bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outbreak ofEnterobacter cloacaeRelated to Understaffing, Overcrowding, and Poor Hygiene Practices
Authors: Harbarth Stephan , Sudre Philippe , Dharan Sasi , Cadenas Mercedes , Pittet Didier 
Published: February 2006

AbstractObjective:To determine the cause and mode of transmission of a cluster of infections due toEnterobacter cloacae.Design and Setting:Retrospective cohort study in a neonatal intensive-care unit (NICU) from December 1996 to January 1997; environmental and laboratory investigations.Subjects:60 infants hospitalized in the NICU during the outbreak period.Main Outcome Measures:Odds ratios (OR) linkingE cloacaecolonization or infection and various exposures. All availableE cloacaeisolates were typed and characterized by contour-clamped homogenous electric-field electrophoresis to confirm possible cross-transmission.Results:Of eight case-patients, two had bacteremia; one, pneumonia; one, soft-tissue infection; and four, respiratory colonization. Infants weighing <2,000 g and born before week 33 of gestation were more likely to become cases (P<.001). Multivariate analysis indicated that the use of multidose vials was independently associated withE cloacaecarriage (OR, 16.3; 95% confidence interval [CI95], 1.8-∞P=011). Molecular studies demonstrated three epidemic clones. Cross-transmission was facilitated by understaffing and overcrowding (up to 25 neonates in a unit designed for 15), with an increased risk ofE cloacaecarriage during the outbreak compared to periods without understaffing and overcrowding (relative risk, 5.97; CI95, 2.2-16.4). Concurrent observation of healthcare worker (HCW) handwashing practices indicated poor compliance. The outbreak was terminated after decrease of work load, increase of hand antisepsis, and reinforcement of single-dose medication.Conclusions:Several factors caused and aggravated this outbreak: (1) introduction ofE cloacaeinto the NICU, likely by two previously colonized infants; (2) further transmission by HCWs' hands, facilitated by substantial overcrowding and understaffing in the unit; (3) possible contamination of multidose vials withE cloacae.Overcrowding and understaffing in periods of increased work load may result in outbreaks of nosocomial infections and should be avoided.
Tuberculosis in Hemodialysis Patients in New Jersey: A Statewide Study
Authors: Simon Teresa A. , Paul Sindy , Wartenberg Daniel , Tokars Jerome I. 
Published: February 2006

AbstractObjective:To study the incidence of tuberculosis (TB), tuberculin skin testing (TST) practices, and infection control practices at outpatient hemodialysis centers.Design:Mail surveys performed in December 1994 and 1995.Main Outcome Measures:The numbers of patients with incident active TB during 1994 and 1995, TST policies during 1994, and TB infection control policies in 1994.Setting:All outpatient dialysis centers in New Jersey.Patients or Participants:Healthcare workers and patients in dialysis centers in New Jersey.Results:Of 47 centers, 41 provided information on TST and TB infection control policies and practices. TSTs were performed on newly hired healthcare workers at all 41 centers and on established workers at 39 centers. In contrast, only 1 center reported performing TSTs on hemodialysis patients; 5 other centers reported screening of patients for TB using chest radiographs. Active TB was reported in 3 of 4,550 chronic hemodialysis patients in 1994 (rate, 66/100,000 patient-years) and in 4 of 4,831 patients in 1995 (rate, 83/100,000 patient-years). Both rates were several times higher than the rate in the New Jersey general population during this period (10.7-10.8/100,000).Conclusion:Although based on small numbers of patients with TB, we found a relatively high incidence of TB among hemodialysis patients in New Jersey. Most centers reported performing TSTs on workers but not on patients. These results suggest the need for improved TB screening and infection control precautions at outpatient dialysis centers.
Costs and Benefits of Measures to Prevent Needlestick Injuries in a University Hospital
Authors: Roudot-Thoraval Françoise , Montagne Olivier , Schaeffer Annette , Dubreuil-Lemaire Marie-Laure , Hachard Danièle , Durand-Zaleski Isabelle 
Published: February 2006

AbstractObjective:To document the costs and the benefits (both in terms of costs averted and of injuries averted) of education sessions and replacement of phlebotomy devices to ensure that needle recapping did not take place.Design:The percentage of recapped needles and the rate of needlestick injuries were evaluated in 1990 and 1997, from a survey of transparent rigid containers in the wards and at the bedside and from a prospective register of all injuries in the workplace. Costs were computed from the viewpoint of the hospital. Positive costs were those of education and purchase of safer phlebotomy devices; negative costs were the prophylactic treatments and follow-up averted by the reduction in injuries.Setting:A 1,050-bed tertiary-care university hospital in the Paris region.Results:Between the two periods, the proportion of needles seen in the containers that had been recapped was reduced from 10% to 2%. In 1990, 127 needlestick (12.7/100,000 needles) and 52 recapping injuries were reported versus 62 (6.4/100,000 needles) and 22 in 1996 and 1997. When the rates were related to the actual number of patients, the reduction was 76 injuries per year. The total cost of information and preventive measures was $325,927 per year. The cost-effectiveness was $4,000 per injury prevented.Conclusion:Although preventive measures taken to ensure reduction of needlestick injuries appear to have been effective (75% reduction in recapping and 50% reduction in injuries), the cost of the safety program was high.
Preventing Central Venous Catheter-Related Infection in a Surgical Intensive-Care Unit
Authors: Bijma Rens , Girbes Armand R. , Kleijer Dick J. , Zwaveling Jan H. 
Published: February 2006

AbstractThe cumulative effect of five measures (introduction of hand disinfection with alcohol, a new type of dressing, a one-bag system for parenteral nutrition, a new intravenous connection device, and surveillance by an infection control practitioner) on central venous catheter colonization and bacteremia was studied. Colonization was significantly reduced (P<.025); the decrease in bacteremia was not statistically significant.
Nosocomial Infections Caused by Multiresistant Pseudomonas aeruginosa
Authors: Arruda Erico A.G. , Marinho Ivan S. , Boulos Marcos , Sinto Sumiko I. , Caiaffa F Helio H. , Mendes Caio M. , Oplustil Carmen P. , Sader Helio , Levy Carlos E. , Levin Anna S. 
Published: February 2006

AbstractA case-control study was done to evaluate factors associated with nosocomial infections by multiresistant Pseudomonas aeruginosa (MRPA). Results showed that MRPA was associated with the use of immunosuppressive and antimicrobial drugs. Five typing methods indicated that the MRPA infections were due to multiple strains rather than a single strain.
Healthcare Worker Compliance With Nosocomial Tuberculosis Control Policies
Authors: LoBue Philip , Catanzaro Antonino 
Published: February 2006

AbstractTo determine compliance with nosocomial tuberculosis control measures, 541 healthcare worker observations were made for 52 patients placed in respiratory isolation. Sixty-four total violations were noted, of which 45% occurred in physicians in training. Overall compliance with tuberculosis control measures appeared to be good, but additional educational efforts are warranted.
Bacterial Contamination of Hospital Physicians' Stethoscopes
Authors: Bernard Louis , Kereveur Anne , Durand Dominique , Gonot Jeanne , Goldstein Fred , Mainardi Jean Luc , Acar Joseph , Carlet Jean 
Published: February 2006

AbstractBecause stethoscopes might be potential vectors of nosocomial infections, this study, conducted in a 450-bed general hospital, was devised to evaluate the bacterial contamination of stethoscopes; bacterial survival on stethoscope membranes; the kinetics of the bacterial load on stethoscope membranes during clinical use; and the efficacy of 70% alcohol or liquid soap for membrane disinfection. Among the 355 stethoscopes tested, 234 carried ≥2 different bacterial species; 31 carried potentially pathogenic bacteria. Although some bacteria deposited onto membranes could survive 6 to 18 hours, none survived after disinfection.
Prevention of Influenza in Long-Term–Care Facilities
Authors: Bradley Suzanne F. ,   Long-Term–Care Committee of the Society for Healthcare Epidemiology of America
Published: February 2006

AbstractInfluenza is a frequent cause of epidemic and endemic respiratory illness in long-term-care facilities (LTCFs), resulting in considerable morbidity and mortality. Detection of influenza outbreaks in this setting can be difficult, because the clinical presentation in older adults is atypical and other pathogens also cause influenza-like illness (ILI) during the influenza season. Use of the standard case definition for influenza has not been effective in detecting episodes in residents of LTCFs. Alternative case-definitions that reflect the atypical presentation of influenza in this population have been recommended but not validated. The use of rapid tests for the detection of influenza in conjunction with more sensitive case definitions of ILI may lead to the earlier detection of influenza outbreaks in LTCFs, earlier initiation of infection control measures, and reduction in transmission.The definition of outbreak, eg, the number of episodes of ILI or episodes of confirmed influenza A that would result in the initiation of antiviral chemoprophylaxis, remains controversial in this setting. The use of newer antivirals could limit the side effects seen in older adults in LTCFs. However, annual vaccination of residents and staff remains the most effective way to prevent the introduction of influenza A or influenza B into LTCFs. In addition, vaccination of LTCF residents reduces rates of illness and pneumonia due to influenza, as well as cardiopulmonary exacerbation, hospitalization, and death.
Structured polychotomous machine diagnosis of multiple cancer types using gene expression
Authors: Koo Ja-Yong , Sohn Insuk , Kim Sujong , Lee Jae Won 
Published: February 2006

Abstract
Motivation: The problem of class prediction has received a tremendous amount of attention in the literature recently. In the context of DNA microarrays, where the task is to classify and predict the diagnostic category of a sample on the basis of its gene expression profile, a problem of particular importance is the diagnosis of cancer type based on microarray data. One method of classification which has been very successful in cancer diagnosis is the support vector machine (SVM). The latter has been shown (through simulations) to be superior in comparison with other methods, such as classical discriminant analysis, however, SVM suffers from the drawback that the solution is implicit and therefore is difficult to interpret. In order to remedy this difficulty, an analysis of variance decomposition using structured kernels is proposed and is referred to as the structured polychotomous machine. This technique utilizes Newton–Raphson to find estimates of coefficients followed by the Rao and Wald tests, respectively, for addition and deletion of import vectors.
Results: The proposed method is applied to microarray data and simulation data. The major breakthrough of our method is efficiency in that only a minimal number of genes that accurately predict the classes are selected. It has been verified that the selected genes serve as legitimate markers for cancer classification from a biological point of view.
Availability: All source codes used are available on request from the authors.
Contact: jykoo@korea.ac.kr
PROFbval: predict flexible and rigid residues in proteins
Authors: Schlessinger Avner , Yachdav Guy , Rost Burkhard 
Published: February 2006

Abstract
Summary: The mobility of a residue on the protein surface is closely linked to its function. The identification of extremely rigid or flexible surface residues can therefore contribute information crucial for solving the complex problem of identifying functionally important residues in proteins. Mobility is commonly measured by B-value data from high-resolution three-dimensional X-ray structures. Few methods predict B-values from sequence. Here, we present PROFbval, the first web server to predict normalized B-values from amino acid sequence. The server handles amino acid sequences (or alignments) as input and outputs normalized B-value and two-state (flexible/rigid) predictions. The server also assigns a reliability index for each prediction. For example, PROFbval correctly identifies residues in active sites on the surface of enzymes as particularly rigid.
Availability:
Contact: profbval@rostlab.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model
Authors: Broët Philippe , Richardson Sylvia 
Published: February 2006

AbstractMotivation: Comparative genomic hybridization array experiments that investigate gene copy number changes present new challenges for statistical analysis and call for methods that incorporate spatial dependence between sequences along the chromosome. For this purpose, we propose a novel method called CGHmix. It is based on a spatially structured mixture model with three states corresponding to genomic sequences that are either unmodified, deleted or amplified. Inference is performed in a Bayesian framework. From the output, posterior probabilities of belonging to each of the three states are estimated for each genomic sequence and used to classify them.Results: Using simulated data, CGHmix is validated and compared with both a conventional unstructured mixture model and with a recently proposed data mining method. We demonstrate the good performance of CGHmix for classifying copy number changes. In Addition, the method provides a good estimate of the false discovery rate. We also present the analysis of a cancer related dataset.Supplementary information: Contact: broet@vjf.inserm.fr
A deterministic motif finding algorithm with application to the human genome
Authors: Hon Lawrence S , Jain Ajay N 
Published: February 2006

Abstract
Motivation: We present a novel algorithm, MaMF, for identifying transcription factor (TF) binding site motifs. The method is deterministic and depends on an indexing technique to optimize the search process. On common yeast datasets, MaMF performs competitively with other methods. We also present results on a challenging group of eight sets of human genes known to be responsive to a diverse group of TFs. In every case, MaMF finds the annotated motif among the top scoring putative motifs. We compared MaMF against other motif finders on a larger human group of 21 gene sets and found that MaMF performs better than other algorithms. We analyzed the remaining high scoring motifs and show that many correspond to other TFs that are known to co-occur with the annotated TF motifs. The significant and frequent presence of co-occurring transcription factor binding sites explains in part the difficulty of human motif finding. MaMF is a very fast algorithm, suitable for application to large numbers of interesting gene sets.
Availability: The software is available for academic research use free of charge by email request.
Contact: ajain@jainlab.org
Supplemental information: Data comprising the benchmarks used in the paper may be downloaded from .
Chemokine Production by Buccal Epithelium as a Distinctive Feature of Pediatric Crohn Disease
Authors: Damen Gerard M , Hol Jeroen , de Ruiter Lilian , Bouquet Jan , Sinaasappel Maarten , van der Woude Janneke , Laman Jon D , Hop Wim C. J , Büller Hans A , Escher Johanna C , Nieuwenhuis Edward E. S 
Published: February 2006

ABSTRACTObjectives:Inflammatory bowel diseases (IBD) represent an aberrant immune response by the mucosal immune system to luminal bacteria. Because the oral mucosa harbors the first epithelial cells that interact with microorganisms, we assessed the immunologic activity of buccal epithelium in children with IBD and adults with Crohn disease.Methods:Buccal epithelial cells were obtained from 17 children and 14 adults with Crohn disease, 18 children with ulcerative colitis, and 40 controls. Cells were cultured with and without microbial stimulation. Chemokine levels were determined in culture supernatants by cytometric bead array and enzyme‐linked immunoabsorbent assay. CXCL‐8 production was studied by immunohistochemical analysis of these cells. CXCL‐8 production by lipopolysaccharide stimulated monocyte‐derived dendritic cells from these patients was determined.Results:Compared with controls, pediatric ulcerative colitis patients, and adult Crohn disease patients, only in children with Crohn disease did buccal epithelial cells exhibit enhanced production of CXCL‐8, CXCL‐9, and CXCL‐10. In vitro stimulation with lipopolysaccharide or zymosan resulted in a further increase of chemokine levels only in cells from pediatric Crohn disease patients. CXCL‐8 production by stimulated monocyte‐derived dendritic cells from children with Crohn disease was equal to that of children with ulcerative colitis.Conclusions:Buccal epithelium of children with Crohn disease is immunologically active, even in the absence of oral lesions. The enhanced chemokine production is associated with pediatric Crohn disease and appears restricted to cells derived from the epithelial barrier. Assessment of chemokine production by buccal epithelial cells may become a new, rapid, noninvasive test for screening and classification of IBD in children.
Meat as a First Complementary Food for Breastfed Infants: Feasibility and Impact on Zinc Intake and Status
Authors: Krebs Nancy F , Westcott Jamie E , Butler Nancy , Robinson Cordelia , Bell Melanie , Hambidge K Michael 
Published: February 2006

ABSTRACTObjective:This study was undertaken to assess the feasibility and effects of consuming either meat or iron‐fortified infant cereal as the first complementary food.Methods:Eighty‐eight exclusively breastfed infants were enrolled at 4 months of age and randomized to receive either pureed beef or iron‐fortified infant cereal as the first complementary food, starting after 5 months and continuing until 7 months. Dietary, anthropometric, and developmental data were obtained longitudinally until 12 months, and biomarkers of zinc and iron status were measured at 9 months.Results:Mean (±SE) daily zinc intake from complementary foods at 7 months for infants in the meat group was 1.9 ± 0.2 mg, whereas that of the cereal group was 0.6 ± 0.1 mg, which is approximately 25% of the estimated average requirement. Tolerance and acceptance were comparable for the two intervention foods. Increase in head circumference from 7 to 12 months was greater for the meat group, and zinc and protein intakes were predictors of head growth. Biochemical status did not differ by feeding group, but approximately 20% of the infants had low (<60 μg/dL) plasma zinc concentrations, and 30% to 40% had low plasma ferritin concentrations (<12 μg/L). Motor and mental subscales did not differ between groups, but there was a trend for a higher behavior index at 12 months in the meat group.Conclusions:Introduction of meat as an early complementary food for exclusively breastfed infants is feasible and was associated with improved zinc intake and potential benefits. The high percentage of infants with biochemical evidence of marginal zinc and iron status suggests that additional investigations of optimal complementary feeding practices for breastfed infants in the United States are warranted.
Management of Fulminating Ulcerative Colitis in Childhood with Chimeric Anti‐CD25 Antibody
Authors: Schwarzer A , Ricciardelli I , Kirkham S , Binnie K , Shah N , Elawad M A , Hill S M , Furman M , Smith V V , Sebire N , Milla P J , Londei M , Lindley K J 
Published: February 2006

ABSTRACTFulminating acute ulcerative colitis (UC) is a potentially life threatening medical emergency. Up to 30% of individuals respond poorly to corticosteroids alone and second line medical or surgical therapies are indicated. We describe the successful use of chimeric anti‐CD25 therapy in 4 such children poorly responsive to combined therapy with intravenous steroids and calcineurin inhibitors with a pretreatment predictive risk of colectomy of 85‐100%. Clinical disease activity scores normalized within 72 hours of anti‐CD25 administration and colonic histology provided evidence of mucosal healing within 10‐14 days. None required emergency colectomy. Anti‐CD25 is efficacious in fulminating UC and randomized placebo controlled trials appear indicated.
A Prospective Study Comparing Oral Sodium Phosphate Solution to a Bowel Cleansing Preparation with Nutrition Food Package in Children
Authors: El‐Baba Mohammad F , Padilla Mary , Houston Carmela , Madani Shailender , Lin Chuan‐Hao , Thomas Ronald , Tolia Vasundhara 
Published: February 2006

ABSTRACTObjective:The inability of children to comply with bowel preparation regimens can result in inadequate visualization of the colon. This study compares the safety, efficacy, and patient acceptance of a prepackaged diet kit plus a magnesium citrate/bisacodyl bowel cleansing regimen with a clear liquid diet and sodium phosphate solution regimen in children undergoing colonoscopy.Methods:Children scheduled for a diagnostic colonoscopy, were randomly assigned to receive a prepackaged diet kit and a magnesium citrate/bisacodyl laxative (group 1), or clear liquids and sodium phosphate solution (group 2). The patients and their parents completed a questionnaire to evaluate acceptance of their assigned regimen before colonoscopy. The endoscopists, blinded to the type of bowel preparation, rated bowel cleansing.Results:Sixty two children (28 males, 34 females) with mean age 12.5 years participated. Thirty six and 26 patients were in groups 1 and 2 respectively. Overall cleansing was rated significantly superior in group 1 compared to group 2 as was amount of retained feces (P = .013 for both). The overall frequency of reported side‐effects was lower in group 1 than (83.3%, 30/36) than in group 2 (100.0%, 26/26) (P = 0.03). The preparations were otherwise equivalent in regards to compliance and patient tolerance.Conclusions:Although both regimens were comparable in adequacy of colon visualization, preparation tolerance, side effects and compliance profile in this pilot study, the prepackaged diet kit with magnesium citrate/bisacodyl laxative resulted in superior colon cleansing.