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Biomedical subjects

C A Andersen

Publications and source records attributed to C A Andersen.

At least 19 recordsLinked to original sources
PubMed2001

Protein secondary structure: category assignment and predictability.

In the last decade, the prediction of protein secondary structure has been optimized using essentially one and the same assignment scheme known as DSSP. We present here a different scheme, which is more predictable. This scheme predicts directly the hydrogen bonds, which stabilize the secondary structures. Single sequence prediction of the new three category assignment gives an overall prediction improvement of 3.1% and 5.1% compared to the DSSP assignment and schemes where the helix category consists of alpha-helix and 3(10)-helix, respectively. These results were achieved using a standard feed-forward neural network with one hidden layer on a data set identical to the one used in earlier work.

Algorithms↗
PubMed2000

Assessing the accuracy of prediction algorithms for classification: an overview.

We provide a unified overview of methods that currently are widely used to assess the accuracy of prediction algorithms, from raw percentages, quadratic error measures and other distances, and correlation coefficients, and to information theoretic measures such as relative entropy and mutual information. We briefly discuss the advantages and disadvantages of each approach. For classification tasks, we derive new learning algorithms for the design of prediction systems by directly optimising the correlation coefficient. We observe and prove several results relating sensitivity and specificity of optimal systems. While the principles are general, we illustrate the applicability on specific problems such as protein secondary structure and signal peptide prediction.

Algorithms↗
PubMed2000

Matching protein beta-sheet partners by feedforward and recurrent neural networks.

Predicting the secondary structure (alpha-helices, beta-sheets, coils) of proteins is an important step towards understanding their three dimensional conformations. Unlike alpha-helices that are built up from one contiguous region of the polypeptide chain, beta-sheets are more complex resulting from a combination of two or more disjoint regions. The exact nature of these long distance interactions remains unclear. Here we introduce two neural-network based methods for the prediction of amino acid partners in parallel as well as anti-parallel beta-sheets. The neural architectures predict whether two residues located at the center of two distant windows are paired or not in a beta-sheet structure. Variations on these architecture, including also profiles and ensembles, are trained and tested via five-fold cross validation using a large corpus of curated data. Prediction on both coupled and non-coupled residues currently approaches 84% accuracy, better than any previously reported method.

Animals↗
PubMed1999

The natural history of early recurrent carotid artery stenosis.

BACKGROUND: Early recurrent carotid stenosis, defined as greater than 50% stenosis within 2 years of a carotid endarterectomy (CEA), occurs in 4% to 19% of patients. These lesions are secondary to myointimal hyperplasia (MH). The natural history of these lesions has been examined prospectively, but the appropriate management of these lesions has not been clearly defined. The vascular surgery service at Madigan Army Medical Center (MAMC) has prospectively collected a cohort of patients with recurrent high-grade carotid stenoses following CEA to determine their natural history and define the ideal therapeutic approach for those lesions. METHODS: Patients undergoing CEA between January 1, 1993, and January 1, 1997, at a single tertiary care institution were followed prospectively with postoperative carotid duplexes at 3-month intervals for the first year and then every 6 months for a year and then annually thereafter. Data were collected regarding patient demographics, type of carotid closure, neurologic morbidity, and death. These results were compared with accepted rates in the literature. Discrete variables were tested for significance by chi-square analysis and Fisher's exact test. A P value less than or equal to 0.05 was considered significant. RESULTS: One hundred and seventy-four (174) patients with 181 operative sites were evaluated. Fourteen patients with 17 sites (9%) had recurrent stenosis. Twelve patients with 14 sites (7%) had stenoses of 50% to 79%. All were asymptomatic. Two patients with 3 sites (2%) had stenoses greater than 80%. Two sites were managed operatively because of neurologic symptoms or preocclusive nature and one remains asymptomatic and stable on serial duplex imaging. All lesions were present at 6 months and those in the 50% to 79% category did not progress in follow-up. Recurrent carotid stenosis occurred to a significantly higher degree in women (women 11 of 60 18.3% versus men 6 of 114 5.3%; P = 0.25), primary closure versus patch angioplasty (primary 6 of 22 27.3% versus patch 11 of 159 6.9%; P = 0.01), and dacron versus polytetrafluoroethylene (PTFE) patch angioplasty (dacron 7 of 36 19.4% versus PTFE 2 of 100 2.0%; P = 0.02). CONCLUSION: Early recurrent stenosis (50% to 79%) is a benign lesion. Patch angioplasty is preferred over primary closure. Dacron patches had a significantly higher rate of recurrent stenosis when compared with PTFE patches. Women undergoing CEA are more prone to recurrent stenosis. Postoperative duplex at 3 and 6 months will identify recurrent carotid stenosis (given a normal duplex prior to discharge following CEA). Moderate high-grade (50% to 79%) stenoses are benign. High-grade (80% to 99%) stenoses require individual management.

Angioplasty↗
PubMed1999

Using sequence motifs for enhanced neural network prediction of protein distance constraints.

Correlations between sequence separation (in residues) and distance (in Angstrom) of any pair of amino acids in polypeptide chains are investigated. For each sequence separation we define a distance threshold. For pairs of amino acids where the distance between C alpha atoms is smaller than the threshold, a characteristic sequence (logo) motif, is found. The motifs change as the sequence separation increases: for small separations they consist of one peak located in between the two residues, then additional peaks at these residues appear, and finally the center peak smears out for very large separations. We also find correlations between the residues in the center of the motif. This and other statistical analysis are used to design neural networks with enhanced performance compared to earlier work. Importantly, the statistical analysis explains why neural networks perform better than simple statistical data-driven approaches such as pair probability density functions. The statistical results also explain characteristics of the network performance for increasing sequence separation. The improvement of the new network design is significant in the sequence separation range 10-30 residues. Finally, we find that the performance curve for increasing sequence separation is directly correlated to the corresponding information content. A WWW server, distanceP, is available at http://www.cbs.dtu.dk/services/distanceP/.

Algorithms↗
PubMed1995

Duplex-guided compression of iatrogenic femoral pseudoaneurysms.

BACKGROUND: Iatrogenic pseudoaneurysms are a major complication following percutaneous cannulations of the femoral artery. Surgical repair has been the traditional treatment modality. Recent reports have introduced duplex-guided compression as a means of nonoperative management of these injuries. We proposed to determine if duplex-guided compression of femoral pseudoaneurysms could be successfully performed, could be done without complication, and could maintain thrombosis on long-term follow-up. STUDY DESIGN: All patients presenting with large groin hematomas following invasive percutaneous femoral artery procedures over a seven-month period were studied using color-flow duplex analysis. Six pseudoaneurysms were discovered and successfully treated with duplex-guided compression. All patients were then followed-up prospectively with both early and long-term repeat duplex analysis. RESULTS: All patients were rescanned 72 hours later and the pseudoaneurysms remained thrombosed. Upon returning for long-term follow-up examination, patients again had duplex confirmation of thrombosis, with a mean follow-up time of 21 months (range, five to 29 months). No complications attributable to this technique have been noted. CONCLUSIONS: This study confirms the clinical usefulness of duplex-guided compression in the evaluation and treatment of iatrogenic femoral pseudoaneurysms.

Adult↗
PubMed1991

Concomitant abdominal aortic aneurysm and colorectal cancer: a decision analysis approach to a therapeutic dilemma.

The therapeutic approach to a patient with concomitant abdominal aortic aneurysm and colorectal carcinoma is not clear. Decision analysis helps clarify decision options and quantify therapeutic outcomes. Variables used in decision analysis include life expectancy after resection for colorectal cancer and abdominal aortic aneurysm, rupture rate of abdominal aortic aneurysm, complications of colorectal The results support the concept that the symptomatic lesion should be treated first. When both lesions are asymptomatic and the aneurysm is 4-5 cm in diameter, it should be resected first, if the colorectal cancer has a less than 5% chance of obstruction or perforation, as is found in noncircumferential lesions. When the aneurysm is greater than 5 cm, it should be resected first if the cancer has a less than 22% chance of obstructing or perforating, as with circumferential lesions. Simultaneous resection should be considered for patients with aneurysms greater than 5 cm and cancers with a greater than 75-80% chance of obstruction or perforation, provided the dual procedures can be performed with a less than 10% operative mortality and less than 50% complication rate.

Aorta, Abdominal↗
PubMed1991

Use of light reflection rheography for diagnosis of axillary or subclavian venous thrombosis.

Noninvasive diagnosis of axillary and subclavian venous thrombosis or documentation of the post-thrombotic syndrome using modalities currently in use is not definitive. Light reflection rheography, which is a reflection of venous pressure changes in the extremity as recorded from the subdermal capillary plexus, was used to correctly diagnose axillary or subclavian venous thrombosis in 11 patients. A positive study was confirmed by phlebography in each instance. There were no instances of false-positive results. The methodology is simple, involving testing of the venous outflow from the upper extremity in response to exercise, application of venous congesting pressure, and measurement of the rate of venous outflow when the congesting pressure is released. Normal respiratory variations of an open venous system are also assessed by this noninvasive modality. The tracing obtained is easy to interpret and provides objective evidence of proximal venous occlusion. The test is not operator-dependent and the instrumentation is relatively inexpensive. We believe that light reflection rheography may be an exciting development in the noninvasive diagnosis of axillary or subclavian venous compromise and merits further trials.

Arm↗
PubMed1984

Asymptomatic carotid arterial disease in patients presenting with angiographically proven coronary artery disease.

Atherosclerosis is a systemic and progressive disease process. However, the patterns of disease and the sequence of arterial involvement need further definition. A select group of patients initially presenting with coronary arterial disease was evaluated for evidence of hemodynamically significant carotid arterial disease. Eight per cent of patients were found to have hemodynamically significant carotid arterial disease by the oculopneumoplethysmography (Gee OPG). This low incidence of carotid arterial disease is in contrast to patients who present with carotid arterial disease who are found to have a high incidence of coronary artery disease. This would suggest that either the coronary artery disease develops first or that there is a specific pattern of atherosclerotic vascular disease where patients have coronary artery disease without hemodynamically significant carotid disease. Long-term follow-up on patients initially presenting with coronary arterial disease will help further define this question.

Adult↗
PubMed1983

Spontaneous pneumothorax. Special considerations.

A review of patients with spontaneous pneumothorax treated at Tripler Army Medical Center (TAMC) between 1977 and 1979 was undertaken to identify areas of strength 1977 and 1979 was undertaken to identify areas of strength and areas of weakness. Fifty patients with a total of 58 pneumothoraces were identified, and their charts were reviewed. Fifty-one pneumothoraces were classified as primary or idiopathic, and seven were secondary to parenchymal disease. Problem areas that were identified included failure to consider catamenial pneumothorax in the differential diagnosis of spontaneous pneumothorax and failure to recognize reexpansion pulmonary edema as a complication of treatment.

Adolescent↗
PubMed1982

Abdominal trauma: the limited role of peritoneal lavage.

Abdominal trauma was reviewed in 103 cases: 88 (85%) resulted from blunt trauma and 15 (15%) from penetrating trauma. Of the 88 cases of blunt abdominal trauma, 22 were felt to have significant intra-abdominal injuries on clinical evaluation alone. On exploration, 20 (91%) had significant injuries, one had a trivial injury, and one had negative exploration. Peritoneal lavage was performed on 66 of the 88 cases of blunt trauma. The results were positive in 36 cases. On exploration, 23 had significant injuries, nine had trivial injuries, and four had negative laparotomies. Twenty-eight lavages were negative; 26 were managed successfully without exploratory laparotomy, but two had significant injuries. Two patients had insignificant return from peritoneal lavage; both had positive laparotomies. Fourteen of 15 patients with penetrating abdominal trauma were managed by exploratory laparotomy and one was observed after negative lavage. Five of six patients explored for gunshot wounds had significant injuries. Of the eight patients explored for stab wounds, only two had significant injuries.

Abdominal Injuries↗
PubMed1981

Prediction of small bowel viability using Doppler ultrasound. Clinical and experimental evaluation.

The operative determination of small bowel viability following strangulation obstruction or mesenteric vascular occlusion remains a problem. In the canine model, Doppler ultrasound was used to predict intestinal viability in segments of small bowel subjected to mesenteric venous occlusion. This was compared with small bowel electromyography and the short- and long-term clinical courses. If flow was consistently heard on the antimesenteric border, the bowel remained viable, had return of slow waves on electromyography, and did not develop strictures during a six-month follow-up period. Four clinical cases are presented where Doppler ultrasound was utilized to supplement the usual methods of determining small bowel viability. Doppler ultrasound is a rapid, noninvasive method of determining small bowel viability.

Animals↗
PubMed1980

Carotid endarterectomy: regional versus general anesthesia.

The records of 421 patients who underwent carotid endarterectomy were reviewed. Between 1967 and 1972 carotid endarterectomy was performed with regional anesthesia in 232 patients. Ten per cent of these patients required the use of general anesthesia and a temporary indwelling shunt, because of the development of neurologic symptoms after temporary cross-clamping (5.6%) or the inability to tolerate regional anesthesia (4.3%). The 30-day mortality was 2.6 per cent. The incidence of fixed neurologic deficits was 2.2 per cent, and the incidence of transient neurologic deficits was 3 per cent. Between 1974 and 1976, 189 carotid endarterectomies were performed with general anesthesia and the routine use of a temporary indwelling shunt. The 30-day mortality was 0.5 per cent. The incidence of fixed neurologic deficits was 2.6 per cent; the incidence of transient neurologic deficits was 2.6 per cent. The use of general anesthesia with a shunt has not significantly changed the mortality or incidence of postoperative neurologic complications when compared with the authors' series performed with regional anesthesia. All patients in whom postoperative strokes occurred had multiple stenotic or occlusive lesions. Special precautions should be taken in this high-risk group.

Anesthesia, Conduction↗