gebhart/patrepeval huggingface dataset:
Light Propagation in Transparent Wood: Efficient Ray‐Tracing Simulation and Retrieving an Effective Refractive Index of Wood Scaffold (2021)

Transparent wood (TW), a biocomposite material demonstrating optical transparency in the visible range, has attracted much interest in recent years due to great potential for ecofriendly applications, for instance, in construction industry and functionalized organic materials. Optical properties of TW, including transparency and haze, depend on a particular structure of cellulose‐based backbone compound, (mis‐)matching of the refractive indices (RIs) between TW compounds, and the polymer matrix. Although there are data of cellulose RIs for various forms of cellulose (fibers, powder, hot‐pressed films, etc.), these values might differ from an effective RI of the TW substrate. Herein, a numerical model of light propagation in the TW, based on the real cellular structure in wood, is presented and applied to estimate an effective RI of the delignified wood reinforcement in the experimentally investigated TW material. Ray‐tracing and rigorous electromagnetic approaches are compared for modeling light propagation in the TW. Ray tracing demonstrates considerably simplified yet accurate and efficient solutions. The work brings substantial progress toward realistic and practical wood modeling for the purpose of applications, materials design, and fundamental studies.
Thermo-mechanical Characteristics Of A Thermal Switch (2005)

An Active Radiat Tile [1] (ART) thermal valve has been fabricated usin StIicon micromachining. Intended for orbital satellite heat control applications, the operational principle f the ART is to control heat flow between two thermall isolated surfaces by bringing the surfaces into intimate mechanical contact using electrostatic actuation. Prototype devices have been tested in vacuum an demonstrate actuation voltages as low as 40 Volts, very good thermal insulation in the OFF state, and a la ease in radiative heat flow in the ON state.
Role of Acetyl-Phosphate in Activation of the Rrp2-RpoN-RpoS Pathway in Borrelia burgdorferi (2010)

Borrelia burgdorferi, the Lyme disease spirochete, dramatically alters its transcriptome and proteome as it cycles between the arthropod vector and mammalian host. During this enzootic cycle, a novel regulatory network, the Rrp2-RpoN-RpoS pathway (also known as the σ(54)-σ(S) sigma factor cascade), plays a central role in modulating the differential expression of more than 10% of all B. burgdorferi genes, including the major virulence genes ospA and ospC. However, the mechanism(s) by which the upstream activator and response regulator Rrp2 is activated remains unclear. Here, we show that none of the histidine kinases present in the B. burgdorferi genome are required for the activation of Rrp2. Instead, we present biochemical and genetic evidence that supports the hypothesis that activation of the Rrp2-RpoN-RpoS pathway occurs via the small, high-energy, phosphoryl-donor acetyl phosphate (acetyl∼P), the intermediate of the Ack-Pta (acetate kinase-phosphate acetyltransferase) pathway that converts acetate to acetyl-CoA. Supplementation of the growth medium with acetate induced activation of the Rrp2-RpoN-RpoS pathway in a dose-dependent manner. Conversely, the overexpression of Pta virtually abolished acetate-induced activation of this pathway, suggesting that acetate works through acetyl∼P. Overexpression of Pta also greatly inhibited temperature and cell density-induced activation of RpoS and OspC, suggesting that these environmental cues affect the Rrp2-RpoN-RpoS pathway by influencing acetyl∼P. Finally, overexpression of Pta partially reduced infectivity of B. burgdorferi in mice. Taken together, these findings suggest that acetyl∼P is one of the key activating molecule for the activation of the Rrp2-RpoN-RpoS pathway and support the emerging concept that acetyl∼P can serve as a global signal in bacterial pathogenesis.
Analytical Electron Microscopy Study of &gamma;&frasl;&gamma;&prime; Phase Equilibria in Ni&ndash;Al&ndash;Ta Alloys (1992)

Phase equilibria between γ and γ′ in Ni-base Ni–Al–Ta alloys have been investigated by analytical electron microscopy (AEM). The chemical compositions of the γ and γ′ phases in the two-phase alloys were determined by an energy dispersive X-ray spectrometer (EDS) and then tie lines in the γ+γ′ two-phase region and the partitioning of Ta in the γ and γ′ phases were evaluated. The ALCHEMI (atom location by channeling enhanced microanalysis) technique revealed that Ta occupies most favorably the Al sites in the γ′ phases irrespective of stoichiometry. The lattice constants of the γ and γ′ phases were determined by convergent beam electron diffraction (CBED). The lattice misfits between the γ and γ′ phases were then calculated from the lattice constants and were compared with those determined from the analysis of the misfit dislocations.
<title>Intercellular fluorescence background on microscope slides: some problems and solutions for automatic analysis</title> (1994)

Although high contrast between signal and the dark background is often claimed as a major advantage of fluorescence staining in cytology and cytogenetics, in practice this is not always the case and in some circumstances the inter-cellular or, in the case of metaphase preparations, the inter-chromosome background can be both brightly fluorescent and vary substantially across the slide or even across a single metaphase. Bright background results in low image contrast, making automatic detection of metaphase cells more difficult. The background correction strategy employed in automatic search must both cope with variable background and be computationally efficient. The method employed in a fluorescence metaphase finder is presented, and the compromises involved are discussed. A different set of problems arise when the analysis is aimed at accurate quantification of the fluorescence signal. Some insight into the nature of the background in the case of comparative genomic hybridization is obtained by image analysis of data obtained from experiments using cell lines with known abnormal copy numbers of particular chromosome types.
<title>Geometric modeling for computer vision</title> (1992)

Computer vision faces the challenge of exploiting the CAD models available for many manufactured objects. Recently, a variety of new algorithms have been developed that rely on symbolic object representations for recognizing curved three-dimensional objects from images. This paper presents a modeling system for constructing these representations from parametric and implicit algebraic surface specifications. A combination of homotopy continuation and curve tracing is used to compute set operations. Specifically, an algorithm for tracing curves defined implicitly in IRn+1 by n polynomial equations in n + 1 variables is presented that correctly characterizes the topology of the intersection curves and respects singular points. The curve tracing algorithm is also used to render line drawings for which parametric representations of occluding contours are unavailable. Hidden lines are easily removed by explicitly constructing an image structure graph of the smooth curve branches and singular points; it is then sufficient to trace a ray at a single point on each curve branch. A preliminary parallel implementation, distributed over a network of SPARC stations, appears promising. For objects modeled by this system algorithms for constructing their aspect graph, computing their stable poses, and recognizing them in different types of images have been developed.
Development and characterization of a scintillating cell imaging dish for radioluminescence microscopy (2018)

Radioluminescence microscopy is an emerging modality that can be used to image radionuclide probes with micron-scale resolution. This technique is particularly useful as a way to probe the metabolic behavior of single cells and to screen and characterize radiopharmaceuticals, but the quality of the images is critically dependent on the scintillator material used to image the cells. In this paper, we detail the development of a microscopy dish made of a thin-film scintillating material, Lu2O3:Eu, that could be used as the blueprint for a future consumable product. After developing a simple quality control method based on long-lived alpha and beta sources, we characterize the radioluminescence properties of various thin-film scintillator samples. We find consistent performance for most samples, but also identify a few samples that do not meet the specifications, thus stressing the need for routine quality control prior to biological experiments. In addition, we test and quantify the transparency of the material, and demonstrate that transparency correlates with thickness. Finally, we evaluate the biocompatibility of the material and show that the microscopy dish can produce radioluminescent images of live single cells.
Higher lung antioxidant enzyme activity persists after single dose of corticosteroids in preterm lambs (1996)

Although administration of exogenous corticosteroids accelerates the late gestational rise in fetal rat and lamb lung antioxidant enzyme activity, the effect of dosing intervals on these responses remains uncertain. We studied the persistence and efficacy of the antioxidant response in fetal lamb lung to a single fetal dose of corticosteroids injected between 121 and 127 days gestational age. Fetal lambs received 0.5 mg/kg of betamethasone (n = 35) or saline (n = 26) by fetal intramuscular injection 24 h, 48 h, 4 days, or 7 days before preterm delivery at 128 days gestation (term = 150 days). After delivery, the lambs were ventilated for 40 min and killed. Total superoxide dismutase, catalase, glutathione peroxidase activities, and lipid hydroperoxide levels were measured, using homogenized lung. The saline-injected controls were similar at all time points. Lung antioxidant enzyme activity was consistently higher and lipid hydroperoxide presence was lower in the betamethasone-treated groups. We conclude that the positive effect of a single fetal dose of betamethasone on lung antioxidant enzyme activity occurs within 24 h after exposure, persists over a period of 7 days without a major change in the magnitude of the response, and leads to a reduction in lipid hydroperoxide formation during immediate postdelivery oxygen exposure.
High-Mobility SiC MOSFETs with Alkaline Earth Interface Passivation (2016)

Alkaline earth elements Sr and Ba provide SiO 2 /SiC interface conditions suitable for obtaining high channel mobility metal-oxide-semiconductor field-effect-transistors (MOSFETs) on the Si-face (0001) of 4H-SiC, without the standard nitric oxide (NO) anneal. The alkaline earth elements Sr and Ba located at/near the SiO 2 /SiC interface result in field-effect mobility (μ FE ) values as high as 65 and 110 cm 2 /V . s, respectively, on 5×10 15 cm -3 Al-doped p-type SiC. As the SiC doping increases, peak mobility decreases as expected, but the peak mobility remains higher for Ba interface layer (Ba IL) devices compared to NO annealed devices. The Ba IL MOSFET field-effect mobility decreases as the temperature is increased to 150 °C, as expected when mobility is phonon-scattering-limited, not interface-trap-limited. This is in agreement with measurements of the interface state density (D IT ) using the high-low C-V technique, indicating that the Ba IL results in lower D IT than that of samples with nitric oxide passivation. Vertical power MOSFET (DMOSFET) devices (1200V, 15A) fabricated with the Ba IL have a 15% lower on-resistance compared to devices with NO passivation. The DMOSFET devices with a Ba IL maintain a stable threshold voltage under NBTI stress conditions of-15V gate bias stress, at 150 °C for 100hrs, indicating no mobile ions. Secondary-ion mass-spectrometry (SIMS) analysis confirms that the Sr and Ba remain predominantly at the SiO 2 /SiC interface, even after high temperature oxide annealing, consistent with the observed high channel mobility after these anneals. The alkaline earth elements result in enhanced SiC oxidation rate, and the resulting gate oxide breakdown strength is slightly reduced compared to NO annealed thermal oxides on SiC.
Safety study of tethered capsule endomicroscopy (TCE) pull back through long segments of the small intestine (2022)

We developed OCT-TCE devices with either guidewire or propylene glycol infusion tethers and tested pullback force and tissue damage over different distances of the small intestine in living swine. For all devices, the maximum force was below our safety threshold of 2N across intestinal lengths of 4m or less. At lengths > 4m, the force was > 4N for the infusion tube devices and > 5N for the guidewire devices, and the proximal intestine showed visible damage matching the tether shape. In conclusion, TCE may be safe for jejunal imaging but likely needs further improvement for ileum imaging in humans.
Full 3D Reconstruction of Non-Rigidly Deforming Objects (2018)

In this article, we discuss enhanced full 360° 3D reconstruction of dynamic scenes containing non-rigidly deforming objects using data acquired from commodity depth or 3D cameras. Several approaches for enhanced and full 3D reconstruction of non-rigid objects have been proposed in the literature. These approaches suffer from several limitations due to requirement of a template, inability to tackle large local deformations and topology changes, inability to tackle highly noisy and low-resolution data, and inability to produce online results. We target online and template-free enhancement of the quality of noisy and low-resolution full 3D reconstructions of dynamic non-rigid objects. For this purpose, we propose a view-independent recursive and dynamic multi-frame 3D super-resolution scheme for noise removal and resolution enhancement of 3D measurements. The proposed scheme tracks the position and motion of each 3D point at every timestep by making use of the current acquisition and the result of the previous iteration. The effects of system blur due to per-point tracking are subsequently tackled by introducing a novel and efficient multi-level 3D bilateral total variation regularization. These characteristics enable the proposed scheme to handle large deformations and topology changes accurately. A thorough evaluation of the proposed scheme on both real and simulated data is carried out. The results show that the proposed scheme improves upon the performance of the state-of-the-art methods and is able to accurately enhance the quality of low-resolution and highly noisy 3D reconstructions while being robust to large local deformations.
Tris(trimethylsilyl)methantellurenylhalogenide (Me3Si)3CTeX (X = Cl, Br, I): Synthese stabiler Alkantellurenylhalogenide (1989)

Tris (trimethylsilyl)methanetellurenyl Halides (Me 3 Si) 3 CTex (X = Cl, Br, I): Synthesis of Stable Alkanetellurenyl Halides The first stable and isolable alkanetellurenyl halides, tris(trimethylsilyl)methanetellurenyl chloride, bromide, and iodide ( 1a – c ) are obtained quantitatively by halogenolysis of bis[tris‐(trimethylsilyl)methyl] ditelluride with SO 2 Cl 2 , Br 2 , and I 2 , respectively. Their synthetic potential is examplified by transformation to methyl tris(trimethylsilyl)methyl telluride ( 2 ) and phenyl tris(trimethylsilyl)methyl telluride ( 3 ).
Influence of Si on the particle growth of AlN ceramics (2014)

Aluminum nitride (AlN) powders doped with various concentrations of Si were investigated to understand the effects of Si on the growth and luminescence of AlN. Certain Si-doping concentrations enhanced the particle growth of AlN and affected the UV emission bands at 280 and 350 nm. Cross-sectional cathodoluminescence images showed that SiNx coated AlN particles on the surface and formed grain boundaries. These grain boundaries may play a critical role in the solid-state reaction and crystal growth of AlN.
Identification and Characterization of IS 2404 and IS 2606 : Two Distinct Repeated Sequences for Detection of Mycobacterium ulcerans by PCR (1999)

Molecular analysis of Mycobacterium ulcerans has revealed two new insertion sequences (ISs), IS2404 and IS2606. IS2404 was identified by complete sequencing of a previously described repetitive DNA segment from M. ulcerans. This element is 1,274 bp long, contains 12-bp inverted repeats and a single open reading frame (ORF) potentially encoding a protein of 327 amino acids (aa), and apparently generates 7-bp direct repeats upon transposition. Amino acid similarity was found between the putative transposase and those encoded by ISs in other bacterial sequences from Aeromonas salmonicida (AsIs1), Escherichia coli (H repeat element), Vibrio cholerae (VcIS1), and Porphyromonas gingivalis (PGIS2). The second IS, IS2606, was discovered by sequence analysis of a HaeIII fragment of M. ulcerans genomic DNA containing a repetitive sequence. This element is 1,404 bp long, with 12-bp inverted repeats and a single ORF potentially encoding a protein of 445 aa. Database searches revealed a high degree of amino acid identity (70%) with the putative transposase of IS1554 from M. tuberculosis. Significant amino acid identity (40%) was also observed with transposases from several other microorganisms, including Rhizobium meliloti (ISRm3), Burkholderia cepacia (IS1356), Corynebacterium diphtheriae, and Yersinia pestis. PCR screening of DNA from 45 other species of mycobacteria with primers for IS2404 confirm that this element is found only in M. ulcerans. However, by PCR, IS2606 was also found in Mycobacterium lentiflavum, another slow-growing member of the genus Mycobacterium that is apparently genetically distinct from M. ulcerans. Testing the sensitivity of PCR based on IS2404 and IS2606 primers demonstrated the ability to detect 0.1 and 1 M. ulcerans genome equivalents, respectively. The ability to detect small numbers of cells by using two gene targets will be particularly useful for analyzing environmental samples, where there may be low concentrations of M. ulcerans among large numbers of other environmental mycobacteria.
DP-space: Bayesian Nonparametric Subspace Clustering with Small-variance Asymptotics (2015)

Subspace clustering separates data points ap-proximately lying on union of affine subspaces into several clusters. This paper presents a novel nonparametric Bayesian subspace cluster-ing model that infers both the number of sub-spaces and the dimension of each subspace from the observed data. Though the posterior infer-ence is hard, our model leads to a very effi-cient deterministic algorithm, DP-space, which retains the nonparametric ability under a small-variance asymptotic analysis. DP-space mono-tonically minimizes an intuitive objective with an explicit tradeoff between data fitness and model complexity. Experimental results demonstrate that DP-space outperforms various competitors in terms of clustering accuracy and at the same time it is highly efficient. 1.
Self‐Immolative Activation of β‐Galactosidase‐Responsive Probes for In Vivo MR Imaging in Mouse Models (2019)

Our lab has developed a new series of self-immolative MR agents for the rapid detection of enzyme activity in mouse models expressing β-galactosidase (β-gal). We investigated two molecular architectures to create agents that detect β-gal activity by modulating the coordination of water to Gd<sup>III</sup> . The first is an intermolecular approach, wherein we designed several structural isomers to maximize coordination of endogenous carbonate ions. The second involves an intramolecular mechanism for q modulation. We incorporated a pendant coordinating carboxylate ligand with a 2, 4, 6, or 8 carbon linker to saturate ligand coordination to the Gd<sup>III</sup> ion. This renders the agent ineffective. We show that one agent in particular (6-C pendant carboxylate) is an extremely effective MR reporter for the detection of enzyme activity in a mouse model expressing β-gal.
Implementation of the transposed Farrow structure (2003)

The Farrow structure provides an efficient way to implement sampling rate increase between arbitrary sampling rates. However, in the case of sampling rate decrease the Farrow structure can only implement filters with poor anti-aliasing properties because the transfer zeros are clustered around the integer multiples of the input sampling rate and not around the multiples of the output sampling rate where aliasing components appear. This problem can be overcome by using the transposed Farrow structure with the transfer zeros clustered around the integer multiples of the output sampling rate. The aliasing components are attenuated using the same polynomial function as for the Farrow structure. The main difference is that this polynomial is determined using the output sampling period as the basic interval, instead of the input sampling period. This paper gives overview and compares two alternative implementation forms for the transposed Farrow structure.
Optimizing laser and probe molecules for multi-photon microscopy (2015)

Multiple fluorescent probes (multi-dyes) and single or multi-laser configurations can significantly extend the applications and accuracy of microscopy. Multiple fluorescent probes enable the user to identify more than one target, but difficulties can arise due to overlapping spectral emissions of the different probes. In particular, spectral overlapping of fluorescent and/or phosphorescent emission signals can lead to incorrect analysis. We present a method to numerically calculate overlapping spectra. An accurate modeling tool would be valuable to predict the best laser-probes combinations for selection and screening stages. We use a numerical method that simulates both time and space so that we can calculate on a near-instantaneous basis the absorption of laser light and electron populations. We can then calculate the intensity of the emitted signal and determine the overlap of the spectra.
Model-Based Meta-Analysis of Relapsing Mouse Model Studies from the Critical Path to Tuberculosis Drug Regimens Initiative Database (2021)

Tuberculosis (TB), the disease caused by Mycobacterium tuberculosis ( Mtb ), remains a leading infectious disease-related cause of death worldwide, necessitating the development of new and improved treatment regimens. Non-clinical evaluation of candidate drug combinations via the relapsing mouse model (RMM) is an important step in regimen development, through which candidate regimens that provide the greatest decrease in probability of relapse following treatment in mice may be identified for further development. Although RMM studies are a critical tool to evaluate regimen efficacy, making comprehensive "apples to apples" comparisons of regimen performance in the RMM has been a challenge, in large part due to the need to evaluate and adjust for variability across studies arising from differences in design and execution. To address this knowledge gap, we performed a model-based meta-analysis on data for 17 unique regimens obtained from a total of 1592 mice across 28 RMM studies. Specifically, a mixed-effects logistic regression model was developed that described the treatment duration-dependent probability of relapse for each regimen and identified relevant covariates contributing to inter-study variability. Using the model, covariate-normalized metrics of interest, namely treatment duration required to reach 50% and 10% relapse probability, were derived and used to compare relative regimen performance. Overall, the model-based meta-analysis approach presented herein enables cross-study comparison of efficacy in the RMM, and provides a framework whereby data from emerging studies may be analyzed in the context of historical data to aid in selecting candidate drug combinations for clinical evaluation as TB drug regimens.