bluuebunny/crossref_metadata_2025_split huggingface dataset:
How Many Nosocomial Infections Are Missed If Identification Is Restricted to Patients With Either Microbiology Reports or Antibiotic Administration?
Authors: Gastmeier Petra , Bräuer Helga , Hauer Thomas , Schumacher Martin , Daschner Franz , Rüden Henning 
Published: February 2006

AbstractObjective:To investigate how many nosocomial infections would be missed if surveillance activities were restricted to patients having either microbiology reports or antibiotic administration.Design:Analysis of data from a large prevalence study on nosocomial infections (Nosocomial Infections in Germany— Surveillance and Prevention).Setting:A total of 14,966 patients were investigated in medical, surgical, obstetric-gynecologic, and intensive-care units of 72 German hospitals representatively selected according to size. Five hundred eighteen patients (3.5%) had at least one nosocomial infection. Microbiology reports were available for 56.6% of these patients on the prevalence day, and 86.3% received antibiotics.Results:Only 31 nosocomially infected patients (6%) would have been missed by using either microbiology reports or antibiotic treatment as an indicator. These indicators of nosocomial infections had a high diagnostic sensitivity for nosocomial pneumonia (98.8%), urinary tract infections (96.3%), and primary bloodstream infections (95.3%), but a lower sensitivity for wound infections (85.4%). Thus, 97.4% of all nosocomial infections were found with this method in intensive-care units and 96.1% in medicine units, but only 89.7% in surgical departments. In 9 (12.5%) of 72 hospitals, the overall sensitivity would have been &lt;80% using a combination of the two indicators. For this reason, the situation in one's own hospital should be checked before using this method.Conclusions:After checking the situation in one's own hospital, the “either-or” approach using the two indicators “microbiology report” and “antibiotic administration” can be recommended as a time-saving measure to diagnose pneumonia, urinary tract, and primary bloodstream infections. For wound infections, additional information obtained by changing dressings or participating in ward rounds is necessary to achieve satisfactory sensitivity in the surveillance of nosocomial infections. Of course, it is necessary that the surveillance staff discard all false positives to ensure a satisfactory specificity.
Use of Personal Protective Equipment and Operating Room Behaviors in Four Surgical Subspecialties: Personal Protective Equipment and Behaviors in Surgery
Authors: Akduman Deniz , Kim Lynn E. , Parks Rodney L. , L'Ecuyer Paul B. , Mutha Sunita , Jeffe Donna B. , Evanoff Bradley A , Fraser Victoria J. 
Published: February 2006

AbstractObjective:To evaluate Universal Precautions (UP) compliance in the operating room (OR).Design:Prospective observational cohort. Trained observers recorded information about (1) personal protective equipment used by OR staff; (2) eyewear, glove, or gown breaks; (3) the nature of sharps transfers; (4) risk-taking behaviors of the OR staff; and (5) needlestick injuries and other blood and body-fluid exposures.Setting:Barnes-Jewish Hospital, a 1,000-bed, tertiary-care hospital affiliated with Washington University School of Medicine, St Louis, Missouri.Participants:OR personnel in four surgical specialties (gynecologic, orthopedic, cardiothoracic, and general). Procedures eligible for the study were selected randomly. Hand surgery and procedures requiring no or a very small incision (eg, arthroscopy, laparoscopy) were excluded.Results:A total of 597 healthcare workers' procedures were observed in 76 surgical cases (200 hours). Of the 597 healthcare workers, 32% wore regular glasses, and 24% used no eye protection. Scrub nurses and medical students were more likely than other healthcare workers to wear goggles. Only 28% of healthcare workers double gloved, with orthopedic surgery personnel being the most compliant. Sharps passages were not announced in 91% of the surgical procedures. In 65 cases (86%), sharps were adjusted manually. Three percutaneous and 14 cutaneous exposures occurred, for a total exposure rate of 22%.Conclusion:OR personnel had poor compliance with UP. Although there was significant variation in use of personal protective equipment between groups, the total exposure rate was high (22%), indicating the need for further training and reinforcement of UP to reduce occupational exposures.
Donor-to-Recipient Transmission of Bacteria as an Unusual Cause of Mediastinitis in a Heart Transplant Recipient
Authors: Burket Jeffrey S. , Chenoweth Carol E. , Meyer Thomas L. , Barg Neil L. 
Published: February 2006

AbstractWe present a 54-year-old male heart transplant recipient who developed mediastinitis caused byKlebsiella oxytocaandVeillonellaspecies. Culture of the donor's bronchus also grewK oxytocaand aVeillonellaspecies. Pulsed-field gel electrophoresis revealed that theK oxytocaisolates had identical banding patterns. This case illustrates transmission of pathogenic bacteria via a contaminated organ.
Memory efficient folding algorithms for circular RNA secondary structures
Authors: Hofacker Ivo L. , Stadler Peter F. 
Published: February 2006

Abstract
Background: A small class of RNA molecules, in particular the tiny genomes of viroids, are circular. Yet most structure prediction algorithms handle only linear RNAs. The most straightforward approach is to compute circular structures from ‘internal’ and ‘external’ substructures separated by a base pair. This is incompatible, however, with the memory-saving approach of the Vienna RNA Package which builds a linear RNA structure from shorter (internal) structures only.
Result: Here we describe how circular secondary structures can be obtained without additional memory requirements as a kind of ‘post-processing’ of the linear structures.
Availability: The circular folding algorithm is implemented in the current version of the of RNAfold program of the Vienna RNA Package, which can be downloaded from
Contact: ivo@tbi.univie.ac.at
Efficient estimation of graphlet frequency distributions in protein–protein interaction networks
Authors: Pržulj N. , Corneil D. G. , Jurisica I. 
Published: February 2006

Abstract
Motivation: Algorithmic and modeling advances in the area of protein–protein interaction (PPI) network analysis could contribute to the understanding of biological processes. Local structure of networks can be measured by the frequency distribution of graphlets, small connected non-isomorphic induced subgraphs. This measure of local structure has been used to show that high-confidence PPI networks have local structure of geometric random graphs. Finding graphlets exhaustively in a large network is computationally intensive. More complete PPI networks, as well as PPI networks of higher organisms, will thus require efficient heuristic approaches.
Results: We propose two efficient and scalable heuristics for finding graphlets in high-confidence PPI networks. We show that both PPI and their model geometric random networks, have defined boundaries that are sparser than the ‘inner parts’ of the networks. In addition, these networks exhibit ‘uniformity’ of local structure inside the networks. Our first heuristic exploits these two structural properties of PPI and geometric random networks to find good estimates of graphlet frequency distributions in these networks up to 690 times faster than the exhaustive searches. Our second heuristic is a variant of a more standard sampling technique and it produces accurate approximate results up to 377 times faster than the exhaustive searches. We indicate how the combination of these approaches may result in an even better heuristic.
Availability: Supplementary information is available at Software implementing the algorithms is available at
Contact: juris@cs.toronto.edu; natasha@igor.ics.uci.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
MAMMOT—a set of tools for the design, management and visualization of genomic tiling arrays
Authors: Ryder E. , Jackson R. , Ferguson-Smith A. , Russell S. 
Published: February 2006

Abstract
Summary: The MAMMOT software suite is a collection of Perl and PHP scripts for designing, annotating and visualizing genome tiling arrays to, for example, facilitate studies into the epigenetics of gene regulation. The web design allows rapid experimental data entry from multiple users, and results can easily be shared between groups and individuals.
Availability:
Contact: e.ryder@gen.cam.ac.uk
Incidence of Crohn Disease in the Czech Republic in the Years 1990 to 2001 and Assessment of Pediatric Population with Inflammatory Bowel Disease
Authors: Pozler Oldrich , Maly Jan , Bonova Oldriska , Dedek Petr , Frühauf Pavel , Havlickova Alena , Janatova Tatiana , Jimramovsky Frantisek , Klimova Lenka , Klusacek Dalibor , Kocourkova Dana , Kolek Antonin , Kotalova Radka , Marx David , Nevoral Jiri , Petro Radim , Petru Ondrej , Plasilova Ivana , Seidl Zbynek , Sekyrova Ivana , Semendak Norbert , Schreierova Irena , Stanek Jan , Sykora Josef , Sulakova Astrid , Toukalkova Lenka , Travnickova Radka , Volf Vladimir , Zahradnicek Lubomir , Zenisková Ivana ,   Czech Collaborative Group for the Study of Chronic Illnesses of the Gastrointestinal Tract in Children
Published: February 2006

ABSTRACTBackground:The aim of this study was to assess the pediatric population that suffered from inflammatory bowel disease (IBD) in the Czech Republic and to determine the incidence of Crohn disease (CD) in children up to 15 years age between 1990 and 2001.Methods:Diagnostic criteria for CD, ulcerative colitis (UC), and indeterminate colitis (IC) were defined. Medical records provided a source of basic information about the children. A standardized protocol was filled out and sent to the coordinator of the study. All protocols were checked to see whether the data corresponded to the defined criteria and then were processed further. The study was retrospective in character for the years 1990 to 1999 and prospective for the years 2000 and 2001.Results:Diagnostic criteria were met in 470 patients with IBD; 201 of them turned 18 years old during the study period. CD was diagnosed in 223 patients. The incidence of CD in children up to 15 years of age increased from 0.25/100,000 in 1990 to 1.25/100,000 in 2001. Eighty‐two percent of children with CD were treated with aminosalicylates in combination with corticosteroids; 29% of patients received azathioprine. Severe growth retardation was recorded in 6.4% of adolescents with CD at the age of 18. UC was diagnosed in 202 patients. Therapy with aminosalicylates only was sufficient for control of the disease in 23% patients; 68% children were treated with corticosteroids, 15 of them (23% of the whole group) received additional azathioprine. Criteria for IC were met in 9.8% of all patients with IBD.Conclusion:This study confirmed an increase in incidence of CD in children younger than 15 years in the Czech Republic.
Clinical Safety of Lactobacillus casei shirota as a Probiotic in Critically Ill Children
Authors: Srinivasan Ramesh , Meyer Rosan , Padmanabhan Ramnarayan , Britto Joseph 
Published: February 2006

ABSTRACTObjective:Diarrhea is frequently observed among critically ill children (CIC) admitted for intensive care. There is increasing evidence that probiotics decrease the incidence of acute infectious and nosocomial and antibiotic induced diarrhea amongst children hospitalized in nonintensive care settings. Despite theoretic advantages for the use of probiotics in CIC, safety has remained a concern in this vulnerable group. The objective of this study was to establish clinical safety (invasive infection/colonization) of Lactobacillus casei shirota (LCS) used as a probiotic in CIC.Methods:Prospective, descriptive pilot study on children admitted to a pediatric intensive care unit. Data regarding safety were collected on the initial recruits to a randomized controlled trial aimed to study the effects of LCS on stool frequency and consistency in CIC. Safety was assessed by bacteriologic surveillance for LCS in surface swabs and endotracheal aspirates (colonization) as well as blood, urine, and sterile body fluid cultures (invasive infection/bacteremia).Results:Safety data were available on 28 patients. LCS was cultured from the feces of five of the six study subjects who opened bowels during their stay on the pediatric intensive care unit. There was no evidence of either colonization or bacteremia with LCS in bacteriologic cultures obtained from study subjects. The preparation was well tolerated with no apparent side effects.Conclusions:Our pilot safety study suggests that the use of LCS as a probiotic in enterally fed CIC is safe.
Serologic and Genetic Markers of Celiac Disease: A Sequential Study in the Screening of First Degree Relatives
Authors: Bonamico Margherita , Ferri Mirella , Mariani Paolo , Nenna Raffaella , Thanasi Enina , Luparia Rita P. L , Picarelli Antonio , Magliocca Fabio M , Mora Barbara , Bardella Maria Teresa , Verrienti Antonella , Fiore Benedetta , Uccini Stefania , Megiorni Francesca , Mazzilli Maria Cristina , Tiberti Claudio 
Published: February 2006

ABSTRACTObjectives:The prevalence of celiac disease (CD) among the relatives and the complications of an undiagnosed CD prompted us to identify a useful disease screening strategy.Methods:We studied 441 first degree relatives of 208 CD patients by immunoglobulin (Ig)A antiendomysium antibodies (EMA) and radioimmunoprecipitation assay (RIA) IgA antitransglutaminase autoantibodies (TGAA). Of these, 364 were typed for human leukocyte antigen‐DRB1, ‐DQA1, and ‐DQB1 genes by the polymerase chain reaction sequence specific primers method. It was suggested to the autoantibody‐positive subjects that they should undergo intestinal biopsy.Results:TGAA were positive in 46 of 439 relatives, EMA in 38; intestinal lesions related to CD were present in 40 subjects. We also found two immunodeficient fathers with duodenal villous atrophy. In three serology‐positive subjects, permission for intestinal biopsy was refused; for another three serology‐positive cases, duodenal mucosa was normal. Thus, the strict CD prevalence resulted 9.5%, the enlarged prevalence 10.9%. The DQ2/DQ8 heterodimers were carried in 231 of 364 subjects and in 38 of 40 biopsy‐proven celiac patients. Three DQ2‐positive parents became positive to the serology during a long‐lasting follow‐up.Conclusions:On the basis of a carefully conducted study, CD prevalence in our series was seen as very high. These data suggest an accurate algorithm to select candidates for intestinal biopsy among CD high‐risk subjects. First, an evaluation of the sensitive RIA TGAA and of total IgA (in IgA deficiency RIA IgG anti‐tissue transglutaminase assay) should be performed. Then, an evaluation of the TGAA and the genetic study would be advisable 2 to 3 years later in negative subjects. Those carrying the DQ2/DQ8 heterodimers should continue the serologic follow‐up; the others need a clinical follow‐up.
Prevalence of Celiac Disease in Brazilian Children with Type 1 Diabetes Mellitus
Authors: Tanure Mariella Guarino , Silva Ivani Novato , Bahia Magda , Penna Francisco José 
Published: February 2006

ABSTRACTObjective:Although the relationship between celiac disease and diabetes mellitus type 1 is well recognized, there are no studies of this association in Brazil. This study aims to identify the prevalence of celiac disease in a group of children with diabetes mellitus type 1 undergoing treatment in the pediatric endocrinology division of a university hospital in Minas Gerais, Brazil.Methods:Immunoglobulin (Ig)A and IgG antigliadin antibodies (enzyme‐linked immunoadsorbent assay) were measured in blood collected from 236 children and adolescents with diabetes mellitus type 1. Patients with antigliadin antibodies then had jejunal biopsy and determination of antiendomysial antibodies by indirect immunofluorescence.Results:Twenty‐one patients had IgA or IgG antigliadin antibodies. Nineteen underwent jejunal biopsy. Six had mucosal alterations compatible with celiac disease; four had nonspecific histologic changes; nine had normal biopsies. Thirteen antigliadin antibody‐positive patients were antiendomysial antibody‐negative; one antiendomysial antibody‐negative patient had celiac disease. The prevalence of celiac disease was 2.6% among 234 patients.Conclusions:Measurement of antigliadin antibodies in patients with diabetes mellitus type 1 helped in the selection of patients to undergo jejunal biopsy. Antiendomysial antibodies were highly specific and moderately sensitive in predicting celiac disease. The prevalence of celiac disease was higher in diabetics than in the general population, suggesting the need for regular screening assessment of diabetic children.
Long‐Term Prognosis of Patients with Biliary Atresia: A 25 Year Summary
Authors: Hung Pei‐Yin , Chen Chiu‐Chiang , Chen Wei‐Jao , Lai Hong‐Shiee , Hsu Wen‐Ming , Lee Po‐Hung , Ho Ming‐Chih , Chen Tony H. H , Ni Yen‐Hsuan , Chen Huey‐Ling , Hsu Hong‐Yuan , Chang Mei‐Hwei 
Published: February 2006

ABSTRACTObjective:The purpose of this study was to delineate the long‐term prognosis of biliary atresia (BA) in Taiwan.Study Design:From 1976 to 2000, 185 children were diagnosed with BA, 22 underwent exploratory laparotomy without Kasai operation, and 163 underwent Kasai operation, of which 141 cases had long‐term follow‐up and formed the basis of this study. The outcome was analyzed.Results:Among the 141 BA children studied who underwent Kasai operation, 115 (81.6%) had recoloration of stools, and 86 (61.0%) became jaundice‐free (bilirubin <20 μmol/L). The resolution of jaundice and the absence of repeated cholangitis contributed to better outcome. Five and 10 year survival rates with native liver were 35% and 31%, respectively. Liver transplantation was performed in 19 patients (all but 2 with a living‐related donor), and 15 (79%) survived. Five and 10 year overall survival rates for BA patients were 41.9% and 40.2%, respectively.Conclusions:The study delineated the long‐term outcome of BA in an Asian country other than Japan. Survival with native liver after a Kasai operation in Taiwan was similar to that in the American and European series. Limited donors for liver transplantation in the years of the study accounted for the poor overall prognosis of BA patients in this series.
Free Sugar and Sugar Alcohol Concentrations in Human Breast Milk
Authors: Cavalli Claudio , Teng Cecilia , Battaglia Frederick C , Bevilacqua Giulio 
Published: February 2006

ABSTRACTObjectives:The goal was to determine the free sugars and polyols in human breast milk, both term and preterm, for comparison with formula milks.Methods:Methodology was developed for the measurement of the free sugars and polyols in breast milk. There were 16 samples collected from women who delivered at term and 17 samples from women delivering preterm. For purposes of comparison, samples were also collected from four commercial formulas for term infants and eight from commercial formulas for preterm infants as well as one sample of cows' milk. All samples were frozen immediately and analyzed by high‐performance liquid chromatography techniques.Results:Except for lactose concentrations, no significant differences were detected for all other sugars and polyols between term and preterm breast milk samples. Within breast milk samples, two patterns emerged, with one group containing additional elution peaks for compounds not yet identified. A second group did not contain these compounds. There were a number of significant differences between breast milk and formulas, particularly for inositol, glycerol, glucose, and galactose. All milks contained significant concentrations of mannose.Conclusions:There are no significant differences among breast milk samples for free sugar and polyol concentrations except lactose. However, some milk contains additional peaks that could be of dietary or genetic origin. Formula milk has relatively high concentrations of glucose and galactose compared with breast milk, suggesting some lactose hydrolysis.
Liver Abscesses in Children: A Single Center Experience in the Developed World
Authors: Muorah M , Hinds R , Verma A , Yu D , Samyn M , Mieli‐Vergani G , Hadžić N 
Published: February 2006

ABSTRACTObjectives:The aim of this study was to investigate the clinical and radiologic features, predisposing risk factors, and complications of children with pyogenic liver abscess (PLA) referred to a tertiary pediatric hepatology center.Methods:We analyzed our database of all children referred to our unit over a 10 year period and performed a case note review of all patients with a radiologically proven PLA.Results:PLA was diagnosed in 15 children (7 boys), 0.5% of all referrals. They presented at a median age of 10 years (range 2 months‐15 years). In three children (2 boys), PLA was the first manifestation of chronic granulomatous disease. Among the others, five had radiologic evidence of other intra‐abdominal pathology (1 with subsequently proven appendicitis), and four developed portal vein thrombosis with portal hypertension. The commonest isolated pathogen was Staphylococcus aureus. Combined treatment with guided aspiration and prolonged intravenous antibiotics was successful in all patients.Conclusion:PLA is a rare diagnosis in children in the developed world. It may be caused by primary neutrophil disorders even in the absence of a previous history of infection. Co‐existent appendicitis, intra‐abdominal sepsis, and ascending pylephlebitis must be sought because these children are at risk of developing portal vein obstruction and portal hypertension. Prolonged intravenous antibiotic treatment guided by microbiologic sensitivities is highly effective.
Sodium Butyrate‐Mediated Sp3 Acetylation Represses Human Insulin‐Like Growth Factor Binding Protein‐3 Expression in Intestinal Epithelial Cells
Authors: White Nicholas R , Mulligan Peter , King Peter J , Sanderson Ian R 
Published: February 2006

ABSTRACTObjectives:Butyrate concentrations in the gastrointestinal tract vary greatly with age. In intestinal epithelial cells, butyrate enhances gene transcription by increasing histone acetylation, rendering the nucleosome open to transcription factors. However, it inhibits human insulin‐like growth factor binding protein (hIGFBP)‐3 expression. We therefore hypothesized that butyrate also acts by regulating transcription factor acetylation.Methods:Gene regulation was examined in Caco‐2 cells. RNA stability was measured after interruption of transcription. The activity of deletion mutations of the hIGFBP‐3 promoter was examined in reporter assays. Transcription factor binding to promoter DNA was analyzed.Results:Butyrate did not increase the transcription of a repressor because it inhibited hIGFBP‐3 mRNA in the absence of protein synthesis. Nor did butyrate decrease the stability of hIGFBP‐3 mRNA. Analysis of the hIGFBP‐3 promoter demonstrated a butyrate‐response element that included the binding sites for p300 and Sp1/Sp3. Transfection of Caco‐2 cells with E1A, an inhibitor of p300 acetyltransferase activity, reversed the butyrate‐induced repression of hIGFBP‐3. Because Sp3 represses the initiation of transcription, we studied whether butyrate induced Sp3 acetylation. Electrophoretic mobility shift assays of nuclei extracted from Caco‐2 cells treated with 5 mmol/L butyrate demonstrated an extra, heavier band in addition to the Sp3‐DNA binding in untreated cells. This corresponded to a protein, detected only in butyrate treated cells, that was identified both by an anti‐Sp3 antibody and by an anti‐acetyl lysine antibody.Conclusions:This study demonstrates that butyrate increases the acetylation of a nonhistone protein, Sp3, catalyzed by p300 acetyltransferase activity.