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At least 271 records · Page 15Linked to original sources

PubMed2004

New procedure for purse-string suture in thoracoscopic esophagectomy with intrathoracic anastomosis.

BACKGROUND: In endoscopic surgery, one of the greatest problems is the difficulty with the reconstructive procedure. This problem frequently makes operating times longer. The authors have performed thoracoscopic esophagectomy and intrathoracic esophagogastric anastomosis for reconstruction using a circular stapler for the esophageal cancer. Although the circular stapler is a useful device for gastrointestinal anastomosis, it was difficult to place a purse-string suture and to fixate the anvil into the proximal esophagus endoscopically. METHODS: The authors devised a new procedure for the placement of the purse-string suture by using an Endo-Stitch device along with a new method to incise the esophageal wall and thereby facilitate fixation of the anvil. RESULTS: The authors attempted this procedure for five patients. The anastomoses were performed successfully. CONCLUSIONS: The new procedure can make endoscopic intrathoracic anastomosis feasible and safe. In addition, this procedure can be applied widely to other endoscopic reconstructions.

Anastomosis, Surgical↗

PubMed2005

Using string kernel to predict signal peptide cleavage site based on subsite coupling model.

Owing to the importance of signal peptides for studying the molecular mechanisms of genetic diseases, reprogramming cells for gene therapy, and finding new drugs for healing a specific defect, it is in great demand to develop a fast and accurate method to identify the signal peptides. Introduction of the so-called {-3,-1, +1} coupling model (Chou, K. C.: Protein Engineering, 2001, 14-2, 75-79) has made it possible to take into account the coupling effect among some key subsites and hence can significantly enhance the prediction quality of peptide cleavage site. Based on the subsite coupling model, a kind of string kernels for protein sequence is introduced. Integrating the biologically relevant prior knowledge, the constructed string kernels can thus be used by any kernel-based method. A Support vector machines (SVM) is thus built to predict the cleavage site of signal peptides from the protein sequences. The current approach is compared with the classical weight matrix method. At small false positive ratios, our method outperforms the classical weight matrix method, indicating the current approach may at least serve as a powerful complemental tool to other existing methods for predicting the signal peptide cleavage site. The software that generated the results reported in this paper is available upon requirement, and will appear at http://www.pami.sjtu.edu.cn/wm.

Models, Genetic↗

PubMed1978

Analysis of 100 cases of missing IUD strings.

In a study of 100 patients with missing IUD strings 69 women had their IUD in utero (4 were pregnant) and 17 had unnoticed expulsions (4 pregnancies); 9 devices were in the peritoneal cavity and one had perforated the cervix. Since the IUD was in the uterine cavity in the majority of these cases, most contraceptors whose IUD strings disappear can be managed in the office or clinic with relatively simple techniques to locate and remove the device.

Abortion, Spontaneous↗

PubMed1996

Association of Drosophila cysteine string proteins with membranes.

Cysteine string proteins are putative synaptic vesicle proteins that lack a transmembrane domain. Our analysis shows that Drosophila cysteine string proteins are extensively modified by hydroxylamine-sensitive fatty acylation. This modification could be responsible for association of csp's with membranes. Extensive deacylation of Dcsp's by a 20 h incubation in 1 M hydroxylamine, pH 7.0, or methanolic KOH produces a protein of 6-7 kDa lower mass than untreated Dcsp's. Surprisingly, the hydroxylamine treatment does not cause release of Dcsp's from membranes. On the other hand, alkaline stripping of membranes isolated from Drosophila brain by 0.1 M sodium carbonate, pH 11.5, causes a significant release of Dcsp's from membranes into the cytosol. These results indicate that fatty acylation may not form the main anchor of Dcsp's in membranes. Taking advantage of the endocytotic block in the Drosophila mutant shibire ts1, we analyzed the acylation states of Dcsp's in two stages during synaptic vesicle recycling and found no evidence for an acylation/deacylation cycle of Dcsp's in the brain nerve terminals.

Acylation↗

PubMed1989

String analysis and energy minimization in the partition of DNA sequences.

Two approaches to the understanding of biological sequences are confronted. While the recognition of particular signals in sequences relies on complex physical interactions, the problem is often analysed in terms of the presence or absence of literal motifs (strings) in the sequence. We present here a test-case for evaluating the potential of this approach. We classify DNA sequences as positive or negative depending on whether they contain a single melted domain in the middle of the sequence, which is a global physical property. Two sets of positive "biological" sequences were generated by a computer simulation of evolutionary divergence along the branches of a phylogenetic tree, under the constraint that each intermediate sequence be positive. These two sets and a set of random positive sequences were subjected to pattern analysis. The observed local patterns were used to construct expert systems to discriminate positive from negative sequences. The experts achieved 79% to 90% success on random positive sequences and up to 99% on the biological sets, while making less than 2% errors on negative sequences. Thus, the global constraints imposed on sequences by a physical process may generate local patterns that are sufficient to predict, with a reasonable probability, the behaviour of the sequences. However, rather large sets of biological sequences are required to generate patterns free of illegitimate constraints. Furthermore, depending upon the initial sequence, the sets of sequences generated on a phylogenetic tree may be amenable or refractory to string analysis, while obeying identical physical constraints. Our study clarifies the relationship between experts' errors on positive and negative sequences, and the contributions of legitimate and illegitimate patterns to these errors. The test-case appears suitable both for further investigations of problems in the theory of sequence evolution and for further testing of pattern analysis techniques.

Base Sequence↗

PubMed1996

Cysteine-string proteins: a cycle of acylation and deacylation?

We used tunicamycin, an inhibitor of protein fatty acylation, to examine the possibility that there is a cycle of acylation and deacylation of cysteine string proteins at nerve terminals. Using both physiological and immunoblot approaches, we obtained no evidence for a cycle of acylation and deacylation that affects these proteins. These data suggest that this lipid modification of cysteine string proteins is relatively more stable than that observed for other nerve ending proteins, like SNAP-25.

Acylation↗

PubMed1995

Cysteine string protein, a DnaJ family member, is present on diverse secretory vesicles.

Synaptic vesicles are the secretory organelles responsible for the regulated secretion of neurotransmission. Proteins associated with or integral components of the lipid bilayer likely represent important components in regulated secretion. CSP (cysteine string protein) is a 34 kDa protein which copurifies with cholinergic synaptic vesicles from the marine ray Torpedo californica. In Drosophila melanogaster deletion of the CSP gene causes impaired presynaptic neuromuscular transmission. A rat brain complementary DNA (cDNA) encoding CSP was isolated and sequence analysis predicts a protein with 86% identity to Torpedo CSP. Rat CSP contains a "J domain" as well as a cysteine rich "string" region. The J domain "fingerprints" the CSP family as members of the universally conserved DnaJ/hsp40 (heat shock protein) chaperone family. Polyclonal antisera raised against a seventeen amino acid peptide representing the carboxy terminus of rat CSP detected a 35 kDa immunoreactive protein in a rat brain synaptic vesicle enriched preparation. A 35 kDa immunoreactive protein that comigrates electrophoretically with rat brain CSP was also detected in zymogen granule membranes. These results establish the presence of a CSP in rat brain and in the zymogen granule of the rat pancreas and suggest that CSPs have a role in exocrine and neural secretion.

Amino Acid Sequence↗

PubMed1984

Diagnosis of typhoid fever using a string capsule device.

Cultures were made from blood, bone marrow, stool and duodenal contents (obtained with string capsules) from 36 patients with bacteriologically proven typhoid fever on admission to hospital. Duodenal content cultures proved to be as sensitive in diagnosis (86%) as bone marrow (75%) and more effective than blood (42%) and stool (26%) cultures in recovery of Salmonella typhi. The sensitivity of duodenal content cultures was not modified by the duration of illness at admission or by previous antibacterial therapy. Even on the seventh day of effective treatment with chloramphenicol, the culture of duodenal contents remained positive in 8 of 17 patients, whereas salmonellae were isolated from stool cultures in only 2 of the same patients. The results obtained with the string capsule, together with the simplicity, economy and acceptability of the procedure, the fact that it can be performed with minimal facilities and the advantages of bacteriological recovery for antibiotic sensitivity testing, suggest that its adoption would be very helpful in efforts to control this disease.

Bacteriological Techniques↗

PubMed1990

The string and the doorknob: profile of a popular approach to dental extraction.

Dental technology and delivery of care constantly improve. At the same time, certain folk traditions and attitudes towards dentistry remain curiously constant. Dental extraction using string is an enduring amateur technique, images of which are still widely perpetuated among the laity, in western society. The historical development of extraction as a treatment modality and the rise of dentistry are discussed in relation to the patient's view of dental therapy. Various examples from art and literature are introduced to give depth and perspective to current popular perceptions. Extraction with string is presented as a metaphor for all extractions and as reflective of the public's continuing psychological sensitivity to surgical intervention in the oral cavity.

Adult↗

PubMed1994

Choice of moving target for a string phantom: II. On the performance testing of Doppler ultrasound systems.

A string phantom was used to test a duplex system using several filaments: braided silk, nylon and O-ring rubber. The estimated pulsatility index was identical for all filaments tested. Range gate registration measurements were identical for all filaments tested. Maximum velocity was underestimated in the region of a strong angular backscatter peak; this was the case for several of the braided silk filaments. This effect was not observed for O-ring rubber. The paper concluded that O-ring rubber is a suitable filament for the testing of several key Doppler quantities. Recalibration of the string phantom velocity indicator is necessary due to the large diameter of the O-ring rubber.

Models, Structural↗

PubMed2006

Suspension string: a new method of aortic valvuloplasty for aortic insufficiency and ventricular septal defect.

In a 4-year-old boy with ventricular septal defect, severe aortic insufficiency, and mild infundibular stenosis, a new method was used to reconstruct the prolapsed aortic cusp. Two ends of a pledged stitch were passed through the aorta at each side of the right, noncoronary commissure and then through another pledget, and were then tied repeatedly in a row. The length of the row of knots was equal to that of the free edge of left coronary or noncoronary leaflet. The remainder of the stitch was passed through a pledget and then the aortic wall at each side of the left and right coronary commissure to the extraaortic wall pledget and were tied. A suspension string was formed by the row of knots and supported by a Teflon (Dupont Teflon, Wilmington, DE) felt pledget sandwich at each of two commissures. The free margin of the prolapsed cusp was attached to the suspension string by a continuous suture. The concomitant anomalies were corrected. The result was satisfactory.

Aortic Valve↗

PubMed2004

Symbol-string sensitivity and children's reading.

In this study of primary school children, a novel 'symbol-string' task is used to assess sensitivity to the position of briefly presented non-alphabetic but letter-like symbols. The results demonstrate that sensitivity in the symbol-string task explains a unique proportion of the variability in children's contextual reading accuracy. Moreover, developmental dyslexic readers show reduced sensitivity in this task, compared to chronological age controls. The results suggest that limitations set by visuo-spatial processes and/or attentional iconic memory resources may constrain children's reading accuracy.

Attention↗

PubMed2005

On exact string matching of unique oligonucleotides.

Unique, gene-specific oligonucleotides are used for many genetic investigations such as polymerase chain reaction, gene cloning, microarray technology and antisense DNA studies. It is a computationally demanding task to extract these oligonucleotides from DNA databases. We studied the problem from the point of view of the string matching problem. We implemented and tested several exact string matching algorithms and modified the implementations to be as effective as possible. Ten different implementations were tested on yeast genomic sequence data. The run times for the best algorithms were significantly improved compared to conventional approaches, while in principle, i.e. in respect of theoretical time complexity, these algorithms do not actually differ essentially from each other.

Algorithms↗

PubMed2005

Assessment of approximate string matching in a biomedical text retrieval problem.

Text-based search is widely used for biomedical data mining and knowledge discovery. Character errors in literatures affect the accuracy of data mining. Methods for solving this problem are being explored. This work tests the usefulness of the Smith-Waterman algorithm with affine gap penalty as a method for biomedical literature retrieval. Names of medicinal herbs collected from herbal medicine literatures are matched with those from medicinal chemistry literatures by using this algorithm at different string identity levels (80-100%). The optimum performance is at string identity of 88%, at which the recall and precision are 96.9% and 97.3%, respectively. Our study suggests that the Smith-Waterman algorithm is useful for improving the success rate of biomedical text retrieval.

Algorithms↗

PubMed2005

Construction of a virtual combinatorial library using SMILES strings to discover potential structure-diverse PPAR modulators.

Based on the structural characters of PPAR modulators, a virtual combinatorial library containing 1226,625 compounds was constructed using SMILES strings. Selected ADME filters were employed to compel compounds having poor drug-like properties from this library. This library was converted to sdf and mol2 files by CONCORD 4.0, and was then docked to PPARgamma by DOCK 4.0 to identify new chemical entities that may be potential drug leads against type 2 diabetes and other metabolic diseases. The method to construct virtual combinatorial library using SMILES strings was further visualized by Visual Basic.net that can facilitate the needs of generating other type virtual combinatorial libraries.

Combinatorial Chemistry Techniques↗

PubMed1997

The DnaJ-like cysteine string protein and exocytotic neurotransmitter release.

The fast, tightly regulated release of neurotransmitters from presynaptic nerve terminals is effected by a complex molecular apparatus. The precise roles of the various proteins involved remain largely conjectural. Cysteine string proteins (CSPs) are novel synaptic vesicle components that have been conserved in evolution. They are characterized by an N-terminus 'J'-domain and a central, multiply palmitoylated string of cysteine residues. Vertebrate CSPs have been implicated in a functional interaction of synaptic vesicles with presynaptic Ca2+ channels. Genetic 'knockout' of CSPs in Drosophila results in a temperature-sensitive breakdown of elicited transmitter release. Here we try to integrate these observations into speculative functional models on the role of this new protein family in synaptic vesicle exocytosis.

Animals↗

PubMed1998

A Xenopus cysteine string protein with a cysteine residue in the J domain.

A cDNA clone encoding a Xenopus cysteine string protein (Xcsp) was isolated and sequenced. The deduced primary sequence of Xcsp is very similar to other vertebrate csps with the exception of a cysteine residue that lies outside of the cysteine-string domain. This cysteine residue replaces a serine that is highly conserved among vertebrate csps, and thus may be of functional importance. Xcsp mRNA appears as a 4.6 kb species on Northern analysis, and immunoblot of Xenopus brain membranes reveals a single, 35 kDa Xcsp that can be deacylated, like other csps.

Amino Acid Sequence↗

PubMed1999

Tendon displacement assessment by pulsed Doppler tissue imaging: validation with a reciprocating string test target.

After hand trauma and surgery, assessment of tendon excursion is important in reconstructive surgery and rehabilitation. Aimed as a more reliable alternative to traditional noninvasive methods, a colour Doppler imaging scanner was adapted to measure longitudinal tendon displacement. Displacement was quantified by integrating the velocity estimated from the zero-crossing rate of the Doppler signal. The system was tested by measuring displaced distances of a rubber string that was moved back and forth. At a determined optimal receiver gain, 1.5-cm string displacements were measured with less than +/- 0.05-cm bias throughout an echo-signal dynamic range of 22 dB; standard deviations were around 0.05 cm. Regression analysis between measured and true displacements in the range 0.5-2.5 cm resulted in a best fit straight line with slope 0.927, intercept 0.041 cm and residual standard error of 0.06 cm. A transfer technique was conceived to ensure accuracy when measuring tendons in the body. This CDI-based pulsed Doppler system merits verification for measurement of tendon excursion in patients.

Biomechanical Phenomena↗