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The spectrum kernel: a string kernel for SVM protein classification.

We introduce a new sequence-similarity kernel, the spectrum kernel, for use with support vector machines (SVMs) in a discriminative approach to the protein classification problem. Our kernel is conceptually simple and efficient to compute and, in experiments on the SCOP database, performs well in comparison with state-of-the-art methods for homology detection. Moreover, our method produces an SVM classifier that allows linear time classification of test sequences. Our experiments provide evidence that string-based kernels, in conjunction with SVMs, could offer a viable and computationally efficient alternative to other methods of protein classification and homology detection.

Artificial Intelligence↗

Haunted by Enron's ghost. National Century Financial Enterprises files for Chapter 11, leaving a string of broken healthcare chains and hospitals.

Some are calling it the Enron of the healthcare industry. Ryder trucks hauled possible evidence from embattled financier National Century Financial Enterprises during an FBI raid. NCFE filed for Chapter 11 bankruptcy protection last week, sending ripples through the industry and contributing to the bankruptcies of a string of national healthcare chains and at least six hospitals.

Bankruptcy↗

[The "grasping tie". I. Introduction to and technical notes of an innovative mechanical tool aimed at formation of "purse string" in digestive surgery].

The grasping tie is an original and mechanical tool, conceived and planned to be used in digestive surgery, to temporary grasp and fasten at the axis of the head or the anvil of a circular stapler the tract of the gut chosen for anastomosis. Its use permit to fix the lower oesophageal stump in total gastrectomy, or that of the rectal stump in the lower rectal resection, respectively to the axis of the circular stapler component for the time necessary to perform the mechanical anastomosis. That is performed by the employment of a thin nylon ribbon, which will be progressively tightened as requested like a one way running knot about the tract of the gut and at the axis of the part of the stapler. The device will be repeatedly activated by an handle located at one of its ends, tightening progressively at the other end a thin nylon ribbon preventively put and laced around the chosen point of the digestive tract to grasp firmly and irreversibly the gut to the axis of the stapler, and then cut away by a trigger of the device in the same end of the handle. The nylon ring will be extracted together with the muscle-mucosal rings once completed the stapler suture, so that nothing of the ribbon remains in the patient. Its function is alternative to the classical tool used to prepare a purse-string suture on a segment of the digestive tract. Its advantages in front of that tool is the minimal space it requires for its use, therefore with operative advantages in fixing the head of the circular stapler in the oesophagus during the reconstructive steps after a total gastrectomy, and in fixing the lower rectum to the axis of anvil of a circular stapler preventively introduced in the anus and extruded. Moreover its employment is advantageous in closing from the outside the two ends of a tract of the gut where a tumour is located, so allowing a safe subsequent manipulation of the gut without oncologic prejudice.

Anastomosis, Surgical↗

[Specific character of movement disorders in children studying string instruments].

Orthopaedic examinations were carried out in 242 children studying string instruments. Various indispositions and deformations of the motor organs were found in 31 children. It has been demonstrated that they were mainly the result of technical errors in holding of the instrument, which caused overloading of the upper extremities and the spine.

Arm↗

Broken retrieval string leads to failed self-removal of a double-J ureteral stent.

Double-J ureteral stents facilitating the drainage of urine from the kidney to the bladder are widely used. Stents designed for patient self-removal are commonplace. We report a case of urosepsis that lead to the incidental discovery of a failed self-removal of a double-J ureteral stent. The retrieval cord broke during self-removal and the patient mistook the string for the stent. Adequate patient education is essential to assure successful self-removal.

Adult↗

[The significance of internal thoracic artery-left anterior descending coronary artery bypass grafting in postoperative angiographic studies--with reference to indication of ITA and factors of string sign].

Internal thoracic artery (ITA) graft for myocardial revascularization has shown superior long-term patency. However, several reports pointed out that the flow capacity of ITA was questionable and the string sign of ITA graft was sometimes observed in the findings of postoperative angiography when the stenosis of the coronary artery was of a lesser degree. We studied pre- and postoperative angiographic findings of 101 patients who underwent ITA grafting to the left anterior descending coronary artery. Postoperative angiography showed that the blood flow from the ITA graft ran through the site of anastomosis only towards the distal end when preoperative stenosis of the native left anterior descending coronary was less than 75%. ITA flow ran bidirectionally (retrogradely and antegradely) when stenosis was within 75 to 90%. Many cases with stenosis of greater than 90% showed the progression of the native lesion, that is, total obstruction of the left anterior descending coronary artery. It becomes clear by statistical study that the postoperative progression of native proximal lesion of the left anterior descending coronary artery correlates neither with the morphological state of the coronary artery nor sites of lesions, but the severity of stenosis. A conclusion has been drawn from angiographic study, that the blood flow from the ITA graft run into two directions; towards the distal and the lesion of the left anterior descending coronary artery, if the free flow through ITA was about 60 ml/min and at the same time, preoperative stenosis of coronary artery was 75% or more.

Adult↗

[Study of Strongyloides stercoralis in the duodenal juice obtained by the examination of a string capsule or the Enterotest].

We present our experience in the investigation of Strongyloides stercoralis in the duodenal juice obtained by the "string capsule" o Enterotest, in 1,511 patients from the Gastroenterology Service of the National Hospital "Edgardo Rebagliati Martins" IPSS, between January 1985 to July 1990. We found 36 patients parasitized with Strongyloides stercoralis, an incidence of 2.4%. This method was good tolerated and have proved to be simple, fast, effective and allowing to examine simultaneously many patients at a very low cost.

Adolescent↗

Stapled transabdominal lower esophageal anastomosis without purse-string suture.

Because of anatomic limitations at the EG junction in total and subtotal gastric resections, gastrointestinal reconstruction is technically challenging. In stapled anastomosis, suboptimal application of a purse-string suture to the distal esophagus may lead to anastomotic breakdown. We describe herein a technique in which this step is eliminated to achieve a sound, full thickness anastomosis with the use of the Roticulator TA 30 and the EEA Premium stapling instruments.

Anastomosis, Surgical↗

[A case report of fibromuscular dysplasia presenting symptoms like moyamoya disease: "string of beads" appearance of the pericallosal artery].

We report a case of fibromuscular dysplasia (FMD) presenting a transient ischemic attack (TIA) like Moyamoya disease. The patient, a 16-year-old woman, had recurrent attacks of right hemiparesis induced by hyperventilation. Neurological examinations revealed no abnormality. Angiography showed severe stenosis of both anterior cerebral arteries at the proximal portion with "string of beads" appearance in the left pericallosal artery, and tubular stenosis of the left internal carotid artery at the level of the second cervical vertebra. Renal artery stenosis was not seen. A cerebral-blood-flow (CBF) study with 133Xe SPECT showed marked reduction of CBF in the left cerebral hemisphere at times of hyperventilation. Extracranial-intracranial bypass surgery was performed and histological examination of the superficial temporal artery (STA) revealed intimal fibroplasia which was compatible with FMD. Postoperative angiography showed good filling of the middle cerebral arteries from the STA. The patient has had no recurrence of TIA for a year since the operation. CBF study showed mild low CBF in the region of the left anterior cerebral arterial circulation at hyperventilation. There is no report of intracranial FMD presenting an ischemic symptom induced by hyperventilation. Clinical diagnosis of Moyamoya disease should be made carefully when extracranial vascular lesion accompanies it.

Adolescent↗

Translocated intra-uterine contraceptive devices and missing strings.

The incidence, clinical presentation, diagnosis, possible aetiology and methods of treatment of translocated intrauterine contraceptive devices (IUCDs) and 'missing strings' are described. Details of 104 such patients, treated at Baragwanath Hospital over a period of 12 months, are given. Four unusual sites of translocation are described.

Adolescent↗

Removable purse-string suture of the bladder neck in transvesical prostatectomy.

Insertion of the provisional Malament purse-string suture of the bladder neck proved an effective haemostatic method of treating serious haemorrhage following suprapubic prostatectomy. In a series of 15 patients, bladder-neck stenosis developed in one case, but in this patient the technique had been used incorrectly. In the other cases there were no serious complications. The method is suitable for bleeding which cannot otherwise be stopped during the operation.

Aged↗

Differentiation of gram-positive and gram-negative bacteria and yeasts using a modification of the "string" test.

Solutions of potassium hydroxide and sodium hydroxide with concentrations between 0.5% and 4% were found to produce mucoid and sticky suspensions when added in drops, using a bacteriological loop, to smears of 609 strains of gram-negative bacteria on glass slides. A total of 461 strains of gram-positive bacteria and yeasts did not produce any mucoid or "string" formation when treated with the same solutions. It was concluded that this modified test could aid in differentiating gram-positive from gram-negative organisms.

Bacteria↗

The retention of vaginal prolapse in the cow using a purse-string suture.

Seventeen cows with prolapsed vaginas were treated by placing a purse-string suture cranial to the external urethral opening to retain the vagina. It was found to be a simple procedure with a high rate of success. Fifteen of the patients responded well to the procedure with a minimum of straining being evident in the post operative period.

Animals↗

Decentralized budgeting: holding the purse strings, part 1.

A decentralized nursing structure allows the head nurse to become actively involved in the planning and budgeting process. In Nursing Decentralization: The El Camino Experience (published in November 1981 by Nursing Resources) the authors describe the development of a budgeting system that supports autonomy, accountability, and authority at the practitioner level. For JONA readers, we present, in two parts, an abridged version of the chapter "Budgeting: Holding the Purse Strings." Part 1, which follows, outlines important steps for the development of a successful and efficient budgeting program that can be adapted to meet the needs of other decentralized organizations. Part 2, which details a typical budget session, will appear in the next issue of JONA.

Budgets↗

The punch and purse-string suture technique.

Palmar hyperhidrosis can be successfully treated by thoracoscopic sympathicotomy, the anterior approach being the most common one. Unfortunately the resulting scars are blemishing. Incision on the upper frontside of thorax leave conspicuous scars and not uncommonly keloids. Likewise the traditional method used for radical excision of naevi leaves large scars in comparison with the size of the mark removed. With the increased awareness of malignant melanoma excision of birthmarks and naevi is increasingly being demanded. There is also a desire for more cosmetically acceptable scars. Is it possible, then, to reduce the size of these scars and make them less conspicuous? In two separate studies a new method has been designed and tested--the punch and purse-string suture technique by which the size of the scars is reduced and of a different shape. In one of the studies, the traditional method and the new technique were compared in the same patient.

Cicatrix↗