bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decrease in Staphylococcus aureus Colonization and Hospital-Acquired Infection in a Medical Intensive Care Unit after Institution of an Active Surveillance and Decolonization Program
Authors: Fraser Thomas G. , Fatica Cynthia , Scarpelli Michele , Arroliga Alejandro C. , Guzman Jorge , Shrestha Nabin K. , Hixson Eric , Rosenblatt Miriam , Gordon Steven M. , Procop Gary W. 
Published: July 2010

Objective.To evaluate the effects of an active surveillance program for Staphylococcus aureus linked to a decolonization protocol on the incidence of healthcare-associated infection and new nasal colonization due to S. aureus.Design.Retrospective quasi-experimental study.Setting.An 18-bed medical intensive care unit at a tertiary care center in Cleveland, Ohio.Methods.From January 1, 2006, through December 31, 2007, all patients in the medical intensive care unit were screened for S. aureus nasal carriage at admission and weekly thereafter. During the preintervention period, January 1 through September 30,2006, only surveillance occurred. During the intervention period, January 1 through December 31,2007, S. aureus carriers received mupirocin intranasally. Beginning in February 2007, carriers also received Chlorhexidine gluconate baths.Results.During the preintervention period, 604 (73.7%) of 819 patients were screened for S. aureus nasal carriage, yielding 248 prevalent carriers (30.3%). During the intervention period, 752 (78.3%) of 960 patients were screened, yielding 276 carriers (28.8%). The incidence of S. aureus carriage decreased from 25 cases in 3,982 patient-days (6.28 cases per 1,000 patient-days) before intervention to 18 cases in 5,415 patient-days (3.32 cases per 1,000 patient-days) (P = .04; relative risk [RR], 0.53 [95% confidence interval {CI}, 0.28-0.97]) and from 9.57 to 4.77 cases per 1,000 at-risk patient-days (P = .02; RR, 0.50 [95% CI, 0.27-0.91]). The incidence of S. aureus hospital-acquired bloodstream infection during the 2 periods was 2.01 and 1.11 cases per 1,000 patient-days, respectively (P = .28). The incidence of S. aureus ventilator-associated pneumonia decreased from 1.51 to 0.18 cases per 1,000 patient-days (P = .03; RR, 0.12 [95% CI, 0.01-0.83]). The total incidence of S. aureus hospital-acquired infection decreased from 3.52 to 1.29 cases per 1,000 patient-days (P = .03; RR, 0.37 [95% CI, 0.14-0.90]).Conclusions.Active surveillance for S. aureus nasal carriage combined with decolonization was associated with a decreased incidence of S. aureus colonization and hospital-acquired infection.
MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus
Authors: Ewing Gregory , Hermisson Joachim 
Published: July 2010

Abstract
Motivation: We have implemented a coalescent simulation program for a structured population with selection at a single diploid locus. The program includes the functionality of the simulator ms to model population structure and demography, but adds a model for deme- and time-dependent selection using forward simulations. The program can be used, e.g. to study hard and soft selective sweeps in structured populations or the genetic footprint of local adaptation. The implementation is designed to be easily extendable and widely deployable. The interface and output format are compatible with ms. Performance is comparable even with selection included.
Availability: The program is freely available from http://www.mabs.at/ewing/msms/ along with manuals and examples. The source is freely available under a GPL type license.
Contact: gregory.ewing@univie.ac.at
Supplementary information: Supplementary data are available at Bioinformatics online.
Clinical and Nutritional Outcomes in Children With Idiopathic Superior Mesenteric Artery Syndrome
Authors: Shiu Jr‐Rung , Chao Hsun‐Chin , Luo Chih‐Cheng , Lai Ming‐Wei , Kong Man‐Shan , Chen Shih‐Yen , Chen Chien‐Chang , Wang Chao‐Jan 
Published: July 2010

ABSTRACTObjective:There are no available data for outcomes in children's idiopathic superior mesenteric artery syndrome (SMAS) strictly treated conservatively. The aim of the study was to evaluate clinical and nutritional outcome in children with idiopathic SMAS.Patients and Methods:A 1‐year prospective observation study of effects of treatment and outcome was performed in 27 children (8 boys, 19 girls) with idiopathic SMAS who underwent an upper gastrointestinal (UGI) series, ultrasound measurement of the aortomesenteric angle, treatment, clinical assessment, growth evaluation, and regular clinical visits for more than 12 months.Results:Mean age of the patients was 11.77 ± 2.15 years. The major clinical complaints were postprandial pain or fullness (88.9%), vomiting (55.6%), and early satiety (51.9%). Eight patients (29.6%) had weight loss. The UGI series revealed typical features of SMAS. The aortomesenteric angle on ultrasound was 10° to 19°. The height of most patients (92.6%) was above the 10th percentile, whereas 15 (55.6%) patients weighed below the 10th percentile. Six patients underwent surgical intervention (3 for obstruction and 3 for persistent anorexia with weight loss), and their clinical symptoms and weight status improved steadily during the follow‐up months. Among the 21 patients not subject to surgical intervention, 11 (52.4%) experienced a reduction of symptoms >50% after 3 months of treatment, and weight‐for‐age percentile increased significantly after 6 months of treatment. Overall, a significant increase in the weight‐for‐age status was seen in the patients with surgical treatment or with medication only after 6 and 12 months of treatment.Conclusions:An aortomesenteric angle <20° is a constant phenomenon in children with idiopathic SMAS. A duodenojejunostomy can effectively relieve the obstructive symptoms, such as anorexia, and improve nutritional status, whereas long‐term medical treatment may aid in relieving the clinical symptoms, promoting appetite, and improving nutritional status in pediatric patients with idiopathic SMAS.
Incidental Gastric Eosinophils in Patients With Eosinophilic Esophagitis: Do They Matter?
Authors: Ammoury Rana F , Rosenman Marc B , Roettcher Donita , Gupta Sandeep K 
Published: July 2010

ABSTRACTBackground and Aim:Some patients with eosinophilic esophagitis (EE) (>15 eosinophils/high‐power field on esophageal mucosal biopsies and lack of response to acid suppression and/or normal pH probe study) demonstrate incidental eosinophilic inflammation of the gastric mucosa. It is unclear whether patients with EE and normal gastric biopsies (EE‐N) are phenotypically different from patients with EE and gastric mucosal abnormalities (EE‐A) (ie, >10 eos/hpf on gastric biopsies). The aim of the study was to compare the clinical features and response to therapy among patients with EE‐N and EE‐A.Patients and Methods:Medical records of all of the EE‐A and a random group of patients with EE‐N diagnosed during an 8‐year period were reviewed. A subgroup analysis of patients treated with swallowed fluticasone with a repeat esophagogastroduodenoscopy within 6 months of starting therapy was also performed.Results:During the study period, 41 patients had EE‐A. When compared to 50 random patients with EE‐N, no clinical differences were noted, including sex, age, presenting symptoms, esophageal histology, and atopy history. Eleven (27%) of the 41 EE‐A and 14 (28%) of the 50 EE‐N patients were treated with swallowed fluticasone, and the response was similar among the groups. The mean esophageal eosinophils/high‐power field among the EE‐A group dropped from 47 to 8 compared with a 46 to 7 drop among the EE‐N group treated with fluticasone therapy (P = 0.91). In 9 (82%) of the 11 patients with EE‐A treated with fluticasone, there was resolution (7 of 9) or significant improvement (2 of 9) of gastric eosinophilia.Conclusions:Patients with EE‐A and EE‐N have similar clinical presentations. Incidental gastric inflammation does not predict a worse response of esophageal inflammation to fluticasone and should not exclude its use in patients with EE‐A. In fact, gastric inflammation responded to swallowed fluticasone in the majority of patients with EE‐A. This observation should foster further investigation into pathogenesis of EE and presumed esophagogastric inflammatory axis.
Thawing Embryonic Stem (ES) Cells from a 96-Well Plate
Authors: Nagy Andras , Gertsenstein Marina , Vintersten Kristina , Behringer Richard 
Published: July 2010

INTRODUCTIONThe most widely used method to alter the genome of embryonic stem (ES) cells is to introduce a specifically designed DNA fragment using electroporation. The DNA will then integrate into the genome of ES cells. Colonies of cells containing the exogenous DNA are then picked, expanded, replica-plated, frozen in 96-well plates, and used as a source for genomic DNA preparation for genotyping. After ES candidate clones are identified by genomic Southern blot or polymerase chain reaction (PCR), the method of rescue of the cells from the frozen 96-well plates is very important. This protocol describes a method for thawing such cells.
Purification of Mediator from HeLa Cell Lines Expressing a Flag-Tagged Mediator Subunit
Authors: Carey Michael F. , Peterson Craig L. , Smale Stephen T. 
Published: July 2010

INTRODUCTIONThe Mediator (Med) complex plays a key role in promoter-specific activation of transcription by RNA polymerase II (Pol II). Med is a major target of activators and can be used in many types of affinity binding and immobilized template studies to evaluate interactions with individual activators. Additionally, all of the Med subunits have been cloned and can be subjected to individual structure-function analyses to learn how a specific activator interacts with a particular subunit. This protocol presents a simple affinity-based method to purify Med complex from HeLa cells stably expressing the Flag-tagged Intersex protein.
In Vivo Imaging of Tumors
Authors: Brown Edward , Munn Lance L. , Fukumura Dai , Jain Rakesh K. 
Published: July 2010

INTRODUCTIONLight microscopy of tumors, as for other thick, scattering tissues such as the brain or the developing embryo, is limited by light penetration and optical access. because of these problems, epifluorescence and confocal microscopy are typically limited to the outer 50-100 μm of the accessible tumor tissue. Most mouse tumors must be exteriorized for examination under the light microscope, a procedure that limits the duration and repeatability of imaging. this protocol describes the generation of chronic window preparations in the mouse. These preparations allow an implanted tumor to grow for several weeks in an optically accessible location in vivo, making it possible to examine the living tumor with high-resolution light microscopy in a repetitive manner. Two chronic window preparations are described: (1) the dorsal skinfold chamber, which allows in vivo imaging of tumors growing in the subcutaneous space, and (2) the cranial window, which allows in vivo imaging of tumors growing on the brain surface.
Electrophysiological Recordings from the Drosophila Giant Fiber System (GFS)
Authors: Allen Marcus J. , Godenschwege Tanja A. 
Published: July 2010

INTRODUCTIONThe giant fiber system (GFS) of Drosophila is a well-characterized neuronal circuit that mediates the escape response in the fly. It is one of the few adult neural circuits from which electrophysiological recordings can be made routinely. This protocol describes a simple procedure for stimulating the giant fiber neurons directly in the brain of the adult fly and obtaining recordings from the output muscles of the GFS: the tergotrochanteral “jump” muscle (TTM) and the large indirect flight muscles (dorsal longitudinal muscles, or DLMs). It is a relatively noninvasive method that allows the investigator to stimulate the giant fibers in the brain and assay the function of several central synapses within this neural circuit by recording from the thoracic musculature.
Enzymatic Method for Extracting Extracellular DNA in Biofilm Matrix
Authors: Wu Jianfeng , Xi Chuanwu 
Published: July 2010

INTRODUCTIONBiofilm is an accumulation of bacterial cells encapsulated in a structurally assembled extracellular polymer matrix that adheres to surfaces. The extracellular polymer matrix is composed mainly of polysaccharides, proteins, and amphiphilic polymers, which are secreted by microorganisms into their environment. Extracellular DNA (eDNA) was recently identified as one of the major components of extracellular polymeric substances (EPSs) and plays an important role in the development of biofilm, especially the early stages, by facilitating initial bacterial attachment and maintaining biofilm structure. More research is needed to fully elucidate the role of eDNA in biofilm development, and such investigations require that extraction of eDNA from the complex biofilm matrix is achieved without any genomic DNA contamination. However, the physical and chemical association of eDNA with extracellular proteins, polysaccharides, and other polymers in the complex matrix of EPS may hinder the liberation of eDNA. Therefore, it is difficult to release eDNA and other materials from the biofilm matrix solely by vortexing or homogenizing, and degradation of certain components of EPSs in the biofilm matrix is necessary in order to release eDNAs that may bind to these compounds. In this protocol, N-glycanase (glycoprotein-degradation hydrolase), dispersin B (biofilm-dispersing glycoside hydrolase), and proteinase K (protein hydrolase) are used to break down biofilm matrix for more efficient and complete extraction of eDNA.
EdU (5-Ethynyl-2′-Deoxyuridine) Labeling of Drosophila Mitotic Neuroblasts: Figure 1.
Authors: Daul Aric L. , Komori Hideyuki , Lee Cheng-Yu 
Published: July 2010

INTRODUCTIONWhen examining mutants that affect cell fate as a result of altered asymmetric division patterns, it is important to determine whether cells are mitotically active. Chemical labeling of newly synthesized DNA (during S-phase) by incorporation of BrdU (5-bromo-2′-deoxyuridine) is informative because this thymidine analog can be used to pulse-label dividing cells and then chased to identify the progeny of dividing cells. Such pulse-chase experiments can provide additional insight by distinguishing actively dividing cells from those that might be arrested at a mitotic checkpoint. EdU (5-ethynyl-2′-deoxyuridine) is another thymidine analog that provides a more sensitive and practical alternative to BrdU. Incorporation of EdU is detected through its reaction with an azide dye that is small enough to penetrate tissues efficiently. Visualization of EdU is rapid and does not interfere with subsequent antibody staining. The use of EdU in labeling Drosophila mitotic neuroblasts is described here.
Efficacy, tolerability and pharmacokinetics of a modified release formulation of ADX10059, a negative allosteric modulator of metabotropic glutamate receptor 5: an esophageal pH‐impedance study in healthy subjects
Authors: Zerbib F. , Keywood C. , Strabach G. 
Published: July 2010

AbstractBackground  Animal studies show metabotropic glutamate receptor 5 inhibition reduces transient lower esophageal sphincter relaxations and increases lower esophageal sphincter tone. A preliminary, single‐day study, demonstrated oral ADX10059 reduced 24‐h esophageal acid exposure and clinical symptoms in gastro‐esophageal reflux disease (GERD) patients, but had suboptimal tolerability, ascribable to the compound’s rapid absorption. This study evaluated ADX10059 modified‐release (MR) formulation pharmacokinetics, tolerability, and pharmacodynamics.Methods  Randomized, double‐blind placebo‐controlled study. Three groups of eight healthy, male subjects received placebo (n = 2) or ADX10059 (n = 6) 50, 125 or 250 mg b.i.d. for 6 days. Esophageal pH‐impedance was performed on day 1 and day 6 of treatment, for 1‐h fasting and for 4 h post refluxogenic meal. Treatment effect was determined by Kruskall–Wallis test and placebo comparison by Wilcoxon rank sum.Key Results  Following placebo, reflux episodes increased from day 1 to day 6. Significant treatment effect was seen for total esophageal acid exposure (P = 0.048) and postprandial number of weakly acidic reflux episodes (P = 0.041). Significant differences from placebo were seen for 125 mg b.i.d.; 250 mg b.i.d. was not more effective than 125 mg b.i.d. Twice daily ADX10059 MR gave satisfactory 24‐h exposure and good tolerability.Conclusions & Inferences  ADX10059 decreased reflux episodes in healthy subjects. The MR formulation is suitable for longer‐term treatment to evaluate symptom control in GERD patients.
Oxidative‐inflammatory damage in cirrhosis: Effect of vitamin E and a fermented papaya preparation
Authors: Marotta Francesco , Yoshida Chisato , Barreto Rafael , Naito Yasuhiro , Packer Lester 
Published: July 2010

AbstractBackground and Aim:  Oxidative DNA damage occurs as an early event in hepatitis C virus (HCV) infection and is an indication of the potential for carcinogenesis. The aim of this study was to test a novel antioxidant/immunomodulator in patients with HCV‐related cirrhosis.Methods:  The study group consisted of 50 patients with HCV‐related cirrhosis with transaminase values less than twofold increased (alanine aminotransferase [ALT] < 80 IU/L). Patients underwent a standardized food‐vitamin composition assessment and were assessed for dietary intake, nutritional status and iron level. Patients were randomly allocated into two groups and then given either α‐tocopherol 900 IU/day or 9 g/day of a fermented papaya preparation (FPP, Immun‐Age, Osato Research Institute, Gifu, Japan) at bedtime for 6 months. Ten healthy subjects served as controls. Patients were checked monthly for: routine tests, redox status (reduced glutathione, glutathione peroxidase, oxidized glutathione, malondialdehyde), plasma α‐tocopherol, 8‐hydroxy‐deoxy‐guanidine (8‐OHdG) level in circulating leukocyte DNA and serum levels of cytokines.Results:  Patients with cirrhosis showed a significant imbalance of redox status (low antioxidants/high oxidative stress markers) (P < 0.005 vs controls). Neither treatment regimen affected transaminases as a whole. However, vitamin E supplementation almost normalized ALT only in the limited vitamin‐E‐deficient subgroup. A significant improvement of redox status was obtained by both regimens. However, only FPP significantly decreased 8‐OHdG and the improvement of cytokine balance with FPP was significantly better than with vitamin E treatment (P < 0.05).Conclusions:  Although the present data seem to suggest a potential supportive role of antioxidants/immunomodulators as FPP in HCV patients, more studies are needed to substantiate their effect on the natural history of the disease.
Australian evidence on student expectations and perceptions of introductory business finance
Authors: Balachandran Balasingham , Skully Michael , Tant Kevin , Watson John 
Published: July 2010

AbstractThis study examines the differences in perceptions and expectations between students at the Caulfield and Peninsula campuses of Monash University with different entrance criteria and degree availability to determine whether two different introductory finance subjects should be offered rather than one. Results reported in this study suggest that students at the Caulfield campus are interested in studying a challenging introductory finance subject, whereas students at the Peninsula campus perceived that introductory finance is ‘difficult’. Capital structure and cost of capital topics are statistically significantly ranked higher by Caulfield students than Peninsula students. The results reported in this study revealed that two different introductory finance subjects would be more effective. The core subject at the finance major campus (Caulfield) follows a traditional structure with more emphasis on finance theory, whereas the new subject at the non‐finance campus (Peninsula) places greater emphasis on applications.
Studying the costs of crime across offender trajectories
Authors: Cohen Mark A. , Piquero Alex R. , Jennings Wesley G. 
Published: July 2010

Research Summary Longitudinal studies of delinquency and crime have generated an important source of descriptive information regarding patterns of offending across the life course, and have helped inform and spur theoretical and methodological contributions. One particular method that has received considerable attention is based on offending trajectories, but applications of this method have not extended much beyond descriptive accounts of offending. This study links offender trajectories to monetary costs associated with criminal offending by members of the Second Philadelphia Birth Cohort. Results indicate that chronic offenders who frequently commit crimes when they are young turn to more serious crimes when they are adults and impose far greater costs than low‐frequency chronic offenders and those whose offending peaks during adolescence. Policy Implications Preventing individuals from becoming high‐rate chronic offenders would yield significant cost savings of more than $200 million. In terms of overall costs, offending frequency accounts for the bulk of costs in the juvenile years, whereas the seriousness of individual crimes drives total costs in the adult years. Moreover, because some trajectory groups impose higher costs in their juvenile years, whereas others impose higher costs in their adult years, policies that target particular (high‐rate chronic) trajectory groups as opposed to all at‐risk youth, for example, have the potential to provide significantly greater benefits at lower costs. These findings suggest that the allocation of prevention and intervention efforts should be targeted differentially across the offender population, with those individuals exhibiting early, frequent, and chronic offending deserving the most attention. Promising programs aimed at such individuals include early childhood prevention programs, such as those based on family–parent training, self‐control improvement, and cognitive therapies.
Candidemia Surveillance in Brazil: Evidence for a Geographical Boundary Defining an Area Exhibiting an Abatement of Infections by
Candida albicans
Group 2 Strains
Authors: Da Matta Daniel A. , Melo Analy S. , Colombo Arnaldo L. , Frade Joao P. , Nucci Marcio , Lott Timothy J. 
Published: July 2010

ABSTRACT

Prospective population surveillance has been conducted for candidemia in Brazil (A. L. Colombo, M. Nucci, B. J. Park, et al., J. Clin. Microbiol. 44:2816-2823, 2006). In the present study, a total of 63 isolates from 61 patients, representing 11 medical centers from nine geographic regions, were characterized by multilocus sequence typing (MLST). A total of 48 unique profiles or diploid sequence types (DSTs) were observed, with nine new sequence types (STs) and 32 new DSTs. There were no apparent correlations between center/region and DST patterns. Subtypes were compared to those in a known characterized reference set, including a large database of strains obtained worldwide. Significantly, only one
C. albicans
group 2 isolate was found in our collection, although isolates from this particular group are commonly found worldwide. These data, combined with information from other previously reported studies, establish a statistically significant diminishment of group 2 strains in Central and South America, including Mexico and portions of the Southwestern United States.