SEARCH · PubMed Health

Results for “STRING”

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 73 records · Page 4Linked to original sources

PubMed1990

Testing ultrasonic pulsed Doppler instruments with a physiologic string phantom.

The spatial, temporal, and frequency resolution of conventional ultrasonic Doppler instruments and the time/space distortions in two-dimensional color Doppler imaging systems can be measured using a pulsatile moving string target. The diameter of the string is small compared with the Doppler sample volume, the velocity (speed and direction), acceleration and timing of the string motions are precisely known with reference to the R wave timing mark, and the spatial location of the string is known. A loop of surgical thread or monofilament fishline running between pulleys is driven by a motor that provides constant string speeds from 0.05 to 150 cm/s and variable string speeds programmed to mimic arterial velocity waveforms from the carotid, aortic, and femoral arteries. Constant string speeds are used to evaluate the Doppler sensitivity, frequency processing, and sample volume size; pulsatile movement of the string provides a physiologic model to evaluate the temporal performance of conventional Doppler systems and the temporal and spatial performance of two-dimensional color Doppler imaging scanners.

Blood Flow Velocity↗

PubMedDate not supplied

The clinical utility of string-PCR test in diagnosing Helicobacter pylori infection.

BACKGROUND/AIMS: Non-invasive string test has been reported as being convenient and capable of yielding bacteria by means of gastric juice sampling in the diagnosis of Helicobacter pylori infection. Molecular methods, such as polymerase chain reaction for the amplification of DNA, are desirable for the detection of minute quantities of H. pylori. We planned to evaluate the diagnostic efficiency of the combination of the string test and polymerase chain reaction and determine whether the string polymerase chain reaction test could obtain more information in conditions where the bacterial load is so low that other diagnostic tests fail to confirm the presence of H. pylori. METHODOLOGY: We enrolled 48 dyspeptic patients, including 29 males and 19 females, with a mean age of 52.5 years. Each patient received endoscopy and biopsy-based tests, including RUT (rapid urease test), cultures, and histology, followed by 13C-UBT (13Carbon urea breath test). We used the string test, (Entero-Test H. pylori, HDC Corporation, CA, US), for gastric juice sampling. The specimen was further analyzed by polymerase chain reaction for the presence of H. pylori with the primer for cagA gene, which is highly prevalent in Taiwan. H. pylori infection was considered as positive when either culture yield was positive, or when two of the other three tests, including RUT, histology, and 13C-UBT, were positive. RESULTS: Of the total 48 patients, 34 patients were H. pylori-positive, and 14 were H. pylori-negative. A fragment of 349 bp of polymerase chain reaction products was detected by agarose gel electrophoresis in 32 out of 34 patients who was classified as H. pylori-positive. The sensitivity, specificity, positive predictive value, and negative predictive value of the string polymerase chain reaction test were 94.12%, 96.97%, 92.86%, and 86.67%, respectively. These results are comparable to 13C-UBT and RUT, and better than histology and culture. One subject, who tested as H. pylori-negative according to the diagnostic criteria, had positive 13C-UBT and string polymerase chain reaction test results. Further sequencing of the DNA obtained from the results of polymerase chain reaction product was performed and it showed 98% identities with the known sequence of cagA strain H. pylori (GenBank accession number: AF249275). CONCLUSIONS: The string polymerase chain reaction test is non-invasive and provides direct bacterial yields. Its diagnostic efficiency is comparable with 13C-UBT and RUT in detecting H. pylori infection. Also, with the assistance of polymerase chain reaction and DNA sequencing, we can diagnose H. pylori infection even when the bacterial load is low. Further application of string polymerase chain reaction test in the genetic analysis of virulent and resistant strains seems promising.

Antigens, Bacterial↗

PubMed2005

Controlled synthesis of target strings in a class of splicing systems.

This article presents an approach for synthesizing target strings in a class of computational models of DNA recombination. The computational models are formalized as splicing systems in the context of formal languages. Given a splicing system (of a restricted type) and a target string to be synthesized, we construct (i) a rule-embedded splicing automaton that recognizes languages containing strings embedded with symbols representing splicing rules, and (ii) an automaton that implicitly recognizes the target string. By manipulating these two automata, we extract all rule sequences that lead to the production of the target string (if that string belongs to the splicing language). An algorithm for synthesizing a certain type of target strings based on such rule sequences is presented.

Algorithms↗

PubMed2006

Preserved hyperaemic response in (distal) string sign left internal mammary artery grafts.

OBJECTIVE: To correlate supraclavicular ultrasonography at rest and in hyperaemic response with angiographically patent and (distal) 'string sign' left internal mammary artery (LIMA) to left anterior descending (LAD) area grafts. METHODS: Fifty-three patients with LIMA to LAD area grafting were prospectively entered in a follow-up study. Arteriography (native and LIMA) was performed at 1.4+/-0.8 years postoperatively and ultrasonography was performed at rest, in hyperaemic response and 2min after hyperaemic response at 1.8+/-0.8 years postoperatively and was compared to arteriography. Ultrasonographic parameters analysed were systolic and diastolic peak velocity, systolic and diastolic velocity integral, diastolic/systolic peak velocity ratio and diastolic/total velocity integral ratio. RESULTS: One patient was excluded because obesity hampered ultrasonography. Arteriography demonstrated functional grafts in 43 patients (group I), sequential distal 'string sign grafts' in 4 patients (group II) and total 'string sign grafts' in 5 patients (group III). Between the groups all ultrasonographic velocities showed a significant linear relation (p<or=0.013) at rest and during maximal hyperaemic response all velocities increased significantly within all groups (p<or=0.018). A significant decrease was found 2min after hyperaemic response and diastolic velocities showed a significant linear relation (p<or=0.032). CONCLUSIONS: String sign LIMA grafts' were found in 9/52 (17.3%) patients. All patent and all 'string sign grafts' showed a shift towards a coronary flow profile in the proximal segment postoperatively. The study revealed the 'functionality' of the patent and the (distal) 'string sign LIMA graft' in regard to myocardial oxygen demand. 'String sign grafts' are 'recruitable' on demand.

Aged↗

PubMed1997

The string measure of the ERP: what does it measure?

The event-related brain potential (ERP) has been investigated extensively inan effort to understand the neurophysiological bases of intelligence. Measures derived from the ERP have been used as indices of intelligence, particularly the string measure of the complexity of the ERP. However, the string measure has been criticised for being non-specific and for being dependent on ERP amplitude. These criticisms were tested by investigating relationships between ERP string measure, ERP amplitude measures, and the ERP power spectrum. It was found that the string measure was non-specific in that it indexes both low and high frequency event-related activity; the string measure is also dependent on ERP amplitude. The string measure is therefore not a valid measure of the ERP. It was concluded that the string measure should be abandoned; human intelligence cannot map in a simple way onto gross measures of scalp-recorded electrocortical activity.

Adult↗

PubMed2003

An example of design optimization for high evolvability: string rewriting grammar.

As an example of the optimization of an evolutionary system design, a string rewriting system is studied. A set of rewriting rules that defines the growth of a string is experimentarily optimized in terms of maximizing the 'replicative capacity', that is the occurrence ratio of self-replicating strings. It is shown that the most optimized rule set allows many strings to self-replicate by using a special character able to copy an original string sequentially. Then, using various different rewriting rule sets, the connectivity between self-replicating strings is studied. A set of 'hyperblobs' covering the self-replicating strings is extracted and their connectivity is studied. The experimental results show that a large replicative capacity assures strong connectivity between self-replicating genotypes, making the system highly evolvable.

Algorithms↗

PubMed2003

Tying everything together: the multiple roles of cysteine string protein (CSP) in regulated exocytosis.

In addition to the core vesicle fusion machinery, the SNARE proteins, a large number of regulatory proteins have been implicated in the process of Ca2+-dependent exocytosis. How these exocytotic proteins are properly targeted and how their myriad interactions are temporally and spatially coordinated is poorly understood. Cysteine string protein (CSP), a secretory vesicle membrane protein and a member of the dnaJ family of co-chaperones, may assist in performing this function. Through its interaction with the ubiquitous chaperone, Hsc70, it is thought that cysteine string protein targets chaperone complexes to the exocytotic machinery to facilitate the correct folding of polypeptides or to regulate the assembly of protein complexes. Since its discovery, there have been conflicting reports from different systems concerned with whether cysteine string protein exerts its effects on exocytosis either up- or down-stream of Ca2+-influx. In this review, we summarize recent experiments that associate cysteine string protein with the regulation of vesicle filling, vesicle docking, Ca2+-channels and the SNARE proteins themselves, hence supporting a role for cysteine string protein as a multifunctional secretory co-chaperone. In addition, we provide an update on the mammalian isoforms of cysteine string protein following the recent discovery of two novel cysteine string proteins.

Amino Acid Sequence↗

PubMed2003

Quasi-collective motion of nanoscale metal strings in metal surfaces.

Mass transport processes on metal surfaces play a key role in epitaxial growth and coarsening processes. They are usually described in terms of independent, statistical diffusion and attachment/detachment of individual metal adatoms or vacancies. Here we present high-speed scanning tunnelling microscopy (video-STM) observations of the dynamic behaviour of five-atom-wide, hexagonally ordered strings of Au atoms embedded in the square lattice of the Au(100)-(1x1) surface that reveal quasi-collective lateral motion of these strings perpendicular to as well as along the string direction. The perpendicular motion can be ascribed to small atomic displacements in the strings induced by propagating kinks, which also provides a mechanism for the exchange of Au atoms between the two string ends, required for motion in string direction. In addition, quasi-one-dimensional transport of Au adatoms along the string boundaries may contribute to the latter phenomenon according to density functional calculations.

Computer Simulation↗

PubMed2005

String tension effects on tennis ball rebound speed and accuracy during playing conditions.

The primary aim of this study was to determine whether variations in rebound speed and accuracy of a tennis ball could be detected during game-simulated conditions when using three rackets strung with three string tensions. Tennis balls were projected from a ball machine towards participants who attempted to stroke the ball cross-court into the opposing singles court. The rebound speed of each impact was measured using a radar gun located behind the baseline of the court. An observer also recorded the number of balls landing in, long, wide and in the net. It was found that rebound speeds for males (110.1+/-10.2 km.h-1; mean+/-s) were slightly higher than those of females (103.6+/-8.6 km.h-1; P<0.05) and that low string tensions (180 N) produced greater rebound speeds (108.1+/-9.9 km.h-1) than high string tensions (280 N, 105.3+/-9.6 km.h-1; P<0.05). This finding is in line with laboratory results and theoretical predictions of other researchers. With respect to accuracy, the type of error made was significantly influenced by the string tension (P<0.05). This was particularly evident when considering whether the ball travelled long or landed in the net. High string tension was more likely to result in a net error, whereas low string tension was more likely to result in the ball travelling long. It was concluded that both gender and the string tension influence the speed and accuracy of the tennis ball.

Adult↗

PubMed1996

High-quality automated DNA sequencing primed with hexamer strings.

The finishing phase of genome sequencing projects is expensive, in part, because of the cost of de novo synthesis of custom primers and the management burden associated with obtaining and using them for primer walking. One approach to reduce these high costs is the use of a presynthesized library of short oligonucleotides (8-10 bases) rather than long primers. The use of such a library eliminates the need for custom synthesis of oligonucleotides, providing the convenience of priming from any site by combining two to three short oligonucleotides to form a string with the required specificity. The first practical implementation of this strategy presented a robust protocol for using hexamer strings with radioisotopic labelling. Whereas versions of this technique have subsequently been implemented on fluorescent sequencers we felt that there was a need to develop and extensively test a protocol that consistently gave read lengths comparable to dye-terminator sequencing with longer primers. We have developed a new two-cycle fluorescent Sequenase terminator procedure for using hexamer strings. We tested this procedure using a set of 32 different 3 hexamer primer strings, each known to be functional to some degree in radioisotopic sequencing, on single-stranded M13mp18 template and ABI 373 DNA sequencers. The overall success rate of priming with these hexamer primer strings is 97% with the failure of only one string. In this case, the corresponding 18-mer primer also failed to produce usable sequence from M13mp18 template. The average read length from reactions successfully primed with the 31 different hexamer strings was 461 bases with > 99% base-calling accuracy. The current protocol is robust enough to be used in virtually any situation where primer walking on single-stranded templates is used. The success rate and read lengths make it universally applicable to the sequencing of single-stranded templates on automated sequencers. It is also amenable to automation.

Automation↗

PubMed2000

A string matching computer-assisted system for dolphin photoidentification.

This paper presents a syntactic/semantic string representation scheme as well as a string matching method as part of a computer-assisted system to identify dolphins from photographs of their dorsal fins. A low-level string representation is constructed from the curvature function of a dolphin's fin trailing edge, consisting of positive and negative curvature primitives. A high-level string representation is then built over the low-level string via merging appropriate groupings of primitives in order to have a less sensitive representation to curvature fluctuations or noise. A family of syntactic/semantic distance measures between two strings is introduced. A composite distance measure is then defined and used as a dissimilarity measure for database search, highlighting both the syntax (structure or sequence) and semantic (attribute or feature) differences. The syntax consists of an ordered sequence of significant protrusions and intrusions on the edge, while the semantics consist of seven attributes extracted from the edge and its curvature function. The matching results are reported for a database of 624 images corresponding to 164 individual dolphins. The identification results indicate that the developed string matching method performs better than the previous matching methods including dorsal ratio, curvature, and curve matching. The developed computer-assisted system can help marine mammalogists in their identification of dolphins, since it allows them to examine only a handful of candidate images instead of the currently used manual searching of the entire database.

Animal Identification Systems↗

PubMed2002

Wave impedances of drill strings and other periodic media.

It is commonly known that wave reflections are caused by abrupt spatial variations in the physical parameter called wave impedance. When a material contains a spatially periodic distribution of wave impedances some very interesting and complex wave propagation phenomena will occur. Two examples of such periodic structures immediately come to mind: the first is a sandwiched structure of two types of plates, say for example, identical layers of thin steel plates interspersed with identical thick aluminum plates; and the second is a large number of identical long thin pipes that are connected from end to end with identical short heavy threaded couplings. The pipe assembly is our primary concern here because it represents the drill string, used worldwide to drill for natural energy resources. We want to understand how waves propagate through drill strings because we want to use them as a means of communication. But while the second structure is our primary concern, it is the study of the first structure, composed of layers, that is the truly historical problem and the source of much of our understanding of this rich set of wave physics. Traditionally, wave propagation in periodic media has been studied as an eigenvalue problem. The eigenvalues themselves yield information about phase velocities, group velocities, passbands, and stopbands. Most often the analysis has stopped there and the eigenvectors have been ignored. Here we turn our attention to the eigenvectors, using them to evaluate the impedance of the periodic structure with particular emphasis on the periodic drill string. As you might expect the impedance of the drill string is a complex number, which is evaluated from a very complicated expression. However, we have discovered that the impedance at two physical locations along the length of each piece of drill pipe in the drill string always reduces to a real number. This is immensely important because it allows us to match the impedance of the drill string to our communication devices. We show how this leads to the effective design of repeaters, noise cancelers, wave terminators, and quarter-wave transformers for a drill-string communication system.

Journal Article↗

PubMed2004

Increase of white matter string vessels in Alzheimer's disease.

String vessels are collagenous structures connected to capillaries. They have no endothelial cells or lumen. We assessed collagen IV-labeled string vessels in the white matter (WM) of subjects with Alzheimer's disease (AD) (n = 12) and non-AD controls (n = 11) using 100 microm celloidin sections. Ten standard fields were digitally captured and the number and length of normal vessels and string vessels were quantified by computerized image analysis. The WM of the AD-diagnosed individuals contained more strings per mm2 (3.95 +/- 0.49) than comparable WM from controls (1.36 +/- 0.39) (p = 0.0005) and had increased total string vessel length in mm/mm2 (AD = 0.29 +/- 0.04; control = 0.10 +/- 0.03; p = 0.0015). There was a 25% increase (not statistically significant) in vessel density in mm/mm2 in AD subjects (AD = 11.88 +/- 0.87; control = 9.53 +/- 0.78; p = 0.06), presumably due to brain atrophy in the white matter. Although vessel length was slightly increased in AD subjects, they still had more than double the string length per total vessel length (AD = 2.88 +/- 0.38) compared to controls (1.36 +/- 0.27) (p = 0.0057). This increase in string vessels in the white matter of AD subjects suggests a decrease in vascular supply in this disease.

Aged↗

PubMed2003

Evaluation of the string test for the detection of Helicobacter pylori.

AIM: Helicobacter pylori can be diagnosed by invasive or non-invasive tests but to obtain bacteria for culture and antibiotic susceptibility testing, an upper GI endoscopy is often required. The string test may be a minimally-invasive alternative method of obtaining H. pylori samples. This study evaluates the sensitivity and specificity of the string test in the diagnosis of H. pylori in comparison with endoscopic means of diagnosis. METHODS: This was a prospective open comparative study of patients with dyspepsia with endoscopy-based tests as gold standard (defined as a positive CLO test and antral histology). Fasting patients swallowed the encapsulated-string (Entero-test Hp), which was withdrawn after 1 hour. The gastric juice from the string was plated onto H. pylori-selective media for culture. Helicobacter pylori was identified by typical colony morphology, gram stain and biochemical test results. RESULTS: Thirty dyspeptic patients were recruited of whom 21 (70 %) were positive for H. pylori according to the gold standard. The sensitivity, specificity, positive predictive value, and negative predictive value for the string test were 38 %, 100 %, 100 % and 41 % respectively, and for endoscopic biopsies 81 %, 100 %, 100 %, 69 % respectively (P=0.004). Logistic regression showed that only abundant growth density from endoscopic biopsy cultures to be a predictor of a positive string test (P=0.018). CONCLUSION: The string test is an alternative method to endoscopy in obtaining H. pylori but has a low sensitivity compared to endoscopic biopsies.

Adult↗

PubMed1991

On the role of refixations in letter strings: the influence of oculomotor factors.

Recent studies of reading and word recognition have shown that eye-movement behavior depends strongly on the position in the word that the eye first fixates; the probability of refixating in a word is lowest with the eye near the middle of the word, and it increases as the eye fixates to either side. It has generally been assumed that the cause for this optimal landing position phenomenon lies in the very strong drop-off of visual acuity even within the fovea; refixation should be more likely when the eye starts from a noncentral position, because here less information can be extracted during one fixation. It may, however, be the case that the phenomenon is caused not by acuity drop-off, but by differences in within-word oculomotor scanning tactics as a function of the position that the eye initially fixates. To test this, in the present experiment we kept visual information constant while we varied the initial fixation position. We used homogeneous strings of letters of different length. One letter in each string was different from the rest (e.g., kkkkkok), and this was the letter that the subject initially fixated. This target letter had to be identified before saccading to a comparison string. The position of the target letter in the string was varied from trial to trial. If, owing to acuity limitations, refixations reflect insufficient information extraction, then, because the target letter is always directly fixated, the pattern of refixations in this condition should be independent of the first fixation position. However, the obtained refixation probability showed a strong dependence on the position of first fixation. The number of refixations was independent of the absolute length of the letter strings, but it seemed to be influenced by the proportion of the string over which the eye had to pass. The larger this proportion, the higher the probability of refixation. The results suggest that to a certain extent refixations in letter strings (or words) reflect properties of the oculomotor system rather than visual information extraction.

Adult↗

PubMed1979

Orthographic regularity, positional frequency, and visual processing of letter strings.

Previous research has demonstrated that familiarity with the orthographic structure within a letter string can facilitate the processing of the component letters. The current research was directed at discovering the psychologically relevant properties of this structure. Two fundamental descriptions were independently varied in the construction of six-letter nonword strings. A probabilistic description based on the frequency of occurrence of letters in each position was factorially combined with a rule-governed description defined in terms of graphemic and phonological constraints. College sophomores and sixth-grade readers were asked to indicate whether or not a predesignated target letter was present in these strings. For both groups of readers, orthographic regularity and summed positional frequency were found to have only a small facilitative effect on reaction time (RT). In contrast, RTs to say "no" increased dramatically with increases in the number of letters in the catch string that were physically similar to the target letter. In another experiment, the letter string was presented for a short duration, followed immediately by masking stimulus and then the target letter. College students indicated whether or not the target was present in the test string. Accuracy of performance was critically dependent on the orthographic regularity and summed positional frequencies of the letters in the test string. No effect of letter similarity was observed. The large differences that were observed between these two tasks were accounted for in terms of the stages of processing that are critical for performance in the tasks.

Adult↗

PubMed1993

A fast algorithm for the optimal alignment of three strings.

Ukkonen's (pair-wise) string alignment technique is extended to the problem of finding an optimal alignment for three strings. The resulting algorithm has worst-case time-complexity O(nd2) and space-complexity O(d3), where the string lengths are ñ and d is the three-way edit-distance based on tree-costs. In practice, the algorithm usually runs in O(n + d3) time. The algorithm is particularly fast when the strings are similar, in which case, d << n. Three-way alignment is an important special case in string alignment. Each internal node in an unrooted, binary evolutionary-tree has three neighbours. The algorithm presented can be used as an iterative step in a heuristic multiple-alignment program for more than three strings.

Algorithms↗

PubMed2003

Key-string segmentation algorithm and higher-order repeat 16mer (54 copies) in human alpha satellite DNA in chromosome 7.

A new key-string segmentation algorithm for identification of alpha satellite DNAs and higher-order repeat (HOR) units was introduced and exemplified. Starting with an initial key string, we determine the dominant key string and HOR. Our key-string algorithm was used to scan the recent GenBank data for human alpha satellite DNA sequence AC017075.8 (193 277 bp) from the centromeric region of chromosome 7. The sequence was computationally segmented into one HOR domain (super-repeat domain) and two non-HOR domains. Dominant key-string GTTTCT provided segmentation in terms of alpha monomers. The HOR is tandemly repeated in 54 copies in the super-repeat (HOR) domain. Five insertions and three deletions in the HOR structure associated with a dominant key string were identified. Concensus HOR was constructed. Divergence of individual HOR copies from concensus amounts to 0.7% on the average, while divergence between 16 monomer variants within each HOR is on the average 20%. In the front and back domain, 199 monomer variants were identified that are not organized in HOR and diverge by 20-40%.

Algorithms↗