bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Retrospective Cohort Study into Acquisition of MRSA and Associated Risk Factors after Implementation of Universal Screening in Scottish Hospitals
Authors: van Velzen E. V. H. , Reilly J. S. , Kavanagh K. , Leanord A. , Edwards G. F. S. , Girvan E. K. , Gould I. M. , MacKenzie F. M. , Masterton R. 
Published: August 2011

Objective.To estimate the proportion of patients who acquire methicillin-resistant Staphylococcus aureus (MRSA) while in hospital and to identify risk factors associated with acquisition of MRSA.Design.Retrospective cohort study.Patients.Adult patients discharged from 36 general specialty wards of 2 Scottish hospitals that had implemented universal screening for MRSA on admission.Methods.Patients were screened for MRSA on discharge from hospital by using multisite body swabs that were tested by culture. Discharge screening results were linked to admission screening results. Genotyping was undertaken to identify newly acquired MRSA in MRSA-positive patients on admission.Results.Of the 5,155 patients screened for MRSA on discharge, 2.9% (95% confidence interval [CI], 2.43–3.34) were found to be positive. In the subcohort screened on both admission and discharge (n = 2,724), 1.3% of all patients acquired MRSA while in hospital (incidence rate, 2.1/1,000 hospital bed-days in this cohort [95% CI, 1.5–2.9]), while 1.3% remained MRSA positive throughout hospital stay. Three risk factors for acquisition of MRSA were identified: age above 64 years, self-reported renal failure, and self-reported presence of open wounds. On a population level, the prevalence of MRSA colonization did not differ between admission and discharge.Conclusions.Cross-transmission of MRSA takes place in Scottish hospitals that have implemented universal screening for MRSA. This study reinforces the importance of infection prevention and control measures to prevent MRSA cross-transmission in hospitals; universal screening for MRSA on admission will in itself not be sufficient to reduce the number of MRSA colonizations and subsequent MRSA infections.
Evaluating a Decade of Exposures to Blood and Body Fluids in an Inner-City Teaching Hospital
Authors: Treakle Amy M. , Schultz Maureen , Giannakos George P. , Joyce Patrick C. , Gordin Fred M. 
Published: August 2011

Objective.To analyze a decade of hospital staff and student exposures to blood and body fluids (BBF) and to identify risk factors relevant to prevention strategies.Design.Retrospective review of a 1999–2008 data set of BBF exposures. The data, maintained by occupational health staff, detailed the type of exposure, the setting in which the exposure occurred, and the occupational group of the BBF-exposed personnel.Setting.Washington DC Veterans Affairs Medical Center (VA-DC), an inner-city tertiary care hospital.Participants.All healthcare workers and staff at the VA-DC.Methods.Review of database.Results.A review of 10 years of data revealed 564 occupational exposures to BBF, of which 66% were caused by needlesticks and 20% were caused by sharp objects. Exposures occurred most often in the acute care setting (which accounted for 39% of exposures) and the operating room (which accounted for 22%). There was a mean of 4.9 exposures per 10,000 acute care patient-days, 0.5 exposures per 10,000 long-term care patient-days, and 0.35 exposures per 10,000 outpatient visits. Housestaff accounted for the highest number of all exposures (196 [35%]). There were, on average, 15.2 exposures per 100 housestaff full-time equivalents. An average of only 1 exposure per year occurred in the hemodialysis center.Conclusions.Occupational exposures to BBF remain common, but rates vary widely by setting and occupational group. Overall rates are steady across a decade, despite the use of various antiexposure devices and provider education programs. Targeting occupational groups and hospital settings that have been shown to have the highest risk rates should become foundational to future preventative strategies.
Point-of-Use Membrane Filtration and Hyperchlorination to Prevent Patient Exposure to Rapidly Growing Mycobacteria in the Potable Water Supply of a Skilled Nursing Facility
Authors: Williams Margaret M. , Chen Tai-Ho , Keane Tim , Toney Nadege , Toney Sean , Armbruster Catherine R. , Butler W. Ray , Arduino Matthew J. 
Published: August 2011

Background.Healthcare-associated outbreaks and pseudo-outbreaks of rapidly growing mycobacteria (RGM) are frequently associated with contaminated tap water. A pseudo-outbreak of Mycobacterium chelonae–M. abscessus in patients undergoing bronchoscopy was identified by 2 acute care hospitals. RGM was identified in bronchoscopy specimens of 28 patients, 25 of whom resided in the same skilled nursing facility (SNF). An investigation ruled out bronchoscopy procedures, specimen collection, and scope reprocessing at the hospitals as sources of transmission.Objective.To identify the reservoir for RGM within the SNF and evaluate 2 water system treatments, hyperchlorination and point-of-use (POU) membrane filters, to reduce RGM.Design.A comparative in situ study of 2 water system treatments to prevent RGM transmission.Setting.An SNF specializing in care of patients requiring ventilator support.Methods.RGM and heterotrophic plate count (HPC) bacteria were examined in facility water before and after hyperchlorination and in a subsequent 24-week assessment of filtered water by colony enumeration on Middlebrook and R2A media.Results.Mycobacterium chelonae was consistently isolated from the SNF water supply. Hyperchlorination reduced RGM by 1.5 log10 initially, but the population returned to original levels within 90 days. Concentration of HPC bacteria also decreased temporarily. RGM were reduced below detection level in filtered water, a 3-log10 reduction. HPC bacteria were not recovered from newly installed filters, although low quantities were found in water from 2-week-old filters.Conclusion.POU membrane filters may be a feasible prevention measure for healthcare facilities to limit exposure of sensitive individuals to RGM in potable water systems.
Clostridium difficile Outbreak Strain BI Is Highly Endemic in Chicago Area Hospitals
Authors: Black Stephanie R. , Weaver Kingsley N. , Jones Roderick C. , Ritger Kathleen A. , Petrella Laurica A. , Sambol Susan P. , Vernon Michael , Burton Stephanie , Garcia-Houchins Sylvia , Weber Stephen G. , Lavin Mary Alice , Gerding Dale , Johnson Stuart , Gerber Susan I. 
Published: August 2011

Objective.Describe the clinical and molecular epidemiology of incident Clostridium difficile infection (CDI) cases in Chicago area acute healthcare facilities (HCFs).Design and Setting.Laboratory, clinical, and epidemiologic information was collected for patients with incident CDI who were admitted to acute HCFs in February 2009. Stool cultures and restriction endonuclease analysis typing of the recovered C. difficile isolates was performed.Patients.Two hundred sixty-three patients from 25 acute HCFs.Results.Acute HCF rates ranged from 2 to 7 patients with CDI per 10,000 patient-days. The crude mortality rate was 8%, with 20 deaths occurring in patients with CDI. Forty-two (16%) patients had complications from CDI, including 4 patients who required partial, subtotal, or total colectomy, 3 of whom died. C. difficile was isolated and typed from 129 of 178 available stool specimens. The BI strain was identified in 79 (61%) isolates. Of patients discharged to long-term care who had their isolate typed, 36 (67%) had BI-associated CDI.Conclusions.Severe disease was common and crude mortality was substantial among patients with CDI in Chicago area acute HCFs in February 2009. The outbreak-associated BI strain was the predominant endemic strain identified, accounting for nearly two-thirds of cases. Focal HCF outbreaks were not reported, despite the presence of the BI strain. Transfer of patients between acute and long-term HCFs may have contributed to the high incidence of BI cases in this investigation.
High Incidence of Multidrug-Resistant Gram-Negative Bacteria Recovered from Afghan Patients at a Deployed US Military Hospital
Authors: Sutter Deena E. , Bradshaw Linda U. , Simkins Lucas H. , Summers Amy M. , Atha Michael , Elwood Robert L. , Robertson Janelle L. , Murray Clinton K. , Wortmann Glenn W. , Hospenthal Duane R. 
Published: August 2011

Objective.To investigate potential sources and risks associated with multidrug-resistant (MDR) bacteria in a deployed US military hospital.Design.Retrospective analysis of factors associated with recovery of MDR bacteria, supplemented by environmental sampling.Setting.The largest US military hospital in Afghanistan.Patients.US and Afghan patients with positive bacterial culture results, from September 2007 through August 2008.Methods.Microbiologic, demographic, and clinical data were analyzed. Potential risk factors included admission diagnosis or mechanism of injury, length of stay, gender, age, and nationality (US or Afghan). Environmental sampling of selected hospital high-touch surfaces and equipment was performed to help elucidate whether environmental MDR bacteria were contributing to nosocomial spread.Results.A total of 266 patients had 411 bacterial isolates that were identified during the study period, including 211 MDR bacteria (51%). Gram-negative bacteria were common among Afghan patients (241 [76%] of 319), and 70% of these were classified as MDR. This included 58% of bacteria recovered from Afghan patients within 48 hours of hospital admission. The most common gram-negative bacteria were Escherichia coli (53% were MDR), Acinetobacter (90% were MDR), and Klebsiella (63% were MDR). Almost one-half of potential extended-spectrum β-lactamase (ESBL) producers were community acquired. Of 100 environmental swab samples, 18 yielded MDR bacteria, including 10 that were Acinetobacter, but no potential ESBL-producing bacteria.Conclusions.Gram-negative bacteria from Afghan patients had high rates of antimicrobial resistance. Patients experiencing Complex trauma and prolonged hospital stays likely contribute to the presence of MDR bacteria in this facility. However, many of these patients had community-acquired cases, which implies high rates of colonization prior to hospital admission.
Effectiveness of Measures to Eradicate Staphylococcus aureus Carriage in Patients with Community-Associated Skin and Soft-Tissue Infections: A Randomized Trial
Authors: Fritz Stephanie A. , Camins Bernard C. , Eisenstein Kimberly A. , Fritz Joseph M. , Epplin Emma K. , Burnham Carey-Ann , Dukes Jonathan , Storch Gregory A. 
Published: August 2011

Background.Despite a paucity of evidence, decolonization measures are prescribed for outpatients with recurrent Staphylococcus aureus skin and soft-tissue infection (SSTI).Objective.Compare the effectiveness of 4 regimens for eradicating S. aureus carriage.Design.Open-label, randomized controlled trial. Colonization status and recurrent SSTI were ascertained at 1 and 4 months.Setting.Barnes-Jewish and St. Louis Children's Hospitals, St. Louis, Missouri, 2007–2009.Participants.Three hundred patients with community-onset SSTI and S. aureus colonization in the nares, axilla, or inguinal folds.Interventions.Participants were randomized to receive no therapeutic intervention (control subjects) or one of three 5-day regimens: 2% mupirocin ointment applied to the nares twice daily, intranasal mupirocin plus daily 4% chlorhexidine body washes, or intranasal mupirocin plus daily dilute bleach water baths.Results.Among 244 participants with 1-month colonization data, modified intention-to-treat analysis revealed S. aureus eradication in 38% of participants in the education only (control) group, 56% of those in the mupirocin group (P = .03 vs controls), 55% of those in the mupirocin and chlorhexidine group (P = .05), and 63% off those in the mupirocin and bleach group (P = .006). Of 229 participants with 4-month colonization data, eradication rates were 48% in the control group, 56% in the mupirocin only group (P = .40 vs controls), 54% in the mupirocin and chlorhexidine group (P = .51), and 71% in the mupirocin and bleach group (P = .02). At 1 and 4 months, recurrent SSTIs were reported by 20% and 36% of participants, respectively.Conclusions.An inexpensive regimen of dilute bleach baths, intranasal mupirocin, and hygiene education effectively eradicated S. aureus over a 4-month period. High rates of recurrent SSTI suggest that factors other than endogenous colonization are important determinants of infection.Trial Registration.ClinicalTrials.gov identifier: NCT00513799.
A survey of electron Bernstein wave heating and current drive potential for spherical tokamaks
Authors: Urban Jakub , Decker Joan , Peysson Yves , Preinhaelter Josef , Shevchenko Vladimir , Taylor Gary , Vahala Linda , Vahala George 
Published: August 2011

The electron Bernstein wave (EBW) is typically the only wave in the electron cyclotron (EC) range that can be applied in spherical tokamaks for heating and current drive (H&CD). Spherical tokamaks (STs) operate generally in high-β regimes, in which the usual EC O- and X-modes are cut off. In this case, EBWs seem to be the only option that can provide features similar to the EC waves—controllable localized H&CD that can be used for core plasma heating as well as for accurate plasma stabilization.
The EBW is a quasi-electrostatic wave that can be excited by mode conversion from a suitably launched O- or X-mode; its propagation further inside the plasma is strongly influenced by the plasma parameters. These rather awkward properties make its application somewhat more difficult. In this paper we perform an extensive numerical study of EBW H&CD performance in four typical ST plasmas (NSTX L- and H-mode, MAST Upgrade, NHTX). Coupled ray-tracing (AMR) and Fokker–Planck (LUKE) codes are employed to simulate EBWs of varying frequencies and launch conditions, which are the fundamental EBW parameters that can be chosen and controlled. Our results indicate that an efficient and universal EBW H&CD system is indeed viable. In particular, power can be deposited and current reasonably efficiently driven across the whole plasma radius. Such a system could be controlled by a suitably chosen launching antenna vertical position and would also be sufficiently robust.
Some eigenvalue problems for vectorial Sturm-Liouville equations with eigenparameter dependent boundary conditions
Authors: Chan Chi-Hua 
Published: August 2011

We investigate the

n
n

-dimensional vectorial Sturm-Liouville equation
\[

y
→

(
x
)
+
[

λ
2

I
n

−
Q
(
x
)
]

y
→

(
x
)
=

0
→

\vec {y}\ (x)+[\lambda ^2 I_n -Q(x)]\vec {y}(x)=\vec {0}

\]
with eigenparameter dependent boundary conditions
\[

y
→

(
0
)
=

0
→

,
A

y
→

′

(
π
)
+
λ

y
→

(
π
)
=

0
→

.

\vec {y}(0)=\vec {0}, A\vec {y}\ ’(\pi )+\lambda \vec {y}(\pi )=\vec {0}.

\]
Under the assumption that

Q
(
x
)

Q(x)

is nonnegative definite in [0,

π
\pi

], we prove that the eigenvalues of the

n
n

-dimensional vectorial Sturm-Liouville equation are real.

For the case

n
=
2

n=2

, we show that the algebraic multiplicity of an eigenvalue of the problem as a zero of the characteristic function
\[

ω
A

(
λ
;
Q
)
=
det
[
A

Y
′

(
π
;

λ
2

;
Q
)
+
λ
Y
(
π
;

λ
2

;
Q
)
]

\omega _A(\lambda ;Q)=\det [AY’(\pi ;\lambda ^2;Q)+\lambda Y(\pi ;\lambda ^2;Q)]

\]
is equal to its geometric multiplicity. By the theory of Hadamard’s factorization, we also prove that the characteristic function

ω
A

(
λ
;
Q
)

\omega _A(\lambda ;Q)

is uniquely determined by the spectral set of the equation. Moreover, we consider the inverse problem for the equation, i.e., how many spectral sets can determine the potential function

Q
(
x
)

Q(x)

uniquely, and we find that three spectral sets are necessary for us to determine the potential function

Q
(
x
)

Q(x)

uniquely.
FDM: a graph-based statistical method to detect differential transcription using RNA-seq data
Authors: Singh Darshan , Orellana Christian F. , Hu Yin , Jones Corbin D. , Liu Yufeng , Chiang Derek Y. , Liu Jinze , Prins Jan F. 
Published: August 2011

Abstract
Motivation: In eukaryotic cells, alternative splicing expands the diversity of RNA transcripts and plays an important role in tissue-specific differentiation, and can be misregulated in disease. To understand these processes, there is a great need for methods to detect differential transcription between samples. Our focus is on samples observed using short-read RNA sequencing (RNA-seq).
Methods: We characterize differential transcription between two samples as the difference in the relative abundance of the transcript isoforms present in the samples. The magnitude of differential transcription of a gene between two samples can be measured by the square root of the Jensen Shannon Divergence (JSD*) between the gene's transcript abundance vectors in each sample. We define a weighted splice-graph representation of RNA-seq data, summarizing in compact form the alignment of RNA-seq reads to a reference genome. The flow difference metric (FDM) identifies regions of differential RNA transcript expression between pairs of splice graphs, without need for an underlying gene model or catalog of transcripts. We present a novel non-parametric statistical test between splice graphs to assess the significance of differential transcription, and extend it to group-wise comparison incorporating sample replicates.
Results: Using simulated RNA-seq data consisting of four technical replicates of two samples with varying transcription between genes, we show that (i) the FDM is highly correlated with JSD* (r=0.82) when average RNA-seq coverage of the transcripts is sufficiently deep; and (ii) the FDM is able to identify 90% of genes with differential transcription when JSD* &gt;0.28 and coverage &gt;7. This represents higher sensitivity than Cufflinks (without annotations) and rDiff (MMD), which respectively identified 69 and 49% of the genes in this region as differential transcribed. Using annotations identifying the transcripts, Cufflinks was able to identify 86% of the genes in this region as differentially transcribed. Using experimental data consisting of four replicates each for two cancer cell lines (MCF7 and SUM102), FDM identified 1425 genes as significantly different in transcription. Subsequent study of the samples using quantitative real time polymerase chain reaction (qRT-PCR) of several differential transcription sites identified by FDM, confirmed significant differences at these sites.
Availability: http://csbio-linux001.cs.unc.edu/nextgen/software/FDM
Contact: darshan@email.unc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Inhibition of Protein Synthesis by TOR Inactivation Revealed a Conserved Regulatory Mechanism of the BiP Chaperone in Chlamydomonas
Authors: Díaz-Troya Sandra , Pérez-Pérez María Esther , Pérez-Martín Marta , Moes Suzette , Jeno Paul , Florencio Francisco J. , Crespo José L. 
Published: August 2011

Abstract
The target of rapamycin (TOR) kinase integrates nutritional and stress signals to coordinately control cell growth in all eukaryotes. TOR associates with highly conserved proteins to constitute two distinct signaling complexes termed TORC1 and TORC2. Inactivation of TORC1 by rapamycin negatively regulates protein synthesis in most eukaryotes. Here, we report that down-regulation of TOR signaling by rapamycin in the model green alga Chlamydomonas reinhardtii resulted in pronounced phosphorylation of the endoplasmic reticulum chaperone BiP. Our results indicated that Chlamydomonas TOR regulates BiP phosphorylation through the control of protein synthesis, since rapamycin and cycloheximide have similar effects on BiP modification and protein synthesis inhibition. Modification of BiP by phosphorylation was suppressed under conditions that require the chaperone activity of BiP, such as heat shock stress or tunicamycin treatment, which inhibits N-linked glycosylation of nascent proteins in the endoplasmic reticulum. A phosphopeptide localized in the substrate-binding domain of BiP was identified in Chlamydomonas cells treated with rapamycin. This peptide contains a highly conserved threonine residue that might regulate BiP function, as demonstrated by yeast functional assays. Thus, our study has revealed a regulatory mechanism of BiP in Chlamydomonas by phosphorylation/dephosphorylation events and assigns a role to the TOR pathway in the control of BiP modification.
The Small GTPase Rab5a Is Essential for Intracellular Transport of Proglutelin from the Golgi Apparatus to the Protein Storage Vacuole and Endosomal Membrane Organization in Developing Rice Endosperm
Authors: Fukuda Masako , Satoh-Cruz Mio , Wen Liuying , Crofts Andrew J. , Sugino Aya , Washida Haruhiko , Okita Thomas W. , Ogawa Masahiro , Kawagoe Yasushi , Maeshima Masayoshi , Kumamaru Toshihiro 
Published: August 2011

AbstractRice (Oryza sativa) glutelins are synthesized on the endoplasmic reticulum as larger precursors, which are then transported via the Golgi to the protein storage vacuole (PSV), where they are processed into acidic and basic subunits. Three independent glutelin precursor mutant4 (glup4) rice lines, which accumulated elevated levels of proglutelin over the wild type, were identified as loss-of-function mutants of Rab5a, the small GTPase involved in vesicular membrane transport. In addition to the plasma membrane, Rab5a colocalizes with glutelins on the Golgi apparatus, Golgi-derived dense vesicles, and the PSV, suggesting that Rab5a participates in the transport of the proglutelin from the Golgi to the PSV. This spatial distribution pattern was dramatically altered in the glup4 mutants. Numerous smaller protein bodies containing glutelin and α-globulin were evident, and the proteins were secreted extracellularly. Moreover, all three independent glup4 allelic lines displayed the novel appearance of a large dilated, structurally complex paramural body containing proglutelins, α-globulins, membrane biomarkers for the Golgi apparatus, prevacuolar compartment, PSV, and the endoplasmic reticulum luminal chaperones BiP and protein disulfide isomerase as well as β-glucan. These results indicate that the formation of the paramural bodies in glup4 endosperm was due to a significant disruption of endocytosis and membrane vesicular transport by Rab5a loss of function. Overall, Rab5a is required not only for the intracellular transport of proglutelins from the Golgi to the PSV in rice endosperm but also in the maintenance of the general structural organization of the endomembrane system in developing rice seeds.