GPSDB: a new database for synonyms expansion of gene and protein names

Summary: We present a new database, GPSDB (Gene and Protein Synonyms DataBase) which collects gene/protein names, in a species specific way, from 14 main biological resources. A web-based search interface gives access to the database: given a gene/protein name, it retrieves all synonyms for this entity and queries Medline with a set of user-selected terms. Availability: GPSDB is freely available from http://biomint.oefai.at/ Contact: [email protected]

Quantifying Phenotypic Variation in Isogenic Caenorhabditis elegans Expressing Phsp-16.2::gfp by Clustering 2D Expression Patterns

Isogenic populations of animals still show a surprisingly large amount of phenotypic variation between individuals. Using a GFP reporter that has been shown to predict longevity and resistance to stress in isogenic populations of the nematode Caenorhabditis elegans, we examined residual variation in expression of this GFP reporter. We found that when we separated the populations into brightest 3% and dimmest 3% we also saw variation in relative expression patterns that distinguished the bright and dim worms. Using a novel image processing method which is capable of directly analyzing worm images, we found that bright worms (after normalization to remove variation between bright and dim worms) had expression patterns that correlated with other bright worms but that dim worms fell into two distinct expression patterns. We have analysed a small set of worms with confocal microscopy to validate these findings, and found that the activity loci in these clusters are caused by extremely bright intestine cells. We also found that the vast majority of the fluorescent signal for all worms came from intestinal cells as well, which may indicate that the activity of intestinal cells is responsible for the observed patterns. Phenotypic variation in C. elegans is still not well understood but our proposed novel method to analyze complex expression patterns offers a way to enable a better understanding

Analysis of unresolved complex mixtures of hydrocarbons extracted from Late Archean sediments by comprehensive two-dimensional gas chromatography (GC×GC)

Author Posting. © Elsevier B.V., 2008. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Organic Geochemistry 39 (2008): 846-867, doi:10.1016/j.orggeochem.2008.03.006.Hydrocarbon mixtures too complex to resolve by traditional capillary gas chromatrography display gas chromatograms with dramatically rising baselines or “humps” of coeluting compounds that are termed unresolved complex mixtures (UCMs). Because the constituents of UCMs are not ordinarily identified, a large amount of geochemical information is never explored. Gas chromatograms of saturated/unsaturated hydrocarbons extracted from Late Archean argillites and greywackes of the southern Abitibi Province of Ontario, Canada contain UCMs with different appearances or “topologies” relating to the intensity and retention time of the compounds comprising the UCMs. These topologies appear to have some level of stratigraphic organization, such that samples collected at any stratigraphic formation collectively are dominated by UCMs that either elute early- (within a window of C15-C20 of n-alkanes), early- to mid- (C15-C30 of n-alkanes), or have a broad UCM that extends through the entire retention time of the sample (from C15-C42 of n-alkanes). Comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC-MS) was used to resolve the constituents forming these various UCMs. Early- to mid- eluting UCMs are dominated by configurational isomers of alkyl-substituted and non substituted polycyclic compounds that contain up to six rings. Late eluting UCMs are composed of C36-C40 mono-, bi-, and tricyclic archaeal isoprenoid diastereomers. Broad UCMs spanning the retention time of compound elution contain nearly the same compounds observed in the early-, mid-, and late retention time UCMs. Although the origin of the polycyclic compounds is unclear, the variations in the UCM topology appear to depend on the concentration of initial compound classes that have the potential to become isomerized. Isomerization of these constituents may have resulted from hydrothermal alteration of organic matter.This project was supported by NASA Exobiology grant #NAG5-13446 to Fabien Kenig. GC×GC analysis was supported by NSF grant IIS-0430835 and the Seaver Foundation to Christopher M. Reddy. Preparation of the archaeal biphytane standard was supported by NSF grant ARC-0520226 to Benjamin Van Mooy

Manipulating Biopolymer Dynamics by Anisotropic Nanoconfinement

How the geometry of nano-sized confinement affects dynamics of biomaterials is interesting yet poorly understood. An elucidation of structural details upon nano-sized confinement may benefit manufacturing pharmaceuticals in biomaterial sciences and medicine. The behavior of biopolymers in nano-sized confinement is investigated using coarse-grained models and molecular simulations. Particularly, we address the effects of shapes of a confinement on protein folding dynamics by measuring folding rates and dissecting structural properties of the transition states in nano-sized spheres and ellipsoids. We find that when the form of a confinement resembles the geometrical properties of the transition states, the rates of folding kinetics are most enhanced. This knowledge of shape selectivity in identifying optimal conditions for reactions will have a broad impact in nanotechnology and pharmaceutical sciences.Comment: to appear in Nano Letter

An Evaluation of Naive Bayes Variants in Content-Based Learning for Spam Filtering

We describe an in-depth analysis of spam-filtering performance of a simple Naive Bayes learner and two extended variants. A set of seven mailboxes comprising about 65,000 mails from seven different users, as well as a representative snapshot of 25,000 mails which were received over 18 weeks by a single user, were used for evaluation. Our main motiva-tion was to test whether two extended variants of Naive Bayes learning, SA-Train and CRM114, were superior to simple Naive Bayes learning, represented by SpamBayes. Surprisingly, we found that the performance of these systems was remarkably similar and that the extended systems have significant weaknesses which are not apparent for the simpler Naive Bayes learner. The simpler Naive Bayes learner, SpamBayes, also offers the most stable performance in that it deteriorates least over time. Over-all, SpamBayes should be preferred over the more complex variants

An Evaluation of Naive Bayes Variants in Content- Based Learning for Spam Filtering

Abstract. We describe an in-depth analysis of spam-filtering performance of a simple Naive Bayes learner and two current variants. A set of seven mailboxes comprising about 65,000 mails from seven different users, as well as a representative snapshot of 25,000 mails which were received over 18 weeks by a single user, were used for evaluation. Our main motivation was to test whether two variants of Naive Bayes learning, SpamAssassin and CRM114, were superior to simple Naive Bayes learning, represented by SpamBayes. Surprisingly, we found that the performance of these systems was remarkably similar and that the extended systems have significant weaknesses which are not apparent for the simpler Naive Bayes learner. The simpler Naive Bayes learner, SpamBayes, also offers the most stable performance in that it deteriorates least over time. Overall, SpamBayes should be preferred over the more complex variants