Detecting Network Soft-failures with the Network Link Outlier Factor (NLOF)

In this paper, we describe and experimentally evaluate the performance of our Network Link Outlier Factor (NLOF) for detecting soft-failures in communication networks. The NLOF is computed using the throughput values derived from NetFlow records. The flow throughput values are clustered in two stages, outlier values are determined within each cluster, and the flow outliers are used to compute the outlier factor or score for each network link. When sampling NetFlow records across the full span of a network, NLOF enables the detection of soft-failures across the span of the network; large NLOF scores correlate well with links experiencing failure

Understanding Oral Diseases: Exploring Opportunities from Filipino Oral Microbiome Research

The human mouth houses the second most diverse microbial community in the body, with almost 700 species of bacteria colonizing the hard surfaces of teeth and the soft tissues of the oral mucosa. To compete in the relatively exposed oral cavity, resident microbes must avoid being replaced by newcomers. This selective constraint, coupled with pressure on the host to cultivate a beneficial microbiome, has rendered a commensal oral microbiota that displays colonization resistance, protecting the human host from invasive species, including pathogens. Current control of dental plaque-related diseases is non-specific and is centered on the removal of plaque by mechanical means. Several new methods based on the modulation of the microbiome that aim at maintaining and re-establishing a healthy oral ecosystem have been developed and has greatly expanded our knowledge of the composition and function of the oral microbiome in health and disease. Promoting a balanced microbiome is therefore important to effectively maintain or restore oral health. This review provides an updated body of knowledge on oral microbiome in health and disease and discusses the implications for modern-day oral healthcare. Filipino Oral Microbiome Research to develop a policy framework for microbiome-based management of dental diseases and opportunities will be discussed

Distinct fos-expressing neuronal ensembles in the ventromedial prefrontal cortex mediate food reward and extinction memories

In operant learning, initial reward-associated memories are thought to be distinct from subsequent extinction-associated memories. Memories formed during operant learning are thought to be stored in “neuronal ensembles.” Thus, we hypothesize that different neuronal ensembles encode reward- and extinction-associated memories. Here, we examined prefrontal cortex neuronal ensembles involved in the recall of reward and extinction memories of food self-administration.Wefirst trained rats to lever press for palatable food pellets for 7 d (1 h/d) and then exposed them to 0, 2, or 7 daily extinction sessions in which lever presses were not reinforced. Twenty-four hours after the last training or extinction session, we exposed the rats to either a short 15 min extinction test session or left them in their homecage (a control condition). We found maximal Fos (a neuronal activity marker) immunoreactivity in the ventral medial prefrontal cortex of rats that previously received 2 extinction sessions, suggesting that neuronal ensembles in this area encode extinction memories. We then used the Daun02 inactivation procedure to selectively disrupt ventral medial prefrontal cortex neuronal ensembles that were activated during the 15 min extinction session following 0 (no extinction) or 2 prior extinction sessions to determine the effects of inactivating the putative food reward and extinction ensembles, respectively, on subsequent nonreinforced food seeking 2 d later. Inactivation of the food reward ensembles decreased food seeking, whereas inactivation of the extinction ensembles increased food seeking. Our results indicate that distinct neuronal ensembles encoding operant reward and extinction memories intermingle within the same cortical area

FUSE Measurements of Far Ultraviolet Extinction. I. Galactic Sight Lines

We present extinction curves that include data down to far ultraviolet wavelengths (FUV; 1050 - 1200 A) for nine Galactic sight lines. The FUV extinction was measured using data from the Far Ultraviolet Spectroscopic Explorer. The sight lines were chosen for their unusual extinction properties in the infrared through the ultraviolet; that they probe a wide range of dust environments is evidenced by the large spread in their measured ratios of total-to-selective extinction, R_V = 2.43 - 3.81. We find that extrapolation of the Fitzpatrick & Massa relationship from the ultraviolet appears to be a good predictor of the FUV extinction behavior. We find that predictions of the FUV extinction based upon the Cardelli, Clayton & Mathis (CCM) dependence on R_V give mixed results. For the seven extinction curves well represented by CCM in the infrared through ultraviolet, the FUV extinction is well predicted in three sight lines, over-predicted in two sight lines, and under-predicted in 2 sight lines. A Maximum Entropy Method analysis using a simple three component grain model shows that seven of the nine sight lines in the study require a larger fraction of grain materials to be in dust when FUV extinction is included in the models. Most of the added grain material is in the form of small (radii < 200 A) grains.Comment: Accepted for publication in the Astrophysical Journal. 31 pages with 7 figure

Size and frequency of natural forest disturbances and Amazon carbon balance

Forest inventory studies in the Amazon indicate a large terrestrial carbon sink. However, field plots may fail to represent forest mortality processes at landscape-scales of tropical forests. Here we characterize the frequency distribution of disturbance events in natural forests from 0.01 ha to 2,651 ha size throughout Amazonia using a novel combination of forest inventory, airborne lidar and satellite remote sensing data. We find that small-scale mortality events are responsible for aboveground biomass losses of B1.28 Pg C y 1 over the entire Amazon region. We also find that intermediate-scale disturbances account for losses of B0.01 Pg C y 1 , and that the largest-scale disturbances as a result of blow-downs only account for losses of B0.003 Pg C y 1 . Simulation of growth and mortality indicates that even when all carbon losses from intermediate and large-scale disturbances are considered, these are outweighed by the net biomass accumulation by tree growth, supporting the inference of an Amazon carbon sink

Erratum: "Photoionization Modeling of Oxygen K Absorption in the Interstellar Medium, the Chandra Grating Spectra of XTE J1817-330" (2013, Apj, 768, 60)

In the published version of this paper, there are some minor inaccuracies in the absorption-line wavelengths listed in Table 4 as a result of a faulty reduction procedure of the Obs6615 spectrum. The shifts have been detected in a comparison with the wavelengths listed for this spectrum in the Chandra Transmission Grating Catalog and Archive (TGCat8). They are due to incorrect centroid positions of the zero-order image in both reductions as determined by the tgdetect utility which, when disentangled, yield the improved line positions of the amended Table 4 given below. It must also be pointed out that other quantitative findings of the original paper: 1. Table 5, p. 9: the column density (NH), ionization parameter, oxygen abundance of the warmabs model and the normalization and photon index of the power-law model; 2. Table 6, p. 9: the hydrogen column density of the warmabs fit; 3. Table 7, p. 9: the present oxygen equivalent widths of XTE J1817-330; and 4. Table 8, p. 10: the present oxygen column densities of XTE J1817-330 derived from both the curve of growth and warmabs model fit have been revised in the new light and are, within the estimated uncertainty ranges, in good accord with the new rendering

Relationship between latent and rebound viruses in a clinical trial of anti-HIV-1 antibody 3BNC117.

A clinical trial was performed to evaluate 3BNC117, a potent anti-HIV-1 antibody, in infected individuals during suppressive antiretroviral therapy and subsequent analytical treatment interruption (ATI). The circulating reservoir was evaluated by quantitative and qualitative viral outgrowth assay (Q2VOA) at entry and after 6 mo. There were no significant quantitative changes in the size of the reservoir before ATI, and the composition of circulating reservoir clones varied in a manner that did not correlate with 3BNC117 sensitivity. 3BNC117 binding site amino acid variants found in rebound viruses preexisted in the latent reservoir. However, only 3 of 217 rebound viruses were identical to 868 latent viruses isolated by Q2VOA and near full-length sequencing. Instead, 63% of the rebound viruses appeared to be recombinants, even in individuals with 3BNC117-resistant reservoir viruses. In conclusion, viruses emerging during ATI in individuals treated with 3BNC117 are not the dominant species found in the circulating latent reservoir, but frequently appear to represent recombinants of latent viruses

Rice Galaxy: An open resource for plant science

Background: Rice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies and high-density genotyping platforms for genome variation analysis and gene discovery. Germplasm collections representing rice diversity, improved varieties, and elite breeding materials are accessible through rice gene banks for use in research and breeding, with many having genome sequences and high-density genotype data available. Combining phenotypic and genotypic information on these accessions enables genome-wide association analysis, which is driving quantitative trait loci discovery and molecular marker development. Comparative sequence analyses across quantitative trait loci regions facilitate the discovery of novel alleles. Analyses involving DNA sequences and large genotyping matrices for thousands of samples, however, pose a challenge to non−computer savvy rice researchers. Findings: The Rice Galaxy resource has shared datasets that include high-density genotypes from the 3,000 Rice Genomes project and sequences with corresponding annotations from 9 published rice genomes. The Rice Galaxy web server and deployment installer includes tools for designing single-nucleotide polymorphism assays, analyzing genome-wide association studies, population diversity, rice−bacterial pathogen diagnostics, and a suite of published genomic prediction methods. A prototype Rice Galaxy compliant to Open Access, Open Data, and Findable, Accessible, Interoperable, and Reproducible principles is also presented. Conclusions: Rice Galaxy is a freely available resource that empowers the plant research community to perform state-of-the-art analyses and utilize publicly available big datasets for both fundamental and applied science

Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics

Saber-toothed cats (Machairodontinae) are among the most widely recognized representatives of the now largely extinct Pleistocene megafauna. However, many aspects of their ecology, evolution, and extinction remain uncertain. Although ancient-DNA studies have led to huge advances in our knowledge of these aspects of many other megafauna species (e.g., mammoths and cave bears), relatively few ancient-DNA studies have focused on saber-toothed cats [1–3], and they have been restricted to short fragments of mitochondrial DNA. Here we investigate the evolutionary history of two lineages of saber-toothed cats (Smilodon and Homotherium) in relation to living carnivores and find that the Machairodontinae form a well-supported clade that is distinct from all living felids. We present partial mitochondrial genomes from one S. populator sample and three Homotherium sp. samples, including the only Late Pleistocene Homotherium sample from Eurasia [4]. We confirm the identification of the unique Late Pleistocene European fossil through ancient-DNA analyses, thus strengthening the evidence that Homotherium occurred in Europe over 200,000 years later than previously believed. This in turn forces a re-evaluation of its demography and extinction dynamics. Within the Machairodontinae, we find a deep divergence between Smilodon and Homotherium (∼18 million years) but limited diversity between the American and European Homotherium specimens. The genetic data support the hypothesis that all Late Pleistocene (or post-Villafrancian) Homotherium should be considered a single species, H. latidens, which was previously proposed based on morphological data [5, 6]. Paijmans et al. present ancient DNA from some of the most recognized extinct Pleistocene megafauna: the saber-toothed cats. The results elucidate the evolutionary history of these iconic carnivores and provide genetic evidence that saber-toothed cats existed in Europe over 200,000 years later than previously believed.This project received funding from the European Research Council (consolidator grant GeneFlow no. 310763 to M.H.), European Union’s Seventh Framework Programme for research, technological development, and demonstration (grant no. FP7-PEOPLE-2011-IEF-298820 to R.B.), and Lundbeck Foundation (grant no. R52-A5062 to M.L.Z.-M.)