bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dispersion in the large-deviation regime. Part 2. Cellular flow at large Péclet number
Authors: Haynes P. H. , Vanneste J. 
Published: March 2014

AbstractA standard model for the study of scalar dispersion through the combined effect of advection and molecular diffusion is a two-dimensional periodic flow with closed streamlines inside periodic cells. Over long time scales, the dispersion of a scalar released in this flow can be characterized by an effective diffusivity that is a factor$\mathit{Pe}^{1/2}$larger than molecular diffusivity when the Péclet number$\mathit{Pe}$is large. Here we provide a more complete description of dispersion in this regime by applying the large-deviation theory developed in Part 1 of this paper. Specifically, we derive approximations to the rate function governing the scalar concentration at large time$t$by carrying out an asymptotic analysis of the relevant family of eigenvalue problems. We identify two asymptotic regimes and, for each, make predictions for the rate function and spatial structure of the scalar. Regime I applies to distances$|\boldsymbol {x}|$from the scalar release point that satisfy$|\boldsymbol {x}|= O(\mathit{Pe}^{1/4} t)$. The concentration in this regime is isotropic at large scales, is uniform along streamlines within each cell, and varies rapidly in boundary layers surrounding the separatrices between adjacent cells. The results of homogenization theory, yielding the$O(\mathit{Pe}^{1/2})$effective diffusivity, are recovered from our analysis in the limit$|\boldsymbol {x}|\ll \mathit{Pe}^{1/4} t$. Regime II applies when$|\boldsymbol {x}|=O(\mathit{Pe}\, t/{\rm log}\, \mathit{Pe})$and is characterized by an anisotropic concentration distribution that is localized around the separatrices. A novel feature of this regime is the crucial role played by the dynamics near the hyperbolic stagnation points. A consequence is that in part of the regime the dispersion can be interpreted as resulting from a random walk on the lattice of stagnation points. The two regimes overlap so that our asymptotic results describe the scalar concentration over a large range of distances$|\boldsymbol {x}|$. They are verified against numerical solutions of the family of eigenvalue problems yielding the rate function.
Spanwise reflection symmetry breaking and turbulence control: plane Couette flow
Authors: Chagelishvili G. , Khujadze G. , Foysi H. , Oberlack M. 
Published: March 2014

AbstractWe propose and analyse a new strategy of shear flow turbulence control that can be realized by the following steps: (i) imposing specially designed seed velocity perturbations, which are non-symmetric in the spanwise direction, at the walls of a flow; (ii) the configuration of the latter ensures a gain of shear flow energy and the breaking of turbulence spanwise reflection symmetry: this leads to the generation of spanwise mean flow; (iii) that changes the self-sustained dynamics of turbulence and results in a considerable reduction of the turbulence level and the production of turbulent kinetic energy. In fact, by this strategy the shear flow transient growth mechanism is activated and the formed spanwise mean flow is an intrinsic, nonlinear composition of the controlled turbulence and not directly introduced in the system. In the present paper, a weak near-wall volume forcing is designed to impose the velocity perturbations with required characteristics in the flow. The efficiency of the proposed scheme has been demonstrated by direct numerical simulation using plane Couette flow as a representative example. A promising result was obtained: after a careful parameter selection, the forcing reduces the turbulence kinetic energy and its production by up to one-third. The strategy can be naturally applied to other wall-bounded flows, e.g. channel and boundary-layer flows. Of course, the considered volume force is theoretical and hypothetical. Nevertheless, it helps to gain knowledge concerning the design of the seed velocity field that is necessary to be imposed in the flow to achieve a significant reduction of the turbulent kinetic energy. This is convincing with regard to a new control strategy, which could be based on specially constructed blowing/suction or riblets, by employing the insight gained by the comprehension of the results obtained using the investigated methodology in this paper.
Offsetting obstacles of any shape for robot motion planning
Authors: Laskar Md Nasir Uddin , Viet Hoang Huu , Choi Seung Yoon , Ahmed Ishtiaq , Lee Sungyoung , Chung Tae Choong 
Published: March 2014

SUMMARYWe present an algorithm for offsetting the workspace obstacles of a circular robot. Our method has two major steps: It finds the raw offset curve for both lines and circular arcs, and then removes the global invalid loops to find the final offset. To generate the raw offset curve and remove global invalid loops, O(n) and O((n+k)log m) computational times are needed respectively, where n is the number of vertices in the original polygon, k is the number of self-intersections and m is the number of segments in the raw offset curve, where m ≤ n. Any local invalid loops are removed before generating the raw offset curve by invoking a pair-wise intersection detection test (PIDT). In the PIDT, two intersecting entities are checked immediately after they are computed, and if the test is positive, portions of the intersecting segments are removed. Our method works for conventional polygons as well as the polygons that contain circular arcs. Our algorithm is simple and very fast, as each sub-process of the algorithm can be completed in linear time except the last one, which is nearly linear. Therefore, the overall complexity of the algorithm is nearly linear. By applying our simple and efficient approach, offsetting obstacles of any shape make it possible to construct a configuration space that ensures optimized motion planning.
Hobbes on the International Rule of Law
Authors: Dyzenhaus David 
Published: March 2014

Perhaps the most influential passage on the rule of law in international law comes from chapter 13 of Thomas Hobbes's Leviathan. In the course of describing the miserable condition of mankind in the state of nature, Hobbes remarks to readers who might be skeptical that such a state ever existed that they need only look to international relations—the relations between independent states—to observe one:But though there had never been any time, wherein particular men were in a condition of warre one against another; yet in all times, Kings, and Persons of Soveraigne authority, because of their Independency, are in continuall jealousies, and in the state and posture of Gladiators; having their weapons pointing, and their eyes fixed on one another; that is, their Forts, Garrisons, and Guns upon the Frontiers of their Kingdomes; and continuall Spyes upon their neighbours; which is a posture of War.
Improving Signal to Noise in Labeled Biological Specimens Using Energy-Filtered TEM of Sections with a Drift Correction Strategy and a Direct Detection Device
Authors: Ramachandra Ranjan , Bouwer James C. , Mackey Mason R. , Bushong Eric , Peltier Steven T. , Xuong Nguyen-Huu , Ellisman Mark H. 
Published: March 2014

AbstractEnergy filtered transmission electron microscopy techniques are regularly used to build elemental maps of spatially distributed nanoparticles in materials and biological specimens. When working with thick biological sections, electron energy loss spectroscopy techniques involving core-loss electrons often require exposures exceeding several minutes to provide sufficient signal to noise. Image quality with these long exposures is often compromised by specimen drift, which results in blurring and reduced resolution. To mitigate drift artifacts, a series of short exposure images can be acquired, aligned, and merged to form a single image. For samples where the target elements have extremely low signal yields, the use of charge coupled device (CCD)-based detectors for this purpose can be problematic. At short acquisition times, the images produced by CCDs can be noisy and may contain fixed pattern artifacts that impact subsequent correlative alignment. Here we report on the use of direct electron detection devices (DDD’s) to increase the signal to noise as compared with CCD’s. A 3× improvement in signal is reported with a DDD versus a comparably formatted CCD, with equivalent dose on each detector. With the fast rolling-readout design of the DDD, the duty cycle provides a major benefit, as there is no dead time between successive frames.
Anglican Stories: Bible, Liturgy and Church
Authors: McGowan Andrew 
Published: March 2014

AbstractWhile Anglicans differ on many issues, they share not only a common history but a common interest in telling and retelling it. Essays in the present issue exemplify the concentration of these stories on three areas: the Bible, Liturgy and the Church itself. Historical or systematic attempts to define Anglicanism founder if attempts to identify essential elements are too prescriptive; but the shared reality and reflection on it constitute a characteristic form of Anglican theological practice.
Terahertz absorption characteristics of nickel–chromium film in a microbolometer focal plane array
Authors: Gou Jun , Jiang Yadong , Wang Jun 
Published: March 2014

Nickel–chromium (NiCr) thin film acted as a terahertz (THz) absorption layer in uncooled infrared (IR) microbolometers operated in the THz spectral range. Nanoscale NiCr thin films with different thicknesses were deposited on the diaphragms of 320 × 240 IR focal plane arrays (IRFPAs). The experiments suggested that the THz absorption of NiCr film increased with the increased frequency. Absorption for a lower frequency decreased whereas that for a higher frequency increased with the decreased film thickness. Optimised absorption for different spectral ranges was achieved by adjusting the NiCr film thickness. A 30 nm NiCr film provided the largest absorption in 0.5–1.5 THz whereas an 8 nm NiCr film showed the greatest contribution in 2–2.5 THz. The THz absorption characteristics of the pixel membrane structure in the IRFPAs coupled with a thin metallic film were modelled and analysed. A good agreement was obtained between the calculations and the measurements.
EphA7 signaling guides cortical dendritic development and spine maturation
Authors: Clifford Meredith A. , Athar Wardah , Leonard Carrie E. , Russo Alexandra , Sampognaro Paul J. , Van der Goes Marie-Sophie , Burton Denver A. , Zhao Xiumei , Lalchandani Rupa R. , Sahin Mustafa , Vicini Stefano , Donoghue Maria J. 
Published: March 2014

Significance
The stereotyped generation and maturation of neurons during development is essential for well-coordinated brain function in maturity. This study characterizes the role of the membrane-bound receptor tyrosine kinase EphA7 in cerebral cortical dendritic elaboration and dendritic spine formation and synaptic function. Results indicate that EphA7 restricts dendritic elaboration early in corticogenesis and promotes dendritic spine formation and synaptic maturation later in a neuron’s life. These results identify EphA7 as a signaling molecule in the molecular machinery that drives neuronal maturation and synaptic function, signaling that may impact our understanding of neurodevelopmental disorders.
Mapping protein conformational heterogeneity under pressure with site-directed spin labeling and double electron–electron resonance
Authors: Lerch Michael T. , Yang Zhongyu , Brooks Evan K. , Hubbell Wayne L. 
Published: March 2014

Significance
Excited states of proteins play functional roles, but their low population and conformational flexibility pose a challenge for characterization by most spectroscopic techniques. Here, this challenge is met by combining high hydrostatic pressure, which reversibly populates excited states, and site-directed spin labeling with double electron–electron resonance (DEER) spectroscopy, which resolves distinct conformational substates of proteins by measuring distances between spin-labeled pairs. We present a method for trapping high-pressure equilibria of proteins by rapid freezing under pressure, followed by depressurization and acquisition of DEER data at atmospheric pressure. The methodology is applied to myoglobin, revealing unique information on the length scale of helical fluctuations in the pressure-populated as compared with the pH-populated molten globule states of the apo-protein.
Multidrug-Resistant Gram-Negative Bloodstream Infections among Residents of Long-Term Care Facilities
Authors: Venkatachalam Indumathi , Yang Hsu Li , Fisher Dale , Lye David C. , Lin Ling Moi , Tambyah Paul , Perl Trish M. 
Published: March 2014

Objective.Prevalence of multidrug-resistant (MDR) gram-negative (GN) bacteria is increasing globally and is complicated by patient movement between acute and long-term care facilities (LTCFs). In Asia, the contribution of LTCFs as a source of MDR GN infections is poorly described. We aimed to define the association between residence in LTCFs and MDR GN bloodstream infections (BSIs).Design.Secondary analysis of data from an observational cohort.Setting.Two tertiary referral hospitals in Singapore, including the 1,400-bed Tan Tock Seng Hospital and the 1,600-bed Singapore General Hospital.Participants.Adult patients with healthcare-onset (HCO) or hospital-onset (HO) GN BSI.Methods.Patients were identified from hospital databases using standard definitions. Risk factors for both MDR GN HCO and HO BSI were analyzed using a multivariable logistic regression model.Results.A total of 675 episodes of GN BSI occurred over a 31-month period. Residence in a LTCF was an independent risk factor for developing MDR GN BSI (odds ratio [OR], 5.1 [95% confidence interval (CI), 2.2–11.9]; P < .01) when antibiotics were not used within the preceding 30 days. This risk persisted beyond the first 48 hours of hospitalization (OR, 3.4 [95% CI, 1.3–9.0]; P = .01). Previous culture growing an MDR organism (OR, 1.8 [95% CI, 1.3–2.7]; P < .01), previous antibiotic use (OR, 1.8 [95% CI, 1.2–2.6]; P < .01), and intensive care unit stay (OR, 2.2 [95% CI, 1.2–3.9]; P = .01), increased the risk of MDR GN BSI.Conclusions.Residence in a LTCF is an independent risk factor for MDR GN BSI. Attempts to contain MDR GN bacteria in large Asian cities, where the proportion of the population that is elderly is projected to increase, should include infection prevention strategies that engage LTCFs.
Piecewise-constant and low-rank approximation for identification of recurrent copy number variations
Authors: Zhou Xiaowei , Liu Jiming , Wan Xiang , Yu Weichuan 
Published: March 2014

Abstract
Motivation:  The post-genome era sees urgent need for more novel approaches to extracting useful information from the huge amount of genetic data. The identification of recurrent copy number variations (CNVs) from array-based comparative genomic hybridization (aCGH) data can help understand complex diseases, such as cancer. Most of the previous computational methods focused on single-sample analysis or statistical testing based on the results of single-sample analysis. Finding recurrent CNVs from multi-sample data remains a challenging topic worth further study.
Results:  We present a general and robust method to identify recurrent CNVs from multi-sample aCGH profiles. We express the raw dataset as a matrix and demonstrate that recurrent CNVs will form a low-rank matrix. Hence, we formulate the problem as a matrix recovering problem, where we aim to find a piecewise-constant and low-rank approximation (PLA) to the input matrix. We propose a convex formulation for matrix recovery and an efficient algorithm to globally solve the problem. We demonstrate the advantages of PLA compared with alternative methods using synthesized datasets and two breast cancer datasets. The experimental results show that PLA can successfully reconstruct the recurrent CNV patterns from raw data and achieve better performance compared with alternative methods under a wide range of scenarios.
Availability and implementation:  The MATLAB code is available at http://bioinformatics.ust.hk/pla.zip .
Contact: xwan@comp.hkbu.edu.hk or eeyu@ust.hk
An R package to analyse LC/MS metabolomic data: MAIT (Metabolite Automatic Identification Toolkit)
Authors: Fernández-Albert Francesc , Llorach Rafael , Andrés-Lacueva Cristina , Perera Alexandre 
Published: March 2014

Abstract
Summary: Current tools for liquid chromatography and mass spectrometry for metabolomic data cover a limited number of processing steps, whereas online tools are hard to use in a programmable fashion. This article introduces the Metabolite Automatic Identification Toolkit (MAIT) package, which makes it possible for users to perform metabolomic end-to-end liquid chromatography and mass spectrometry data analysis. MAIT is focused on improving the peak annotation stage and provides essential tools to validate statistical analysis results. MAIT generates output files with the statistical results, peak annotation and metabolite identification.
Availability and implementation: http://b2slab.upc.edu/software-and-downloads/metabolite-automatic-identification-toolkit/ .
Contact: francesc.fernandez.albert@upc.edu
Supplementary information: Supplementary data are available at Bioinformatics online
Lung Ultrasound Predicts Interstitial Syndrome and Hemodynamic Profile in Parturients with Severe Preeclampsia
Authors: Zieleskiewicz Laurent , Contargyris Claire , Brun Clément , Touret Maxime , Vellin Armand , Antonini François , Muller Laurent , Bretelle Florence , Martin Claude , Leone Marc 
Published: March 2014

Abstract

Background:
The role of lung ultrasound has never been evaluated in parturients with severe preeclampsia. The authors’ first aim was to assess the ability of lung ultrasound to detect pulmonary edema in severe preeclampsia. The second aim was to highlight the relation between B-lines and increased left ventricular end-diastolic pressures.

Methods:
This prospective cohort study was conducted in a level-3 maternity during a 12-month period. Twenty parturients with severe preeclampsia were consecutively enrolled. Both lung and cardiac ultrasound examinations were performed before (n = 20) and after delivery (n = 20). Each parturient with severe preeclampsia was compared with a control healthy parturient. Pulmonary edema was determined using two scores: the B-pattern and the Echo Comet Score. Left ventricular end-diastolic pressures were assessed by transthoracic echocardiography.

Results:
Lung ultrasound detected interstitial edema in five parturients (25%) with severe preeclampsia. A B-pattern was associated to increased mitral valve early diastolic peak E (116 vs. 90 cm/s; P = 0.05) and to increased E/E’ ratio (9.9 vs. 6.6; P < 0.001). An Echo Comet Score of greater than 25 predicted an increase in filling pressures (E/E’ ratio >9.5) with a sensitivity and specificity of 1.00 (95% CI, 0.69 to 1.00) and 0.82 (95% CI, 0.66 to 0.92), respectively.

Conclusions:
In parturients with severe preeclampsia, lung ultrasound detects both pulmonary edema and increased left ventricular end-diastolic pressures. The finding of a B-pattern should restrict the use of fluid. However, these preliminary results are associations from a single sample. They need to be replicated in a larger, definitive study.
Cellular Registration without Behavioral Recall of Olfactory Sensory Input under General Anesthesia
Authors: Samuelsson Andrew R. , Brandon Nicole R. , Tang Pei , Xu Yan 
Published: March 2014

Abstract

Background:
Previous studies suggest that sensory information is “received” but not “perceived” under general anesthesia. Whether and to what extent the brain continues to process sensory inputs in a drug-induced unconscious state remain unclear.

Methods:
One hundred seven rats were randomly assigned to 12 different anesthesia and odor exposure paradigms. The immunoreactivities of the immediate early gene products c-Fos and Egr1 as neural activity markers were combined with behavioral tests to assess the integrity and relationship of cellular and behavioral responsiveness to olfactory stimuli under a surgical plane of ketamine–xylazine general anesthesia.

Results:
The olfactory sensory processing centers could distinguish the presence or absence of experimental odorants even when animals were fully anesthetized. In the anesthetized state, the c-Fos immunoreactivity in the higher olfactory cortices revealed a difference between novel and familiar odorants similar to that seen in the awake state, suggesting that the anesthetized brain functions beyond simply receiving external stimulation. Reexposing animals to odorants previously experienced only under anesthesia resulted in c-Fos immunoreactivity, which was similar to that elicited by familiar odorants, indicating that previous registration had occurred in the anesthetized brain. Despite the “cellular memory,” however, odor discrimination and forced-choice odor-recognition tests showed absence of behavioral recall of the registered sensations, except for a longer latency in odor recognition tests.

Conclusions:
Histologically distinguishable registration of sensory processing continues to occur at the cellular level under ketamine–xylazine general anesthesia despite the absence of behavioral recognition, consistent with the notion that general anesthesia causes disintegration of information processing without completely blocking cellular communications.
Improving Patient Safety Culture in Primary Care: A Systematic Review
Authors: Verbakel Natasha J. , Langelaan Maaike , Verheij Theo J. M. , Wagner Cordula , Zwart Dorien L. M. 
Published: March 2014

Background
Patient safety culture, described as shared values, attitudes and behavior of staff in a health-care organization, gained attention as a subject of study as it is believed to be related to the impact of patient safety improvements. However, in primary care, it is yet unknown, which effect interventions have on the safety culture.

Objectives
To review literature on the use of interventions that effect patient safety culture in primary care.

Methods
Searches were performed in PubMed, EMBASE, CINAHL, and PsychINFO on March 4, 2013. Terms defining safety culture were combined with terms identifying intervention and terms indicating primary care. Inclusion followed if the intervention effected patient safety culture, and effect measures were reported.

Results
The search yielded 214 articles from which two were eligible for inclusion. Both studies were heterogeneous in their interventions and outcome; we present a qualitative summary. One study described the implementation of an electronic medical record system in general practices as part of patient safety improvements. The other study facilitated 2 workshops for general practices, one on risk management and another on significant event audit. Results showed signs of improvement, but the level of evidence was low because of the design and methodological problems.

Conclusions
These studies in general practice provide a first understanding of improvement strategies and their effect in primary care. As the level of evidence was low, no clear preference can be determined. Further research is needed to help practices make an informed choice for an intervention.