The best practice for preparation of samples from FTA®cards for diagnosis of blood borne infections using African trypanosomes as a model system

Background: Diagnosis of blood borne infectious diseases relies primarily on the detection of the causative agent in the blood sample. Molecular techniques offer sensitive and specific tools for this although considerable difficulties exist when using these approaches in the field environment. In large scale epidemiological studies, FTA®cards are becoming increasingly popular for the rapid collection and archiving of a large number of samples. However, there are some difficulties in the downstream processing of these cards which is essential for the accurate diagnosis of infection. Here we describe recommendations for the best practice approach for sample processing from FTA®cards for the molecular diagnosis of trypanosomiasis using PCR. Results: A comparison of five techniques was made. Detection from directly applied whole blood was less sensitive (35.6%) than whole blood which was subsequently eluted from the cards using Chelex®100 (56.4%). Better apparent sensitivity was achieved when blood was lysed prior to application on the FTA cards (73.3%) although this was not significant. This did not improve with subsequent elution using Chelex®100 (73.3%) and was not significantly different from direct DNA extraction from blood in the field (68.3%). Conclusions: Based on these results, the degree of effort required for each of these techniques and the difficulty of DNA extraction under field conditions, we recommend that blood is transferred onto FTA cards whole followed by elution in Chelex®100 as the best approach

First-principles characterization of ferromagnetic Mn5Ge3 for spintronic applications

In the active search for potentially promising candidates for spintronic applications, we focus on the intermetallic ferromagnetic Mn5Ge3 compound and perform accurate first-principles FLAPW calculations within density functional theory. Through a careful investigation of the bulk electronic and magnetic structure, our results for the total magnetization, atomic magnetic moments, metallic conducting character and hyperfine fields are found to be in good agreement with experiments, and are elucidated in terms of a hybridization mechanism and exchange interaction. In order to assess the potential of this compound for spin-injection purposes, we calculate Fermi velocities and degree of spin-polarization; our results predict a rather high spin-injection efficiency in the diffusive regime along the hexagonal c-axis. Magneto-optical properties, such as L_2,3 X-ray magnetic circular dichroism, are also reported and await comparison with experimental data.Comment: 10 pages with 6 figures, to appear in Phys. Rev.

Spin-phonon coupling effects in transition-metal perovskites:a DFT+UU and hybrid-functional study

Spin-phonon coupling effects, as reflected in phonon frequency shifts between ferromagnetic (FM) and G-type antiferromagnetic (AFM) configurations in cubic CaMnO$_3$, SrMnO$_3$, BaMnO$_3$, LaCrO$_3$, LaFeO$_3$ and La$_2$(CrFe)O$_6$, are investigated using density-functional methods. The calculations are carried out both with a hybrid-functional (HSE) approach and with a DFT+$U$ approach using a $U$ that has been fitted to HSE calculations. The phonon frequency shifts obtained in going from the FM to the AFM spin configuration agree well with those computed directly from the more accurate HSE approach, but are obtained with much less computational effort. We find that in the $A$MnO$_3$ materials class with $A$=Ca, Sr, and Ba, this frequency shift decreases as the A cation radius increases for the $\Gamma$ phonons, while it increases for R-point phonons. In La$M$O$_3$ with $M$=Cr, Fe, and Cr/Fe, the phonon frequencies at $\Gamma$ decrease as the spin order changes from AFM to FM for LaCrO$_3$ and LaFeO$_3$, but they increase for the double perovskite La$_2$(CrFe)O$_6$. We discuss these results and the prospects for bulk and superlattice forms of these materials to be useful as multiferroics.Comment: 13 pages, 7 figures, 9 table

Theoretical prediction of multiferroicity in double perovskite Y2_2NiMnO6_6

We put forward double perovskites of the R$_2$NiMnO$_6$ family (with $R$ a rare-earth atom) as a new class of multiferroics on the basis of {\it ab initio} density functional calculations. We show that changing $R$ from La to Y drives the ground-state from ferromagnetic to antiferromagnetic with $\uparrow\uparrow\downarrow\downarrow$ spin patterns. This E$^*$-type ordering breaks inversion symmetry and generates a ferroelectric polarization of few $\mu C/cm^2$. By analyzing a model Hamiltonian we understand the microscopic origin of this transition and show that an external electric field can be used to tune the transition, thus allowing electrical control of the magnetization.Comment: 4 pages, 3 figure

Polar distortions in hydrogen bonded organic ferroelectrics

Although ferroelectric compounds containing hydrogen bonds were among the first to be discovered, organic ferroelectrics are relatively rare. The discovery of high polarization at room temperature in croconic acid [Nature \textbf{463}, 789 (2010)] has led to a renewed interest in organic ferroelectrics. We present an ab-initio study of two ferroelectric organic molecular crystals, 1-cyclobutene-1,2-dicarboxylic acid (CBDC) and 2-phenylmalondialdehyde (PhMDA). By using a distortion-mode analysis we shed light on the microscopic mechanisms contributing to the polarization, which we find to be as large as 14.3 and 7.0\,$\mu$C/cm$^{2}$ for CBDC and PhMDA respectively. These results suggest that it may be fruitful to search among known but poorly characterized organic compounds for organic ferroelectrics with enhanced polar properties suitable for device applications.Comment: Submitte

Earthquake Early Warning System for Structural Drift Prediction Using Machine Learning and Linear Regressors

In this work, we explored the feasibility of predicting the structural drift from the first seconds of P-wave signals for On-site Earthquake Early Warning (EEW) applications. To this purpose, we investigated the performance of both linear least square regression (LSR) and four non-linear machine learning (ML) models: Random Forest, Gradient Boosting, Support Vector Machines and K-Nearest Neighbors. Furthermore, we also explore the applicability of the models calibrated for a region to another one. The LSR and ML models are calibrated and validated using a dataset of ∼6,000 waveforms recorded within 34 Japanese structures with three different type of construction (steel, reinforced concrete, and steel-reinforced concrete), and a smaller one of data recorded at US buildings (69 buildings, 240 waveforms). As EEW information, we considered three P-wave parameters (the peak displacement, Pd, the integral of squared velocity, IV2, and displacement, ID2) using three time-windows (i.e., 1, 2, and 3 s), for a total of nine features to predict the drift ratio as structural response. The Japanese dataset is used to calibrate the LSR and ML models and to study their capability to predict the structural drift. We explored different subsets of the Japanese dataset (i.e., one building, one single type of construction, the entire dataset. We found that the variability of both ground motion and buildings response can affect the drift predictions robustness. In particular, the predictions accuracy worsens with the complexity of the dataset in terms of building and event variability. Our results show that ML techniques perform always better than LSR models, likely due to the complex connections between features and the natural non-linearity of the data. Furthermore, we show that by implementing a residuals analysis, the main sources of drift variability can be identified. Finally, the models trained on the Japanese dataset are applied the US dataset. In our application, we found that the exporting EEW models worsen the prediction variability, but also that by including correction terms as function of the magnitude can strongly mitigate such problem. In other words, our results show that the drift for US buildings can be predicted by minor tweaks to models

Ab-initio study of the relation between electric polarization and electric field gradients in ferroelectrics

The hyperfine interaction between the quadrupole moment of atomic nuclei and the electric field gradient (EFG) provides information on the electronic charge distribution close to a given atomic site. In ferroelectric materials, the loss of inversion symmetry of the electronic charge distribution is necessary for the appearance of the electric polarization. We present first-principles density functional theory calculations of ferroelectrics such as BaTiO3, KNbO3, PbTiO3 and other oxides with perovskite structures, by focusing on both EFG tensors and polarization. We analyze the EFG tensor properties such as orientation and correlation between components and their link with electric polarization. This work supports previous studies of ferroelectric materials where a relation between EFG tensors and polarization was observed, which may be exploited to study ferroelectric order when standard techniques to measure polarization are not easily applied.Comment: 9 pages, 6 figures, 5 tables, corrected typos, as published in Phys. Rev.

Characterisation of the Trypanosoma brucei rhodesiense isolates from Tanzania using serum resistance associated gene as molecular marker

Serum resistance associated (SRA) gene has been found to confer resistance to the innate trypanolytic factor (TLF) found in normal human serum; thus allowing Trypanosoma brucei brucei to survive exposure to normal human serum. This study was carried out to examine the presence of SRA gene and identify the origin of T. b. rhodesiense isolates from three districts in Tanzania, namely Kibondo, Kasulu and Urambo. Twenty-six T. b. rhodesiense isolates and two references T. b. rhodesiense isolates from Kenya were examined for SRA gene using simple Polymerase Chain Reaction technique. The gene was found to be present in all 26 T. b. rhodesiense isolates including the two references isolates from Kenya. The SRA gene was confirmed to be specific to T. b. rhodesiense since it could not be amplified from all other Trypanozoon including T. b. gambiense; and gave an amplified fragment of the expected size (3.9kb), confirming that all these isolates were T. b. rhodesiense of the northern variant. Although the geographic distributions of T. b. gambiense and T. b. rhodesiense are clearly localized to west/central Africa and eastern Africa, respectively, natural movement of people and recent influx of large number of refugees into Tanzania from the Democratic Republic of Congo, could have brought T. b. gambiense in western Tanzania. The overlap in distribution of both of these pathogenic sub-species could result in erroneous diagnoses since both trypanosome sub-species are morphologically identical, and currently serologic methods have low specificity. Both the susceptible and resistant T.b. rhodesiense isolates possessed the SRA gene suggesting that there is no correlation between drug resistance and presence of SRA gene. The use of SRA gene helps to confirm the identity and diversity of some of the isolates resistant to various drugs. Keywords: Trypanosoma brucei rhodesiense, resistance, SRA gene, PCR, TanzaniaTanzania Health Research Bulletin Vol. 9 (1) 2007: pp.25-3