Browse
Submit Data
Databases
API
Help

Dataset Information

7 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of variant-pairing tendencies in lenticular martensite microstructures based on rank-1 connection.

ABSTRACT: Herein, variant-pairing tendencies of lenticular martensite in an Fe-30Ni-0.3C (wt%) alloy are analyzed based on rank-1 connection at martensite/martensite junction planes (JPs) to facilitate the understanding of martensite microstructure. The degree of incompatibility (θ) at the JPs successfully explained their observed frequency; in the actual microstructure, variant pairs with a small θ form preferentially. The experimentally obtained JPs were consistent with theoretical ones. To the best of our knowledge, this is the first study to confirm the validity of variant-pair crystallography in steel based on rank-1 connection, both theoretically and experimentally. Diamond, composite-spear, and composite-kink clusters are considered. The cumulative θ at the JPs can suppress diamond cluster formation because it exceeds the θ of a single variant pair, and the diamond cluster is not observed experimentally. However, θ at the JPs cancel out in composite-spear (CS) and composite-kink (CK) clusters, but CK clusters are rarely observed experimentally, while a few CS clusters are observed. This demonstrates the analytical limitations of 2D approaches used to evaluate the frequency of variant pairs and clusters. These two variant clusters have a narrow window of 2D observation because the orientation relationships between JPs and intersection lines between two habit planes affect the areas of JPs.

SUBMITTER: Shinohara Y

PROVIDER: S-EPMC8298466 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Variant selection in surface martensite.

Project description:A significant variant selection is reported in isothermal martensite formed on the surface of an Fe-30%?Ni sample. The selection phenomenon is modelled using different descriptions of the martensitic phase transformation. In particular, matrices based on the phenomenological theory of martensite crystallography, the Jaswon and Wheeler distortion, and the continuous face centred cubic-body centred cubic distortion are compared. All descriptions allow good predictions of the variant selection. However, the Jaswon and Wheeler distortion and the continuous distortion better account for other features of the surface martensite, such as the {225}? habit plane and the accommodation mechanism by twin-related variant pairing.

| S-EPMC5713143 | biostudies-literature

Optically-Induced Cell Fusion on Cell Pairing Microstructures.

Project description:Cell fusion is a critical operation for numerous biomedical applications including cell reprogramming, hybridoma formation, cancer immunotherapy, and tissue regeneration. However, unstable cell contact and random cell pairings have limited efficiency and yields when utilizing traditional methods. Furthermore, it is challenging to selectively perform cell fusion within a group of cells. This study reports a new approach called optically-induced cell fusion (OICF), which integrates cell-pairing microstructures with an optically-induced, localized electrical field. By projecting light patterns onto a photoconductive film (hydrogen-rich, amorphous silicon) coated on an indium-tin-oxide (ITO) glass while an alternating current electrical field was applied between two such ITO glass slides, "virtual" electrodes could be generated that could selectively fuse pairing cells. At 10 kHz, a 57% cell paring rate and an 87% fusion efficiency were successfully achieved at a driving voltage of 20 V(pp), suggesting that this new technology could be promising for selective cell fusion within a group of cells.

| S-EPMC4766562 | biostudies-other

Transcriptomic pan-cancer analysis using rank-based Bayesian inference.

Project description:The analysis of whole genomes of pan-cancer data sets provides a challenge for researchers, and we contribute to the literature concerning the identification of robust subgroups with clear biological interpretation. Specifically, we tackle this unsupervised problem via a novel rank-based Bayesian clustering method. The advantages of our method are the integration and quantification of all uncertainties related to both the input data and the model, the probabilistic interpretation of final results to allow straightforward assessment of the stability of clusters leading to reliable conclusions, and the transparent biological interpretation of the identified clusters since each cluster is characterized by its top-ranked genomic features. We applied our method to RNA-seq data from cancer samples from 12 tumor types from the Cancer Genome Atlas. We identified a robust clustering that mostly reflects tissue of origin but also includes pan-cancer clusters. Importantly, we identified three pan-squamous clusters composed of a mix of lung squamous cell carcinoma, head and neck squamous carcinoma, and bladder cancer, with different biological functions over-represented in the top genes that characterize the three clusters. We also found two novel subtypes of kidney cancer that show different prognosis, and we reproduced known subtypes of breast cancer. Taken together, our method allows the identification of robust and biologically meaningful clusters of pan-cancer samples.

| S-EPMC10061294 | biostudies-literature

Analysis of Age-Related White Matter Microstructures Based on Diffusion Tensor Imaging.

Project description:Population aging has become a serious social problem. Accordingly, many researches are focusing on changes in brains of the elderly. In this study, we used multiple parameters to analyze age-related changes in white matter fibers. A sample cohort of 58 individuals was divided into young and middle-age groups and tract-based spatial statistics (TBSS) were used to analyze the differences in fractional anisotropy (FA), mean diffusion (MD), axial diffusion (AD), and radial diffusion (RD) between the two groups. Deterministic fiber tracking was used to investigate the correlation between fiber number and fiber length with age. The TBSS analysis revealed significant differences in FA, MD, AD, and RD in multiple white matter fibers between the two groups. In the middle-age group FA and AD were lower than in young people, whereas the MD and RD values were higher. Deterministic fiber tracking showed that the fiber length of some fibers correlated positively with age. These fibers were observed in the splenium of corpus callosum (SCC), the posterior limb of internal capsule (PLIC), the right posterior corona radiata (PCR_R), the anterior corona radiata (ACR), the left posterior thalamic radiation (include optic radiation; PTR_L), and the left superior longitudinal fasciculus (SLF_L), among others. The results showed that the SCC, PLIC, PCR_R, ACR, PTR_L, and SLF_L significantly differed between young and middle-age people. Therefore, we believe that these fibers could be used as image markers of age-related white matter changes.

| S-EPMC8273390 | biostudies-literature

A rank-based sequence aligner with applications in phylogenetic analysis.

Project description:Recent tools for aligning short DNA reads have been designed to optimize the trade-off between correctness and speed. This paper introduces a method for assigning a set of short DNA reads to a reference genome, under Local Rank Distance (LRD). The rank-based aligner proposed in this work aims to improve correctness over speed. However, some indexing strategies to speed up the aligner are also investigated. The LRD aligner is improved in terms of speed by storing [Formula: see text]-mer positions in a hash table for each read. Another improvement, that produces an approximate LRD aligner, is to consider only the positions in the reference that are likely to represent a good positional match of the read. The proposed aligner is evaluated and compared to other state of the art alignment tools in several experiments. A set of experiments are conducted to determine the precision and the recall of the proposed aligner, in the presence of contaminated reads. In another set of experiments, the proposed aligner is used to find the order, the family, or the species of a new (or unknown) organism, given only a set of short Next-Generation Sequencing DNA reads. The empirical results show that the aligner proposed in this work is highly accurate from a biological point of view. Compared to the other evaluated tools, the LRD aligner has the important advantage of being very accurate even for a very low base coverage. Thus, the LRD aligner can be considered as a good alternative to standard alignment tools, especially when the accuracy of the aligner is of high importance. Source code and UNIX binaries of the aligner are freely available for future development and use at http://lrd.herokuapp.com/aligners. The software is implemented in C++ and Java, being supported on UNIX and MS Windows.

| S-EPMC4136772 | biostudies-literature

Amorphous martensite in β-Ti alloys.

Project description:Martensitic transformations originate from a rigidity instability, which causes a crystal to change its lattice in a displacive manner. Here, we report that the martensitic transformation on cooling in Ti-Zr-Cu-Fe alloys yields an amorphous phase instead. Metastable β-Ti partially transforms into an intragranular amorphous phase due to local lattice shear and distortion. The lenticular amorphous plates, which very much resemble α'/α″ martensite in conventional Ti alloys, have a well-defined orientation relationship with the surrounding β-Ti crystal. The present solid-state amorphization process is reversible, largely cooling rate independent and constitutes a rare case of congruent inverse melting. The observed combination of elastic softening and local lattice shear, thus, is the unifying mechanism underlying both martensitic transformations and catastrophic (inverse) melting. Not only do we reveal an alternative mechanism for solid-state amorphization but also establish an explicit experimental link between martensitic transformations and catastrophic melting.

| S-EPMC5802800 | biostudies-literature

Rank-based principal stratum sensitivity analyses.

Project description:We describe rank-based approaches to assess principal stratification treatment effects in studies where the outcome of interest is only well-defined in a subgroup selected after randomization. Our methods are sensitivity analyses, in that estimands are identified by fixing a parameter and then we investigate the sensitivity of results by varying this parameter over a range of plausible values. We present three rank-based test statistics and compare their performance through simulations, and provide recommendations. We also study three different bootstrap approaches for determining levels of significance. Finally, we apply our methods to two studies: an HIV vaccine trial and a prostate cancer prevention trial.

| S-EPMC5753805 | biostudies-literature

Stress-induced detwinning and martensite transformation in an austenite Ni-Mn-Ga alloy with martensite cluster under uniaxial loading.

Project description:Stress-induced martensitic detwinning and martensitic transformation during step-wise compression in an austenite Ni-Mn-Ga matrix with a martensite cluster under uniaxial loading have been investigated by electron backscatter diffraction, focusing on the crystallographic features of microstructure evolution. The results indicate that detwinning occurs on twins with a high Schmid factor for both intra-plate and inter-plate twins in the hierarchical structure, resulting in a nonmodulated (NM) martensite composed only of favourable variants with [001]NM orientation away from the compression axis. Moreover, the stress-induced martensitic transformation occurs at higher stress levels, undergoing a three-stage transformation from austenite to a twin variant pair and finally to a single variant with increasing compressive stress, and theoretical calculation shows that the corresponding crystallographic configuration is accommodated to the compression stress. The present research not only provides a comprehensive understanding of martensitic variant detwinning and martensitic transformation under compression stress, but also offers important guidelines for the mechanical training process of martensite.

| S-EPMC6503927 | biostudies-literature

Lenticular Imaging: A New Experimental and Quantitative Analysis of Capsular Dynamics, "Choi-Apple View".

Project description:PurposeDevelopment of a means for quantitative estimation of lenticular and zonular dynamics by using real-time imaging of human autopsy eyes during implantation of different intraocular lens (IOL) models.MethodsIsolated lenticular structures from human autopsy eyes were prepared in vitro. The following IOLs were implanted: a one-piece C-loop haptic IOL, a three-piece C-loop haptic IOL, and a one-piece plate-type IOL. The amount of deformation of lenticular structures during implantation was calculated and the movements visualized with two cameras. The results were transformed to two-dimensional graphs using a newly developed image-processing algorithm.ResultsFor both one-piece plate-type and one-piece C-loop haptic IOLs, the amount of capsular bag deformation from its initial shape was greater in the direction of posterior center of the capsule, as detected by side camera, than in the direction of the equator (or periphery), as detected by front camera. The mean peak deformation values were 51% and 36% (as measured by side and front cameras, respectively) for one-piece plate-type IOL and 25% and 20% for one-piece C-loop haptic IOL. For three-piece C-loop haptic IOL, the capsular bag distention was almost equal in both posterior and peripheral directions, with mean peak deformation values reaching 39% and 38%.ConclusionsThe new experimental means of lenticular imaging and quantified dynamics from two different angles allowed three-dimensional understanding of specific behavior of each IOL. Our model not only exposes the capsular bag for recording during implantation, but also objectively compares the individual movement values and reveals different zonular and capsular stress patterns, depending on IOL model.Translational relevanceThe novel "Choi-Apple View" allows a three-dimensional quantitative analysis of capsular dynamics and IOL implantation behavior.

| S-EPMC6528741 | biostudies-literature

PenDA, a rank-based method for personalized differential analysis: Application to lung cancer.

Project description:The hopes of precision medicine rely on our capacity to measure various high-throughput genomic information of a patient and to integrate them for personalized diagnosis and adapted treatment. Reaching these ambitious objectives will require the development of efficient tools for the detection of molecular defects at the individual level. Here, we propose a novel method, PenDA, to perform Personalized Differential Analysis at the scale of a single sample. PenDA is based on the local ordering of gene expressions within individual cases and infers the deregulation status of genes in a sample of interest compared to a reference dataset. Based on realistic simulations of RNA-seq data of tumors, we showed that PenDA outcompetes existing approaches with very high specificity and sensitivity and is robust to normalization effects. Applying the method to lung cancer cohorts, we observed that deregulated genes in tumors exhibit a cancer-type-specific commitment towards up- or down-regulation. Based on the individual information of deregulation given by PenDA, we were able to define two new molecular histologies for lung adenocarcinoma cancers strongly correlated to survival. In particular, we identified 37 biomarkers whose up-regulation lead to bad prognosis and that we validated on two independent cohorts. PenDA provides a robust, generic tool to extract personalized deregulation patterns that can then be used for the discovery of therapeutic targets and for personalized diagnosis. An open-access, user-friendly R package is available at https://github.com/bcm-uga/penda.

| S-EPMC7274464 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data