An Experimental Evaluation of the Computational Cost of a DPI Traffic Classifier

A common belief in the scientific community is that traffic classifiers based on deep packet inspection (DPI) are far more expensive in terms of computational complexity compared to statistical classifiers. In this paper we counter this notion by defining accurate models for a deep packet inspection classifier and a statistical one based on support vector machines, and by evaluating their actual processing costs through experimental analysis. The results suggest that, contrary to the common belief, a DPI classifier and an SVM-based one can have comparable computational costs. Although much work is left to prove that our results apply in more general cases, this preliminary analysis is a first indication of how DPI classifiers might not be as computationally complex, compared to other approaches, as we previously though

Comparing P2PTV Traffic Classifiers

Peer-to-Peer IP Television (P2PTV) applications represent one of the fastest growing application classes on the Internet, both in terms of their popularity and in terms of the amount of traffic they generate. While network operators require monitoring tools that can effectively analyze the traffic produced by these systems, few techniques have been tested on these mostly closed-source, proprietary applications. In this paper we examine the properties of three traffic classifiers applied to the problem of identifying P2PTV traffic. We report on extensive experiments conducted on traffic traces with reliable ground truth information, highlighting the benefits and shortcomings of each approach. The results show that not only their performance in terms of accuracy can vary significantly, but also that their usability features suggest different effective aspects that can be integrate

Evaluation of the BovineSNP50 genotyping array in four South African cattle populations

The BovineSNP50 genotyping array is a product with a wide range of applications in cattle such as genome-wide association studies, identification of copy number variation and investigation of genetic relationships among cattle breeds. It also holds potential for genomic selection, especially for traits that are expensive and difficult to measure. The successfulness of this chip for any of these applications depends on the degree of polymorphisms in the cattle breeds. The SNP50 array has not been validated in any South African cattle population and this could lead to overestimating the number of polymorphic SNPs available for application in it. This study is a first attempt to evaluate the Bovine64SNP50 genotyping array in the South African cattle population. Ninety six bovine samples, consisting of 45 Holstein, 29 Nguni, 12 Angus and 10 Nguni x Angus crossbred animals, were genotyped with the BovineSNP50 infinium assay. The results of this study demonstrated that 40 555 SNPs were polymorphic (MAF >0.05) in these breeds and indicate potential for application in South African cattle populations. Genomic information generated from the BovineSNP50 can now be applied in genetic prediction, genetic characterization and genome-wide association studies.The authors would like to thank the ARC-Biotechnology Platform for making their laboratory resources available for genotyping samples. Financial support from the ARC is greatly appreciated. Provision of semen on Holstein bulls by Taurus Co-operative is also acknowledged.http://www.sasas.co.za/am201

Genetic diversity and population structure in South African, French and Argentinian angora goats from genome-wide SNP data

The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have been kept geographically and genetically distinct. Due to country-specific selection and breeding strategies, there is a need to characterize the populations on a genetic level. In this study we analysed genetic variability of Angora goats from three distinct geographical regions using the standardized 50k Goat SNP Chip. A total of 104 goats (AR: 30; FR: 26; SA: 48) were genotyped. Heterozygosity values as well as inbreeding coefficients across all autosomes per population were calculated. Diversity, as measured by expected heterozygosity (HE) ranged from 0.371 in the SA population to 0.397 in the AR population. The SA goats were the only population with a positive average inbreeding coefficient value of 0.009. After merging the three datasets, standard QC and LD-pruning, 15 105 SNPs remained for further analyses. Principal component and clustering analyses were used to visualize individual relationships within and between populations. All SA Angora goats were separated from the others and formed a well-defined, unique cluster, while outliers were identified in the FR and AR breeds. Apparent admixture between the AR and FR populations was observed, while both these populations showed signs of having some common ancestry with the SA goats. LD averaged over adjacent loci within the three populations per chromosome were calculated. The highest LD values estimated across populations were observed in the shorter intervals across populations. The Ne for the Angora breed was estimated to be 149 animals ten generations ago indicating a declining trend. Results confirmed that geographic isolation and different selection strategies caused genetic distinctiveness between the populations.S1 Fig. Admixture plots for K = 2–4 showing population structure of different Angora subpopulations.The authors thank Margarita Cano (supplying Argentinean Angora DNA samples), Hector Taddeo (for historical information on the Argentinian Angora breed) and Capgenes (supplying French Angora DNA samples and historical information on the French Angora breed).The Argentinian part (MP) of the project was financially supported by Instituto Nacional de Tecnologia Agropecuaria PNBIO1131033 project. The South African researchers acknowledge the National Research Foundation (grants KIC14011761093 (CV) and TP13073024535 (EVMK)) and the University of Pretoria Genomics Research Institute (CV) for financial support.http://www.plosone.orgam2016Animal and Wildlife Science

Cellulose acetate phthalate, a common pharmaceutical excipient, inactivates HIV-1 and blocks the coreceptor binding site on the virus envelope glycoprotein gp120

BACKGROUND: Cellulose acetate phthalate (CAP), a pharmaceutical excipient used for enteric film coating of capsules and tablets, was shown to inhibit infection by the human immunodeficiency virus type 1 (HIV-1) and several herpesviruses. CAP formulations inactivated HIV-1, herpesvirus types 1 (HSV-1) and 2 (HSV-2) and the major nonviral sexually transmitted disease (STD) pathogens and were effective in animal models for vaginal infection by HSV-2 and simian immunodeficiency virus. METHODS: Enzyme-linked immunoassays and flow cytometry were used to demonstrate CAP binding to HIV-1 and to define the binding site on the virus envelope. RESULTS: 1) CAP binds to HIV-1 virus particles and to the envelope glycoprotein gp120; 2) this leads to blockade of the gp120 V3 loop and other gp120 sites resulting in diminished reactivity with HIV-1 coreceptors CXCR4 and CCR5; 3) CAP binding to HIV-1 virions impairs their infectivity; 4) these findings apply to both HIV-1 IIIB, an X4 virus, and HIV-1 BaL, an R5 virus. CONCLUSIONS: These results provide support for consideration of CAP as a topical microbicide of choice for prevention of STDs, including HIV-1 infection

Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers

The Nguni cattle breed is a landrace breed adapted to different ecological regions of South Africa. A number of ecotypes are recognised based on phenotype within the breed, but it is not known if they are genetically distinct. In this study, molecular characterisation was performed on Makhathini (MAK), Pedi (PED), Shangaan (SHA) and Venda (VEN) Nguni cattle ecotypes. Two Nguni cattle populations, not kept as separate ecotypes, from the University of Fort Hare (UFH) and Agricultural Research Council Loskop South farm (LOS) were also included. Genotypic data was generated for 189 unrelated Nguni cattle selected based on pedigree records using 22 microsatellite markers. The expected heterozygosity values varied from 69 % (UFH) to 72 % (PED) with a mean number of alleles ranging from 6.0 to 6.9. The F ST estimate demonstrated that 4.8 % of the total genetic variation was due to the genetic differentiation between the populations and 92.2 % accounted for differences within the populations. The genetic distances and structure analysis revealed the closest relationship between MAK, PEDI and SHA ecotypes, followed by SHA and VEN. The UFH population clustered with the MAK ecotype, indicating that they are more genetically similar, while the LOS cattle grouped as a distinct cluster. Results suggest that the genetic differentiation between the PED and SHA ecotypes is low and can be regarded as one ecotype based on limited genetic differences. The results of this study can be applied as a point of reference for further genetic studies towards conservation of Nguni cattle ecotypes.Limpopo Department of Agriculture and Agricultural Research Council - Animal Production Institute (ARC-API).http://link.springer.com/journal/112502017-02-20hb201

Chiral indolylarylsulfone non-nucleoside reverse transcriptase inhibitors as new potent and broad spectrum anti-HIV-1 agents

We designed and synthesized a series of chiral indolyarylsulfones (IASs) as new HIV-1 NNRTIs. The new IASs 8–37 showed potent inhibition of the HIV-1 WT NL4-3 strain and of the mutant K103N, Y181C, Y188L, and K103N–Y181C HIV-1 strains. Six racemic mixtures, 8, 23–25, 31, and 33, were separated at semipreparative level into their pure enantiomers. The (R)-8 enantiomer bearing the chiral (α-methylbenzyl) was superior to the (S)-counterpart. IAS derivatives bearing the (S) alanine unit, (S)-23, (S,R)-25, (S)-31, and (S)-33, were remarkably more potent than the corresponding (R)-enantiomers. Compound 23 protected hippocampal neuronal cells from the excitotoxic insult, while efavirenz (EFV) did not contrast the neurotoxic effect of glutamate. The present results highlight the chiral IASs as new NNRTIs with improved resistance profile against the mutant HIV-1 strains and reduced neurotoxic effects