The Effect of Al and Ti Additions on Solid Solution Strengthening and Precipitation Hardening in CoNiFe Medium-Entropy Alloys.

The effect of Al and Ti additions on the microstructure and properties of CoNiFe alloys was studied in this paper. The investigations were conducted on four specially designed and produced arc furnace alloys (from 3 to 5 components, with medium to high entropy). Samples in various states were analyzed, i.e., as-cast, after homogenization, after solution heat treatment, and after solution heat treatment and aging. The obtained samples were characterized by: SEM observations, EDS, XRD, TEM analyses, and finally, hardness measurements. The solid solution strengthening coming from the addition of 5 at. pct. Al was negligible, while the effect from the 5 at. pct. of Ti addition was significant. The precipitation hardening effect related to the presence of the (CoNi)3Ti phase caused by the Ti addition is comparable with the total effect of the Al and Ti addition, which caused the precipitation of (NiCo)3AlTi.

Mapping of lattice distortion in martensitic steel-Comparison of different evaluation methods of EBSD patterns.

To visualize the varying tetragonal distortions in high carbon martensitic steels by EBSD, two different approaches have been applied on backscattered Kikuchi diffraction (BKD) patterns. A band-edge refinement technique called Refined Accuracy (RA) (Oxford Instruments) is compared with a technique called Pattern Matching (PM), which optimizes the fit to a simulated BKD signal. RA distinguishes between hypothetical phases of different fixed c/a, while PM determines a best fitting continuous c/a by projective transformation of a master pattern. Both techniques require stored BKD patterns. The sensitivity of the c/a-determination was tested by investigating the microstructure of a ferritic steel with an expected c/a=1. The influence of the Kikuchi pattern noise on c/a was compared for a single or 40 averaged frames per measuring point, and turned out to be not significant. The application of RA and PM on the martensitic microstructure delivered qualitatively similar maps of c/a. The comparison of RA and PM shows that RA is suitably fast and precise during mapping the martensite c/a ratio in analyses of high carbon martensite, especially for fast initial surveys. As RA leads quantitatively to higher noise in c/a, the PM analysis can be used for higher precision results.

Crystallization Kinetics Analysis of the Binary Amorphous Mg72Zn28 Alloy.

The aim of the study was to analyze the crystallization kinetics of the Mg72Zn28 metallic glass alloy. The crystallization kinetics of Mg72Zn28 metallic glass were investigated by differential scanning calorimetry and X-ray diffraction. The phases formed during the crystallization process were identified as α-Mg and complex Mg12Zn13 phases. Activation energies for the glass transition temperature, crystallization onset, and peak were calculated based on the Kissinger model. The activation energy calculated from the Kissinger model was Eg = 176.91, Ex = 124.26, Ep1 = 117.49, and Ep2 = 114.48 kJ mol-1, respectively.

In vitro cytocompatibility and antibacterial studies on biodegradable Zn alloys supplemented by a critical assessment of direct contact cytotoxicity assay.

In vitro cytotoxicity assessment is indispensable in developing new biodegradable implant materials. Zn, which demonstrates an ideal corrosion rate between Mg- and Fe-based alloys, has been reported to have excellent in vivo biocompatibility. Therefore, modifications aimed at improving Zn's mechanical properties should not degrade its biological response. As sufficient strength, ductility and corrosion behavior required of load-bearing implants has been obtained in plastically deformed Zn-3Ag-0.5Mg, the effect of simultaneous Ag and Mg additions on in vitro cytocompatibility and antibacterial properties was studied, in relation to Zn and Zn-3Ag. Direct cell culture on samples and indirect extract-based tests showed almost no significant differences between the tested Zn-based materials. The diluted extracts of Zn, Zn-3Ag, and Zn-3Ag-0.5Mg showed no cytotoxicity toward MG-63 cells at a concentration of ≤12.5%. The cytotoxic effect was observed only at high Zn2+ ion concentrations and when in direct contact with metallic samples. The highest LD50 (lethal dose killing 50% of cells) of 13.4 mg/L of Zn2+ ions were determined for the Zn-3Ag-0.5Mg. Similar antibacterial activity against Escherichia coli and Staphylococcus aureus was observed for Zn and Zn alloys, so the effect is attributed mainly to the released Zn2+ ions exhibiting bactericidal properties. Most importantly, our experiments indicated the limitations of water-soluble tetrazolium salt-based cytotoxicity assays for direct tests on Zn-based materials. The discrepancies between the WST-8 assay and SEM observations are attributed to the interference of Zn2+ ions with tetrazolium salt, therefore favoring its transformation into formazan, giving false cell viability quantitative results.

Fabrication of stainless-steel microfibers with amorphous-nanosized microstructure with enhanced mechanical properties.

Metallic glasses (MG) have attracted much attention due to their superior hardness and good corrosion resistance. However, designing new MG compositions is still a big challenge, and their integration into different systems is limited when they are in the shape of bulk materials. Here, we present a new method for the fabrication of MG in the form of microfibers which could greatly help them to be integrated within different systems. The newly proposed technique has the ability to form MG structure from commercially available alloy compositions thanks to its significantly improved quenching rate(~ 108 K.s-1). In this technique, individual melt droplets are ejected on a rotating wheel forming a thin film which are ruptured upon solidification leading to the formation of MG microfibers. In this regard, we have fabricated microfibers from a commercial DIN 1.4401 stainless-steel which could form a completely amorphous structure confirmed by DSC, XRD, and HRTEM. The fabricated MG microfibers show an increased hardness for more than two-fold from 3.5 ± 0.17 GPa for the as-received stainless-steel to 7.77 ± 0.60 GPa for the amorphous microfibers. Subsequent heat-treatment of the microfibers resulted in a nanocrystalline structure with the presence of amorphous regions when the hardness increases even further to 13.5 ± 2.0 GPa. We propose that confinement of both shear transformation zones and dislocations in the heat-treated MG microfibers plays a major role in enhancing strength.

Human exposome assessment platform.

The Human Exposome Assessment Platform (HEAP) is a research resource for the integrated and efficient management and analysis of human exposome data. The project will provide the complete workflow for obtaining exposome actionable knowledge from population-based cohorts. HEAP is a state-of-the-science service composed of computational resources from partner institutions, accessed through a software framework that provides the world's fastest Hadoop platform for data warehousing and applied artificial intelligence (AI). The software, will provide a decision support system for researchers and policymakers. All the data managed and processed by HEAP, together with the analysis pipelines, will be available for future research. In addition, the platform enables adding new data and analysis pipelines. HEAP's final product can be deployed in multiple instances to create a network of shareable and reusable knowledge on the impact of exposures on public health.

Transmission Kikuchi diffraction: The impact of the signal-to-noise ratio.

Signal optimization for transmission Kikuchi diffraction (TKD) measurements in the scanning electron microscope is investigated by a comparison of different sample holder designs. An optimized design is presented, which uses a metal shield to efficiently trap the electron beam after transmission through the sample. For comparison, a second holder configuration allows a significant number of the transmitted electrons to scatter back from the surface of the sample holder onto the diffraction camera screen. It is shown that the secondary interaction with the sample holder leads to a significant increase in the background level, as well as to additional noise in the final Kikuchi diffraction signal. The clean TKD signal of the optimized holder design with reduced background scattering makes it possible to use small signal changes in the range of 2% of the camera full dynamic range. As is shown by an analysis of the power spectrum, the signal-to-noise ratio in the processed Kikuchi diffraction patterns is improved by an order of magnitude. As a result, the optimized design allows an increase in pattern signal to noise ratio which may lead to increase in measurement speed and indexing reliability.

Kikuchi pattern simulations of backscattered and transmitted electrons.

We discuss a refined simulation approach which treats Kikuchi diffraction patterns in electron backscatter diffraction (EBSD) and transmission Kikuchi diffraction (TKD). The model considers the result of two combined mechanisms: (a) the dynamical diffraction of electrons emitted coherently from point sources in a crystal and (b) diffraction effects on incoherent diffuse intensity distributions. Using suitable parameter settings, the refined simulation model allows to reproduce various thickness- and energy-dependent features which are observed in experimental Kikuchi diffraction patterns. Excess-deficiency features are treated by the effect of gradients in the incoherent background intensity. Based on the analytical two-beam approximation to dynamical electron diffraction, a phenomenological model of excess-deficiency features is derived, which can be used for pattern matching applications. The model allows to approximate the effect of the incident beam geometry as a correction signal for template patterns which can be reprojected from pre-calculated reference data. As an application, we find that the accuracy of fitted projection centre coordinates in EBSD and TKD can be affected by changes in the order of 10 - 3 - 10 - 2 if excess-deficiency features are not considered in the theoretical model underlying a best-fit pattern matching approach. Correspondingly, the absolute accuracy of simulation-based EBSD strain determination can suffer from biases of a similar order of magnitude if excess-deficiency effects are neglected in the simulation model.

Fine-tuning of mechanical properties in a Zn-Ag-Mg alloy via cold plastic deformation process and post-deformation annealing.

In recent years, Zn-based materials have been extensively investigated as potential candidates for biodegradable implant applications. The introduction of alloying elements providing solid-solution strengthening and second phase strengthening seems crucial to provide a suitable platform for the thermo-mechanical strengthening of Zn alloys. In this study, a systematic investigation of the microstructure, crystallographic texture, phase composition, and mechanical properties of a Zn-3Ag-0.5Mg (wt%) alloy processed through combined hot extrusion (HE) and cold rolling (CR), followed by short-time heat treatment (CR + HT) at 200 °C was conducted. Besides, the influence of different annealing temperatures on the microstructure and mechanical properties was studied. An adequate combination of processing conditions during CR and HT successfully addressed brittleness obtained in the high-strength HE Zn-3Ag-0.5Mg alloy. By controlling the microstructure, the most promising results were obtained in the sample subjected to 50% CR reduction and 5-min annealing, which were: ultimate tensile strength of 432 MPa, yield strength of 385 MPa, total elongation to failure of 34%, and Vickers microhardness of 125 HV0.3. The obtained properties clearly exceed the mechanical benchmarks for biodegradable implant materials. Based on the conducted investigation, brittle multi-phase Zn alloys' mechanical performance can be substantially enhanced to provide sufficient plasticity by grain refinement through cold deformation process, followed by short-time annealing to restore proper strength.

Numerical Study on the Dependency of Microstructure Morphologies of Pulsed Laser Deposited TiN Thin Films and the Strain Heterogeneities during Mechanical Testing.

Numerical study of the influence of pulsed laser deposited TiN thin films' microstructure morphologies on strain heterogeneities during loading was the goal of this research. The investigation was based on the digital material representation (DMR) concept applied to replicate an investigated thin film's microstructure morphology. The physically based pulsed laser deposited model was implemented to recreate characteristic features of a thin film microstructure. The kinetic Monte Carlo (kMC) approach was the basis of the model in the first part of the work. The developed kMC algorithm was used to generate thin film's three-dimensional representation with its columnar morphology. Such a digital model was then validated with the experimental data from metallographic analysis of laboratory deposited TiN(100)/Si. In the second part of the research, the kMC generated DMR model of thin film was incorporated into the finite element (FE) simulation. The 3D film's morphology was discretized with conforming finite element mesh, and then incorporated as a microscale model into the macroscale finite element simulation of nanoindentation test. Such a multiscale model was finally used to evaluate the development of local deformation heterogeneities associated with the underlying microstructure morphology. In this part, the capabilities of the proposed approach were clearly highlighted.

Improvement in Hardness and Wear Behaviour of Iron-Based Mn-Cu-Sn Matrix for Sintered Diamond Tools by Dispersion Strengthening.

The work presents the possibility of fabricating materials for use as a matrix in sintered metallic-diamond tools with increased mechanical properties and abrasion wear resistance. In this study, the effect of micro-sized SiC, Al2O3, and ZrO2 additives on the wear behaviour of dispersion-strengthened metal-matrix composites was investigated. The development of metal-matrix composites (based on Fe-Mn-Cu-Sn-C) reinforced with micro-sized particles is a new approach to the substitution of critical raw materials commonly used for the matrix in sintered diamond-impregnated tools used for the machining of abrasive stone and concrete. The composites were prepared using spark plasma sintering (SPS). Apparent density, microstructural features, phase composition, Young's modulus, hardness, and abrasion wear resistance were determined. An increase in the hardness and wear resistance of the dispersion-strengthened composites as compared to the base material (Fe-Mn-Cu-Sn-C) and the commercial alloy Co-20% WC provides metallic-diamond tools with high-performance properties.

Approximant-based orientation determination of quasicrystals using electron backscatter diffraction.

Orientation mapping of quasicrystalline materials is demonstrated using crystalline approximant structures in the technique of electron backscatter diffraction (EBSD). The approximant-based orientations are symmetrised according to the rotational point group of the quasicrystal, including the visualization of orientation maps using proper colour keys for quasicrystal symmetries. Alternatively, approximant-based orientation data can also be treated using pseudosymmetry post-processing options in the EBSD system software, which enables basic grain size estimations. Approximant-based orientation analyses are demonstrated for icosahedral and decagonal quasicrystals.

Refined Calibration Model for Improving the Orientation Precision of Electron Backscatter Diffraction Maps.

For the precise determination of orientations in polycrystalline materials, electron backscatter diffraction (EBSD) requires a consistent calibration of the diffraction geometry in the scanning electron microscope (SEM). In the present paper, the variation of the projection center for the Kikuchi diffraction patterns which are measured by EBSD is calibrated using a projective transformation model for the SEM beam scan positions on the sample. Based on a full pattern matching approach between simulated and experimental Kikuchi patterns, individual projection center estimates are determined on a subgrid of the EBSD map, from which least-square fits to affine and projective transformations can be obtained. Reference measurements on single-crystalline silicon are used to quantify the orientation errors which result from different calibration models for the variation of the projection center.

Machine Learning for detection of viral sequences in human metagenomic datasets.

BACKGROUND: Detection of highly divergent or yet unknown viruses from metagenomics sequencing datasets is a major bioinformatics challenge. When human samples are sequenced, a large proportion of assembled contigs are classified as "unknown", as conventional methods find no similarity to known sequences. We wished to explore whether machine learning algorithms using Relative Synonymous Codon Usage frequency (RSCU) could improve the detection of viral sequences in metagenomic sequencing data. RESULTS: We trained Random Forest and Artificial Neural Network using metagenomic sequences taxonomically classified into virus and non-virus classes. The algorithms achieved accuracies well beyond chance level, with area under ROC curve 0.79. Two codons (TCG and CGC) were found to have a particularly strong discriminative capacity. CONCLUSION: RSCU-based machine learning techniques applied to metagenomic sequencing data can help identify a large number of putative viral sequences and provide an addition to conventional methods for taxonomic classification.

Massively Parallel Implementation of Sequence Alignment with Basic Local Alignment Search Tool Using Parallel Computing in Java Library.

Basic Local Alignment Search Tool (BLAST) is an essential algorithm that researchers use for sequence alignment analysis. The National Center for Biotechnology Information (NCBI)-BLAST application is the most popular implementation of the BLAST algorithm. It can run on a single multithreading node. However, the volume of nucleotide and protein data is fast growing, making single node insufficient. It is more and more important to develop high-performance computing solutions, which could help researchers to analyze genetic data in a fast and scalable way. This article presents execution of the BLAST algorithm on high performance computing (HPC) clusters and supercomputers in a massively parallel manner using thousands of processors. The Parallel Computing in Java (PCJ) library has been used to implement the optimal splitting up of the input queries, the work distribution, and search management. It is used with the nonmodified NCBI-BLAST package, which is an additional advantage for the users. The result application-PCJ-BLAST-is responsible for reading sequence for comparison, splitting it up and starting multiple NCBI-BLAST executables. Since I/O performance could limit sequence analysis performance, the article contains an investigation of this problem. The obtained results show that using Java and PCJ library it is possible to perform sequence analysis using hundreds of nodes in parallel. We have achieved excellent performance and efficiency and we have significantly reduced the time required for sequence analysis. Our work also proved that PCJ library could be used as an effective tool for fast development of the scalable applications.

Electrophoretic deposition of organic/inorganic composite coatings containing ZnO nanoparticles exhibiting antibacterial properties.

To address one of the serious problems associated with permanent implants, namely bacterial infections, novel organic/inorganic coatings containing zinc oxide nanoparticles (nZnO) are proposed. Coatings were obtained by electrophoretic deposition (EPD) on stainless steel 316L. Different deposition conditions namely: deposition times in the range 60-300s and applied voltage in the range 5-30V as well as developing a layered coating approach were studied. Antibacterial tests against gram-positive Staphylococcus aureus and gram-negative Salmonella enteric bacteria confirmed the activity of nZnO to prevent bacterial growth. Coatings composition and morphology were analyzed by thermogravimetric analysis, Fourier transform infrared spectroscopy, scanning electron microscopy and energy dispersive X-ray spectroscopy. Moreover, the corrosion resistance was analyzed by evaluation of the polarization curves in DMEM at 37°C, and it was found that coatings containing nZnO increased the corrosion resistance compared to the bare substrate. Considering all results, the newly developed coatings represent a suitable alternative for the surface modification of metallic implants.

Heteroplasmic substitutions in the entire mitochondrial genomes of human colon cells detected by ultra-deep 454 sequencing.

Mitochondrial DNA (mtDNA) heteroplasmy has been widely described from clinical, evolutionary and analytical points of view. Historically, the majority of studies have been based on Sanger sequencing. However, next-generation sequencing technologies are now being used for heteroplasmy analysis. Ultra-deep sequencing approaches provide increased sensitivity for detecting minority variants. However, a phylogenetic a posteriori analysis revealed that most of the next-generation sequencing data published to date suffers from shortcomings. Because implementation of new technologies in clinical, population, or forensic studies requires proper verification, in this paper we present a direct comparison of ultra-deep 454 and Sanger sequencing for the detection of heteroplasmy in complete mitochondrial genomes of normal colon cells. The spectrum of heteroplasmic mutations is discussed against the background of mitochondrial DNA variability in human populations.

KARDIONET: telecardiology based on GRID technology.

The telecardiological system Kardionet is being developed to support interventional cardiology. The main aim of the system is to collect specific and systemized patient data from the distant medical centers and to organize it in the best possible way to diagnose quickly and choose the medical treatment. It is the distributed GRID type system operating in shortest achievable time. Computational GRID solutions together with distributed archive data GRID support creation, implementation and operations of software using considerable computational power. Kardionet system devoted to cardiology purposes includes specially developed data bases for the multimodal data and metadata, including information on a patient and his/her medical examination results. As Kardionet uses modern technology and methods we expect it could have a considerable impact on telemedicine development in Poland. The presented telecardiological system can provide a number of important gains for the national health care system if it is implemented nationwide.

Molecular dynamics simulations of the first steps of the reaction catalyzed by HIV-1 protease.

The mechanism of the first steps of the reaction catalyzed by HIV-1 protease was studied through molecular dynamics simulations. The potential energy surface in the active site was generated using the approximate valence bond method. The approximate valence bond (AVB) method was parameterized based on density functional calculations. The surrounding protein and explicit water environment was modeled with conventional, classical force field. The calculations were performed based on HIV-1 protease complexed with the MVT-101 inhibitor that was modified to a model substrate. The protonation state of the catalytic aspartates was determined theoretically. Possible reaction mechanisms involving the lytic water molecule are accounted for in this study. The modeled steps include the dissociation of the lytic water molecule and proton transfer onto Asp-125, the nucleophilic attack followed by a proton transfer onto peptide nitrogen. The simulations show that in the active site most preferable energetically are structures consisting of ionized or polarized molecular fragments that are not accounted for in conventional molecular dynamics. The mobility of the lytic water molecule, the dynamics of the hydrogen bond network, and the conformation of the aspartates in the active center were analyzed.