A survey of the testate amoeba genus Difflugia Leclerc, 1815 based on specimens in the E. Penard and C.G. Ogden collections of the Natural History Museum, London. Part 2: Species with shells that are pyriform or elongate.

© 2014 The Author(s). Protistology © 2014 Protozoological Society Affiliated with RAS. All articles published by Protistology are permanently accessible online immediately upon publication, without subscription charges or registration barriers

Irreversible thermodynamics of creep in crystalline solids

We develop an irreversible thermodynamics framework for the description of creep deformation in crystalline solids by mechanisms that involve vacancy diffusion and lattice site generation and annihilation. The material undergoing the creep deformation is treated as a non-hydrostatically stressed multi-component solid medium with non-conserved lattice sites and inhomogeneities handled by employing gradient thermodynamics. Phase fields describe microstructure evolution which gives rise to redistribution of vacancy sinks and sources in the material during the creep process. We derive a general expression for the entropy production rate and use it to identify of the relevant fluxes and driving forces and to formulate phenomenological relations among them taking into account symmetry properties of the material. As a simple application, we analyze a one-dimensional model of a bicrystal in which the grain boundary acts as a sink and source of vacancies. The kinetic equations of the model describe a creep deformation process accompanied by grain boundary migration and relative rigid translations of the grains. They also demonstrate the effect of grain boundary migration induced by a vacancy concentration gradient across the boundary

A simulation model for wind energy storage systems. Volume 1: Technical report

A comprehensive computer program for the modeling of wind energy and storage systems utilizing any combination of five types of storage (pumped hydro, battery, thermal, flywheel and pneumatic) was developed. The level of detail of Simulation Model for Wind Energy Storage (SIMWEST) is consistent with a role of evaluating the economic feasibility as well as the general performance of wind energy systems. The software package consists of two basic programs and a library of system, environmental, and load components. The first program is a precompiler which generates computer models (in FORTRAN) of complex wind source storage application systems, from user specifications using the respective library components. The second program provides the techno-economic system analysis with the respective I/O, the integration of systems dynamics, and the iteration for conveyance of variables. SIMWEST program, as described, runs on the UNIVAC 1100 series computers

Compositional Data Analysis is necessary for simulating and analyzing RNA-Seq data

*Seq techniques (e.g. RNA-Seq) generate compositional datasets, i.e. the number of fragments sequenced is not proportional to the total RNA present. Thus, datasets carry only relative information, even though absolute RNA copy numbers are often of interest. Current normalization methods assume most features are not changing, which can lead to misleading conclusions when there are large shifts. However, there are few real datasets and no simulation protocols currently available that can directly benchmark methods when such large shifts occur. We present absSimSeq, an R package that simulates compositional data in the form of RNA-Seq reads. We tested several tools used for RNA-Seq differential analysis: sleuth, DESeq2, edgeR, limma, sleuth and ALDEx2 (which explicitly takes a compositional approach). For these tools, we compared their standard normalization to either “compositional normalization”, which uses log-ratios to anchor the data on a set of negative control features, or RUVSeq, another tool that directly uses negative control features. We show that common normalizations result in reduced performance with current methods when there is a large change in the total RNA per cell. Performance improves when spike-ins are included and used by a compositional approach, even if the spike-ins have substantial variation. In contrast, RUVSeq, which normalizes count data rather than compositional data, has poor performance. Further, we show that previous criticisms of spike-ins did not take into account the compositional nature of the data. We conclude that absSimSeq can generate more representative datasets for testing performance, and that spike-ins should be more broadly used in a compositional manner to minimize misleading conclusions from differential analyses

Minimal basilar membrane motion in low-frequency hearing

Low-frequency hearing is critically important for speech and music perception, but no mechanical measurements have previously been available from inner ears with intact low-frequency parts. These regions of the cochlea may function in ways different from the extensively studied high-frequency regions, where the sensory outer hair cells produce force that greatly increases the sound-evoked vibrations of the basilar membrane. We used laser interferometry in vitro and optical coherence tomography in vivo to study the low-frequency part of the guinea pig cochlea, and found that sound stimulation caused motion of a minimal portion of the basilar membrane. Outside the region of peak movement, an exponential decline in motion amplitude occurred across the basilar membrane. The moving region had different dependence on stimulus frequency than the vibrations measured near the mechanosensitive stereocilia. This behavior differs substantially from the behavior found in the extensively studied high-frequency regions of the cochlea

Robustness of Cosmological Simulations I: Large Scale Structure

The gravitationally-driven evolution of cold dark matter dominates the formation of structure in the Universe over a wide range of length scales. While the longest scales can be treated by perturbation theory, a fully quantitative understanding of nonlinear effects requires the application of large-scale particle simulation methods. Additionally, precision predictions for next-generation observations, such as weak gravitational lensing, can only be obtained from numerical simulations. In this paper, we compare results from several N-body codes using test problems and a diverse set of diagnostics, focusing on a medium resolution regime appropriate for studying many observationally relevant aspects of structure formation. Our conclusions are that -- despite the use of different algorithms and error-control methodologies -- overall, the codes yield consistent results. The agreement over a wide range of scales for the cosmological tests is test-dependent. In the best cases, it is at the 5% level or better, however, for other cases it can be significantly larger than 10%. These include the halo mass function at low masses and the mass power spectrum at small scales. While there exist explanations for most of the discrepancies, our results point to the need for significant improvement in N-body errors and their understanding to match the precision of near-future observations. The simulation results, including halo catalogs, and initial conditions used, are publicly available.Comment: 32 pages, 53 figures, data from the simulations is available at http://t8web.lanl.gov/people/heitmann/arxiv, accepted for publication in ApJS, several minor revisions, reference added, main conclusions unchange

X-ray scattering from surfaces: discrete and continuous components of roughness

Incoherent surface scattering yields a statistical description of the surface, due to the ensemble averaging over many independently sampled volumes. Depending on the state of the surface and direction of the scattering vector relative to the surface normal, the height distribution is discrete, continuous, or a combination of the two. We present a treatment for the influence of multimodal surface height distributions on Crystal Truncation Rod scattering. The effects of a multimodal height distribution are especially evident during in situ monitoring of layer-by-layer thin-film growth via Pulsed Laser Deposition. We model the total height distribution as a convolution of discrete and continuous components, resulting in a broadly applicable parameterization of surface roughness which can be applied to other scattering probes, such as electrons and neutrons. Convolution of such distributions could potentially be applied to interface or chemical scattering. Here we find that this analysis describes accurately our experimental studies of SrTiO3 annealing and homoepitaxial growth.Comment: 15 pages, 7 figure

A survey of the testate amoeba genus Difflugia Leclerc, 1815 based on specimens in the E. Penard and C.G. Ogden collections of the Natural History Museum, London. Part 3: Species with shells that are spherical or ovoid

© 2015 The Author(s). Protistology © 2015 Protozoological Society Affiliated with RAS. All articles published by Protistology are permanently accessible online immediately upon publication, without subscription charges or registration barriers. The attached file is the published version of the article

Spin-Charge Coupling in lightly doped Nd2−x_{2-x}Cex_{x}CuO4_4

We use neutron scattering to study the influence of a magnetic field on spin structures of Nd$_2$CuO$_4$. On cooling from room temperature, Nd$_2$CuO$_4$ goes through a series of antiferromagnetic (AF) phase transitions with different noncollinear spin structures. While a c-axis aligned magnetic field does not alter the basic zero-field noncollinear spin structures, a field parallel to the CuO$_2$ plane can transform the noncollinear structure to a collinear one ("spin-flop" transition), induce magnetic disorder along the c-axis, and cause hysteresis in the AF phase transitions. By comparing these results directly to the magnetoresistance (MR) measurements of Nd$_{1.975}$Ce$_{0.025}$CuO$_4$, which has essentially the same AF structures as Nd$_2$CuO$_4$, we find that a magnetic-field-induced spin-flop transition, AF phase hysteresis, and spin c-axis disorder all affect the transport properties of the material. Our results thus provide direct evidence for the existence of a strong spin-charge coupling in electron-doped copper oxides.Comment: 12 pages, 12 figure

Can Reproductive Health Voucher Programs Improve Quality of Postnatal Care? A Quasi-Experimental Evaluation of Kenya’s Safe Motherhood Voucher Scheme

This study tests the group-level causal relationship between the expansion of Kenya’s Safe Motherhood voucher program and changes in quality of postnatal care (PNC) provided at voucher-contracted facilities. We compare facilities accredited since program inception in 2006 (phase I) and facilities accredited since 2010-2011 (phase II) relative to comparable non-voucher facilities. PNC quality is assessed using observed clinical content processes, as well as client-reported outcome measures. Two-tailed unpaired t-tests are used to identify differences in mean process quality scores and client-reported outcome measures, comparing changes between intervention and comparison groups at the 2010 and 2012 data collection periods. Difference-in-differences analysis is used to estimate the reproductive health (RH) voucher program’s causal effect on quality of care by exploiting group-level differences between voucher-accredited and non-accredited facilities in 2010 and 2012. Participation in the voucher scheme since 2006 significantly improves overall quality of postnatal care by 39% (p=0.02), where quality is defined as the observable processes or components of service provision that occur during a PNC consultation. Program participation since phase I is estimated to improve the quality of observed maternal postnatal care by 86% (p=0.02), with the largest quality improvements in counselling on family planning methods (IRR 5.0; p=0.01) and return to fertility (IRR 2.6; p=0.01). Despite improvements in maternal aspects of PNC, we find a high proportion of mothers who seek PNC are not being checked by any provider after delivery. Additional strategies will be necessary to standardize provision of packaged postnatal interventions to both mother and new-born. This study addresses an important gap in the existing RH literature by using a strong evaluation design to assess RH voucher program effectiveness on quality improvement