bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lessons learned in systems change initiatives: benchmarks and indicators
Authors: Kreger Mary , Brindis Claire D. , Manuel Diane M. , Sassoubre Lauren 
Published: May 2007

AbstractMeasuring progress toward systems change, sustainable efforts that address root causes of an issue by changing policies and practices, is a difficult task for communities, evaluators, and foundations. Tracking and documenting changes in resources, power, policy, sustainable funding, structured relationships and roles, and underlying values require multi‐level analyses. Systems change analysts must consider at least four “strata” at once: (1) events and trends, (2) patterns of interaction, (3) context and cultural or social models, and (4) the systems themselves. In this paper we provide a brief overview of systems change; a discussion of collaboratives as one “engine” of social change; a discussion of benchmarks and indicators of collaboratives focused on systems change; and suggestions for further research. The analysis draws upon several analytic frameworks described in the literature. We illustrate these concepts with examples from six systems change initiatives funded by The California Endowment. The need for further research is outlined.
A trial with N‐carbamylglutamate may not detect all patients with NAGS deficiency and neonatal onset
Authors: Nordenström A. , Halldin M. , Hallberg B. , Alm J. 
Published: May 2007

SummaryN‐Acetylglutamate synthase (NAGS) deficiency is a rare urea cycle disorder. An effective treatment, N‐carbamoyl‐l‐glutamic acid (NCGA), is now available, increasing the importance of identifying and treating these patients early. We describe a case with genetically verified NAGS deficiency and neonatal onset of severe hyperammonaemia. The ammonia levels increased above 1400 μmol/L. The patient did not respond to NCGA treatment during the first 15 h, indicating that a delayed response or no response cannot be used as a safe indicator for excluding NAGS deficiency in the acute situation. Hence, conventional treatment should not be delayed by a diagnostic procedure, such as a loading test. Furthermore, at 3 years of age this patient has normal psychomotor development, underlining the possibility of a favourable outcome despite markedly elevated ammonia levels, coma, and seizures in the neonatal period. Including NCGA early in the treatment of patients with hyperammonaemia may be of clinical importance. In order to detect patients with NAGS deficiency and neonatal onset and to optimize care, it is important to use the available treatment strategies to reduce plasma ammonia concentrations without delay. We propose the use of combined symptomatic treatment, i.e. glucose infusion, sodium benzoate, arginine or citrulline, and when indicated haemodialysis, as well as NCGA treatment in all neonates presenting with severe hyperammonaemia. The treatment should be continued until laboratory investigations are complete or indicate another disorder.
Impact of Different Methods for Describing the Extent of Prior Antibiotic Exposure on the Association Between Antibiotic Use and Antibiotic-Resistant Infection
Authors: Hyle Emily P. , Bilker Warren B. , Gasink Leanne B. , Lautenbach Ebbing 
Published: May 2007

Objective.Many studies have investigated the association between prior antibiotic use and antibiotic resistance. However, methods used in past studies to describe the extent of prior antibiotic use (eg, use of the 2 categories exposure versus no exposure and measurement of duration of exposure) have not been reviewed. The impact of the use of different methods for quantifying the use of antibiotics is unknown. The objectives of this study were to characterize past approaches to describing the extent of antibiotic use and to identify the impact of the use of different methods on associations between use of specific antibiotics and infection with an antibiotic-resistant-organism.Methods.We conducted a systematic review of studies that investigated risk factors for extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and Klebsiella species to identify variability in past approaches to describing the extent of antibiotic use. We then reanalyzed a data set from a prior study of risk factors for infection with ESBL-producing E. coli and Klebsiella species. We developed 2 separate multivariable models: 1 in which prior antibiotic use was described as a categorical variable (eg, exposure or no exposure) and 1 in which antibiotic use was described as a continuous variable (eg, measured in antibiotic-days). These models were compared qualitatively.Setting.Large academic medical center.Results.The 25 articles included in the systematic review revealed a variety of methods used to describe the extent of prior antibiotic exposure. Only 1 study justified its approach. Results from the 2 multivariable models that used different methodologic approaches differed substantially. Specifically, use of third-generation cephalosporins was a risk factor for infection with ESBL-producing E. coli and Klebsiella species when antibiotic use was described as a continuous variable but not when antibiotic use was described as a categorical variable.Conclusions.There has been no consistent method for assessing the extent of prior antibiotic exposure. The use of different methods may substantially alter the identified antimicrobial risk factors, which has important implications for the resultant interventions regarding antimicrobial use.
Epidemiology and Genetic Diversity of Methicillin-ResistantStaphylococcus aureusStrains in Residential Care Homes for Elderly Persons in Hong Kong
Authors: Ho Pak-Leung , Wang Teresa K. F. , Ching Patricia , Mak Gannon C. , Lai Eileen , Yam Wing-Cheong , Seto Wing-Hong 
Published: May 2007

Objective.To determine the prevalence and molecular epidemiology of methicillin-resistantStaphylococcus aureus(MRSA) strains among residents in residential care homes for the elderly in Hong Kong.Design.Cross-sectional and descriptive study.Participants.A total of 949 residents in 13 residential care homes for elderly persons in Hong Kong in January 2005.Methods.MRSA colonization was assessed by culture of swab specimens from anterior nares and active skin lesions. Characteristics of residents were obtained by a standard questionnaire. All MRSA isolates were analyzed by polymerase chain reaction for their staphylococcal cassette chromosome (SCC)meccontent and were typed by pulsed-field gel electrophoresis (PFGE) and multilocus sequencing.Results.MRSA colonization was detected in 27 residents (2.8%). No MRSA was found in 2 facilities. The rate of MRSA carriage in the other 11 facilities ranged from 1.9% to 4.2%. In univariate analysis, functional immobility (odds ratio [OR], 1.4), history of hospital admission (OR, 2.3), and the use of nebulized medication (OR, 5.4) were significantly associated with MRSA colonization. The isolates had 11 unique antibiograms, with 14 isolates susceptible to all but 1 or 2 of the non-β-lactam antimicrobial agents tested. The isolates exhibited SCCmectypes I (1 isolate), II (2 isolates), III (1 isolate), IV/IVA (10 isolates), and V (13 isolates). No isolates had the Panton-Valentine leukocidin genes. PFGE analysis clustered all except 1 isolate into 7 PFGE types, designated HKU10 to HKU70. Between 1 and 4 unique PFGE types were found in the individual residential care facilities.Conclusion.This study documented the emergence of SCCmec types IV and V among genetically diverse MRSA strains in residential care homes for elderly persons in Hong Kong.
Risk of Transmission Associated With Live Attenuated Vaccines Given to Healthy Persons Caring for or Residing With an Immunocompromised Patient
Authors: Kamboj Mini , Sepkowitz Kent A. 
Published: May 2007

Objective.Persons who receive live attenuated vaccine may occasionally transmit the vaccine strain to others. The risk of such transmission is a concern, especially for persons who provide care to immunocompromised patients (ie, family and healthcare workers [HCWs]). Since the Advisory Committee on Immunization Practices released guidelines 10 years ago, several new live attenuated products have been introduced, and additional information on older vaccines has become available. To better define the risk of transmission associated with live vaccines, we reviewed the currently available literature.Results.A review of the medical literature revealed no major risk of transmission associated with any live attenuated vaccine. A theoretical risk continues to exist for the live attenuated intranasal influenza vaccine and the smallpox vaccine.Conclusions.The available data support routine vaccination with live attenuated vaccines for all household contacts of immunocompromised patients and for HCWs caring for such Patients. The benefit for immunocompromised patients of providing herd immunity against this group of potentially devastating pathogens outweighs the risk, if any, of secondary transmission.
Exposure to Pulmonary Tuberculosis in a Neonatal Intensive Care Unit: Unique Aspects of Contact Investigation and Management of Hospitalized Neonates
Authors: Nania Joseph Jacob , Skinner Jena , Wilkerson Kathie , Warkentin Jon V. , Thayer Valerie , Swift Melanie , Schaffner William , Talbot Thomas R. 
Published: May 2007

Objective.We describe the investigation of a tuberculosis (TB) exposure in which a neonatal intensive care unit (NICU) respiratory therapist was the index patient, as well as the rationale by which exposed infants were managed and possible explanations for the lack of transmission to these patients.Design.Description of an exposure investigation.Setting.Academic, level IV NICU of a tertiary care children's hospital.Participants.Contacts of a respiratory therapist with pulmonary TB disease, including household members, healthcare coworkers, and infant patients.Results.In addition to 5 household contacts, 248 healthcare coworkers and 180 infant patients were identified as possibly exposed during the 24 days that the index patient worked between December 3, 2004, and January 30, 2005. Tuberculin skin tests (TSTs) were performed for 233 of the 235 contacts with the greatest degree of exposure (household and coworker contacts) who had a previously documented negative TST result or whose TST status was unknown prior to the investigation. No cases of latent tuberculosis infection or TB disease were identified. Because of characteristics of the index case, the exposure duration and setting, the infants' small lung volumes, and lack of evidence of transmission to higher-risk contacts, infants were not clinically evaluated or empirically treated for TB disease. Surveillance for subsequent illness was carried out by primary healthcare providers and parents. No TB disease or unexplained illness in these infants was reported in the 20 months following the exposure.Conclusion.After limited hospital exposure to a healthcare worker with pulmonary TB disease who is not highly contagious, neonates can be safely managed without specific evaluation for TB disease or empirical treatment.
Impact of Different Methods of Feedback to Clinicians After Postprescription Antimicrobial Review Based on the Centers for Disease Control and Prevention's 12 Steps to Prevent Antimicrobial Resistance Among Hospitalized Adults
Authors: Cosgrove Sara E. , Patel Alpa , Song Xiaoyan , Miller Robert E. , Speck Kathleen , Banowetz Amy , Hadler Rachel , Sinkowitz-Cochran Ronda L. , Cardo Denise M. , Srinivasan Arjun 
Published: May 2007

Objectives.To evaluate (1) the framework of the 12 Steps to Prevent Antimicrobial Resistance Among Hospitalized Adults that is part of the Centers for Disease Control and Prevention (CDC) Campaign to Prevent Antimicrobial Resistance in Healthcare Settings, with regard to steps addressing antimicrobial use; and (2) methods of feedback to clinicians regarding antimicrobial use after postprescription review.Design.Prospective intervention to identify and modify inappropriate antimicrobial therapy.Setting.A 1,000-bed, tertiary care teaching hospital.Patients.Inpatients in selected medicine and surgery units receiving broad-spectrum antimicrobials for 48-72 hours.Interventions.We created a computer-based clinical-event detection system that automatically identified inpatients taking broad-spectrum and “reserve” antimicrobials for 48-72 hours. Although prior approval was required for initial administration of broad-spectrum and reserve antimicrobials, once approval was obtained, therapy with the antimicrobials could be continued indefinitely at the discretion of the treating clinician. Therapy that was ongoing at 48-72 hours was reviewed by an infectious diseases pharmacist or physician, and when indicated feedback was provided to clinicians to modify or discontinue therapy. Feedback was provided via a direct telephone call, a note on the front of the medical record, or text message sent to the clinician's pager. The acceptance rate of feedback was recorded and recommendations were categorized according to the 12 steps recommended by the CDC.Results.Interventions were recommended for 334 (30%) of 1,104 courses of antimicrobial therapy reviewed. A total of 87% of interventions fit into one of the CDC's 12 steps of prevention: 39% into step 3 (“target the pathogen”), 1% into step 4 (“access experts”), 3% into steps 7 and 8 (“treat infection, not colonization or contamination”), 18% into step 9 (“say ‘no’ to vancomycin”), and 26% into step 10 (“stop treatment when no infection”). The rate of compliance with recommendations to improve antimicrobial use was 72%. No differences in compliance were seen with the different methods of feedback.Conclusions.Nearly one-third of antimicrobial courses did not follow the CDC's recommended 12 steps for prevention of antimicrobial resistance. Clinicians demonstrated high compliance with following suggestions made after postprescription review, suggesting that it is a useful approach to decreasing and improving antimicrobial use among inpatients.
Increase in the Rate of Sternal Surgical Site Infection After Coronary Artery Bypass Graft: A Marker of Higher Severity of Illness
Authors: Fakih Mohamad G. , Sharma Mamta , Khatib Riad , Berriel-Cass Dorine , Meisner Susan , Harrington Steven , Saravolatz Louis 
Published: May 2007

Objective.To evaluate factors related to a gradual rise in sternal surgical site infection (SSI) rates.Design.Retrospective cohort study.Setting.A 608-bed, tertiary care teaching hospital.Patients.All patients who underwent coronary artery bypass graft (CABG) from January 2000 through September 2004.Results.Of 3,578 patients who underwent CABG, 144 (4%) had sternal SSI. There was an increase in infection rate, with a marked reduction in the number of operations per year. The percentage of patients with peripheral vascular disease increased from 12% to 24.3% (P < .001), and the percentage with congestive heart failure increased from 17% to 22% (P < .001). Between 2002 and 2004, the mean duration of surgery increased from 233 to 290 minutes (P < .001), the percentage of patients with a National Nosocomial Infections Surveillance System (NNIS) risk index of 2 increased from 14.3% to 38% (P < .001), and the percentage of patients with a postoperative stay in the intensive care unit of greater than 72 hours increased from 29% to 40.6% (P < .001). Multivariate analysis showed diabetes mellitus, peripheral vascular disease, obesity, duration of surgery, and postoperative stay in the intensive care unit of greater than 72 hours to be independently associated with infection.Conclusions.An increase in infection in the CABG population not associated with an outbreak may be a reflection of a change in the severity of illness. Preoperative, intraoperative, and postoperative markers for increased infection risk may be used, in addition to the NNIS risk index, to assess the patient population risk.
T-Pile—a package for thermodynamic calculations for biomolecules
Authors: Gront Dominik , Kolinski Andrzej 
Published: May 2007

AbstractSummary: Molecular dynamics and Monte Carlo, usually conducted in canonical ensemble, deliver a plethora of biomolecular conformations. Proper analysis of the simulation data is a crucial part of biophysical and bioinformatics studies. Sequence alignment problem can be also formulated in terms of Boltzmann distribution. Therefore tools for efficient analysis of canonical ensemble data become extremely valuable. T-Pile package, presented here provides a user-friendly implementation of most important algorithms such as multihistogram analysis and reweighting technique. The package can be used in studies of virtually any system governed by Boltzmann distribution.Availability: T-Pile can be downloaded from: http://biocomp.chem.uw.edu.pl/services/tpile. These pages provide a comprehensive tutorial and documentation with illustrative examples of applications.Contact: dgront@chem.uw.edu.plSupplementary information: Supplementary data are available at Bioinformatics online.
Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations
Authors: Toleno Donna M. , Morrell Peter L. , Clegg Michael T. 
Published: May 2007

AbstractMotivation: Errors in nucleotide sequence and SNP genotyping data are problematic when inferring haplotypes. Previously published methods for error detection in haplotype data make use of pedigree information; however, for many samples, individuals are not related by pedigree. This article describes a method for detecting errors in haplotypes by considering the recombinational history implied by the patterns of variation, three SNPs at a time.Results: Coalescent simulations provide evidence that the method is robust to high levels of recombination as well as homologous gene conversion, indicating that patterns produced by both proximate and distant SNPs may be useful for detecting unlikely three-site haplotypes.Availability: The perl script implementing the described method is called EDUT (Error Detection Using Triplets) and is available on request from the authors.Contact: mclegg@uci.eduSupplementary information: Supplementary data are available at Bioinformatics online.
An evaluation of automated homology modelling methods at low target–template sequence similarity
Authors: Dalton James A. R. , Jackson Richard M. 
Published: May 2007

AbstractMotivation: There are two main areas of difficulty in homology modelling that are particularly important when sequence identity between target and template falls below 50%: sequence alignment and loop building. These problems become magnified with automatic modelling processes, as there is no human input to correct mistakes. As such we have benchmarked several stand-alone strategies that could be implemented in a workflow for automated high-throughput homology modelling. These include three new sequence-structure alignment programs: 3D-Coffee, Staccato and SAlign, plus five homology modelling programs and their respective loop building methods: Builder, Nest, Modeller, SegMod/ENCAD and Swiss-Model. The SABmark database provided 123 targets with at least five templates from the same SCOP family and sequence identities ≤50%.Results: When using Modeller as the common modelling program, 3D-Coffee outperforms Staccato and SAlign using both multiple templates and the best single template, and across the sequence identity range 20–50%. The mean model RMSD generated from 3D-Coffee using multiple templates is 15 and 28% (or using single templates, 3 and 13%) better than those generated by Staccato and Salign, respectively. 3D-Coffee gives equivalent modelling accuracy from multiple and single templates, but Staccato and SAlign are more successful with single templates, their quality deteriorating as additional lower sequence identity templates are added. Evaluating the different homology modelling programs, on average Modeller performs marginally better in overall modelling than the others tested. However, on average Nest produces the best loops with an 8% improvement by mean RMSD compared to the loops generated by Builder.Contact: r.m.jackson@leeds.ac.uk.Supplementary information: Supplementary data are available at Bioinformatics online.
Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays
Authors: Laakso Marko , Tuupanen Sari , Karhu Auli , Lehtonen Rainer , Aaltonen Lauri A. , Hautaniemi Sampsa 
Published: May 2007

AbstractMotivation: Single nucleic polymorphisms (SNPs) are one of the most abundant genetic variations in the human genome. Recently, several platforms for high-throughput SNP analysis have become available, capable of measuring thousands of SNPs across the genome. Tools for analysing and visualizing these large genetic data sets in biologically relevant manner are rare. This hinders effective use of the SNP-array data in research on complex diseases, such as cancer.Results: We describe a computational framework to analyse and visualize SNP-array data, and link the results in relevant databases. Our major objective is to develop methods for identifying DNA regions that likely harbour recessive mutations. Thus, the algorithms are designed to have high sensitivity and the identified regions are ranked using a scoring algorithm. We have also developed annotation tools that automatically query gene IDs, exon counts, microarray probe IDs, etc. In our case study, we apply the methods for identifying candidate regions for recessively inherited colorectal cancer predisposition and suggest directions for wet-lab experiments.Availability: R-package implementation is available at http://www.ltdk.helsinki.fi/sysbio/csb/downloads/CohortComparator/Contact: sampsa.hautaniemi@helsinki.fiSupplementary information: Supplementary data are available at Bioinformatics online.
Statistical prediction of protein–chemical interactions based on chemical structure and mass spectrometry data
Authors: Nagamine Nobuyoshi , Sakakibara Yasubumi 
Published: May 2007

AbstractMotivation: Prediction of interactions between proteins and chemical compounds is of great benefit in drug discovery processes. In this field, 3D structure-based methods such as docking analysis have been developed. However, the genomewide application of these methods is not really feasible as 3D structural information is limited in availability.Results: We describe a novel method for predicting protein–chemical interaction using SVM. We utilize very general protein data, i.e. amino acid sequences, and combine these with chemical structures and mass spectrometry (MS) data. MS data can be of great use in finding new chemical compounds in the future. We assessed the validity of our method in the dataset of the binding of existing drugs and found that more than 80% accuracy could be obtained. Furthermore, we conducted comprehensive target protein predictions for MDMA, and validated the biological significance of our method by successfully finding proteins relevant to its known functions.Availability: Available on request from the authors.Contact: yasu@bio.keio.ac.jpSupplementary information: Appendix–technical details of method, Supplementary Table 1–7 and Supplementary Figure 1.