bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting calcium‐binding sites in proteins—A graph theory and geometry approach
Authors: Deng Hai , Chen Guantao , Yang Wei , Yang Jenny J. 
Published: April 2006

AbstractIdentifying calcium‐binding sites in proteins is one of the first steps towards predicting and understanding the role of calcium in biological systems for protein structure and function studies. Due to the complexity and irregularity of calcium‐binding sites, a fast and accurate method for predicting and identifying calcium‐binding protein is needed. Here we report our development of a new fast algorithm (GG) to detect calcium‐binding sites. The GG algorithm uses a graph theory algorithm to find oxygen clusters of the protein and a geometric algorithm to identify the center of these clusters. A cluster of four or more oxygen atoms has a high potential for calcium binding. High performance with about 90% site sensitivity and 80% site selectivity has been obtained for three datasets containing a total of 123 proteins. The results suggest that a sphere of a certain size with four or more oxygen atoms on the surface and without other atoms inside is necessary and sufficient for quickly identifying the majority of the calcium‐binding sites with high accuracy. Our finding opens a new avenue to visualize and analyze calcium‐binding sites in proteins facilitating the prediction of functions from structural genomic information. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Risk Factors for and Clinical Outcomes of Bloodstream Infections Caused by Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae
Authors: Kang Cheol-In , Kim Sung-Han , Kim Dong Min , Park Wan Beom , Lee Ki-Deok , Kim Hong-Bin , Oh Myoung-don , Kim Eui-Chong , Choe Kang-Won 
Published: April 2006

AbstractObjective:To evaluate risk factors and treatment outcomes of bloodstream infections caused by extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-KP).Design:Retrospective case-control study. Stored blood isolates of K. pneumoniae were tested for ESBL production by NCCLS guidelines, double-disk synergy test, or both.Setting:A 1,500-bed, tertiary-care university hospital and referral center.Patients:Sixty case-patients with bacteremia due to ESBL-KP were compared with 60 matched control-patients with non-ESBL-KP.Results:There were no significant differences in age, gender, APACHE II score, or underlying diseases between the groups. Independent risk factors for infections caused by ESBL-KP were urinary catheterization, invasive procedure within the previous 72 hours, and an increasing number of antibiotics administered within the previous 30 days. Complete response rate, evaluated 72 hours after initial antimicrobial therapy, was higher among control-patients (13.3% vs 36.7%; P = .003). Treatment failure rate was higher among case-patients (35.0% vs 15%; P = .011). Overall 30-day mortality rate was 30% for case-patients and 28.3% for control-patients (P = .841). Case-patients who received imipenem or ciprofloxacin as a definitive antibiotic had 10.5% mortality. The mortality rate for initially ineffective therapy was no higher than that for initially effective therapy (9.1% vs 11.1%; P = 1.000), but statistical power was low for evaluating mortality in the absence of septic shock.Conclusion:For K. pneumoniae bacteremia, patients with ESBL-KP had a higher initial treatment failure rate but did not have higher mortality if antimicrobial therapy was appropriately adjusted in this study with limited statistical power.
Incidence of Urinary Tract Infection Following Transrectal Ultrasound Guided Prostate Biopsy at a Tertiary-Care Medical Center in Lebanon
Authors: Otrock Zaher K. , Oghlakian Gerard O. , Salamoun Mariana M. , Haddad Maurice , Bizri Abdul Rahman N. 
Published: April 2006

AbstractObjective:To determine the incidence of urinary tract infections (UTIs) following transrectal ultrasound guided needle biopsy of the prostate (TRUBP) and the bacteriology of these infections.Design:Retrospective evaluation of the charts and records of all patients who underwent TRUBP between June 1, 2002, and August 31, 2003.Setting:American University of Beirut Medical Center, a tertiary-care center in Lebanon.Patients:Two hundred seven patients underwent TRUBP. All received prophylactic antibiotics. One hundred twenty (58%) received ciprofloxacin alone, whereas 87 (42%) received both ciprofloxacin and gentamicin. Sixty-one patients (29.5%) had an enema prior to the procedure, whereas 146 (70.5%) did not.Results:Thirteen patients (6.3%) were admitted with UTI. All had rigors and fever on admission. Symptoms appeared at a mean of 2.7 days and the mean hospital stay was 9.2 days. The mean duration of antibiotic treatment was 23.2 days. Ten (77%) of the patients had positive bacteriology. Urine cultures were positive in 8 (61.5%) of the patients and blood cultures in 6 (46.2%). All positive cultures grew Escherichia coli resistant to ciprofloxacin, with 5 isolates producing extended-spectrum beta-lactamases.Conclusions:TRUBP continues to be associated with significant infectious complications, especially UTI. Given the increasing incidence of antibiotic resistance mainly among the Enterobacteriaceae, antimicrobial prophylaxis practices should be reevaluated and the universal administration of quinolones alone or in combination with aminoglycosides should be reconsidered.
A Cluster of Nosocomial Klebsiella oxytoca Bloodstream Infections in a University Hospital
Authors: Sardan Yesim Cetinkaya , Zarakolu Pinar , Altun Belgin , Yildirim Aycan , Yildirim Gonul , Hascelik Gulsen , Uzun Omrum 
Published: April 2006

AbstractBackground:On February 19, 2003, four patients (patients 1-4) in the neurology ward underwent cranial magnetic resonance angiography (MRA) and developed fever within 1 hour afterward. Klebsiella oxytoca was isolated from blood cultures of patients 1 through 3.Objective:To identify the source of this cluster of nosocomial K. oxytoca bloodstream infections.Design:Outbreak investigation.Setting:A 1,000-bed university hospital.Methods:The infection control team reviewed patient charts and interviewed nursing staff about the preparation and administration of parenteral fluids. The procedure of cranial MRA was observed. Arbitrarily primed polymerase chain reaction (AP-PCR) was performed to show the clonal relationship among these three strains.Results:AP-PCR revealed that three K. oxytoca isolates had the same molecular profile. Cranial MRA was found to be the only common source among these patients. During MRA, before injection of the contrast medium, normal saline solution was infused to check the functioning of the intravenous catheter. Use of the solution for multiple patients was routine, but the access diaphragm of the bottle was not cleansed. The bottle of normal saline solution used on February 19 had already been discarded and the culture sample taken from the solution on the day of observation was sterile.Conclusions:We speculate that normal saline solution became contaminated during manipulation and that successive uses might have been responsible for this cluster. Poor aseptic techniques employed during successive uses appear to be the most likely route of contamination. Use of parenteral solutions for multiple patients was discontinued..
Improving the Rates of Inpatient Pneumococcal Vaccination: Impact of Standing Orders Versus Computerized Reminders to Physicians
Authors: Coyle Christina M. , Currie Brian P. 
Published: April 2006

AbstractObjective:To determine the impact of interventions using standing orders and computerized reminders to physicians on inpatient pneumococcal vaccination rates relative to a control group.Design:Open trial of the following approaches, each on a different ward: (1) standing orders for vaccination of eligible consenting patients, (2) computerized reminders to physicians, and (3) usual practice.Setting And Patients:Four hundred twenty-four patients were admitted to three 30-bed inpatient medical wards during a 4-month period in 1999 at one hospital. Unvaccinated patients 65 years or older and competent to give oral consent were included.Intervention:A pharmacist activated a standing orders protocol for vaccination of all eligible consenting patients on one ward and computerized reminders to physicians on a second ward. A third ward served as a control group.Results:Forty-two patients met inclusion criteria and accepted vaccination in the standing orders arm versus 35 patients in the computerized reminder arm. Vaccination rates on the standing orders ward included 98% of those eligible and accepting vaccination, 73% of eligible patients, and 28% of all patients admitted. Rates on the computerized reminder ward were 23%, 15%, and 7%, respectively. All of the rates from the standing orders ward were significantly greater than those from the computerized reminder ward (P < .0001). Only 0.6% of all patients on the control arm were vaccinated.Conclusion:Although both interventions were effective in increasing inpatient pneumococcal vaccination rates relative to baseline practice, physician independent initiation of standing orders was clearly more effective.
Surveillance for Transmission and antibiotic Adverse Events Among Neonates and Adults Exposed to a Healthcare Worker With Pertussis
Authors: Friedman Dara S. , Robinette Curtis C. , Schauer Stephanie L. , Salvi Susan , Klapholz Henry , Treadwell Thomas , Wortzman Jerry , Bisgard Kristine M. , Lett Susan M. 
Published: April 2006

AbstractBackground:During a hospital obstetric rotation, a medical student demonstrated classic symptoms of pertussis. The diagnosis was confirmed by isolation of Bordetella pertussis. Because this exposure occurred in a high-risk hospital setting, control measures were undertaken to prevent transmission and illness.Objectives:To identify secondary cases of pertussis, to determine compliance with chemoprophylaxis recommendations, and to monitor for adverse events associated with chemoprophylaxis following a hospital exposure to pertussis.Patients:More than 500 individuals were potentially exposed, including 168 neonates; antimicrobial chemoprophylaxis was administered to 281 individuals. Fifty-eight neonates and 194 adults began azithromycin chemoprophylaxis; 18 neonates and 2 adults began erythromycin chemoprophylaxis.Methods:Active surveillance was instituted for (1) secondary cases of pertussis among healthcare coworkers, obstetric patients, their neonates, and labor companions and (2) antibiotic compliance and tolerance.Results:No secondary cases of pertussis were confirmed by laboratory tests; however, 26 suspected cases and 5 clinically compatible cases were identified. Antibiotic courses were completed by 95% of the individuals who initiated therapy. Neonates taking azithromycin had statistically significantly less gastrointestinal distress compared with neonates taking erythromycin (12% vs 50%; P = .002); there were no cases of infantile hypertrophic pyloric stenosis.Conclusions:Although it was not possible to assess the effectiveness of the antibiotic regimens, the lack of laboratory-confirmed secondary cases suggests control measures were successful. Data from the 58 neonates who received azithromycin suggest it may be well tolerated in this age group.
Catheter-Associated Urinary Tract Infections in Intensive Care Units Can Be Reduced by Prompting Physicians to Remove Unnecessary Catheters
Authors: Huang Wei-Chun , Wann Shue-Ren , Lin Shoa-Lin , Kunin Calvin M. , Kung Ming-Ho , Lin Chin-Hsun , Hsu Chien-Wei , Liu Chun-Peng , Lee Susan Shin-Jung , Liu Yung-Ching , Lai Kwok-Hung , Lin Tzu-Wen 
Published: April 2006

AbstractObjective:Indwelling urinary catheters are the most common source of infections in intensive care units (ICUs). The aim of this study was to evaluate the efficacy of nurse-generated daily reminders to physicians to remove unnecessary urinary catheters 5 days after insertion.Design:A time-sequence nonrandomized intervention study.Setting:Adult ICUs (medical, surgical, cardiovascular surgical, neurosurgical, and coronary care) of a tertiary-care university medical center.Patients:All patients admitted to the adult ICUs during a 2-year period. The study consisted of a 12-month observational phase (15,960 patient-days) followed by a 12-month intervention phase (15,525 patient-days).Intervention:Daily reminders to physicians from the nursing staff to remove unnecessary urinary catheters 5 days after insertion.Results:The duration of urinary catheterization was significantly reduced during the intervention phase (from 7.0 ± 1.1 days to 4.6 ± 0.7 days; P < .001). The rate of catheter-associated urinary tract infection (CAUTI) was also significantly reduced (from 11.5 ± 3.1 to 8.3 ± 2.5 patients with CAUTI per 1,000 catheter-days; P = .009). There was a linear relationship between the monthly average duration of catheterization and the rate of CAUTI (r = 0.50; P = .01). The excess monthly cost of antibiotics for CAUTI was reduced by 69% (from $4,021 ± $1,800 to $1,220 ± $941; P = .004).Conclusion:This study demonstrated that a simple measure instituted as part of a continuous quality improvement program significantly reduced the duration of urinary catheterization, rate of CAUTI, and additional costs of antibiotics to manage CAUTI.
Nosocomial Pertussis Outbreak Among Adult Patients and Healthcare Workers
Authors: Bassinet Laurence , Matrat Mireille , Njamkepo Elisabeth , Aberrane Said , Housset Bruno , Guiso Nicole 
Published: April 2006

AbstractWe describe a pertussis outbreak among adult patients in a French general hospital following transmission from a healthcare worker. This index case transmitted pertussis to other healthcare workers, who, in turn, contaminated other staff and two immuno-suppressed patients. This raises questions about infection control.
Should Electronic Faucets Be Recommended in Hospitals?
Authors: Chaberny Iris F. , Gastmeier Petra 
Published: April 2006

AbstractMicrobiological examinations of electronic faucets newly installed in a hospital kitchen revealed high bacteria counts and Pseudomonas aeruginosa during a 6-month period of observation. Our data suggest that the use of electronic faucets poses a potential risk for nosocomial infection in high-risk areas of hospitals.
Colonization of Personal Digital Assistants Carried by Healthcare Professionals
Authors: Hassoun Ali , Vellozzi Ernestine M. , Smith Miriam A. 
Published: April 2006

AbstractThis study evaluated personal digital assistant (PDA) microbial colonization before and after cleaning with alcohol. Samples from 75 PDAs were processed. Before cleaning, 96% of the samples were culture positive. After cleaning, 75% became culture negative. PDAs cleaned with an alcohol swab demonstrated significant reduction in colonization.
Rapid Creation of a Temporary Isolation Ward for Patients With Severe Acute Respiratory Syndrome in Taiwan
Authors: Fung Chang-Phone , Hsieh Tsorng-Liu , Tan Kuang-Huan , Loh Chin-Hui , Wu Jiunn-Sheng , Li Chien-Chung , Chang Feng-Yee , Siu L. K. , Yen Moh-Yun , Wang Lih-Shinn , Wong Wing-Wai , Kao Wei-Fong , Hsu Jia-Hui , Lin Ting-Hsiang , Huang Fu-Yuan , Lee Chen-Hsen 
Published: April 2006

AbstractObjectives:To rapidly establish a temporary isolation ward to handle an unexpected sudden outbreak of severe acute respiratory syndrome (SARS) and to evaluate the implementation of exposure control measures by healthcare workers (HCWs) for SARS patients.Design:Rapid creation of 60 relatively negative pressure isolation rooms for 196 suspected SARS patients transferred from 19 hospitals and daily temperature recordings of 180 volunteer HCWs from 6 medical centers.Setting:A military hospital.Results:Of the 196 patients, 34 (17.3%) met the World Health Organization criteria for probable SARS with positive results of serologic testing for SARS-associated coronavirus (SARS-CoV), reverse transcriptase polymerase chain reaction (RT-PCR) from nasopharyngeal or throat swabs for SARS-CoV, or both. Seventy-four patients had suspected SARS based on unprotected exposure to SARS patients; three of them had positive results on RT-PCR but negative serologic results. The remaining 88 patients did not meet the criteria for a probable or suspected SARS diagnosis. Of the 34 patients with probable SARS, 13 were transferred to medical centers to receive mechanical ventilation due to rapid deterioration of chest x-ray results, and three patients died of SARS despite intensive therapy in medical centers. During the study period, one nurse developed probable SARS due to violation of infection control measures, but there was no evidence of cross-transmission to other HCWs.Conclusions:Despite the use of full personal protection equipment, the facility failed to totally prevent exposures of HCWs to SARS but minimized the risk of nosocomial transmission. Better training and improvements in infection control infrastructure may limit the impact of SARS.
A Large-Volume Nebulizer Would Not Be an Infectious Source for Severe Acute Respiratory Syndrome
Authors: Wan Gwo-Hwa , Tsai Ying-Huang , Wu Yao-Kuang , Tsao Kuo-Chien 
Published: April 2006

AbstractWe attempted to detect the presence of airborne SARS-coronavirus (CoV) in a healthcare setting when a patient with SARS used a humidifier or a large-volume nebulizer (LVN). All of the air samples from the humidifier and LVN were found to have negative SARS-CoV-specific DNA products.
Transmission of Tuberculosis Among Patients With Human Immunodeficiency Virus at a University Hospital in Brazil
Authors: Resende Mariângela R. , Villares Maria Cecília B. , Ramos Marcelo de C. 
Published: April 2006

AbstractThis study evaluated the IS6220-RFLP patterns of 109 Mycobacterium tuberculosis isolates of patients with HIV cared for at a Brazilian university hospital. Thirteen clusters involving 35 (32.1%) individuals were identified. Nosocomial transmission was possible in 5 cases. Strategies to prevent M. tuberculosis transmission should be implemented in hospitals in developing countries.
Timing of Intravenous Administration Set Changes: A Systematic Review
Authors: Gillies Donna , O'Riordan Libba , Wallen Margaret , Rankin Karen , Morrison Anne , Nagy Sue 
Published: April 2006

AbstractObjective:To determine the optimal time interval for the routine replacement of intravenous administration sets when crystalloids or parenteral nutrition are administered via a central or peripheral catheter in an acute care setting.Design:Systematic review of all randomized or systematically allocated controlled trials addressing the frequency of replacing intravenous administration sets.Methods:The Cochrane Controlled Trials Register (June 2001) and the Ovid databases (Medline, CINAHL, and CancerLit-July 2001) were searched. Bibliographies, relevant conference proceedings, and any product information were also checked for references.Results:Eighteen studies were selected for review. The 12 included studies were separated into 3 intravenous administration set change comparisons; 24 hours versus 48 hours or more; 48 hours versus 72 hours or more; and 72 hours versus 96 hours or more. There was good evidence that changing intravenous administration sets every 72 hours or more does not increase the risk of infusate-related bloodstream infection (BSI) in patients with central or peripheral catheters and a fair level of evidence that it does not increase the risk of catheter-related BSI. There were insufficient data regarding the incidence of BSI among patients receiving parenteral nutrition, particularly lipid-containing parenteral nutrition.Conclusions:It appears that intravenous administration sets containing crystalloids can be changed in patients with central or peripheral catheters every 72 hours or more without increasing the risk of BSI. However, it is not possible to conclude that intravenous administration sets containing parenteral nutrition, particularly lipid-containing parenteral nutrition, can be changed at this interval.
Infectivity of Prion Protein Bound to Stainless Steel Wires: A Model for Testing Decontamination Procedures for Transmissible Spongiform Encephalopathies
Authors: Yan Zheng-xin , Stitz Lothar , Heeg Peter , Pfaff Eberhard , Roth Klaus 
Published: April 2006

AbstractObjectives:To establish an animal model to study transmissible spongiform encephalopathy using hamsters and steel wires contaminated with infectious brain materials as transfer vehicles, and, based on this model, to test decontamination procedures against the infectious prion proteins on the steel wires as a near real situation bioassay.Design:Infectious brain materials were given to healthy hamsters intracerebrally either as a suspension or as dried materials on the surface of steel wires. The animals were observed for 18 months. During this period, animals showing definitive clinical signs were euthanized. Decontamination studies were performed by reprocessing contaminated steel wires with different disinfection agents and procedures before implantation.Results:Pathological prion proteins were able to bind to the steel wires and caused disease after the contaminated wires were implanted in the brains of hamsters. When the contaminated wires were treated with different reprocessing procedures before implantation, infectivity was reduced, which was manifested directly by prolonged survival time of the test animals. These results show that this model can be used as a bioassay to validate reprocessing procedures for surgical instruments.Conclusions:At the time of submission of this article, only the group of hamsters incubated with wires reprocessed with an alkaline detergent, followed by sterilization with a modified cycle in a hydrogen peroxide gas plasma sterilizer (4 injections), showed no clinical signs of disease and remained alive. Two animals from the group receiving sodium hydroxide followed by autoclaving (at 134° C for 18 minutes) died. Furthermore, the tested enzymatic cleaning agent seemed to have no positive effect.
Compliance with Local Guidelines for Antibiotic Prophylaxis in Surgery
Authors: Pons-Busom Montserrat , Aguas-Compaired Margarita , Delás Jordi , Eguileor-Partearroyo Begoña 
Published: April 2006

AbstractObjectives:To describe the development and implementation of a local protocol for antibiotic prophylaxis in surgery and to assess compliance with these guidelines using a computer-based system.Design:One 5-week prospective period (phase 1) followed by three 1-week, cross-sectional assessments (phases 2, 3, and 4).Setting:Pharmacy of a 350-bed acute care teaching hospital in Barcelona, Spain.Methods:In phase 1, 395 forms for antibiotic prescribing delivered to the pharmacy were reviewed. Nonadherence was defined as the prescription of an antibiotic (or doses) different from what the protocol specified. In phases 2, 3, and 4, antibiotic prescribing forms for all elective procedures (630 patients) performed during 1-week periods were analyzed.Results:A total of 1,047 patients (mean age, 58.9 ± 17.3 years) were included. Cefazolin was administered in 41% of procedures. Overall compliance with antibiotic prescribing forms was 83.3%. There was a statistically significant increase in compliance with guidelines throughout the four phases of the study, from 80.3% in phase 1 to 87.8% in phase 4 (P < .042), as well as adherence to completing forms for surgical procedures, from 51% in phase 2 to 77.6% in phase 4 (P < .001). The main reason for non-adherence was that some procedures had not been included in the protocol in phase 2.Conclusion:Surgeons sensitized to the implementation of local antibiotic prophylaxis guidelines showed a high degree of compliance with them, using both the procedure established for antibiotic prescribing and the antimicrobials recommended for particular operations.