PubMed Health⌕ Search

Biomedical subjects

R Shamir

Publications and source records attributed to R Shamir.

At least 19 recordsLinked to original sources
PubMed2000

An algorithm for clustering cDNA fingerprints.

Clustering large data sets is a central challenge in gene expression analysis. The hybridization of synthetic oligonucleotides to arrayed cDNAs yields a fingerprint for each cDNA clone. Cluster analysis of these fingerprints can identify clones corresponding to the same gene. We have developed a novel algorithm for cluster analysis that is based on graph theoretic techniques. Unlike other methods, it does not assume that the clusters are hierarchically structured and does not require prior knowledge on the number of clusters. In tests with simulated libraries the algorithm outperformed the Greedy method and demonstrated high speed and robustness to high error rate. Good solution quality was also obtained in a blind test on real cDNA fingerprints.

Algorithms↗
PubMed2000

Dietary therapy for children with hypercholesterolemia.

Accumulating evidence clearly shows that atherosclerosis begins in youth. The National Cholesterol Education Program (NCEP) has recommended that children at high risk of developing coronary artery disease as adults be screened so that those with elevated low-density lipoprotein (LDL) cholesterol levels can be treated, primarily by modification of diet. The initial approach to these youthful patients is to use the NCEP step I diet. This diet provides calories and nutrients that support normal growth and development, but limits saturated fat and total fat intake to no more than 10 and 30 percent of total calories, respectively, and cholesterol intake to no more than 100 mg per 1,000 kcal per day, to a maximum of 300 mg. If the goal of reducing the LDL cholesterol level to below 130 mg per dL (3.35 mmol per L) is not achieved, the more restrictive step II diet should be initiated. However, the step II diet may not provide sufficient calories and nutrients to support normal growth and development; therefore, trained nutritionists may be required to effectively manage a child on this diet.

Adolescent↗
PubMed2000

Faecal occult blood in children with coeliac disease.

UNLABELLED: It has recently been suggested that in adults with coeliac disease, faecal blood loss may play a role in the development of iron deficiency. A group of 45 children diagnosed with coeliac disease during 1996 and 1997 were therefore prospectively evaluated for the presence of gluten in their diet, iron deficiency anaemia, and faecal occult blood. Sixty children admitted for elective surgery or asthma served as controls. Faecal occult blood was found in four iron deficient children on normal diet, of whom three were newly diagnosed. Occult blood loss disappeared in three of the four children when gluten was removed from their diet. Faecal occult blood was found in 26.7% of children on gluten-containing diet, but not in children on gluten-free diet (P = 0.01), or in control children (P = 0.001). CONCLUSION: Our data suggest that the incidence of occult blood loss in coeliac disease occurs mainly in newly diagnosed cases and responds to a gluten-free diet. Occult blood testing may not be warranted in the absence of iron deficiency anaemia nor in children with iron deficiency anaemia who are on a gluten-free diet.

Adolescent↗
PubMed2000

Serum transferrin receptor in children and adolescents with inflammatory bowel disease.

UNLABELLED: Iron studies are difficult to interpret in patients with chronic inflammatory states such as inflammatory bowel disease (IBD). Serum transferrin receptor (TfR) has been reported to be a reliable tool for the diagnosis of iron deficiency in adults. Our aim was to evaluate the role of serum TfR in diagnosing iron deficiency in children and adolescents with IBD. A total of 63 consecutive patients with IBD, aged 9 to 22 years (median 15 years), were tested for serum haemoglobin level, mean corpuscular volume (MCV), and serum iron, transferrin, ferritin and serum TfR levels. Those found to be anaemic were compared with seven age-matched subjects with iron deficiency anaemia (IDA) and 24 age-matched children without signs of anaemia or inflammation. Of the 63 patients with IBD, 26 had anaemia. Based on ferritin levels and MCV indices, anaemia was classified as IDA in 11 patients and as anaemia of chronic disease (ACD) in 15 patients. Mean serum TfR level in normal controls was 3.5 mg/l (range 1.2-8.2 mg/l). Mean (+/-SD) serum TfR levels were significantly lower in the IBD patients with ACD (5.3 +/- 2.3 mg/l) than in the IBD patients with IDA (8.2 +/- 3.1 mg/l) (P < 0.05). Serum TfR levels above 5 mg/l identified 10/11 IBD patients with IDA. The calculated TfR/ferritin ratio was 84 (range 17-367) for controls and 133 (range 6.4-1840) for IBD patients. A cut-off level of 350 (91% sensitivity, 100% specificity, 100% positive predictive value, 98% negative predictive value) was established for the diagnosis of IDA in IBD. CONCLUSION: The results suggest that serum transferrin receptor is a useful parameter for the diagnosis of iron deficiency in inflammatory bowel disease, in particular, the transferrin receptor/ferritin ratio with a cut-off level > or = 350.

Adolescent↗
PubMed2000

An algorithm combining discrete and continuous methods for optical mapping.

Optical mapping is a novel technique for generating the restriction map of a DNA molecule by observing many single, partially digested copies of it, using fluorescence microscopy. The real-life problem is complicated by numerous factors: false positive and false negative cut observations, inaccurate location measurements, unknown orientations, and faulty molecules. We present an algorithm for solving the real-life problem. The algorithm combines continuous optimization and combinatorial algorithms applied to a nonuniform discretization of the data. We present encouraging results on real experimental data and on simulated data.

Algorithms↗
PubMed2000

A fast algorithm for joint reconstruction of ancestral amino acid sequences.

A dynamic programming algorithm is developed for maximum-likelihood reconstruction of the set of all ancestral amino acid sequences in a phylogenetic tree. To date, exhaustive algorithms that find the most likely set of ancestral states (joint reconstruction) have running times that scale exponentially with the number of sequences and are thus limited to very few taxa. The time requirement of our new algorithm scales linearly with the number of sequences and is therefore applicable to practically any number of taxa. A detailed description of the new algorithm and an example of its application to cytochrome b sequences are provided.

Algorithms↗
PubMed2000

Liver enzyme abnormalities in gram-negative bacteremia of premature infants.

BACKGROUND: Hyperbilirubinemia and liver enzyme abnormalities are commonly observed in sepsis. However, the frequency in premature neonates and the specific relation to gram-negative bacteria are not known. PATIENTS AND METHODS: Charts of all preterm infants who had positive blood cultures for either gram-negative bacteria or coagulase-negative staphylococci were reviewed. Neonates with gram-negative bacteremia (n = 54) were compared with neonates with coagulase-negative staphylococcal bacteremia (n = 31). In addition infants with gram-negative bacteremia and elevated liver enzymes (n = 25) were compared with infants with gram-negative bacteremia and normal liver enzymes (n = 29). RESULTS: Liver enzyme abnormalities accompanied 46.3% (25 of 54) of gram-negative bacteremia and 12.9% (4 of 31) of episodes of coagulase-negative staphylococcal bacteremia (P = 0.002). Serum concentrations of liver enzymes were significantly higher in infants with gram-negative bacteremia than in those with coagulase-negative staphylococcal bacteremia (P < 0.0001), but no difference in alkaline phosphatase serum values was observed. Infants with gram-negative bacteremia and elevated liver enzymes were not fed for a longer period than infants with gram-negative bacteremia and normal liver enzymes (7.3 +/- 6.3 days vs. 4.0 +/- 4.3 days, P = 0.03), and this was accompanied by significant conjugated hyperbilirubinemia (P < 0.0001). Ventilation, total parenteral nutrition and medications were not responsible for the observed differences. Klebsiella pneumoniae bacteremia was commonly associated with elevated liver enzymes (12 of 18), whereas none of the infants with Pseudomonas aeruginosa bacteremia had elevated liver enzymes. CONCLUSIONS: Gram-negative bacteremia is commonly associated with cholestasis in premature neonates. Liver enzyme abnormalities are more common than elevated conjugated bilirubin, not all gram-negative bacteria have the same effect and the lack of enteral feeding seems to play a more significant role than the administration of parenteral nutrition.

Bacteremia↗
PubMed2000

The effect of cisapride on total parenteral nutrition-associated cholestasis in rats.

BACKGROUND: Cholestasis is a frequent problem in patients on total parenteral nutrition. Cisapride has a prokinetic effect on the biliary system, but its effect on hepatic excretory function is unknown. OBJECTIVES: To study the effect of cisapride on TPN-induced cholestasis in a rat model. METHODS: Bile flow and bile salt secretion rate were measured in rats given TPN. There were four groups of 8 to 13 animals each. After a one hour baseline period during which all four groups received i.v. saline infusion, two groups received a TPN solution for another 2 hours, while saline was infused in the two control groups. At the beginning of the second hour, 2 mg/kg cisapride was injected i.v. as a bolus into one experimental and one control group. Bile was collected from the common bile duct. RESULTS: At the end of the third hour, TPN caused a significant reduction in bile flow (P < 0.02) and bile salt secretion rate (P < 0.001) (61.24 vs. 50.74 microliters/min/kg, and 1.173 vs. 0.799 mumol/min/kg, respectively). Addition of cisapride abolished the cholestatic effect of TPN. CONCLUSIONS: Cisapride has a protective effect against TPN-associated cholestasis. This may have clinical significance, and further studies are warranted.

Animals↗
PubMed2000

Spectrum alignment: efficient resequencing by hybridization.

Recent high-density microarray technologies allow, in principle, the determination of all k-mers that appear along a DNA sequence, for k = 8 - 10 in a single experiment on a standard chip. The k-mer contents, also called the spectrum of the sequence, is not sufficient to uniquely reconstruct a sequence longer than a few hundred bases. We have devised a polynomial algorithm that reconstructs the sequence, given the spectrum and a homologous sequence. This situation occurs, for example, in the identification of single nucleotide polymorphisms (SNPs), and whenever a homologue of the target sequence is known. The algorithm is robust, can handle errors in the spectrum and assumes no knowledge of the k-mer multiplicities. Our simulations show that with realistic levels of SNPs, the algorithm correctly reconstructs a target sequence of length up to 2,000 nucleotides when a polymorphic sequence is known. The technique is generalized to handle profiles and HMMs as input instead of a single homologous sequence.

Algorithms↗
PubMed2000

CLICK: a clustering algorithm with applications to gene expression analysis.

Novel DNA microarray technologies enable the monitoring of expression levels of thousands of genes simultaneously. This allows a global view on the transcription levels of many (or all) genes when the cell undergoes specific conditions or processes. Analyzing gene expression data requires the clustering of genes into groups with similar expression patterns. We have developed a novel clustering algorithm, called CLICK, which is applicable to gene expression analysis as well as to other biological applications. No prior assumptions are made on the structure or the number of the clusters. The algorithm utilizes graph-theoretic and statistical techniques to identify tight groups of highly similar elements (kernels), which are likely to belong to the same true cluster. Several heuristic procedures are then used to expand the kernels into the full clustering. CLICK has been implemented and tested on a variety of biological datasets, ranging from gene expression, cDNA oligo-fingerprinting to protein sequence similarity. In all those applications it outperformed extant algorithms according to several common figures of merit. CLICK is also very fast, allowing clustering of thousands of elements in minutes, and over 100,000 elements in a couple of hours on a regular workstation.

Algorithms↗
PubMed1999

Carboxyl ester lipase overexpression in rat hepatoma cells and CEL deficiency in mice have no impact on hepatic uptake or metabolism of chylomicron-retinyl ester.

To study the role of carboxyl ester lipase (CEL) in hepatic retinoid (vitamin A) metabolism, we investigated uptake and hydrolysis of chylomicron (CM)-retinyl esters (RE) by rat hepatoma (McArdle-RH7777) cells stably transfected with a rat CEL cDNA. We also studied tissue uptake of CM-RE in CEL-deficient mice generated by targeted disruption of the CEL gene. CEL-transfected cells secreted active enzyme into the medium. However, both control and CEL-transfected cells accumulated exogenously added CM-RE or CM remnant (CMR)-derived RE in equal amounts. Serum clearance of intravenously injected CM-RE and cholesteryl ester were not different between wild-type and CEL-deficient mice. Also, the uptake of the two compounds by the liver and other tissues did not differ. These data indicate that the lack of CEL expression does not affect the uptake of dietary CM-RE by the liver or other tissues. Moreover, the percentage of retinol formed in the liver after CM-RE uptake, the levels of retinol and retinol-binding protein in serum, and retinoid levels in various tissues did not differ, indicating that CEL deficiency does not affect hepatic retinoid metabolism and retinoid distribution throughout the body. Surprisingly, in both pancreas and liver of wild-type, heterozygous, and homozygous CEL-deficient mice, the levels of bile salt-dependent retinyl ester hydrolase (REH) activity were similar. This indicates that in the mouse pancreas and liver an REH enzyme activity, active in the presence of bile salt and distinct from CEL, is present, compatible with the results from our accompanying paper that the intestinal processing and absorption of RE were unimpaired in CEL-deficient mice.

Animals↗
PubMed1999

Parenteral selenium supplementation in extremely low birth weight infants: inadequate dosage but no correlation with hypothyroidism.

OBJECTIVE: Selenium is an essential trace element, known to be important in thyroid metabolism. We speculated that parenteral selenium supplementation is inadequate in preterm infants and may contribute to the development of hypothyroidism. STUDY DESIGN: Serum selenium and thyroid function were evaluated on day 10 of life in extremely low birth weight infants. Selenium intake provided by parenteral nutrition was prospectively evaluated. RESULTS: Selenium intake was close to the recommended 2 micrograms/kg per day. Serum selenium values were 0.54 +/- 0.13 microM (mean +/- SD, n = 29). Selenium serum levels were low in 26 of 29 infants. In infants with subnormal serum selenium levels, free T4 was transiently low in 10 of 26 infants but was normal in 16 of 26 infants. No significant correlation was found between serum selenium levels and hypothyroidism. CONCLUSION: Current selenium supplementation guidelines may be inadequate in extremely low birth weight infants. However, selenium deficiency does not seem to play a major role in neonatal hypothyroidism.

Birth Weight↗
PubMed1999

Construction of physical maps from oligonucleotide fingerprints data.

A new algorithm for the construction of physical maps from hybridization fingerprints of short oligonucleotide probes has been developed. Extensive simulations in high-noise scenarios show that the algorithm produces an essentially completely correct map in over 95% of trials. Tests for the influence of specific experimental parameters demonstrate that the algorithm is robust to both false positive and false negative experimental errors. The algorithm was also tested in simulations using real DNA sequences of C. elegans, E. coli, S. cerevisiae, and H. sapiens. To overcome the non-randomness of probe frequencies in these sequences, probes were preselected based on sequence statistics and a screening process of the hybridization data was developed. With these modifications, the algorithm produced very encouraging results.

Algorithms↗
PubMed1999

An algorithm combining discrete and continuous methods for optical mapping.

Optical mapping is a novel technique for generating the restriction map of a DNA molecule by observing many single, partially digested, copies of it, using fluorescence microscopy. The real-life problem is complicated by numerous factors: false positive and false negative cut observations, inaccurate location measurements, unknown orientations and faulty molecules. We present an algorithm for solving the real-life problem. The algorithm combines continuous optimization and combinatorial algorithms, applied to a non-uniform discretization of the data. We present encouraging results on real experimental data.

Algorithms↗
PubMed1998

QT interval in children and infants receiving cisapride.

OBJECTIVES: Life-threatening arrhythmias and prolonged QT interval have been reported in adults and children using cisapride, a medication structurally similar to procainamide. Premature infants have reduced activity of cytochrome p-450, the system responsible for metabolism of cisapride, which could lead to QT prolongation. Therefore, we prospectively studied premature infants and children receiving cisapride to analyze the effect of prolonged cisapride therapy on QT interval. DESIGN: Premature infants in a neonatal intensive care unit and children seen at a pediatric gastroenterology clinic in a tertiary care hospital had electrocardiography-analyzed and -corrected QT interval measured before cisapride (0.8/mg/kg per day) therapy, and again after 1 month of therapy. If baseline electrocardiography was not performed initially, it was obtained after cessation of therapy. RESULTS: A total of 30 children participated in the study. Mean corrected QT interval was similar at baseline and at 1 month after therapy. Significant QT prolongation was not found, and no adverse effects were recorded. CONCLUSIONS: Corrected QT interval during prolonged cisapride therapy at 0.8 mg/kg per day appears to be similar for premature infants and children. An inherent trend toward QT prolongation was not detected in either group. In the absence of other risk factors that alter cisapride metabolism or predispose to arrhythmia, cisapride may be safe for use in premature infants as well as in children. Additional studies are needed to confirm these data.

Arrhythmias, Cardiac↗
PubMed1998

Management of acute gastroenteritis in children in Israel.

OBJECTIVE: Diarrheal diseases are a major cause of morbidity and mortality worldwide. Guidelines about the use of oral rehydration solutions (ORS) and dietary management of acute gastroenteritis (GE) were recently revised and published by the American Academy of Pediatrics (AAP). Study aims were to examine Israeli pediatricians' knowledge and implementation of the revised AAP guidelines, the effect of medical school (Israeli versus foreign medical graduates) on the physicians' practice, and the effect of the type of practice (community vs hospital-based) on the management of gastroenteritis. METHODS: A multiple-choice, written questionnaire was distributed at two pediatrics annual meetings. RESULTS: A total of 87 pediatricians completed the questionnaire. They were aware of 73% of the current AAP guidelines and followed 60% of the guidelines. Most pediatricians (83%) use ORS for treatment of dehydration in GE, but 60% of pediatricians believe that full-strength feeds are inappropriate in the presence of GE, and 67% of them do not recommend full-strength formulas. In addition, 37% of the pediatricians stop feeding temporarily in the presence of GE, in contrast to the 1996 AAP guidelines. There were no differences in knowledge and management practices among pediatricians graduating in Israel, Europe, or the United States, and no differences between pediatricians working in an ambulatory setting or in a hospital. CONCLUSIONS: Pediatricians in Israel, regardless of country of origin, medical school, or place of practice, are aware of the correct use of ORS but do not follow nutritional practices recommended recently by the AAP. These findings suggest that steps for implementing the guidelines are needed in Israel and most probably worldwide.

Acute Disease↗
PubMed1998

Intravenous amino acids, cholestasis and kwashiorkor.

Kwashiorkor dermatosis has not been reported in children on parenteral nutrition (PN). We report a case of kwashiorkor developing in a partially PN dependent patient with cholestasis, when amino acids were removed from the PN solution in an effort to control the cholestasis. Although the kwashiorkor dermatosis improved within 24 hours after the addition of amino acids (1 g/kg) to the PN solution, the cholestasis worsened.

Amino Acids↗