bluuebunny/crossref_metadata_2025 huggingface dataset:
Linear stability analysis and nonlinear simulation of the channeling effect on viscous fingering instability in miscible displacement
Authors: Shahnazari M. R. , Maleka Ashtiani I. , Saberi A.
Published: March 2018

In this paper, the effect of channeling on viscous fingering instability of miscible displacement in porous media is studied. In fact, channeling is introduced as a solution to stabilize the viscous fingering instability. In this solution, narrow channels were placed next to the walls, and by considering an exponential function to model the channeling effect, a heterogeneous media is assumed. In linear stability analysis, the governing equations are transferred to Fourier space, and by introducing a novel numerical method, the transferred equations are analyzed. The growth rate based on the wave number diagram has been drawn up in three sections of the medium. It is found that the flow becomes more stable at the center and unstable along the walls when the permeability ratio is increased. Also when the permeability ratio is approximately equal to one, the channeling has no significant effect. In nonlinear simulations, by using stream function and vortices, new equations have been rewritten and it is shown that channeling has a profound effect on the growth of the fingers and mechanisms. In addition to the superposition of velocity vectors and concentration contours, the development of instability is investigated using the mixing length and sweep efficiency diagram. The results show that although channeling reduces instability, it increases the displacement process time.
Dynamical simulation of electron transfer processes in self-assembled monolayers at metal surfaces using a density matrix approach
Authors: Prucker V. , Bockstedte M. , Thoss M. , Coto P. B.
Published: March 2018

A single-particle density matrix approach is introduced to simulate the dynamics of heterogeneous electron transfer (ET) processes at interfaces. The characterization of the systems is based on a model Hamiltonian parametrized by electronic structure calculations and a partitioning method. The method is applied to investigate ET in a series of nitrile-substituted (poly)(p-phenylene)thiolate self-assembled monolayers adsorbed at the Au(111) surface. The results show a significant dependence of the ET on the orbital symmetry of the donor state and on the molecular and electronic structure of the spacer.
A particle manipulation method and its experimental study based on opposed jets
Authors: Zhang Qin , Fan Jibin , Wang Han , Aoyama Hisayuki
Published: March 2018

A particle manipulation method was presented in this paper based on opposed jets. In such a method, particles were trapped near the stagnation point of the flow field and moved by controlling the position of the stagnation point. The hold direction of the flow to the particle was changed by changing the orientation of the opposed-jet flow field where a particle is trapped. Subsequently, the directional and quantitative movement of the particle in any direction was achieved. Taking micron particles as examples, we analyzed the control mechanism of particles based on opposed jets and evaluated the influence of jet velocity, inner diameter, distance of end face, radial error, and position of capillaries on the particle control performance by simulations. The feasibility of the proposed method was proved by a great number of experiments, and the results demonstrated that particles with the arbitrary size and shape can be trapped and moved directionally and quantitatively by constructing an opposed-jet flow field. The trapping and position control of particles can be manipulated without any contact with proper flow field parameters.
Crystal growth kinetics of triblock Janus colloids
Authors: Reinhart Wesley F. , Panagiotopoulos Athanassios Z.
Published: March 2018

We measure the kinetics of crystal growth from a melt of triblock Janus colloids using non-equilibrium molecular dynamics simulations. We assess the impact of interaction anisotropy by systematically varying the size of the attractive patches from 40% to 100% coverage, finding substantially different growth behaviors in the two limits. With isotropic particles, the interface velocity is directly proportional to the subcooling, in agreement with previous studies. With highly anisotropic particles, the growth curves are well approximated by using a power law with exponent and prefactor that depend strongly on the particular surface geometry and patch fraction. This nonlinear growth appears correlated to the roughness of the solid-liquid interface, with the strongest growth inhibition occurring for the smoothest crystal faces. We conclude that crystal growth for patchy particles does not conform to the typical collision-limited mechanism, but is instead an activated process in which the rate-limiting step is the collective rotation of particles into the proper orientation. Finally, we show how differences in the growth kinetics could be leveraged to achieve kinetic control over polymorph growth, either enhancing or suppressing metastable phases near solid-solid coexistence lines.
A flexible optically re-writable color liquid crystal display
Authors: Zhang Yihong , Sun Jiatong , Liu Yang , Shang Jianhua , Liu Hao , Liu Huashan , Gong Xiaohui , Chigrinov Vladimir , Kowk Hoi Sing
Published: March 2018

It is very difficult to make a liquid crystal display (LCD) that is flexible. However, for an optically re-writable LCD (ORWLCD), only the spacers and the substrates need to be flexible because the driving unit and the display unit are separate and there are no electronics in the display part of ORWLCD. In this paper, three flexible-spacer methods are proposed to achieve this goal. A cholesteric liquid crystal colored mirror with a polarizer behind it is used as the colored reflective backboard of an ORWLCD. Polyethersulfone substrates and flexible spacers are used to make the optically re-writable cell insensitive to mechanical force.
Rotational and fine structure of open-shell molecules in nearly degenerate electronic states
Authors: Liu Jinjun
Published: March 2018

An effective Hamiltonian without symmetry restriction has been developed to model the rotational and fine structure of two nearly degenerate electronic states of an open-shell molecule. In addition to the rotational Hamiltonian for an asymmetric top, this spectroscopic model includes the energy separation between the two states due to difference potential and zero-point energy difference, as well as the spin-orbit (SO), Coriolis, and electron spin-molecular rotation (SR) interactions. Hamiltonian matrices are computed using orbitally and fully symmetrized case (a) and case (b) basis sets. Intensity formulae and selection rules for rotational transitions between a pair of nearly degenerate states and a nondegenerate state have also been derived using all four basis sets. It is demonstrated using real examples of free radicals that the fine structure of a single electronic state can be simulated with either a SR tensor or a combination of SO and Coriolis constants. The related molecular constants can be determined precisely only when all interacting levels are simulated simultaneously. The present study suggests that analysis of rotational and fine structure can provide quantitative insights into vibronic interactions and related effects.
Molecular simulation of capillary phase transitions in flexible porous materials
Authors: Shen Vincent K. , Siderius Daniel W. , Mahynski Nathan A.
Published: March 2018

We used flat-histogram sampling Monte Carlo to study capillary phase transitions in deformable adsorbent materials. Specifically, we considered a pure adsorbate fluid below its bulk critical temperature within a slit pore of variable pore width. The instantaneous pore width is dictated by a number of factors, such as adsorbate loading, reservoir pressure, fluid-wall interaction, and bare adsorbent properties. In the slit pores studied here, the bare adsorbent free energy was assumed to be biparabolic, consisting of two preferential pore configurations, namely, the narrow pore and the large pore configurations. Four distinct phases could be found in the adsorption isotherms. We found a low-pressure phase transition, driven primarily by capillary condensation/evaporation and accompanied by adsorbent deformation in response. The deformation can be a relatively small contraction/expansion as seen in elastic materials, or a large-scale structural transformation of the adsorbent. We also found a high-pressure transition driven by excluded volume effects, which tends to expand the material and thus results in a large-scale structural transformation of the adsorbent. The adsorption isotherms and osmotic free energies can be rationalized by considering the relative free energy differences between the basins of the bare adsorbent free energy.
Sn2+—Stabilization in MASnI3 perovskites by superhalide incorporation
Authors: Xiang Junxiang , Wang Kan , Xiang Bin , Cui Xudong
Published: March 2018

Sn-based hybrid halide perovskites are a potential solution to replace Pb and thereby reduce Pb toxicity in MAPbI3 perovskite-based solar cells. However, the instability of Sn2+ in air atmosphere causes a poor reproducibility of MASnI3, hindering steps towards this goal. In this paper, we propose a new type of organic metal-superhalide perovskite of MASnI2BH4 and MASnI2AlH4. Through first-principles calculations, our results reveal that the incorporation of BH4 and AlH4 superhalides can realize an impressive enhancement of oxidation resistance of Sn2+ in MASnI3 perovskites because of the large electron transfer between Sn2+ and [BH4]−/[AlH4]−. Meanwhile, the high carrier mobility is preserved in these superhalide perovskites and only a slight decrease is observed in the optical absorption strength. Our studies provide a new path to attain highly stable performance and reproducibility of Sn-based perovskite solar cells.
Anionic water pentamer and hexamer clusters: An extensive study of structures and energetics
Authors: Ünal Aslı , Bozkaya Uğur
Published: March 2018

An extensive study of structures and energetics for anionic pentamer and hexamer clusters is performed employing high level ab initio quantum chemical methods, such as the density-fitted orbital-optimized linearized coupled-cluster doubles (DF-OLCCD), coupled-cluster singles and doubles (CCSD), and coupled-cluster singles and doubles with perturbative triples [CCSD(T)] methods. In this study, sixteen anionic pentamer clusters and eighteen anionic hexamer clusters are reported. Relative, binding, and vertical detachment energies (VDE) are presented at the complete basis set limit (CBS), extrapolating energies of aug4-cc-pVTZ and aug4-cc-pVQZ custom basis sets. The largest VDE values obtained at the CCSD(T)/CBS level are 9.9 and 11.2 kcal mol−1 for pentamers and hexamers, respectively, which are in very good agreement with the experimental values of 9.5 and 11.1 kcal mol−1. Our binding energy results, at the CCSD(T)/CBS level, indicate strong bindings in anionic clusters due to hydrogen bond interactions. The average binding energy per water molecules is −5.0 and −5.3 kcal mol−1 for pentamers and hexamers, respectively. Furthermore, our results demonstrate that the DF-OLCCD method approaches to the CCSD(T) quality for anionic clusters. The inexpensive analytic gradients of DF-OLCCD compared to CCSD or CCSD(T) make it very attractive for high-accuracy studies.
Communication: Density functional theory model for multi-reference systems based on the exact-exchange hole normalization
Authors: Laqua Henryk , Kussmann Jörg , Ochsenfeld Christian
Published: March 2018

The correct description of multi-reference electronic ground states within Kohn-Sham density functional theory (DFT) requires an ensemble-state representation, employing fractionally occupied orbitals. However, the use of fractional orbital occupation leads to non-normalized exact-exchange holes, resulting in large fractional-spin errors for conventional approximative density functionals. In this communication, we present a simple approach to directly include the exact-exchange-hole normalization into DFT. Compared to conventional functionals, our model strongly improves the description for multi-reference systems, while preserving the accuracy in the single-reference case. We analyze the performance of our proposed method at the example of spin-averaged atoms and spin-restricted bond dissociation energy surfaces.
High-frequency elastic moduli of two-dimensional Yukawa fluids and solids
Authors: Khrapak Sergey , Klumov Boris
Published: March 2018

An approach to calculate high-frequency bulk and shear moduli of two-dimensional (2D) weakly screened Yukawa fluids and solids is presented. Elastic moduli are directly related to sound velocities and other important characteristics of the system. In this article, we discuss these relations and present an exemplary calculation of the longitudinal, transverse, and instantaneous sound velocities and derive a differential equation for the Einstein frequency. Simple analytical results presented demonstrate good accuracy when compared with numerical calculations. The obtained results can be particularly useful in the context of 2D colloidal and complex (dusty) plasma monolayers.
A noninvasive light driven technique integrated microfluidics for zebrafish larvae transportation
Authors: Mani Karthick , Hsieh Yu-Che , Panigrahi Bivas , Chen Chia-Yuan
Published: March 2018

Transferring the zebrafish larvae on an imaging platform has long been performed manually by the use of forceps or through mechanical pumping. These methods induce detrimental damages to the fragile bodies of zebrafish larvae during the transportation. To address this issue, in this work we are devising a light driven technique to transport zebrafish larvae within a microfluidic environment. In particular, an optomotor behavioral response of the zebrafish larvae was controlled through the computer animated moving gratings for their transportation within a microfluidics chamber. It was observed that with an optimum grating frequency of 1.5 Hz and a grating width ratio of 1:1, a 5 days-post fertilization zebrafish larva can be transported within minimum and maximum time periods of 0.63 and 2.49 s, respectively. This proposed technique can be utilized towards multi-automatic transportation of zebrafish larvae within the microfluidic environment as well as the zebrafish core facility.
Astaxanthin counteracts the effects of heat shock on the maturation of bovine oocytes
Authors: Ispada J. , Rodrigues T. A. , Risolia P. H. B. , Lima R. S. , Gonçalves D. R. , Rettori D. , Nichi M. , Feitosa W. B. , Paula-Lopes F. F.
Published: March 2018

The cellular mechanisms induced by elevated temperature on oocytes are not fully understood. However, there is evidence that some of the deleterious effects of heat shock are mediated by a heat-induced increase in reactive oxygen species (ROS). In this context, carotenoid antioxidants might have a thermoprotective effect. Therefore, the objective of this study was to determine the role of astaxanthin (AST) on oocyte ROS production and on the redox profile and developmental competency of cumulus-oocyte complexes (COCs) after 14 h heat shock (41°C) during in vitro maturation (IVM). Exposure of oocytes to heat shock during IVM increased ROS and reduced the ability of the oocyte to cleave and develop to the blastocyst stage. However, 12.5 and 25 nM astaxanthin rescued these negative effects of heat shock; astaxanthin counteracted the heat shock-induced increase in ROS and restored oocyte developmental competency. There was no effect of astaxanthin on maturation medium lipid peroxidation or on glutathione peroxidase and catalase activity in oocytes and cumulus cells. However, astaxanthin stimulated superoxide dismutase (SOD) activity in heat-shocked cumulus cells. In conclusion, direct heat shock reduced oocyte competence, which was restored by astaxanthin, possibly through regulation of ROS and SOD activity in oocytes and COCs.
Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding
Authors: Le Daniel D. , Shimko Tyler C. , Aditham Arjun K. , Keys Allison M. , Longwell Scott A. , Orenstein Yaron , Fordyce Polly M.
Published: March 2018

Significance

Transcription factors (TFs) are key proteins that bind DNA targets to coordinate gene expression in cells. Understanding how TFs recognize their DNA targets is essential for predicting how variations in regulatory sequence disrupt transcription to cause disease. Here, we develop a high-throughput assay and analysis pipeline capable of measuring binding energies for over one million sequences with high resolution and apply it toward understanding how nucleotides flanking DNA targets affect binding energies for two model yeast TFs. Through systematic comparisons between models trained on these data, we establish that considering dinucleotide (DN) interactions is sufficient to accurately predict binding and further show that sites used by TFs in vivo are both energetically and mutationally distant from the highest affinity sequence.
TWEAK and RIPK1 mediate a second wave of cell death during AKI
Authors: Martin-Sanchez Diego , Fontecha-Barriuso Miguel , Carrasco Susana , Sanchez-Niño Maria Dolores , Mässenhausen Anne von , Linkermann Andreas , Cannata-Ortiz Pablo , Ruiz-Ortega Marta , Egido Jesus , Ortiz Alberto , Sanz Ana Belen
Published: March 2018

Significance

Acute kidney injury (AKI) has a mortality of 50%. There is no satisfactory therapy and the incidence is increasing. The etiology of AKI is heterogeneous, and this has therapeutic implications. Here we show that necroptosis plays a role in a second wave of tubular cell death in experimental toxic AKI. This second wave of death is triggered by TWEAK activation of the Fn14 receptor and contributes to persistence of injury. We previously observed that the initial wave of cell death was ferroptosis dependent and necroptosis independent. The identification of a pathway contributing to AKI persistence may facilitate the design of therapies, as exemplified by the protection afforded by RIPK1 inhibitors when administered after AKI had been induced.
Myosin 1b promotes axon formation by regulating actin wave propagation and growth cone dynamics
Authors: Iuliano Olga , Yoshimura Azumi , Prospéri Marie-Thérèse , Martin René , Knölker Hans-Joachim , Coudrier Evelyne
Published: March 2018

Single-headed myosin 1 has been identified in neurons, but its function in these cells is still unclear. We demonstrate that depletion of myosin 1b (Myo1b), inhibition of its motor activity, or its binding to phosphoinositides impairs the formation of the axon, whereas overexpression of Myo1b increases the number of axon-like structures. Myo1b is associated with growth cones and actin waves, two major contributors to neuronal symmetry breaking. We show that Myo1b controls the dynamics of the growth cones and the anterograde propagation of the actin waves. By coupling the membrane to the actin cytoskeleton, Myo1b regulates the size of the actin network as well as the stability and size of filopodia in the growth cones. Our data provide the first evidence that a myosin 1 plays a major role in neuronal symmetry breaking and argue for a mechanical control of the actin cytoskeleton both in actin waves and in the growth cones by this myosin.
ESCRT-III is required for scissioning new peroxisomes from the endoplasmic reticulum
Authors: Mast Fred D. , Herricks Thurston , Strehler Kathleen M. , Miller Leslie R. , Saleem Ramsey A. , Rachubinski Richard A. , Aitchison John D.
Published: March 2018

Dynamic control of peroxisome proliferation is integral to the peroxisome’s many functions. The endoplasmic reticulum (ER) serves as a source of preperoxisomal vesicles (PPVs) that mature into peroxisomes during de novo peroxisome biogenesis and support growth and division of existing peroxisomes. However, the mechanism of PPV formation and release from the ER remains poorly understood. In this study, we show that endosomal sorting complexes required for transport (ESCRT)-III are required to release PPVs budding from the ER into the cytosol. Absence of ESCRT-III proteins impedes de novo peroxisome formation and results in an aberrant peroxisome population in vivo. Using a cell-free PPV budding assay, we show that ESCRT-III proteins Vps20 and Snf7 are necessary to release PPVs from the ER. ESCRT-III is therefore a positive effector of membrane scission for vesicles budding both away from and toward the cytosol. These findings have important implications for the evolutionary timing of emergence of peroxisomes and the rest of the internal membrane architecture of the eukaryotic cell.
Termination of T cell priming relies on a phase of unresponsiveness promoting disengagement from APCs and T cell division
Authors: Bohineust Armelle , Garcia Zacarias , Beuneu Hélène , Lemaître Fabrice , Bousso Philippe
Published: March 2018

T cells are primed in secondary lymphoid organs by establishing stable interactions with antigen-presenting cells (APCs). However, the cellular mechanisms underlying the termination of T cell priming and the initiation of clonal expansion remain largely unknown. Using intravital imaging, we observed that T cells typically divide without being associated to APCs. Supporting these findings, we demonstrate that recently activated T cells have an intrinsic defect in establishing stable contacts with APCs, a feature that was reflected by a blunted capacity to stop upon T cell receptor (TCR) engagement. T cell unresponsiveness was caused, in part, by a general block in extracellular calcium entry. Forcing TCR signals in activated T cells antagonized cell division, suggesting that T cell hyporesponsiveness acts as a safeguard mechanism against signals detrimental to mitosis. We propose that transient unresponsiveness represents an essential phase of T cell priming that promotes T cell disengagement from APCs and favors effective clonal expansion.
Taking Reductionism to the Limit: How to Rebut the Antireductionist Argument from Infinite Limits
Authors: Saatsi Juha , Reutlinger Alexander
Published: March 2018

This article analyzes the antireductionist argument from renormalization group explanations of universality and shows how it can be rebutted if one assumes that the explanation in question is captured by the counterfactual dependence account of explanation.
Fundamentality and Time’s Arrow
Authors: Loew Christian
Published: March 2018

The distribution of matter in our universe is strikingly time asymmetric. Most famously, the Second Law of Thermodynamics says that entropy tends to increase toward the future but not toward the past. But what explains this time-asymmetric distribution of matter? In this article, I explore the idea that time itself has a direction by drawing from recent work on grounding and metaphysical fundamentality. I will argue that positing such a direction of time, in addition to time-asymmetric boundary conditions (such as the so-called past hypothesis), enables a better explanation of the thermodynamic asymmetry than is available otherwise.
Comparison of measurement capability with 100 μmol/mol of carbon monoxide in nitrogen
Authors: Lee Jeongsoon , Lee JinBok , Lim Jeongsik , Tarhan l , Liu Hsin-Wang , Aggarwal Shankar G
Published: March 2018

Carbon monoxide (CO) in nitrogen was one of the first types of gas mixtures used in an international key comparison. The comparison dates back to 1998 (CCQMK1a) [1]. Since then, many National Metrology Institutes (NMIs) have developed calibration and measurement capabilities (CMCs) for these mixtures. Recently, NMIs in the APMP region have actively participated in international comparisons to provide domestic services. At the 2013 APMP meeting, several NMIs requested a CO comparison to establish CO/N2 certification for industrial applications, which was to be coordinated by KRISS. Consequently, this comparison provides an opportunity for APMP regional NMIs to develop CO/N2 CMC claims.

The goal of this supplementary comparison is to support CMC claim for carbon monoxide in the N2 range of 50–2000 μmol/mol. An extended range may be supported as described in the GAWG strategy for comparisons and CMC claims.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Integrated Forehead and Temporal Augmentation Using 3D Printing-Assisted Methyl Methacrylate Implants
Authors: Hirohi Toshitsugu , Nagai Koji , Ng Donald , Harii Kiyonori
Published: March 2018

Background

Achieving aesthetic results with forehead augmentation procedures remains challenging. We have developed a method of integrated forehead and temporal augmentation using a three-dimensional (3D) printing-assisted methyl methacrylate implant.

Objectives

The study objective was to assess the importance of combined temporal augmentation when performing forehead augmentation.

Methods

We identified 34 patients (from 2000 to 2010) who underwent forehead augmentation with a methyl methacrylate implant contoured in situ during surgery and 41 patients (from 2010 to 2016) who underwent integrated forehead and temporal augmentation with a prefabricated methyl methacrylate implant. We conducted a retrospective chart review of patient data including operation time, complications, and instances of revision surgery. Two blinded plastic surgeons scored the aesthetic results of the operations on a 4-point scale (1, poor, to 4, excellent) based on preoperative and posttreatment photographs.

Results

The integrated augmentation method resulted in a lower frequency of posttreatment implant removal (one [2%] vs. six [18%]; P < .05), a lower frequency of filler injection for touch up (one [2%] vs. six [18%]; P < .05), and higher mean aesthetic scores (3.7 ± 0.5 vs. 2.2 ± 1.0; P < . 001) compared to the forehead augmentation method. There was no statistically significant difference in surgical complications between the two groups.

Conclusions

Integrated forehead and temporal augmentation using a 3D printing-assisted methyl methacrylate implant may be the optimal available procedure, enabling the custom fabrication of contours requested by the patient and providing a rejuvenating and balancing effect on facial appearance.

Level of Evidence: 3
MetaboCraft: building a Minecraft plugin for metabolomics
Authors: Megalios Anargyros , Daly Rónán , Burgess Karl
Published: March 2018

Motivation

The rapid advances in metabolomics pose a significant challenge in presentation and interpretation of results. Development of new, engaging visual aids is crucial to advancing our understanding of new findings.

Results

We have developed MetaboCraft, a Minecraft plugin which creates immersive visualizations of metabolic networks and pathways in a 3D environment and allows the results of user experiments to be viewed in this context, presenting a novel approach to exploring the metabolome.

Availability and implementation

https://github.com/argymeg/MetaboCraft/; https://hub.docker.com/r/ronandaly/metabocraft/

Supplementary information

Supplementary data are available at Bioinformatics online.
scanPAV: a pipeline for extracting presence–absence variations in genome pairs
Authors: Giordano Francesca , Stammnitz Maximilian R , Murchison Elizabeth P , Ning Zemin
Published: March 2018

Motivation

The recent technological advances in genome sequencing techniques have resulted in an exponential increase in the number of sequenced human and non-human genomes. The ever increasing number of assemblies generated by novel de novo pipelines and strategies demands the development of new software to evaluate assembly quality and completeness. One way to determine the completeness of an assembly is by detecting its Presence–Absence variations (PAV) with respect to a reference, where PAVs between two assemblies are defined as the sequences present in one assembly but entirely missing in the other one. Beyond assembly error or technology bias, PAVs can also reveal real genome polymorphism, consequence of species or individual evolution, or horizontal transfer from viruses and bacteria.

Results

We present scanPAV, a pipeline for pairwise assembly comparison to identify and extract sequences present in one assembly but not the other. In this note, we use the GRCh38 reference assembly to assess the completeness of six human genome assemblies from various assembly strategies and sequencing technologies including Illumina short reads, 10× genomics linked-reads, PacBio and Oxford Nanopore long reads, and Bionano optical maps. We also discuss the PAV polymorphism of seven Tasmanian devil whole genome assemblies of normal animal tissues and devil facial tumour 1 (DFT1) and 2 (DFT2) samples, and the identification of bacterial sequences as contamination in some of the tumorous assemblies.

Availability and implementation

The pipeline is available under the MIT License at https://github.com/wtsi-hpag/scanPAV.

Supplementary information

Supplementary data are available at Bioinformatics online.
Two low-order nonconforming finite element methods for the Stokes flow in three dimensions
Authors: Hu Jun , Schedensack Mira
Published: March 2018

In this paper, we propose two low-order nonconforming finite element methods (FEMs) for the three-dimensional Stokes flow that generalize the nonconforming FEM of Kouhia & Stenberg (1995, A linear nonconforming finite element method for nearly incompressible elasticity and Stokes flow. Comput. Methods Appl. Mech. Eng, 124, 195–212). The finite element spaces proposed in this paper consist of two globally continuous components (one piecewise affine and one enriched component) and one component that is continuous at the midpoints of interior faces. We prove that the discrete Korn inequality and a discrete inf–sup condition hold uniformly in the mesh size and also for a nonempty Neumann boundary. Based on these two results, we show the well-posedness of the discrete problem. Two counterexamples prove that there is no direct generalization of the Kouhia–Stenberg FEM to three space dimensions: the finite element space with one nonconforming and two conforming piecewise affine components does not satisfy a discrete inf–sup condition with piecewise constant pressure approximations, while finite element functions with two nonconforming and one conforming component do not satisfy a discrete Korn inequality.
Dispersively formed quasi-periodic fast magnetosonic wavefronts due to the eruption of a nearby mini-filament
Authors: Shen Yuandeng , Song Tengfei , Liu Yu
Published: March 2018

Observational analysis is performed to study the excitation mechanism and propagation properties of a quasi-periodic fast-propagating (QFP) magnetosonic wave. The QFP wave was associated with the eruption of a nearby mini-filament and a small B4 Geostationary Operational Environmental Satellite (GOES) flare, which may indicate that the generation of a QFP wave does not require much flare energy. The propagation of the QFP wave was along a bundle of funnel-shaped open loops with a speed of about 1100 ± 78 km s−1 and an acceleration of −2.2 ± 1.1 km s−2. Periodicity analysis indicates that the periods of the QFP wave are 43 ± 6 and 79 ± 18 s. For the first time, we find that the periods of the QFP wave and the accompanying flare are inconsistent, which is different from the findings reported in previous studies. We propose that the present QFP wave was possibly caused by the mechanism of dispersive evolution of the initially broad-band disturbance resulting from the nearby mini-filament eruption.
On the evolutionary status and pulsations of the recently discovered blue large-amplitude pulsators (BLAPs)
Authors: Romero Alejandra D , Córsico A H , Althaus L G , Pelisoli I , Kepler S O
Published: March 2018

The blue large-amplitude pulsators (BLAPs) constitute a new class of pulsating stars. They are hot stars with effective temperatures of ∼30 000 K and surface gravities of log g ∼ 4.9, that pulsate with periods in the range 20−40 min. Until now, their origin and evolutionary state, as well as the nature of their pulsations, were not been unveiled. In this paper, we propose that the BLAPs are the hot counterpart of the already known pulsating pre-extremely low mass (pre-ELM) white dwarf (WD) stars, that are He-core low-mass stars resulting from interacting binary evolution. Using fully evolutionary sequences, we show that the BLAPs are well represented by pre-ELM WD models with high effective temperature and stellar masses ∼0.34 M⊙. From the analysis of their pulsational properties, we find that the observed variabilities can be explained by high-order non-radial g-mode pulsations or, in the case of the shortest periods, also by low-order radial modes, including the fundamental radial mode. The theoretical modes with periods in the observed range are unstable due to the κ mechanism associated with the Z-bump in the opacity at log T ∼ 5.25.
The duration of reionization constrains the ionizing sources
Authors: Sharma Mahavir , Theuns Tom , Frenk Carlos
Published: March 2018

We investigate how the nature of the galaxies that reionized the Universe affects the duration of reionization. We contrast two sets of models: one in which galaxies on the faint side of the luminosity function dominate the ionizing emissivity, and a second in which the galaxies on the bright side of the luminosity function dominate. The faint end of the luminosity function evolves slowly, therefore the transition from mostly neutral to mostly ionized state takes a much longer time in the first set of models compared to the second. Existing observational constraints on the duration of this transition are relatively weak, but taken at face value prefer the model in which galaxies on the bright side play a major role. Measurements of the kinetic Sunyaev–Zeldovich effect in the cosmic microwave background from the epoch of reionization also point in the same direction.
Stress in Patients With (Un)ruptured Intracranial Aneurysms vs Population-Based Controls
Authors: de Wilde Arno , Greebe Paut , Rinkel Gabriël J E , Algra Ale
Published: March 2018

BACKGROUND

Stress is associated with increased risk of stroke and might predispose to presence and rupture of intracranial aneurysms.

OBJECTIVE

To study the association of recent and lifelong stress with unruptured intracranial aneurysm (UIA) and aneurysmal subarachnoid hemorrhage (ASAH).

METHODS

In 227 UIA patients (mean age 61 ± 11 yr), 490 ASAH patients (59 ± 11 yr), and 775 controls (51 ± 15 yr) who were randomly retrieved from the general population, we assessed occurrence of major life events and perceived stress during the preceding 12 mo and the entire life. With multivariable logistic regression analysis, we calculated odds ratios (ORs) with 95% confidence intervals (95% CIs) for 4 categories of life events (financial-related, work-related, children-related, and death of family members) and for periods of perceived stress at home and at work (never vs sometimes, often, or always). We adjusted for sex, age, alcohol consumption, smoking, and hypertension.

RESULTS

The 4 categories of life events and perceived stress at work had ORs ranging from 0.4 to 1.7, of which financial stress for UIA was statistically significant (95% CI: 1.1-2.5). ORs for chronic perceived stress at home in the previous year were 4.3 (95% CI: 1.8-10.3) for UIA and 2.5 (1.2-5.5) for ASAH, and for lifelong exposure 5.7 (2.2-14.5) for UIA and 3.0 (1.3-7.0) for ASAH.

CONCLUSION

For some components of stress, there may be a relation with UIA and ASAH. The mechanisms underlying this relation should be unraveled; strategies to improve coping with stress may reduce the risk of rupture in patients with unruptured aneurysms.
Central nervous system involvement in children and adolescents with rhabdomyosarcoma. A report from the AIEOP Soft Tissue Sarcoma Committee
Authors: Pierobon Marta , Ferrari Andrea , Scarzello Giovanni , Tamburini Angela , Quaglietta Lucia , Ruggiero Antonio , Milano Giuseppe Maria , Zin Angelica , Bisogno Gianni
Published: March 2018

Background

Rhabdomyosarcoma (RMS) is a highly malignant tumor typically affecting children and adolescents. Central nervous system (CNS) dissemination is rare in RMS patients, but seems to have a particularly negative impact. The aim of this study was to analyze treatment and outcome of patients with RMS and evidence of CNS disease who were registered in the protocols coordinated by the Italian Soft Tissue Sarcoma Committee from March 1979 to December 2016.

Methods

We analyzed 39 patients with CNS disease. Depending on when their CNS disease was identified, we grouped patients as: Group A, at diagnosis; Group B, progression during treatment; Group C, at first relapse.

Results

Six patients were in Group A (2.7% of metastatic RMS patients at diagnosis); 24 were in Group B and 9 in Group C (6.5% of patients with tumor progression/relapse included in the protocols). Only 5 patients (4 in Group A, 1 in Group B) survived the event and are alive in complete remission with a median follow-up of 17.5 years. These 5 patients received systemic chemotherapy and craniospinal radiotherapy, and 2 of them also received intrathecal therapy with topotecan.

Conclusions

CNS involvement at diagnosis is a rare and prognostically negative event in RMS patients, but not always fatal when it is found at diagnosis. It is more frequent during or shortly after treatment, and the more dismal prognosis in these cases underscores the need to improve our ability to identify patients at risk of CNS dissemination in order to attempt more effective treatments that can sterilize the meninges.
Color Coding of a Sterile Field to Aid in Recognition of Visual Cognition and Learning
Authors: Hannon Michele A. , Raymond Roberta A.
Published: March 2018

This study used color coding to determine if color promotes visual cognition and learning for students to identify the sterile field while inserting an indwelling catheter. Novice students have trouble identifying the sterile field. It was theorized that adding color would help students identify what is and is not sterile. Thirty students in the control group were instructed using a standard non-color-coded catheter kit; 30 students in the experimental group were instructed using a red color-coded catheter kit. All students were validated using the standard non-colored-coded kit. The experimental group performed better on overall sterility.
Using Simulation With Nursing Students to Promote Affirmative Practice Toward the Lesbian, Gay, Bisexual, and Transgender Population: A Multisite Study
Authors: Maruca Annette T. , Diaz Desiree A. , Stockmann Cherrill , Gonzalez Laura
Published: March 2018

AIM

The aim of this research was to evaluate the impact of a transgender simulation on nursing students’ affirmative practice when caring for a transgender person.

BACKGROUND

There is a paucity of research that assesses the attitudes of nursing students toward lesbian, gay, bisexual, and transgender (LGBT) persons and a deficit in nursing curricula regarding LGBT content.

METHOD

A nonexperimental, pretest-posttest design was used to evaluate nursing students’ affirmative practice when caring for a transgender patient using the Gay Affirmative Practice Scale.

RESULTS

A Wilcoxon signed-rank test revealed a statistical significance in Gay Affirmative Practice scores after the simulation with a small effect size. These results suggest that the transgender simulation supported nursing students’ attitudes and affirmative practice when providing nursing care to a transgender person.

CONCLUSION

Experiential learning in nursing education is an effective approach to teach cultural competence and sensitivity in caring for vulnerable populations.
Relationships Between the ACGME Resident and Faculty Surveys and Program Pass Rates on the ABIM Internal Medicine Certification Examination
Authors: Holt Kathleen D. , Miller Rebecca S. , Vasilias Jerry , Byrne Lauren M. , Cable Christian , Grosso Louis , Bellini Lisa M. , McDonald Furman S.
Published: March 2018

Purpose

The Accreditation Council for Graduate Medical Education (ACGME) has surveyed residents since 2003, and faculty since 2012. Surveys are designed to assess program functioning and specify areas for improvement. The purpose of this study was to assess the association of the ACGME’s resident and faculty surveys with residency-program-specific performance on the American Board of Internal Medicine (ABIM) certification exam.

Method

Data were available from residents and faculty in 375 U.S. ACGME-accredited internal medicine programs from the 2012–2013, 2013–2014, and 2014–2015 academic years. Analysis of variance and correlations were used to examine the relationship between noncompliance with ACGME program requirements as assessed by the resident and faculty surveys, and ABIM program pass rates.

Results

Noncompliance reported on the resident and faculty surveys was highest for programs not meeting the ACGME program requirement of an 80% pass rate on the ABIM certification examination. This relationship was significant for overall noncompliance, both within the resident (P < .001) and faculty (P < .05) surveys, for many areas within the two surveys (correlations ranged between −.07 and −.25, and P values ranged between .20 and < .001), and for the highest levels of noncompliance across areas of the resident (P < .001) and faculty (P < .04) surveys.

Conclusions

ACGME resident and faculty surveys were significantly associated with ABIM program pass rates, supporting the importance of these surveys within the ACGME’s Next Accreditation System.
Mindfulness-Based Neurodevelopmental Care
Authors: Petteys Annie R. , Adoumie Dominique
Published: March 2018

Background/Purpose:

Experiences of premature birth and neonatal intensive care unit (NICU) hospitalizations result in stress and family separation that have far-reaching implications. Prior studies of neonatal neurodevelopmental care show improved infant outcomes. Previous studies of mindfulness show improved stress and health outcomes in varied disease processes. No neonatal studies of parent training in mindfulness-based neurodevelopmental care exist. This study examines the impact of parent education and participation in mindfulness-based neurodevelopmental care on parent outcomes (stress, bonding, and satisfaction) and infant length of stay (LOS).

Methods:

This randomized controlled trial pilot study utilized a convenience sample of 55 parent–infant dyads. Parametric and nonparametric statistical tests examined differences in and between study groups in demographics and dependent study variables (stress, bonding, satisfaction, and LOS).

Results:

No statistically significant differences in parent outcomes were seen between groups. However, experimental group (EG) parents showed a significant reduction in stress scores from enrollment to discharge (P= .012) and EG infants had significantly shorter LOS (P= .026-.047) than control.

Implications for Practice and Research:

While further research to confirm study results is warranted, changes in current NICU practices to incorporate additional parent education in mindfulness-based neurodevelopmental care may help alleviate parent stress and decrease LOS that impact financial, physical, and psychosocial outcomes for patients, families, healthcare systems, and society.
How does information on the harms and benefits of cervical cancer screening alter the intention to be screened?: a randomized survey of Norwegian women
Authors: Iyer Anita L. , Bundorf M. Kate , Gyrd-Hansen Dorte , Goldhaber-Fiebert Jeremy D. , Cyr Pascale-Renée , Sønbø Kristiansen Ivar
Published: March 2018

Cervical cancer (CC) is the 13th most frequent cancer among women in Norway, but the third most common among women aged 25–49 years. The national screening program sends information letters to promote screening participation. We aimed to evaluate how women’s stated intention to participate in screening and pursue treatment changed with the provision of additional information on harms associated with screening, and to assess women’s preferences on the timing and source of such information. We administered a web-based questionnaire to a panel of Norwegian women aged 25–69 years and randomized into three groups on the basis of when in the screening process additional information was introduced: (i) invited for routine screening, (ii) recommended an additional test following detection of cellular abnormalities, and (iii) recommended precancer treatment. A fourth (control) group did not receive any additional information. Results show that among 1060 respondents, additional information did not significantly alter women’s stated intentions to screen. However, it created decision uncertainty on when treatment was recommended (8.76–9.09 vs. 9.40; 10-point Likert scale; P=0.004). Over 80% of women favored receiving information on harms and 59% preferred that information come from a qualified public health authority. Nearly 90% of women in all groups overestimated women’s lifetime risk of CC. In conclusion, additional information on harms did not alter Norwegian women’s stated intention to screen for CC; yet, it resulted in greater decision uncertainty to undergo precancer treatment. Incorporating information on harms into invitation letters is warranted as it would increase women’s ability to make informed choices.
Comparative Evaluation of Gemcabene and Peroxisome Proliferator–Activated Receptor Ligands in Transcriptional Assays of Peroxisome Proliferator–Activated Receptors: Implication for the Treatment of Hyperlipidemia and Cardiovascular Disease
Authors: Bisgaier Charles L. , Oniciu Daniela C. , Srivastava Rai Ajit K.
Published: March 2018

Gemcabene, a late-stage clinical candidate, has shown efficacy for LDL-C, non-HDL cholesterol, apoB, triglycerides, and hsCRP reduction, all risk factors for cardiovascular disease. In rodents, gemcabene showed changes in targets, including apoC-III, apoA-I, peroxisomal enzymes, considered regulated through peroxisome proliferator–activated receptor (PPAR) gene activation, suggesting a PPAR-mediated mechanism of action for the observed hypolipidemic effects observed in rodents and humans. In the current study, the gemcabene agonist activity against PPAR subtypes of human, rat, and mouse were compared with known lipid lowering PPAR activators. Surprisingly, gemcabene showed no or little PPAR-α transactivation compared with reference agonists, which showed concentration-dependent transactivation against human PPAR-α of 2.4- to 30-fold (fenofibric acid), 17-fold (GW590735), and 2.3- to 25-fold (WY-14643). These agents also showed robust transactivation of mouse and rat PPAR-α in a concentration-dependent manner. The known PPAR-δ agonists, GW1516, L165041, and GW0742, showed potent agonist activity against human, mouse, and rat receptors (ranging from 165- to 396-fold). By contrast, gemcabene at the highest concentration tested (300 μM) showed no response in mouse and rat and a marginal response against human PPAR-δ receptors (3.2-fold). For PPAR-γ, gemcabene showed no agonist activity against all 3 species at 100 μM and marginal activity (3.6- to 5-fold) at 300 μM. By contrast, the known agonists, rosiglitazone, indomethacin, and muraglitazar showed strong activation against the mouse, rat, and human PPAR-γ receptors. No clear antagonist activity was observed with gemcabene against any PPAR subtypes for all 3 species over a wide range of concentrations. In summary, the transactivation studies rule out gemcabene as a direct agonist or antagonist of PPAR-α, PPAR-γ, and PPAR-δ receptors of these 3 species. These data suggest that the peroxisomal effects observed in rodents and the lipid regulating effects observed in rodents and humans are not related to a direct activation of PPAR receptors by gemcabene.