Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Data Compression”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 937 records · Page 52Linked to original sources

Experimental induction of equine protozoal myeloencephalitis in horses using Sarcocystis sp. sporocysts from the opossum (Didelphis virginiana).

Sarcocystis sp. sporocysts isolated from eight feral opossums (Didelphis virginiana) were pooled and fed to 18 commercially reared budgerigars (Melopsittacus undulatus), 14 wild-caught sparrows (Passer domesticus), one wild-caught slate-colored Junco (Junco hyemalis) and five weanling horses (Equus caballus). All budgerigars died within 5 weeks post inoculation (wpi). Histologic examination revealed meronts within the pulmonary epithelia and typical Sarcocystis falcatula sarcocysts developing in the leg muscles. Sparrows were euthanized 13 and 17 wpi and their carcasses were fed to four laboratory raised opossums. Sporocysts were detected in the feces of two opossums on 15 days post inoculation (dpi) and in a third opossum on 40 dpi. Fecal samples from the fourth opossum remained negative; however, sporocysts were found in intestinal digests from all four opossums. Sporocysts were not found in feces or intestinal digest of an additional opossum that was fed three uninoculated sparrows. Five foals were fed sporocysts (Foals 2, 3, 4, 5, and 7) and two foals were maintained as uninoculated controls (Foals 1 and 6). Sporocysts from two additional feral opossums also were fed to foals. Foal 5 was given 0.05 mg kg-1 dexamethasone sodium phosphate daily beginning 2 days before inoculation for a total of 2 weeks. Horse sera were tested three times per week, and cerebrospinal fluid (CSF) samples were tested biweekly for anti-Sarcocystis neurona antibodies by Western blot analysis. No foals had any S. neurona-specific antibodies by Western blot analysis prior to sporocysts ingestion. Seroconversion occurred in Foals 3, 5, and 7 by 24 dpi, followed by positive CSF tests on 28 dpi. Foals 2 and 4 seroconverted by 40 dpi. Cerebrospinal fluid from Foal 2 tested positive by 42 dpi, but Foal 4 remained seronegative throughout the study. Sera and CSF from control Foals 1 and 6 remained seronegative. All foals with positive CSF developed neurologic clinical signs. Neurologic disease was evident in Foals 2 and 3 by 42 dpi and in Foal 7 by 28 dpi. The severity of clinical signs progressed to marked spasticity, hypermetria and ataxia in Foal 7 by the end of the trial. Necropsy examination of inoculated foals did not reveal gross lesions; however, microscopic lesions consistent with equine protozoal myeloencephalitis (EPM) were found in Foals 2, 3, and 7. Protozoa were not observed in the tissue sections. Microscopic lesions consistent with EPM were not found in Foals 4 and 5 or in uninoculated control Foals 1 and 6. Foal 5 had unilateral non-inflammatory lesions in the cervical and thoracic spinal cord consistent with cord compression. These data indicate that the opossum is a definitive host of S. neurona.

Animals↗

Internal carotid blood flow velocity in children with cerebral palsy by Doppler Ultrasound method.

Cerebral blood flow assessed noninvasively by Doppler ultrasound technique in 30 children with cerebral palsy. The average maximal blood velocity (A/L) and end-diastolic blood velocity (d) of internal carotid artery were measured before and during brief digital compression of contralateral common carotid artery. Both A/L and d values in children with cerebral palsy were significantly lower than those observed in normal healthy children. In 13 children with spastic hemiplegia, no significant difference in either A/L or d was seen between the non-affected side and affected side both before and during brief digital compression. This data suggests that mean cerebral blood flow decreases in our children with cerebral palsy, and that no lateralization of the decrease in hemispheric cerebral circulation in hemiplegic children may explain by supposing the existence of generalized bilateral brain damage in those subjects.

Adolescent↗

Venous leg ulcer pain and its characteristics.

This study investigated the prevalence, severity and characteristics of pain associated with venous leg ulceration. Sixty-five patients suffering with venous leg ulceration were randomised to one of three treatment groups over a 12-week treatment period. All patients received short-stretch compression bandaging. Data were collected by use of a visual analogue scale and the McGill Pain Questionnaire. Seventy per cent of patients reported pain on entry to the study and within 2 weeks of effective treatment initial pain was dramatically reduced. Patients typically described their pain as throbbing, sharp, itchy, sore and tender. The affective nature of pain was often described as tiring and patients evaluated their pain as being annoying and nagging. This study highlights the importance of pain associated with venous leg ulceration.

Adult↗

Percutaneous plasma decompression alters cytokine expression in injured porcine intervertebral discs.

BACKGROUND CONTEXT: Discectomy is a surgical technique commonly used to treat bulging or herniated discs causing nerve root compression. Clinical data suggest discectomy may also help patients with contained discs and no clear neural compromise. However, the mechanisms of clinical efficacy are uncertain, and consequently bases for treatment optimization are limited. PURPOSE: To determine the effect of percutaneous plasma decompression on the histologic, morphologic, biochemical and biomechanical features of degenerating intervertebral discs. STUDY DESIGN: An adult porcine model of disc degeneration was used to establish a degenerative baseline against which to evaluate discectomy efficacy. OUTCOME MEASURES: Cytokines interleukin (IL)-1, IL-6, IL-8, and tumor necrosis factor (TNF)-alpha were measured from tissue samples using enzyme-linked immunosorbent assay. Histology and morphology images were rated for degenerative findings (of cells and matrix) in both the nucleus and annulus. Proteoglycan content was determined, and intact specimen stiffness and flexibility were measured biomechanically. Magnetic resonance images were collected for biomechanical specimens. METHODS: Using a retroperitoneal surgical approach, stab incisions were made in four or five lumbar discs per spine in 12 minipigs. Animals were allocated into one of three groups: 6-week recovery, 12-week recovery and percutaneous plasma decompression using an electrosurgical device at 6 weeks with recovery for 6 additional weeks. Four additional animals served as controls. RESULTS: Discs treated with discectomy had a significant increase in IL-8 and a decrease in IL-1 as compared with the 12-week, nontreated discs. There were no significant differences in morphologic and biomechanical parameters or proteoglycan content between treated discs and time-matched, nontreated discs. CONCLUSIONS: Our results demonstrate that percutaneous plasma discectomy alters the expression of inflammatory cytokines in degenerated discs, leading to a decrease in IL-1 and an increase in IL-8. Whereas both IL-1 and IL-8 have hyperalgesic properties, IL-1 is likely to be a more important pathophysiologic factor in painful disc disorders than IL-8. Therefore, the alteration in cytokine expression that we observed is consistent with this effect as a mechanism of pain relief after discectomy. In addition, given that IL-1 is catabolic in injured tissue and IL-8 is anabolic, our results suggest that a percutaneous plasma discectomy may be capable of initiating a repair response in the disc.

Animals↗

Paraphrasing for condensation in journal abstracting.

When authors of empirical science articles write abstracts, they employ a wide variety of distinct linguistic operations which interact to condense and rephrase a subset of sentences from the source text. An on-going comparison of biological and biomedical journal articles with their author-written abstracts is providing a basis for a more linguistically detailed model of abstract derivation using syntactic representations of selected source sentences. The description makes use of rich dictionary information to formulate paraphrasing rules of differing degrees of generality, including some which are sublanguage-specific, and others which appear valid in several languages when formulated using "lexical functions" to express important semantic relationships between lexical items. Some paraphrase operations may use both lexical functions and rhetorical relations between sentences to reformulate larger chunks of text in a concise abstract sentence. The descriptive framework is computable and utilizes existing linguistic resources.

Abstracting and Indexing↗

Detection of sugar adulterants in apple juice using fourier transform infrared spectroscopy and chemometrics.

Fourier transform infrared spectroscopy and attenuated total reflection sampling have been used to detect adulteration of single strength apple juice samples. The sample set comprised 224 authentic apple juices and 480 adulterated samples. Adulterants used included partially inverted cane syrup (PICS), beet sucrose (BS), high fructose corn syrup (HFCS), and a synthetic solution of fructose, glucose, and sucrose (FGS). Adulteration was carried out on individual apple juice samples at levels of 10, 20, 30, and 40% w/w. Spectral data were compressed by principal component analysis and analyzed using k-nearest neighbors and partial least squares regression techniques. Prediction results for the best classification models achieved an overall (authentic plus adulterated) correct classification rate of 96.5, 93.9, 92.2, and 82.4% for PICS, BS, HFCS, and FGS adulterants, respectively. This method shows promise as a rapid screening technique for the detection of a broad range of potential adulterants in apple juice.

Beverages↗

Genomic messaging system and DNA mark-up language for information-based personalized medicine with clinical and proteome research applications.

The convergence of clinical medicine and the Life Sciences, commencing with opportunities in clinical trials and clinically linked medical research, presents many novel challenges. The Genomic Messaging System (GMS) described here was originally developed as a tool for assembling clinical genomic records of individual and collective patients, and was then generalized to become a flexible workflow component that will link clinical records to a variety of computational biology research tools, for research and ultimately for a more personalized, focused, and preventative healthcare system. Prominent among the applications linked are protein science applications, including the rapid automated modeling of patient proteins with their individual structural polymorphisms. In an initial study, GMS formed the basis of a fully automated system for modeling patient proteins with structural polymorphisms as a basis for drug selection and ultimately design on an individual patient basis.

Clinical Medicine↗

Development of an emergency medical video multiplexing transport system. Aiming at the nation wide prehospital care on ambulance.

The Emergency Medical Video Multiplexing Transport System (EMTS) is designed to support prehospital cares by delivering high quality live video streams of patients in an ambulance to emergency doctors in a remote hospital via satellite communications. The important feature is that EMTS divides a patient's live video scene into four pieces and transports the four video streams on four separate network channels. By multiplexing four video streams, EMTS is able to transport high quality videos through low data transmission rate networks such as satellite communications and cellular phone networks. In order to transport live video streams constantly, EMTS adopts Real-time Transport Protocol/Real-time Control Protocol as a network protocol and video stream data are compressed by Moving Picture Experts Group 4 format. As EMTS combines four video streams with checking video frame numbers, it uses a refresh packet that initializes server's frame numbers to synchronize the four video streams.

Ambulances↗

Development of an Emergency Medical Video Multiplexing Transport System (EMTS): aiming at the nation-wide prehospital care in ambulance.

The Emergency Medical Video Multiplexing Transport System (EMTS) is designed to support prehospital care by delivering high quality patient's live video streams in an ambulance to emergency doctors in a remote hospital on the basis of satellite communications. The feature is that EMTS divides a patient's live video scene into four pieces and transports the four video streams on four separate network channels. By multiplexing the four video streams, EMTS is able to transport high quality videos through low data transmission rate networks such as satellite communications and cellular phone networks. In order to transport live video streams constantly, EMTS adopts Real-Time Transport Protocol/Real-Time Control Protocol as a network protocol, and video stream data are compressed by Moving Picture Experts Group 4 format. As EMTS combines four video streams with checking video frame numbers, it uses a refresh packet that initializes server's frame numbers to synchronize the four video streams.

Ambulances↗

Fred Hollows lecture: digital screening for eye disease.

The purpose of this study was to explore progress, in the adaptation to community screening for blinding eye disease, of digital imaging devices and technology for storage and transmission. Available imaging systems were compared to gold standard clinical photography in terms of sensitivity and specificity for diagnosis of common blinding eye conditions. Since the use of expensive non-portable imaging devices is likely to be limited for widespread community screening purposes, a portable fundus camera (Nidek, Chiyoda-ku, Japan) and a prototype monocular digital indirect ophthalmoscope constructed at the Lions Eye Institute (LEI) were selected for comparative trials for the screening of optic disc cupping, glaucoma and clinical signs of diabetic retinopathy. Fifty-one eyes of 27 consecutive patients being assessed at the LEI clinic for glaucoma were dilated and photographed with a Zeiss retinal camera, and digital images were taken with the portable Nidek NM100 fundus camera (Carl Zeiss, Oberkochen, Germany) or with a prototype digital monocular indirect ophthalmoscope. Vertical cup: disc ratios (VCDR) were measured on the disc photographs by one ophthalmologist while three other clinicians were presented with compressed digital images in random order to estimate VCDR. Field trials were also carried out to demonstrate the practicality of compression, local storage and then transmission by mobile telephone ISDN lines and satellite, of optic discs and fundus images of patients with diabetes in either rural Western Australia or Surabaya, Indonesia. Kappa values of correlations of measurement of agreement between measured and estimated VCDR were 0.87, 0.45 and 0.84, respectively, for the three observers, corresponding to a specificity of 79-97% and a sensitivity of 70-95%. The portable Nidek fundus camera was also assessed for specificity and sensitivity in the diagnosis of diabetic retinopathy in comparison to standard Zeiss fundus camera photographs. Of 49 eyes in 25 consecutive patients attending the LEI clinic for assessment of diabetic retinopathy, three ophthalmologists assessed photographs and images in random order. When used for screening diabetic retinopathy, the digital images of the Nidek camera were graded as adequate quality in only 56% of eyes compared to 93% of the photographs. The kappa value of agreement in analysis of diabetic retinopathy was only 0.30. The prototype digital monocular indirect ophthalmoscope compared favourably with the Nidek camera. At 1:5 compression, images of size 36 kB transmitted from Surabaya to Perth took 29 s on the mobile telephone, while uncompressed images took 170 s. Images compressed 1:5 were transmitted in 60 s using the satellite telephone, while the uncompressed images took 240 s. Satellite transmission was more expensive but the lines were more stable than telephone connections from Indonesia. Digital imaging is becoming a powerful tool for ophthalmology in clinical records, teaching and research, and interoffice diagnostic opinions. It also has enormous potential for community screening for blinding eye diseases, such as glaucoma and diabetic retinopathy. Inexpensive portable imaging devices that are easy to use, and on which local health workers might be trained, must be developed and validated in terms of sensitivity and specificity of performance. The technology of image capture, image compression, transmission, data base storage and analysis is rapidly evolving and becoming less expensive.

Diabetic Retinopathy↗

First-order mean spherical approximation for attractive, repulsive, and multi-Yukawa potentials.

The first-order mean spherical approximation (FMSA) theory proposed by Tang et al. [Fluid Phase Equilib., 134, 21(1997)] is applied for studying several typical Yukawa fluids, including attractive, repulsive, and multi-Yukawa cases. The FMSA study is particularly advantageous in providing thermodynamics and structure information in a simple, analytical, and consistent manner. Comparisons with the latest reported computer simulation data for compressibility factor, internal energy, and radial distribution function show that FMSA performs very well and the performance is very close to the full MSA and to several other theories, developed individually for the above-mentioned cases or properties. The present study provides solid evidence to support FMSA applications to more complex fluids.

Journal Article↗

Relative benefits of linear analogue and advanced digital hearing aids.

Speech recognition performance and self-reported benefit from linear analogue and advanced (digital) hearing aids were compared in 100 first-time hearing aid users with mild-to-moderate sensorineural hearing loss fitted monaurally with a behind-the-ear (BTE) hearing aid in a single-blind randomized crossover trial. Subjects used each aid for 5 weeks in turn, with aid order balanced across subjects. Three alternative models of digital hearing aid were assigned to subjects according to a balanced design. Aid type was disguised to keep subjects blind within practical limitations. Aided speech recognition performance in noise was measured at speech levels of 65 and 75dB at a speech-to-noise ratio (SNR) of +2dB for closed sets of single words. Self-rated benefit was measured using the Abbreviated Profile of Hearing Aid Benefit (APHAB) and the Glasgow Hearing Aid Benefit Profile (GHABP). Quality of life, hearing aid use and user preferences were also assessed. Speech recognition scores with the digital aids were significantly better at 75dB than with the analogue aids Self-reported benefit (APHAB, GHABP) and improvement in quality of life were generally not significantly different between analogue and digital aids, although aversiveness measured with the APHAB was significantly lower with digital aids, and satisfaction measured with the GHABP was greater. The digital aids were preferred significantly more often than the analogue aids, with 61 subjects choosing their digital aid, 26 choosing the analogue aid, and nine being equivocal. Overall, this study shows advantages for advanced digital over simple linear analogue aids in terms of both objective and subjective outcomes, although average differences are not large.

Adult↗

Directional bonding in compacted microcrystalline cellulose.

The mechanical properties of compacts of microcrystalline cellulose (MCC) and silicified microcrystalline cellulose (SMCC) were evaluated by tensile testing, diametric compression testing, and compression testing. For tensile and compression testing, cubic specimens were carefully machined from MCC and SMCC compacts, and the tensile and compression strengths were evaluated both normal and parallel to the compaction direction. The cubic tensile strengths were compared to values obtained from the diametric compression test. The results obtained using the diametric compression test suggested compacts of SMCC exhibit greater strength than those of MCC. In addition, the cubes machined from compacts of MCC and SMCC exhibited directional strength; the direction normal to the compaction direction display ed the greater tensile strength, and the parallel direction had greater compression strength. The diametric compression test afforded strength values with reduced spread compared to the values collected from the cubic tensile test, suggesting that the errors involved in collecting diametric compression test data of compacts are less than those for the cubic tensile test. Analysis of the cubes using X-ray diffraction (XRD) suggested that they display directional structural anisotropy, with the direction normal to the compaction direction being more crystalline than the parallel direction. However, it is not clear whether the difference in the directional strength is solely a consequence of the increased crystallinity or a culmination of crystallographic and mechanical keying effects.

Algorithms↗

Fast reconstruction of 3D time-of-flight PET data by axial rebinning and transverse mashing.

Faster scintillators like LaBr(3) and LSO have sparked renewed interest in PET scanners with time-of-flight (TOF) information. The TOF information adds another dimension to the data set compared to conventional three-dimensional (3D) PET with the size of the projection data being multiplied by the number of TOF bins. Here we show by simulations and analytical reconstruction that angular sampling for two-dimensional (2D) TOF PET can be reduced significantly compared to what is required for conventional 2D PET. Fully 3D TOF PET data, however, have a wide range of oblique and transverse angles. To make use of the smaller necessary angular sampling we reduce the 3D data to a set of 2D histoprojections. This is done by rebinning the 3D data to 2D data and by mashing these 2D data into a limited number of angles. Both methods are based on the most likely point given by the TOF measurement. It is shown that the axial resolution loss associated with rebinning reduces with improved timing resolution and becomes less than 1 mm for a TOF resolution below 300 ps. The amount of angular mashing that can be applied without tangential resolution loss increases with improved TOF resolution. Even quite coarse angular mashing (18 angles out of 324 measured angles for 424 ps) does not significantly reduce image quality in terms of the contrast or noise. The advantages of the proposed methods are threefold. Data storage is reduced to a limited number of 2D histoprojections with TOF information. Compared to listmode format we have the advantage of a predetermined storage space and faster reconstruction. The method does not require the normalization of projections prior to rebinning and can be applied directly to measured listmode data.

Algorithms↗

Using personal digital assistants to access drug information.

The use of personal digital assistants (PDAs) to access drug information in a health system is described. Given the widespread use of PDAs at an 872-bed university health system, an opportunity existed to provide current drug information to physicians via these devices. As part of the health system's intranet, extensive online content had been made available through a browser; extension to PDAs was a natural next step. There were two primary requirements: the ability to synchronize information with the database server when a PDA was used and the development of content and applications by using existing staff. Mobile enterprise software was chosen that supports multiple PDA platforms, is easy to use, and does not require programming skills. The software works through customized "channels," or collections of information from a content provider. The customized channel service works over the Internet. Two channels of content were created, an ambulatory care channel and an inpatient care channel. The ambulatory care channel contains a list of preferred ambulatory care agents, poison control information, the locations of outpatient pharmacies, drug information, and safety tips for prescribing. The inpatient channel contains the inpatient formulary, current news and events, information on currrent drug shortages and recalls, pharmacy contact information, and medication safety tips. When a user synchronizes his or her PDA, the software contacts the department's intranet servers and processes the request. The data are compressed and downloaded to the user's PDA. A university health system successfully used PDAs to access drug and other information.

Clinical Pharmacy Information Systems↗

Efficient similarity search in protein structure databases by k-clique hashing.

MOTIVATION: Graph-based clique-detection techniques are widely used for the recognition of common substructures in proteins. They permit the detection of resemblances that are independent of sequence or fold homologies and are also able to handle conformational flexibility. Their high computational complexity is often a limiting factor and prevents a detailed and fine-grained modeling of the protein structure. RESULTS: We present an efficient two-step method that significantly speeds up the detection of common substructures, especially when used to screen larger databases. It combines the advantages from both clique-detection and geometric hashing. The method is applied to an established approach for the comparison of protein binding-pockets, and some empirical results are presented. AVAILABILITY: Upon request from the authors.

Algorithms↗

MinSet: a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database.

MOTIVATION: The size of current protein databases is a challenge for many Bioinformatics applications, both in terms of processing speed and information redundancy. It may be therefore desirable to efficiently reduce the database of interest to a maximally representative subset. RESULTS: The MinSet method employs a combination of a Suffix Tree and a Genetic Algorithm for the generation, selection and assessment of database subsets. The approach is generally applicable to any type of string-encoded data, allowing for a drastic reduction of the database size whilst retaining most of the information contained in the original set. We demonstrate the performance of the method on a database of protein domain structures encoded as strings. We used the SCOP40 domain database by translating protein structures into character strings by means of a structural alphabet and by extracting optimized subsets according to an entropy score that is based on a constant-length fragment dictionary. Therefore, optimized subsets are maximally representative for the distribution and range of local structures. Subsets containing only 10% of the SCOP structure classes show a coverage of >90% for fragments of length 1-4. AVAILABILITY: http://mathbio.nimr.mrc.ac.uk/~jkleinj/MinSet. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Algorithms↗