58 research outputs found
The SOFG Anatomy Entry List (SAEL):an annotation tool for functional genomics data
A great deal of data in functional genomics studies needs to be annotated with
low-resolution anatomical terms. For example, gene expression assays based on
manually dissected samples (microarray, SAGE, etc.) need high-level anatomical
terms to describe sample origin. First-pass annotation in high-throughput assays (e.g.
large-scale in situ gene expression screens or phenotype screens) and bibliographic
applications, such as selection of keywords, would also benefit from a minimum
set of standard anatomical terms. Although only simple terms are required, the
researcher faces serious practical problems of inconsistency and confusion, given
the different aims and the range of complexity of existing anatomy ontologies. A
Standards and Ontologies for Functional Genomics (SOFG) group therefore initiated
discussions between several of the major anatomical ontologies for higher vertebrates.
As we report here, one result of these discussions is a simple, accessible, controlled
vocabulary of gross anatomical terms, the SOFG Anatomy Entry List (SAEL).
The SAEL is available from http://www.sofg.org and is intended as a resource
for biologists, curators, bioinformaticians and developers of software supporting
functional genomics. It can be used directly for annotation in the contexts described
above. Importantly, each term is linked to the corresponding term in each of the
major anatomy ontologies. Where the simple list does not provide enough detail or
sophistication, therefore, the researcher can use the SAEL to choose the appropriate
ontology and move directly to the relevant term as an entry point. The SAEL links will
also be used to support computational access to the respective ontologies
The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration
The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or âontologiesâ. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform, and new ontologies being created, on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved in the future
LSST: from Science Drivers to Reference Design and Anticipated Data Products
(Abridged) We describe here the most ambitious survey currently planned in
the optical, the Large Synoptic Survey Telescope (LSST). A vast array of
science will be enabled by a single wide-deep-fast sky survey, and LSST will
have unique survey capability in the faint time domain. The LSST design is
driven by four main science themes: probing dark energy and dark matter, taking
an inventory of the Solar System, exploring the transient optical sky, and
mapping the Milky Way. LSST will be a wide-field ground-based system sited at
Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m
effective) primary mirror, a 9.6 deg field of view, and a 3.2 Gigapixel
camera. The standard observing sequence will consist of pairs of 15-second
exposures in a given field, with two such visits in each pointing in a given
night. With these repeats, the LSST system is capable of imaging about 10,000
square degrees of sky in a single filter in three nights. The typical 5
point-source depth in a single visit in will be (AB). The
project is in the construction phase and will begin regular survey operations
by 2022. The survey area will be contained within 30,000 deg with
, and will be imaged multiple times in six bands, ,
covering the wavelength range 320--1050 nm. About 90\% of the observing time
will be devoted to a deep-wide-fast survey mode which will uniformly observe a
18,000 deg region about 800 times (summed over all six bands) during the
anticipated 10 years of operations, and yield a coadded map to . The
remaining 10\% of the observing time will be allocated to projects such as a
Very Deep and Fast time domain survey. The goal is to make LSST data products,
including a relational database of about 32 trillion observations of 40 billion
objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures
available from https://www.lsst.org/overvie
Photochemical dihydrogen production using an analogue of the active site of [NiFe] hydrogenase
The photoproduction of dihydrogen (H2) by a low molecular weight analogue of the active site of [NiFe] hydrogenase has been investigated by the reduction of the [NiFe2] cluster, 1, by a photosensitier PS (PS = [ReCl(CO)3(bpy)] or [Ru(bpy)3][PF6]2). Reductive quenching of the 3MLCT excited state of the photosensitiser by NEt3 or N(CH2CH2OH)3 (TEOA) generates PSâąâ, and subsequent intermolecular electron transfer to 1 produces the reduced anionic form of 1. Time-resolved infrared spectroscopy (TRIR) has been used to probe the intermediates throughout the reduction of 1 and subsequent photocatalytic H2 production from [HTEOA][BF4], which was monitored by gas chromatography. Two structural isomers of the reduced form of 1 (1aâąâ and 1bâąâ) were detected by Fourier transform infrared spectroscopy (FTIR) in both CH3CN and DMF (dimethylformamide), while only 1aâąâ was detected in CH2Cl2. Structures for these intermediates are proposed from the results of density functional theory calculations and FTIR spectroscopy. 1aâąâ is assigned to a similar structure to 1 with six terminal carbonyl ligands, while calculations suggest that in 1bâąâ two of the carbonyl groups bridge the Fe centres, consistent with the peak observed at 1714 cmâ1 in the FTIR spectrum for 1bâąâ in CH3CN, assigned to a Îœ(CO) stretching vibration. The formation of 1aâąâ and 1bâąâ and the production of H2 was studied in CH3CN, DMF and CH2Cl2. Although the more catalytically active species (1aâąâ or 1bâąâ) could not be determined, photocatalysis was observed only in CH3CN and DMF
Design, Performance, and Calibration of the CMS Hadron-Outer Calorimeter
The CMS hadron calorimeter is a sampling calorimeter with brass absorber and plastic scintillator tiles with wavelength shifting fibres for carrying the light to the readout device. The barrel hadron calorimeter is complemented with an outer calorimeter to ensure high energy shower containment in the calorimeter. Fabrication, testing and calibration of the outer hadron calorimeter are carried out keeping in mind its importance in the energy measurement of jets in view of linearity and resolution. It will provide a net improvement in missing \et measurements at LHC energies. The outer hadron calorimeter will also be used for the muon trigger in coincidence with other muon chambers in CMS
Design, Performance, and Calibration of CMS Hadron-Barrel Calorimeter Wedges
Extensive measurements have been made with pions, electrons and muons on four production wedges of the Compact Muon Solenoid (CMS) hadron barrel (HB) calorimeter in the H2 beam line at CERN with particle momenta varying from 20 to 300 GeV/c. Data were taken both with and without a prototype electromagnetic lead tungstate crystal calorimeter (EB) in front of the hadron calorimeter. The time structure of the events was measured with the full chain of preproduction front-end electronics running at 34 MHz. Moving-wire radioactive source data were also collected for all scintillator layers in the HB. These measurements set the absolute calibration of the HB prior to first pp collisions to approximately 4%
Design, Performance and Calibration of the CMS Forward Calorimeter Wedges
We report on the test beam results and calibration methods using charged particles of the CMS Forward Calorimeter (HF). The HF calorimeter covers a large pseudorapidity region (3\l |\eta| \le 5), and is essential for large number of physics channels with missing transverse energy. It is also expected to play a prominent role in the measurement of forward tagging jets in weak boson fusion channels. The HF calorimeter is based on steel absorber with embedded fused-silica-core optical fibers where Cherenkov radiation forms the basis of signal generation. Thus, the detector is essentially sensitive only to the electromagnetic shower core and is highly non-compensating (e/h \approx 5). This feature is also manifest in narrow and relatively short showers compared to similar calorimeters based on ionization. The choice of fused-silica optical fibers as active material is dictated by its exceptional radiation hardness. The electromagnetic energy resolution is dominated by photoelectron statistics and can be expressed in the customary form as a/\sqrt{E} + b. The stochastic term a is 198% and the constant term b is 9%. The hadronic energy resolution is largely determined by the fluctuations in the neutral pion production in showers, and when it is expressed as in the electromagnetic case, a = 280% and b = 11%
Design, Performance, and Calibration of CMS Hadron Endcap Calorimeters
Detailed measurements have been made with the CMS hadron calorimeter endcaps (HE) in response to beams of muons, electrons, and pions. Readout of HE with custom electronics and hybrid photodiodes (HPDs) shows no change of performance compared to readout with commercial electronics and photomultipliers. When combined with lead-tungstenate crystals, an energy resolution of 8\% is achieved with 300 GeV/c pions. A laser calibration system is used to set the timing and monitor operation of the complete electronics chain. Data taken with radioactive sources in comparison with test beam pions provides an absolute initial calibration of HE to approximately 4\% to 5\%
Energy Response and Longitudinal Shower Profiles Measured in CMS HCAL and Comparison With Geant4
The response of the CMS combined electromagnetic and hadron calorimeter to beams of pions with momenta in the range 5-300 GeV/c has been measured in the H2 test beam at CERN. The raw response with the electromagnetic compartment calibrated to electrons and the hadron compartment calibrated to 300 GeV pions may be represented by sigma = (1.2) sqrt{E} oplus (0.095) E. The fraction of energy visible in the calorimeter ranges from 0.72 at 5 GeV to 0.95 at 300 GeV, indicating a substantial nonlinearity. The intrinsic electron to hadron ratios are fit as a function of energy and found to be in the range 1.3-2.7 for the electromagnetic compartment and 1.4-1.8 for the hadronic compartment. The fits are used to correct the non-linearity of the e pi response to 5% over the entire measured range resulting in a substantially improved resolution at low energy. Longitudinal shower profile have been measured in detail and compared to Geant4 models, LHEP-3.7 and QGSP-2.8. At energies below 30 GeV, the data, LHEP and QGSP are in agreement. Above 30 GeV, LHEP gives a more accurate simulation of the longitudinal shower profile
Synchronization and Timing in CMS HCAL
The synchronization and timing of the hadron calorimeter (HCAL) for the Compact Muon Solenoid has been extensively studied with test beams at CERN during the period 2003-4, including runs with 40 MHz structured beam. The relative phases of the signals from different calorimeter segments are timed to 1 ns accuracy using a laser and equalized using programmable delay settings in the front-end electronics. The beam was used to verify the timing and to map out the entire range of pulse shapes over the 25 ns interval between beam crossings. These data were used to make detailed measurements of energy-dependent time slewing effects and to tune the electronics for optimal performance
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