SEARCH · PubMed Health

Results for “Filing”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 487 records · Page 27Linked to original sources

PubMed1975

The large data base file structure dilemma.

This paper first presents a brief tutorial on the principal random file organization methods for handling two major applications--Transaction oriented systems and information storage and retrieval systems. It then addresses a particular large data base dilemma, not satisfactorily resolved by any of these methods, and which is currently under active investigation. Two approaches to a solution are described. One is called the hybrid inverted list; the other is based upon an old technique called super-imposed coding. The former has been implemented and has recently been installed in an operational system. Some statistics related to file characteristics in this application are provided, but operational cost and performance statistics are not yet available.

Computers↗

PubMed2005

Influence of boundaries of nanoporous crystals on molecular exchange under the conditions of single-file diffusion.

We study the tracer exchange of molecules between the phase adsorbed in one-dimensional channels and the surrounding gas phase by molecular dynamics simulations. Under the conditions of single-file diffusion, a novel boundary effect is observed. The shape of the tracer-exchange concentration profiles deviates from those obtained under the conditions of normal diffusion. Compared to the profiles for normal diffusion, which correspond to the same degree of exchange, the equilibrium concentration is reached faster at the boundaries and slower in the middle part of the channel in the case of single-file diffusion. This boundary effect is observed for the system neopentane in AlPO4-5 (which was chosen as a reference system), as well as for modified systems. The effect can be understood considering two diffusion mechanisms which occur in parallel. First, the diffusion of the whole chain of particles, that is, the center-of-mass diffusion, obeying the laws of normal diffusion. Second, the individual movement of the particles relative to the center of mass of the chain. The second mechanism admits additional displacements which, on average, lead to an accelerated exchange of the marginal particles.

Journal Article↗

PubMed2000

Object features, object locations, and object files: which does selective attention activate and when?

The representation within which attention operates was investigated in 3 experiments. The task was similar to that of R. Egly, J. Driver, and R. D. Rafal (1994). Participants had to detect the presence of a target at 1 of 4 ends of 2 shapes, differing in color and form. A precue appeared at 1 of the 4 possible corners. The 2 shapes occupied either the same or different locations in the cuing and target displays. The results showed that the cued object location was attended whether or not space was task relevant, whereas the cued object features (color and form) were attended only when these were task relevant. Moreover, when object file continuity was maintained through continuous movement, attention was found to follow the cued object file as it moved while also accruing to the cued location.

Adult↗

PubMed2005

A uniform proteomics MS/MS analysis platform utilizing open XML file formats.

The analysis of tandem mass (MS/MS) data to identify and quantify proteins is hampered by the heterogeneity of file formats at the raw spectral data, peptide identification, and protein identification levels. Different mass spectrometers output their raw spectral data in a variety of proprietary formats, and alternative methods that assign peptides to MS/MS spectra and infer protein identifications from those peptide assignments each write their results in different formats. Here we describe an MS/MS analysis platform, the Trans-Proteomic Pipeline, which makes use of open XML file formats for storage of data at the raw spectral data, peptide, and protein levels. This platform enables uniform analysis and exchange of MS/MS data generated from a variety of different instruments, and assigned peptides using a variety of different database search programs. We demonstrate this by applying the pipeline to data sets generated by ThermoFinnigan LCQ, ABI 4700 MALDI-TOF/TOF, and Waters Q-TOF instruments, and searched in turn using SEQUEST, Mascot, and COMET.

Archaeal Proteins↗

PubMed2000

Interaction between noise and file compression and its effect on the recognition of caries in digital imaging.

OBJECTIVES: To determine the interaction between image noise and file compression, with special emphasis on the accuracy of caries diagnosis. METHODS: Fifty-nine bitewing radiographs of patients were taken simultaneously with Ektaspeed Plus (Eastman-Kodak, Rochester, NY, USA) film without lead foil and the Digora storage phosphor system (Soredex, Helsinki, Finland). Three different levels of Gaussian noise were added to the original digital images which were then compressed with JPEG 53. Seven observers evaluated the presence and depth of caries lesions on selected approximal surfaces on a 5-point scale. The results of JPEG 27 compression from a previous study were also included. ROC analysis was used together with multivariate analysis of variance (MANOVA). RESULTS: JPEG 27 and 53 reduced the file size down to 7% and 4.6% of the original respectively. ROC curve analysis showed no significant difference between image conditions (original, JPEG 27, and JPEG 53) at the same noise level. JPEG 27 and 53 had larger Az scores than their original counterparts at the same noise level. However, MANOVA showed that for depth estimation of enamel lesions JPEG 53 resulted in a higher observer error. CONCLUSIONS: Both JPEG 53 and 27 could reduce some of the adverse effect of noise from the image by removing high spatial frequencies. JPEG 53, resulting in a compression ratio of 1:21, does not compromise the diagnostic performance in general. JPEG 53 compression may however affect the ability to detect enamel lesions.

Artifacts↗

PubMed2000

Comparison of observer performance in determining the position of endodontic files with physical measures in the evaluation of dental X-ray imaging systems.

OBJECTIVE: To examine the feasibility of substituting observers determining the accuracy of endodontic measurements for measurements of physical qualities in comparison of digital imaging systems. METHODS: Sensors from six digital imaging systems were compared for signal-to-noise ratio (SNR), modulation transfer function (MTF) and detective quantum efficiency (DQE). A total of 45 canals in teeth from human cadavers were instrumented to their apical foramina. Endodontic files, ranging in size from size 8 to size 20, were glued in place at random distances from the apical foramina spanning a range of +/- 3 mm. The teeth were imaged with the six digital systems and dental X-ray film. Fifteen dentists independently measured the distance from the end of the file to the apical foramen. Results were expressed as the measurement error. Measurement error was compared to SNR, MTF and DQE for each digital system. RESULTS: CDR (Schick, New York, NY, USA), Digora (Sordex, Helsinki, Finland) and Dexis (Provision Dental Systems, Palo Alto, CA, USA) produced the highest SNR values followed closely by RVG-4 (Trophy, Croissy-Beavborg, France). Sens-A-Ray (Dent-X/Regam Medical Systems, Sundsvall, Sweden), Dexis and the RVG-4 produced the best MTF results. Dexis had the greatest DQE. The mean measurement errors (in mm) were: Film 0.65, Dexis 0.69, CDR 0.71, RVG-4 0.74, Digora 0.89, Sens-A-Ray 0.97, and Visualix-2 (Gendex, Monza, Italy) 0.98. CONCLUSIONS: Digital systems closely approximate film in their accuracy when used for endodontic measurement providing that the assessment instruments have similar resolving power. DQE was the best physical predictor of system accuracy when compared with endodontic length measurements. MTF and SNR alone did not accurately predict observer precision.

Cadaver↗

PubMed1998

Influence of file handle attachments on tactile discrimination: an evaluation by dental students.

This study used a simulator to determine the effectiveness of two file-handle sleeves that are claimed to improve tactile discrimination and the ease of manipulation of endodontic hand instruments. Thirty final-year dental undergraduates inserted files into instrument setting rods until a putty resistance was felt, following which depth of penetration into the material was measured with a microscope. Results were analysed statistically. Despite favourable comments from participants in the trial, the devices failed to deliver enhanced tactile discrimination.

Dental Instruments↗

PubMed2002

Shaping ability of GTTM Rotary Files in simulated resin root canals.

AIM: The aim of this study was to determine the shaping ability of GT Rotary Files in simulated root canals. METHODOLOGY: Forty canals with four different shapes in terms of angle (40 degrees and 60 degrees) and position of curvature (straight section before curve: 8 and 12 mm) were prepared using a crown-down/stepback technique. Pre-operative and post-operative pictures, recorded using an image analysis system, were super-imposed and aberrations recorded. Measurements were carried out at 5 different points: at the canal orifice (0): half-way to the orifice in the straight section (HO); the beginning of the curve (BC); the apex of the curve (AC): the endpoint (EP). RESULTS: Two instrument fractures occurred and 9 instruments were deformed. Overall, eight zips and one ledge were created. There were significant differences (P < 0.001) for the total width of the canals between the various canal shapes at AC, BC and HO. There were significant differences (P < 0.001) for the amount of resin removed from the outer aspect of the curve at AC, BC and HO; and for the amount of resin removed from the inner aspect of the curve at all five measuring points (0, AC and EP (P < 0.05) and HO and BC (P < 0.001)). Mean transportation was towards the inner aspect of the canal in canals with straight sections of 12 mm regardless the curve angle; towards the outer aspect in canals with straight sections of 8 mm and 40 degrees curves at all the five measuring points, and at AC, BC and HO when the curve was 60 degrees. CONCLUSIONS: Under the conditions of this study, GT Rotary Files produced acceptable canal shapes. In narrow and curved canals, the length of the straight section of the canal determines the direction of transportation more than the angle of the curve. In the 60 degrees curves, a high incidence of instrument deformation was found when using the 0.04 tapered instruments.

Dental Alloys↗

PubMed1976

[Logetronic micro-film in radiological diagnosis with an integrated system of filming and filing(author's transl)].

The results of one year's routine use of primary microfilm in a large diagnostic radiological institute is reviewed. Positive views were treated by electronic contrast enhancement in an integrated system of immediate filming and filing. The resulting changes and improvements in running the department are described. This involves a fundamental reorganisation of the department, as well as equipment which is not yet commercially available. The latter had therefore to be improvised and is described. Similar procedures introduced elsewhere are critically evaluated. The advantages of immediate filming are stressed and a comparison with conventional large film filing demonstrates its financial advantages. Logical application of the method results in saving in personnel and material, but implies that the radiologist must be prepared to change to positive films in routine diagnosis. By using microfilm positives with a resolution of 4.0 pairs of lines per mm., the results equal those from large film negatives.

Archives↗

PubMed2005

Soluble stochastic dynamics of quasi-one-dimensional single-file fluid self-diffusion.

We solve a model of random-walk stochastic dynamics for hard single-file fluids in the experimentally important quasi-one-dimensional regime. This is a nontrivial extension of exact solution beyond one dimension. We point out that quasi-one-dimensional single-file self-diffusion of one-component hard fluids of diameter a under stochastic forces is equivalent at long time to a one-dimensional hard-rod fluid with the same linear density but a different diameter, a(eff). This effective diameter is controlled by the details of the relative dynamics between the transverse and longitudinal directions. There are two regimes of limiting behavior. For very fast transverse motion, the system is likely (but we cannot prove rigorously) to be equivalent to the soluble-oriented hard-rectangle or cylinder systems, with a(eff)=a. With very slow transverse motion, the self-diffusion dynamics is described by an equivalent soluble one-dimensional mixture of fluids with a(eff)=a(ave), the average longitudinal separation between nearest-neighbor particles at contact. We have explored our theoretical predictions with Monte Carlo simulations.

Journal Article↗

PubMed2004

Removal of NOx from flue gas with iron filings reduction following complex absorption in ferrous chelates aqueous solutions.

A novel process for removal of nitrogen oxides (NOx) from flue gases with iron filings reduction following complex absorption in iron-ethylenediaminetetraacetic acid aqueous solution is proposed. The reaction mechanism involved in the process is discussed briefly. The parameters influencing the process, including the concentration of ferrous chelates, initial pH, amount of iron filings, temperature, flow rate of the flue gas, and inlet nitric oxide concentration and oxygen content of the flue gas, are researched in detail. The optimal NOx removal conditions are established. The regeneration and circular utilization of the absorption solution also is studied.

Absorption↗

PubMed1992

Kinetic analysis of water transport through a single-file pore.

We apply the diagrammatic method developed by Hill (1977. Free Energy Transduction in Biology. Academic Press, New York) to analyze single-file water transport. We use this formalism to derive explicit expressions for the osmotic and diffusive permeabilities Pf and Pd of a pore. We first consider a vacancy mechanism of transport analogous to the one-vacancy pore model previously used by Kohler and Heckmann (1979. J. Theor. Biol. 79:381-401). (a) For the general one-vacancy case, we find that the permeability ratio can be expressed by Pf/Pd = (Pf/Pd)eqf(wA,wB), where the second factor is a function of the water activities in the two adjoining compartments A and B. As a consequence, the permeability ratio in general can effectively differ from its value at equilibrium. We also find that n - 1 less than or equal to (Pf/Pd)eq less than or equal to n, a result already proposed by Kohler and Heckmann (1979. J. Theor. Biol. 79:381-401). (b) When vacancy states are transient intermediates, the model can be reduced to a diagram consisting of only fully occupied states. Such a diagram resembles the one describing a no-vacancy mechanism of transport (c), but in spite of the similarity the expressions obtained for the permeability coefficients still retain the basic relationships of the original (a) nonreduced one-vacancy model. (c) We then propose a kinetic description of a no-vacancy mechanism of single-file water transport. In this case, the expressions derived for Pf and Pd are formally equivalent to those obtained by Finkelstein and Rosenberg (1979. Membrane Transport Processes. Vol. 3. C.F. Stevens and R.W. Tsien, editors, Raven Press, New York. 73-88.) A main difference with the vacancy mechanism is that here the permeability coefficients are independent of the water activities.

Biological Transport↗

PubMed2026

QPL-enabled HTSlib library: accelerating sequence file compression using Intel IAA.

SUMMARY: Sequence analysis workflows require the accessibility of large datasets, which require state-of-the-art compression tools. These compression tools, such as Samtools, often rely on HTSlib as a GZip implementation, but are still limited by throughput on time-intensive compression. QPL-HTSLib offers order of magnitude speedups for the compression and decompression of the SAM and BAM file formats commonly used in genomics workflows at the cost of a slightly larger compressed file, and is a drop-in replacement for HTSlib on Intel systems. AVAILABILITY AND IMPLEMENTATION: QPL-HTSLib is freely available on Github as an open-source software project.

Journal Article↗

PubMed1996

TAXOKEY: a universal taxonomic key program using DOS text files and graphics.

A program (TAXOKEY.EXE), requiring only a few keystrokes to use, is described as a universal taxonomic key in the identification of plant and animal species by IBM-compatible personal computers. A DOS text file serves as the database for a key that can be dichotomous or with multiple choices. TAXOKEY can optionally display colour or monochrome screen pictures to illustrate the keys. Additional programs are described that are used to make the keys and check for errors, as well as convert .PCX graphic images for use with TAXOKEY. A second text file can be searched by TAXOKEY for information on particular species descriptions, notes and references.

Anatomy, Comparative↗

PubMed2000

SISEQ: manipulation of multiple sequence and large database files for common platforms.

UNLABELLED: A multiple sequence file converter for common platforms, SISEQ,is described, which performs extraction of DNA sequences that correspond to CDS or RNA field of a large database file as well as subsequent multi-sequence conversions for phylogenetic or molecular biological analysis. Command-line interface as well as a GUI and a script-driven operation mode are provided. AVAILABILITY: The program is freely available to academic users in the form of Macintosh FAT binary, DOS executable, or UNIX source code at http://www.molbiol.saitama-u.ac.jp/ñaoki/ Software.html. CONTACT: naokisat@molbiol.saitama-u.ac.jp

DNA↗

PubMed1990

Free molecular biological software available from the EMBL file server.

A new service provided by EMBL (EMBL Software File Server) is described that will make free molecular biology software available to anyone with computer network access. MS-DOS, Apple Macintosh and VAX/VMX are supported at the moment. The programs will be delivered by normal electronic mail; conversion mechanisms will transform binary files to ASCII to allow mail transfer. This service will also help authors to distribute their software conveniently.

Computer Communication Networks↗

PubMed2025

Parsing GTF and FASTA files using the eccLib Library.

SUMMARY: Leveraging the Python/C API, eccLib was developed as a high-performance library designed for parsing genomic files and analysing genomic contexts. To the best of the authors' knowledge, it is the fastest Python-based solution available. With eccLib, users can efficiently parse GTF/GFFv3 and FASTA files and utilize the provided methods for additional analysis. AVAILABILITY AND IMPLEMENTATION: This library is implemented in C and distributed under the GPL-3.0 licence. It is compatible with any system that has the Python interpreter (CPython) installed. The use of C enables numerous optimizations at both the implementation and algorithmic levels, which are either unachievable or impractical in Python.

Software↗

PubMed1996

HPLC quantitation of a very hydrophilic 3-hydroxypyridin-4-one chelator using a simple separation procedure and the baseline file subtraction method.

The lack of a method to isolate very hydrophilic 3-hydroxypyridin-4-ones (HPs) from blood has prevented determination of their pharmacokinetics. The objective of this study is to develop method to quantitate these compounds. A simple sample preparation method coupled with high-performance liquid chromatography is used to quantitate 1-[ethan-1-ol]-2-methyl-3- hydroxypyridin-4-one, a very hydrophilic HP, in plasma. Plasma proteins are precipitated by trichloroacetic acid. The baseline file subtraction method is used to improve the resolution of this HP in the presence of interfering chromatographic peaks that could not be resolved from the HP by the methods investigated. The method is used to determine the pharmacokinetics of this HP in rabbits. The precision of the pharmacokinetic results is comparable or better than the results obtained from seven more lipophilic HPs that were separated by a published method. The new method is slightly modified and used in a study of the pharmacokinetics of this HP in the rat, and precision is comparable with results obtained with two more lipophilic HPs determined by the published method. Baseline file subtraction is useful when other methods cannot be used to adequately resolve a hydrophilic analyte from coeluting interfering substances.

Animals↗