Biomedical subjects

Scott White

Publications and source records attributed to Scott White.

4 recordsLinked to original sources

PubMed2006

Generative model for feedback networks.

We propose a model for network formation and study some of its statistical properties. The motivation for the model comes from the growth of several kinds of real networks (i.e., kinship and trading networks, networks of corporate alliances, networks of autocatalytic chemical reactions). These networks grow either by establishing closer connections by adding links in the existing network or by adding new nodes. A node in these networks lacks the information of the entire network. In order to establish a closer connection to other nodes it starts a search in the neighboring part of the network and waits for a possible feedback from a distant node that received the "searching signal." Our model imitates this behavior by growing the network via the addition of a link that creates a cycle in the network or via the addition of a new node with a link to the network. The forming of a cycle creates feedback between the two ending nodes. After choosing a starting node, a search is made for another node at a suitable distance; if such a node is found, a link is established between this and the starting node, otherwise (such a node cannot be found) a new node is added and is linked to the starting node. We simulate this algorithm and find that we cannot reject the hypothesis that the empirical degree distribution is a q-exponential function, which has been used to model long-range processes in nonequilibrium statistical mechanics.

Journal Article↗

PubMed2005

Phasing in the presence of radiation damage.

In the accurate estimation of small signals, redundancy of observations is often seen as an essential tool for the experimenter. This is particularly true during macromolecular structure determination by single-wavelength anomalous dispersion (SAD), where the exploitable signal can be less than a few percent. At the most intense undulator synchrotron beamlines, the effect of radiation damage can be such that all usable signal is obscured. Here the magnitude of this effect in experiments performed at the Se K-edge is quantified. Six successive data sets were collected on the same crystal, interspersed with two exposures to the X-ray beam during which data were not collected. It is shown that the very first data set has excellent phasing statistics, whereas these statistics degrade for the later data sets. Merging several data sets into one, highly redundant, data set only gave moderate improvements as a result of the presence of radiation damage. Part of the damage could be corrected for using a linear interpolation scheme. Interpolation of the data to a low-dose as well as to a high-dose data set allowed us to combine the SAD method with the radiation-damage induced phasing (RIP) technique, which further improved the experimental phases, especially after density modification. Some recommendations are given on how to mitigate the effect of radiation damage during structure determination.

Bacterial Proteins↗

PubMed2005

SNPsFinder--a web-based application for genome-wide discovery of single nucleotide polymorphisms in microbial genomes.

UNLABELLED: Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variations in closely related microbial species, strains or isolates. Some SNPs confer selective advantages for microbial pathogens during infection and many others are powerful genetic markers for distinguishing closely related strains or isolates that could not be distinguished otherwise. To facilitate SNP discovery in microbial genomes, we have developed a web-based application, SNPsFinder, for genome-wide identification of SNPs. SNPsFinder takes multiple genome sequences as input to identify SNPs within homologous regions. It can also take contig sequences and sequence quality scores from ongoing sequencing projects for SNP prediction. SNPsFinder will use genome sequence annotation if available and map the predicted SNP regions to known genes or regions to assist further evaluation of the predicted SNPs for their functional significance. SNPsFinder can generate PCR primers for all predicted SNP regions according to user's input parameters to facilitate experimental validation. The results from SNPsFinder analysis are accessible through the World Wide Web. AVAILABILITY: The SNPsFinder program is available at http://snpsfinder.lanl.gov/. SUPPLEMENTARY INFORMATION: The user's manual is available at http://snpsfinder.lanl.gov/UsersManual/

Algorithms↗

PubMedDate not supplied

Retapamulin ointment twice daily for 5 days vs oral cephalexin twice daily for 10 days for empiric treatment of secondarily infected traumatic lesions of the skin.

INTRODUCTION: Retapamulin is a novel, topical antibacterial of the pleuromutilin class in development for the treatment of secondarily infected traumatic lesions of the skin. METHODS: The efficacy, safety, and tolerability of topical retapamulin ointment, 1% for 5 days twice daily was evaluated in 2 identical, randomized, double-blind, double-dummy, multicenter studies vs oral cephalexin, 500 mg twice daily for 10 days, in 1904 patients with secondarily infected traumatic lesions. RESULTS: Clinical success rates were 89.5% in protocol-adherent patients receiving retapamulin compared with 91.9% for cephalexin (treatment difference, -2.5% [95% confidence interval, -5.4% to 0.5%]). In patients with Staphylococcus aureus or Streptococcus pyogenes at baseline, clinical success was 89.2% (365/409) for retapamulin and 92.6% (63/68) for cephalexin. Safety and tolerability were similar between treatments. Noncompliance (defined as using or taking <80% of doses) was recorded in 8.0% (51/636) of patients taking cephalexin compared with 0.39% (5/1268) of patients receiving retapamulin. CONCLUSIONS: Retapamulin offers a novel, effective, and convenient topical treatment for secondarily infected traumatic lesions.

Administration, Oral↗