bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effectiveness of Continuous Passive Motion in an Inpatient Rehabilitation Hospital After Total Knee Replacement: A Matched Cohort Study
Authors: Herbold Janet Anne , Bonistall Kristen , Blackburn Marielle 
Published: September 2012

ObjectiveTo examine the use of continuous passive motion (CPM) as an adjunct to physical therapy after total knee replacement in patients who were transferred to an inpatient rehabilitation facility (IRF) and to compare the effectiveness of CPM on active range of motion (AROM), functional tasks, destination after discharge, the need for home care services, and the ambulation device at discharge.DesignMatched cohort study.SettingIRF.ParticipantsPatients admitted to a rehabilitation setting after total knee replacement surgery with an initial AROM for knee flexion of less than 75° at admission to the IRF. From this initial population, a matched sample of 61 patient pairs was included in the analysis (61 who used the CPM and 61 who did not receive the adjunct therapy).InterventionUse of CPM for 2 hours per day as an adjunct to the 3 hours of physical and occupational therapy customary in an IRF.Main OutcomesPrimary outcomes were discharge active knee flexion ROM and flexion gain. Secondary outcomes were motor, cognitive, and total Functional Independence Measure scores; discharge ambulation device; destination after discharge; and the need for home care services after the inpatient stay.ResultsThe outcome variables of 61 matched pairs of CPM users and non‐CPM users were reported. No statistically significant differences were found in any of the outcome variables that were compared in this matched case design, including AROM knee, flexion gain, discharge to the community, need for home care services after discharge, and discharge with cane/no device. No significant difference was found in all functional scores as measured by the Functional Independence Measure scale.ConclusionFor this population, we determined at one facility that less than 30% are provided with a CPM as an adjunct to physical therapy. Using a matched cohort design, we compared CPM use with non‐CPM use and determined that the application of CPM may not significantly influence ROM gain.
Particle capture and low-Reynolds-number flow around a circular cylinder
Authors: Espinosa-Gayosso Alexis , Ghisalberti Marco , Ivey Gregory N. , Jones Nicole L. 
Published: September 2012

AbstractParticle capture, whereby suspended particles contact and adhere to a solid surface (a ‘collector’), is an important mechanism in a range of environmental processes. In aquatic systems, typically characterized by low collector Reynolds numbers ($\mathit{Re}$), the rate of particle capture determines the efficiencies of a range of processes such as seagrass pollination, suspension feeding by corals and larval settlement. In this paper, we use direct numerical simulation (DNS) of a two-dimensional laminar flow to accurately quantify the rate of capture of low-inertia particles by a cylindrical collector for $\mathit{Re}\leq 47$ (i.e. a range where there is no vortex shedding). We investigate the dependence of both the capture rate and maximum capture angle on both the collector Reynolds number and the ratio of particle size to collector size. The inner asymptotic expansion of Skinner (Q. J. Mech. Appl. Maths, vol. 28, 1975, pp. 333–340) for flow around a cylinder is extended and shown to provide an excellent framework for the prediction of particle capture and flow close to the leading face of a cylinder up to $\mathit{Re}= 10$. Our results fill a gap between theory and experiment by providing, for the first time, predictive capability for particle capture by aquatic collectors in a wide (and relevant) Reynolds number and particle size range.
Symplectic T7, T8 singularities and Lagrangian tangency orders
Authors: Domitrz Wojciech , Trȩbska Żaneta 
Published: September 2012

AbstractWe study the local symplectic algebra of curves. We use the method of algebraic restrictions to classify symplectic T7, T8 singularities. We define discrete symplectic invariants (the Lagrangian tangency orders) and compare them with the index of isotropy. We use these invariants to distinguish symplectic singularities of classical T7 singularity. We also give the geometric description of symplectic classes of the singularity.
The immune response to tuberculosis infection in the setting ofHelicobacter pyloriand helminth infections
Authors: PERRY S. , CHANG A. H. , SANCHEZ L. , YANG S. , HAGGERTY T. D. , PARSONNET J. 
Published: September 2012

SUMMARYWe screened 176 healthy, adult (aged 18–55 years) US refugees from tuberculosis (TB)-endemic countries to evaluate whether cytokine responses to latent TB infection (LTBI) are modified in the setting of concurrentH. pyloriand helminth infection. As measured by the Quantiferon-TB GOLD interferon-γ release assay, a total 38 (22%) subjects had LTBI, of which 28 (74%) also wereH. pyloriseropositive and/or helminth infected. Relative to ten subjects with LTBI only, 16 subjects with concurrentH. pyloriinfection had significantly elevated levels of IFN-γ, and nine subjects with bothH. pyloriand helminth infection had significantly elevated levels of IFN-γ, IL-2, IL-13, and IL-5.H. pyloriis associated with enhanced IFN-γ responses to TB, even in the setting of concurrent helminth infection. Efficacy of TB vaccines may vary with the co-existence of these three infections in the developing world.
Prevalence, risk factors and molecular epidemiology of methicillin-resistantStaphylococcus aureus(MRSA) colonization in residents of long-term care facilities in Luxembourg, 2010
Authors: MOSSONG J. , GELHAUSEN E. , DECRUYENAERE F. , DEVAUX A. , PERRIN M. , EVEN J. , HEISBOURG E. 
Published: September 2012

SUMMARYA prevalence survey of methicillin-resistantStaphylococcus aureus(MRSA) was performed in 2010 in 19 long-term care facilities in Luxembourg. Of the 954 participating residents, 69 (7·2%) were colonized by MRSA. Previous history of MRSA [odds ratio (OR) 7·20, 95% confidence interval (CI) 3·19–16·27], quinolone therapy in the previous year (OR 2·27, 95% CI 1·17–4·41) and ⩾24 h care administered per week (OR 4·29, 95% CI 1·18–15·56) were independent risk factors for MRSA colonization. More than 75% of strains were of clonal complex (CC)5, mainlyspa-type t003 or sequence type (ST)225 and ST710, which is a rapidly emerging lineage prevalent in central Europe. Five residents were colonized by livestock-associated genotypes belonging to CC398. Previously dominant CC8 strains have recently been replaced by more resistant CC5 strains in Luxembourg.
TNFα enhances TLR3‐dependent effects on MMP‐9 expression in human mesangial cells
Authors: Merkle Monika , Ribeiro Andrea , Köppel Simone , Wörnle Markus 
Published: September 2012

AbstractThe role of MMPs (matrix metalloproteinases) in kidney diseases has been widely accepted, where they can regulate inflammatory response because of their effects on both recruitment and survival of inflammatory cells. TNFα (tumour necrosis factor α) has also been implicated in the pathogenesis of inflammatory kidney diseases, including forms of glomerulonephritis associated with viral diseases. Previously, we established the functional linkage between viral receptors of the innate immune system, the TLRs (Toll‐like receptors) and control of MMP activity in human MC (mesangial cells). Expression levels of MMP‐2, MMP‐7, MMP‐9, TIMP‐1 (tissue inhibitor of metalloproteinase 1) and TIMP‐2 in human MC in culture were analysed by RT‐PCR (reverse transcription–PCR). TNFα significantly enhanced the TLR3‐dependent induction of MMP‐9 in human MC. Expression levels of MMP‐2, TIMP‐1 and TIMP‐2 were not significantly affected by the activation of TLR3 or TNFα stimulation. No significant MMP‐7 expression was found. We conclude that the role of MMP‐9 in chemotaxis, activation and proliferation of inflammatory cells is amplified by TNFα originating from infiltrating cells, especially monocytes, producing a regulatory loop that potentially leads to a self‐propagating inflammation.
Personal Protective Equipment Management and Policies: European Network for Highly Infectious Diseases Data from 48 Isolation Facilities in 16 European Countries
Authors: Iaco Giuseppina De , Puro Vincenzo , Fusco Francesco Maria , Schilling Stefan , Maltezou Helena C. , Brouqui Philippe , Gottschalk René , Bannister Barbara , Brodt Hans-Reinhard , Siikamaki Heli , Perronne Christian , Brantsæter Arne Broch , Fjellet Anne Lise , Ippolito Giuseppe ,   European Network for Highly Infectious Diseases Working Group
Published: September 2012

Objective.To collect data about personal protective equipment (PPE) management and to provide indications for improving PPE policies in Europe.Design.Descriptive, cross-sectional survey.Setting and Participants.Data were collected in 48 isolation facilities in 16 European countries nominated by National Health Authorities for the management of highly infectious diseases (HIDs).Methods.Data were collected through standardized checklists at on-site visits during February-November 2009. Indications for adequate PPE policies were developed on the basis of a literature review, partners' expert opinions, and the collected data.Results.All facilities have procedures for the selection of PPE in case of HID, and 44 have procedures for the removal of PPE. In 40 facilities, different levels of PPE are used according to a risk assessment process, and in 8 facilities, high-level PPE (eg, positive-pressure complete suits or Trexler units) is always used. A fit test is performed at 25 of the 40 facilities at which it is applicable, a seal check is recommended at 25, and both procedures are used at 17. Strategies for promoting and monitoring the correct use of PPE are available at 42 facilities. In case of a sudden increase in demand, 44 facilities have procedures for rapid supply of PPE, whereas 14 facilities have procedures for decontamination and reuse of some PPE.Conclusions.Most isolation facilities devote an acceptable level of attention to PPE selection and removal, strategies for the promotion of the correct use of PPE, and ensuring adequate supplies of PPE. Fit test and seal check procedures are still not widely practiced. Moreover, policies vary widely between and within European countries, and the development of common practice procedures is advisable.Infect Control Hosp Epidemiol2012;33(10):1008-1016
Daily Disinfection of High-Touch Surfaces in Isolation Rooms to Reduce Contamination of Healthcare Workers' Hands
Authors: Kundrapu Sirisha , Sunkesula Venkata , Jury Lucy A. , Sitzlar Brett M. , Donskey Curtis J. 
Published: September 2012

In a randomized nonblinded trial, we demonstrated that daily disinfection of high-touch surfaces in rooms of patients with Clostridium difficile infection and methicillin-resistant Staphylococcus aureus colonization reduced acquisition of the pathogens on hands after contacting high-touch surfaces and reduced contamination of hands of healthcare workers caring for the patients.Infect Control Hosp Epidemiol 2012;33(10):1039-1042
Epidemiology and Healthcare Costs of Incident Clostridium difficile Infections Identified in the Outpatient Healthcare Setting
Authors: Kuntz Jennifer L. , Johnson Eric S. , Raebel Marsha A. , Petrik Amanda F. , Yang Xiuhai , Thorp Micah L. , Spindel Steven J. , Neil Nancy , Smith David H. 
Published: September 2012

Objective.To describe the epidemiology and healthcare costs of Clostridium difficile infection (CDI) identified in the outpatient setting.Design.Population-based, retrospective cohort study.Patients.Kaiser Permanente Colorado and Kaiser Permanente Northwest members between June 1, 2005, and September 30, 2008.Methods.We identified persons with incident CDI and classified CDI by whether it was identified in the outpatient or inpatient healthcare setting. We collected information about baseline variables and follow-up healthcare utilization, costs, and outcomes among patients with CDI. We compared characteristics of patients with CDI identified in the outpatient versus inpatient setting.Results.We identified 3,067 incident CDIs; 56% were identified in the outpatient setting. Few strong, independent predictors of diagnostic setting were identified, although a previous stay in a nonacute healthcare institution (odds ratio [OR], 1.45 [95% confidence interval (CI), 1.13-1.86]) was statistically associated with outpatient-identified CDI, as was age from 50 to 59 years (OR, 1.64 [95% CI, 1.18-2.29]), 60 to 69 years (OR, 1.37 [95% CI, 1.03-1.82]), and 70 to 79 years (OR, 1.36 [95% CI, 1.06-1.74]), when compared with persons aged 80-89 years.Conclusions.We found that more than one-half of incident CDIs in this population were identified in the outpatient setting. Patients with outpatient-identified CDI were younger with fewer comorbidities, although they frequently had previous exposure to healthcare. These data suggest that practitioners should be aware of CDI and obtain appropriate diagnostic testing on outpatients with CDI symptoms.Infect Control Hosp Epidemiol 2012;33(10):1031-1038
Active Surveillance and Decolonization of Methicillin-Resistant Staphylococcus aureus on Admission to Neonatal Intensive Care Units in Hong Kong: A Cost-Effectiveness Analysis
Authors: You Joyce H. S. , Chan C. Y. , Wong M. Y. , Ip Margaret 
Published: September 2012

Objective.To examine potential clinical outcomes and cost of active methicillin-resistant Staphylococcus aureus (MRSA) surveillance with and without decolonization in neonatal intensive care units (NICUs) from the perspective of healthcare providers in Hong Kong.Design.Decision analysis modeling.Setting.NICU.Patients.Hypothetical cohort of patients admitted to an NICU.Methods.We designed a decision tree to simulate potential outcomes of active MRSA surveillance with and without decolonization in patients admitted to an NICU. Outcome measures included total direct medical cost per patient, MRSA infection rate, and MRSA-associated mortality rate. Model inputs were derived from the literature. Sensitivity analyses evaluated the impact of uncertainty in all model variables.Results.In the base-case analysis, active surveillance plus decolonization showed a lower expected MRSA infection rate (0.911% vs 1.759%), MRSA-associated mortality rate (0.223% vs 0.431%), and total cost per patient (USD 47,294 vs USD 48,031) compared with active surveillance alone. Sensitivity analyses showed that active surveillance plus decolonization cost less and had lower event rates if the incidence risk ratio of acquiring MRSA infections in carriers after decolonization was less than 0.997. In 10,000 Monte Carlo simulations, active surveillance plus decolonization was significantly less costly than active surveillance alone 99.9% of the time, and both the MRSA infection rate and the MRSA-associated mortality rate were significantly lower 99.9% of the time.Conclusions.Active surveillance plus decolonization for patients admitted to NICUs appears to be cost saving and effective in reducing the MRSA infection rate and the MRSA-associated mortality rate if addition of decolonization to active surveillance reduces the risk of MRSA infection.Infect Control Hosp Epidemiol 2012;33(10):1024-1030
Finding differentially expressed regions of arbitrary length in quantitative genomic data based on marked point process model
Authors: Hatsuda Hiroshi 
Published: September 2012

Abstract
Motivation: High-throughput nucleotide sequencing technologies provide large amounts of quantitative genomic data at nucleotide resolution, which are important for the present and future biomedical researches; for example differential analysis of base-level RNA expression data will improve our understanding of transcriptome, including both coding and non-coding genes. However, most studies of these data have relied on existing genome annotations and thus are limited to the analysis of known transcripts.
Results: In this article, we propose a novel method based on a marked point process model to find differentially expressed genomic regions of arbitrary length without using genome annotations. The presented method conducts a statistical test for differential analysis in regions of various lengths at each nucleotide and searches the optimal configuration of the regions by using a Monte Carlo simulation. We applied the proposed method to both synthetic and real genomic data, and their results demonstrate the effectiveness of our method.
Availability: The program used in this study is available at https://sites.google.com/site/hiroshihatsuda/.
Contact: H.Hatsuda@warwick.ac.uk
Graphlet-based edge clustering reveals pathogen-interacting proteins
Authors: Solava R. W. , Michaels R. P. , Milenković T. 
Published: September 2012

Abstract
Motivation: Prediction of protein function from protein interaction networks has received attention in the post-genomic era. A popular strategy has been to cluster the network into functionally coherent groups of proteins and assign the entire cluster with a function based on functions of its annotated members. Traditionally, network research has focused on clustering of nodes. However, clustering of edges may be preferred: nodes belong to multiple functional groups, but clustering of nodes typically cannot capture the group overlap, while clustering of edges can. Clustering of adjacent edges that share many neighbors was proposed recently, outperforming different node clustering methods. However, since some biological processes can have characteristic ‘signatures’ throughout the network, not just locally, it may be of interest to consider edges that are not necessarily adjacent.
Results: We design a sensitive measure of the ‘topological similarity’ of edges that can deal with edges that are not necessarily adjacent. We cluster edges that are similar according to our measure in different baker's yeast protein interaction networks, outperforming existing node and edge clustering approaches. We apply our approach to the human network to predict new pathogen-interacting proteins. This is important, since these proteins represent drug target candidates.
Availability: Software executables are freely available upon request.
Contact: tmilenko@nd.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Trajectory-oriented Bayesian experiment design versus Fisher A-optimal design: an in depth comparison study
Authors: Weber Patrick , Kramer Andrei , Dingler Clemens , Radde Nicole 
Published: September 2012

AbstractMotivation: Experiment design strategies for biomedical models with the purpose of parameter estimation or model discrimination are in the focus of intense research. Experimental limitations such as sparse and noisy data result in unidentifiable parameters and render-related design tasks challenging problems. Often, the temporal resolution of data is a limiting factor and the amount of possible experimental interventions is finite. To address this issue, we propose a Bayesian experiment design algorithm to minimize the prediction uncertainty for a given set of experiments and compare it to traditional A-optimal design.Results: In an in depth numerical study involving an ordinary differential equation model of the trans-Golgi network with 12 partly non-identifiable parameters, we minimized the prediction uncertainty efficiently for predefined scenarios. The introduced method results in twice the prediction precision as the same amount of A-optimal designed experiments while introducing a useful stopping criterion. The simulation intensity of the algorithm's major design step is thereby reasonably affordable. Besides smaller variances in the predicted trajectories compared with Fisher design, we could also achieve smaller parameter posterior distribution entropies, rendering this method superior to A-optimal Fisher design also in the parameter space.Availability: Necessary software/toolbox information are available in the supplementary material. The project script including example data can be downloaded from http://www.ist.uni-stuttgart.de/%7eweber/BayesFisher2012.Contact: patrick.weber@ist.uni-stuttgart.deSupplementary Information: Supplementary data are available at Bioinformatics online.
Reveal—visual eQTL analytics
Authors: Jäger Günter , Battke Florian , Nieselt Kay 
Published: September 2012

Abstract
Motivation: The analysis of expression quantitative trait locus (eQTL) data is a challenging scientific endeavor, involving the processing of very large, heterogeneous and complex data. Typical eQTL analyses involve three types of data: sequence-based data reflecting the genotypic variations, gene expression data and meta-data describing the phenotype. Based on these, certain genotypes can be connected with specific phenotypic outcomes to infer causal associations of genetic variation, expression and disease.
To this end, statistical methods are used to find significant associations between single nucleotide polymorphisms (SNPs) or pairs of SNPs and gene expression. A major challenge lies in summarizing the large amount of data as well as statistical results and to generate informative, interactive visualizations.
Results: We present Reveal, our visual analytics approach to this challenge. We introduce a graph-based visualization of associations between SNPs and gene expression and a detailed genotype view relating summarized patient cohort genotypes with data from individual patients and statistical analyses.
Availability: Reveal is included in Mayday, our framework for visual exploration and analysis. It is available at http://it.inf.uni-tuebingen.de/software/reveal/.
Contact: guenter.jaeger@uni-tuebingen.de
A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst
Authors: Buettner Florian , Theis Fabian J. 
Published: September 2012

Abstract
Motivation: Single-cell experiments of cells from the early mouse embryo yield gene expression data for different developmental stages from zygote to blastocyst. To better understand cell fate decisions during differentiation, it is desirable to analyse the high-dimensional gene expression data and assess differences in gene expression patterns between different developmental stages as well as within developmental stages. Conventional methods include univariate analyses of distributions of genes at different stages or multivariate linear methods such as principal component analysis (PCA). However, these approaches often fail to resolve important differences as each lineage has a unique gene expression pattern which changes gradually over time yielding different gene expressions both between different developmental stages as well as heterogeneous distributions at a specific stage. Furthermore, to date, no approach taking the temporal structure of the data into account has been presented.
Results: We present a novel framework based on Gaussian process latent variable models (GPLVMs) to analyse single-cell qPCR expression data of 48 genes from mouse zygote to blastocyst as presented by (Guo et al., 2010). We extend GPLVMs by introducing gene relevance maps and gradient plots to provide interpretability as in the linear case. Furthermore, we take the temporal group structure of the data into account and introduce a new factor in the GPLVM likelihood which ensures that small distances are preserved for cells from the same developmental stage. Using our novel framework, it is possible to resolve differences in gene expressions for all developmental stages. Furthermore, a new subpopulation of cells within the 16-cell stage is identified which is significantly more trophectoderm-like than the rest of the population. The trophectoderm-like subpopulation was characterized by considerable differences in the expression of Id2, Gata4 and, to a smaller extent, Klf4 and Hand1. The relevance of Id2 as early markers for TE cells is consistent with previously published results.
Availability: The mappings were implemented based on Prof. Neil Lawrence's FGPLVM toolbox1; extensions for relevance analysis and including the structure of the data can be obtained from one of the authors' homepage.2
Contact: f.buettner@helmholtz-muenchen.de