Strain-induced phase transformation under compression in a diamond anvil cell: Simulations of a sample and gasket

Combined high pressure phase transformations (PTs) and plastic flow in a sample within a gasket compressed in diamond anvil cell (DAC) are studied for the first time using finite element method. The key point is that phase transformations are modelled as strain-induced, which involves a completely different kinetic description than for traditional pressure-induced PTs. The model takes into account, contact sliding with Coulomb and plastic friction at the boundaries between the sample, gasket, and anvil. A comprehensive computational study of the effects of the kinetic parameter, ratio of the yield strengths of high and low-pressure phases and the gasket, sample radius, and initial thickness on the PTs and plastic flow is performed. A new sliding mechanism at the contact line between the sample, gasket, and anvil called extrusion-based pseudoslip is revealed, which plays an important part in producing high pressure. Strain-controlled kinetics explains why experimentally determined phase transformation pressure and kinetics (concentration of high pressure phase vs. pressure) differ for different geometries and properties of the gasket and the sample: they provide different plastic strain, which was not measured. Utilization of the gasket changes radial plastic flow toward the center of a sample, which leads to high quasi-homogeneous pressure for some geometries. For transformation to a stronger high pressure phase, plastic strain and concentration of a high-pressure phase are also quasi-homogeneous. This allowed us to suggest a method of determining strain-controlled kinetics from experimentation, which is not possible for weaker and equal-strength high-pressure phases and cases without a gasket. Some experimental phenomena are reproduced and interpreted. Developed methods and obtained results represent essential progress toward the understanding of PTs under compression in the DAC. This will allow one optimal design of experiments and conditions for synthesis of new high pressure phases

The Wide Integral Field Infrared Spectrograph: Commissioning Results and On-sky Performance

We have recently commissioned a novel infrared ($0.9-1.7$ $\mu$m) integral field spectrograph (IFS) called the Wide Integral Field Infrared Spectrograph (WIFIS). WIFIS is a unique instrument that offers a very large field-of-view (50$^{\prime\prime}$ x 20$^{\prime\prime}$) on the 2.3-meter Bok telescope at Kitt Peak, USA for seeing-limited observations at moderate spectral resolving power. The measured spatial sampling scale is $\sim1\times1^{\prime\prime}$ and its spectral resolving power is $R\sim2,500$ and $3,000$ in the $zJ$ ($0.9-1.35$ $\mu$m) and $H_{short}$ ($1.5-1.7$ $\mu$m) modes, respectively. WIFIS's corresponding etendue is larger than existing near-infrared (NIR) IFSes, which are mostly designed to work with adaptive optics systems and therefore have very narrow fields. For this reason, this instrument is specifically suited for studying very extended objects in the near-infrared such as supernovae remnants, galactic star forming regions, and nearby galaxies, which are not easily accessible by other NIR IFSes. This enables scientific programs that were not originally possible, such as detailed surveys of a large number of nearby galaxies or a full accounting of nucleosynthetic yields of Milky Way supernova remnants. WIFIS is also designed to be easily adaptable to be used with larger telescopes. In this paper, we report on the overall performance characteristics of the instrument, which were measured during our commissioning runs in the second half of 2017. We present measurements of spectral resolving power, image quality, instrumental background, and overall efficiency and sensitivity of WIFIS and compare them with our design expectations. Finally, we present a few example observations that demonstrate WIFIS's full capability to carry out infrared imaging spectroscopy of extended objects, which is enabled by our custom data reduction pipeline.Comment: Published in the Proceedings of SPIE Astronomical Telescopes and Instrumentation 2018. 17 pages, 13 figure

Computer-Aided Histopathological Characterisation of Endometriosis Lesions.

Endometriosis is a common gynaecological condition characterised by the growth of endometrial tissue outside the uterus and is associated with pain and infertility. Currently, the gold standard for endometriosis diagnosis is laparoscopic excision and histological identification of endometrial epithelial and stromal cells. There is, however, currently no known association between the histological appearance, size, morphology, or subtype of endometriosis and disease prognosis. In this study, we used histopathological software to identify and quantify the number of endometrial epithelial and stromal cells within excised endometriotic lesions and assess the relationship between the cell contents and lesion subtypes. Prior to surgery for suspected endometriosis, patients provided menstrual and abdominal pain and dyspareunia scores. Endometriotic lesions removed during laparoscopic surgery were collected and prepared for immunohistochemistry from 26 patients. Endometrial epithelial and stromal cells were identified with Cytokeratin and CD10 antibodies, respectively. Whole slide sections were digitised and the QuPath software was trained to automatically detect and count epithelial and stromal cells across the whole section. Using this classifier, we identified a significantly larger number of strongly labelled CD10 stromal cells (p = 0.0477) in deeply infiltrating lesions (99,970 ± 2962) compared to superficial lesions (2456 ± 859). We found the ratio of epithelial to stromal cells was inverted in deeply infiltrating endometriosis lesions compared to superficial peritoneal and endometrioma lesions and we subsequently identified a correlation between total endometrial cells and abdominal pain (p = 0.0005) when counted via the automated software. Incorporating histological software into current standard diagnostic pipelines may improve endometriosis diagnosis and provide prognostic information in regards to severity and symptoms and eventually provide the potential to personalise adjuvant treatment decisions

Coupled plastic flow and phase transformation under compression of materials in a diamond anvil cell: Effects of transformation kinetics and yield strength

The large-strain problem on phase transformations (PTs) under compression in a diamond anvil cell is studied in detail using the finite-element method. The combined effect of transformation kinetics and ratios of the yield strengths of low- and high-pressure phases is examined. Some experimental phenomena (e.g., plateaus in pressure distribution and plasticflow to the center of a sample) are reproduced. Results are applied to interpretation of experimental data and characterization of strain-induced PTs.The following article appeared in Journal of Applied Physics 111 (2012): 023518 and may be found at http://dx.doi.org/10.1063/1.3677977.</p

MultiMetEval: comparative and multi-objective analysis of genome-scale metabolic models

Comparative metabolic modelling is emerging as a novel field, supported by the development of reliable and standardized approaches for constructing genome-scale metabolic models in high throughput. New software solutions are needed to allow efficient comparative analysis of multiple models in the context of multiple cellular objectives. Here, we present the user-friendly software framework Multi-Metabolic Evaluator (MultiMetEval), built upon SurreyFBA, which allows the user to compose collections of metabolic models that together can be subjected to flux balance analysis. Additionally, MultiMetEval implements functionalities for multi-objective analysis by calculating the Pareto front between two cellular objectives. Using a previously generated dataset of 38 actinobacterial genome-scale metabolic models, we show how these approaches can lead to exciting novel insights. Firstly, after incorporating several pathways for the biosynthesis of natural products into each of these models, comparative flux balance analysis predicted that species like Streptomyces that harbour the highest diversity of secondary metabolite biosynthetic gene clusters in their genomes do not necessarily have the metabolic network topology most suitable for compound overproduction. Secondly, multi-objective analysis of biomass production and natural product biosynthesis in these actinobacteria shows that the well-studied occurrence of discrete metabolic switches during the change of cellular objectives is inherent to their metabolic network architecture. Comparative and multi-objective modelling can lead to insights that could not be obtained by normal flux balance analyses. MultiMetEval provides a powerful platform that makes these analyses straightforward for biologists. Sources and binaries of MultiMetEval are freely available from https://github.com/PiotrZakrzewski/MetEv​al/downloads

Local Ferromagnetism in Microporous Carbon with the Structural Regularity of Zeolite Y

Magnetization M(H,T) measurements have been performed on microporous carbon (MC) with a three-dimensional nano-array structure corresponding to that of a zeolite Y supercage. The obtained results unambiguously demonstrate the occurrence of high-temperature ferromagnetism in MC, probably originating from a topological disorder associated with curved graphene sheets. The results provide evidence that the ferromagnetic behavior of MC is governed by isolated clusters in a broad temperature range, and suggest the occurrence of percolative-type transition with the temperature lowering. A comparative analysis of the results obtained on MC and related materials is given.Comment: To be published in Physical Review B (2003

Multiple-Point and Multiple-Time Correlations Functions in a Hard-Sphere Fluid

A recent mode coupling theory of higher-order correlation functions is tested on a simple hard-sphere fluid system at intermediate densities. Multi-point and multi-time correlation functions of the densities of conserved variables are calculated in the hydrodynamic limit and compared to results obtained from event-based molecular dynamics simulations. It is demonstrated that the mode coupling theory results are in excellent agreement with the simulation results provided that dissipative couplings are included in the vertices appearing in the theory. In contrast, simplified mode coupling theories in which the densities obey Gaussian statistics neglect important contributions to both the multi-point and multi-time correlation functions on all time scales.Comment: Second one in a sequence of two (in the first, the formalism was developed). 12 pages REVTeX. 5 figures (eps). Submitted to Phys.Rev.

Volatile constituents and behavioral change induced by Cymbopogon winterianus leaf essential oil in rodents

Cymbopogon winterianus Jowitt (‘Java citronella’) is an important essential oil yielding aromatic grass cultivated in India and Brazil and its volatile essential oils extracted from its leaves are used in perfumery, cosmetics, pharmaceuticals and flavoring industries. However, there is no report on any psychopharmacological study of C. winterianus leaf essential oil (LEO) available to date. In this study, the pharmacological effects of the LEO were investigated in animal models and its phytochemical analyses. GC-MS analysis showed a mixture of monoterpenes, as citronellal (36.19%), geraniol (32.82%) and citronellol (11.37%). LEO exhibited an inhibitory effect on the locomotor activity of mice, an antinociceptive effect by increasing the reaction time in the writhing and capsaicin tests. All doses induced a significant increase in the sleeping time of animals not having modified however, the latency. The LEO did not alter the remaining time of the animals on the rota-rod apparatus. These results suggest a possible central effect.Key words: Cymbopogon winterianus, essential oil, CNS, behavioral effects, analgesic

Unravelling the size distribution of social groups with information theory on complex networks

The minimization of Fisher's information (MFI) approach of Frieden et al. [Phys. Rev. E {\bf 60} 48 (1999)] is applied to the study of size distributions in social groups on the basis of a recently established analogy between scale invariant systems and classical gases [arXiv:0908.0504]. Going beyond the ideal gas scenario is seen to be tantamount to simulating the interactions taking place in a network's competitive cluster growth process. We find a scaling rule that allows to classify the final cluster-size distributions using only one parameter that we call the competitiveness. Empirical city-size distributions and electoral results can be thus reproduced and classified according to this competitiveness, which also allows to correctly predict well-established assessments such as the "six-degrees of separation", which is shown here to be a direct consequence of the maximum number of stable social relationships that one person can maintain, known as Dunbar's number. Finally, we show that scaled city-size distributions of large countries follow the same universal distribution