bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining multiple microarrays in the presence of controlling variables
Authors: Park Taesung , Yi Sung-Gon , Shin Young Kee , Lee SeungYeoun 
Published: May 2006

AbstractMotivation: Microarray technology enables the monitoring of expression levels for thousands of genes simultaneously. When the magnitude of the experiment increases, it becomes common to use the same type of microarrays from different laboratories or hospitals. Thus, it is important to analyze microarray data together to derive a combined conclusion after accounting for the differences. One of the main objectives of the microarray experiment is to identify differentially expressed genes among the different experimental groups. The analysis of variance (ANOVA) model has been commonly used to detect differentially expressed genes after accounting for the sources of variation commonly observed in the microarray experiment.Results: We extended the usual ANOVA model to account for an additional variability resulting from many confounding variables such as the effect of different hospitals. The proposed model is a two-stage ANOVA model. The first stage is the adjustment for the effects of no interests. The second stage is the detection of differentially expressed genes among the experimental groups using the residuals obtained from the first stage. Based on these residuals, we propose a permutation test to detect the differentially expressed genes. The proposed model is illustrated using the data from 133 microarrays collected at three different hospitals. The proposed approach is more flexible to use, and it is easier to accommodate the individual covariates in this model than using the meta-analysis approach.Availability: A set of programs written in R will be electronically sent upon request.Contact: tspark@stats.snu.ac.kr
Distance-based clustering of CGH data
Authors: Liu Jun , Mohammed Jaaved , Carter James , Ranka Sanjay , Kahveci Tamer , Baudis Michael 
Published: May 2006

Abstract
Motivation: We consider the problem of clustering a population of Comparative Genomic Hybridization (CGH) data samples. The goal is to develop a systematic way of placing patients with similar CGH imbalance profiles into the same cluster. Our expectation is that patients with the same cancer types will generally belong to the same cluster as their underlying CGH profiles will be similar.
Results: We focus on distance-based clustering strategies. We do this in two steps. (1) Distances of all pairs of CGH samples are computed. (2) CGH samples are clustered based on this distance. We develop three pairwise distance/similarity measures, namely raw, cosine and sim. Raw measure disregards correlation between contiguous genomic intervals. It compares the aberrations in each genomic interval separately. The remaining measures assume that consecutive genomic intervals may be correlated. Cosine maps pairs of CGH samples into vectors in a high-dimensional space and measures the angle between them. Sim measures the number of independent common aberrations. We test our distance/similarity measures on three well known clustering algorithms, bottom-up, top-down and k-means with and without centroid shrinking. Our results show that sim consistently performs better than the remaining measures. This indicates that the correlation of neighboring genomic intervals should be considered in the structural analysis of CGH datasets. The combination of sim with top-down clustering emerged as the best approach.
Availability: All software developed in this article and all the datasets are available from the authors upon request.
Contact: juliu@cise.ufl.edu
Protein classification using probabilistic chain graphs and the Gene Ontology structure
Authors: Carroll Steven , Pavlovic Vladimir 
Published: May 2006

AbstractMotivation: Probabilistic graphical models have been developed in the past for the task of protein classification. In many cases, classifications obtained from the Gene Ontology have been used to validate these models. In this work we directly incorporate the structure of the Gene Ontology into the graphical representation for protein classification. We present a method in which each protein is represented by a replicate of the Gene Ontology structure, effectively modeling each protein in its own ‘annotation space’. Proteins are also connected to one another according to different measures of functional similarity, after which belief propagation is run to make predictions at all ontology terms.Results: The proposed method was evaluated on a set of 4879 proteins from the Saccharomyces Genome Database whose interactions were also recorded in the GRID project. Results indicate that direct utilization of the Gene Ontology improves predictive ability, outperforming traditional models that do not take advantage of dependencies among functional terms. Average increase in accuracy (precision) of positive and negative term predictions of 27.8% (2.0%) over three different similarity measures and three subontologies was observed.Availability: C/C++/Perl implementation is available from authors upon request.Contact: vladimir@cs.rutgers.edu
Dilated Intercellular Spaces
Authors: Ravelli Alberto M. , Villanacci Vincenzo , Ruzzenenti Nella , Grigolato Piergiovanni , Tobanelli Pamela , Klersy Catherine , Rindi Guido 
Published: May 2006

ABSTRACTObjectives:Dilated intercellular spaces (DIS) in the esophageal epithelium have been identified by electron microscopy as marker of acid reflux damage in experimental animals and adults with gastroesophageal reflux disease (GERD). We aimed to identify and quantify DIS by light microscopy in pediatric GERD and esophagitis.Methods:We prospectively took esophageal biopsies in 70 consecutive pediatric patients, 48 of whom had GERD symptoms. On hematoxylin and eosin‐stained sections esophagitis was scored histologically, and DIS were graded as 0 (absent), + (small and focal), ++ (moderate) or +++ (large and diffuse). A computerized image analysis identified total, cellular and nuclear areas and DIS were quantified as percentage of total minus cellular area.Results:Forty of 48 GERD patients had histological esophagitis (33 G1, 4 G2, 3 G3, 1 of which with Barrett esophagus), and all 40 had DIS (33 +, 4 ++, 3 +++) with 100% interobserver agreement; 15 of 29 (55%) had abnormal pH study (reflux index, 5.7%‐36%). In 30 patients the esophagus was histologically normal. DIS values were 2.21% ± 2.60% (range, 0.11%‐12%) in patients with esophagitis and 0.44% ± 0.13% (0.2%‐0.7%) in patients with normal histology (P < 0.00001), with 0.71% bearing 70% sensitivity and 100% specificity for GERD versus controls. Five other children with esophagitis unrelated to GERD (eosinophilic, Candida, food allergy) also had DIS + to +++, and median DIS area was 5% (1.3%‐12%).Conclusions:DIS can be detected and evaluated by light microscopy, and the image analysis used provides an objective quantification of DIS and supports the light microscopy evaluation. DIS are a morphological feature of GERD and esophagitis in infancy and childhood.
Superior Mesenteric Artery Syndrome in Children
Authors: Biank Vincent , Werlin Steven 
Published: May 2006

ABSTRACTObjectives:Superior mesenteric artery syndrome (SMAS), Wilkie syndrome or cast syndrome is a rare condition that usually presents with symptoms of mid to upper gastrointestinal obstruction due to the compression of the duodenum between the abdominal aorta, posteriorly, and the superior mesenteric artery, anteriorly. The aim of this study was to analyze the clinical characteristics, means of diagnosis and management of SMAS in a pediatric population.Methods:Retrospective chart review of all patients at the Children's Hospital of Wisconsin with SMAS from 1985 to 2005.Results:Twenty‐two cases of SMAS where diagnosed at Children's Hospital of Wisconsin between 1985 and 2005 [14, (64%) female]. Symptoms developed 1 to 393 days (median 5 days) before diagnosis. Presenting symptoms included abdominal pain (59%), vomiting (50%), nausea (40%), early satiety (32%) and anorexia (18%). Diagnosis was made by upper‐gastrointestinal radiography in 18 (82%), by computed tomography in 2 (9%) and at laparotomy in 2 (9%). One patient was treated surgically after medical management failed. Mean length of treatment was 65 days (range 13‐169), with a mean length of hospitalization of 21 days (range 0‐68 days).Conclusion:SMAS usually presents more acutely than chronically with symptoms of small bowel obstruction. Weight loss is not necessary for SMAS development. Prior neurological injury may be a risk factor for development of SMAS. Upper gastrointestinal radiography remains the primary means of diagnosis. SMAS is typically successfully managed medically. Surgical intervention should be reserved for patients' refractory to medical therapy. The expected outcome of SMAS is excellent.
Endoscopic Management of Sphincter of Oddi Dysfunction in Children
Authors: Varadarajulu Shyam , Wilcox C. Mel 
Published: May 2006

ABSTRACTBackground:Data on sphincter of Oddi dysfunction (SOD) in children are scant. Most children diagnosed with SOD are treated by biliary sphincterotomy with suboptimal results. The efficacy and safety of pancreatic and dual sphincterotomy in children with SOD has not been previously reported.Objective:To evaluate the efficacy and safety of pancreatic and dual sphincterotomy in children with SOD.Materials and Methods:Prospective evaluation of all children who underwent endoscopic retrograde cholangiopancreatogram (ERCP) with sphincter of Oddi manometry for evaluation of suspected SOD over a 3‐year period. Children diagnosed with SOD underwent pancreatic or dual sphincterotomy with prophylactic pancreatic stenting.Results:SOD was diagnosed by sphincter of Oddi manometry in 6 of 11 children who underwent ERCP for suspected SOD. Of the 6 children (mean age, 11 years; range, 5‐16; 4 girls) with SOD, 3 presented with recurrent pancreatitis and 3 with postcholecystectomy pain. Pancreatic sphincter hypertension was noted in all 6 patients; concomitant biliary sphincter hypertension was noted in 3 patients with postcholecystectomy pain. Patients with recurrent pancreatitis underwent pancreatic sphincterotomy and those with postcholecystectomy pain underwent dual sphincterotomy. Prophylactic pancreatic stents were placed in all patients. One girl experienced mild post‐ERCP pancreatitis. At a mean follow‐up of 583 days (range, 325‐1445), 4 patients were asymptomatic, 1 experienced partial symptom relief and 1 had recurrent symptoms.Conclusions:As in adults, pancreatic and dual sphincterotomy, in expert hands, is effective and safe in a subgroup of children with SOD. Prospective, randomized trials with larger number of patients are required to validate the efficacy of endotherapy in children with SOD.
Anti‐rotavirus Antibodies in Human Milk
Authors: Asensi María Teresa , Martínez‐Costa Cecilia , Buesa Javier 
Published: May 2006

ABSTRACTObjective:To analyze anti‐rotavirus antibodies in human milk in order to determine their isotypes and neutralizing activity on rotavirus strains representing different viral serotypes.Methods:One hundred seventy‐three milk samples (65 colostrum, 55 transitional milk and 53 mature milk) obtained from 65 mothers were analyzed along with 49 serum samples collected just before delivery. Total immunoglobulin A (IgA) and rotavirus‐specific IgA and immunoglobulins G (IgG) antibodies were determined in milk and serum by enzyme‐linked immunosorbent assay. Neutralizing activity was evaluated by an immunoperoxidase focus reduction assay. Milk IgA was purified by binding to the lectin jacalin, elution and ultrafiltration.Results:Total IgA antibodies were detected in all serum and milk samples analyzed. IgA levels decreased sharply during the replacement of colostrum by transitional milk, and more gradually from transitional to mature milk. These differences in IgA concentration during the 3 periods were statistically significant. Anti‐rotavirus antibodies detected in human milk were exclusively of the IgA type, whereas both IgA and IgG anti‐rotavirus antibodies were present in serum samples. Both milk and serum samples showed in vitro neutralization of the infectivity of rotavirus strains SA11, Wa and VA70, this activity being stronger toward the human rotavirus strain Wa. No correlation was however found between the inhibitory effect on rotavirus and the concentrations of IgA in human milk and serum samples.Conclusion:Anti‐rotavirus antibodies are only partly responsible for the neutralizing activity detected in milk and serum. This result suggests that other components possessing suppressive activity against rotavirus must also be present.
Usefulness of Nonbreath‐hold 1‐Shot Magnetic Resonance Cholangiopancreatography for the Evaluation of Choledochal Cyst in Children
Authors: Suzuki Mitsuyoshi , Shimizu Toshiaki , Kudo Takahiro , Suzuki Ryuyo , Ohtsuka Yoshikazu , Yamashiro Yuichiro , Shimotakahara Akihiko , Yamataka Atsuyuki 
Published: May 2006

ABSTRACTObjective:The aim of this study was to clarify the usefulness of magnetic resonance cholangiopancreatography (MRCP) for the evaluation of choledochal cyst in children.Subjects and methods:MRCP was performed preoperatively in 33 patients. The MRCP findings were compared with those of endoscopic retrograde cholangiopancreatography or intraoperative cholangiopancreatography.Results:In all 33 patients, MRCP could detect choledochal cyst. The detection rate of a cyst in the main pancreatic duct was 62.2%, of abnormal union of the pancreaticobiliary junction (AUPBJ) was 53.3%, of dilatation or abnormalities of the main pancreatic duct was 75.0% and of a protein plug or stone was 76.9%. In patients under 2 years of age (group A), these findings were significantly lower than those of patients above 2 years of age (group B) [main pancreatic duct: 16.6% (1/6) vs 73.1% (19/26), P < 0.01; AUPBJ: 0.0% (0/6) vs 66.7% (16/24), P < 0.05; and protein plug or stone: 0.0% (0/2) vs 90.9% (10/11), P < 0.05]. The detection rate of AUPBJ in the patients with fusiform dilatation was superior to that of those with cystic dilatation [70% (14/20) vs 20% (2/10), P < 0.05]. In the patients with fusiform dilatation, the detection rate in group A was significantly lower than that in group B [0.0% (0/3) vs 82.4% (14/17), P < 0.01]; however, there was no significant difference between the 2 groups in the detection of cystic dilatation.Conclusion:In patients older than 2 years, MRCP should be the first‐choice method for confirming the diagnosis and for ensuring accurate visualization of the pancreaticobiliary system.
Probiotic Intervention in Neonates‐Will Permanent Colonization Ensue?
Authors: Gueimonde Miguel , Kalliomäki Marko , Isolauri Erika , Salminen Seppo 
Published: May 2006

ABSTRACTThe presence of Lactobacillus rhamnosus GG at 6 and 12 months in the feces of 128 infants receiving the strain or placebo for 6 months after birth was monitored. No permanent establishment of the strain was found, but transient colonization was observed at 6 months of age. The presence of the strain at the end of the administration period was correlated with a reduced prevalence of atopic eczema later in life.
6‐Thioguanine‐related Chronic Hepatotoxicity and Variceal Haemorrhage in Children Treated for Acute Lymphoblastic Leukaemia‐A Dual‐centre Experience
Authors: Ravikumara Madhur , Hill Frank G.H. , Wilson David C. , Gillett Peter M. , Thomas Angela , Brown R. , Darbyshire Philip J. , McKiernan Patrick J. 
Published: May 2006

ABSTRACTBackground:6‐Thioguanine treatment in childhood acute lymphoblastic leukaemia (ALL) has been shown to cause hepatic veno‐occlusive disease, but this usually resolved with drug withdrawal. Recent reports suggested that treatment of ALL with 6‐thioguanine can lead to chronic hepatotoxicity and portal hypertension. We describe our experience from 2 UK centres of chronic hepatotoxicity in children receiving maintenance 6‐thioguanine for ALL in the national leukaemia protocol ALL 97/99.Methods:Retrospective review of children who were referred with liver disease secondary to 6‐thioguanine treatment of ALL was performed. A paediatric pathologist blinded to the clinical features reviewed liver histology slides.Results:Ten of 75 children (13%) treated with 6‐thioguanine in both centres were referred at a median of 6 months (range, 2‐29) after discontinuation of chemotherapy. In 8 cases, referral was due to persistent thrombocytopenia and splenomegaly. Two children presented with acute variceal bleeding. All had thrombocytopenia at referral, and ultrasonography showed coarse hepatic echo texture and splenomegaly in all. Endoscopy showed oesophageal varices in 7 and gastric varices in 1. Nine underwent liver biopsy that showed features compatible with nodular regenerative hyperplasia in 5 cases. After a median follow‐up of 36 months, a further child has had a variceal haemorrhage and all but 2 children remain thrombocytopenic.Conclusions:6‐Thioguanine‐induced chronic hepatotoxicity is a significant complication in children treated with this agent for ALL. Children may present several months to years after discontinuation of 6‐thioguanine. All children given maintenance treatment of ALL with this agent should be screened, and affected children require long‐term surveillance.
Changes of Gut Microbiota and Immune Markers During the Complementary Feeding Period in Healthy Breast‐fed Infants
Authors: Amarri S. , Benatti F. , Callegari M.L. , Shahkhalili Y. , Chauffard F. , Rochat F. , Acheson K.J. , Hager C. , Benyacoub J. , Galli E. , Rebecchi A. , Morelli L. 
Published: May 2006

IntroductionLittle is known about changes in intestinal microbiota during the important period of complementary feeding (weaning). This descriptive study investigated changes of selected gut microbiota and markers of gut permeability and the immune system in breast fed infants during the complementary feeding period.Methods22 healthy, exclusively breast fed infants (from birth to 4 months) with no antibiotic intake during the month prior to the study, were followed from 4 to 9 months of age. Faecal and saliva samples were collected at the start of the study (V0) and at monthly intervals (V1—V5) for measurement of selective gut microbiota (bifidobacteria, lactobacilli, vancomycin‐insensitive lactobacilli, enterobacteria, enterococci, Clostridium perfringens) using semi‐selective media. Immune markers (α‐1‐antitrypsin, eosinophil cationic protein (ECP), secretory IgA and TNF‐α were measured in saliva and secretory IgA and TNF‐α in faecal samples.ResultsHigh stool bifidobacteria counts at the start of the study (7.99 1 1.95 log10 CFU/g faeces) remained stable throughout the 5 months of complementary feeding while counts of enterobacteria and enterococci increased with age (P < 0.05 and P = 0.02 respectively). Vancomycin‐insensitive lactobacilli increased significantly during weaning from V0 to V3 (P < 0.01), and then decreased slightly (V4). Faecal Clostridium perfringens remained below the detection limit during the study and parameters measured in saliva did not change. Faecal ECP decreased significantly from 1.011.4 (V0) to 0.510.9 mg/mg protein (V5) P = 0.03.ConclusionAge and/or diet modifications during complementary feeding had no impact on faecal bifidobacteria counts but increased those of enterobacteria and enterococci. Transient increases in faecal lactobacilli and vancomycininsensitive lactobacilli counts were observed. The reduction in faecal ECP may indicate a decrease in gut permeability (reinforcement of gut mucosa integrity) during the weaning period with age.
Probiotics in Gastrointestinal Diseases in Children
Authors: Szajewska Hania , Setty Mala , Mrukowicz Jacek , Guandalini Stefano 
Published: May 2006

ABSTRACTThe use of probiotics, once discussed primarily in the context of alternative medicine, is now entering mainstream medicine. However, only a few of the potential health benefits attributed to probiotics have been confirmed in well‐designed, well‐conducted, randomized, controlled trials. This is especially true in the pediatric population. We review here the available evidence on efficacy of probiotics in children in the prevention and treatment of gastrointestinal diseases. Although we restrict our analysis to the pediatric age, whenever potentially relevant information is available only from adult studies, they are examined as well. Probiotics have been most extensively studied in the treatment of diarrheal diseases, where their efficacy can be considered well established. Studies documenting effects in other childhood gastrointestinal illnesses are few, although some preliminary results are promising. Furthermore, only a limited number of probiotic strains have been tested, and, as the effects of different probiotic microorganisms are not equivalent, results cannot be generalized. Thus, at present, we have some positive certainties, lots of exciting promises and many unanswered questions.
Feeding Preterm Infants After Hospital Discharge
Authors:   ESPGHAN Committee on Nutrition:, Aggett Peter J. , Agostoni Carlo , Axelsson Irene , De Curtis Mario , Goulet Olivier , Hernell Olle , Koletzko Berthold , Lafeber Harry N. , Michaelsen Kim F. , Puntis John W.L. , Rigo Jacques , Shamir Raanan , Szajewska Hania , Turck Dominique , Weaver Lawrence T. 
Published: May 2006

ABSTRACTSurvival of small premature infants has markedly improved during the last few decades. These infants are discharged from hospital care with body weight below the usual birth weight of healthy term infants. Early nutrition support of preterm infants influences long‐term health outcomes. Therefore, the ESPGHAN Committee on Nutrition has reviewed available evidence on feeding preterm infants after hospital discharge. Close monitoring of growth during hospital stay and after discharge is recommended to enable the provision of adequate nutrition support. Measurements of length and head circumference, in addition to weight, must be used to identify those preterm infants with poor growth that may need additional nutrition support. Infants with an appropriate weight for postconceptional age at discharge should be breast‐fed when possible. When formula‐fed, such infants should be fed regular infant formula with provision of long‐chain polyunsaturated fatty acids. Infants discharged with a subnormal weight for postconceptional age are at increased risk of long‐term growth failure, and the human milk they consume should be supplemented, for example, with a human milk fortifier to provide an adequate nutrient supply. If formula‐fed, such infants should receive special postdischarge formula with high contents of protein, minerals and trace elements as well as an long‐chain polyunsaturated fatty acid supply, at least until a postconceptional age of 40 weeks, but possibly until about 52 weeks postconceptional age. Continued growth monitoring is required to adapt feeding choices to the needs of individual infants and to avoid underfeeding or overfeeding.