Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm

Clustering protein sequences according to inferred homology is a fundamental step in the analysis of many large data sets. Since the publication of the Markov Clustering (MCL) algorithm in 2002, it has been the centerpiece of several popular applications. Each of these approaches generates an undirected graph that represents sequences as nodes connected to each other by edges weighted with a BLAST-based metric. MCL is then used to infer clusters of homologous proteins by analyzing these graphs. The various approaches differ only by how they weight the edges, yet there has been very little direct examination of the relative performance of alternative edge-weighting metrics. This study compares the performance of four BLAST-based edge-weighting metrics: the bit score, bit score ratio (BSR), bit score over anchored length (BAL), and negative common log of the expectation value (NLE). Performance is tested using the Extended CEGMA KOGs (ECK) database, which we introduce here. All metrics performed similarly when analyzing full-length sequences, but dramatic differences emerged as progressively larger fractions of the test sequences were split into fragments. The BSR and BAL successfully rescued subsets of clusters by strengthening certain types of alignments between fragmented sequences, but also shifted the largest correct scores down near the range of scores generated from spurious alignments. This penalty outweighed the benefits in most test cases, and was greatly exacerbated by increasing the MCL inflation parameter, making these metrics less robust than the bit score or the more popular NLE. Notably, the bit score performed as well or better than the other three metrics in all scenarios. The results provide a strong case for use of the bit score, which appears to offer equivalent or superior performance to the more popular NLE. The insight that MCL-based clustering methods can be improved using a more tractable edge-weighting metric will greatly simplify future implementations. We demonstrate this with our own minimalist Python implementation: Porthos, which uses only standard libraries and can process a graph with 25 m + edges connecting the 60 k + KOG sequences in half a minute using less than half a gigabyte of memory.https://doi.org/10.1186/s12859-015-0625-xhttps://doi.org/10.1186/s12859-015-0690-

Hubble Space Telescope STIS Observations of GRB 000301C: CCD Imaging and Near-Ultraviolet MAMA Spectroscopy

We present Space Telescope Imaging Spectrograph observations of the optical transient (OT) counterpart of the γ-ray burster GRB 000301C obtained 5 days after the burst, on 2000 March 6. CCD clear-aperture imaging reveals a R ≃ 21.50 ± 0.15 source with no apparent host galaxy. An 8000 s, 1150 Å 18 on the line of sight to the OT. This measured redshift is conservatively a lower limit to the GRB redshift. However, as all other GRBs that have deep Hubble Space Telescope images appear to lie on the stellar field of a host galaxy, and as the large H I column density measured here and in later ground-based observations is unlikely on a random line of sight, we believe we are probably seeing absorption from H I in the host galaxy. In any case, this represents the largest direct redshift determination of a γ-ray burster to date. Our data are compatible with an OT spectrum represented by a power law with an intrinsic index α = 1.2 (f_ν ∝ ν^(-α)) and no extinction in the host galaxy, or with α = 0.5 and extinction by SMC-like dust in the OT rest frame with A_V = 0.15. The large N_(H I) and the lack of a detected host are similar to the situation for damped Lyα absorbers at z > 2

HST/STIS observations of GRB000301C: CCD imaging and NUV MAMA spectroscopy

We present HST/STIS observations of the optical counterpart (OT) of the gamma-ray burster GRB 000301C obtained on 2000 March 6, five days after the burst. CCD clear aperture imaging reveals a R ~ 21.50+/-0.15 source with no apparent host galaxy. An 8000 s, 1150 < lambda/A < 3300 NUV-MAMA prism spectrum shows a relatively flat continuum (in f_lambda) between 2800 and 3300 A, with a mean flux 8.7 (+0.8,-1.6)+/- 2.6 10^(-18) ergs/s/cm^2/A, and a sharp break centered at 2797+/-25 A. We interpret it as HI Lyman break at z = 2.067+/-0.025 indicating the presence of a cloud with a HI column density log(HI) > 18 on the line-of-sight to the OT. This value is conservatively a lower limit to the GRB redshift. However, the facts that large N(HI) system are usually considered as progenitors of present day galaxies and that other OTs are found associated with star forming galaxies strongly suggest that it is the GRB redshift. In any case, this represents the largest direct redshift determination of a gamma-ray burster to date. Our data are compatible with an OT spectrum represented by a power-law with an intrinsic index \alpha = 1.2((f_nu \propto nu^-alpha) and no extinction in the host galaxy or with alpha = 0.5 and extinction by a SMC-like dust in the OT rest-frame with A_V = 0.15. The large N(HI) and the lack of detected host is similar to the situation for damped Ly-alpha absorbers at z > 2.Comment: Replaced by final version. 10 p., 2 fig. Scheduled to appear in ApJ 555 n2 Jul 10, 2001. Minor changes, both redshift and mean near UV flux are revised with slightly larger values, due to a wrong offset sign in the wavelength calibratio

Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease

The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease. While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Through the sequencing of the 16S rRNA gene and of whole community DNA we provide a glimpse at the global genetic, metabolic, and ecological changes associated with periodontitis in 15 subgingival plaque samples, four from each of two periodontitis patients, and the remaining samples from three healthy individuals. We also demonstrate the power of whole-metagenome sequencing approaches in characterizing the genomes of key players in the oral microbiome, including an unculturable TM7 organism. We reveal the disease microbiome to be enriched in virulence factors, and adapted to a parasitic lifestyle that takes advantage of the disrupted host homeostasis. Furthermore, diseased samples share a common structure that was not found in completely healthy samples, suggesting that the disease state may occupy a narrow region within the space of possible configurations of the oral microbiome. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease. Despite a modest level of sequencing (∼2 lanes Illumina 76 bp PE) and high human DNA contamination (up to ∼90%) we were able to partially reconstruct several oral microbes and to preliminarily characterize some systems-level differences between the healthy and diseased oral microbiomes

Hubble Space Telescope STIS Observations of GRB 000301C: CCD Imaging and Near-Ultraviolet MAMA Spectroscopy

We present Space Telescope Imaging Spectrograph observations of the optical transient (OT) counterpart of the γ-ray burster GRB 000301C obtained 5 days after the burst, on 2000 March 6. CCD clear-aperture imaging reveals a R ≃ 21.50 ± 0.15 source with no apparent host galaxy. An 8000 s, 1150 Å 18 on the line of sight to the OT. This measured redshift is conservatively a lower limit to the GRB redshift. However, as all other GRBs that have deep Hubble Space Telescope images appear to lie on the stellar field of a host galaxy, and as the large H I column density measured here and in later ground-based observations is unlikely on a random line of sight, we believe we are probably seeing absorption from H I in the host galaxy. In any case, this represents the largest direct redshift determination of a γ-ray burster to date. Our data are compatible with an OT spectrum represented by a power law with an intrinsic index α = 1.2 (f_ν ∝ ν^(-α)) and no extinction in the host galaxy, or with α = 0.5 and extinction by SMC-like dust in the OT rest frame with A_V = 0.15. The large N_(H I) and the lack of a detected host are similar to the situation for damped Lyα absorbers at z > 2

The Stakes in Bayh-Dole: Public Values Beyond the Pace of Innovation

Evaluation studies of the Bayh-Dole Act are generally concerned with the pace of innovation or the transgressions to the independence of research. While these concerns are important, I propose here to expand the range of public values considered in assessing Bayh-Dole and formulating future reforms. To this end, I first examine the changes in the terms of the Bayh-Dole debate and the drift in its design. Neoliberal ideas have had a definitive influence on U.S. innovation policy for the last thirty years, including legislation to strengthen patent protection. Moreover, the neoliberal policy agenda is articulated and justified in the interest of “competitiveness.” Rhetorically, this agenda equates competitiveness with economic growth and this with the public interest. Against that backdrop, I use Public Value Failure criteria to show that values such as political equality, transparency, and fairness in the distribution of the benefits of innovation, are worth considering to counter the “policy drift” of Bayh-Dole

ACC/AHA guidelines for the evaluation and management of chronic heart failure in the adult: Executive summary. A report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines (Committee to Revise the 1995 Guidelines for the Evaluation and Management of Heart Failure)

"Heart failure (HF) is a major public health problem in the United States. Nearly 5 million patients in this country have HF, and nearly 500,000 patients are diagnosed with HF for the first time each year. The disorder is the underlying reason for 12 to 15 million office visits and 6.5 million hospital days each year (1). During the last 10 years, the annual number of hospitalizations has increased from approximately 550,000 to nearly 900,000 for HF as a primary diagnosis and from 1.7 to 2.6 million for HF as a primary or secondary diagnosis (2). Nearly 300,000 patients die of HF as a primary or contributory cause each year, and the number of deaths has increased steadily despite advances in treatment. HF is primarily a disease of the elderly (3). Approximately 6% to 10% of people older than 65 years have HF (4), and approximately 80% of patients hospitalized with HF are more than 65 years old (2). HF is the most common Medicare diagnosis-related group, and more Medicare dollars are spent for the diagnosis and treatment of HF than for any other diagnosis (5). The total inpatient and outpatient costs for HF in 1991 were approximately $38.1 billion, which was approximately 5.4$500 million annually is spent on drugs for the treatment of HF. The American College of Cardiology (ACC) and the American Heart Association (AHA) first published guidelines for the evaluation and management of HF in 1995 (6). Since that time, a great deal of progress has been made in the development of both pharmacological and nonpharmacological approaches to treatment for this common, costly, disabling, and generally fatal disorder. For this reason, the 2 organizations believed that the time was right to reassess and update these guidelines, fully recognizing that the optimal therapy of HF remains a work in progress and that future guidelines will supersede these.

Penilaian Kinerja Keuangan Koperasi di Kabupaten Pelalawan

This paper describe development and financial performance of cooperative in District Pelalawan among 2007 - 2008. Studies on primary and secondary cooperative in 12 sub-districts. Method in this stady use performance measuring of productivity, efficiency, growth, liquidity, and solvability of cooperative. Productivity of cooperative in Pelalawan was highly but efficiency still low. Profit and income were highly, even liquidity of cooperative very high, and solvability was good