorithm into fineRADstructure—a complete, easy to use, and fast population inference package for RADseq data (https://github.com/millanek/fineRADstructure; last accessed February 24, 2018). Finally, with two example data sets, we illustrate its use, benefits, and robustness to missing RAD alleles in double digest RAD sequencing
5 minutes with Milan Vojnovic
No full textProfessor Milan Vojnovic is a Chair in Data Science in the Department of Statistics, London School and Economics & Political Science. With the publication of Contest Theory, we took the opportunity to interview the author to find out more about his book and how it relates to his career
Radicals formation in supersonic plasma jet
No full textTitle: Creation of radicals in electric discharge supersonic plasma jet Author: Milan MaSat Department: Department of Surface and Plasma Science Supervisor: Prof. RNDr. Milan Tichy, DrSc. Supervisor's e-mail address: [email protected] Abstract: Free radicals are the key intermediates and propagators of chemical reactions in Earth's atmosphere. Study of their structure and chemical properties is vital for understanding the processes in atmosphere. But their high reactivity brings the need for specific research methods. In-situ preparation and non-invasive detection and characterization techniques are needed. Most commonly used laboratory techniques such as photodissociation or electric discharge generate radicals at temperatures that are significantly higher then those under atmospheric conditions, which we intendto model. In this work, I was developing a source of cold radicals and experimental techniques for measuring their properties. 1 combined plasma source, which creates sufficient concentrations of radicals with supersonic expansion in which the translational and internal degrees of freedom are cooled deeply below the room temperature. For their characterization I used high-resolution spectroscopy utilizing near infrared laser diodes. I also developed and built electronic circuits and software..
Why do voters back corrupt and dishonest politicians? Interview with Milan Vaishnav
No full textA candidate with criminal allegations hanging over them will repel voters – or will they? Not necessarily. In India, a third of the MPs elected in 2014 faced an ongoing criminal case. Milan Vaishnav, the author of a new book about the nexus of crime and democracy in India, talks to Ros Taylor about the appeal of a strongman who can ‘get things done’, even if it means breaking the law – and considers whether some US voters share the same instincts
Towards reliable detection of introgression in the presence of among-species rate variation.
No full textThe role of interspecific hybridization has recently seen increasing attention, especially in the context of diversification dynamics. Genomic research has now made it abundantly clear that both hybridization and introgression - the exchange of genetic material through hybridization and backcrossing - are far more common than previously thought. Besides cases of ongoing or recent genetic exchange between taxa, an increasing number of studies report "ancient introgression" - referring to results of hybridization that took place in the distant past. However, it is not clear whether commonly used methods for the detection of introgression are applicable to such old systems, given that most of these methods were originally developed for analyses at the level of populations and recently diverged species, affected by recent or ongoing genetic exchange. In particular, the assumption of constant evolutionary rates, which is implicit in many commonly used approaches, is more likely to be violated as evolutionary divergence increases. To test the limitations of introgression detection methods when being applied to old systems, we simulated thousands of genomic datasets under a wide range of settings, with varying degrees of among-species rate variation and introgression. Using these simulated datasets, we showed that some commonly applied statistical methods, including the D-statistic and certain tests based on sets of local phylogenetic trees, can produce false-positive signals of introgression between divergent taxa that have different rates of evolution. These misleading signals are caused by the presence of homoplasies occurring at different rates in different lineages. To distinguish between the patterns caused by rate variation and genuine introgression, we developed a new test that is based on the expected clustering of introgressed sites along the genome, and implemented this test in the program Dsuite
The history and organization of the Workshop on Population and Speciation Genomics.
No full textWith the advent of high-throughput genome sequencing, bioinformatics training has become essential for research in evolutionary biology and related fields. However, individual research groups are often not in the position to teach students about the most up-to-date methodology in the field. To fill this gap, extended bioinformatics courses have been developed by various institutions and provide intense training over the course of two or more weeks. Here, we describe our experience with the organization of a course in one of the longest-running extended bioinformatics series of workshops, the Evomics Workshop on Population and Speciation Genomics that takes place biennially in the UNESCO world heritage town of Český Krumlov, Czech Republic. We list the key ingredients that make this workshop successful in our view, explain the routine for workshop organization that we have optimized over the years, and describe the most important lessons that we have learned from it. We report the results of a survey conducted among past workshop participants that quantifies measures of effective teaching and provide examples of how the workshop setting has led to the cross-fertilisation of ideas and ultimately scientific progress. We expect that our account may be useful for other groups aiming to set up their own extended bioinformatics courses
Le congrès de Milan (enregistrement 1/2)
No full textConférence - débats donnée par Guy Bouchauveau et Chistian Cuxac sur le congrès de Milan en 1880 dans le cadre de la commémoration du Bicentenaire de la mort de l'Abbé de l'Epée. Chacun des deux orateurs expose en même temps les tenants et les aboutissants du congrès de Milan.00:00:00 - 00:03:27 Introduction sur le congrès de Milan 00:03:31 - 00:08:20 10 et 11 septembre 1880 : qu'est ce que le congrès de Milan ? Quand aurait-il pu intervenir ? 00:08:22 - 00:15:30 Congrès de Milan : quels congressistes, quels éléments le préparent ? 00:15:31 - 00:25:55 Les stratégies des oralistes français pour imposer l'oralisme. 00:25:56 - 00:35:39 Les arguments développés pendant le congrès (médicaux, mimétiques, religieux). Les arguments non dits (rejet du corps, planification de la destruction des langues minoritaires) 00:35:39 - 00:38:50 Etat des lieux de l'enseignement aux enfants sourds en 1880 en France : éducation socialement discriminantes dans de petites institutions oralistes. 00:38:54 - 00:42:35 Résolutions du congrès de Milan 00:42:35 - 00:52:27 Effets du congrès de Milan 00:52:27 - 00:55:49 Congrès de Milan, la suite : La méthode oraliste pure subit un coup de grâce en 1909 dans un article de Binet. 00:55:57 - 00:56:35 Dessin conclusif de Guy Bouchauveau 00:56:35 - 00:58:08 Conclusion de Christian Cuxac (interprète : Elisabeth Kraut) 00:58:13 - 00:59:23 Conclusion de Guy Bouchauveau (voix Elisabeth Kraut
D statistics
No full textThis table gives values of Patterson’s D(h1, h2, h3, h4) for all combinations of samples of the cichlid species given in Supplementary Table S1 of Malinsky et al. 2018, where the outgroup (h4) is fixed as N. brichardi from Lake Tanganyika. Note that the different geographic variants of A. calliptera were treated separately
CHARM OF AUTHOR INTERVENTION:NARRATIVE THEORETICAL ANALYSIS ON MILAN KUNDERA’S WORKS
No full textArticle discusses the narrative of "interference" theory. The discussion with the author’s intervention and then gives a detailed and profound discussion. The author uses four ways to carry out the intervention, such as "deliberate go away, having no intention of sneaking, into the intention of the highlights, at random creative". This article talks about the creation of a detailed narrative analysis and has a further exploration about the effect of narrative. Under such theory frame and the synthesis, this article is attempting a utilization of the narrative theory to the text explanation
f statistics
No full textThis table gives values of the f4 admixture ratio f(h1, h2, h3, h4) ([see SOM18 in ref. 31, and fG in ref. 48 in Malinsky et al. 2018] for all combinations of species for which D(h1,h2,h3,h4)>0. The outgroup (h4) is fixed as N. brichardi from Lake Tanganyika. Note that the different geographic variants of A. calliptera were treated separately
- …
