Few smooth d-polytopes with n lattice points

We prove that, for fixed n there exist only finitely many embeddings of Q-factorial toric varieties X into P^n that are induced by a complete linear system. The proof is based on a combinatorial result that for fixed nonnegative integers d and n, there are only finitely many smooth d-polytopes with n lattice points. We also enumerate all smooth 3-polytopes with at most 12 lattice points. In fact, it is sufficient to bound the singularities and the number of lattice points on edges to prove finiteness.Comment: 20+2 pages; major revision: new author, new structure, new result

Feedback-amplified electrochemical dual-plate boron-doped diamond microtrench detector for flow injection analysis

An electrochemical flow cell with a boron‐doped diamond dual‐plate microtrench electrode has been developed and demonstrated for hydroquinone flow injection electroanalysis in phosphate buffer pH 7. Using the electrochemical generator‐collector feedback detector improves the sensitivity by one order of magnitude (when compared to a single working electrode detector). The diffusion process is switched from an analyte consuming “external” process to an analyte regenerating “internal” process with benefits in selectivity and sensitivity

Biowep: a workflow enactment portal for bioinformatics applications

<p>Abstract</p> <p>Background</p> <p>The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS), can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing.</p> <p>Results</p> <p>We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved.</p> <p>Conclusion</p> <p>We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical databases and analysis software and the creation of effective workflows can significantly improve automation of in-silico analysis. Biowep is available for interested researchers as a reference portal. They are invited to submit their workflows to the workflow repository. Biowep is further being developed in the sphere of the Laboratory of Interdisciplinary Technologies in Bioinformatics – LITBIO.</p

A novel method for the absolute fluorescence yield measurement by AIRFLY

One of the goals of the AIRFLY (AIR FLuorescence Yield) experiment is to measure the absolute fluorescence yield induced by electrons in air to better than 10% precision. We introduce a new technique for measurement of the absolute fluorescence yield of the 337 nm line that has the advantage of reducing the systematic uncertainty due to the detector calibration. The principle is to compare the measured fluorescence yield to a well known process - the Cerenkov emission. Preliminary measurements taken in the BFT (Beam Test Facility) in Frascati, Italy with 350 MeV electrons are presented. Beam tests in the Argonne Wakefield Accelerator at the Argonne National Laboratory, USA with 14 MeV electrons have also shown that this technique can be applied at lower energies.Comment: presented at the 5th Fluorescence Workshop, El Escorial - Madrid, Spain, 16 - 20 September 200

Temperature and Humidity Dependence of Air Fluorescence Yield measured by AIRFLY

The fluorescence detection of ultra high energy cosmic rays requires a detailed knowledge of the fluorescence light emission from nitrogen molecules over a wide range of atmospheric parameters, corresponding to altitudes typical of the cosmic ray shower development in the atmosphere. We have studied the temperature and humidity dependence of the fluorescence light spectrum excited by MeV electrons in air. Results for the 313.6 nm, 337.1 nm, 353.7 nm and 391.4 nm bands are reported in this paper. We found that the temperature and humidity dependence of the quenching process changes the fluorescence yield by a sizeable amount (up to 20%) and its effect must be included for a precise estimation of the energy of ultra high energy cosmic rays.Comment: presented at the 5th Fluorescence Workshop, El Escorial - Madrid, Spain, 16 - 20 September 2007, to appear in Nuclear Instruments and Methods

PhyloPat: phylogenetic pattern analysis of eukaryotic genes

BACKGROUND: Phylogenetic patterns show the presence or absence of certain genes or proteins in a set of species. They can also be used to determine sets of genes or proteins that occur only in certain evolutionary branches. Phylogenetic patterns analysis has routinely been applied to protein databases such as COG and OrthoMCL, but not upon gene databases. Here we present a tool named PhyloPat which allows the complete Ensembl gene database to be queried using phylogenetic patterns. DESCRIPTION: PhyloPat is an easy-to-use webserver, which can be used to query the orthologies of all complete genomes within the EnsMart database using phylogenetic patterns. This enables the determination of sets of genes that occur only in certain evolutionary branches or even single species. We found in total 446,825 genes and 3,164,088 orthologous relationships within the EnsMart v40 database. We used a single linkage clustering algorithm to create 147,922 phylogenetic lineages, using every one of the orthologies provided by Ensembl. PhyloPat provides the possibility of querying with either binary phylogenetic patterns (created by checkboxes) or regular expressions. Specific branches of a phylogenetic tree of the 21 included species can be selected to create a branch-specific phylogenetic pattern. Users can also input a list of Ensembl or EMBL IDs to check which phylogenetic lineage any gene belongs to. The output can be saved in HTML, Excel or plain text format for further analysis. A link to the FatiGO web interface has been incorporated in the HTML output, creating easy access to functional information. Finally, lists of omnipresent, polypresent and oligopresent genes have been included. CONCLUSION: PhyloPat is the first tool to combine complete genome information with phylogenetic pattern querying. Since we used the orthologies generated by the accurate pipeline of Ensembl, the obtained phylogenetic lineages are reliable. The completeness and reliability of these phylogenetic lineages will further increase with the addition of newly found orthologous relationships within each new Ensembl release

Search for Gravitational Waves Associated with 39 Gamma-Ray Bursts Using Data from the Second, Third, and Fourth LIGO Runs

We present the results of a search for short-duration gravitational-wave bursts associated with 39 gamma-ray bursts (GRBs) detected by gamma-ray satellite experiments during LIGO's S2, S3, and S4 science runs. The search involves calculating the crosscorrelation between two interferometer data streams surrounding the GRB trigger time. We search for associated gravitational radiation from single GRBs, and also apply statistical tests to search for a gravitational-wave signature associated with the whole sample. For the sample examined, we find no evidence for the association of gravitational radiation with GRBs, either on a single-GRB basis or on a statistical basis. Simulating gravitational-wave bursts with sine-gaussian waveforms, we set upper limits on the root-sum-square of the gravitational-wave strain amplitude of such waveforms at the times of the GRB triggers. We also demonstrate how a sample of several GRBs can be used collectively to set constraints on population models. The small number of GRBs and the significant change in sensitivity of the detectors over the three runs, however, limits the usefulness of a population study for the S2, S3, and S4 runs. Finally, we discuss prospects for the search sensitivity for the ongoing S5 run, and beyond for the next generation of detectors.Comment: 24 pages, 10 figures, 14 tables; minor changes to text and Fig. 2; accepted by Phys. Rev.

All-sky LIGO Search for Periodic Gravitational Waves in the Early S5 Data

We report on an all-sky search with the LIGO detectors for periodic gravitational waves in the frequency range 50--1100 Hz and with the frequency's time derivative in the range -5.0E-9 Hz/s to zero. Data from the first eight months of the fifth LIGO science run (S5) have been used in this search, which is based on a semi-coherent method (PowerFlux) of summing strain power. Observing no evidence of periodic gravitational radiation, we report 95% confidence-level upper limits on radiation emitted by any unknown isolated rotating neutron stars within the search range. Strain limits below 1.E-24 are obtained over a 200-Hz band, and the sensitivity improvement over previous searches increases the spatial volume sampled by an average factor of about 100 over the entire search band. For a neutron star with nominal equatorial ellipticity of 1.0E-6, the search is sensitive to distances as great as 500 pc--a range that could encompass many undiscovered neutron stars, albeit only a tiny fraction of which would likely be rotating fast enough to be accessible to LIGO. This ellipticity is at the upper range thought to be sustainable by conventional neutron stars and well below the maximum sustainable by a strange quark star.Comment: 6 pages, 1 figur

Search for gravitational waves from binary inspirals in S3 and S4 LIGO data

We report on a search for gravitational waves from the coalescence of compact binaries during the third and fourth LIGO science runs. The search focused on gravitational waves generated during the inspiral phase of the binary evolution. In our analysis, we considered three categories of compact binary systems, ordered by mass: (i) primordial black hole binaries with masses in the range 0.35 M(sun) < m1, m2 < 1.0 M(sun), (ii) binary neutron stars with masses in the range 1.0 M(sun) < m1, m2 < 3.0 M(sun), and (iii) binary black holes with masses in the range 3.0 M(sun)< m1, m2 < m_(max) with the additional constraint m1+ m2 < m_(max), where m_(max) was set to 40.0 M(sun) and 80.0 M(sun) in the third and fourth science runs, respectively. Although the detectors could probe to distances as far as tens of Mpc, no gravitational-wave signals were identified in the 1364 hours of data we analyzed. Assuming a binary population with a Gaussian distribution around 0.75-0.75 M(sun), 1.4-1.4 M(sun), and 5.0-5.0 M(sun), we derived 90%-confidence upper limit rates of 4.9 yr^(-1) L10^(-1) for primordial black hole binaries, 1.2 yr^(-1) L10^(-1) for binary neutron stars, and 0.5 yr^(-1) L10^(-1) for stellar mass binary black holes, where L10 is 10^(10) times the blue light luminosity of the Sun.Comment: 12 pages, 11 figure