The Alloy Theoretic Automated Toolkit: A User Guide

Although the formalism that allows the calculation of alloy thermodynamic properties from first-principles has been known for decades, its practical implementation has so far remained a tedious process. The Alloy Theoretic Automated Toolkit (ATAT) drastically simplifies this procedure by implementing decision rules based on formal statistical analysis that frees the researchers from a constant monitoring during the calculation process and automatically "glues" together the input and the output of various codes, in order to provide a high-level interface to the calculation of alloy thermodynamic properties from first-principles. ATAT implements the Structure Inversion Method (SIM), also known as the Connolly-Williams method, in combination with semi-grand-canonical Monte Carlo simulations. In order to make this powerful toolkit available to the wide community of researchers who could benefit from it, this article present a concise user guide outlining the steps required to obtain thermodynamic information from ab initio calculations.Comment: 15 pages, 4 figure

The Effect of Lattice Vibrations on Substitutional Alloy Thermodynamics

A longstanding limitation of first-principles calculations of substitutional alloy phase diagrams is the difficulty to account for lattice vibrations. A survey of the theoretical and experimental literature seeking to quantify the impact of lattice vibrations on phase stability indicates that this effect can be substantial. Typical vibrational entropy differences between phases are of the order of 0.1 to 0.2 k_B/atom, which is comparable to the typical values of configurational entropy differences in binary alloys (at most 0.693 k_B/atom). This paper describes the basic formalism underlying ab initio phase diagram calculations, along with the generalization required to account for lattice vibrations. We overview the various techniques allowing the theoretical calculation and the experimental determination of phonon dispersion curves and related thermodynamic quantities, such as vibrational entropy or free energy. A clear picture of the origin of vibrational entropy differences between phases in an alloy system is presented that goes beyond the traditional bond counting and volume change arguments. Vibrational entropy change can be attributed to the changes in chemical bond stiffness associated with the changes in bond length that take place during a phase transformation. This so-called ``bond stiffness vs. bond length'' interpretation both summarizes the key phenomenon driving vibrational entropy changes and provides a practical tool to model them.Comment: Submitted to Reviews of Modern Physics 44 pages, 6 figure

Analysis and Reuse of Plots Using Similarity and Analogy

Abstract: A plot is a partially ordered set of events. Plot analysis is a relevant source of knowledge about the agents behavior when accessing data stored in the database. It relies on logical logs which register the actions of individual agents. This paper proposes techniques to analyze and reuse plots based on the concepts of similarity and analogy, borrowed from cognitive science and linguistics. The concept of similarity is applied to organize plots as a library, and to explore the reuse of plots in the same domain. By contrast, the concept of analogy helps reuse plots across different domains. The techniques proposed in this paper find applications in areas such as computer games and emergency response information systems, as well as some traditional business applications

X-ray reflectivity of an Sb delta-doping layer in silicon

X‐ray reflectivity measurements were made on Si(001) crystals containing a delta‐doping layer of Sb atoms a few nanometers below the surface. The measurements show the Sb doping profile to be abrupt towards the substrate side of the sample and to decay towards the surface with a characteristic decay length of 1.01 nm

Evidence of a new state in 11^{11}Be observed in the 11^{11}Li β\beta-decay

Coincidences between charged particles emitted in the $\beta$-decay of $^{11}$Li were observed using highly segmented detectors. The breakup channels involving three particles were studied in full kinematics allowing for the reconstruction of the excitation energy of the $^{11}$Be states participating in the decay. In particular, the contribution of a previously unobserved state at 16.3 MeV in $^{11}$Be has been identified selecting the $\alpha$ + $^7$He$\to\alpha$ + $^6$He+n channel. The angular correlations between the $\alpha$ particle and the center of mass of the $^6$He+n system favors spin and parity assignment of 3/2$^-$ for this state as well as for the previously known state at 18 MeV.Comment: 13 pages, 6 figure

In vitro digestion and lactase treatment influence uptake of quercetin and quercetin glucoside by the Caco-2 cell monolayer

BACKGROUND: Quercetin and quercetin glycosides are widely consumed flavonoids found in many fruits and vegetables. These compounds have a wide range of potential health benefits, and understanding the bioavailability of flavonoids from foods is becoming increasingly important. METHODS: This study combined an in vitro digestion, a lactase treatment and the Caco-2 cell model to examine quercetin and quercetin glucoside uptake from shallot and apple homogenates. RESULTS: The in vitro digestion alone significantly decreased quercetin aglycone recovery from the shallot digestate (p < 0.05), but had no significant effect on quercetin-3-glucoside recovery (p > 0.05). Digestion increased the Caco-2 cell uptake of shallot quercetin-4'-glucoside by 2-fold when compared to the non-digested shallot. Despite the loss of quercetin from the digested shallot, the bioavailability of quercetin aglycone to the Caco-2 cells was the same in both the digested and non-digested shallot. Treatment with lactase increased quercetin recovery from the shallot digestate nearly 10-fold and decreased quercetin-4'-glucoside recovery by more than 100-fold (p < 0.05), but had no effect on quercetin recovery from apple digestates. Lactase treatment also increased shallot quercetin bioavailability to the Caco-2 cells approximately 14-fold, and decreased shallot quercetin-4'-glucoside bioavailability 23-fold (p < 0.05). These Caco-2 cells had lactase activity similar to that expressed by a lactose intolerant human. CONCLUSIONS: The increase in quercetin uptake following treatment with lactase suggests that dietary supplementation with lactase may increase quercetin bioavailability in lactose intolerant humans. Combining the digestion, the lactase treatment and the Caco-2 cell culture model may provide a reliable in vitro model for examining flavonoid glucoside bioavailability from foods

Measurement of the inelastic branch of the 14^{14}O(α,p)17^{17}F reaction: Implications for explosive burning in novae and x-ray bursters

A measurement of the inelastic component of the key astrophysical resonance in the 14O(α,p)17F reaction for burning and breakout from hot carbon-nitrogen-oxygen (CNO) cycles is reported. The inelastic component is found to be comparable to the ground-state branch and will enhance the 14O(α,p)17F reaction rate. The current results for the reaction rate confirm that the 14O(α,p)17F reaction is unlikely to contribute substantially to burning and breakout from the CNO cycles under novae conditions. The reaction can, however, contribute strongly to the breakout from the hot CNO cycles under the more extreme conditions found in x-ray bursters

Neurocognitive functioning in school-aged cystinosis patients

Contains fulltext : 89600.pdf (publisher's version ) (Closed access)INTRODUCTION: Cystinosis is an autosomal recessive disorder leading to intralysosomal cystine accumulation in various tissues. It causes renal Fanconi syndrome and end stage renal failure around the age of 10 years if not treated with cysteamine. Children with cystinosis seem to have a normal intelligence but frequently show learning difficulties. These problems may be due to specific neurocognitive deficits rather than impaired renal function. Whether cysteamine treatment can improve cognitive functioning of cystinosis patients is thus far unknown. We aim to analyze neurocognitive functioning of school-aged cystinosis patients treated with cysteamine in order to identify specific deficits that can lead to learning difficulties. PATIENTS AND METHODS: Fourteen Dutch and Belgian school-aged cystinosis patients were included. Glomerular filtration rate was estimated using the Schwartz formula. Children were tested for general intelligence, visual-motor integration, inhibition, interference, sustained attention, accuracy, planning, visual memory, processing speed, motor planning, fluency and speed, and behavioural and emotional functioning using standardized methods. RESULTS: Glomerular filtration rate ranged from 22 to 120 ml min(-1) 1.73 m(-2). Median full-scale intelligence was below the average of a normal population (87, range 60-132), with a discrepancy between verbal (median 95, range 60-125) and performance (median 87, range 65-130) intelligence. Over 50% of the patients scored poorly on visual-motor integration, sustained attention, visual memory, planning, or motor speed. The other tested areas showed no differences between patients' and normal values. CONCLUSION: Neurocognitive diagnostics are indicated in cystinosis patients. Early recognition of specific deficits and supervision from special education services might reduce learning difficulties and improve school careers.1 december 201

Representation and exclusion in partial democracies: the role of civil society organisations

The ‘third democratic wave’ that rose in the 1990s has receded in many countries, as incum-bent regimes have manipulated electoral processes and regressive political movements have exploited class, ethnic and sectarian antagonism to undermine political order. Such events have led many to question the importance of democratic processes. The papers in this special section challenge both the uncritical advocates and over-critical naysayers of the third wave by treating democratisation as a long-term and contested transition from closed to open ac-cess societies, where elections represent a necessary but not sufficient mechanism to guarantee representation for excluded groups. The three papers focus on the critical role of civil society organisations (CSOs) in securing representation for marginal actors, drawing on the cases of Bangladesh and Uganda. In doing so the contributions illustrate the challenges that CSOs confront in situations marked by the problems of clientelism, capture and exclusion