Magnetic properties of a spin system in a longitudinal magnetic field

2004-2005 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Accelerating exhaustive pairwise metagenomic comparisons

In this manuscript, we present an optimized and parallel version of our previous work IMSAME, an exhaustive gapped aligner for the pairwise and accurate comparison of metagenomes. Parallelization strategies are applied to take advantage of modern multiprocessor architectures. In addition, sequential optimizations in CPU time and memory consumption are provided. These algorithmic and computational enhancements enable IMSAME to calculate near optimal alignments which are used to directly assess similarity between metagenomes without requiring reference databases. We show that the overall efficiency of the parallel implementation is superior to 80% while retaining scalability as the number of parallel cores used increases. Moreover, we also show thats equential optimizations yield up to 8x speedup for scenarios with larger data.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

Genome-wide profiling of uncapped mRNA

Gene transcripts are under extensive posttranscriptional regulation, including the regulation of their stability. A major route for mRNA degradation produces uncapped mRNAs, which can be generated by decapping enzymes, endonucleases, and small RNAs. Profiling uncapped mRNA molecules is important for the understanding of the transcriptome, whose composition is determined by a balance between mRNA synthesis and degradation. In this chapter, we describe a method to profile these uncapped mRNAs at the genome scale

Comparison of 20nm silver nanoparticles synthesized with and without a gold core: Structure, dissolution in cell culture media, and biological impact on macrophages

Widespread use of silver nanoparticles raises questions of environmental and biological impact. Many synthesis approaches are used to produce pure silver and silver-shell gold-core particles optimized for specific applications. Since both nanoparticles and silver dissolved from the particles may impact the biological response, it is important to understand the physicochemical characteristics along with the biological impact of nanoparticles produced by different processes. The authors have examined the structure, dissolution, and impact of particle exposure to macrophage cells of two 20 nm silver particles synthesized in different ways, which have different internal structures. The structures were examined by electron microscopy and dissolution measured in Rosewell Park Memorial Institute media with 10% fetal bovine serum. Cytotoxicity and oxidative stress were used to measure biological impact on RAW 264.7 macrophage cells. The particles were polycrystalline, but 20 nm particles grown on gold seed particles had smaller crystallite size with many high-energy grain boundaries and defects, and an apparent higher solubility than 20 nm pure silver particles. Greater oxidative stress and cytotoxicity were observed for 20 nm particles containing the Au core than for 20 nm pure silver particles. A simple dissolution model described the time variation of particle size and dissolved silver for particle loadings larger than 9 μg/ml for the 24-h period characteristic of many in-vitro studies

Historical Differences in School Term Length and Measured Blood Pressure: Contributions to Persistent Racial Disparities among US-Born Adults

Introduction Legally mandated segregation policies dictated significant differences in the educational experiences of black and white Americans through the first half of the 20th century, with markedly lower quality in schools attended by black children. We determined whether school term length, a common marker of school quality, was associated with blood pressure and hypertension among a cohort of older Americans who attended school during the de jure segregation era. Methods National Health and Nutrition Examination Survey I and II data were linked to state level historical information on school term length. We used race and gender-stratified linear regression models adjusted for age, state and year of birth to estimate effects of term length on systolic and diastolic blood pressure (SBP and DBP) and hypertension for US-born adults. We also tested whether correcting years of schooling for term length differences attenuated estimated racial disparities. Results Among black women, 10% longer school term was associated with lower SBP, DBP and hypertension prevalence (2.1 mmHg, 1.0 mmHg, and 5.0 percentage points respectively). Associations for whites and for black men were not statistically significant. Adjustment for education incorporating corrections for differences in school term length slightly attenuated estimated racial disparities. Conclusions Longer school term length predicted better BP outcomes among black women, but not black men or whites

Towards segmentation and spatial alignment of the human embryonic brain using deep learning for atlas-based registration

We propose an unsupervised deep learning method for atlas based registration to achieve segmentation and spatial alignment of the embryonic brain in a single framework. Our approach consists of two sequential networks with a specifically designed loss function to address the challenges in 3D first trimester ultrasound. The first part learns the affine transformation and the second part learns the voxelwise nonrigid deformation between the target image and the atlas. We trained this network end-to-end and validated it against a ground truth on synthetic datasets designed to resemble the challenges present in 3D first trimester ultrasound. The method was tested on a dataset of human embryonic ultrasound volumes acquired at 9 weeks gestational age, which showed alignment of the brain in some cases and gave insight in open challenges for the proposed method. We conclude that our method is a promising approach towards fully automated spatial alignment and segmentation of embryonic brains in 3D ultrasound

Ultrahigh power and energy density in partially ordered lithium-ion cathode materials

The rapid market growth of rechargeable batteries requires electrode materials that combine high power and energy and are made from earth-abundant elements. Here we show that combining a partial spinel-like cation order and substantial lithium excess enables both dense and fast energy storage. Cation overstoichiometry and the resulting partial order is used to eliminate the phase transitions typical of ordered spinels and enable a larger practical capacity, while lithium excess is synergistically used with fluorine substitution to create a high lithium mobility. With this strategy, we achieved specific energies greater than 1,100 Wh kg–1 and discharge rates up to 20 A g–1. Remarkably, the cathode materials thus obtained from inexpensive manganese present a rare case wherein an excellent rate capability coexists with a reversible oxygen redox activity. Our work shows the potential for designing cathode materials in the vast space between fully ordered and disordered compounds

Dynamic changes of mechanical properties induced by friction in the Archard wear model

© 2019 Elsevier B.V. Fretting is small-amplitude, oscillatory motion between two bodies leading to surface damage. During the fretting process, a tribologically transformed structure (TTS) which has different mechanical properties and microstructure than the starting material is formed on the surface. The commonly-used Archard wear equation relating wear volume to the hardness of the worn material does not account for changes in mechanical properties induced by friction in fretting. To investigate that effect, ball-on-plane fretting tests were conducted on three engineering materials (type 316 stainless steel, pure copper, and titanium alloy Ti-6Al-4V) against an alumina ball to generate TTS layers. The evolution of mechanical properties and microstructures of TTS layers were investigated using nanoindentation and focused ion beam-scanning electron microscope (FIB-SEM). Wear volumes after different fretting cycles were measured with a white light interference microscope. Results show that the mechanical properties of TTS layers evolve differently on different materials during the fretting process. Microstructures of TTS layers also vary from one material to the other. A modified wear model that accounts for friction-induced dynamic changes in mechanical properties is proposed. In these tests the modified model was able to predict the wear volume of 316 steel and pure copper more accurately than the classical Archard model, but it was less successful in predicting wear on Ti6Al4V where there is added complexity from changing microstructure, oxidation, porosity and cracking

The carbon cycle in Mexico: past, present and future of C stocks and fluxes

PublishedThe Supplement related to this article is available online at doi:10.5194/bg-13-223-2016-supplement.We modeled the carbon (C) cycle in Mexico with a process-based approach. We used different available products (satellite data, field measurements, models and flux towers) to estimate C stocks and fluxes in the country at three different time frames: present (defined as the period 2000–2005), the past century (1901–2000) and the remainder of this century (2010–2100). Our estimate of the gross primary productivity (GPP) for the country was 2137 ± 1023 TgC yr−1 and a total C stock of 34 506 ± 7483 TgC, with 20 347 ± 4622 TgC in vegetation and 14 159 ± 3861 in the soil. Contrary to other current estimates for recent decades, our results showed that Mexico was a C sink over the period 1990–2009 (+31 TgC yr−1) and that C accumulation over the last century amounted to 1210 ± 1040 TgC. We attributed this sink to the CO2 fertilization effect on GPP, which led to an increase of 3408 ± 1060 TgC, while both climate and land use reduced the country C stocks by −458 ± 1001 and −1740 ± 878 TgC, respectively. Under different future scenarios, the C sink will likely continue over the 21st century, with decreasing C uptake as the climate forcing becomes more extreme. Our work provides valuable insights on relevant driving processes of the C cycle such as the role of drought in drylands (e.g., grasslands and shrublands) and the impact of climate change on the mean residence time of soil C in tropical ecosystems.The lead author (G. Murray-Tortarolo) thanks CONACYT-CECTI, the University of Exeter and Secretaría de Educación Pública (SEP) for their funding of this project. The authors extend their thanks to Carlos Ortiz Solorio and to the Colegio de Posgraduados for the field soil data and to the Alianza Redd+ Mexico for the field biomass data. This project would not have been possible without the valuable data from the CMIP5 models. A. Arneth, G. Murray-Tortarolo, A. Wiltshire and S. Sitch acknowledge the support of the European Commission-funded project LULCC4C (grant no. 603542). A. Wiltshire was partsupported by the Joint UK DECC/Defra Met Office Hadley Centre Climate Programme (GA01101)

Relativistic Mean-Field Theory Equation of State of Neutron Star Matter and a Maxwellian Phase Transition to Strange Quark Matter

The equation of state of neutron star matter is examined in terms of the relativistic mean-field theory, including a scalar-isovector $\delta$-meson effective field. The constants of the theory are determined numerically so that the empirically known characteristics of symmetric nuclear matter are reproduced at the saturation density. The thermodynamic characteristics of both asymmetric nucleonic matter and $\beta$-equilibrium hadron-electron $npe$-plasmas are studied. Assuming that the transition to strange quark matter is an ordinary first-order phase transition described by Maxwell's rule, a detailed study is made of the variations in the parameters of the phase transition owing to the presence of a $\delta$-meson field. The quark phase is described using an improved version of the bag model, in which interactions between quarks are accounted for in a one-gluon exchange approximation. The characteristics of the phase transition are determined for various values of the bag parameter within the range $B\in[60,120]$ $MeV/fm^{3}$ and it is shown that including a $\delta$-meson field leads to a reduction in the phase transition pressure $P_{0}$ and in the concentrations $n_{N}$ and $n_{Q}$ at the phase transition point.Comment: 17 pages, 8 figure