Hot Spot Position Research Articles

Effects of soil moisture content on reflectance anisotropy — Laboratory goniometer measurements and RPV model inversions

Abstract Optical methods to study soil moisture content (SMC) are often based on empirically or physically based models that relate changes in reflectance intensity to SMC. The effects of SMC on the reflectance anisotropy, however, have not received much attention. In this paper the effects of SMC on the anisotropic reflectance behaviour of soils were studied. Biconical reflectance factors (BCRFs) of five different soil samples were acquired at 60 positions covering the full hemisphere in the optical domain at different SMC levels using Wageningen University's laboratory goniometer facility. In addition, we inverted the Rahman–Pinty–Verstraete (RPV) model against the measured BCRFs in the principal plane. The results show that the anisotropic reflectance behaviour of soils is strongly influenced by the SMC. Dry soils displayed strong backward scattering behaviour, with a maximum reflectance close to the hotspot position. An increase of the SMC level up to the soil's saturation point caused the soils to scatter more in the forward direction and induced a weakening of the hotspot effect. Oversaturated soils displayed a strong sun-glint-like reflectance peak in the anti-solar direction. The RPV model fitted the measured BCRFs in the principal plane up to saturated SMC levels in general with an R 2 > 0.9. It was not possible to fit the model through observations of oversaturated soils, since the RPV model is not capable of simulating specular reflectance. The asymmetry parameter ( Θ ) of the RPV model, which controls the proportion of forward and backward scattering, showed a strong correlation to SMC for individual samples. This correlation remained significant when we considered all samples together with a maximum R 2 of 0.797 at 2123 nm, indicating that reflectance anisotropy contained information on the water content of soils. The amplitude parameter ( ρ 0 ), which is closely related to the reflectance intensity, only had a maximum R 2 of 0.622 at 1921 nm. This indicated that reflectance anisotropy contained more information on SMC than the level of spectral reflectance as such.

Effects of magnetron arrangement and power combination on temperature field uniformity of microwave drying of carrot

ABSTRACTThe effects of magnetron arrangement and power combination on the temperature field uniformity of microwave (MW) drying of carrot were investigated in this study. Using one magnetron resulted in poor temperature field uniformity. However, when two magnetrons were applied, the Td (temperature dispersion between the maximum temperature value and the minimum temperature value among detectors) at different hot spots was lower than that obtained for the single magnetron. Td was 3–10°C when a combination of three magnetrons (α, β, and γ) was used at powers of 400, 500, and 600 W (except for the hot spot of “the highest temperature point”). This method of infrared temperature control-intermittent MW heating could reduce Td significantly in different hot spot positions and improve the uniformity of the temperature field.

Influence of the local heating position on the terahertz emission power from high-Tc superconducting Bi2Sr2CaCu2O8+δ mesas

Simultaneous measurements of spectroscopic terahertz emissions from and SiC photoluminescent local temperature T(r) distributions of high transition temperature Tc superconducting Bi2Sr2CaCu2O8+δ rectangular mesa devices were made. A local region with T(r) > Tc known as a hot spot can emerge with current bias changes. When the hot spot position was moved to a mesa end by locally heating the mesa surface with a laser beam, the intensity of the emission increased, but no changes to its frequency or line width were observed. These results suggest that higher power radiation is attainable by adjusting the hot spot position.

The mutational pattern of primary lymphoma of the central nervous system determined by whole-exome sequencing.

To decipher the mutational pattern of primary CNS lymphoma (PCNSL), we performed whole-exome sequencing to a median coverage of 103 × followed by mutation verification in 9 PCNSL and validation using Sanger sequencing in 22 PCNSL. We identified a median of 202 (range: 139-251) potentially somatic single nucleotide variants (SNV) and 14 small indels (range: 7-22) with potentially protein-changing features per PCNSL. Mutations affected the B-cell receptor, toll-like receptor, and NF-κB and genes involved in chromatin structure and modifications, cell-cycle regulation, and immune recognition. A median of 22.2% (range: 20.0-24.7%) of somatic SNVs in 9 PCNSL overlaps with the RGYW motif targeted by somatic hypermutation (SHM); a median of 7.9% (range: 6.2-12.6%) affects its hotspot position suggesting a major impact of SHM on PCNSL pathogenesis. In addition to the well-known targets of aberrant SHM (aSHM) (PIM1), our data suggest new targets of aSHM (KLHL14, OSBPL10, and SUSD2). Among the four most frequently mutated genes was ODZ4 showing protein-changing mutations in 4/9 PCNSL. Together with mutations affecting CSMD2, CSMD3, and PTPRD, these findings may suggest that alterations in genes having a role in CNS development may facilitate diffuse large B-cell lymphoma manifestation in the CNS. This may point to intriguing mechanisms of CNS tropism in PCNSL.

Recombination in the human Pseudoautosomal region PAR1.

The pseudoautosomal region (PAR) is a short region of homology between the mammalian X and Y chromosomes, which has undergone rapid evolution. A crossover in the PAR is essential for the proper disjunction of X and Y chromosomes in male meiosis, and PAR deletion results in male sterility. This leads the human PAR with the obligatory crossover, PAR1, to having an exceptionally high male crossover rate, which is 17-fold higher than the genome-wide average. However, the mechanism by which this obligatory crossover occurs remains unknown, as does the fine-scale positioning of crossovers across this region. Recent research in mice has suggested that crossovers in PAR may be mediated independently of the protein PRDM9, which localises virtually all crossovers in the autosomes. To investigate recombination in this region, we construct the most fine-scale genetic map containing directly observed crossovers to date using African-American pedigrees. We leverage recombination rates inferred from the breakdown of linkage disequilibrium in human populations and investigate the signatures of DNA evolution due to recombination. Further, we identify direct PRDM9 binding sites using ChIP-seq in human cells. Using these independent lines of evidence, we show that, in contrast with mouse, PRDM9 does localise peaks of recombination in the human PAR1. We find that recombination is a far more rapid and intense driver of sequence evolution in PAR1 than it is on the autosomes. We also show that PAR1 hotspot activities differ significantly among human populations. Finally, we find evidence that PAR1 hotspot positions have changed between human and chimpanzee, with no evidence of sharing among the hottest hotspots. We anticipate that the genetic maps built and validated in this work will aid research on this vital and fascinating region of the genome.

Spectral investigation of hot spot and cavity resonance effects on the terahertz radiation from high-Tc superconducting Bi2Sr2CaCu2O8+δ mesas

Terahertz (THz) electromagnetic radiation emitted from single and series-connected rectangular mesa devices of high-Tc superconducting Bi2Sr2CaCu2O8+δ is investigated spectroscopically during simultaneous temperature distribution observations using a microcrystalline SiC photoluminescence technique. In single mesas, a hot-spot region with its temperature T locally exceeding Tc was observed to jump suddenly in position under small current I-bias changes. Although these hot-spot position jumps cause large changes in the output power with small changes in I, as long as the voltage V per junction number N is kept constant, they do not affect the output frequency f, which is given by the ac Josephson frequency fJ. f can lock onto that of a particular mesa cavity resonance frequency fc, which enhances the emission power and serves as the primary mechanism for the synchronization of the emissions from each of the intrinsic Josephson junctions in the mesa.

Systematic Analysis of Large Enzyme Families: Identification of Specificity‐ and Selectivity‐Determining Hotspots

AbstractA general strategy is described that integrates data mining of enzyme families and molecular modeling of enzyme–substrate interactions to identify selectivity hotspots and to design focused variant libraries for changed regio‐ and stereoselectivity. This strategy is demonstrated for two case studies; the design of cytochrome P450 monooxygenases with improved regioselectivity and of thiamine diphosphate dependent enzymes with improved stereoselectivity. In both families, two selectivity hotspots are found in almost all sequences, and simple, generic rules are established to predict the effect of mutations at these positions on selectivity. The crucial role of the hotspot positions is validated for an increasing number of enzymes by designing variants with improved or switched selectivity.

Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences

BackgroundCoalescent simulation is pivotal for understanding population evolutionary models and demographic histories, as well as for developing novel analytical methods for genetic association studies for DNA sequence data. A plethora of coalescent simulators are developed, but selecting the most appropriate program remains challenging.ResultsWe extensively compared performances of five widely used coalescent simulators – Hudson’s ms, msHOT, MaCS, Simcoal2, and fastsimcoal, to provide a practical guide considering three crucial factors, 1) speed, 2) scalability and 3) recombination hotspot position and intensity accuracy. Although ms represents a popular standard coalescent simulator, it lacks the ability to simulate sequences with recombination hotspots. An extended program msHOT has compensated for the deficiency of ms by incorporating recombination hotspots and gene conversion events at arbitrarily chosen locations and intensities, but remains limited in simulating long stretches of DNA sequences. Simcoal2, based on a discrete generation-by-generation approach, could simulate more complex demographic scenarios, but runs comparatively slow. MaCS and fastsimcoal, both built on fast, modified sequential Markov coalescent algorithms to approximate standard coalescent, are much more efficient whilst keeping salient features of msHOT and Simcoal2, respectively. Our simulations demonstrate that they are more advantageous over other programs for a spectrum of evolutionary models. To validate recombination hotspots, LDhat 2.2 rhomap package, sequenceLDhot and Haploview were compared for hotspot detection, and sequenceLDhot exhibited the best performance based on both real and simulated data.ConclusionsWhile ms remains an excellent choice for general coalescent simulations of DNA sequences, MaCS and fastsimcoal are much more scalable and flexible in simulating a variety of demographic events under different recombination hotspot models. Furthermore, sequenceLDhot appears to give the most optimal performance in detecting and validating cross-over hotspots.

Computational tools for designing smart libraries.

Traditional directed evolution experiments are often time-, labor- and cost-intensive because they involve repeated rounds of random mutagenesis and the selection or screening of large mutant libraries. The efficiency of directed evolution experiments can be significantly improved by targeting mutagenesis to a limited number of hot-spot positions and/or selecting a limited set of substitutions. The design of such "smart" libraries can be greatly facilitated by in silico analyses and predictions. Here we provide an overview of computational tools applicable for (a) the identification of hot-spots for engineering enzyme properties, and (b) the evaluation of predicted hot-spots and selection of suitable amino acids for substitutions. The selected tools do not require any specific expertise and can easily be implemented by the wider scientific community.

Probing the Location of Hot Spots by Surface-Enhanced Raman Spectroscopy: Toward Uniform Substrates

Wide applications of surface plasmon resonance rely on the in-depth understanding of the near-field distribution over a metallic nanostructure. However, precisely locating the strongest electric field in a metallic nanostructure still remains a great challenge in experiments because the field strength decays exponentially from the surface. Here, we demonstrate that the hot spot position for gold nanoparticles over a metal film can be precisely located using surface-enhanced Raman spectroscopy (SERS) by rationally choosing the probe molecules and excitation wavelengths. The finite difference time domain simulation verifies the experimental results and further reveals that the enhancement for the above system is sensitive to the distance between nanoparticles and the metal film but insensitive to the distance of nanoparticles. On the basis of this finding, we propose and demonstrate an approach of using a nanoparticles-on-metal film substrate as a uniform SERS substrate. This work provides a convenient way to probe the location of strong near-field enhancement with SERS and will have important implications in both surface analysis and surface plasmonics.

Plasmonic Nanoclusters with Rotational Symmetry: Polarization-Invariant Far-Field Response vs Changing Near-Field Distribution

Flexible control over the near- and far-field properties of plasmonic nanostructures is important for many potential applications, such as surface-enhanced Raman scattering and biosensing. Generally, any change in the polarization of the incident light leads to a change in the nanoparticle's near-field distribution and, consequently, in its far-field properties as well. Therefore, producing polarization-invariant optical responses in the far field from a changing near field remains a challenging issue. In this paper, we probe experimentally the optical properties of cruciform pentamer structures--as an example of plasmonic oligomers--and demonstrate that they exhibit such behavior due to their symmetric geometrical arrangement. We demonstrate direct control over hot spot positions in sub-20 nm gaps, between disks of 145 nm diameter at a wavelength of 850 nm, by means of scattering scanning near-field optical microscopy. In addition, we employ the coupled dipole approximation method to define a qualitative model revealing the relationship between the near and far field in such structures. The near-field profiles depend on particular mode superpositions excited by the incident field and, thus, are expected to vary with the polarization. Consequently, we prove analytically that the far-field optical properties of pentamers have to be polarization-independent due to their rotational symmetry.

Failure assessment diagrams for circular hollow section X- and K-joints

This paper reports the failure assessment curves for semi-elliptical surface cracks located at hot-spot positions in the circular hollow section X- and K-joints. The failure assessment curves derive from the square root of the ratio between the linear–elastic and the elastic–plastic energy release rates, computed from the domain-integral approach. This study examines both the material and geometric dependence of the failure assessment curves. The area reduction factor, used in defining the strength of the cracked joints, imposes a significant effect on the computed failure assessment curve. The failure assessment curves indicate negligible variations with respect to the crack-front locations and the material yield strength. The crack depth ratio exerts a stronger effect on the computed failure assessment curve than does the crack aspect ratio. This study proposes a parametric expression for the failure assessment curves based on the geometric parameters for surface cracks in circular hollow section X- and K-joints.

Templated silver nanocube arrays for single-molecule SERS detection

We describe the self-assembly of silver nanocubes (AgNC) into dense bowl-shaped arrays using a template made from polystyrene nanospheres (PSNS). Interestingly, we found that most AgNCs were arranged facet-to-facet. When used as substrates for surface-enhanced Raman scattering (SERS), we observed that the SERS hot spot positions were located at the corners of the cubes. This was confirmed using the formation of a self-assembled monolayer (SAM) of 1-dodecanethiol (DDT) covering the cubes' facet surface, whilst the pinholes in the DDT SAM at the corners were subsequently filled with 2-mercaptopyridine (MPy). Due to the high enhancement from the densely arranged AgNCs, single molecule detection was achieved from this SERS substrate and evidenced using the bi-analyte Raman technique.

“Digitally” Addressable Focusing of Light into a Subwavelength Hot Spot

We show that a plasmonic metamaterial can act as a far-field to near-field transformer that focuses a free-space beam of light into a subwavelength energy hot spot at a prescribed location with a spot size only a small fraction of the wavelength. The hot spot position on the metamaterial can be prescribed and moved at will from one metamolecule of the array to another in a "digital" fashion simply by modulating the input phase profile, thus providing new opportunities for imaging and optical data processing.

Thermal distribution monitoring of the container data center by a fast infrared image fusion technique

This paper develops a thermal distribution monitoring (TDM) method for a container data center (CDC). First, the image is divided into hot and non-hot regions and their corner and edge features are extracted. Then, the regions that are blended by fast infrared image fusion (FIIF) technique, named as hot spot fusion; otherwise, non-hot spot fusion. In the experiments, the study tests seven benchmarks from Octets, SPi Corporation, and Kimura’s literature. The results show the proposed method achieves good performance for recognizing physical position of hot spots. We also test five actual Inventec CDC images which consist of angles from 0 to 45 degree in different field of view (FOV). The method is validated to be applicable to the container data center or ordinary data center with high density of equipment. The experimental results show that the image fusion is efficient to find hot spot position for the management information system (MIS).

Three-dimensional numerical analysis of terahertz radiation emitted from intrinsic Josephson junctions with hot spots

In this study, we numerically investigate the terahertz radiation from mesa-structured intrinsic Josephson junctions (IJJs) using a three-dimensional calculation model. We assume an in-phase mode of the phase differences and calculate electromagnetic fields inside and outside of the IJJs simultaneously. We consider the appearance of a hot spot in the mesa where ${j}_{c}$ locally decreases and investigate the change of the radiation power with varying hot-spot positions. The radiation powers for three different hot-spot positions are calculated as functions of voltage. We observe strong radiation when the ac Josephson frequency satisfies the cavity resonance condition. Transverse-magnetic modes ${\text{TM}}_{m,n}$ whose indices $m$ and $n$ are even appear regardless of the positions of hot spots. Meanwhile, the ${\text{TM}}_{m,n}$ cavity modes whose $m$ or $n$ are odd appear only when the hot spots break the reflectional symmetry of the mesa structure. Moreover, we calculate the radiation patterns emitted by the IJJs at these cavity resonance conditions. The radiation patterns reflect the existence of two types of internal modes, that is, a uniform background mode and a cavity resonance mode.

Avaliação da detecção de focos de calor por sensoriamento remoto para o Parque Nacional do Itatiaia

Palavras-chave: deteccao de incendios florestais, relatorio de ocorrencia de incendios, sensoriamento remoto. AbstRAct - The remote sensing detection of hotspots is an important part of the monitoring system of forest fires for two major Brazilian federal agencies elated to preventing and combating these occurrences, IBAMA and ICMBio. To evaluate the effectiveness and accuracy of data from the Vegetation Fires Database of the National Institute of Space Research, we used the following two data sources: data recorded by the Center for the Prevention and Combat of Fire in Itatiaia National Park from 2008 to 2010 and data about areas of large fires that occurred in the Park in 2001, 2007 and 2010, obtained by interpretation of satellite images from LANDSAT 5 and CBERS 2. We analyzed information from the AQUA, TERRA, ERS-2, MGS- 02 and NOAA and GOES satellites series for the aforementioned area and period to study a total of 92 hotspots, whose data were compared to those from 101 records of fire occurrence. Ninety-six percent of hotspot detections were omitted in relation to fires reported. The TERRA and AQUA satellites, which carry MODIS sensors, showed the best results in the detection of fires and in the accuracy of the hotspot's position in relation to the burned area.

Mitochondrial DNA in a population of individuals from the City of São Paulo. DNA extraction from head and pubic hair and blood

In biological samples with low copy DNA or DNA degraded samples, such as hair and pubic hair, there is a greater probability of obtaining a mitochondrial DNA profile. Hair and pubic hair are often found at crime scenes; in cases of sexual violence is common to find the suspect's pubic hair in the victim's body. This study analyzed, blood, head and pubic hair samples of 25 males to perform the analysis of mtDNA. Each three hair shafts were grouped and divided into 0.5 cm sections: with the bulbs, and the other with 2 cm, the proximal portion, without the bulbs. The DNA extraction of hair samples was performed using QIAamp DNA Micro Kit (QIAGEN) and the PCR amplification of HV1 and HV2 carried out. The amplified products were purified and sequenced using Big Dye™ Terminator and ABI 3130 (Applied Biosystems). To insure that hair samples were from the same individual, the AmpFLSTR Identifiler Kit ® (Applied Biosystems) were used. The success rate of genotyping of hair samples with the bulb was: 56% for head hairs and in 64% for pubic hair samples, for a complete profile of the 15 STR (Identifiler). There was no statistically significant difference between the DNA concentration samples from hair with bulb and without bulb, as well as samples of pubic hair with bulb and without bulb. The overall success rate obtained with the extraction method used was approximately 60% and the success rate obtained in the sequencing was higher for pubic hair, both with and without bulb, than in head hair samples. Partial profiles of HV1 and HV2 were observed in most cases. Point heteroplasmy was detected in a sample of hair without bulb at hotspot position 16192 and another individual showed point heteroplasmy in pubic hair sample with bulb and without bulb at position 204, also observed in the blood sample of the same individual. In the preliminary results, 193 different haplotypes were detected; the most frequent haplotype was shared by 3 individuals. The most frequent lineage observed was African, showing the contribution of this haplotype group in São Paulo City population. This data were used to analyze and to compare the haplotypes of hair samples.

A model to predict the effects of soil structure on denitrification and N 2O emission

► Dual porous model of soil that closely reproduces experimental water retention. ► Simplified to critical percolation path with hotspots positioned 10 μm or 100 μm away. ► Denitrification and nitrification assumed to occur in micro-porous hot-spot zones. ► A priori diffusion and kinetics reproduce experimental CO 2 , N 2 O and N 2 emissions. ► Model shows sensitivity of O 2 thresholds, rate coefficients and hotspot positions. A model of the void space of soil is presented, and used for the a priori biophysical simulation of denitrification. The model comprises a single critical percolation channel through a 5 cm stack of four unit cells of a dual-porous void structure. Together, the micro- and macro-porous structures closely replicate the full water retention characteristic of a sandy clay loam soil from the Woburn Experimental Farm operated by Rothamsted Research, UK. Between 1 and 10 micro-porous hot-spot zones of biological activity were positioned at equally spaced distances within 5 cm from the surface, and at either 10 μm or 100 μm from the critical percolation channel. Nitrification and denitrification reactions within the hotspots were assumed to follow Michaelis–Menten kinetics, with estimated values of rate coefficients. Estimates were also made of the threshold values of oxygen concentration below which the anaerobic processes would commence. The pore network was fully saturated following addition of an aqueous ‘amendment’ of nitrate and glucose which started the reactions, and which mirrored an established laboratory protocol. Diffusion coefficients for Fickian and Crank-Nicolson calculations were taken from the literature, and were corrected for the tortuosity of the micro-porosity. The model was used to show the amount of carbon dioxide, nitrous oxide and molecular nitrogen emerging from the simulated soil with time. Adjustment of the rate coefficient and oxygen threshold concentrations, within the context of a sensitivity analysis, gave emission curves in good agreement with previous experimental measurements. Positioning of the hot-spot zones away from the critical percolation path slowed the increase and decline in emission of the gases. The model and its parameters can now be used for modelling the effect of soil compaction and saturation on the emission of nitrous oxide.

Identification of an Anchor Residue for CheA-CheY Interactions in the Chemotaxis System of Escherichia coli

Transfer of a phosphoryl group from autophosphorylated CheA (P-CheA) to CheY is an important step in the bacterial chemotaxis signal transduction pathway. This reaction involves CheY (i) binding to the P2 domain of P-CheA and then (ii) acquiring the phosphoryl group from the P1 domain. Crystal structures indicated numerous side chain interactions at the CheY-P2 binding interface. To investigate the individual contributions of the P2 side chains involved in these contacts, we analyzed the effects of eight alanine substitution mutations on CheA-CheY binding interactions. An F214A substitution in P2 caused ∼1,000-fold reduction in CheA-CheY binding affinity, while Ala substitutions at other P2 positions had small effects (E171A, E178A, and I216A) or no detectable effects (H181A, D202A, D207A, and C213A) on binding affinity. These results are discussed in relation to previous in silico predictions of hot-spot and anchor positions at the CheA-CheY interface. We also investigated the consequences of these mutations for chemotaxis signal transduction in living cells. CheA(F214A) was defective in mediating localization of CheY-YFP to the large clusters of signaling proteins that form at the poles of Escherichia coli cells, while the other CheA variants did not differ from wild-type (wt) CheA (CheA(wt)) in this regard. In our set of mutants, only CheA(F214A) exhibited a markedly diminished ability to support chemotaxis in motility agar assays. Surprisingly, however, in FRET assays that monitored receptor-regulated production of phospho-CheY, CheA(F214A) (and each of the other Ala substitution mutants) performed just as well as CheA(wt). Overall, our findings indicate that F214 serves as an anchor residue at the CheA-CheY interface and makes an important contribution to the binding energy in vitro and in vivo; however, loss of this contribution does not have a large negative effect on the overall ability of the signaling pathway to modulate P-CheY levels in response to chemoattractants.