Large-Scale Atom Probe Tomography Data Mining: Methods and Application to Inform Hydrogen Behavior.

A large number of atom probe tomography (APT) datasets from past experiments were collected into a database to conduct statistical analyses. An effective way of handling the data is shown, and a study on hydrogen is conducted to illustrate the usefulness of this approach. We propose to handle a large collection of APT spectra as a point cloud and use a city block distance-based metric to measure dissimilarity between spectra.

Processing APT Spectral Backgrounds for Improved Quantification.

We describe a method to estimate background noise in atom probe tomography (APT) mass spectra and to use this information to enhance both background correction and quantification. Our approach is mathematically general in form for any detector exhibiting Poisson noise with a fixed data acquisition time window, at voltages varying through the experiment. We show that this accurately estimates the background observed in real experiments.

Blockade of TGF-β signaling to enhance the antitumor response is accompanied by dysregulation of the functional activity of CD4CD25Foxp3 and CD4CD25Foxp3 T cells.

Background: The pleiotropic cytokine, transforming growth factor (TGF)-β, and CD4CD25Foxp3 regulatory T cells (Tregs) play a critical role in actively suppressing antitumor immune responses. Evidence shows that TGF-β produced by tumor cells promotes tolerance via expansion of Tregs. Our group previously demonstrated that blockade of TGF-β signaling with a small molecule TGF-β receptor I antagonist (SM16) inhibited primary and metastatic tumor growth in a T cell dependent fashion.

A Gas-Phase Reaction Cell for Modern Atom Probe Systems.

In this work, we demonstrate a new system for the examination of gas interactions with surfaces via atom probe tomography. This system provides capability of examining the surface and subsurface interactions of gases with a wide range of specimens, as well as a selection of input gas types. This system has been primarily developed to aid the investigation of hydrogen interactions with metallurgical samples, to better understand the phenomenon of hydrogen embrittlement.

DF-Fit: A Robust Algorithm for Detection of Crystallographic Information in Atom Probe Tomography Data.

We report on a new algorithm for the detection of crystallographic information in three-dimensional, as retained in atom probe tomography (APT), with improved robustness and signal detection performance. The algorithm is underpinned by one-dimensional distribution functions (DFs), as per existing algorithms, but eliminates an unnecessary parameter as compared to current methods.By examining traditional DFs in an automated fashion in real space, rather than using Fourier transform approaches, we utilize an error metric based upon the expected value for a spatially random distribution for detecting crystallography.

Autophagosome-based strategy to monitor apparent tumor-specific CD8 T cells in patients with prostate cancer.

The immune system plays an essential role in eradicating cancer in concert with various treatment modalities. In the absence of autologous tumor material, no standardized method exists to assess T cell responses against the many antigens that may serve as cancer rejection antigens. Thus, development of methods to screen for therapy-induced anti-tumor responses is a high priority that could help tailor therapy.

Single-Ion Deconvolution of Mass Peak Overlaps for Atom Probe Microscopy.

Due to the intrinsic evaporation properties of the material studied, insufficient mass-resolving power and lack of knowledge of the kinetic energy of incident ions, peaks in the atom probe mass-to-charge spectrum can overlap and result in incorrect composition measurements. Contributions to these peak overlaps can be deconvoluted globally, by simply examining adjacent peaks combined with knowledge of natural isotopic abundances. However, this strategy does not account for the fact that the relative contributions to this convoluted signal can often vary significantly in different regions of the analysis volume; e.

Atom Probe Analysis of Ex Situ Gas-Charged Stable Hydrides.

In this work, we report on the atom probe tomography analysis of two metallic hydrides formed by pressurized charging using an ex situ hydrogen charging cell, in the pressure range of 200-500 kPa (2-5 bar). Specifically we report on the deuterium charging of Pd/Rh and V systems. Using this ex situ system, we demonstrate the successful loading and subsequent atom probe analysis of deuterium within a Pd/Rh alloy, and demonstrate that deuterium is likely present within the oxide-metal interface of a native oxide formed on vanadium.

An atom probe perspective on phase separation and precipitation in duplex stainless steels.

Three-dimensional chemical imaging of Fe-Cr alloys showing Fe-rich (α)/Cr-rich (α') phase separation is reported using atom probe tomography techniques. The extent of phase separation, i.e.

A Semi-automated Approach to Preparing Antibody Cocktails for Immunophenotypic Analysis of Human Peripheral Blood.

Immunophenotyping of peripheral blood by flow cytometry determines changes in the frequency and activation status of peripheral leukocytes during disease and treatment. It has the potential to predict therapeutic efficacy and identify novel therapeutic targets. Whole blood staining utilizes unmanipulated blood, which minimizes artifacts that can occur during sample preparation.

Mining information from atom probe data.

Whilst atom probe tomography (APT) is a powerful technique with the capacity to gather information containing hundreds of millions of atoms from a single specimen, the ability to effectively use this information creates significant challenges. The main technological bottleneck lies in handling the extremely large amounts of data on spatial-chemical correlations, as well as developing new quantitative computational foundations for image reconstruction that target critical and transformative problems in materials science. The power to explore materials at the atomic scale with the extraordinary level of sensitivity of detection offered by atom probe tomography has not been not fully harnessed due to the challenges of dealing with missing, sparse and often noisy data.

Detailed characterization of tumor infiltrating lymphocytes in two distinct human solid malignancies show phenotypic similarities.

Background: We examined the phenotype and function of lymphocytes collected from the peripheral blood (PBL) and tumor (TIL) of patients with two different solid malignancies: colorectal cancer liver metastases (CRLM) and ovarian cancer (OVC).

Methods: Tumor and corresponding peripheral blood were collected from 16 CRLM and 22 OVC patients; immediately following resection they were processed and analyzed using a multi-color flow cytometry panel. Cytokine mRNA from purified PBL and TIL CD4(+) T cells were also analyzed by qPCR.

OX40 is a potent immune-stimulating target in late-stage cancer patients.

OX40 is a potent costimulatory receptor that can potentiate T-cell receptor signaling on the surface of T lymphocytes, leading to their activation by a specifically recognized antigen. In particular, OX40 engagement by ligands present on dendritic cells dramatically increases the proliferation, effector function, and survival of T cells. Preclinical studies have shown that OX40 agonists increase antitumor immunity and improve tumor-free survival.

Level set methods for modelling field evaporation in atom probe.

Atom probe is a nanoscale technique for creating three-dimensional spatially and chemically resolved point datasets, primarily of metallic or semiconductor materials. While atom probe can achieve local high-level resolution, the spatial coherence of the technique is highly dependent upon the evaporative physics in the material and can often result in large geometric distortions in experimental results. The distortions originate from uncertainties in the projection function between the field evaporating specimen and the ion detector.

Defining clusters in APT reconstructions of ODS steels.

Oxide nanoclusters in a consolidated Fe-14Cr-2W-0.3Ti-0.3Y₂O₃ ODS steel and in the alloy powder after mechanical alloying (but before consolidation) are investigated by atom probe tomography (APT).

Tumor-derived autophagosome vaccine: mechanism of cross-presentation and therapeutic efficacy.

Purpose: We previously reported that autophagy in tumor cells plays a critical role in cross-presentation of tumor antigens and that autophagosomes are efficient antigen carriers for cross-priming of tumor-reactive CD8(+) T cells. Here, we sought to characterize further the autophagosome-enriched vaccine named DRibble (DRiPs-containing blebs), which is derived from tumor cells after inhibition of protein degradation, and to provide insights into the mechanisms responsible for their efficacy as a novel cancer immunotherapy.

Experimental Design: DRibbles were characterized by Western blot and light or transmission electron microscopy.

Crystallographic structural analysis in atom probe microscopy via 3D Hough transformation.

Whereas the atom probe is regarded almost exclusively as a technique for 3D chemical microanalysis of solids with the highest chemical and spatial resolution, we demonstrate that the technique can be used for detailed crystallographic determinations. We present a new method for the quantitative determination of crystal structure (plane spacings and angles) using a Hough transformation of the reconstructed atom probe data. The resolving power is shown to be high enough to identify poorly established, discontinuous planes that are typical in semiconducting materials.

Exhaustive expansion: A novel technique for analyzing complex data generated by higher-order polychromatic flow cytometry experiments.

Background: The complex data sets generated by higher-order polychromatic flow cytometry experiments are a challenge to analyze. Here we describe Exhaustive Expansion, a data analysis approach for deriving hundreds to thousands of cell phenotypes from raw data, and for interrogating these phenotypes to identify populations of biological interest given the experimental context.

Methods: We apply this approach to two studies, illustrating its broad applicability.

Spatial resolution in atom probe tomography.

This article addresses gaps in definitions and a lack of standard measurement techniques to assess the spatial resolution in atom probe tomography. This resolution is known to be anisotropic, being better in-depth than laterally. Generally the presence of atomic planes in the tomographic reconstruction is considered as being a sufficient proof of the quality of the spatial resolution of the instrument.

Depletion of tumor-induced Treg prior to reconstitution rescues enhanced priming of tumor-specific, therapeutic effector T cells in lymphopenic hosts.

We reported previously that vaccination of reconstituted, lymphopenic mice resulted in a higher frequency of tumor-specific effector T cells with therapeutic activity than vaccination of normal mice. Here, we show that lymphopenic mice reconstituted with spleen cells from tumor-bearing mice (TBM), a situation that resembles the clinical condition, failed to generate tumor-specific T cells with therapeutic efficacy. However, depletion of CD25(+) Treg from the spleen cells of TBM restored tumor-specific priming and therapeutic efficacy.

Disruption of TGF-beta signaling prevents the generation of tumor-sensitized regulatory T cells and facilitates therapeutic antitumor immunity.

Regulatory T (Treg) cells represent a major roadblock to the induction of antitumor immunity through vaccine approaches. TGF-beta is a cytokine implicated in the generation and maintenance of Treg cells, as well as in their suppressive function. These experiments examined whether the generation of tumor-sensitized Treg cells was TGF-beta dependent and evaluated whether TGF-beta produced by Treg cells blocked the priming of tumor-specific T cells in vaccinated reconstituted lymphopenic mice.

Cancer immunotherapy: the role regulatory T cells play and what can be done to overcome their inhibitory effects.

Since multiple lines of experimental and clinical data clearly identified regulatory T cells as an integral part of the immune response, these cells have become a major focus of investigation in tumor immunology. Regulatory T cells are in place to dampen ongoing immune responses and to prevent autoimmunity, but they also have profound effects in blocking therapeutic anti-tumor activity. Therefore regulatory T cells are seen as a major hurdle that must be overcome in order for cancer immunotherapy to reach its therapeutic potential.

Qualification of the tomographic reconstruction in atom probe by advanced spatial distribution map techniques.

New and improved spatial distribution map (SDM) methods are developed to identify and extract crystallographic information within atom probe tomography three-dimensional (3D) reconstructions. Detailed structural information is retrieved by combining z-SDM offset distribution analyses computed in multiple crystallographic directions, accurately determining inter-planar spacings and crystallographic angles. The advantages of this technique in comparison to applying the complete z-SDM and complementary xy-SDM analysis to a single crystallographic direction are investigated.

Characterization of the class I-restricted gp100 melanoma peptide-stimulated primary immune response in tumor-free vaccine-draining lymph nodes and peripheral blood.

Purpose: The aim of this study was to characterize the primary gp100(209-2M)-specific T-cell response in vaccine-draining, metastases-free lymph nodes and peripheral blood of peptide-vaccinated stage I to III melanoma patients.

Experimental Design: After two or three gp100(209-2M) vaccinations, sentinel lymph nodes that drained both the primary tumor and adjacent vaccine sites were excised concomitant with wide excision of the tumor. Comparative 7-color flow cytometry phenotype analysis was done on gp100 tetramer-positive CD8(+) T cells from sentinel lymph nodes, closely proximate time-related peripheral blood mononuclear cells (PBMC) collected 2 to 4 weeks after sentinel lymph node excision, and on PBMC collected 6 months later after 7 or 11 more immunizations.

Phenotype and functional characterization of long-term gp100-specific memory CD8+ T cells in disease-free melanoma patients before and after boosting immunization.

Purpose: Effective cancer vaccines must both drive a strong CTL response and sustain long-term memory T cells capable of rapid recall responses to tumor antigens. We sought to characterize the phenotype and function of gp100 peptide-specific memory CD8+ T cells in melanoma patients after primary gp100(209-2M) immunization and assess the anamnestic response to boosting immunization.

Experimental Design: Eight-color flow cytometry analysis of gp100-specific CD8+ T cells was done on peripheral blood mononuclear cells collected shortly after the primary vaccine regimen, 12 to 24 months after primary vaccination, and after boosting immunization.