The Interpretation of X-Ray and Electron Signals Generated in Thin or Layered Targets

This work outlines the development of a comprehensive theory for the electron probe microanalyser and scanning electron microscope or SEM, that is intended to serve as a framework of understanding for those employing electron beam methods and as a basis for improved correction procedures. There is particular emphasis on applications to layered and non-uniform specimens. Starting from a simple Gaussian depth distribution of electrons and making assumptions about the X-ray production, a series of predictions of X-ray and electron signals are made for various target configurations. When compared with experimental measurements a series of interesting discoveries follow, which, taken altogether, lead to a more refined model with the promise of more accurate analyses and a better understanding of the physics involved

Optical Microreflectometry and Microscopy of Chalcopyrite Specimens: Reflectance Calculation and Comparison to Backscattered Electron Microscopy

A model was developed to calculate the optical reflectance of an absorbing substrate covered by multiple thin layers of absorbing materials. Both multiple homogeneous thin layers and thin surface layers of mixed phases were modeled. Reflectance versus wavelength was measured for polished chalcopyrite (CuFeS2) and compared to calculated data. The identity and thickness of surface compounds used to calculate reflectance curves were partially determined using X-ray photoelectron and Auger electron spectroscopies. Very good agreement between theoretical and experimental reflectance curves were observed as a function of surface composition. The hue (color) and luminosity (brightness) of the polished surface were also calculated from both experimental and theoretical curves and were found to also be valuable for evaluating surface composition. Contrast in optical photomicrographs resulting from both luminosity and hue was illustrated. Secondary and backscattered electron microscopy were also used to image chalcopyrite polished surfaces which were naturally oxidized by an exposure before and after ion etching. For a substrate covered with thin layers, the resulting backscattered coefficient was calculated as a function of the backscattered coefficient for the surface and the substrate, respectively. The variations of the relative difference between the effective backscattered coefficients vs the primary beam energy exhibited a maximum for a critical thickness difference of the surface layer. The dependence of the variations in thickness of the oxidized layer with the crystallographic orientation changes of the substrate as well as the resulting contrasts of the optical and electron images were discussed

Spectral Decomposition of Wavelength Dispersive X-Ray Spectra: Implications for Quantitative Analysis in the Electron Probe Microanalyzer

The line shapes of Kα, Lα,β and Mα X-ray peaks of pure elements were analyzed by means of commercial wavelength dispersive spectrometers (WDS) attached to an electron probe micro-analyzer (EPMA). A pseudo-Voigt function, i.e., a linear combination of Gaussian and Lorentzian distributions, was used as a fitting profile for the X-ray peaks, with Gaussian offsets incorporated in the short wavelength (high energy) side to describe the observed asymmetry. The asymmetry of X-ray peaks resulting from both instrumental distortions and satellite bands may lead to discrepancies in quantitative analysis with the EPMA as a function of the procedure used for deriving X-ray intensities from WDS spectra, e.g., peak height, peak area, or peak decomposition. These effects have been illustrated by analyzing gold-copper metallic alloys and minerals containing gold at trace levels

Cathodoluminescence Applied to the Microcharacterization of Mineral Materials: A Present Status in Experimentation and Interpretation

Experimentation and interpretation of cathodoluminescence (CL) microscopy and spectroscopy applied to the microcharacterization of material minerals are reviewed. The origins of the intrinsic (host lattice) and extrinsic (impurities) luminescence emissions in crystals are briefly discussed. Merits and limitations of the available techniques are illustrated. CL emission changes as a function of the incident electron dose are illustrated for the case of natural quartz and sphalerite (ZnS) crystals. These effects are discussed in terms of the development of bulk charging, production of heat, diffusion of impurities, and creation of lattice defects induced by the incident ionizing particles. Although CL emission is mostly extrinsic in origin there is no general rule for identifying the nature of impurities from the CL emission spectra of minerals. However there is potential for using CL spectroscopy for trace element analysis as presented for the case of minerals containing rare-earth luminescent ions. The CL emission is a signature of the crystal-chemistry properties of minerals and hence contains potential genetic information. Some of the applications of CL emissions in the geosciences are summarized

Diseño y puesta en funcionamiento de un SIG como herramienta para el estudio del turismo y su planificación en las regiones del archipiélago de Las Canarreos y Cienfuegos-Trinidad-Topes de Collantes, Cuba

Today, geographic information systems are being used as a platform for managing hugh volumes of information related to the decision making process withing different fields. Given the great variety of touristic resources that Cuba has, different systems have been generated at the Faculty of Geography of the University of Havana, oriented to tourism plainning and study. In this article, two of those results are presented involving different territories: Los Canarreos Archipielago and Cienfuegos -Trinidad - Topes de Collantes region.En la época actual, los Sistemas de Información Geográfica están siendo cada vez más utilizados como plataforma para el manejo de grandes volúmenes de información relacionados con la toma de decisiones en diferentes ramas. Dada la gran variedad de recursos turísticos con que Cuba cuenta y dado el incremento de la actividad en el país, se han generado por la Facultad de Geografía de la Universidad de La Habana diferentes sistemas orientados al estudio y la planificación del turismo. En el presente trabajo se presentan dos de estos resultados vinculados con territorios específicos: El Archipiélago de los Canarreos y la región Cienfuegos-Trinidad-Topes de Collaiites

Early evaluation of the effectiveness and cost-effectiveness of ctDNA-guided selection for adjuvant chemotherapy in stage II colon cancer

Background: Current patient selection for adjuvant chemotherapy (ACT) after curative surgery for stage II colon cancer (CC) is suboptimal, causing overtreatment of high-risk patients and undertreatment of low-risk patients. Postoperative circulating tumor DNA (ctDNA) could improve patient selection for ACT. Objectives: We conducted an early model-based evaluation of the (cost-)effectiveness of ctDNA-guided selection for ACT in stage II CC in the Netherlands to assess the conditions for cost-effective implementation. Methods: A validated Markov model, simulating 1000 stage II CC patients from diagnosis to death, was supplemented with ctDNA data. Five ACT selection strategies were evaluated: the current guideline (pT4, pMMR), ctDNA-only, and three strategies that combined ctDNA status with pT4 and pMMR status in different ways. For each strategy, the costs, life years, quality-adjusted life years (QALYs), recurrences, and CC deaths were estimated. Sensitivity analyses were performed to assess the impact of the costs of ctDNA testing, strategy adherence, ctDNA as a predictive biomarker, and ctDNA test performance. Results: Model predictions showed that compared to current guidelines, the ctDNA-only strategy was less effective (+2.2% recurrences, −0.016 QALYs), while the combination strategies were more effective (−3.6% recurrences, +0.038 QALYs). The combination strategies were not cost-effective, since the incremental cost-effectiveness ratio was €67,413 per QALY, exceeding the willingness-to-pay threshold of €50,000 per QALY. Sensitivity analyses showed that the combination strategies would be cost-effective if the ctDNA test costs were lower than €1500, or if ctDNA status was predictive of treatment response, or if the ctDNA test performance improved substantially. Conclusion: Adding ctDNA to current high-risk clinicopathological features (pT4 and pMMR) can improve patient selection for ACT and can also potentially be cost-effective. Future studies should investigate the predictive value of post-surgery ctDNA status to accurately evaluate the cost-effectiveness of ctDNA testing for ACT decisions in stage II CC.</p

Modeling Personalized Adjuvant TreaTment in EaRly stage coloN cancer (PATTERN)

Aim: To develop a decision model for the population-level evaluation of strategies to improve the selection of stage II colon cancer (CC) patients who benefit from adjuvant chemotherapy. Methods: A Markov cohort model with a one-month cycle length and a lifelong time horizon was developed. Five health states were included; diagnosis, 90-day mortality, death other causes, recurrence and CC death. Data from the Netherlands Cancer Registry were used to parameterize the model. Transition probabilities were estimated using parametric survival models including relevant clinical and pathological covariates. Subsequently, biomarker status was implemented using external data. Treatment effect was incorporated using pooled trial data. Model development, data sources used, parameter estimation, and internal and external validation are described in detail. To illustrate the use of the model, three example strategies were evaluated in which allocation of treatment was based on (A) 100% adherence to the Dutch guidelines, (B) observed adherence to guideline recommendations and (C) a biomarker-driven strategy. Results: Overall, the model showed good internal and external validity. Age, tumor growth, tumor sidedness, evaluated lymph nodes, and biomarker status were included as covariates. For the example strategies, the model predicted 83, 87 and 77 CC deaths after 5 years in a cohort of 1000 patients for strategies A, B and C, respectively. Conclusion: This model can be used to evaluate strategies for the allocation of adjuvant chemotherapy in stage II CC patients. In future studies, the model will be used to estimate population-level long-term health gain and cost-effectiveness of biomarker-based selection strategies

Modeling Personalized Adjuvant TreaTment in EaRly stage coloN cancer (PATTERN)

Aim To develop a decision model for the population-level evaluation of strategies to improve the selection of stage II colon cancer (CC) patients who benefit from adjuvant chemotherapy. Methods A Markov cohort model with a one-month cycle length and a lifelong time horizon was developed. Five health states were included; diagnosis, 90-day mortality, death other causes, recurrence and CC death. Data from the Netherlands Cancer Registry were used to parameterize the model. Transition probabilities were estimated using parametric survival models including relevant clinical and pathological covariates. Subsequently, biomarker status was implemented using external data. Treatment effect was incorporated using pooled trial data. Model development, data sources used, parameter estimation, and internal and external validation are described in detail. To illustrate the use of the model, three example strategies were evaluated in which allocation of treatment was based on (A) 100% adherence to the Dutch guidelines, (B) observed adherence to guideline recommendations and (C) a biomarker-driven strategy. Results Overall, the model showed good internal and external validity. Age, tumor growth, tumor sidedness, evaluated lymph nodes, and biomarker status were included as covariates. For the example strategies, the model predicted 83, 87 and 77 CC deaths after 5 years in a cohort of 1000 patients for strategies A, B and C, respectively. Conclusion This model can be used to evaluate strategies for the allocation of adjuvant chemotherapy in stage II CC patients. In future studies, the model will be used to estimate population-level long-term health gain and cost-effectiveness of biomarker-based selection strategies.Financial support for this study was provided by a grant from ZonMw (Grant number: 848015007). ZonMw had no role in designing the study, interpreting the data, writing the manuscript, and publishing the report

Proteins in stool as biomarkers for non-invasive detection of colorectal adenomas with high risk of progression

Screening to detect colorectal cancer (CRC) in an early or premalignant state is an effective method to reduce CRC mortality rates. Current stool-based screening tests, e.g. fecal immunochemical test (FIT), have a suboptimal sensitivity for colorectal adenomas and difficulty distinguishing adenomas at high risk of progressing to cancer from those at lower risk. We aimed to identify stool protein biomarker panels that can be used for the early detection of high-risk adenomas and CRC. Proteomics data (LC–MS/MS) were collected on stool samples from adenoma (n = 71) and CRC patients (n = 81) as well as controls (n = 129). Colorectal adenoma tissue samples were characterized by low-coverage whole-genome sequencing to determine their risk of progression based on specific DNA copy number changes. Proteomics data were used for logistic regression modeling to establish protein biomarker panels. In total, 15 of the adenomas (15.8%) were defined as high risk of progressing to cancer. A protein panel, consisting of haptoglobin (Hp), LAMP1, SYNE2, and ANXA6, was identified for the detection of high-risk adenomas (sensitivity of 53% at specificity of 95%). Two panels, one consisting of Hp and LRG1 and one of Hp, LRG1, RBP4, and FN1, were identified for high-risk adenomas and CRCs detection (sensitivity of 66% and 62%, respectively, at specificity of 95%). Validation of Hp as a biomarker for high-risk adenomas and CRCs was performed using an antibody-based assay in FIT samples from a subset of individuals from the discovery series (n = 158) and an independent validation series (n = 795). Hp protein was significantly more abundant in high-risk adenoma FIT samples compared to controls in the discovery (p = 0.036) and the validation series (p = 9e-5). We conclude that Hp, LAMP1, SYNE2, LRG1, RBP4, FN1, and ANXA6 may be of value as stool biomarkers for early detection of high-risk adenomas and CRCs

Comparison of NTRK fusion detection methods in microsatellite-instability-high metastatic colorectal cancer

Tropomyosin receptor kinase (TRK) inhibitors have been approved for metastatic solid tumors harboring NTRK fusions, but the detection of NTRK fusions is challenging. International guidelines recommend pan-TRK immunohistochemistry (IHC) screening followed by next generation sequencing (NGS) in tumor types with low prevalence of NTRK fusions, including metastatic colorectal cancer (mCRC). RNA-based NGS is preferred, but is expensive, time-consuming, and extracting good-quality RNA from FFPE tissue is challenging. Alternatives in daily clinical practice are warranted. We assessed the diagnostic performance of RNA-NGS, FFPE-targeted locus capture (FFPE-TLC), fluorescence in situ hybridization (FISH), and the 5'/3' imbalance quantitative RT-PCR (qRT-PCR) after IHC screening in 268 patients with microsatellite-instability-high mCRC, the subgroup in which NTRK fusions are most prevalent (1-5%). A consensus result was determined after review of all assay results. In 16 IHC positive tumors, 10 NTRK fusions were detected. In 33 IHC negative samples, no additional transcribed NTRK fusions were found, underscoring the high sensitivity of IHC. Sensitivity of RNA-NGS, FFPE-TLC, FISH, and qRT-PCR was 90%, 90%, 78%, and 100%, respectively. Specificity was 100% for all assays. Robustness, defined as the percentage of samples that provided an interpretable result in the first run, was 100% for FFPE-TLC, yet more limited for RNA-NGS (85%), FISH (70%), and qRT-PCR (70%). Overall, we do not recommend FISH for the detection of NTRK fusions in mCRC due to its low sensitivity and limited robustness. We conclude that RNA-NGS, FFPE-TLC, and qRT-PCR are appropriate assays for NTRK fusion detection, after enrichment with pan-TRK IHC, in routine clinical practice