Depth Distribution Profiles Research Articles

Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.

We hypothesize that sample species abundance, sequencing depth, and taxonomic relatedness influence the recovery of metagenome-assembled genomes (MAGs). To test this hypothesis, we assessed MAG recovery in three in silico microbial communities composed of 42 species with the same richness but different sample species abundance, sequencing depth, and taxonomic distribution profiles using three different pipelines for MAG recovery. The pipeline developed by Parks and colleagues (8K) generated the highest number of MAGs and the lowest number of true positives per community profile. The pipeline by Karst and colleagues (DT) showed the most accurate results (~ 92%), outperforming the 8K and Multi-Metagenome pipeline (MM) developed by Albertsen and collaborators. Sequencing depth influenced the accurate recovery of genomes when using the 8K and MM, even with contrasting patterns: the MM pipeline recovered more MAGs found in the original communities when employing sequencing depths up to 60 million reads, while the 8K recovered more true positives in communities sequenced above 60 million reads. DT showed the best species recovery from the same genus, even though close-related species have a low recovery rate in all pipelines. Our results highlight that more bins do not translate to the actual community composition and that sequencing depth plays a role in MAG recovery and increased community resolution. Even low MAG recovery error rates can significantly impact biological inferences. Our data indicates that the scientific community should curate their findings from MAG recovery, especially when asserting novel species or metabolic traits.

Исследование структур на основе GaP методом электрохимического вольт-фарадного профилирования

Gallium phosphide substrate structures with different crystallographic orientation and degree of doping have been studied by means of electrochemical capacitance-voltage (ECV) profiling. A brief description of the ECV profiling as well as its advantages over the conventional capacitance-voltage technique are given. The ECV measurement modes for GaP structures has been worked out, and the necessary electrolyte meets the requirement of polishing character during etching the samples has been selected. During the experiment, the current-voltage and capacitance-voltage characteristics were measured, by which the type of conductivity for each of the samples was determined. Depth distribution profiles of majority charge carrier concentration were obtained. The doping uniformity of samples with p- and n-type impurities is shown up to a depth of 1 μm.

The influence of implantation of Mg+ ions and subsequent annealing on the composition, electronic structures, emission and optical properties of CdF2

Relevance. In the case of bombardment with Mg metal ions, the changes are accompanied by the introduction of metal atoms and the formation of various types of compounds. Thus, CdF2 is intensively decomposed into components in the near-surface layer in the process of ion implantation. A small part of these components can be sprayed from the surface. Due to the high chemical activity, almost all of the liberated fluorine atoms again enter into a chemical bond with both the atoms of the alloying element and the atoms of cadmium. Consequently, three-component compounds are formed in the near-surface layer. Therefore, it is necessary to define the electronic states, band energy, and optical parameters of CdF2 and Cd0.6Mg0.4F2 films. Purpose. The composition, structure, and properties of CdF2 implanted with Mg+ ions in combination with thermal and laser annealing for the first time were the research aims. Methodology. The experimental studies were carried out at a vacuum of at least 10-7 Pa using the methods of Auger electron spectroscopy (AES) and ultraviolet photoelectron spectroscopy (UVES). The depth distribution profiles of atoms were determined by the AES method in combination with layer-by-layer etching of the surface with Ar+ ions with E0=2-3 keV. Results. CdF2 is intensively decomposed into components in the near-surface layer in the process of ion implantation. Consequently, three-component compounds are formed in the near-surface layer. Band-energy parameters and densities of the state of electrons in the valence band of this film are determined. Conclusions. The effect of the implantation of Mg+ ions on the composition and electronic structure of single-crystal CdF2/Si(III) films was studied for the first time. The densities of electronic states, band-energy and optical parameters of CdF2 and Cd0.6Mg0.4F2 films have been determined

A high sensitivity microbeam RBS setup for heavy elements implantation profiles analysis

This work presents a new setup that integrates heavy ion RBS with microbeam technology combined with high detection solid angle for the measurement of the depth profile and areal distribution of heavy elements in silicon using a Si microbeam. Focussed 2.4 MeV Si2+ ions were scanned over the frontal or lateral surface of silicon wafers to measure both the areal concentrations and depth profiles of all elements heavier than silicon. Tests were done on samples with Pt concentration range of 4 × 10 12–2 × 10 14 at/cm 3 that was diffused via the Pt-Silicide surface layer process from one lateral surface into the 400 µm thick Si wafers. It is important to note that employing a Si ion beam instead of the conventional He ion beam serves the purpose of not only increasing the backscattering cross section, as in well-established heavy element RBS, but also reducing pileup by eliminating scattering from the Si substrate, which is essential for sensitive analysis. This allows a significant increase in microbeam currents without increasing the count rate in large area detectors. A set of two large area PIN diodes (10x10 mm) were used in an optimized configuration resulting in 1,04 sr detection solid angle. Additionally, an appropriate microbeam collimator was used to shield the PIN diodes from events caused by forward scattering and scattering of the Si ion beam halo from different components in the reaction chamber. Lateral scans of the silicon wafer were performed by focussed Si ions, with ∼10 µm spot size and of the nA range beam currents. The RBS intensity maps containing the Pt depth profile were obtained with a sensitivity of 6.7 × 109 at/cm2.

Experimental and model study of LIBS depth profile for multilayer deposition materials

The patterns of erosion and deposition occurred in the plasma-facing materials (PFMs) of a magnetic confinement fusion device are crucial for the investigation of plasma-wall interaction (PWI). The deposition behavior can be identified by the elemental depth profile of the deposition layer. As an effective remote monitoring method for the wall in nuclear fusion devices, laser-induced breakdown spectroscopy (LIBS) shows excellent potential for the depth profiling of the deposition layer on the PFMs. However, some potentially influencing factors lead to the difficulty of distinguishing and identifying the interfaces between the deposition layers and substrate. The measuring accuracy of the deposition layer thickness plays an essential role in PWI research. In this paper, depth profiling of multilayer samples with Ni layers on Cu were performed using LIBS with an ns-pulse laser. The experiment was carried out under 5 × 10−5 mbar to simulate the operation of a nuclear fusion device. Meanwhile, a two-dimensional model for multi-pulse LIBS depth analysis based on the laser beam profile factor and interface roughness factor was established to reconstruct and predict the elemental depth profile distribution of NiCu multilayer materials. The correlation coefficients between the experimental and modeling data were all >0.99. We introduced a locating approach for the interface based on model prediction, and the relative errors of all Ni layer thicknesses were < 5.1%, demonstrating the feasibility and accuracy of the model. All the results show that the two-dimensional numerical model can improve the accuracy of LIBS depth profile on layer thickness analysis and further promote the application of in situ LIBS diagnosis in PWI research.

Alleviating Defect and Oxidation in Tin Perovskite Solar Cells Using a Bidentate Ligand

Tin-perovskite solar cells (Sn-PSCs) have low energy conversion efficiency and stability due to facile oxidation of Sn2+ during precursor solution preparation and film growth. Herein, we introduced formohydrazide (FHZ) as a bidentate ligand into the Sn-halide perovskite (Sn-HaP) to improve the optoelectronic properties. This approach is found to be effective for the suppression of Sn-oxidation and interfacial energy band modulation. The depth profile distribution confirmed that the FHZ additive is primarily located on surfaces and the hole transport layer (HTL)/Sn-HaP interface with partly capping at the grain boundaries, which offers a reducing ambient in the Sn-HaP film. Therefore, the device with FHZ demonstrated a device efficiency of 12.87% (9.93% control) with enhanced open circuit voltage from ∼0.734 to 0.874 V and improved operational device stability. The device analysis suggests that the FHZ additive alleviates the bulk and interface defect in the Sn-PSC with −NH2 and −O═C bidentate bonding to Sn-HaP, which is supported by theoretical calculations. Thus, this work corroborates the importance of multidentate ligands for modulating the film morphology and defect chemistry in the Sn-perovskite for high efficiency and superior device stability.

О РАСЧЕТЕ РАДИОЯРКОСТНОЙ ТЕМПЕРАТУРЫ ГРУНТА ЛУНЫ

Microwave radiometers have proven to be useful tools for studying the thermal regime of the atmosphere and the Earth's surface. Similar devices were recommended for inclusion in the composition of scientific radio equipment designed to study other bodies of the solar system, in particular the moon. The degree of understanding of the physical foundations of the experiments and the accuracy of their theoretical description is the coincidence of the results of measurements and numerical simulation of radio brightness temperature. The paper discusses the mechanism for calculating this value, deriving a recurrent formula convenient for calculating the radio brightness temperature from the Moon's soil. The algorithm is built for flat-layered soil. The depth distribution profile of physical temperature and complex permittivity for this problem are a priori information.

Pd-Fe alloy film with high magnetic gradient: structural and magnetic properties

An epitaxial film of the Pd-Fe alloy 116 nm thick with an iron concentration varying in depth from 2 at.% to 50 at.% has been synthesized. An experimental depth distribution profile of iron was obtained as a result of stepwise etching of the film surface with Ar+ ions. Profiling has shown that, as a result of annealing, the impurity was redistributed in the film, and a layer of the L10-phase with a constant concentration was formed near the film surface. After removal of the L10-phase, the film exhibits &amp;quot;easy-plane&amp;quot; anisotropy. The study of spin-wave resonance spectra showed the presence of several modes of standing spin waves, the number of which depends on the residual film thickness. Keywords: graded magnetic materials, molecular beam epitaxy, palladium-iron alloys, X-ray diffraction, spin-wave resonance.

Пленка сплава Pd-Fe с большим градиентом магнитной примеси: структурные и магнитные свойства

An epitaxial film of the Pd-Fe alloy 116 nm thick with an iron concentration varying in depth from 2 at.% to 50 at.% has been synthesized. An experimental depth distribution profile of iron was obtained as a result of stepwise etching of the film surface with Ar+ ions. Profiling showed that, as a result of annealing, the impurity was redistributed in the film, and a layer of the L10-phase with a constant concentration was formed near the film surface. After removal of the L10-phase, the film exhibits easy-plane anisotropy. The study of spin-wave resonance spectra showed the presence of several modes of standing spin waves, the number of which depends on the residual film thickness.

Determination of nuclear graphite impurities by prompt gamma activation analysis to support decommissioning operations

Elemental composition of non-irradiated nuclear grade graphite was determined by Prompt Gamma Activation Analysis (PGAA) to quantitively assess some neutron activation precursors. The knowledge of these data is paramount for an accurate radiological characterization of the material before decommissioning of graphite-moderated nuclear reactors. Bulk results of most of the nuclides were consistent with benchmark Inductively Coupled Plasma–Mass Spectrometry (ICP-MS) and literature data. In the case of 14N and 35Cl, depth distribution profiles were observed and quantified for the first time. These outcomes could shine a light on 14C and 36Cl depth distribution profiles and fractional release during leaching experiments.

Assessment of erosion rate in a rainfed agricultural area on the Northwestern coast of Egypt using 137Cs measurements

In the present work, the use of the fallout radionuclide 137Cs as a tracer for estimating soil redistribution rates over the past 60 years was tested in Egypt at an agricultural field with a smooth slope (0–10%) located in Ras El-Hekma on the Northwestern coast. The average annual soil erosion rate was derived from 137Cs inventories (Bq m−2) and by using the conversion Diffusion and Migration Model (DMM). The activity concentrations of 137Cs with uncertainty ranging between 7.5 and 20.9% were measured using HPGe gamma spectrometry. Approximately exponential shape for the distribution of 137Cs activity concentration was observed within the upper 20 cm of the soil profile associated with the reference site while for the study sites, the 137Cs depth distribution profiles indicate generally an increase of activity reaching a maximum peak of 137Cs usually at a depth of 10–15 cm followed by an abrupt exponential decrease of 137Cs activity concentration with depth. The measured average reference inventory for this area was 697 Bq m−2 with a coefficient of variation of 23%. This value is close to the estimated reference inventory using the conversion model, which was 744 Bq m−2. Transect sampling strategy was adopted at the study area where three parallel transects were chosen based on the common slope. The estimated average annual erosion rate for the three transects was found to be 7.5 t ha−1 y−1, and sediment delivery ratio was approximately 98%, which shows the moderate vulnerability of the Ras El-Hekma area to water erosion.

Rare earth element and neodymium isotopes of the eastern US GEOTRACES Equatorial Pacific Zonal Transect (GP16)

Dissolved rare earth element ([REE]) and neodymium isotopic (εNd) data from the US GEOTRACES Eastern Equatorial Pacific Transect (EPZT) are presented. These data are compared to watermass distributions (Peters et al., 2018), particulate data (Lam et al., 2018) and carbonate species data (Bates, 2018) to evaluate present theories of REE and εNd geochemistry, given that the Pacific has been notably intractable in relation to these ideas (Jones et al., 2008). The [REEs] have typical depth profile distributions (e.g., [La] ranges from ∼5 to 15 pmol/kg in the surface, increasing with depth to values of ∼40 pmol/kg), as does εNd (ranging from ∼-1 to -6 εNd; similar to previous Pacific data). However, despite the unsurprising nature of these data, several apparent inconsistencies with respect to current models for REE/εNd geochemistry arise. These are: (1) While εNd remarkably maintains watermass distribution information, there is a significant (+1.4 εNd) offset in the data compared to published end-member compositions, indicating a strong but largely consistent non-conservative component; (2) Reversible scavenging seems an unlikely mechanism for redistribution of [REE] and εNd in the water column; (3) There does not appear to be any correlation of [REE] to carbonate ion concentration, and; (4) There are indications of influence from a benthic flux, but the evidence is ambiguous.

Investigation of the effects on dose calculations of correction-based algorithms in different tissue medium

The aim of this study is to determine the effects of correction-based algorithms on dose distributions in the inhomogeneous medium and dosimetric parameters depending on the algorithms preferred in breast and lung treatment plans. In the treatment planning system (TPS) in which the Pencil Beam Convolution (PBC) dose calculation algorithm is used, dose calculations were performed in different correction-based algorithms Modified Batho and Equivalent Tissue-Air Ratio (ETAR) for soft tissue, bone and air medium. Rectilinear virtual phantoms were created in TPS for soft tissue, bone and air materials, and deep dose values and dose distribution profiles at lateral depth were obtained. Intensity modulated radiotherapy (IMRT) treatment planning technique was applied to 20 patients with breast and lung cancer diagnosis on computed tomography (CT) sections, and dose calculations were performed. Different dosimetric parameters obtained within the target volume were calculated. Although the effects of correction-based algorithms on dose values depending on the depth and dose distribution profiles in lateral depth were calculated below 1% in dose calculations performed on soft tissue virtual phantom, dose profiles were obtained as approximately 20% in bone and air medium. It was concluded that correction-based algorithms in the different inhomogeneous mediums have a significant effect on the dose values calculated in TPS.

Impacts of oak deforestation and rainfed cultivation on soil redistribution processes across hillslopes using 137Cs techniques

BackgroundAs one of the main components of land-use change, deforestation is considered the greatest threat to global environmental diversity with possible irreversible environmental consequences. Specifically, one example could be the impacts of land-use changes from oak forests into agricultural ecosystems, which may have detrimental impacts on soil mobilization across hillslopes. However, to date, scarce studies are assessing these impacts at different slope positions and soil depths, shedding light on key geomorphological processes.MethodsIn this research, the Caesium-137 (137Cs) technique was applied to evaluate soil redistribution and soil erosion rates due to the effects of these above-mentioned land-use changes. To achieve this goal, we select a representative area in the Lordegan district, central Iran. 137Cs depth distribution profiles were established in four different hillslope positions after converting natural oak forests to rainfed farming. In each hillslope, soil samples from three depths (0–10, 10–20, and 20–50 cm) and in four different slope positions (summit, shoulder, backslope, and footslope) were taken in three transects of about 20 m away from each other. The activity of 137Cs was determined in all the soil samples (72 soil samples) by a gamma spectrometer. In addition, some physicochemical properties and the magnetic susceptibility (MS) of soil samples were measured.ResultsErosion rates reached 51.1 t·ha− 1·yr− 1 in rainfed farming, whereas in the natural forest, the erosion rate was 9.3 t·ha− 1·yr− 1. Magnetic susceptibility was considerably lower in the cultivated land (χhf = 43.5 × 10− 8 m3·kg− 1) than in the natural forest (χhf = 55.1 × 10− 8 m3·kg− 1). The lower soil erosion rate in the natural forest land indicated significantly higher MS in all landform positions except at the summit one, compared to that in the rainfed farming land. The shoulder and summit positions were the most erodible hillslope positions in the natural forest and rainfed farming, respectively.ConclusionsWe concluded that land-use change and hillslope positions played a key role in eroding the surface soils in this area. Moreover, land management can influence soil erosion intensity and may both mitigate and amplify soil loss.

Soil organic carbon fractions in the Great Plains of the United States: an application of mid-infrared spectroscopy

Spectroscopy is a powerful means of increasing the availability of soil data necessary for understanding carbon cycling in a changing world. Here, we develop a calibration transfer methodology to appropriately apply an existing mid infrared (MIR) spectral library with analyte data on the distribution of soil organic carbon (SOC) into particulate (POC), mineral-associated (MAOC), and pyrogenic (PyC) forms to nearly 8000 soil samples collected in the Great Plains ecoregion of the United States. We then use this SOC fraction database in combination with a machine learning-based predictive soil mapping approach to explore the controls on the distribution of fractions through soil profiles and across the region. The relative abundance of each fraction had unique depth distribution profiles with POC fraction dropping exponentially with depth, the MAOC fraction having a broad distribution with a maxima at 35–50 cm, and the PyC fraction showed a slight subsurface maxima (10–20 cm) and then a steady decline with increasing depth. Within the Great Plains ecoregion, clay content was a strong control on the total amount and relative proportion of each fraction in both the surface and subsoil horizons. Sandy soils and soils in cool semi-arid regions contained significantly more POC relative to the MAOC and PyC fractions. Cultivated soils had significantly less SOC than grassland soils with losses following a predictable pattern: POC > MAOC ≫ PyC. This SOC fraction database and resulting maps can now form the basis for improved representation of SOC dynamics in biogeochemical models.

Integration of electrochemical capacitance–voltage characteristics: a new procedure for obtaining free charge carrier depth distribution profiles with high resolution

A novel electrochemical profiling technique consisting in integration capacitance–voltage characteristics was proposed, developed and proven. The aim is to overcome the insufficient resolution in charge carrier concentration measurements during commonly used electrochemical capacitance–voltage profiling. This is very actual task for modern low-dimensional optoelectronics. According to the introduced “profiling window”, after each etching step the coordinate interval is selected, the concentration distribution in which is to be matched itself and by the first derivative at the edges with the concentration in adjacent intervals. To achieve these conditions the minimum dissipation factor should be maintained for each C–V characteristic at the corresponding etching depth. The method allows both to obtain general free charge carrier concentration depth distribution over unlimited structure depth and to achieve necessary resolution in key regions, even if they are lying at a high depth. Particularly, in GaAs-based heterostructure concentration profile of deep-lying quantum well and a delta layer (ultra-thin (2 nm) profile of dopant with extremely high concentration) were confidently distinguished with magnitude difference of 20% in the dip region in between. Besides, we have shown how quantum-confined objects of different origins give different concentration responses when electrochemical capacitance–voltage profiling with sequential etching. An explanation for this dissimilarity is given.

Irradiation induced elongation of Fe nanoparticles embedded in silica films

ABSTRACT Irradiation with swift heavy ions causes the deformation of Ferric nanoparticles in direction of the ion beam. Fe nanoparticles with mean diameter of about 20 nm were prepared by gas flow sputtering and subsequently confined within silica films. Two silica films wherein two different densities of Fe nanoparticles are encapsulated were irradiated with 50 MeV Ag ions with fluences of few 1014 ions.cm−2 at 300 K and normal incidence. Transmission electron microscopy analysis shows that the spherical Fe nanoparticles are deformed into prolate nanorods aligned in direction of the incident ion beam. The depth distribution profiles of irradiated particles reveal the presence of a critical fluence above which the elongation kinetics becomes dependent on the nanoparticles density. Analysis indicates that for the lower density particles, a saturation length is reached under irradiation to fluence between 3–4 × 1014 ions.cm−2. However, for the higher density, collective growth into aligned nanowires is presumed to take place. Hysteresis curves of the saturation magnetization and coercivity indicate an increasing magnetic anisotropy, which can be correlated with the deformation of nanoparticles in the direction of the ion beam.

Quantification of Chlorosomal Bacteriochlorophylls Using Absorption Spectra of Green Sulfur Bacteria in Natural Water

A non-extraction method for determining the concentration of chlorosomal bacteriochlorophylls (Bchl), photosynthetic pigments of green sulfur bacteria has been developed and tested. The method is based on the measurement of optical density spectra of microorganisms directly in natural water and is aimed at simplifying Bchl concentration measurements, reducing the measurement time and eliminating toxic solvents from the experiments. Comparison of the results of Bchl concentration determination by the traditional method based on the measurement of absorption spectra of pigment extracts and the new method that is based on the measurement of long wavelength absorption band of Bchl in bacterial cells in natural water showed a high correlation coefficient from 0.9866 to 0.9991 for different series of samples. The depth distribution profiles of Bchl concentration obtained from the absorption spectra of natural water in some meromictic reservoirs of the White Sea region in September 2019 and Lake Mogilnoye (Barents Sea) in June 2019 are presented.

Representation and illustration of the initial parameters in GATE 8.1 monte carlo simulation of an Elekta Versa-HD linear accelerator

The purpose of this study is to validate GATE 8.1 Radiotherapy Monte Carlo (MC) simulation of a 6 MV Elekta Versa-HD linear accelerator at King Abdulaziz University Hospital (KAUH). The simulation data using GATE 8.1 was benchmarked against measured data at KAUH. The simulation comprises treatment head, Multi-Leaf Collimators (MLCs), and homogeneous water phantom, whereas the measured data was performed using MP3 phantom and PTW 31,010, 0.125 cm3 Semiflex Chamber. Dose depth distribution and dose profiles were carried out at three different field sizes 10x10, 20x20, and 30 × 30 cm2. The calculated TPR20,10 for the simulated data was found to be 0.658, 1.1% less than the measured TPR20,10 which was found to be 0.666. The obtained results indicate good agreement between the simulated and measured data, where Gamma Index 3%/3 mm criteria reached values of 97% and 90% for relative dose and dose profiles, respectively.

Depthprofile distribution of Cs and its toxicity for canola plants grown on arid rainfed soils as affected by increasing K-inputs

Radioactive cesium (Cs) is more likely to be trans-located via rainfall into surrounding environments. Upon Cs-contaminated water reaching soil, Cs is retained on soil components, mainly organic matter and clay fraction. This study aims are i) comparing the relative ability of five arid soils, differing in their textural and chemical properties, to accumulate Cs when subjected to Cs-artificially contaminated rain droplets and ii) testing whether K fertilizer can decrease the uptake of Cs and its translocation within plants or not. A lab experiment was then conducted to simulate artificial rain droplets contaminated with 1000 becquerel (Bq) of 134Cs L−1 precipitated on soil columns each of 10.5 cm inner diameter at a rate of 1.15 mL cm−2 over a period of 2-months. At least 89% of 134Cs accumulated within the uppermost 5-cm layer of these soils. Another greenhouse experiment was set to test the hypothesis which indicates that Cs uptake increases unexpectedly by supplying plants with K-fertilizers. In this experiment, canola (Brassica napus L.) seeds were cultivated into three K-deficient soils (Typic Haplotorrent, Typic Haplocalcid, and Typic Torripsamment) which were contaminated with 100 mg Cs kg−1 soil (stable-Cs was used instead of radioactive-Cs to designate its behavior on the long run). Canola plants were fertilized with 0, 80 and 120 mg K2SO4 kg−1 soil. Results carried on Typic Haplotorrent soil confirmed the aforementioned assumption as K-addition increased Cd-uptake up to 40.1%. Contradictory results were achieved in the other two soils where Cs-uptake decreased by 21.5 and 15.3% in Typic Haplocalcid and Typic Torripsamment soils, respectively due to the application of the aforementioned dose of K. In the K non-amended soils, Cs shoot-root translocation factor was >1; yet, it was <1 in response to K addition, regardless of its application rate.