Mapping the Space of Genomic Signatures

We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is computed for each pair of graphical representations of DNA sequences, and the distances are visualized as a Molecular Distance Map: Each point on the map represents a DNA sequence, and the spatial proximity between any two points reflects the degree of structural similarity between the corresponding sequences. The graphical representation of DNA sequences utilized, Chaos Game Representation (CGR), is genome- and species-specific and can thus act as a genomic signature. Consequently, Molecular Distance Maps could inform species identification, taxonomic classifications and, to a certain extent, evolutionary history. The image distance employed, Structural Dissimilarity Index (DSSIM), implicitly compares the occurrences of oligomers of length up to $k$ (herein $k=9$) in DNA sequences. We computed DSSIM distances for more than 5 million pairs of complete mitochondrial genomes, and used Multi-Dimensional Scaling (MDS) to obtain Molecular Distance Maps that visually display the sequence relatedness in various subsets, at different taxonomic levels. This general-purpose method does not require DNA sequence homology and can thus be used to compare similar or vastly different DNA sequences, genomic or computer-generated, of the same or different lengths. We illustrate potential uses of this approach by applying it to several taxonomic subsets: phylum Vertebrata, (super)kingdom Protista, classes Amphibia-Insecta-Mammalia, class Amphibia, and order Primates. This analysis of an extensive dataset confirms that the oligomer composition of full mtDNA sequences can be a source of taxonomic information.Comment: 14 pages, 7 figures. arXiv admin note: substantial text overlap with arXiv:1307.375

A noninvasive method for in situ determination of mating success in female American lobsters (Homarus americanus)

Despite being one of the most productive fisheries in the Northwest Atlantic, much remains unknown about the natural reproductive dynamics of American lobsters. Recent work in exploited crustacean populations (crabs and lobsters) suggests that there are circumstances where mature females are unable to achieve their full reproductive potential due to sperm limitation. To examine this possibility in different regions of the American lobster fishery, a reliable and noninvasive method was developed for sampling large numbers of female lobsters at sea. This method involves inserting a blunt-tipped needle into the female's seminal receptacle to determine the presence or absence of a sperm plug and to withdraw a sample that can be examined for the presence of sperm. A series of control studies were conducted at the dock and in the laboratory to test the reliability of this technique. These efforts entailed sampling 294 female lobsters to confirm that the presence of a sperm plug was a reliable indicator of sperm within the receptacle and thus, mating. This paper details the methodology and the results obtained from a subset of the total females sampled. Of the 230 female lobsters sampled from George's Bank and Cape Ann, MA (size range = 71-145 mm in carapace length), 90.3% were positive for sperm. Potential explanations for the absence of sperm in some females include: immaturity (lack of physiological maturity), breakdown of the sperm plug after being used to fertilize a clutch of eggs, and lack of mating activity. The surveys indicate that this technique for examining the mating success of female lobsters is a reliable proxy that can be used in the field to document reproductive activity in natural populations

Zahmah social force model for pedestrian movement

The Social Force Model is one of the well-known approaches that could successfully simulate pedestrian’s movement realistically. However, it is not suitable to simulate a complex pedestrian movement. Hence, this research proposed a novel model which improved the Social Force Model for simulating high density crowd such as Tawaf. Tawaf is an Islamic ritual, which requires agents to encircle the Kaabah. This ritual has been complex yet unique, due to its capacity, density, and various demographic backgrounds of the agents. A certain set of rules that must be followed by each agent, which introduces anomalies in the flow around the Kaabah. The agents also will be assigned with unique attributes such as; gender, walking speed and intention outlook to make the simulations more realistic. The findings of this research will contribute to the simulation activities of pedestrians in a highly dense population

Reheating as a surface effect

We describe a new mechanism for reheating the Universe through evaporation of a surface charge of a fragmented inflaton condensate. We show that for a range of Yukawa coupling of the inflaton to the matter sector evaporation gives rise to a much smaller reheat temperature compared to the standard perturbative decay. As a consequence, reheating through a surface effect could solve the gravitino and moduli over production problem in inflationary models without fine tuning the Yukawa sector.Comment: 4 page

Supervision Of Civil Society In The Implementation Of Government Village Kakara B

The village is a social institution that was passed on from generation to generation by the people. the new order of government is concerned homogenize the internal order of the village is so diverse in this country. The government wants the village as an instrument of development of effective and efficient. With the Law No. 6 of 2014 on the village, the village returned as part of the right of people, so the presence of village autonomy, which the village organize independently of government. From this, the village was given the authority to regulate and manage their own household and are expected to manage the potential that exists in villages both in the field of human resources, and natural resources, to find out the surveillance society in the implementation of governmental tasks, the researchers malakukan direct research with the number of informants as many as 14 people.Supervision is very important in a government, to encourage and anticipate deviations will occur. In this study informant revealed that the villagers have not been up correcting the results of the work done by the village government, it is because the government never set up a room for deliberation, so that what is done by the village government in particular on the budget the village fund managed by the government does not know then how the budget has been realized by building rural infrastructure, and the rest of the village community fund budget management never know, because the government is not accountable for the village community. In other words, the government should better evaluate the performance and the need to implement corrective actions so that the results of the work in accordance with the plan

Season of Grazing Interacts with Soil Texture, Selecting for Associations of Biocrust Morphogroups

Livestock grazing, a widespread land use in semi-arid systems, is often placed in opposition to the perpetuation of biological soil crusts (“biocrusts”: lichens, mosses, and algal crusts including cyanobacteria) that live on the soil surface and provide ecosystem functions. The composition of biocrusts and vascular plants varies with climate, soils, and disturbance. In general, ruderal mosses and light algal crusts make up greater proportions of biocrusts in the presence of disturbance, although morphogroups of biocrusts respond differently to various disturbances. It is unknown if there are scenarios under which grazing can occur and ruderal components of biocrust could be maintained. We examine the hypothesis that soil surface texture-moisture interactions influence the ability of biocrusts to withstand trampling, reasoning that finer-textured soils are firmer (therefore serving as a better substrate for biocrusts) when dry and that coarser-textured are firmer when wet. We test these relationships within Birds of Prey, National Conservation Area (Boise, Idaho, USA). Results demonstrate two associations of biocrusts, dependent on season of grazing: one dominated by light algal crusts and lichens that frequently occurs with wet season grazing, and a second dominated by tall mosses and cup lichens that frequently occurs with dry season grazing. High cover of the invasive annual grass, Bromus tectorum (L.) was observed on sites with coarse-textured soils, and high sand content, that are grazed at relatively high intensities, creating unstable surfaces, and likely putting biocrusts at greater susceptibility to trampling. Results suggest that livestock management that accounts for soil texture and moisture could be used to maintain cover of ruderal biocrusts on fine-textured soils, that are grazed in the dry season, at low intensity. We discuss our findings in the context of managing for species of interest. Our findings are timely as varying the season of grazing is increasingly discussed as a means of favoring desirable native perennial grasses. Although ruderal morphogroups of biocrusts are not interpreted as having equivalent ecosystem functions compared to intact biocrusts, their contributions to soil stability, fertility, hydrology, and weed abatement could increase if they were more intentionally targeted by management

Semispectral measures as convolutions and their moment operators

The moment operators of a semispectral measure having the structure of the convolution of a positive measure and a semispectral measure are studied, with paying attention to the natural domains of these unbounded operators. The results are then applied to conveniently determine the moment operators of the Cartesian margins of the phase space observables.Comment: 7 page

MSSM Higgses as the source of reheating and all matter

We consider the possibility that the dark energy responsible for inflation is deposited into extra dimensions outside of our observable universe. Reheating and all matter can then be obtained from the MSSM flat direction condensate involving the Higgses $H_u$ and $H_d$, which acquires large amplitude by virtue of quantum fluctuations during inflation. The reheat temperature is $T_{RH} \lesssim 10^9$ GeV so that there is no gravitino problem. We find a spectral index $n_s\approx 1$ with a very weak dependence on the Higgs potential.Comment: 4 page