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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↗
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↗
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↗
PubMed1984

New hope for identifying the unidentified. The National Crime Information Center unidentified person/missing person files.

The National Crime Information Center Unidentified Person/Missing Person Files offer computer comparison of descriptive data on unidentified dead and living persons with data entered on missing persons. Completion of a simple, but detailed standard form allows entry of descriptors of physical characteristics, fingerprint classification, dentition, anthropologic and x-ray findings, optic prescriptions, medical devices, surgical procedures, serology, jewelry, and clothes. Medical and law enforcement agencies collect the descriptive data on the unidentified; families and law enforcement agencies collect missing persons information. Entry for both is via law enforcement regional or state NCIC computer terminals. Continuous comparison and cross search of both files is initiated upon entry of either form.

Autopsy↗
PubMed1988

Use of a computer data file for storage of heat resistance data on bacterial spores.

The use of a computer data file to compile published heat resistance data on bacterial spores is described. Information relating to sporulation, heating and recovery of the spores, in addition to decimal reduction times at different temperatures has been stored. The data file was constructed using Minitab and an indexer program on a VAX 11/750 computer operating on VMS. Storage of the data in this way enables rapid manipulation and analysis of large quantities of information relating to heat resistance of bacterial spores.

Clostridium↗
PubMed1977

The Protein Data Bank. A computer-based archival file for macromolecular structures.

The Protein Data Bank is a computer-based archival file for macromolecular structures. The Bank stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies. Text included in each data entry gives pertinent information for the structure at hand (e.g. species from which the molecule has been obtained, resolution of diffraction data, literature citations and specifications of secondary structure). In addition to atomic co-ordinates and connectivities, the Protein Data Bank stores structure factors and phases, although these latter data are not placed in any uniform format. Input of data to the Bank and general maintenance functions are carried out at Brookhaven National Laboratory. All data stored in the Bank are available on magnetic tape for public distribution, from Brookhaven (to laboratories in the Americas), Tokyo (Japan), and Cambridge (Europe and worldwide). A master file is maintained at Brookhaven and duplicate copies are stored in Cambridge and Tokyo. In the future, it is hoped to expand the scope of the Protein Data Bank to make available co-ordinates for standard structural types (e.g. alpha-helix, RNA double-stranded helix) and representative computer programs of utility in the study and interpretation of macromolecular structures.

Computers↗
PubMed1984

Non-selective conductance in calcium channels of frog muscle: calcium selectivity in a single-file pore.

Voltage-clamp studies were carried out to compare currents through Ca2+ channels (ICa) with Na+ currents (Ins) through a non-selective cation conductance blocked by micromolar concentrations of external Ca2+. The gating of both currents was found to have similar time and voltage dependence. The amplitudes of ICa and Ins varied widely, but Ins was always large in fibres with large ICa, and small in fibres with small ICa. Both ICa and Ins were blocked by the specific Ca2+ channel blocker nifedipine, with half-blockage concentrations that were virtually identical (KD = 0.9 microM for ICa and 0.7 microM for Ins). ICa and Ins were also equally sensitive to block by diltiazem (KD = 80 microM). These parallels between Ins and ICa are most easily explained if Ins flows through Ca2+ channels. Apparently, Ca2+ channels bear high-affinity Ca2+-binding sites, and are highly permeable to monovalent cations when Ca2+ is absent. Ba2+ currents (IBa) and ICa were measured in external solutions containing mixtures of Ba2+ and Ca2+. IBa is blocked by Ca2+, as is Ins. Adding Ba2+ to Ca2+ produces only small or no increases in current, as if Ba2+ is only sparingly permeant when Ca2+ is present. Membrane currents in Ba2+/Ca2+ mixtures show anomalous mole-fraction behaviour, suggesting that Ca2+ channels are single-file, multi-ion pores. Complex current transients are observed under maintained depolarizations in Na+/Ca2+ and Ba2+/Ca2+ mixtures. They suggest that in ion mixtures, Ca2+ channels transport Ca2+ in preference to Na+ and Ba2+. Hence Ca2+ channels are selective for Ca2+, even though current amplitudes suggest that the Na+ or Ba2+ permeabilities in the absence of Ca2+ are as high as, or higher than, the Ca2+ permeability. We conclude that the selective permeability of Ca2+ channels depends on the presence of Ca2+. In model calculations, our observations are explained as a consequence of Ca2+ channels being single-file pores. It is proposed that Ca2+ channels derive much of their ion selectivity from high-affinity Ca2+ binding sites located in an otherwise unselective aqueous pore.

Action Potentials↗
PubMed1977

Maintenance and use of cumulative haematology files on a laboratory computer.

A system is described for the maintenance of cumulative haematology records for selected patients using a laboratory minicomputer with limited storage capacity. Records are indexed by the patient's name and location since, as in the majority of hospital laboratories, there is no unique numbering scheme which covers all patients. The computer system imitates the procedures of manual filing, listing uncertain record matches for human decision. Applications include the production of a regularly updated printing of of cumulative files, the preparation of graphs from cumulative blood count records, and the provision of a summary and follow-up service for general practitioners.

Computers↗
PubMed1984

Data-base management system on a CT scanner computer: application to teaching file and procedure records.

A prototype relational data-base management system was installed on computed tomographic (CT) scanner computers at two hospitals. This was used to create computerized indices for a teaching file and a record of CT procedures. Several problems commonly encountered when maintaining and using a radiologic teaching file were solved. Interesting cases were easily retrieved for teaching, conferences, or publication because the system permits rapid search on the basis of patient name, identification number, date, diagnosis, special description, or a combination of these data. The procedure record index contains these data as well as administrative and technical data on all CT examinations. These data are entered into the data base semiautomatically. The result is an extensive set of records that is easily accessible and requires a minimum of manpower to maintain.

Computers↗
PubMed1992

A standard file format for data from DNA sequencing instruments.

There are now a number of machines for determining DNA sequences. These devices are currently of two types: those such as the Applied Biosystems 373A and the Pharmacia A.L.F. which interpret the sequences of samples as they run on gels within the machine, and those, such as the Bio-Rad and Amersham readers that scan and analyse conventional autoradiographs. Both types of machine can produce their data in the form of traces which represent the band intensity of each of the four base types at each position in the sequence. At present all the machines write files in different formats. We describe a machine independent format for storing data derived from automatic sequencing machines. Files in this format can store the derived sequence, the traces and a set of confidence measures for each base. We have adopted the format as the standard for our sequence handling software.

Databases, Factual↗
PubMed1994

Graphic file compression on a Macintosh.

AutoDoubler, Compact Pro, DiskDoubler, StuffIt Deluxe, and StuffIt SpaceSaver compression applications for the Macintosh were tested for size of compressed files, and time to compress and expand. EPS, TIFF, PICT and Photoshop native format file types were used, in 1-bit, 8-bit greyscale, 8-bit colour (indexed), 24-bit colour (red, blue, green (RGB)), and 32-bit colour (cyan, magenta, yellow, black (CMYK)) modes. JPEG compression is illustrated by comparing an uncompressed image with three images compressed at different rates.

Computer Graphics↗
PubMed1975

Automatic and manual indexing performance in a small file of medical literature.

A test of the performance of an automatic indexing procedure based on the processing of the full text of medical journal articles shows results comparable to those achieved using Excerpta Medica and MEDLARS manual indexing. A file of nineteen documents was partitioned by sixteen questions, for each of which two search strategies in each indexing language were formulated. The results were compared to ideal answers chosen by a fourth-year medical student who read the entire file and posed the questions.

Abstracting and Indexing↗
PubMedDate not supplied

[Scanning electron microscope study of chemically disinfected endodontic files].

Forty stainless steel endodontic files were observed at scanning electron microscopy after being subjected to ten disinfection cycles of 10 minutes each one, immersed in different chemical disinfectants. Corrosion was not observed on the surface of the files in circumstances that this study was made.

Corrosion↗
PubMed1991

[S.E.M. study of surface condition of ultrasonic K files].

The present study was not about the interest of the association of ultrasonic instrumentation with irrigation in the root canal therapy, but about the wear of the K files themselves. The results showed with the assistance of the sono-synergistic system, files are almost as clean as the sterile are. This is important for the prevention of possible contamination.

Dental Cavity Preparation↗
PubMed1991

[Magneto-optical disk filing system for oral diagnostic reports and their synchronized images].

The rewritable and compact media of magneto-optical disk (MOD) is firstly applied to store medical images with spoken reporting. The MOD has multi-media function of communication and filing. Our system is optimized in terms of recording length of speech based upon our clinical research. The results will have influences over the future PACS. One of their examples is possibility of multimedia PACS with images, speeches and demographic data. Another example is prevention of dispersion of images which have no interpretations by radiologists. Our next step is to recognize filed speech in background processing for printing reports.

Optical Storage Devices↗
PubMed1990

Endodontic file design and dynamics in automated root canal preparation. Concepts, materials and methods.

Many treatment failures in endodontics are caused by problems that occurred during canal preparation. This article reviews principles of endodontic instrument design and analyzes the design as it relates to an automated handpiece. After a review of the problems of automation, there will be an introduction of a new automated handpiece and a new modified file known as the Anticurvature File.

Equipment Design↗