Robocrystallographer: Automated crystal structure text descriptions and analysis

Our ability to describe crystal structure features is of crucial importance when attempting to understand structure-property relationships in the solid state. In this paper, the authors introduce robocrystallographer, an open-source toolkit for analyzing crystal structures. This package combines new and existing open-source analysis tools to provide structural information, including the local coordination and polyhedral type, polyhedral connectivity, octahedral tilt angles, component-dimensionality, and molecule-within-crystal and fuzzy prototype identification. Using this information, robocrystallographer can generate text-based descriptions of crystal structures that resemble descriptions written by human crystallographers. The authors use robocrystallographer to investigate the dimensionalities of all compounds in the Materials Project database and highlight its potential in machine learning studies

High Thermoelectric Performance and Defect Energetics of Multipocketed Full Heusler Compounds

We report a first-principles density-functional study of electron-phonon interactions in and thermoelectric transport properties of the full Heusler compounds Sr2BiAu and Sr2SbAu. Our results show that ultrahigh intrinsic bulk thermoelectric performance across a wide range of temperatures is physically possible and point to the presence of multiply degenerate and highly dispersive carrier pockets as the key factor for achieving this. Sr2BiAu, which features ten energy-aligned low-effective-mass pockets (six along Γ-X and four at L), is predicted to deliver n-type zT=0.4-4.9 at T=100-700 K. Comparison with the previously investigated compound Ba2BiAu shows that the additional L pockets in Sr2BiAu significantly increase its low-temperature power factor to a maximum value of 12 mW m-1 K-2 near T=300 K. However, at high temperatures the power factor of Sr2BiAu drops below that of Ba2BiAu because the L states are heavier and subject to strong scattering by phonon deformation, as opposed to the lighter Γ-X states, which are limited by polar-optical scattering. Sr2SbAu is predicted to deliver a lower n-type zT=3.4 at T=750 K due to appreciable misalignment between the L and Γ-X carrier pockets, generally heavier scattering, and a slightly higher lattice thermal conductivity. Soft acoustic modes, which are responsible for the low lattice thermal conductivity, also increase the vibrational entropy and high-temperature stability of these Heusler compounds, suggesting that their experimental synthesis may be feasible. The dominant intrinsic defects are found to be Au vacancies, which drive the Fermi level towards the conduction band and work in favor of n-doping

Effect of Electrode Geometry on Sensor Response

We have demonstrated the feasibility of using a finite-element program to study the effect of electrode geometry on the performance of an oxide gas sensor. The gas concentration is varied within the sensor. The program is general enough to be extended to complex three-dimensional geometries. For the simpler cases we consider, we find that at a given temperature the back contact sensor will be more selective for moderately reactive gases than for less or more reactive ones, which is in general agreement with the observations made on Figaro gas sensors. We also find that the performance of the sensor improves by using interlacing electrodes, as expected

A first step to accelerating fingerprint matching based on deformable minutiae clustering

Fingerprint recognition is one of the most used biometric methods for authentication. The identification of a query fingerprint requires matching its minutiae against every minutiae of all the fingerprints of the database. The state-of-the-art matching algorithms are costly, from a computational point of view, and inefficient on large datasets. In this work, we include faster methods to accelerating DMC (the most accurate fingerprint matching algorithm based only on minutiae). In particular, we translate into C++ the functions of the algorithm which represent the most costly tasks of the code; we create a library with the new code and we link the library to the original C# code using a CLR Class Library project by means of a C++/CLI Wrapper. Our solution re-implements critical functions, e.g., the bit population count including a fast C++ PopCount library and the use of the squared Euclidean distance for calculating the minutiae neighborhood. The experimental results show a significant reduction of the execution time in the optimized functions of the matching algorithm. Finally, a novel approach to improve the matching algorithm, considering cache memory blocking and parallel data processing, is presented as future work.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Comparison of the tetrahedron method to smearing methods for the electronic density of states

The electronic density of states (DOS) highlights fundamental properties of materials that oftentimes dictate their properties, such as the band gap and Van Hove singularities. In this short note, we discuss how sharp features of the density of states can be obscured by smearing methods (such as the Gaussian and Fermi smearing methods) when calculating the DOS. While the common approach to reach a "converged" density of states of a material is to increase the discrete k-point mesh density, we show that the DOS calculated by smearing methods can appear to converge but not to the correct DOS. Employing the tetrahedron method for Brillouin zone integration resolves key features of the density of states far better than smearing methods

A genome-wide study of Hardy–Weinberg equilibrium with next generation sequence data

Statistical tests for Hardy–Weinberg equilibrium have been an important tool for detecting genotyping errors in the past, and remain important in the quality control of next generation sequence data. In this paper, we analyze complete chromosomes of the 1000 genomes project by using exact test procedures for autosomal and X-chromosomal variants. We find that the rate of disequilibrium largely exceeds what might be expected by chance alone for all chromosomes. Observed disequilibrium is, in about 60% of the cases, due to heterozygote excess. We suggest that most excess disequilibrium can be explained by sequencing problems, and hypothesize mechanisms that can explain exceptional heterozygosities. We report higher rates of disequilibrium for the MHC region on chromosome 6, regions flanking centromeres and p-arms of acrocentric chromosomes. We also detected long-range haplotypes and areas with incidental high disequilibrium. We report disequilibrium to be related to read depth, with variants having extreme read depths being more likely to be out of equilibrium. Disequilibrium rates were found to be 11 times higher in segmental duplications and simple tandem repeat regions. The variants with significant disequilibrium are seen to be concentrated in these areas. For next generation sequence data, Hardy–Weinberg disequilibrium seems to be a major indicator for copy number variation.Peer ReviewedPostprint (published version

Anthracycline-Induced Cardiotoxicity: Cardiac Monitoring by Continuous Wave-Doppler Ultrasound Cardiac Output Monitoring and Correlation to Echocardiography

Background: Anthracyclines are agents with a well-known cardiotoxicity. The study sought to evaluate the hemodynamic response to an anthracycline using real-time continuous-wave (CW)-Doppler ultrasound cardiac output monitoring (USCOM) and echocardiography in combination with serum biomarkers. Methods: 50 patients (26 male, 24 female, median age 59 years) suffering from various types of cancer received an anthracycline-based regimen. Patients' responses were measured at different time points (T0 prior to infusion, T1 6 h post infusion, T2 after 1 day, T3 after 7 days, and T4 after 3 months) with CW-Doppler ultrasound (T0-T4) and echocardiography (T1, T4) for hemodynamic parameters such as stroke volume (SV; SVUSCOM ml) and ejection fraction (EF; EFechocardiography%) and with NT-pro-BNP and hs-Troponin T (T0-T4). Results: During the 3-month observation period, the relative decrease in the EF determined by echocardiography was -2.1% (Delta T0-T4, T0 71 +/- 7.8%, T4 69.5 +/- 7%, p = 0.04), whereas the decrease in SV observed using CW-Doppler was -6.5% (Delta T0-T4, T0 54 +/- 19.2 ml, T4 50.5 +/- 20.6 ml, p = 0.14). The kinetics for serum biomarkers were inversely correlated. Conclusions: Combining real-time CW-Doppler USCOM and serum biomarkers is feasible for monitoring the immediate and chronic hemodynamic changes during an anthracycline-based regimen; the results obtained were comparable to those from echocardiography

Optimizing CIGB-300 intralesional delivery in locally advanced cervical cancer

Background:We conducted a phase 1 trial in patients with locally advanced cervical cancer by injecting 0.5 ml of the CK2-antagonist CIGB-300 in two different sites on tumours to assess tumour uptake, safety, pharmacodynamic activity and identify the recommended dose.Methods:Fourteen patients were treated with intralesional injections containing 35 or 70 mg of CIGB-300 in three alternate cycles of three consecutive days each before standard chemoradiotherapy. Tumour uptake was determined using 99 Tc-radiolabelled peptide. In situ B23/nucleophosmin was determined by immunohistochemistry.Results:Maximum tumour uptake for CIGB-300 70-mg dose was significantly higher than the one observed for 35 mg: 16.1±8.9 vs 31.3±12.9 mg (P=0.01). Both, AUC 24h and biological half-life were also significantly higher using 70 mg of CIGB-300 (P<0.001). Unincorporated CIGB-300 diffused rapidly to blood and was mainly distributed towards kidneys, and marginally in liver, lungs, heart and spleen. There was no DLT and moderate allergic-like reactions were the most common systemic side effect with strong correlation between unincorporated CIGB-300 and histamine levels in blood. CIGB-300, 70 mg, downregulated B23/nucleophosmin (P=0.03) in tumour specimens.Conclusion:Intralesional injections of 70 mg CIGB-300 in two sites (0.5 ml per injection) and this treatment plan are recommended to be evaluated in phase 2 studies.Fil: Sarduy, M. R.. Medical-surgical Research Center; CubaFil: García, I.. Centro de Ingeniería Genética y Biotecnología; CubaFil: Coca, M. A.. Clinical Investigation Center; CubaFil: Perera, A.. Clinical Investigation Center; CubaFil: Torres, L. A.. Clinical Investigation Center; CubaFil: Valenzuela, C. M.. Centro de Ingeniería Genética y Biotecnología; CubaFil: Baladrón, I.. Centro de Ingeniería Genética y Biotecnología; CubaFil: Solares, M.. Hospital Materno Ramón González Coro; CubaFil: Reyes, V.. Center For Genetic Engineering And Biotechnology Havana; CubaFil: Hernández, I.. Isotope Center; CubaFil: Perera, Y.. Centro de Ingeniería Genética y Biotecnología; CubaFil: Martínez, Y. M.. Medical-surgical Research Center; CubaFil: Molina, L.. Medical-surgical Research Center; CubaFil: González, Y. M.. Medical-surgical Research Center; CubaFil: Ancízar, J. A.. Centro de Ingeniería Genética y Biotecnología; CubaFil: Prats, A.. Clinical Investigation Center; CubaFil: González, L.. Centro de Ingeniería Genética y Biotecnología; CubaFil: Casacó, C. A.. Clinical Investigation Center; CubaFil: Acevedo, B. E.. Centro de Ingeniería Genética y Biotecnología; CubaFil: López Saura, P. A.. Centro de Ingeniería Genética y Biotecnología; CubaFil: Alonso, Daniel Fernando. Universidad Nacional de Quilmes; ArgentinaFil: Gómez, R.. Elea Laboratories; ArgentinaFil: Perea Rodríguez, S. E.. Center For Genetic Engineering And Biotechnology Havana; Cuba. Centro de Ingeniería Genética y Biotecnología; Cub

Decolorization of synthetic melanoidins-containing wastewater by a bacterial consortium

The presence of melanoidins in molasses wastewater leads to water pollution both due to its dark brown color and its COD contents. In this study, a bacterial consortium isolated from waterfall sediment was tested for its decolorization. The identification of culturable bacteria by 16S rDNA based approach showed that the consortium composed of Klebsiella oxytoca, Serratia mercescens, Citrobacter sp. and unknown bacterium. In the context of academic study, prevention on the difficulties of providing effluent as well as its variations in compositions, several synthetic media prepared with respect to color and COD contents based on analysis of molasses wastewater, i.e., Viandox sauce (13.5% v/v), caramel (30% w/v), beet molasses wastewater (41.5% v/v) and sugarcane molasses wastewater (20% v/v) were used for decolorization using consortium with color removal 9.5, 1.13, 8.02 and 17.5%, respectively, within 2 days. However, Viandox sauce was retained for further study. The effect of initial pH and Viandox concentration on decolorization and growth of bacterial consortium were further determined. The highest decolorization of 18.3% was achieved at pH 4 after 2 day of incubation. Experiments on fresh or used medium and used or fresh bacterial cells, led to conclusion that the limitation of decolorization was due to nutritional deficiency. The effect of aeration on decolorization was also carried out in 2 L laboratory-scale suspended cell bioreactor. The maximum decolorization was 19.3% with aeration at KLa = 2.5836 h-1 (0.1 vvm)

Male predominance of pneumonia and hospitalization in pandemic influenza A (H1N1) 2009 infection

<p>Abstract</p> <p>Background</p> <p>Pandemic influenza A (H1N1) disproportionately affects different age groups. The purpose of the current study was to describe the age and gender difference of pandemic influenza A (H1N1) cases that lead to pneumonia, hospitalization or ICU admission.</p> <p>Methods</p> <p>Data were collected retrospectively between May 2009 and December 2009. All of the diagnoses of H1N1 were confirmed by real-time reverse-transcription polymerase chain reaction (RT-PCR).</p> <p>Results</p> <p>During the study period there were 3402 cases of RT-PCR positive H1N1, among which 1812 were males and 1626 were adults (> 15 years of age). 6% (206/3402) of patients required hospitalization, 3.6% (122/3402) had infiltrates on chest radiographs, and 0.70% (24/3402) were admitted to intensive care unit (ICU). The overall fatality rate was 0.1% (4/3402). The rate of hospitalization was sharply increased in patients ≥ 50 years of age especially in male. Out of 122 pneumonia patients, 68.8% (84 patients) were male. Among the patients admitted to the ICU, 70.8% (17 patients) were male. Approximately 1 of 10 H1N1-infected patients admitted to the ICU were ≥ 70 years of age.</p> <p>Conclusions</p> <p>Among the confirmed cases of H1N1, the ICU admission rate was < 1% and the case fatality rate was 0.1%. Male had a significantly higher rate of pneumonia and hospital admission. These findings should be taken into consideration when developing vaccination and treatment strategies.</p