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PubMed1998

Compression of strings with approximate repeats.

We describe a model for strings of characters that is loosely based on the Lempel Ziv model with the addition that a repeated substring can be an approximate match to the original substring; this is close to the situation of DNA, for example. Typically there are many explanations for a given string under the model, some optimal and many suboptimal. Rather than commit to one optimal explanation, we sum the probabilities over all explanations under the model because this gives the probability of the data under the model. The model has a small number of parameters and these can be estimated from the given string by an expectation-maximization (EM) algorithm. Each iteration of the EM algorithm takes O(n2) time and a few iterations are typically sufficient. O(n2) complexity is impractical for strings of more than a few tens of thousands of characters and a faster approximation algorithm is also given. The model is further extended to include approximate reverse complementary repeats when analyzing DNA strings. Tests include the recovery of parameter estimates from known sources and applications to real DNA strings.

Algorithms↗

PubMed2003

Induction of string rescues the neuroblast proliferation defect in trol mutant animals.

In trol mutants, neuroblasts fail to exit G1 for S phase. Increasing string expression in trol mutants rescues the number of S phase neuroblasts without an increase in M phase neuroblasts. Decreasing string expression further decreased the number of S phase neuroblasts. Coexpression of cyclin E and string did not produce additional S phase cells. Unlike cyclin E, cdk2, and cdk2AF, elevated expression of neither cyclin A, cyclin D, nor cdk1AF was able to promote S phase progression in arrested neuroblasts, indicating that String-induced activity of a Cyclin A or Cyclin D complex is unlikely to drive trol neuroblasts into S phase. Biochemical analyses revealed a rapid increase of Cyclin E-Cdk2 kinase activity to wild-type levels upon increased string expression. These results suggest that Drosophila Cdc25 may directly or indirectly increase the kinase activity of Cyclin E-Cdk2 complexes in vivo, thus driving arrested neuroblasts into cell division.

Alleles↗

PubMed1981

The string test: an early behavioral change in thiamine deficiency.

Thiamine deficiency is a useful animal model of the interaction between biochemistry and behavior. Although numerous biochemical changes have been detected in thiamine deficiency, studies of behavioral changes are relatively scarce. We have modified and quantitated the string test, originally described by Miquel and Blasco, for application to thiamine-deficient rats. The string test is reproducible with time, and control rats have a narrow range of scores. 50% of rats treated with thiamine-deficient diet and pyrithiamine, a centrally-acting thiamine antagonist, have persistently decreased string test scores. This decrease is already present on day 5 of treatment, long before the onset of weight loss or neurological symptoms. Rats treated with oxythiamine, a peripherally acting thiamine antagonist, do not have decreased string test scores, even when anorectic and moribund. These findings suggest that impaired string test performance is a central system effect of thiamine deficiency, and that it may also be a useful behavioral parameter to follow in other animal models of metabolic encephalopathies.

Animals↗

PubMed1998

Intrinsic membrane association of Drosophila cysteine string proteins.

Cysteine string proteins (csps) are highly conserved constituents of vertebrate and invertebrate secretory organelles. Biochemical and immunoprecipitation experiments implied that vertebrate csps were integral membrane proteins that were tethered to the outer leaflet of secretory vesicles via the fatty acyl residues of their extensively acylated cysteine string. Independently, work of others suggested that Drosophila csps were peripheral membrane proteins that were anchored to membranes by a mechanism that was independent of the cysteine string and its fatty acyl residues. We extended these investigation and found first that sodium carbonate treatment partially stripped both csps and the integral membrane protein, synaptotagmin, from Drosophila membranes. Concomitantly, carbonate released fatty acids into the medium, arguing that it has a mild, solubilizing effect on these membranes. Second, we observed that Drosophila csps behaved like integral membrane proteins in Triton X-114 partitioning experiments. Third, we found that when membrane-bound csps were deacylated, they remained membrane bound. Moreover, it appeared that hydrophobic interactions were necessary for this persistent membrane association of csps. Thus, neither reducing conditions, urea, nor chaotropic agents displaced deacylated csps from membranes. Only detergents were effective in solubilizing deacylated csps. Finally, by virtue of the inaccessibility of deacylated csps to thiol alkylation by the membrane-impermeant alkylating reagent, iodoacetic acid, we inferred that it was the cysteine string domain that mediated the membrane association of deacylated csps. Thus, we conclude that under physiological conditions csps are integral membrane proteins of secretory organelles, and that the cysteine string domain plays a vital role in the membrane association of these proteins.

Acylation↗

PubMed2003

Nutritive evaluation of the seed, germinated seed, and string bean of Erythrina americana and the detoxification of the material by boiling.

The nutritive and toxicological values of the dry seeds, germinated seeds, and string beans of Erythrina americana were studied using raw and boiled samples. Raw germinated seeds had a higher protein content and lower fiber content than dry seeds. The whole string bean had lower protein content and higher fiber content. However, the seeds of the green pod showed the same protein concentration as the dry seeds (dry basis). Boiling and elimination of broth was beneficial in diminishing the alkaloid concentration in all the samples. The trypsin inhibitors, lectins, and tannins were also diminished as was expected. The raw string bean showed the lowest LD(50). Although the total essential amino acids content of the boiled germinated seeds was increased, the quality of protein, protein efficiency ratio (PER), was lower than in boiled dry seeds, and in these, the PER was similar to the control (casein). The present results suggest that for the protein quality and low alkaloid content, the boiled dry seeds and string beans could be used for animal feeding. It could be interesting to test the raw string beans in ruminants since in this stage E. americana showed the lowest toxicity.

Animal Feed↗

PubMed1999

Evaluation of two string tests for obtaining gastric juice for culture, nested-PCR detection, and combined single- and double-stranded conformational polymorphism discrimination of Helicobacter pylori.

We have compared two gastric string tests for obtaining gastric juice for culture of Helicobacter pylori and for nested-PCR detection and PCR-based combined single- and double-stranded conformational polymorphism (SDSCP) discrimination of infecting strains. String test specimens were obtained from one seropositive volunteer for 13 consecutive weeks. The distal 10 cm of each string was suspended in 1 ml saline and quantitatively cultured. An additional nine volunteers with histories of upper-gastrointestinal complaints were given a string test for culture and nested-PCR assay. H. pylori isolates and/or gastric juice from each volunteer were extracted for DNA and analyzed by PCR-based SDSCP. Quantitative culture showed that the Entero-test was four times as sensitive as the Gastro-test but was more prone to contamination by oral flora. However, the two string tests are equally sensitive by PCR assays. Thus, the Gastro-test is more suitable for culture detection of H. pylori, since it is less prone to oral contamination and its shorter length is better tolerated. SDSCP analysis of H. pylori DNA from four PCR-positive volunteers without requiring culture showed four distinct profiles, indicating different infecting strains. SDSCP analysis of strains isolated before and after treatment of one volunteer had the same SDSCP profile, suggesting endogenous reinfection by the same strain.

Female↗

PubMed2004

Chloroplasts in Living Cells and the String-of-Grana Concept of Chloroplast Structure Revisited.

In 1980, Wildman et al. (Bot Gaz 141: 24-36) proposed a three-dimensional model for chloroplast structure whereby the grana were arranged in non-overlapping rows, like beads on a string. This string-of-grana model was developed from phase microscope analysis of living cells and partially disrupted, isolated chloroplasts. However, models based on analyses by various electron microscope (EM) techniques (which inevitably encompass a relatively small fraction of the whole chloroplast) indicated that grana are interconnected in all directions by intergranal lamellae and not just along a single 'string.' Hence the string-of-grana model was not widely accepted. Recently, confocal laser scanning microscopy (CLSM) of both living and fixed cells, which gives views of the three-dimensional disposition of grana by imaging Photosystem II fluorescence over much larger sample volumes, that is, the entire chloroplast, has revealed that, although many grana are apparently not in any discernible arrangement, some are indeed present in strings of varying lengths in a range of taxa. The topic therefore warrants revisiting, using techniques, for example, such as EM tomography to assess the degree of variation in the geometry of intergranal connections in whole chloroplasts, and its possible functional consequences and developmental origins.

Journal Article↗

PubMed1991

The role of articulation in the parsing and retention of letter strings in tachistoscopic free recall.

In Mewhort and Campbell's (1981) model of visual word recognition, a scan-parse mechanism transfer information from a character buffer to a short-term store and is largely responsible for the familiarity effects observed in tachistoscopic free recall. Although Mewhort and Campbell do not elaborate on the role of articulation in this task, they do suggest that the scan-parse mechanism acts prior to any involvement of articulatory processes (see Mewhort & Campbell, 1980). However, proponents of working memory (see Baddeley, 1986) are clear that articulation is necessary for the transfer of visual information to a phonological short-term store. In order to clarify the role of articulation in the parsing and retention of letter string, we asked subjects to undertake a tachistoscopic free-recall task, involving first- and fourth-order letter strings, with and without articulatory suppression and/or unattended speech. Unattended speech was observed to interfere with recall, but only when subjects were free to articulate the strings. This implies that subjects were retrieving information from the phonological store and that articulation is necessary for the registration of visual information in this store. The lack of interaction between order-of-approximation and suppression supports the view that the scan-parse mechanism acts independently of articulation. It appears, therefore, that letter strings are parsed at a stage preceding their transfer of the pharmacological store. Finally, the results indicate that subjects are able to draw directly on a representation of the parsed components of a letter string and may do so when phonological storage is difficult.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed2002

Cysteine-string protein in inner hair cells of the organ of Corti: synaptic expression and upregulation at the onset of hearing.

Cysteine-string protein is a vesicle-associated protein that plays a vital function in neurotransmitter release. We have studied its expression and regulation during cochlear maturation. Both the mRNA and the protein were found in primary auditory neurons and the sensory inner hair cells. More importantly, cysteine-string protein was localized on synaptic vesicles associated with the synaptic ribbon in inner hair cells and with presynaptic differentiations in lateral and medial olivocochlear terminals -- the cell bodies of which lie in the auditory brainstem. No cysteine-string protein was expressed by the sensory outer hair cells suggesting that the distinct functions of the two cochlear hair cell types imply different mechanisms of neurotransmitter release. In developmental studies in the rat, we observed that cysteine-string protein was present beneath the inner hair cells at birth and beneath outer hair cells by postnatal day 2 only. We found no expression in the inner hair cells before about postnatal day 12, which corresponds to the period during which the first cochlear action potentials could be recorded. In conclusion, the close association of cysteine-string protein with synaptic vesicles tethered to synaptic ribbons in inner hair cells and its synchronized expression with the appearance and maturation of the cochlear potentials strongly suggest that this protein plays a fundamental role in sound-evoked glutamate release by inner hair cells. This also suggests that this role may be common to ribbon synapses and conventional central nervous system synapses.

Aging↗

PubMed2002

Pecking at other birds and at string enrichment devices by adult laying hens.

1. Bunches of white string (polypropylene twine) are particularly attractive pecking stimuli for both chicks and adult laying hens. Furthermore, these devices can retain the birds' interest over lengthy periods. It has also been demonstrated that birds with trimmed feathers elicit feather pecking. The present study was designed to determine whether string devices would retain their attractiveness in the presence of a competing stimulus: a trimmed hen. 2. Lohmann Brown hens were reared in 20 groups of 5 in floor pens with perches from 17 weeks of age. They were exposed to one of two treatments when they were 23 weeks old. One hen was removed from every pen and the feathers on her rump were trimmed. Immediately before her return two string devices were suspended from a perch in treatment 1 whereas no devices were included in treatment 2. Pecking behaviours were immediately observed for 30 min; this procedure was repeated later that day. The devices remained in the pens used in treatment 1 and these birds were observed again for 15 min after 14 d. 3. The string devices were pecked earlier and more than either the trimmed or untrimmed hens. Furthermore, the devices were still being pecked 2 weeks after their introduction. 4. The virtual absence of severe feather pecking and of aggressive head pecks precluded test of our hypothesis that the devices would divert potentially injurious pecking away from other birds. However, the fact that the birds showed sustained interest in the devices, even in the presence of a competing stimulus, supports our proposal that string may represent a practicable and effective form of environmental enrichment.

Animal Husbandry↗

PubMed1986

Facilitation in letter detection with sequentially presented homophonic strings.

A consistent phonology between sequentially presented pseudoword quadrigrams was found to improve performance in a letter-detection task. Each of 8 subjects was required to judge whether an M appeared in either the initial or terminal position of letter strings. The letter N was used as a foil. For each presentation, two quadrigrams appeared sequentially, the first for 20 ms and the second for a duration that allowed approximately 75% overall accuracy. The strings differed only by the letter next to the one on the opposite end of the string from the M or N. Subjects were not told that two strings were exposed on each presentation, and when asked, none reported having been aware of this. Nevertheless, detection was significantly better when the two strings were homophones (e.g., SERM, SIRM) than when they were not (e.g., SARM, SORM). Results are discussed in terms of phonological access to the mental lexicon.

Discrimination Learning↗

PubMedDate not supplied

String vibration dampers do not reduce racket frame vibration transfer to the forearm.

In this study, we examined the effect of string vibration damping devices on reducing racket frame vibration transfer to the forearm. Twenty participants volunteered to hold a tennis racket stationary in a forehand and backhand stroking position while tennis balls were fired at 20 m x s(-1) towards two impact locations, the node of vibration and the dead spot. A three-way analysis of variance with repeated measures on damping condition, impact location and stroke condition was performed on the data. The resonant frequency of the hand-held racket was found to be approximately 120 Hz. No significant differences in amplitude of vibration at the resonant frequency were found for the wrist or the elbow when damped and non-damped impacts were compared. Impacts at the dead spot produced greater amplitudes of vibration (P < 0.01) but no interaction between impact location and string dampers was evident. The string dampers had no effect on the grip force used or the muscle electrical activity in the forearm after impact. In conclusion, we found that string dampers do not reduce the amount of racket frame vibration received at the forearm. We suggest that string dampers remain a popular accessory among tennis players because of their acoustic effects and psychological support rather than any mechanical advantage.

Adult↗

PubMed1999

The effect of tennis racket string vibration dampers on racket handle vibrations and discomfort following impacts.

In this study, we evaluated the effect of the use of tennis racket string vibration dampers on racket handle vibrations, and perceptions of hand and arm discomfort experienced by tennis players owing to stationary racket impacts. Twenty tennis players (10 males, 10 females) aged 18-29 years volunteered for the study. Two different racket models were impacted at the geometric centre of the racket face and 100 mm distal to the centre both with and without string vibration dampers in place. The participants could neither see nor hear the impacts, and they indicated their discomfort immediately after each impact using a visual analogue scale. An analysis of variance (2 x 2 x 2 factorial) was performed on the scaled discomfort ratings with the factors damping condition, racket type and impact location. No significant differences in discomfort ratings between damped and undamped impacts or between the two racket types were found. Also, central impacts were found to be more comfortable than impacts 100 mm distal to the centre (P< 0.05). There were no significant interaction effects. Vibration traces from an accelerometer mounted on the racket handle revealed that string vibration dampers quickly absorbed high-frequency string vibration without attenuating the lower-frequency frame vibration. In conclusion, we found no evidence to support the contention that string vibration dampers reduce hand and arm impact discomfort.

Adolescent↗

PubMed1988

String wrapping versus massage for reducing digital volume.

The purposes of this study were 1) to compare the relative effectiveness of two common methods of treating hand edema, retrograde massage and string wrapping, and 2) to compare these two methods with two techniques of combining them. Fifty-six digits of the hands of 14 subjects were studied. Because all of the subjects demonstrated generalized hand edema, comparisons of different digits of the same subject could be made on each visit. Effectiveness rankings of the treatment methods were made after each visit. A clear pattern of effectiveness emerged that suggested that superimposing massage on an already-wrapped digit was more effective than either massage or string wrapping alone. Average circumferential reductions of digits further supported the hypothesis that a combination of string wrapping and massage would be more effective than the individual string-wrapping or massage techniques. No significant difference in effectiveness was found between massage and string wrapping when used singularly.

Adult↗

PubMed1985

Collection of duodenal bile in infants and children by the string test.

Present methods for collection of duodenal bile may be difficult to perform and may involve the use of sedation and roentgenograms. The string test (Entero-Test Pediatric, HDC Corporation, Mountain View, CA) has replaced the need for intestinal intubation for diagnosis of giardiasis and bacterial overgrowth. The present study investigated the use of the string test for collection of duodenal bile. Fifteen children were administered string tests. No complications were encountered. The distal end of the string had yellow pigmented fluid that contained bilirubin conjugates in quantity and quality compatible with duodenal bile. The study demonstrates that the string test is a useful procedure for collection of duodenal bile samples in infants and children.

Bacterial Infections↗

PubMed1989

Hepatobiliary scintigraphy and the string test in the evaluation of neonatal cholestasis.

We evaluated [99mTc]diisopropylphenyl-carbamoylmethylimidodiacetic acid ([99mTc]DISIDA) cholescintigraphy with measurement of duodenal fluid radioactivity collected by the string test in patients with neonatal cholestasis. Twenty-six infants with prolonged jaundice and acholic stools were studied prospectively. Twelve patients had neonatal hepatitis, 12 biliary atresia, and one each Alagille syndrome and alpha 1-antitrypsin deficiency liver disease. All infants except the biliary atresia patients and four of the neonatal hepatitis patients revealed bowel activity on scan 6 h after tracer administration. At 24 h, three of these latter patients with neonatal hepatitis and two of the patients with biliary atresia revealed bowel activity. String radioactive counts for neonatal hepatitis ranged from 99,574 to 967,205 cpm (374,504 +/- 232,210 cpm; mean +/- SD) and for biliary atresia from 8,342 to 370,346 cpm (117,149 +/- 98,698 cpm; mean +/- SD). While neither test alone was capable of correctly differentiating among all patients, those patients with biliary atresia had either a negative hepatobiliary scan at 24 h or string radioactive count below 197,007 cpm. Disparity between the hepatobiliary scan and the string radioactive counts mandates further diagnostic investigation. These data suggest that simultaneous administration of the string test with hepatobiliary scintigraphy is advantageous in the evaluation of infants with cholestatic jaundice.

Acute Disease↗

PubMed2002

Kaluza-Klein states versus winding states: can both be above the string scale?

Closed strings in extra compactified dimensions give rise to both Kaluza-Klein states and winding states. Since the masses of these states play a reciprocal role, it is often believed that either the lightest Kaluza-Klein states or the lightest winding states must be at or below the string scale. In this Letter, we demonstrate the contrary, showing that there exist toroidal compactifications for which all Kaluza-Klein states as well as all winding states are heavier than the string scale. Within the context of low-scale string theories, this implies that it may be possible to cross the string scale without detecting any states associated with spacetime compactification.

Journal Article↗

PubMed2003

Open-closed string duality at tree level.

We study the decay of unstable D-branes in string theory in the presence of an electric field, and show that the classical open string theory results for various properties of the final state agree with the properties of closed string states into which the system is expected to decay. This suggests a duality between tree level open string theory on unstable D-branes and closed strings at high density.

Journal Article↗