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Biomedical subjects

D Shasha

Publications and source records attributed to D Shasha.

7 recordsLinked to original sources
PubMed1999

Brachytherapy in the treatment of colorectal malignancies.

By precisely delivering a single, high dose fraction of intraoperative radiation under direct visualization while excluding surrounding normal dose-limiting tissues, IORT has improved the therapeutic ratio of tumor control to morbidity. Both IOERT and HDR-IORT represent effective means of delivering this therapy, and either may be chosen with equal confidence, depending upon the facilities available, physician preference, and the clinical situation. The extraordinary efforts often required in the management of these highly selected patients is justified by the improvement achieved in the enhanced local control rates and increased cure rates. Preoperative chemoradiation therapy followed by gross total resection and IORT affords the patient the highest likelihood of local control and survival. The importance of aggressive surgery in achieving gross total resection with pathologically negative margins is reflected by the dramatic correlation reported between margin status and local control. The high complication rate associated with this multidisciplinary therapy is, no doubt, multifactorial and may be attributed to the advanced disease state at presentation and the intensive multidisciplinary treatments administered. In an effort to eradicate disease and prolong survival, many consider these elevated complication rates acceptable, particularly in light of the complexity of these cases, as well as the morbidity and mortality associated with persistent disease in the pelvis.

Brachytherapy↗
PubMed1999

New techniques for DNA sequence classification.

DNA sequence classification is the activity of determining whether or not an unlabeled sequence S belongs to an existing class C. This paper proposes two new techniques for DNA sequence classification. The first technique works by comparing the unlabeled sequence S with a group of active motifs discovered from the elements of C and by distinction with elements outside of C. The second technique generates and matches gapped fingerprints of S with elements of C. Experimental results obtained by running these algorithms on long and well conserved Alu sequences demonstrate the good performance of the presented methods compared with FASTA. When applied to less conserved and relatively short functional sites such as splice-junctions, a variation of the second technique combining fingerprinting with consensus sequence analysis gives better results than the current classifiers employing text compression and machine learning algorithms.

Algorithms↗
PubMed1998

Elective irradiation of the N0 neck in squamous cell carcinoma of the upper aerodigestive tract.

The decision of how to optimally manage the clinically negative neck is based on the likelihood of clinically inapparent disease and the efficacy of salvage therapy. The criteria of decision for elective management of the neck takes into account the site, size, depth of infiltration, grading of the primary lesion, clinical and radiologic evaluation, and patient wishes. Diagnostic procedures currently used in evaluating head and neck cancer patients with nodal disease are reviewed. Elective irradiation of the N0 neck in patients with squamous cell carcinoma of the head and neck is an effective means of maintaining locoregional control. The impact of elective nodal treatment on disease free survival and overall survival is discussed.

Carcinoma, Squamous Cell↗
PubMed1998

The role of brachytherapy in head and neck cancer.

By precision dose delivery to a well-defined target, brachytherapy fulfills the complementary goals of delivering sufficient dose for tumor cell kill while sparing normal adjacent structures. The unique properties of this modality, either used alone or implemented in a combined modality setting with surgery or external-beam irradiation, offer an ideal means of enhancing the therapeutic ratio by exploiting the effect of local therapies while respecting normal tissue tolerance. Brachytherapy also provides an effective technique for the retreatment of patients with recurrent, persistent, or second primary head and neck malignant tumors in a previously irradiated region. The benefits of this treatment modality are reflected in excellent reported local control rates, shortened overall treatment times, reduced functional deficits, improved quality of life, and decreased costs. Successful brachytherapy relies, however, on close collaborative efforts between radiation oncologists and surgeons, careful assessment of the patient, precise planning, and technique that adheres to the rules of a system. Brachytherapy has been clearly identified as an effective, safe, and appealing modality in the treatment of head and neck malignancies.

Brachytherapy↗
PubMed1996

Complementary classification approaches for protein sequences.

We have studied five methods of protein classification and have applied them to the 768 groups of related proteins in the PROSITE catalog. Four of these methods are based on searching a database of blocks, and the other uses the frequently occurring motifs found in the protein families combined with a fingerprint technique. Our experimental results show that the block-based methods perform well when taking into account the probability of amino acids occurring in a block. Furthermore, the five methods give information that is complementary to each other. Thus, using the five methods together, one can obtain high confidence classifications (if the results agree) or suggest alternative hypotheses (if the results disagree). We also list those proteins whose current families documented in the PROSITE catalog differ from those suggested by our results. There are remarkably few of them, which is a testimony to the quality of PROSITE.

Amino Acid Sequence↗
PubMed1994

Discovering active motifs in sets of related protein sequences and using them for classification.

We describe a method for discovering active motifs in a set of related protein sequences. The method is an automatic two step process: (1) find candidate motifs in a small sample of the sequences; (2) test whether these motifs are approximately present in all the sequences. To reduce the running time, we develop two optimization heuristics based on statistical estimation and pattern matching techniques. Experimental results obtained by running these algorithms on generated data and functionally related proteins demonstrate the good performance of the presented method compared with visual method of O'Farrell and Leopold. By combining the discovered motifs with an existing fingerprint technique, we develop a protein classifier. When we apply the classifier to the 698 groups of related proteins in the PROSITE catalog, it gives information that is complementary to the BLOCKS protein classifier of Henikoff and Henikoff. Thus, using our classifier in conjunction with theirs, one can obtain high confidence classifications (if BLOCKS and our classifier agree) or suggest a new hypothesis (if the two disagree).

Algorithms↗