Orientation Variants Research Articles

A Chimeric ORF Fusion Phenotypic Reporter for Cryptococcus neoformans.

The plethora of genome sequences produced in the postgenomic age has not resolved many of our most pressing biological questions. Correlating gene expression with an interrogatable and easily observable characteristic such as the surrogate phenotype conferred by a reporter gene is a valuable approach to gaining insight into gene function. Many reporters including lacZ, amdS, and the fluorescent proteins mRuby3 and mNeonGreen have been used across all manners of organisms. Described here is an investigation into the creation of a robust, synthetic, fusion reporter system for Cryptococcus neoformans that combines some of the most useful fluorophores available in this system with the versatility of the counter-selectable nature of amdS. The reporters generated include multiple composition and orientation variants, all of which were investigated for differences in expression. Evaluation of known promoters from the TEF1 and GAL7 genes was undertaken, elucidating novel expression tendencies of these biologically relevant C. neoformans regulators of transcription. Smaller than lacZ but providing multiple useful surrogate phenotypes for interrogation, the fusion ORF serves as a superior whole-cell assay compared to traditional systems. Ultimately, the work described here bolsters the array of relevant genetic tools that may be employed in furthering manipulation and understanding of the WHO fungal priority group pathogen C. neoformans.

Ferroelasticity in Two-Dimensional Hybrid Ruddlesden-Popper Perovskites Mediated by Cross-Plane Intermolecular Coupling and Metastable Funnel-like Phases.

Ferroelasticity is a phenomenon in which a material exhibits two or more equally stable orientation variants and can be switched from one form to another under an applied stress. Recent works have demonstrated that two-dimensional layered organic-inorganic hybrid Ruddlesden-Popper perovskites can serve as ideal platforms for realizing ferroelasticity, however, the ferroelastic (FE) behavior of structures with a single octahedra layer such as (BA)2PbI4 [BA = CH3(CH2)3NH3+] has remained elusive. Herein, by using a combined first-principles and metadynamics approach, the FE behavior of (BA)2PbI4 under mechanical and thermal stresses is uncovered. FE switching is mediated by cross-plane intermolecular coupling, which could occur through multiple rotational modes, rendering the formation of FE domains and several metastable paraelastic (PE) phases. Such metastable phases are akin to wrinkled structures in other layered materials and can act as a "funnel" of hole carriers. Thermal excitation tends to flatten the kinetic barriers of the transition pathways between orientation variants, suggesting an enhanced concentration of metastable PE states at high temperatures, while halogen mixing with Br raises these barriers and conversely lowers the concentration of PE states. These findings reveal the rich structural diversity of (BA)2PbI4 domains, which can play a vital role in enhancing the optoelectronic properties of the perovskite and raise exciting prospects for mechanical switching, shape memory, and information processing.

Strong Substrate Influence on Atomic Structure and Properties of Epitaxial VO2 Thin Films

AbstractThe metal–insulator transition (MIT) observed in vanadium dioxide has been a topic of great research interest for past decades, with the underlying physics yet not fully understood due to the complex electron interactions and structures involved. The ability to understand and tune the MIT behavior is of vital importance from the perspective of both underlying fundamental science as well as potential applications. In this work, scanning transmission electron microscopy (STEM) is used to investigate cross‐section lamella of the VO2 films deposited using pulsed laser deposition on three substrates: c‐cut sapphire, TiO2(101) and TiO2(001). Advanced STEM imaging is performed in which also the oxygen atom columns are resolved. The overall film quality and structures on atomic and nanoscale are linked to the electrical transition characteristics. Relatively poor MIT characteristics are observed on c‐sapphire due to the presence of very small domains with six orientation variants, and on TiO2 (001) due to the presence of cracks induced by stress relaxation. However, the MIT on TiO2 (101) behaves favorably, despite similar stress relaxation which, however, only leads to domain boundaries but no cracks.

Unlocking the mysterious polytypic features within vaterite CaCO3

Calcium carbonate (CaCO3), the most abundant biogenic mineral on earth, plays a crucial role in various fields such as hydrosphere, biosphere, and climate regulation. Of the four polymorphs, calcite, aragonite, vaterite, and amorphous CaCO3, vaterite is the most enigmatic one due to an ongoing debate regarding its structure that has persisted for nearly a century. In this work, based on systematic transmission electron microscopy characterizations, crystallographic analysis and machine learning aided molecular dynamics simulations with ab initio accuracy, we reveal that vaterite can be regarded as a polytypic structure. The basic phase has a monoclinic lattice possessing pseudohexagonal symmetry. Direct imaging and atomic-scale simulations provide evidence that a single grain of vaterite can contain three orientation variants. Additionally, we find that vaterite undergoes a second-order phase transition with a critical point of ~190 K. These atomic scale insights provide a comprehensive understanding of the structure of vaterite and offer advanced perspectives on the biomineralization process of calcium carbonate.

Effect of cyclic loading on microstructure and crack propagation in additively manufactured biomaterial Co–Cr–Mo alloy

Cobalt–Chromium–Molybdenum (Co–Cr–Mo) alloys are commonly used for artificial hip and knee joint metallic implants. These components are subjected to repetitive loads during service. Therefore, materials used for such applications must exhibit a high fatigue crack resistance. In this research, Co–28Cr–6Mo (wt.-%) powder was utilized as a feedstock in a laser powder bed fusion process to produce test coupons. The coupons were then subjected to load-controlled cyclic material tests in the low cycle fatigue regime to study mechanical response and microstructural changes of the material. With the progressing number of cycles, a continuous increase in macroscopic plastic strain was observed. The electron backscattered diffraction analysis revealed that cyclic loading caused deformation-induced face-centered cubic (FCC) → hexagonal close-packed (HCP) phase transformation. In addition, the phase transition generated an accumulation of plastic strain at the FCC/HCP interface giving rise to crack nucleation. The crack propagation path along HCP orientation variants with high mechanical work and strain hardening mechanism is discussed.

Multivariant microstructure evolution in Ti-alloys: insights from a quantitative phase-field study

Abstract In the present work, we employ a CALPHAD-integrated physics-based quantitative multi-phase field model to study the microstructure evolution in a multi-phase Ti-alloy. In this model we use the free energies obtained from TTTI3 thermodynamic database for Ti-based alloys using a CALPHAD approach. For numerical implementation of the model, we solve the governing equations in their weak form using the open-source MOOSE finite element framework. Our model is successfully able to capture all the possible orientational variants in Ti- alloy system. Moreover, we elucidate the complex interaction between the variants using two- and multi-particle simulations. We show that the elastic energies associated with the variants play significant role in their growth behavior. We also explore the effect of anisotropy in interfacial energy on the variant evolution.

Habit plane determination from reconstructed parent phase orientation maps

This study details the development and validation of a new algorithm that determines the dominant habit plane of a transformed child phase from orientation maps of a single planar cross-section. The method describes the habit plane in terms of its five-parameter grain boundary character and couples it to the specific orientation relationship of the identified orientation variant. The symmetry operations associated with the specific orientation relationship of the variants are applied to transform habit plane traces as determined in the specimen-fixed reference frame into the parent or child reference frame, allowing for the fitting of the habit plane. Our algorithm stands out by its robustness, computational efficiency, automation and ability to operate on fully transformed microstructures. Four automated methods for habit plane trace determination are proposed and compared. Detailed sensitivity analysis reveals that the proposed algorithm is exceptionally robust against poor accuracy in the measured traces and distortions in the orientation map, but more sensitive to inaccuracies propagated from parent grain reconstruction. Validation on a synthetic microstructure with a known habit plane returned consistent results when applied to high and low carbon steels with different prior austenite grain sizes and orientation map resolutions. The habit planes were not significantly affected by the austenite grain sizes. The habit plane of the steel with 0.35 wt% C was close to (111)γ whereas the habit plane of steel with 0.71 wt% C was closer to (575)γ, in close agreement with previous work using two-surface stereological analysis and transmission electron microscopy-based trace analysis.

Orientation relationships, orientational variants and the embedding approach.

For phase transformations within polycrystalline materials, the connection between the crystal orientations of parent grains and those of child grains is usually expressed in terms of (theoretical or measured) orientation relationships. This paper introduces a new approach to various problems associated with orientation relationships: (i) estimation, (ii) whether or not a single orientation relationship fits the data adequately, (iii) whether or not a set of children comes from a common parent, and (iv) reconstruction of a parent or of grain boundaries. The approach is an extension to the crystallographic context of the well established embedding approach to directional statistics. It is inherently statistical, producing precise probabilistic statements. Explicit coordinate systems are not used and arbitrary thresholds are avoided.

Thermal switch based on ferroelasticity VA-N binary compounds

Ferroelastic materials possess two or more equally stable orientation variants and can be effectively modulated via external fields, including stress and electronic field. In this paper, taking the VA-N ferroelastic materials as examples, we propose a thermal switch device based on their ferroelastic characteristics. The results show that the VA-N binary compound exhibits excellent ferroelasticity, high reversible elastic strain (5.5%–54.1%), and suitable switching energy barriers (0.012–0.386 eV/atom) in both δ and α phases. Utilizing the advanced on-the-fly machine learning potential, we obtain physically well-defined quadratic dispersion curves in the long-wavelength limit and further evaluate their lattice thermal conductivity of δ and α phase VA-N binary compounds. Due to the difference in phonon group velocities, the lattice thermal conductivity of VA-N binary compounds along the armchair direction is obviously smaller than that along the zigzag direction. Such remarkable anisotropy and easily switchable features based on ferroelasticity endow reversible and real-time regulation of thermal conductivity of VA-N binary compounds. The ferroelastic-based thermal switch hosts high switch ratios range from 2.08 to 5.99 and does not require additional energy to maintain the modulation state. The results presented herein provide a pavement for designing next-generation thermal switches and propose a reliable solution for eliminating the nonphysical pseudo-phenomenon of phonon dispersion curve violation of quadratic dispersion in the long-wavelength limit.

Oriented secondary magnetite micro-inclusions in plagioclase from oceanic gabbro

Abstract Plagioclase-hosted submicrometer to micrometer-sized oriented needle- and lath-shaped magnetite micro-inclusions with their elongation direction aligned parallel to the plagioclase [001] (PL[001]) direction were investigated using correlated optical, scanning electron, and scanning transmission electron microscopy. The PL[001] magnetite micro-inclusions formed from older generations of differently oriented magnetite micro-inclusions by recrystallization during hydrothermal alteration. Six orientation variants of PL[001] magnetite micro-inclusions occur, and they share the same shape orientation but differ in their crystallographic orientation relationships to the plagioclase host. The magnetite-plagioclase interfaces are facetted. High-resolution scanning transmission electron microscopy revealed that interface facets are aligned parallel to low-index lattice planes corresponding to oxygen layers of either magnetite or plagioclase. In addition, the linkage between prominent crystal structure elements of magnetite and plagioclase across the interfaces and accommodation mechanisms minimizing misfit between the two crystal structures were discerned. Combined evidence suggests that the shape and shape orientation, as well as the crystallographic orientation relationships between the magnetite micro-inclusions and the plagioclase host, are crystallographically controlled. The close crystal-structural link between magnetite precipitates and plagioclase host ensures a low-energy configuration driving recrystallization of older generations of differently orientated magnetite micro-inclusions into those that are aligned parallel to PL[001] and facilitates the underlying reaction kinetics. Due to their single to pseudo-single domain characteristics, the plagioclase-hosted magnetite micro-inclusions are particularly robust carriers of natural remanent magnetization. Recrystallization of differently oriented preexisting magnetite micro-inclusions into magnetite micro-inclusions with uniform shape orientation parallel to PL[001] has interesting consequences for the magnetic anisotropy of magnetite-bearing plagioclase grains.

Using ferroelastic variant switching to tune ferromagnetic properties of 1T′ CrX2 (X=S, Se) for local strain modulated spin valves

In this paper, density functional theory calculations are adopted to systematically study the magnetic-structure anisotropy association and strain induced structure variants switching behavior of ferroelastic $1{\mathrm{T}}^{\ensuremath{'}}\text{\ensuremath{-}}{\mathrm{CrS}}_{2}$ and ${\mathrm{CrSe}}_{2}$. We find that the easy magnetization axis is always perpendicular to Cr-Cr zigzag chain in the ferromagnetic (FM) $1{\mathrm{T}}^{\ensuremath{'}}$ phase. In addition, the mechanical strain can alter the relative thermodynamic stability among the three different crystal orientation variants of both the FM and nonmagnetic (NM) $1{\mathrm{T}}^{\ensuremath{'}}$ phase. These two facts lay the ground for strain-controlled magnetic moment rotation of the FM $1{\mathrm{T}}^{\ensuremath{'}}$ phase. A prototypical design and operating mechanism of a strain-controlled $1{\mathrm{T}}^{\ensuremath{'}}$-FM/NM/FM heterostructure spin valve are presented. Our finding offers a potential solution to reduce energy consumption in miniaturized spintronics devices.

Anisotropic correlations in higher manganese silicides

Anisotropic correlations are vital for understanding the thermoelectric transport properties of higher manganese silicides (HMSs). In this work, we establish the implications of anisotropy on thermoelectric performance by examining the orientational variants in melt-grown single crystal and directional configurations of spark plasma sintered polycrystalline specimens of HMS. Single crystal specimen aligned perpendicular to the c-axis (i.e., along the cleavage ab-plane) exhibited high electrical and thermal conductivity, while the maximum Seebeck coefficient was measured along the c-axis direction. Similarly, polycrystalline specimens exhibited a weakened anisotropy with an enhanced weighted mobility and reduced thermal conductivity than their monocrystal counterpart resulting in a relatively higher thermoelectric figure-of-merit (zT). The characteristic MnSi striations were found to be predominantly grown perpendicular to the c-axis in melt-grown single crystals while peritectic decomposition during sintering is commonly observed in sintered polycrystals thereby emanating an inherently disordered and modulated lattice structure in the synthesized HMS crystals. It was observed that the zT for single and polycrystalline HMSs could be erroneously estimated if charge and phonon transport properties are measured in different directions. This study offers newer insights into the structure-property relationships of HMSs and demonstrates the need for more careful considerations in addressing the anisotropic behavior and microstructural evolutions that prevails in HMS crystals.

γ″ variant-sensitive deformation behaviour of Inconel 718 superalloy

• This study reveals, for the first time, the micro-mechanism of deformation of γ″ strengthened superalloys using neutron diffraction. • Inconel 718 samples with different γ″ variant distributions were prepared by different stress ageing heat treatments. • The γ″ variant-sensitive deformation behavior was studied by interpreting the stress-lattice strain curves. • Compressive-aged sample shows larger yield strength compared to the tensile-aged sample • The difference in strengthening arises from the interactions between dislocations and different γ″ variants. Strengthening in Inconel 718 superalloy is derived from dislocation interaction with γ″ precipitates, which exist in disk-shaped three possible orientation variants with their {100} habit plane normal to each other. The interactions between dislocations and γ″ precipitates vary according to the γ″ orientation variants, which makes the deformation behaviour complicated and difficult to reveal experimentally. In this work, γ″ variant distributions of Inconel 718 samples were tailored by ageing heat treatment under either tensile or compressive stress. The γ″ variant-sensitive deformation behaviours were then studied by in situ tensile tests via neutron diffraction at room temperature. It is demonstrated that yielding first takes place in grains oriented with <110> parallel to the loading direction. An identical lattice strain response to applied stress of both the γ matrix and the γ″ precipitates was observed during yielding, suggesting that dislocations shearing through the γ″ precipitates is predominant at this stage. Variations in yield strength for samples with different γ″ variant distributions were observed, which can be attributed to different strengthening that arises from interactions between dislocation and different γ″ variants.

Sex and Sexuality in Autism Spectrum Disorders: A Scoping Review on a Neglected but Fundamental Issue.

ASD consists of a set of permanent neurodevelopmental conditions, which are studded with social and communication differences, limited interests, and repetitive behaviors. Individuals with ASD have difficulty reading eye gestures and expressions, and may also have stereotyped or repetitive language, excessive adherence to routines, fixed interests, and rigid thinking. However, sexuality in adolescents and young adults with ASD is still a poorly studied and neglected issue. This review aims to evaluate sexual function and behavior in individuals with ASD to foster a greater understanding of this important, although often overlooked, issue. This review was conducted by searching peer-reviewed articles published between 01 June 2000 and 31 May 2022 using the following databases: PubMed, Embase, Cochrane Database, and Web of Science. A comprehensive search was conducted using the terms: "Autism" OR "ASD" AND "Sexuality" OR "Romantic relation" OR "sexual behavior" AND/OR "sexual awareness". After an accurate revision of 214 full manuscripts, 11 articles satisfied the inclusion/exclusion criteria. This review found that, although individuals with ASD may have sexual functioning, their sexuality is characterized by higher prevalence rates of gender dysphoria and inappropriate sexual behavior. Furthermore, sexual awareness is reduced in this patient population, and the prevalence of other variants of sexual orientation (i.e., homosexuality, asexuality, bisexuality, etc.) is higher in adolescents with ASD than in non-autistic peers. Sexual health and education should be included in the care path of patients with ASD in order to improve their quality of life and avoid/reduce inappropriate and risky behaviors.

Eutectoid decomposition of βNb5Si3 → αNb5Si3 + Nbss in Nbss/Nb5Si3 in-situ composites revealed by electron microscopy

Eutectoid decomposition of βNb5Si3 → αNb5Si3 + Nbss in Nbss/Nb5Si3 in-situ composites has been systematically investigated by electron microscopy. βNb5Si3 would transform into different αNb5Si3 orientation variants around 1075 °C. There is no inherent orientation relationship (OR) between βNb5Si3 and αNb5Si3, which might be regulated by the diffusive nature of the transformation. Numerous Nbss precipitates would form within αNb5Si3 with crystallographic OR of <001>Nb// < 001>α. This transformation is promoted by formation of dislocations and the diffusion of Nb at elevated temperatures, which will propagate from Nbss/βNb5Si3 interfaces to the interior of βNb5Si3 grains.

Entrepreneurial responsible orientation in small and medium businesses: the case of Pakistan

PurposeThe identification of a successful mix of strategic orientations is a big challenge for corporate sustainability and management research. To this end, the purpose of this paper is to explore and analyze the interrelationships among multiple variants of strategic orientations (i.e. entrepreneurial orientation (EO), market orientation (MO), technology orientation (TO) and sustainability orientation (SO)) that lead to the superior performance of sustainability-oriented small and medium enterprises (SMEs) in a developing country context.Design/methodology/approachThis study utilized the case-study method to explore a detailed and comprehensive understanding of the interplay among multiple strategic orientations. The data were collected from the top management of SMEs working in Pakistan through semi-structured interviews, complemented with the data obtained through a structured survey and the firms’ documentary evidence. Interviews were content analyzed to reveal more rigorous and comprehensive results.FindingsThe findings of this study suggest that the strategic framework of successful firms utilizes the aspects from multiple orientations (EO, MO and SO) to create an appropriate alignment that ensures superior performance in a highly dynamic environment.Originality/valueThe key finding of this study is the identification of a configurational framework, Entrepreneurial Responsible Orientation, if successfully implemented, it has the potential to drive sustainable performance of the small firms particularly, and sustainable development of the country, generally.

Ferroelectric HfO2 and the importance of strain

Ferroelectric oxides based on ${\mathrm{HfO}}_{2}$ show tremendous promise for the next generation of memory and logic devices. The ferroelectric polymorph is one of several that can be derived from the high symmetry cubic fluorite structure of ${\mathrm{HfO}}_{2}$. A single grain of ${\mathrm{HfO}}_{2}$ may consist of a coherent mixture of multiple orientational and translational variants of different polymorphs. Here, we use symmetry-adapted strain-order parameters to elucidate the relationship between the different ${\mathrm{HfO}}_{2}$ polymorphs and their symmetrically equivalent variants. We use first-principles electronic structure methods to identify minimum energy pathways and map them in subspaces of the symmetry-adapted strain order parameters. We next investigate the atomic structure of domain boundaries that separate coexisting variants of ferroelectric ${\mathrm{HfO}}_{2}$. We rely on Gibbsian excess quantities and a precise specification of mechanical boundary conditions to describe the thermodynamic properties of domain boundaries. Our first-principles calculations show that the O and Hf shuffle arrangement within a domain boundary is closely related to the intermediate shuffle patterns of the homogeneous pathways between ferroelectric variants. Furthermore, the preferred structure within a boundary is very sensitive to local strain constraints imposed by the adjacent ferroelectric variants, leading to highly anisotropic domain boundary energies.

Identification of a coherent twin relationship from high-resolution reciprocal-space maps.

Twinning is a common crystallographic phenomenon which is related to the formation and coexistence of several orientation variants of the same crystal structure. It may occur during symmetry-lowering phase transitions or during the crystal growth itself. Once formed, twin domains play an important role in defining physical properties: for example, they underpin the giant piezoelectric effect in ferroelectrics, superelasticity in ferroelastics and the shape-memory effect in martensitic alloys. Regrettably, there is still a lack of experimental methods for the characterization of twin domain patterns. Here, a theoretical framework and algorithm are presented for the recognition of ferroelastic domains, as well as the identification of the coherent twin relationship using high-resolution reciprocal-space mapping of X-ray diffraction intensity around split Bragg peaks. Specifically, the geometrical theory of twinned ferroelastic crystals [Fousek & Janovec (1969). J. Appl. Phys. 40, 135-142] is adapted for the analysis of the X-ray diffraction patterns. The necessary equations are derived and an algorithm is outlined for the calculation of the separation between the Bragg peaks, diffracted from possible coherent twin domains, connected to one another via a mismatch-free interface. It is demonstrated that such separation is always perpendicular to the planar interface between mechanically matched domains. For illustration purposes, the analysis is presented of the separation between the peaks diffracted from tetragonal and rhombohedral domains in the high-resolution reciprocal-space maps of BaTiO3 and PbZr1-xTixO3 crystals. The demonstrated method can be used to analyse the response of multi-domain patterns to external perturbations such as electric field, change of temperature or pressure.

The variant graph approach to improved parent grain reconstruction

The variant graph is a new, hybrid algorithm that combines the strengths of established global grain graph and local neighbor level voting approaches, while alleviating their shortcomings, to reconstruct parent grains from orientation maps of partially or fully phase-transformed microstructures. The variant graph algorithm is versatile and is capable of reconstructing transformation microstructures from any parent-child combination by clustering together child grains based on a common parent orientation variant. The main advantage of the variant graph over the grain graph is its inherent ability to more accurately detect prior austenite grain boundaries.A critical examination of Markovian clustering and neighbor level voting as methods to reconstruct prior austenite orientations is first conducted. Following this, the performance of the variant graph algorithm is showcased by reconstructing the prior austenite grains and boundaries from an example low-carbon lath martensite steel microstructure. Programmatic extensions to the variant graph algorithm for specific morphological conditions and the merging of variants with small mutual disorientation angles are also proposed. The accuracy of the reconstruction and the computational performance of the variant graph algorithm is either on-par or outperforms alternate methods for parent grain reconstruction.The variant graph algorithm is implemented as a new addition to the functionalities for phase transformation analysis in MTEX 5.8 and is freely available for download by the community.

Ideafix: a decision tree-based method for the refinement of variants in FFPE DNA sequencing data.

Increasingly, treatment decisions for cancer patients are being made from next-generation sequencing results generated from formalin-fixed and paraffin-embedded (FFPE) biopsies. However, this material is prone to sequence artefacts that cannot be easily identified. In order to address this issue, we designed a machine learning-based algorithm to identify these artefacts using data from >1 600 000 variants from 27 paired FFPE and fresh-frozen breast cancer samples. Using these data, we assembled a series of variant features and evaluated the classification performance of five machine learning algorithms. Using leave-one-sample-out cross-validation, we found that XGBoost (extreme gradient boosting) and random forest obtained AUC (area under the receiver operating characteristic curve) values >0.86. Performance was further tested using two independent datasets that resulted in AUC values of 0.96, whereas a comparison with previously published tools resulted in a maximum AUC value of 0.92. The most discriminating features were read pair orientation bias, genomic context and variant allele frequency. In summary, our results show a promising future for the use of these samples in molecular testing. We built the algorithm into an R package called Ideafix (DEAmination FIXing) that is freely available at https://github.com/mmaitenat/ideafix.