cRIsp: Crowdsourcing Representation Information to Support Preservation

In this paper, we describe a new collaborative approach to the collection of representation information to ensure long term access to digital content. Representation information is essential for successful rendering of digital content in the future. Manual collection and maintenance of representation information has so far proven to be highly resource intensive and is compounded by the massive scale of the challenge, especially for repositories with no format limitations. This solution combats these challenges by drawing upon the wisdom and knowledge of the crowd to identify online sources of representation information, which are then collected, classified, and managed using existing tools. We suggest that nominations can be harvested and preserved by participating established web archives, which themselves could obviously benefit from such extensive collections. This is a low cost, low resource approach to collecting essential representation information of widespread relevance

PCA and K-Means decipher genome

In this paper, we aim to give a tutorial for undergraduate students studying statistical methods and/or bioinformatics. The students will learn how data visualization can help in genomic sequence analysis. Students start with a fragment of genetic text of a bacterial genome and analyze its structure. By means of principal component analysis they ``discover'' that the information in the genome is encoded by non-overlapping triplets. Next, they learn how to find gene positions. This exercise on PCA and K-Means clustering enables active study of the basic bioinformatics notions. Appendix 1 contains program listings that go along with this exercise. Appendix 2 includes 2D PCA plots of triplet usage in moving frame for a series of bacterial genomes from GC-poor to GC-rich ones. Animated 3D PCA plots are attached as separate gif files. Topology (cluster structure) and geometry (mutual positions of clusters) of these plots depends clearly on GC-content.Comment: 18 pages, with program listings for MatLab, PCA analysis of genomes and additional animated 3D PCA plot

Enhanced relativistic harmonics by electron nanobunching

It is shown that when an few-cycle, relativistically intense, p-polarized laser pulse is obliquely incident on overdense plasma, the surface electrons may form ultra-thin, highly compressed layers, with a width of a few nanometers. These electron "nanobunches" emit synchrotron radiation coherently. We calculate the one-dimensional synchrotron spectrum analytically and obtain a slowly decaying power-law with an exponent of 4/3 or 6/5. This is much flatter than the 8/3 power of the BGP (Baeva-Gordienko-Pukhov) spectrum, produced by a relativistically oscillating bulk skin layer. The synchrotron spectrum cut-off frequency is defined either by the electron relativistic $\gamma$-factor, or by the thickness of the emitting layer. In the numerically demonstrated, locally optimal case, the radiation is emitted in the form of a single attosecond pulse, which contains almost the entire energy of the full optical cycle.Comment: to appear in Physics of Plasma

Too Little, Too Late: How the Tidal Evolution of Hot Jupiters affects Transit Surveys of Clusters

The tidal evolution of hot Jupiters may change the efficiency of transit surveys of stellar clusters. The orbital decay that hot Jupiters suffer may result in their destruction, leaving fewer transiting planets in older clusters. We calculate the impact tidal evolution has for different assumed stellar populations, including that of 47~Tuc, a globular cluster that was the focus of an intense HST search for transits. We find that in older clusters one expects to detect fewer transiting planets by a factor of two for surveys sensitive to Jupiter-like planets in orbits out to 0.5~AU, and up to a factor of 25 for surveys sensitive to Jupiter-like planets in orbits out to 0.08~AU. Additionally, tidal evolution affects the distribution of transiting planets as a function of semi-major axis, producing larger orbital period gaps for transiting planets as the age of the cluster increases. Tidal evolution can explain the lack of detected exoplanets in 47~Tuc without invoking other mechanisms. Four open clusters residing within the {\em Kepler} fields of view have ages that span 0.4-8~Gyr--if {\em Kepler} can observe a significant number of planets in these clusters, it will provide key tests for our tidal evolution hypothesis. Finally, our results suggest that observers wishing to discover transiting planets in clusters must have sufficient accuracy to detect lower mass planets, search larger numbers of cluster members, or have longer observation windows to be confident that a significant number of transits will occur for a population of stars.Comment: 23 pages including 6 figures, accepted to Ap

Investigation into the metal contamination of the Plankenburg and Diep Rivers, Western Cape, South Africa

Metal contamination in the Plankenburg and Diep Rivers (Western Cape) was investigated over a 12 and 9 month period, respectively. Aluminium (Al), copper (Cu), iron (Fe), lead (Pb), manganese (Mn), nickel (Ni) and zinc (Zn) concentrations were determined using the nitric acid digestion method and analysed by inductively coupled plasma atomic emission spectrometry (ICP-AES). For both rivers the Al and Fe concentrations were higher than that for all the other metals analysed for in sediment and water samples. The highest concentrations recorded in the Plankenburg River were 13.6 mgE.-1 (water . Week 18, Site B) and 15 018 mgEkg-1 (sediment . Week 1, Site C) for Al, and 48 mgE.-1 (water . Week 43, Site A) and 14 363.8 mgEkg-1 (sediment . Week 1, Site A) for Fe. The highest concentrations recorded in the Diep River were 4 mgE.-1 (water . Week 1, Site A) and 19 179 mgEkg-1 (sediment . Week 1, Site C) for Al, and 513 mgE.-1 (water . Week 27, Site A) and 106 379.5 mgEkg-1 (sediment . Week 9, Site C) for Fe. For most of the metals analysed the concentrations were higher than the recommended water quality guidelines as stipulated by the Department of Water Affairs and Forestry, the Canadian Council for the Ministers of the Environment and the accepted eworld averagef. Point sources of pollution could not be conclusively identified, but runoff from both industrial and residential areas could have contributed to the increased concentrations. Metal concentrations should be routinely monitored and the guidelines should be updated and revised based on the current state of the rivers and pollution sources

Discrete Charge Dielectric Model of Electrostatic Energy

Studies on nanoscale materials merit careful development of an electrostatics model concerning discrete point charges within dielectrics. The discrete charge dielectric model treats three unique interaction types derived from an external source: Coulomb repulsion among point charges, direct polarization between point charges and their associated surface charge elements, and indirect polarization between point charges and surface charge elements formed by other point charges. The model yields the potential energy, U(N), stored in a general $N$ point charge system differing from conventional integral formulations, $1/2\int{\bm E}\cdot{\bm D}dV$ and $1/2\int\rho\Phi dV$, in a manner significant to the treatment of few electron systems.Comment: 1 figure, 2 parts, ep

Short communication: Isolation and identification of bacterial pollutants from the Berg and Plankenburg Rivers in the Western Cape, South Africa

Bacterial species present in the Berg and Plankenburg Rivers (Western Cape, South Africa) were isolated from water and biofilm samples and population shifts between sampling sites were phylogenetically identified. Deoxyribonucleic acid (DNA) extraction of representative isolates was performed and amplified using 2 different primer sets. Various Enterobacteriaceae species were present at all of the sites, confirming faecal contamination. Phylogenetic analyses also showed that, in general, Gram-negative micro-organisms dominated at all of the sites sampled in both the Berg and Plankenburg river systems. Pathogens and opportunistic pathogens, such as Pseudomonas aeruginosa, Staphylococcus sp., and Bacillus cereus, were isolated from the Berg River. Similarly, in the Plankenburg River system, Aeromonas sp., Acinetobacter sp., Stenotrophomonas sp. and Yersinia enterocolitica were also isolated. This raises major health concerns as human population densities along both rivers are high, thus resulting in increased human exposure to these organisms

Identification of metal-tolerant organisms isolated from the Plankenburg River, Western Cape, South Africa

The ability of biofilms to resist pollutants makes them advantageous for use in bioremediation. The objective of this investigation was to isolate metal-tolerant micro-organisms from a site along the Plankenburg River. Microbial biofilms cultivated in multi-channelled flow cells were exposed to varying concentrations of aluminium (Al), iron (Fe), copper (Cu), manganese (Mn), nickel (Ni) and zinc (Zn), stained with the BacLightTM viability probe, visualised using epifluorescence microscopy and analysed using ScionImage. Exposure to the highest Al, Fe, Cu and Mn concentrations increased the percentages of dead cells. A difference in live and dead cells after exposure to varying Zn and Ni concentrations was not evident. When exposed to the lowest concentrations, no notable difference could be detected in comparison with the untreated control. Possible metal-tolerant micro-organisms were identified from the exposed flow cells using polymerase chain reaction (PCR) and deoxyribonucleic acid (DNA) sequencing, followed by ClustalX alignment and phylogenetic analysis. Phylogenetic analysis identified a variety of organisms, including Bacillus sp., Pseudomonas sp., Delftia tsuruhatensis strain A90, Kocuria kristinae strain 6J-5b, Comamonas testosteroni WDL7, Stenotrophomonas maltophilia strain 776, Staphylococcus sp. MOLA:313, Micrococcus sp. TPR14, Sphingomonas sp. 8b-1 and Microbacterium sp. PAO-12. Two major clusters could be distinguished based on their Gram-reactions.Keywords: BacLightTM viability probe, biofilms, phylogenetic analysis, river water, ScionImag