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Biomedical subjects

R Shamir

Publications and source records attributed to R Shamir.

At least 19 recordsLinked to original sources
PubMed2007

Wireless video capsule in pediatric patients with functional abdominal pain.

OBJECTIVES: Upper endoscopy (esophagogastroduodenoscopy [EGD]) has a limited role, if any, in the evaluation of functional abdominal pain (FAP). Nevertheless, children with intractable FAP are occasionally referred to EGD to rule out intestinal pathology. We evaluated the role of wireless video capsule endoscopy (VCE) in children referred for EGD with a diagnosis of FAP. PATIENTS AND METHODS: Ten children older than 10 years of age were prospectively enrolled. Children were first studied with the PillCam SB (VCE; Given Imaging, Yokneam, Israel) followed by standard EGD within 2 weeks. After the completion of the study, a questionnaire of tolerance and content regarding the 2 procedures was completed by the patients. RESULTS: Physical examinations and laboratory tests were within normal limits in all of the patients. Patients swallowed the endoscopic capsules without difficulty. There were no complications. VCE identified gastritis in 4 patients (confirmed by biopsies), whereas EGD detected erosive gastritis in only 1 of the 4 children. EGD detected no duodenal abnormalities. VCE detected Crohn disease in the small intestine and cecum in 1 patient. VCE was ranked by 8 patients as convenient and as a preferable procedure compared with EGD. CONCLUSION: The results of this small cohort suggest that in children with FAP, VCE is more sensitive than EGD for detection of macroscopic gastric and small bowel pathologies.

Abdominal Pain↗
PubMed2006

ATM haplotypes and breast cancer risk in Jewish high-risk women.

While genetic factors clearly play a role in conferring breast cancer risk, the contribution of ATM gene mutations to breast cancer is still unsettled. To shed light on this issue, ATM haplotypes were constructed using eight SNPs spanning the ATM gene region (142 kb) in ethnically diverse non-Ashkenazi Jewish controls (n=118) and high-risk (n=142) women. Of the 28 haplotypes noted, four were encountered in frequencies of 5% or more and accounted for 85% of all haplotypes. Subsequently, ATM haplotyping of high-risk, non-Ashkenazi Jews was performed on 66 women with breast cancer and 76 asymptomatic. One SNP (rs228589) was significantly more prevalent among breast cancer cases compared with controls (P=4 x 10(-9)), and one discriminative ATM haplotype was significantly more prevalent among breast cancer cases (33.3%) compared with controls (3.8%), (P< or =10(-10)). There was no significant difference in the SNP and haplotype distribution between asymptomatic high-risk and symptomatic women as a function of disease status. We conclude that a specific ATM SNP and a specific haplotype are associated with increased breast cancer risk in high-risk non-Ashkenazi Jews.

Adult↗
PubMed2006

Parallel induction of ATM-dependent pro- and antiapoptotic signals in response to ionizing radiation in murine lymphoid tissue.

The ATM protein kinase, functionally missing in patients with the human genetic disorder ataxia-telangiectasia, is a master regulator of the cellular network induced by DNA double-strand breaks. The ATM gene is also frequently mutated in sporadic cancers of lymphoid origin. Here, we applied a functional genomics approach that combined gene expression profiling and computational promoter analysis to obtain global dissection of the transcriptional response to ionizing radiation in murine lymphoid tissue. Cluster analysis revealed a prominent pattern characterizing dozens of genes whose response to irradiation was Atm-dependent. Computational analysis identified significant enrichment of the binding site signatures of NF-kappaB and p53 among promoters of these genes, pointing to the major role of these two transcription factors in mediating the Atm-dependent transcriptional response in the irradiated lymphoid tissue. Examination of the response showed that pro- and antiapoptotic signals were simultaneously induced, with the proapoptotic pathway mediated by p53 targets, and the prosurvival pathway by NF-kappaB targets. These findings further elucidate the molecular network induced by IR, point to novel putative NF-kappaB targets, and suggest a mechanistic model for cellular balancing between pro- and antiapoptotic signals induced by IR in lymphoid tissues, which has implications for cancer management. The emerging model suggests that restoring the p53-mediated apoptotic arm while blocking the NF-kappaB-mediated prosurvival arm could effectively increase the radiosensitivity of lymphoid tumors.

Animals↗
PubMed2006

Image-guided system with miniature robot for precise positioning and targeting in keyhole neurosurgery.

This paper describes a novel image-guided system for precise automatic targeting in minimally invasive keyhole neurosurgery. The system consists of the MARS miniature robot fitted with a mechanical guide for needle, probe or catheter insertion. Intraoperatively, the robot is directly affixed to a head clamp or to the patient's skull. It automatically positions itself with respect to predefined targets in a preoperative CT/MRI image following an anatomical registration with an intraoperative 3D surface scan of the patient's facial features and registration jig. We present the system architecture, surgical protocol, custom hardware (targeting and registration jig), and software modules (preoperative planning, intraoperative execution, 3D surface scan processing, and three-way registration). We also describe a prototype implementation of the system and in vitro registration experiments. Our results indicate a system-wide target registration error of 1.7 mm (standard deviation = 0.7 mm), which is close to the required 1.0-1.5 mm clinical accuracy in many keyhole neurosurgical procedures.

Magnetic Resonance Imaging↗
PubMed2005

Robot-assisted image-guided targeting for minimally invasive neurosurgery: planning, registration, and in-vitro experiment.

This paper present a novel image-guided system for precise automatic targeting in keyhole minimally invasive neurosurgery. The system consists of a miniature robot fitted with a mechanical guide for needle/probe insertion. Intraoperatively, the robot is directly affixed to a head clamp or to the patient skull. It automatically positions itself with respect to predefined targets in a preoperative CT/MRI image following an anatomical registration with a intraoperative 3D surface scan of the patient facial features. We describe the preoperative planning and registration modules, and an in-vitro registration experiment of the entire system which yields a target registration error of 1.7 mm (std = 0.7 mm).

Craniotomy↗
PubMed2005

Prevalence and significance of mutations in the familial Mediterranean fever gene in patients with Crohn's disease.

The concurrence of Crohn's disease (CD) and familial Mediterranean fever was repeatedly reported. In this study we determined the distribution and contribution of MEFV gene mutations to CD susceptibility and clinical heterogeneity. An Israeli cohort of 209 CD patients (120 men and 89 women) was investigated for mutations in the MEFV gene. A detailed chart review, interview and physical examination were used to determine sociodemographic and clinical characteristics. MEFV and NOD2/CARD15 genotypes were analyzed in all patients and a genotype-phenotype correlation analysis was undertaken. The results of this study do not implicate MEFV mutations as major modifiers in CD. However, the E148Q MEFV variant was associated with susceptibility to perianal disease. More specifically, 19% (9/47) of CD patients with perianal disease carried the E148Q mutation compared to 6.7% (11/162) of CD patients without perianal involvement (OR 3.26, 95% CI 1.2-8.8, P=0.02). Although, for all mutations taken together, the prevalence of MEFV gene mutations among CD patients and controls was similar, the hypothesis that E148Q mutation modulates the phenotypic expression of CD is corroborated by the results of this study and needs to be further evaluated.

Adolescent↗
PubMed2004

Bone quantitative ultrasound and nutritional status in severely handicapped institutionalized children and adolescents.

BACKGROUND & AIMS: Children with cerebral palsy (CP) have a high prevalence of pathologic fractures. Bone quantitative ultrasonography (QUS) has emerged as a radiation-free method for the assessment of bone quality and fracture risk. In this study, we applied QUS technique in order to investigate bone status in handicapped institutionalized children and adolescents. METHODS: This cross-sectional study included 87 handicapped institutionalized patients. Measurements of the velocity of ultrasound wave, speed of sound (SOS), at distal radius and midshaft tibia, were performed using Omnisense 7000S analyser (Sunlight Ltd., Tel Aviv, Israel). In addition, all the participants had a thorough evaluation of nutritional status, demographic and clinical characteristics. RESULTS: Forty-five of patients had either radius or tibia bone SOS lower than -1 SD, and 21% had either radius or tibia bone SOS lower than -2.5 SD. Using step-wise regression analysis, female gender (P=0.003) and stature (P=0.008) were correlated with radius SOS. Age (P=0.03) and fracture history (P=0.04) were negatively correlated with tibia SOS. CONCLUSION: In this group of children and adolescents with CP one-fifth had poor bone status as suggested by low tibia/radius SOS assessed by QUS. Female gender, stature, age and fracture history were significantly correlated with poor bone status.

Adolescent↗
PubMed2004

Reconstructing chain functions in genetic networks.

Deciphering the mechanisms that control gene expression in the cell is a fundamental question in molecular biology. This task is complicated by the large number of possible regulation relations in the cell, and the relatively small amount of available experimental data. Recently, a new class of regulation functions called chain functions was suggested. Many signal transduction pathways can be accurately modeled by chain functions, and the restriction to chain functions greatly reduces the vast search space of regulation relations. In this paper we study the computational problem of reconstructing a chain function using a minimum number of experiments, in each of which only few genes are perturbed. We give optimal reconstruction schemes for several scenarios and show their application in reconstructing the regulation of galactose utilization in yeast.

Computational Biology↗
PubMed2004

The influence of oral insulin on the development of autoimmune diabetes in NOD mice fed a hypoallergenic diet.

BACKGROUND: Autoimmune diabetes can be prevented in animal models by hypoallergenic diets. Moreover, in animal models, oral administration of insulin can suppress the development of autoimmune diabetes and clinical trials on prevention of human Type 1 diabetes by oral administration of insulin are already taking place. However, it has been reported that autoimmune diabetes can be induced by oral administration of an auto-antigen (insulin), and great caution is therefore warranted when applying the oral tolerance approach to prevent Type 1 diabetes. AIM: To evaluate the effect of orally administered insulin on the development of autoimmune diabetes in non-obese diabetic mice fed a hypoallergenic diet. METHODS: Four groups of mice were fed regular mouse chow (group 1, control mice), hypoallergenic diet, using the hydrolyzed infant formula Pregistimil (group 2), and Pregistimil with oral insulin (4 U/l of drinking water, group 3; and 8 U/l of drinking water, group 4). RESULTS: At 210 days of age, 11/20 (55%) mice in group 1 developed diabetes. In contrast, none of the mice from the Pregistimil-fed groups (0/16, 0/14, 0/17) developed the disease (p<0.001). The incidence of infiltrated islets and the severity of insulitis, at age 90 days, was significantly lower in mice fed with the hypoallegenic diet than in controls (p=0.028). CONCLUSIONS: In NOD mice fed a diet that prevents the development of diabetes, oral insulin supplementation appears to be safe, since it does not promote the development of clinical diabetes.

Administration, Oral↗
PubMed2003

Scoring clustering solutions by their biological relevance.

MOTIVATION: A central step in the analysis of gene expression data is the identification of groups of genes that exhibit similar expression patterns. Clustering gene expression data into homogeneous groups was shown to be instrumental in functional annotation, tissue classification, regulatory motif identification, and other applications. Although there is a rich literature on clustering algorithms for gene expression analysis, very few works addressed the systematic comparison and evaluation of clustering results. Typically, different clustering algorithms yield different clustering solutions on the same data, and there is no agreed upon guideline for choosing among them. RESULTS: We developed a novel statistically based method for assessing a clustering solution according to prior biological knowledge. Our method can be used to compare different clustering solutions or to optimize the parameters of a clustering algorithm. The method is based on projecting vectors of biological attributes of the clustered elements onto the real line, such that the ratio of between-groups and within-group variance estimators is maximized. The projected data are then scored using a non-parametric analysis of variance test, and the score's confidence is evaluated. We validate our approach using simulated data and show that our scoring method outperforms several extant methods, including the separation to homogeneity ratio and the silhouette measure. We apply our method to evaluate results of several clustering methods on yeast cell-cycle gene expression data. AVAILABILITY: The software is available from the authors upon request.

Algorithms↗
PubMed2003

Rofecoxib reduces polyp recurrence in familial polyposis.

The long-term (mean of 16.4 +/- 4.2 months) efficacy and safety of rofecoxib (a specific COX-2 inhibitor) in maintaining the colon free of polyps in familial polyposis patients was assessed. Eight patients were treated with rofecoxib 25 mg every day. Sigmoidoscopy/colonoscopy was performed at study entry and every six months. At each endoscopy the number, size, and histological grade of all polyps were assessed, and the polyps were removed. The drug was well tolerated with no significant adverse events throughout the study. A highly significant reduction in the rate of polyp formation (70-100%) was observed in all patients from a mean number of 15.1 +/- 11.7 at baseline to 6.0 +/- 5.8 at one year and 1.6 +/- 1.6 at the end of follow-up (P = 0.016 and 0.008, respectively). No patient developed cancer or high-grade adenoma. In conclusion, Long-term use of rofecoxib is well tolerated and effective in inhibiting polyp formation in polyposis patients.

Adenomatous Polyposis Coli↗
PubMed2003

Chain functions and scoring functions in genetic networks.

One of the grand challenges of system biology is to reconstruct the network of regulatory control among genes and proteins. High throughput data, particularly from expression experiments, may gradually make this possible in the future. Here we address two key ingredients in any such 'reverse engineering' effort: The choice of a biologically relevant, yet restricted, set of potential regulation functions, and the appropriate score to evaluate candidate regulatory relations. We propose a set of regulation functions which we call chain functions, and argue for their ubiquity in biological networks. We analyze their complexity and show that their number is exponentially smaller than all boolean functions of the same dimension. We define two new scores: one evaluating the fitness of a candidate set of regulators of a particular gene, and the other evaluating a candidate function. Both scores use established statistical methods. Finally, we test our methods on experimental gene expression data from the yeast galactose pathway. We show the utility of using chain functions and the improved inference using our scores in comparison to several extant scores. We demonstrate that the combined use of the two scores gives an extra advantage. We expect both chain functions and the new scores to be helpful in future attempts to infer regulatory networks.

Galactose↗
PubMed2003

Faecal elastase 1 levels in premature and full term infants.

BACKGROUND: Determination of faecal elastase 1 (FE1) is a simple, relatively inexpensive, non-invasive, highly specific and sensitive test for determining pancreatic function. Secretion of pancreatic enzymes varies during infancy, but there are almost no specific data on the ontogeny of elastase 1 in human babies. AIM: To study FE1 levels in preterm and term babies, and to determine the possible effect of gestational and postconceptual age on these levels. METHODS: Serial stool samples were collected and tested for FE1 level from 77 premature and full term infants. FE1 levels were determined by a commercially available enzyme linked immunosorbent assay (ELISA) kit. RESULTS: A total of 232 stool samples were collected from 77 neonates. The FE1 level measured in the first stool sample (meconium) was below normal (200 micro g/g stool) in all samples regardless of gestational age. Sixty three neonates had at least two samples tested for FE1 level. The mean (SD) level of FE1 in sample 1 was 45.9 (51.1) micro g/g stool and was significantly (p < 0.001) lower than in sample 2 (243.0 (164.9) micro g/g stool). The lower the gestational age of the newborn, the more time it took for FE1 to reach normal levels. CONCLUSIONS: FE1 levels in meconium are low, and studies in meconium should be avoided if pancreatic sufficiency is to be determined. FE1 reaches normal levels by day 3 in term newborns and by 2 weeks in infants born before 28 weeks gestation. Normal levels are reached sooner in infants of more advanced gestational age who start enteral feeding earlier.

Aging↗
PubMed2003

Insulin in human milk: postpartum changes and effect of gestational age.

OBJECTIVE: To determine if human milk insulin (HMI) concentrations are affected by gestational age and postnatal age. DESIGN AND SETTING: An observational study carried out in a level III neonatal intensive care unit. Insulin concentrations were determined in human milk of 90 parturient mothers who delivered between 30 and 41 weeks gestation. Samples were collected on days 3 and 10 after delivery. RESULTS: HMI concentrations for mothers of preterm infants were not significantly different from those of full term infants, on either day 3 or 10 post partum. When results for all 90 mothers were pooled, regardless of gestational age, HMI concentration fell significantly from day 3 to day 10 (50.1 (34.6) v 41.1 (28.5) microU/ml; p = 0.01; mean (SD)). However, this decrease was only significant for mothers delivering at term (37-41 weeks). CONCLUSIONS: HMI concentrations were not influenced by gestational age at delivery. They decreased post partum, mainly in mothers of term infants. The postnatal changes in HMI concentrations and the effects of oral insulin on the immature intestinal mucosa warrant further investigation.

Female↗
PubMed2003

The prevalence of coeliac disease antibodies in patients with the antiphospholipid syndrome.

High prevalence of coeliac disease (CD) has been reported in various autoimmune disorders, buthas not been studied in the antiphospholipid syndrome (APS). We aimed to establish the prevalence of CD antibodies in a cohort of APS patients, and to examine whether CD may be responsible for some of the manifestations of APS. Fifty-seven patients (47 females, 10 males) with APS were studied for clinical manifestations and serological markers of the disease, as well as the presence of anti-endomysial antibodies using an ELISA assay (EMA-ELISA). Control subjects were 171 healthy individuals, age- and sex-matched (141 females). Eight patients with APS (14%, six females) were found to have EMA-ELISA antibodies, compared with 2/141 (1.1%) of controls (P = 0.0003). Antibodies against beta2-glycoprotein-I (beta2GPI) epitopes (GRTCPKPDDLP) were more prevalent in EMA-positive patients than in EMA-negative patients (P = 0.006). Vasculitic skin lesions were significantly more common in EMA-ELISA-positive compared with EMA-ELISA-negative patients(62.5 versus 16.3%, P = 0.01). Among the skin manifestations, superficial cutaneous necrosis (37.5 versus 2%, P = 0.007) was more prevalent in EMA-ELISA-positive than in EMA-ELISA-negative patients. EMA-ELISA antibodies are common in APS, and their presence is associated with high prevalence of antibodies recognizing certain beta2-glycoprotein epitopes, and with cutaneous manifestations of APS.

Adult↗
PubMed2002

Skin level division of percutaneous endoscopic gastrostomy without endoscopy retrieval: a hazardous procedure.

Percutaneous endoscopic gastrostomy (PEG) has become the method of choice for long-term enteral access in the pediatric population. Since its introduction, several common complications have been described. Less well known is the danger of removing or replacing a PEG by cutting the device at skin level without endoscopic assistance to ensure the complete removal of all parts. The aim of the present work is to describe a patient in whom gastrostomy parts were retained after PEG removal, causing bowel obstruction and perforation.

Child, Preschool↗