Inference of historical population-size changes with allele-frequency data

With up to millions of nearly neutral polymorphisms now being routinely sampled in population-genomic surveys, it is possible to estimate the site-frequency spectrum of such sites with high precision. Each frequency class reflects a mixture of potentially unique demographic histories, which can be revealed using theory for the probability distributions of the starting and ending points of branch segments over all possible coalescence trees. Such distributions are completely independent of past population history, which only influences the segment lengths, providing the basis for estimating average population sizes separating tree-wide coalescence events. The history of population-size change experienced by a sample of polymorphisms can then be dissected in a model-flexible fashion, and extension of this theory allows estimation of the mean and full distribution of long-term effective population sizes and ages of alleles of specific frequencies. Here, we outline the basic theory underlying the conceptual approach, develop and test an efficient statistical procedure for parameter estimation, and apply this to multiple population-genomic datasets for the microcrustacean Daphnia pulex

A preliminary investigation of strains and fracturing in small hydro-stone beams due to impact loading

Every structure has a fundamental frequency which is sometimes referred to as its first natural frequency. If a periodic force acts on the structure whose frequency is equal to that of the natural frequency of the structure, a vibration is set up whose amplitude would approach infinity if it were not for the presence of damping. Since damping is always present, steady state conditions will finally be reached provided that the applied force is not so great that it will cause the structure to fail. The amplitude of the vibration will be a function of the applied force and the damping capacity of the structure. Steady state conditions will also be finally obtained if a periodic force acts on a structure whose frequency is not equal to the natural frequency of the structure. In this case, the amplitude of the vibration will be a function of the magnitude of the applied force, the damping capacity of the structure, and the ratio of the frequency of the applied force to the natural frequency. The maximum amplitude is obtained when the ratio is equal to 1. An impulse will excite vibrations also, but no steady state harmonic conditions will be obtained. Either the structure will fail or it will return back to the initial state on account of the presence of damping. The mining engineer is interested in the impact loading of structures, because this is the type of force supplied by the action of explosives. This is a preliminary investigation of the strain time history in a small hydro-stone beam due to a suddenly applied force. The impact loading was obtained by dropping steel balls from various heights on the beam. The purpose of the first part of this project was to determine the influence of a number of variables on the strain. The factors which were studied are: a variation in the height of drop and in the weight of the balls; and the effect of the size of the variable resistance wire strain gage on the dynamic strain record. The object of the second part of this project was to investigate the strains present in a small hydro-stone beam when it is subjected to an impact loading which is sufficiently large to cause the beam to fail --Introduction, pages 1-2

Multivariate Statistical Analysis in the Real and Complex Domains

This book explores topics in multivariate statistical analysis, relevant in the real and complex domains. It utilizes simplified and unified notations to render the complex subject matter both accessible and enjoyable, drawing from clear exposition and numerous illustrative examples. The book features an in-depth treatment of theory with a fair balance of applied coverage, and a classroom lecture style so that the learning process feels organic. It also contains original results, with the goal of driving research conversations forward. This will be particularly useful for researchers working in machine learning, biomedical signal processing, and other fields that increasingly rely on complex random variables to model complex-valued data. It can also be used in advanced courses on multivariate analysis. Numerous exercises are included throughout

Fur: Find unique genomic regions for diagnostic PCR

Unique marker sequences are highly sought after in molecular diagnostics. Nevertheless, there are only few programs available to search for marker sequences, compared to the many programs for similarity search. We therefore wrote the program Fur for Finding Unique genomic Regions.Fur takes as input a sample of target sequences and a sample of closely related neighbors. It returns the regions present in all targets and absent from all neighbors. The recently published program genmap can also be used for this purpose and we compared it to fur. When analyzing a sample of 33 genomes representing the major phylogroups of E.coli, fur was 40 times faster than genmap but used three times more memory. On the other hand, genmap yielded three times more markers, but they were less accurate when tested in silico on a sample of 237 E.coli genomes. We also designed phylogroup-specific PCR primers based on the markers proposed by genmap and fur, and tested them by analyzing their virtual amplicons in GenBank. Finally, we used fur to design primers specific to a Lactobacillus species, and found excellent sensitivity and specificity in vitro.Fur sources and documentation are available from https://github.com/evolbioinf/fur. The compiled software is posted as a docker container at https://hub.docker.com/r/haubold/fox.Supplementary data are available at Bioinformatics online

Multivariate Statistical Analysis in the Real and Complex Domains

This book explores topics in multivariate statistical analysis, relevant in the real and complex domains. It utilizes simplified and unified notations to render the complex subject matter both accessible and enjoyable, drawing from clear exposition and numerous illustrative examples. The book features an in-depth treatment of theory with a fair balance of applied coverage, and a classroom lecture style so that the learning process feels organic. It also contains original results, with the goal of driving research conversations forward. This will be particularly useful for researchers working in machine learning, biomedical signal processing, and other fields that increasingly rely on complex random variables to model complex-valued data. It can also be used in advanced courses on multivariate analysis. Numerous exercises are included throughout

Comparative Analysis of Super-Kamiokande and SNO Solar-Neutrino Data and the Photospheric Magnetic Field

We analyze Super-Kamiokande, SNO, and photospheric magnetic-field data for the common time interval, namely the SNO D2O phase. Concerning rotational modulation, the magnetic-field power spectrum shows the strongest peaks at the second and sixth harmonics of the solar synodic rotation frequency [3 nu(rot) and 7 nu(rot)]. The restricted Super-Kamiokande dataset shows strong modulation at the second harmonic. The SNO D2O dataset shows weak modulation at that frequency, but strong modulation in the sixth-harmonic frequency band. We estimate the significance level of the correspondence of the Super-Kamiokande second-harmonic peak with the corresponding magnetic-field peak to be 0.0004, and the significance level of the correspondence of the SNO D2O sixth-harmonic peak with the corresponding magnetic-field peak to be 0.009. By estimating the amplitude of the modulation of the solar neutrino flux at the second harmonic from the restricted Super-Kamiokande dataset, we find that the weak power at that frequency in the SNO D2O power spectrum is not particularly surprising. Concerning 9.43 yr-1, we find no peak at this frequency in the power spectrum formed from the restricted Super-Kamiokande dataset, so it is no surprise that this peak does not show up in the SNO D2O dataset, either.Comment: 32 pages, 8 tables, 16 figure

WSO/UV: World Space Observatory/Ultraviolet

We summarize the capabilities of the World Space Observatory (UV) Project (WSO/UV). An example of the importance of this project (with a planned launch date of 2007/8) for the study of Classical Novae is given.Comment: 4 pages, To appear in the proceeedings of the "Classical Nova Explosions" conference, eds. M. Hernanz and J. Jose, AI