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At least 145 records · Page 8Linked to original sources
PubMed1980

Ion movements in gramicidin pores. An example of single-file transport.

Experimental results on ion movement through gramicidin membrane channels are presented and discussed in terms of ion transport in the simplest single-file pore (for review see Urban, B.W. and Hladky, S.B. (1979) Biochim. Biophys. Acta 554, 410-429). Single-channel conductance and bi-ionic potential data for Na+, K+, Cs+, NH4+ and Tl+ are used to assign values to the rate constants of the model. Not all of the rate constants can be determined uniquely and simplifications are introduced to reduce the number of free parameters. The simplified model gives good quantitative fits to the experimental results for Na+, K+, Cs+ and NH4+. For Tl+, although the model accounts qualitatively for the salient features of the results, the quantitative agreement is less satisfactory. Predictions calculated from the model and the fitted rate constants are compared with independent data from blocking and tracer-flux measurements. In agreement with experiment, the model shows that only Tl+ blocks the Na+ conductance significantly. Furthermore, the exponent, n, in the tracer flux ratio rises, as observed, well above unity. The values for the rate constants suggest internal consistency of the model in that entry is always slower to singly occupied pores than to empty pores while exit is always faster from doubly as compared to singly occupied pores. The agreement between model prediction and experimental results suggests that the main features of ion transport in the gramicidin channel arise from cation-cation interaction in a single-file pore.

Cations, Monovalent↗
PubMed1988

An image filing system for the implementation of image processing algorithms in a research environment.

An image filing system (IFS) has been written to facilitate the implementation and testing of image processing algorithms in a research environment. A programming substrate has been developed to provide applications with routines for acquiring, displaying, and manipulating images without regard for the underlying information format. Images of diverse modalities are cataloged and tracked through a series of image operations with descriptive pointers to all antecedents. This paper presents the design and implementation of the image filing system and describes one of the major image processing applications developed in the IFS environment.

Algorithms↗
PubMedDate not supplied

Clinical application of a magneto-optical disk image filing system/image save and carry (ISAC) system.

We propose the utilization of portable magneto optical disks for image filing. The main problems in PACS are the need for a high-speed local area network (LAN) and a large mass storage device. An image filing system--image save and carry (ISAC)--is one solution for these problems in present PACS and requires minimal additional hardware and cost for the installation. Whenever a patient is examined, the clerk carries the medical record and the ISAC magneto-optical disk for recording image data, and after inspection records the image data into the magneto-optical disk. We investigated the number of image retrievals done for inpatients and outpatients in 1988 at our radiation therapy department. The data storage requirements were on the average 18.5 MB for outpatients and 173.9 MB for inpatients. An ISAC display console needs also an easy-to-use man/machine interface for specifying images and image display characteristics in order to realize the ISAC system.

Computer Systems↗
PubMed1992

Oral diagnostic reporting and synchronized image filing using magneto-optical disks.

An experimental radiologic reporting system has been developed and tested. The rewritable and compact magneto-optical disk (MOD) is applied to storing medical images with oral diagnostic reports of these radiologic images. The disk is 5.25 inches in diameter, has 600 MB memory capacity, is erasable, light and compact. Advantages are simultaneous recording of radiologic images and their oral reports by radiologists, and application to circulation of media inside the hospital as well as to filing of medical images. The MOD has a multimedia function of communication and filing. When medical images are taken and stored, oral interpretation by radiologists can be simultaneously added. Physicians can get information of the images and their reports by oral speech at the same time in front of computer workstation. Furthermore, integration of a voice recognition capability is now being undertaken.

Image Processing, Computer-Assisted↗
PubMed1992

Identification of fractures from computerized Medicare files.

Study of non-hip fractures, which are a serious public health problem for persons greater than or equal to 65 years of age, has been hindered by the absence of an economical method for case identification. We assessed the utility of computerized Medicare inpatient, emergency room, hospital outpatient department and physician claims for identifying fractures in an elderly Tennessee Medicaid population. We used these files for 1987 to identify 3086 possible fractures and reviewed medical records for a sample of 1440. Using this sample, we developed a definition of probable fractures that excluded claims unlikely to represent newly diagnosed fractures. For all fractures, this definition had a positive predictive value of 94%, which for individual fracture sites, ranged from 79% (tibia/fibula) to 98% (hip). Of fractures in the reviewed sample, 91% were identified as probable fractures; this upper bound for sensitivity varied between 75% (femoral shaft) and 100% (patella). These data suggest that computerized Medicare files can be used for rapid and economical fracture ascertainment among persons greater than or equal to 65 years of age. However, further work is needed to obtain better estimates of sensitivity.

Aged↗
PubMed1991

A comparison of weights of debris extruded apically by conventional filing and Canal Master techniques.

Sixty extracted human teeth were divided into three groups of 20 each. Apically extruded debris and irrigant were collected, dried, and weighed by the following three instrumentation techniques: (a) group 1, filing 1 mm short of the foramen; (b) group 2, Canal Master instrumentation to the foramen; and (c) group 3, filing to the foramen (for a relative comparison). The results indicated that all three groups were significantly different from one another. Group 1 had the least amount of debris extruded. Of the two groups instrumented to the foramen, group 3 had twice as much debris extruded as group 2. An apical dentinal plug was frequently found in group 1 and was probably a major reason why this group had the least amount of extruded debris. The significance of this dentinal plug and possible indications for instrumentation to the foramen are discussed.

Analysis of Variance↗
PubMed1990

Comparison of the Canal Master endodontic instrument and K-type files for enlargement of curved root canals.

Twenty mandibular molars with 40 mesial curved root canals were instrumented with a circumferential technique using K files and the Canal Master instrumentation technique by junior dental students whose only endodontic experience had been completion of a preclinical endodontic course. Preoperative and postoperative radiographs were taken facially and mesially with instruments in place. The canals were evaluated radiographically for transportation 1 mm and 4 mm from the apex. The mesial roots were cross-sectioned at the same level. The sections were evaluated for roundness of the canal preparation. It was concluded that the Canal Master instrumentation technique transported the root canal less and produced rounder preparations than the K file circumferential technique. There appears to be a greater tendency for breakage with the Canal Master.

Dental Pulp Cavity↗
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↗
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↗