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At least 307 records · Page 17Linked to original sources

PubMed1993

A programmable Doppler string test object.

A prototype water filled ultrasound string test object is presented for performance checks on Doppler ultrasound systems. The string motion produces realistic and reproducible Doppler wave forms on the system by means of a programmable stepper motor. Wave forms can be generated using a computer, and programmed into the device. The test object can be used to check Doppler calculation parameters, such as pulsatility index and resistance index, as well as range gate registration and wall filter function. The test object is water filled, and the lack of attenuation did prove to be a problem on some systems. The object was tested using five different duplex and colour scanners, and found to be sufficiently reproducible for use as a field test object for Doppler ultrasound machines. The device is compact and portable, making it suitable for checks in the field for both longterm monitoring of performance and inter-machine comparisons.

Humans↗

PubMed2000

Antegrade ureteral stent placement: positioning without use of a retraction string.

PURPOSE: To evaluate a simple method of antegrade ureteral stent insertion allowing optimal positioning of the stent without the use of a retraction string. PATIENTS AND METHODS: Seventeen stents were placed in sixteen patients with ureteral obstruction. Materials included a long vascular introducer sheath and radiopaque markers on the tips of both the sheath and the pusher catheter. For optimal positioning of the proximal pigtail in the renal pelvis, the distal end of the sheath was used to hold a large portion of the pigtail in the extended state prior to its deployment. RESULTS: All stent placements were successful. In one case, the tip of the proximal pigtail was caught in a lower-pole calix. In another case, repeat stent placement was necessary because of recurrent stricture several months after removal of the first stent. All stents functioned properly, as demonstrated by follow-up nephrostography 2 or 3 days after each procedure. CONCLUSION: The insertion method we describe is simple, easy to perform, and fast and avoids the risks associated with the use of a retraction string.

Adult↗

PubMed1993

FASTPAT: a fast and efficient algorithm for string searching in DNA sequences.

A new string searching algorithm is presented aimed at searching for the occurrence of character patterns in longer character texts. The algorithm, specifically designed for nucleic acid sequence data, is essentially derived from the Boyer-Moore method (Comm. ACM, 20, 762-772, 1977). Both pattern and text data are compressed so that the natural 4-letter alphabet of nucleic acid sequences is considerably enlarged. The string search starts from the last character of the pattern and proceeds in large jumps through the text to be searched. The data compression and searching algorithm allows one to avoid searching for patterns not present in the text as well as to inspect, for each pattern, all text characters until the exact match with the text is found. These considerations are supported by empirical evidence and comparisons with other methods.

Algorithms↗

PubMed2026

Treemble: a graphical tool to generate Newick strings from phylogenetic tree images.

SUMMARY: Phylogenetic trees are ubiquitous and central to biology, but most published trees are available only as visual diagrams and not in the machine-readable Newick format. There are, thus, thousands of published trees in the scientific literature that are unavailable for follow-up analyses, comparisons, and supertree construction. Experts can easily read such diagrams, but the manual construction of a Newick string from a diagram is laborious, error-prone, and time-consuming. Previous attempts to semi-automate the reading of tree images relied on image processing techniques. These often encounter difficulties as typical published tree diagrams contain various graphical elements and annotations that overlap the branches, such as error bars on internal nodes. Here we introduce Treemble, a user-friendly desktop application for generating Newick strings from tree images. The user simply clicks to mark node locations, assisted by a deep learning-based node detection tool, and Treemble algorithmically assembles the tree from the node coordinates alone. Treemble also facilitates the automatic reading of tip name labels and can be used for both rectangular and circular trees. AVAILABILITY AND IMPLEMENTATION: Treemble is a native desktop application for macOS and Windows and is freely available, with documentation, at treemble.org. Source code is available at github.com/John-Allard/Treemble. The trained node detection model is available at huggingface.co/John-Allard/treemble-1.

Phylogeny↗

PubMed2005

The fragment assembly string graph.

We present a concept and formalism, the string graph, which represents all that is inferable about a DNA sequence from a collection of shotgun sequencing reads collected from it. We give time and space efficient algorithms for constructing a string graph given the collection of overlaps between the reads and, in particular, present a novel linear expected time algorithm for transitive reduction in this context. The result demonstrates that the decomposition of reads into kmers employed in the de Bruijn graph approach described earlier is not essential, and exposes its close connection to the unitig approach we developed at Celera. This paper is a preliminary piece giving the basic algorithm and results that demonstrate the efficiency and scalability of the method. These ideas are being used to build a next-generation whole genome assembler called BOA (Berkeley Open Assembler) that will easily scale to mammalian genomes.

Algorithms↗

PubMed1998

Cysteine string protein (CSP) is an insulin secretory granule-associated protein regulating beta-cell exocytosis.

Cysteine string proteins (CSPs) are novel synaptic vesicle-associated protein components characterized by an N-terminal J-domain and a central palmitoylated string of cysteine residues. The cellular localization and functional role of CSP was studied in pancreatic endocrine cells. In situ hybridization and RT-PCR analysis demonstrated CSP mRNA expression in insulin-producing cells. CSP1 mRNA was present in pancreatic islets; both CSP1 and CSP2 mRNAs were seen in insulin-secreting cell lines. Punctate CSP-like immunoreactivity (CSP-LI) was demonstrated in most islets of Langerhans cells, acinar cells and nerve fibers of the rat pancreas. Ultrastructural analysis showed CSP-LI in close association with membranes of secretory granules of cells in the endo- and exocrine pancreas. Subcellular fractionation of insulinoma cells showed CSP1 (34/36 kDa) in granular fractions; the membrane and cytosol fractions contained predominantly CSP2 (27 kDa). The fractions also contained proteins of 72 and 70 kDa, presumably CSP dimers. CSP1 overexpression in INS-1 cells or intracellular administration of CSP antibodies into mouse ob/ob beta-cells did not affect voltage-dependent Ca2+-channel activity. Amperometric measurements showed a significant decrease in insulin exocytosis in individual INS-1 cells after CSP1 overexpression. We conclude that CSP is associated with insulin secretory granules and that CSP participates in the molecular regulation of insulin exocytosis by mechanisms not involving changes in the activity of voltage-gated Ca2+-channels.

Animals↗

PubMed2000

STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.

The repeated occurrence of genes in each other's neighbourhood on genomes has been shown to indicate a functional association between the proteins they encode. Here we introduce STRING (search tool for recurring instances of neighbouring genes), a tool to retrieve and display the genes a query gene repeatedly occurs with in clusters on the genome. The tool performs iterative searches and visualises the results in their genomic context. By finding the genomically associated genes for a query, it delineates a set of potentially functionally associated genes. The usefulness of STRING is illustrated with an example that suggests a functional context for an RNA methylase with unknown specificity.

Genes, Bacterial↗

PubMed1997

The "round block" purse-string suture: a simple method to close skin defects with minimal scarring.

We report the use of a subcuticular purse-string suture for closure of surgical skin defects, a simple maneuver that we have found to be very useful in closing difficult wounds and reducing scarring. The purse-string suture is performed with a large nonabsorbable suture that is passed intradermally and left in situ at least 4 weeks. This technique has been applied in 196 patients for a total of 221 sutures over a period of 2 years, being used to close skin defects from 2 x 2 to 8 x 11 cm in many areas of the body. All the patients showed, at closure, a large number of concentric redundant folds as well as considerable distortion of nearby structures; both improved impressively over a period of 2 to 3 weeks and became nearly normal at the time of suture removal (4 to 8.2 weeks, mean 5.7 weeks). The initially very limited and almost circular scar oriented itself along the skin tension lines over a period of a few weeks and, when matured, was always shorter than the original defect. In general, minimal scar widening occurred when we used larger sutures (more than 0-1) that were left longer (more than 6 weeks). Complications have been 23 cases of dehiscence (10.4 percent) in 23 patients (between the fifth and sixteenth days, mean 6.7 days); they were caused by the bad quality of the skin and by the use of too small sutures that cut through the dermis. The "round block" suture has many advantages: 1. It is a simple, inexpensive, and rapid technique for closing wounds by expanding the surrounding skin and often avoiding the use of skin grafts and/or local flaps. 2. It can minimize scarring; the final scars are shorter than the original defect and usually of very good quality. 3. It allows a very useful temporary closure that stretches the surrounding skin while waiting for the definitive histologic report. If this method is not chosen as a definitive closure, later repair with local flaps may be facilitated. 4. For the reasons expressed above, it never compromises the final result even in cases of dehiscence. The main disadvantage is the acceptability of the method on the part of patients, who need to be carefully prepared for both the gross initial distortion and the long time the suture has to be retained; nevertheless, patient satisfaction with the final results in generally very high, especially in large excisions of the face.

Adolescent↗

PubMed2002

Circular excision of hemangioma and purse-string closure: the smallest possible scar.

Localized cutaneous infantile hemangioma acts like a tissue expander. This rapidly growing tumor can destroy elastic fibers or cause ulceration resulting in telangiectases, cutaneous laxity, scarring, and fibrofatty residuum. Although surgeons may dispute indications and timing, most would agree that the scar of resection should be minimized. For this reason, circular excision and purse-string closure is particularly applicable for hemangioma at any stage of its evolution. The purposes of this study were to: (1) analyze the results of circular excision/purse-string closure in all three phases of the life cycle of hemangioma; (2) quantify dimensional changes after resection; and (3) compare the scars after theoretical single-stage lenticular excision with those after staged circular excision/purse-string closure. The authors retrospectively analyzed their experience in 25 children with localized hemangioma who underwent circular excision/purse-string closure from 1997 to 2000. Each hemangioma was measured preoperatively and the scars were measured at most recent follow-up (minimum, 6 months). Preoperative and postoperative dimensions were analyzed using SPSS statistical software. The study included 22 girls and three boys, with an average time to follow-up evaluation of 13.1 months. Twenty-one lesions were in the face and scalp, and five were in the extremity. Five tumors were resected in the proliferative phase (either because of ulceration, bleeding, or visual complications) and 21 were excised in the involuting or involuted phase. Six patients had a second-stage procedure: three had another circular excision and three had later lenticular excision. After single circular excision/purse-string closure, the mean long-axial diameter (length) decreased by 45 percent, the mean short-axial width (width) decreased by 73 percent, and the mean scar area was only 15 percent of the original area. All these differences were statistically significant (p = 0.001). The average width/length ratio decreased by 50 percent, indicating a tendency for scars to linearize. There was no difference in linearization for the three phases of hemangioma (p > 0.05); extremity scars became more linear that those on the face (p = 0.01). The authors devised a formula for scar length after lenticular excision/linear closure, assuming a conventional excisional ratio of 3:1 for a circular lesion. Using this equation, the authors predicted that mean scar length after circular excision, followed by lenticular excision, would be 72 percent shorter than the calculated scar that would result from conventional lenticular excision. In three patients who underwent this two-stage approach, the resultant scar was 69 percent shorter. Circular excision of hemangioma and purse-string closure reduces both the longitudinal and transverse dimensions and converts a large circular lesion into a small ellipsoid scar. If subsequent revision to a linear scar is desirable, its length will be the same or slightly less than the diameter of the original lesion. No other excision and closure technique results in a smaller scar. Another advantage of this method is minimal distortion of surrounding structures.

Child↗

PubMed2002

Purse string-formed plication of the SMAS with fixation to the zygomatic bone.

The superficial musculoaponeurotic system (SMAS) operation revolutionized face-lift procedures. The idea of having one direction of traction with suturing and fixation of SMAS to a stable structure is gaining popularity. The author's contribution is the fixation of the SMAS and the extension of the supraplatysmal plane to the zygomatic bone periosteum to achieve stable traction and fixation. This procedure has not been described before in medical literature. The purse string-formed plication of the SMAS is a procedure in which the soft tissue (SMAS, parotid fascia, and the extension of the supraplatysmal plane) is plicated and fixed to the periosteum of the zygomatic bone. This superficial operation avoids entering the deeper planes, which could result in severe complications. The procedure fills the cheeks and gives a more natural look than standard face lifts. A total of 250 patients underwent this procedure. The suspension achieved seemed to be more stable than some SMASectomy techniques. Complication rates and recovery times were low. The purse string-formed plication of the SMAS is a safe, quick, and simple procedure with effective results suitable for younger patients with good skin conditions.

Adult↗

PubMed2003

Reexamination of string phase and shear thickening in simple fluids.

In 1984, Erpenbeck observed a shear-induced alignment of particles into strings in nonequilibrium molecular dynamics simulations of hard spheres. Since then, it has remained unclear if this effect was genuine or if it arose from the use of a thermostat which assumed an incorrect form for the velocity profile. All studies performed up to now have focused on improving the accuracy with which the velocity profile is determined. We propose here a radically different approach: we apply a recently developed configurational expression for the temperature. This expression does not require any knowledge of the streaming velocity profile. Using a configurational thermostat, we show that the string phase is an artifact and we observe a shear-thickening regime, as seen in experiments on concentrated "hard-sphere"-like colloidal dispersions.

Journal Article↗

PubMed2004

Nucleation rate of critical droplets on an elastic string in a phi6 potential.

We obtain the nucleation rate of critical droplets for an elastic string moving in a phi(6) local potential and subject to noise and damping forces. The critical droplet is a bound soliton-antisoliton pair that carries a section of the string out of the metastable central minimum into one of the stable side minima. The frequencies of small oscillations about the critical droplet are obtained from a Heun equation. We solve the Fokker-Planck equation for the phase-space probability density by projecting it onto the eigenfunction basis obtained from the Heun equation. We employ Farkas' "flux-overpopulation" method to obtain boundary conditions for solving the Fokker-Planck equation; these restrict the validity of our solution to the moderate to heavy damping regime. We present results for the rate as a function of temperature, well depth, and damping.

Journal Article↗

PubMed2005

Analytical derivation of thermodynamic characteristics of lipid bilayer from a flexible string model.

We introduce a flexible string model of the hydrocarbon chain and derive an analytical expression for the lateral pressure profile across the hydrophobic core of the membrane. The pressure profile influences the functioning of the embedded proteins and is difficult to measure experimentally. In our model the hydrocarbon chain is represented as a flexible string of finite thickness with a given bending rigidity. In the mean-field approximation we substitute the entropic repulsion between neighboring chains in a lipid membrane by an effective potential. The effective potential is determined self-consistently. The arbitrary chain conformation is expanded over eigenfunctions of the self-adjoint operator of the chain energy density. The lateral pressure distribution across the bilayer is calculated using the path integral technique. We found that the pressure profile is mainly formed by the sum of the partial contributions of a few discrete lowest-energy "eigenconformations." The dependences on temperature and area per lipid of the lateral pressure produced by the hydrocarbon chains are found. We also calculated the chain contribution to the area compressibility modulus and the temperature coefficient of area expansion.

Compressive Strength↗

PubMed2000

Gravitational wave bursts from cosmic strings

Cusps of cosmic strings emit strong beams of high-frequency gravitational waves (GW). As a consequence of these beams, the stochastic ensemble of gravitational waves generated by a cosmological network of oscillating loops is strongly non-Gaussian, and includes occasional sharp bursts that stand above the rms GW background. These bursts might be detectable by the planned GW detectors LIGO/VIRGO and LISA for string tensions as small as G&mgr; approximately 10(-13). The GW bursts discussed here might be accompanied by gamma ray bursts.

Journal Article↗

PubMed2000

Transverse momentum distributions and their forward-backward correlations in the percolating color string approach

The forward-backward correlations in the p(T) distributions at midrapidity, which present a clear signature of nonlinear effects in particle production, are studied in the model of percolating color strings. Quantitative predictions are given for these correlations at SPS, RHIC, and LHC energies. Interaction of strings also naturally explains the flattening of p(T) distributions and increase of with energy and atomic number for nuclear collisions.

Journal Article↗

PubMed2001

Behavior of boundary string field theory associated with integrable massless flow.

We put forward an idea that the boundary entropy associated with integrable massless flow of thermodynamic Bethe ansatz (TBA) is identified with tachyon action of boundary string field theory. We show that the temperature parametrizing a massless flow in the TBA formalism can be identified with tachyon energy for the classical action at least near the ultraviolet fixed point, i.e., the open string vacuum.

Journal Article↗

PubMed2002

Overpopulation of Omega; in pp collisions: a way to distinguish statistical hadronization from string dynamics.

The Omega/Omega ratio originating from string decays is predicted to be larger than unity in proton-proton interactions at SPS energies ( E(lab) = 160 GeV). The antiomega dominance increases with decreasing beam energy. This surprising behavior is caused by the combinatorics of quark-antiquark production in small and low-mass strings. Since this behavior is not found in a statistical description of hadron production in proton-proton collisions, it may serve as a key observable to probe the hadronization mechanism in such collisions.

Journal Article↗

PubMed2002

A class of exact classical solutions to string theory.

We show that the recently obtained class of spacetimes for which all of the scalar curvature invariants vanish (which can be regarded as generalizations of pp-wave spacetimes) are exact solutions in string theory to all perturbative orders in the string tension scale. As a result the spectrum of the theory can be explicitly obtained, and these spacetimes are expected to provide some hints for the study of superstrings on more general backgrounds. Since these Lorentzian spacetimes suffer no quantum corrections to all loop orders they may also offer insights into quantum gravity.

Journal Article↗