scholarly journals Local and Integral Techniques in Metal Compositional Analysis of Archaeological Objects with Surface Corrosion Layers and Small Sample Quantities

2018 ◽  
Vol 4 (26) ◽  
pp. 203-221 ◽  
Author(s):  
Anastasiya Yu. Loboda ◽  
◽  
Elena Yu. Tereshhenko ◽  
Anna V. Antipenko ◽  
Vasiliy M. Retivov ◽  
...  
Keyword(s):  
Compositional Analysis ◽  
Small Sample ◽  
Surface Corrosion ◽  
Archaeological Objects

Computer-Aided Analysis of Oriented Crystallites by Diffraction Pattern Simulation and Tilt-Stage Control in a TEM

1997 ◽  
Vol 3 (S2) ◽  
pp. 1015-1016
Author(s):  
L.E. Thomas ◽  
L.A. Chariot ◽  
J.T. Stanley
Keyword(s):  
Small Sample ◽  
Hot Water ◽  
Metal Corrosion ◽  
Desktop Computer ◽  
Cross Sectional ◽  
Surface Corrosion ◽  
Computer Aided ◽  
Columnar Grains ◽  
Diffraction Patterns ◽  
Convergent Beam

Electron diffraction patterns taken in the transmission electron microscope (TEM) provide information about crystal structures and orientations in small sample areas. Extracting this information and manipulating local crystal orientations has become a great deal easier with the availability of desktop computer programs that allow simulation matching of experimental patterns and crystallographic control of sample tilting in the TEM. This presentation will illustrate an application of computer-aided crystallography for analyzing oriented crystallites in an experimentally complex material.The surface corrosion films that form on reactive metals such as hafnium or zirconium in hot water provided our example. Cross-sectional examinations of the corrosion films revealed a columnar microstructure of monoclinic HfO2/ZrO2 grains extending normal to the metal/corrosion-film interface.The columnar grains were only about 50 nm in width, and thus were too small to analyze individually by selected-area diffraction. Local strains in the films smeared the diffraction fine structure so there was little hope for analysis by convergent-beam diffraction methods.

Texture and Compositional Analysis in Archaeology

2011 ◽  
pp. 229-255
Author(s):  
Juan A. Barceló
Keyword(s):  
Compositional Analysis ◽  
Perceptual Information ◽  
Shape Information ◽  
Archaeological Materials ◽  
Local Properties ◽  
Perceptual Variability ◽  
Surface Discontinuity ◽  
Visual Variety ◽  
Micro Topography ◽  
Archaeological Objects

In this section, we will consider archaeological textures as the archaeological element’s surface attributes having either tactile or visual variety, which characterize its appearance. The surfaces of archaeological objects, artifacts, and materials are not uniform but contain many variations; some of them are of visual or tactile nature. Such variations go beyond the peaks and valleys characterizing surface micro-topography, which is the obvious frame of reference for “textures” in usual speaking. Archaeological materials have variations in the local properties of their surfaces like albedo and color variations, uniformity, density, coarseness, roughness, regularity, linearity, directionality, frequency, phase, hardness, brightness, bumpiness, specularity, reflectivity, transparency, and so on. Texture is the name we give to the perception of these variations. What we are doing here is introducing a synonym for “perceptual variability” or “surface discontinuity.” It is a kind of perceptual information complementing shape information.

scholarly journals LOCOM: A logistic regression model for testing differential abundance in compositional microbiome data with false discovery rate control

2021 ◽  
Author(s):  
Yingtian Hu ◽  
Glen Satten ◽  
Yijuan Hu
Keyword(s):  
Logistic Regression ◽  
False Discovery Rate ◽  
Compositional Analysis ◽  
R Package ◽  
Small Sample ◽  
Metagenomic Sequencing ◽  
False Discovery ◽  
Small Sample Sizes ◽  
Low Sensitivity ◽  
Microbiome Data

Abstract Motivation: Compositional analysis is based on the premise that a relatively small proportion of taxa are differentially abundant", while the ratios of the relative abundances of the remaining taxa remain unchanged. Most existing methods of compositional analysis such as ANCOM or ANCOM-BC use log-transformed data, but log-transformation of data with pervasive zero counts is problematic, and these methods cannot always control the false discovery rate (FDR). Further, high-throughput microbiome data such as 16S amplicon or metagenomic sequencing are subject to experimental biases that are introduced in every step of the experimental workflow. McLaren, Willis and Callahan [1] have recently proposed a model for how these biases affect relative abundance data. Methods: Motivated by [1], we show that the (log) odds ratios in a logistic regression comparing counts in two taxa are invariant to experimental biases. With this motivation, we propose LOCOM, a robust logistic regression approach to compositional analysis, that does not require pseudocounts. We use a Firth bias-corrected estimating function to account for sparse data. Inference is based on permutation to account for overdispersion and small sample sizes. Traits can be either binary or continuous, and adjustment for continuous and/or discrete confounding covariates is supported. Results: Our simulations indicate that LOCOM always preserved FDR and had much improved sensitivity over existing methods. In contrast, ANCOM often had inflated FDR; ANCOM-BC largely controlled FDR but still had modest inflation occasionally; ALDEx2 generally had low sensitivity. LOCOM and ANCOM were robust to experimental biases in every situation, while ANCOM-BC and ALDEx2 had elevated FDR when biases at causal and non-causal taxa were differentially distributed. The flexibility of our method for a variety of microbiome studies is illustrated by the analysis of data from two microbiome studies. Availability and implementation: Our R package LOCOM is available on GitHub at https://github.com/yijuanhu/LOCOM in formats appropriate for Macintosh or Windows.

Primary and Secondary Gold Sources of Quaternary Placers of Western Spain: a Morphotextural and Compositional Analysis of the Fresnedoso Deposit.

2021 ◽  
Author(s):  
Kelvin Dos Santos Alves ◽  
Santos Barrios Sánchez ◽  
Juan Gómez Barreiro ◽  
Raul Merinero Palomares ◽  
Rafael Pablo Lozano Fernández ◽  
...  
Keyword(s):  
Cold Work ◽  
Compositional Analysis ◽  
Small Sample ◽  
Primary Sources ◽  
Gold Placer ◽  
Gold Particles ◽  
Western Spain ◽  
Type 3

<p>In this contribution we have investigated the Fresnedoso Quaternary gold placer (Western Spain), analyzing the morphotextural and microchemical evolution of gold particles. The statistical analysis has revealed the presence of two populations of particles being consistent with primary sources situated at a distal [20 - 50 km] and a proximal [2.5 - 10 km] range. The gold morphology and chemistry point to a recycling (and potentially undiscovered) Tertiary paleoplacers. The discovery of primary laminar morphologies points to lode deposits in small-flat veins hosted in Precambrian metasediments (Schist Greywacke Complex). All these findings suggest that the Fresnedoso gold deposit is formed by mono and polycyclic particles. We have tested previous transport distance vs Flattening indexes (CFI, Shilo) models resulting in useful framework for exploration of undiscovered ores, even with a small sample dimension. Chemical analysis of the different gold morphologies depicted that the Fresnedoso gold is a AuAg bimetallic alloy. Three groups were identified based on the texture and composition of the gold particles: Type 1 (Au1= Au89-94Ag11-6), Type 2 (Au2= Au99 Ag1) and Type 3 (Au3~ Au >99). Particle's cores (gold Type 1) show a compositional range that could be interpreted as differences in primary sources, spatial dispersion of sources or the actuation of secondary processes, probably in an orogenic gold context. Microchemical heterogeneity in the particles is probably due to secondary processes. A conceptual model has been elaborated to explain particle's microchemical domains represented by gold Type 2 (rim) and Type 3 (micro-aggregates) as the result of two different de-alloying stages: A) initial Ag-leaching at the rim and/or through microcracks and grainboundaries (Type 2), B) Total reset of the primary chemical fingerprint, with porous microtexture and the precipitation of gold with iron oxyhydroxides and clays (Type 3). This model suggests a silver de-alloying mechanism favored in a chlorine-iron-rich environment as in the case of laterites. Deformation and eventually recrystallization mechanisms associated with the fluvial transport (mechanical cold-work), cooperated in the evolution of the particles (Dos Santos et al. 2020).</p><p>References </p><p>Dos Santos Alves, K., Barrios Sánchez, S., Gómez Barreiro, J., Merinero Palomares,R. and Compaña Prieto, J.M. (2020). "Morphological and compositional analysis of alluvial gold: The Fresnedoso gold placer (Spain)." Ore Geology Reviews : 103489.</p>

scholarly journals LOCOM: A logistic regression model for testing differential abundance in compositional microbiome data with false discovery rate control

2021 ◽  
Author(s):  
Yingtian Hu ◽  
Glen A. Satten ◽  
Yi-Juan Hu
Keyword(s):  
Logistic Regression ◽  
False Discovery Rate ◽  
Compositional Analysis ◽  
R Package ◽  
Small Sample ◽  
Metagenomic Sequencing ◽  
False Discovery ◽  
Small Sample Sizes ◽  
Low Sensitivity ◽  
Microbiome Data

AbstractMotivationCompositional analysis is based on the premise that a relatively small proportion of taxa are “differentially abundant”, while the ratios of the relative abundances of the remaining taxa remain unchanged. Most existing methods of compositional analysis such as ANCOM or ANCOM-BC use log-transformed data, but log-transformation of data with pervasive zero counts is problematic, and these methods cannot always control the false discovery rate (FDR). Further, high-throughput microbiome data such as 16S amplicon or metagenomic sequencing are subject to experimental biases that are introduced in every step of the experimental workflow. McLaren, Willis and Callahan [1] have recently proposed a model for how these biases affect relative abundance data.MethodsMotivated by [1], we show that the (log) odds ratios in a logistic regression comparing counts in two taxa are invariant to experimental biases. With this motivation, we propose LOCOM, a robust logistic regression approach to compositional analysis, that does not require pseudocounts. We use a Firth bias-corrected estimating function to account for sparse data. Inference is based on permutation to account for overdispersion and small sample sizes. Traits can be either binary or continuous, and adjustment for continuous and/or discrete confounding covariates is supported.ResultsOur simulations indicate that LOCOM always preserved FDR and had much improved sensitivity over existing methods. In contrast, ANCOM often had inflated FDR; ANCOM-BC largely controlled FDR but still had modest inflation occasionally; ALDEx2 generally had low sensitivity. LOCOM and ANCOM were robust to experimental biases in every situation, while ANCOM-BC and ALDEx2 had elevated FDR when biases at causal and non-causal taxa were differentially distributed. The flexibility of our method for a variety of microbiome studies is illustrated by the analysis of data from two microbiome studies.Availability and implementationOur R package LOCOM is available on GitHub at https://github.com/yijuanhu/LOCOM in formats appropriate for Macintosh or Windows.

Probing the ultrastructure of the mitotic and meiotic spindle in eggs: An expeditious approach based on semi-thin (0.25 μm) serial sections

1983 ◽  
Vol 41 ◽  
pp. 552-555
Author(s):  
Conly L. Rieder ◽  
S. Bowser ◽  
R. Nowogrodzki ◽  
K. Ross ◽  
G. Sluder
Keyword(s):  
Small Sample Size ◽  
Small Sample ◽  
Meiotic Spindle ◽  
Serial Sections ◽  
Mitotic Apparatus ◽  
Thin Sections ◽  
Cell Cycles ◽  
Ultrastructural Studies

Eggs have long been a favorite material for studying the mechanism of karyokinesis in-vivo and in-vitro. They can be obtained in great numbers and, when fertilized, divide synchronously over many cell cycles. However, they are not considered to be a practical system for ultrastructural studies on the mitotic apparatus (MA) for several reasons, the most obvious of which is that sectioning them is a formidable task: over 1000 ultra-thin sections need to be cut from a single 80-100 μm diameter egg and of these sections only a small percentage will contain the area or structure of interest. Thus it is difficult and time consuming to obtain reliable ultrastructural data concerning the MA of eggs; and when it is obtained it is necessarily based on a small sample size.We have recently developed a procedure which will facilitate many studies concerned with the ultrastructure of the MA in eggs. It is based on the availability of biological HVEM's and on the observation that 0.25 μm thick serial sections can be screened at high resolution for content (after mounting on slot grids and staining with uranyl and lead) by phase contrast light microscopy (LM; Figs 1-2).

Compositional Analysis of III-V Interface Lattice Images

1980 ◽  
Vol 38 ◽  
pp. 318-319
Author(s):  
A. Olsen ◽  
J.C.H. Spence ◽  
P. Petroff
Keyword(s):  
Crystal Structure ◽  
Image Matching ◽  
Compositional Analysis ◽  
Depth Of Field ◽  
Limit Set ◽  
High Contrast ◽  
Resolution Limit ◽  
Fourier Image ◽  
Lattice Images ◽  
True Structure

Since the point resolution of the JEOL 200CX electron microscope is up = 2.6Å it is not possible to obtain a true structure image of any of the III-V or elemental semiconductors with this machine. Since the information resolution limit set by electronic instability (1) u0 = (2/πλΔ)½ = 1.4Å for Δ = 50Å, it is however possible to obtain, by choice of focus and thickness, clear lattice images both resembling (see figure 2(b)), and not resembling, the true crystal structure (see (2) for an example of a Fourier image which is structurally incorrect). The crucial difficulty in using the information between Up and u0 is the fractional accuracy with which Af and Cs must be determined, and these accuracies Δff/4Δf = (2λu2Δf)-1 and ΔCS/CS = (λ3u4Cs)-1 (for a π/4 phase change, Δff the Fourier image period) are strongly dependent on spatial frequency u. Note that ΔCs(up)/Cs ≈ 10%, independent of CS and λ. Note also that the number n of identical high contrast spurious Fourier images within the depth of field Δz = (αu)-1 (α beam divergence) decreases with increasing high voltage, since n = 2Δz/Δff = θ/α = λu/α (θ the scattering angle). Thus image matching becomes easier in semiconductors at higher voltage because there are fewer high contrast identical images in any focal series.

High Spatial Resolution Compositional Analysis at Interfaces

1980 ◽  
Vol 38 ◽  
pp. 356-359
Author(s):  
John B. Vander Sande ◽  
Thomas F. Kelly ◽  
Douglas Imeson
Keyword(s):  
Electron Microscope ◽  
High Spatial Resolution ◽  
Compositional Analysis ◽  
Scanning Transmission Electron Microscope ◽  
Thin Specimen ◽  
X Ray ◽  
Volume Of Interest ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Electron Energy Loss

In the scanning transmission electron microscope (STEM) a fine probe of electrons is scanned across the thin specimen, or the probe is stationarily placed on a volume of interest, and various products of the electron-specimen interaction are then collected and used for image formation or microanalysis. The microanalysis modes usually employed in STEM include, but are not restricted to, energy dispersive X-ray analysis, electron energy loss spectroscopy, and microdiffraction.

Validating the Factor Structure of the Stigma of Suicide Scale–Short Form Spanish Version Among Healthcare Students

Crisis ◽  
2020 ◽  
pp. 1-5
Author(s):  
Ruthmarie Hernández-Torres ◽  
Paola Carminelli-Corretjer ◽  
Nelmit Tollinchi-Natali ◽  
Ernesto Rosario-Hernández ◽  
Yovanska Duarté-Vélez ◽  
...  
Keyword(s):  
Factor Structure ◽  
Structural Equation ◽  
Short Form ◽  
Small Sample Size ◽  
Small Sample ◽  
Spanish Version ◽  
Equation Modeling ◽  
Cross Sectional ◽  
Healthcare Students ◽  
Spanish Speaking

Abstract. Background: Suicide is a leading cause of death among Spanish-speaking individuals. Suicide stigma can be a risk factor for suicide. A widely used measure is the Stigma of Suicide Scale-Short Form (SOSS-SF; Batterham, Calear, & Christensen, 2013 ). Although the SOSS-SF has established psychometric properties and factor structure in other languages and cultural contexts, no evidence is available from Spanish-speaking populations. Aim: This study aims to validate a Spanish translation of the SOSS-SF among a sample of Spanish-speaking healthcare students ( N = 277). Method: We implemented a cross-sectional design with quantitative techniques. Results: Following a structural equation modeling approach, a confirmatory factor analysis (CFA) supported the three-factor model proposed by Batterham and colleagues (2013) . Limitations: The study was limited by the small sample size and recruitment by availability. Conclusion: Findings suggest that the Spanish version of the SOSS-SF is a valid and reliable tool with which to examine suicide stigma among Spanish-speaking populations.

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