bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kikuchi ultrafast nanodiffraction in four-dimensional electron microscopy
Authors: Yurtsever Aycan , Zewail Ahmed H. 
Published: January 2011

Coherent atomic motions in materials can be revealed using time-resolved X-ray and electron Bragg diffraction. Because of the size of the beam used, typically on the micron scale, the detection ofnanoscalepropagating waves in extended structures hitherto has not been reported. For elastic waves of complex motions, Bragg intensities contain all polarizations and they are not straightforward to disentangle. Here, we introduce Kikuchi diffraction dynamics, using convergent-beam geometry in an ultrafast electron microscope, to selectively probe propagating transverse elastic waves with nanoscale resolution. It is shown that Kikuchi band shifts, which are sensitive only to the tilting of atomic planes, reveal the resonance oscillations, unit cell angular amplitudes, and the polarization directions. For silicon, the observed wave packet temporal envelope (resonance frequency of 33 GHz), the out-of-phase temporal behavior of Kikuchi’s edges, and the magnitude of angular amplitude (0.3 mrad) and polarizationelucidate the nature of the motion: one that preserves the mass density (i.e., no compression or expansion) but leads to sliding of planes in the antisymmetric shear eigenmode of the elastic waveguide. As such, the method of Kikuchi diffraction dynamics, which is unique to electron imaging, can be used to characterize the atomic motions of propagating waves and their interactions with interfaces, defects, and grain boundaries at the nanoscale.
Estimating the Proportion of Healthcare-Associated Infections That Are Reasonably Preventable and the Related Mortality and Costs
Authors: Umscheid Craig A. , Mitchell Matthew D. , Doshi Jalpa A. , Agarwal Rajender , Williams Kendal , Brennan Patrick J. 
Published: January 2011

Objective.To estimate the proportion of healthcare-associated infections (HAIs) in US hospitals that are “reasonably preventable,” along with their related mortality and costs.Methods.To estimate preventability of catheter-associated bloodstream infections (CABSIs), catheter-associated urinary tract infections (CAUTIs), surgical site infections (SSIs), and ventilator-associated pneumonia (VAP), we used a federally sponsored systematic review of interventions to reduce HAIs. Ranges of preventability included the lowest and highest risk reductions reported by US studies of “moderate” to “good” quality published in the last 10 years. We used the most recently published national data to determine the annual incidence of HAIs and associated mortality. To estimate incremental cost of HAIs, we performed a systematic review, which included costs from studies in general US patient populations. To calculate ranges for the annual number of preventable infections and deaths and annual costs, we multiplied our infection, mortality, and cost figures with our ranges of preventability for each HAI.Results.AS many as 65%–70% of cases of CABSI and CAUTI and 55% of cases of VAP and SSI may be preventable with current evidence-based strategies. CAUTI may be the most preventable HAI. CABSI has the highest number of preventable deaths, followed by VAP. CABSI also has the highest cost impact; costs due to preventable cases of VAP, CAUTI, and SSI are likely less.Conclusions.Our findings suggest that 100% prevention of HAIs may not be attainable with current evidence-based prevention strategies; however, comprehensive implementation of such strategies could prevent hundreds of thousands of HAIs and save tens of thousands of lives and billions of dollars.
Validity of ICD-9-CM Coding for Identifying Incident Methicillin-Resistant Staphylococcus aureus (MRSA) Infections: Is MRSA Infection Coded as a Chronic Disease?
Authors: Schweizer Marin L. , Eber Michael R. , Laxminarayan Ramanan , Furuno Jon P. , Popovich Kyle J. , Hota Bala , Rubin Michael A. , Perencevich Eli N. 
Published: January 2011

Background and Objective.Investigators and medical decision makers frequently rely on administrative databases to assess methicillin-resistant Staphylococcus aureus (MRSA) infection rates and outcomes. The validity of this approach remains unclear. We sought to assess the validity of the International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM) code for infection with drug-resistant microorganisms (V09) for identifying culture-proven MRSA infection.Design.Retrospective cohort study.Methods.All adults admitted to 3 geographically distinct hospitals between January 1, 2001, and December 31, 2007, were assessed for presence of incident MRSA infection, defined as an MRSA-positive clinical culture obtained during the index hospitalization, and presence of the V09 ICD-9-CM code. The k statistic was calculated to measure the agreement between presence of MRSA infection and assignment of the V09 code. Sensitivities, specificities, positive predictive values, and negative predictive values were calculated.Results.There were 466,819 patients discharged during the study period. Of the 4,506 discharged patients (1.0%) who had the V09 code assigned, 31% had an incident MRSA infection, 20% had prior history of MRSA colonization or infection but did not have an incident MRSA infection, and 49% had no record of MRSA infection during the index hospitalization or the previous hospitalization. The V09 code identified MRSA infection with a sensitivity of 24% (range, 21%–34%) and positive predictive value of 31% (range, 22%–53%). The agreement between assignment of the V09 code and presence of MRSA infection had a k coefficient of 0.26 (95% confidence interval, 0.25–0.27).Conclusions.In its current state, the ICD-9-CM code V09 is not an accurate predictor of MRSA infection and should not be used to measure rates of MRSA infection.
Effect of Accounting for Multiple Concurrent Catheters on Central Line–Associated Bloodstream Infection Rates: Practical Data Supporting a Theoretical Concern
Authors: Aslakson Rebecca A. , Romig Mark , Galvagno Samuel M. , Colantuoni Elizabeth , Cosgrove Sara E. , Perl Trish M. , Pronovost Peter J. 
Published: January 2011

Background.Central line-associated bloodstream infection (CLABSI) rates are gaining importance as they become publicly reported metrics and potential pay-for-performance indicators. However, the current conventional method by which they are calculated may be misleading and unfairly penalize high-acuity care settings, where patients often have multiple consurrent central venous catheters (CVCs).Objective.We compared the conventional method of calculating CLABSI rates, in which the number of catheter-days is used (1 patient with n catheters for 1 day has 1 catheter-day), with a new method that accounts for multiple concurrent catheters (1 patient with n catheters for 1 day has n catheter-days), to determine whether the difference appreciably changes the estimated CLABSI rate.Design.Cross-sectional survey.Setting.Academic, tertiary care hospital.Patients.Adult patients who were consecutively admitted from June 10 through July 9, 2009, to a cardiac-surgical intensive care unit and a surgical intensive and surgical intermediate care unit.Results.Using the conventional method, we counted 485 catheter-days throughout the study period, with a daily mean of 18.6 catheter-days (95% confidence interval, 17.2-20.0 catheter-days) in the 2 intensive care units. In contrast, the new method identified 745 catheter-days, with a daily mean of 27.5 catheter-days (95% confidence interval, 25.6-30.3) in the 2 intensive care units. The difference was statistically significant (P < .001). The new method that accounted for multiple concurrent CVCs resulted in a 53.6% increase in the number of catheter-days; this increased denominator decreases the calculated CLABSI rate by 36%.Conclusions.The undercounting of catheter-days for patients with multiple concurrent CVCs that occurs when the conventional method of calculating CLABSI rates is used inflates the CLABSI rate for care settings that have a high CVC burden and may not adjust for underlying medical illness. Additional research is needed to validate and generalize our findings.
Peripherally Inserted Central Venous Catheter–Associated Bloodstream Infections in Hospitalized Adult Patients
Authors: Ajenjo M. Cristina , Morley James C. , Russo Anthony J. , McMullen Kathleen M. , Robinson Catherine , Williams Robert C. , Warren David K. 
Published: January 2011

Background.Limited data on the risk of peripherally inserted central venous catheter-associated bloodstream infections (PICC BSIs) in hospitalized patients are available. In 2007, dedicated intravenous therapy nurses were no longer available to place difficult peripheral intravenous catheters or provide PICC care Barnes-Jewish Hospital.Objectives.To determine the hospital-wide incidence of PICC BSIs and to assess the effect of discontinuing intravenous therapy service on PICC use and PICC BSI rates.Setting.A 1,252-bed tertiary care teaching hospital.Methods.A 31-month retrospective cohort study was performed. PICC BSIs were defined using National Healthcare Safety Network criteria.Results.In total, 163 PICC BSIs were identified (3.13 BSIs per 1,000 catheter-days). PICC use was higher in intensive care units (ICUs) than non-ICU areas (PICC utilization ratio, 0.109 vs 0.059 catheter-days per patient-day for ICU vs non-ICU; rate ratio [RR], 1.84 [95% confidence interval {CI}, 1.78-1.91]). PICC BSI rates were higher in ICUs (4.79 vs 2.79 episodes per 1,000 catheter-days; RR, 1.7 [95% CI, 1.10-2.61]). PICC use increased hospital-wide after the intravenous therapy service was discontinued (0.049 vs 0.097 catheter-days per patient-day; P = .01), but PICC BSI rates did not change (2.68 vs 3.63 episodes per 1,000 catheter-days; P = .06). Of PICC BSIs, 73% occurred in non-ICU patients.Conclusions.PICC use and PICC BSI rates were higher in ICUs; however, most of the PICC BSIs occurred in non-ICU areas. Reduction in intravenous therapy services was associated with increased PICC use across the hospital, but PICC BSI rates did not increase.
Is Continuous Subglottic Suctioning Cost-Effective for the Prevention of Ventilator-Associated Pneumonia?
Authors: Hallais Corinne , Merle Véronique , Guitard Pierre-Gildas , Moreau Anne , Josset Valérie , Thillard Denis , Haghighat Suzanne , Veber Benoit , Czernichow Pierre 
Published: January 2011

Objective.To establish whether continuous subglottic suctioning (CSS) could be cost-effective.Design.Cost-benefit analysis, based on a hypothetical replacement of conventional ventilation (CV) with CSS.Setting.A surgical intensive care unit (SICU) of a tertiary care university hospital in France.Patients.All consecutive patients receiving ventilation in the SICU in 2006.Methods.Efficacy data for CSS were obtained from the literature and applied to the SICU of our hospital. Costs for CV and CSS were provided by the hospital pharmacy; costs for ventilator-associated pneumonia (VAP) were obtained from the literature. The cost per averted VAP episode was calculated, and a sensitivity analysis was performed on VAP incidence and on the number of tubes required for each patient.Results.At our SICU in 2006, 416 patients received mechanical ventilation for 3,487 ventilation-days, and 32 VAP episodes were observed (7.9 episodes per 100 ventilated patients; incidence density, 9.2 episodes per 10,000 ventilation-days). Based on the hypothesis of a 29% reduction in the risk of VAP with CSS than CV, 9 VAP episodes could have been averted. The additional cost of CSS for 2006 was estimated to be €10,585.34. The cost per averted VAP episode was €1,176.15. Assuming a VAP cost of €4,387, a total of 3 averted VAP episodes would neutralize the additional cost. For a low VAP incidence of 6.6%, the cost per averted VAP would be €1,323. If each patient required 2 tubes during ventilation, the cost would be €1,383.69 per averted VAP episode.Conclusion.Replacement of CV with CSS was cost-effective even when assuming the most pessimistic scenario of VAP incidence and costs.
Effect of Patterns of Transferring Patients among Healthcare Institutions on Rates of Nosocomial Methicillin-ResistantStaphylococcus aureusTransmission: A Monte Carlo Simulation
Authors: Lesosky Maia , McGeer Allison , Simor Andrew , Green Karen , Low Don E. , Raboud Janet 
Published: January 2011

Objective.To determine the effect of the rate and pattern of patient transfers among institutions within a single metropolitan area on the rates of methicillin-resistantStaphylococcus aureus(MRSA) transmission among patients in hospitals and nursing homes.Methods.A stochastic, discrete-time, Monte Carlo simulation was used to model the rate and spread of MRSA transmission among patients in medical institutions within a single metropolitan area. Admission, discharges, transfers, and nosocomial transmission were simulated with respect to different interinstitutional transfer strategies and various situational scenarios, such as outlier institutions with high transmission rates.Results.The simulation results indicated that transfer patterns and transfer rate changes do not affect nosocomial MRSA transmission. Outlier institutions with high transmission rates affect the systemwide rate of nosocomial infections differently, depending on institution type.Conclusion.It is worth effort to understanding disease-transmission dynamics and interinstitutional transfer patterns for the management of recently introduced diseases or strains. Once endemic in a system, other strategies for transmission control need to be implemented.
Estimates of nuclear DNA content in 98 species of brown algae (Phaeophyta)
Authors: Phillips Naomi , Kapraun Donald F. , Gómez Garreta Amelia , Ribera Siguan M. Antonia , Rull Jorde L. , Salvador Soler Noemi , Lewis Raymond , Kawai Hiroshi 
Published: January 2011

Abstract

Background and aims
Brown algae are critical components of marine ecosystems around the world. However, the genome of only one species of the class has so far been sequenced. This contrasts with numerous sequences available for model organisms such as higher plants, flies or worms. The present communication expands our coverage of DNA content information to 98 species of brown algae with a view to facilitating further genomic investigations of the class.

Methodology
The DNA-localizing fluorochrome DAPI (4′,6-diamidino-2-phenylindole) and the red blood cell (chicken erythrocyte) standard were used to estimate 2C values by static microspectrophotometry.

Principal results
2C DNA contents are reported for 98 species of brown algae, almost doubling the number of estimates available for the class. The present results also expand the reported DNA content range to 0.2–3.6 pg, with several species of Fucales and Laminariales containing apparent polyploid genomes with 2C = 1.8–3.6 pg.

Conclusions
The data provide DNA content values for 12 of the 19 recognized orders of brown algae spanning the breadth of the class. Despite earlier contentions concerning DNA content and the presence of oogamy, the present results do not support a correlation between phylogenetic placement and genome size. The closest sister groups to the brown algae have genome sizes on the order of 0.3 pg (e.g. Schizocladiophyceae), suggesting that this may be the ancestral genome size. However, DNA content ranges widely across the class.
Succinct data structures for assembling large genomes
Authors: Conway Thomas C. , Bromage Andrew J. 
Published: January 2011

Abstract
Motivation: Second-generation sequencing technology makes it feasible for many researches to obtain enough sequence reads to attempt the de novo assembly of higher eukaryotes (including mammals). De novo assembly not only provides a tool for understanding wide scale biological variation, but within human biomedicine, it offers a direct way of observing both large-scale structural variation and fine-scale sequence variation. Unfortunately, improvements in the computational feasibility for de novo assembly have not matched the improvements in the gathering of sequence data. This is for two reasons: the inherent computational complexity of the problem and the in-practice memory requirements of tools.
Results: In this article, we use entropy compressed or succinct data structures to create a practical representation of the de Bruijn assembly graph, which requires at least a factor of 10 less storage than the kinds of structures used by deployed methods. Moreover, because our representation is entropy compressed, in the presence of sequencing errors it has better scaling behaviour asymptotically than conventional approaches. We present results of a proof-of-concept assembly of a human genome performed on a modest commodity server.
Availability: Binaries of programs for constructing and traversing the de Bruijn assembly graph are available from http://www.genomics.csse.unimelb.edu.au/succinctAssembly.
Contact: tom.conway@nicta.com.au
Supplementary information: Supplementary data are available at Bioinformatics online.
S (+)-Ketamine Suppresses Desensitization of γ-Aminobutyric Acid Type B Receptor-mediated Signaling by Inhibition of the Interaction of γ-Aminobutyric Acid Type B Receptors with G Protein–coupled Receptor Kinase 4 or 5
Authors: Ando Yuko , Hojo Minoru , Kanaide Masato , Takada Masafumi , Sudo Yuka , Shiraishi Seiji , Sumikawa Koji , Uezono Yasuhito 
Published: January 2011

Background
Intrathecal baclofen therapy is an established treatment for severe spasticity. However, long-term management occasionally results in the development of tolerance. One of the mechanisms of tolerance is desensitization of γ-aminobutyric acid type B receptor (GABABR) because of the complex formation of the GABAB2 subunit (GB2R) and G protein-coupled receptor kinase (GRK) 4 or 5. The current study focused on S(+)-ketamine, which reduces the development of morphine tolerance. This study was designed to investigate whether S(+)-ketamine affects the GABABR desensitization processes by baclofen.

Methods
The G protein-activated inwardly rectifying K channel currents induced by baclofen were recorded using Xenopus oocytes coexpressing G protein-activated inwardly rectifying K channel 1/2, GABAB1a receptor subunit, GB2R, and GRK. Translocation of GRKs 4 and 5 and protein complex formation of GB2R with GRKs were analyzed by confocal microscopy and fluorescence resonance energy transfer analysis in baby hamster kidney cells coexpressing GABAB1a receptor subunit, fluorescent protein-tagged GB2R, and GRKs. The formation of protein complexes of GB2R with GRKs was also determined by coimmunoprecipitation and Western blot analysis.

Results
Desensitization of GABABR-mediated signaling was suppressed by S(+)-ketamine in a concentration-dependent manner in the electrophysiologic assay. Confocal microscopy revealed that S(+)-ketamine inhibited translocation of GRKs 4 and 5 to the plasma membranes and protein complex formation of GB2R with the GRKs. Western blot analysis also showed that S(+)-ketamine inhibited the protein complex formation of GB2R with the GRKs.

Conclusion
S(+)-Ketamine suppressed the desensitization of GABABR-mediated signaling at least in part through inhibition of formation of protein complexes of GB2R with GRK 4 or 5.
Midazolam Suppresses Maturation of Murine Dendritic Cells and Priming of Lipopolysaccharide-induced T Helper 1-type Immune Response
Authors: Ohta Noriyuki , Ohashi Yoshifumi , Takayama Chihiro , Mashimo Takashi , Fujino Yuji 
Published: January 2011

Background
Dendritic cells (DCs), as antigen-presenting cells, play a key role in the induction and regulation of adaptive immune response. Midazolam is reported to have immunomodulatory properties that affect immune cells. However, the effect of midazolam on DCs has not been characterized. We examined the immunomodulatory properties of midazolam on DC-mediated immune response.

Methods
After allowing murine bone marrow-derived DCs induced by granulocyte macrophage colony stimulating factor to mature, we analyzed their expression of costimulatory molecules (CD80 and CD86), major histocompatibility complex class II molecules, and the secretion of interleukin-12 p40. In vitro, we evaluated the effect of midazolam on maturing DCs in mixed cell cultures containing DCs and T cells. In vivo, we investigated the contact-hypersensitivity response.

Results
Midazolam suppressed the expression of CD80, CD86, and major histocompatibility complex class II molecules from murine DCs. Treated with midazolam, DCs also secreted less interleukin-12 p40. In mixed cell cultures with CD3-positive T cells, midazolam-treated DCs showed less propensity to stimulate the proliferation of CD3-positive T cells and the secretion of interferon-γ from CD4-positive T cells. Midazolam-treated DCs impaired the induction of contact-hypersensitivity response. Treatment with ligands for peripheral benzodiazepine receptor inhibited the up-regulation of CD80 during DC maturation.

Conclusion
Midazolam inhibits the functional maturation of murine DCs and interferes with DC induction of T helper 1 immunity in the whole mouse. In addition, it appears that the immunomodulatory effect of midazolam is mediated via the action of midazolam on the peripheral benzodiazepine receptor.
The Late Ordovician deglaciation sequence of the SW Murzuq Basin (Libya)
Authors: Moreau Julien 
Published: January 2011

ABSTRACTRocks of Late Ordovician to Silurian age are well exposed on the western rim of the Murzuq Basin (Ghat‐Tikiumit area, Libya) where seismic‐scale exposures allow spectacular insights into the growth and decay of the Late Ordovician (Hirnantian) ice sheet. The final deglaciation left a complex topography with a combination of subglacial morphologies and proglacial depositional systems. This paper documents the glacial and proglacial palaeo‐topography that controls the accumulation of a postglacial transgressive depositional system and the Rhuddanian (Early Silurian) shales. The glacial relief directly contributed to an important hiatus, with the Rhuddanian deposits at the base of the remnant glacial troughs being 3 Ma older than at the top of the topographic highs. The source‐rock in the Murzuq Basin is of Early Rhuddanian age, so it is present only in the deepest part whereas geomorphic traps are formed within the highs of the relict postglacial topography. The transgressive system, recognised for its good reservoir potential, is considered to play a key‐role in the petroleum system, linking the source rock deposited in the ancient topographic lows with the reservoir rocks in the topographic highs. This study aims to demonstrate the importance of palaeo‐glaciological reconstructions for petroleum exploration of the Ordovician–Silurian in North Africa.