gebhart/patrepeval huggingface dataset:
Geometric Approach to Estimation of Volumetric Distortions (2016)

The problem of measuring geometrical distortions is not trivial for volumetric domains. There exist intrinsic

restrictions and constrains on higher dimensional mappings. Moreover, according to Liouville theorem, most

existing techniques for 2D data can not be directly applied to volumetric objects. In this work we approximate

continuous deformations by piecewise affine functions defined on tetrahedral meshes. Our aim is to study

a few types of geometrical distortions that can be expressed as functions of singular values of a Jacobian.

We employ the proposed methods of estimating conformal and isometric distortions to analyze volumetric

data. In particular, we examine parametrization of tetrahedral models to a ball. Distortions produced by the

resulting spatial mappings depict intrinsic structure of domains, and therefore can be employed in such tasks

as detection of abnormalities and comparison (i.e. similarity assessment) between 3D objects. This geometric

approach and results are highly relevant to various applications in Computer Vision, Computer Graphics, 3D

Printing and Medical Imaging.
Image analysis of bone tissue remodelling around biomaterials (2007)

There is a need to develop faster and more reliable histomorphometrical methods for evaluating the implant integration in bone tissue when working on 2D-cut and ground sections. There is a need for reliable 3D methods in order to provide a better insight in bone modelling and remodelling around implants. We foresee that extracting information obtained with different techniques will help us to gain more in our understanding of integration of biomaterials. We present an automatic method for performing quantitative measurements of implant integration on the histological images. Quantifications involved bone to implant contact as well as bone area inside the threads of the implant. The segmentation was based on discriminant analysis and involved a supervised training where the bone, implant and soft tissue regions has been marked manually. The method is compared to the time consuming and subjective manual measuring of the same features performed in the light-microscope. The area measurements of the automatic method correspond well with the manual method. However, significant difference in the length values of the estimation of the bone to implant contact were observed, revealing greater numbers for the automatic method compared to the manual. These differences are most likely due to staining artifacts. We also present SRµCT 3D imaging of samples and observations made so far. The volumes have been segmented using thresholding. The current work involves an improvement of the segmentation in order to obtain correct analysis. Furthermore, manual annotation is very time consuming and difficult for the volumes. In order to work around this deficiency, the 3D samples have been sliced and histologically imaged. These images are easier to annotate and can therefore provide a ground truth. Methods for registration, i.e. finding 2D slice in the 3D volume are being investigated.
Investigations of Chemical Vapor Deposition of GaN Using Synchrotron Radiation (2001)

We apply synchrotron X-ray analysis techniques to probe the surface structure of GaN films during synthesis by metallorganic chemical vapor deposition (MOCVD). Our approach is to observe the evolution of surface structure and morphology in real-time using grazing incidence X-ray scattering (GIXS). This technique combines the ability of X-rays to penetrate the chemical vapor deposition environment for in situ measurements, with the sensitivity of GIXS to atomic scale structure. Examples are presented from some of our studies of growth modes and surface evolution as a function of process conditions that illustrate the capabilities of synchrotron X-ray analysis during MOCVD growth. We focus on studies of the homoepitaxial growth mode, island coarsening dynamics, and effects of impurities. © 2001 The Electrochemical Society. All rights reserved.
On-chip optical interconnection by using integrated III-V laser diode and photodetector with silicon waveguide (2010)

On-chip integration of III-V laser diodes and photodetectors with silicon nanowire waveguides is demonstrated. Through flip-chip bonding of GaInNAs/GaAs laser diodes directly onto the silicon substrate, efficient heat dissipation was realized and characteristic temperatures as high as 132K were achieved. Spot-size converters for the laser-to-waveguide coupling were used, with efficiencies greater than 60%. The photodetectors were fabricated by bonding of InGaAs/InP wafers directly to silicon waveguides and formation of metal-semiconductor-metal structures, giving responsivities as high as 0.74 A/W. Both laser diode and the photodetector were integrated with a single silicon waveguide to demonstrate a complete on-chip optical transmission link.
Torsional vibrations of quartz crystal beams (2002)

An exact solution of a partial differential equation including elastic compliance constant s'/sub 56/, with respect to stress function /spl psi/ has been found for torsional modes of vibration of an arbitrary (singly, doubly, triply) rotated beam with a pair of parallel, free edges. The solution is obtained by relaxing the condition that the edge planes are perpendicular to the main faces of the beam. That is, the edges are off perpendicular by the angle /spl Theta/=arctan(-s'/sub 56//s'/sub 55/). The exact solution can reduce the difference of the calculated and measured values for a thickness-to-width ratio which gives the first order temperature coefficient /spl alpha/=0. Also, a comparatively large-inclination of the edge cuts is required to reduce the unwanted, complicated mode shapes to simple ones.
Application of Chromeless Phase Lithography (CPL) masks in ArF lithography (2002)

The challenges of low k1 lithography require unique solutions at all levels of the lithography process. Chromeless phase lithography (CPL) is a promising technique that uses a 2-beam imaging strategy and a unique OPC application for enhanced CD uniformity through pitch. It is particularly effective when combined with a high numerical aperture (NA) and off-axis illumination (OAI). In addition to its imaging benefits, CPL masks offer many advantages in the manufacturing of the mask over other approaches. The manufacturing strategy and methodology employed to fabricate CPL masks will be discussed. The technical challenges of mask production will also be highlighted. Application of CPL to production ArF images were characterized through simulations and experimental data demonstrating the capability of this technique to produce complex structures.
Prion protein hereditary amyloidosis: parenchymal and vascular (1996)

Prion protein (PrP) amyloidosis is a feature of Gerstmann-Sträussler-Scheinker disease (GSS) and prion protein cerebral amyloid angiopathy (PrP-CAA). GSS and PrP-CAA are associated with point mutations of the prion protein gene (PRNP); there is a broad spectrum of clinical presentations and the main signs are ataxia, spastic paraparesis, extrapyramidal signs and dementia. In GSS, parenchymal amyloid may be associated with spongiform changes or neurofibrillary lesions; in PrP-CAA, vascular amyloid is associated with neurofibrillary lesions. In the two diseases, a major component of the amyloid fibrils is a 7 kDa peptide, approximately spanning residues 81–150 of PrP.
High-output power near-ultraviolet and violet light-emitting diodes fabricated on patterned sapphire substrates using metalorganic vapor phase epitaxy (2004)

The external quantum efficiency (EQE, &eta;<sub>e</sub>) of conventional near-ultraviolet (NUV) light-emitting diodes (LEDs) with an InGaN multi-quantum-well (MQW) structure is limited by high dislocation density and by the narrow escape cone due to total internal reflection at the GaN/air or sapphire/air interface. We have fabricated the NUV and violet InGaN-MQW-LEDs with the high EQE on the patterned-sapphire substrate (PSS) using a single growth process by metal-organic vapor phase epitaxy (MOVPE). The PSS with parallel grooves along the <11-20><sub>GaN</sub> direction or the <1-100><sub>GaN</sub> direction was fabricated by a standard photolithography and subsequent reactive ion etching (RIE). In this study, fabricated the LED on the PSS with parallel grooves along the <11-20><sub>GaN</sub> direction. The GaN layer grown by lateral epitaxy on a patterned substrate (LEPS) has dislocation density of 1.5x10<sup>8</sup> cm<sup>-2</sup>. The LEPS-NUV (or violet)-LED chips were mounted on the Si bases in a flip-chip bonding arrangement. When the LEPS-NUV-LED (the emission peak wavelength &lambda;p: 382 nm) was operated at a forward-bias current of 20 mA at room temperature (RT), the output power (P<sub>o</sub>) and the EQE were 15.6 mW and 24%, respectively. When the LEPS-violet-LED (&lambda;p: 405 nm) was operated at a forward-bias current of 20 mA at RT, the P<sub>o</sub> and the EQE were 26.3 mW and 43%, respectively. Furthermore, we obtained the P<sub>o</sub> of approximately 61 mW at 50 mA and 111 mW at 100 mA, respectively. It was revealed that the PSS is very effective in reducing the dislocation density and for increasing the extraction efficiency due to the multiple scattering of the emission light at the GaN/patterned sapphire interface.
Anti-Müllerian Hormone Recruits BMPR-IA in Immature Granulosa Cells (2013)

Anti-Müllerian hormone (AMH) is a member of the TGF-β superfamily secreted by the gonads of both sexes. This hormone is primarily known for its role in the regression of the Müllerian ducts in male fetuses. In females, AMH is expressed in granulosa cells of developing follicles. Like other members of the TGF-β superfamily, AMH transduces its signal through two transmembrane serine/threonine kinase receptors including a well characterized type II receptor, AMHR-II. The complete signalling pathway of AMH involving Smads proteins and the type I receptor is well known in the Müllerian duct and in Sertoli and Leydig cells but not in granulosa cells. In addition, few AMH target genes have been identified in these cells. Finally, while several co-receptors have been reported for members of the TGF-β superfamily, none have been described for AMH. Here, we have shown that none of the Bone Morphogenetic Proteins (BMPs) co-receptors, Repulsive guidance molecules (RGMs), were essential for AMH signalling. We also demonstrated that the main Smad proteins used by AMH in granulosa cells were Smad 1 and Smad 5. Like for the other AMH target cells, the most important type I receptor for AMH in these cells was BMPR-IA. Finally, we have identified a new AMH target gene, Id3, which could be involved in the effects of AMH on the differentiation of granulosa cells and its other target cells.
Improving Execution Speed of FPGA using Dynamically Reconfigurable Technique (2007)

This paper studies issues concerning dynamically reconfigurable FPGA (DRFPGA). It reports the architecture and performance of Flexible Processor III (FP3), a newly proposed DRFPGA. The FP3 employs a new shift register-type temporal interconnect to reduce operation delay. Designed and fabricated in 0.35mum 2P3M CMOS technology, FP3 works correctly as a multi-context FPGA. Our experimental results show that there exist cases where the best user circuit speed was achieved when 2 contexts were in use for a benchmark circuit. This is because of the reduction of buffers in the critical path by temporal partitioning.
Evolving Design Rules for the Inverse Granular Packing Problem (2014)

If a collection of identical particles is poured into a container, different shapes will fill to different densities. But what is the shape that fills a container as close as possible to a pre-specified, desired density? We demonstrate a solution to this inverse-packing problem by framing it in the context of artificial evolution. By representing shapes as bonded spheres, we show how shapes may be mutated, simulated, and selected to produce particularly dense or loose packing aggregates, both with and without friction. Moreover, we show how motifs emerge linking these shapes together. The result is a set of design rules that function as an effective solution to the inverse packing problem for given packing procedures and boundary conditions. Finally, we show that these results are verified by experiments on 3D-printed prototypes used to make packings in the real world.
Approximate Bayesian framework for 3D reconstruction in a volumetric PIV/PTV measurement (2021)

Non-invasive flow velocity measurement techniques like volumetric Particle Image Velocimetry (PIV) (Elsinga et al., 2006; Adrian and Westerweel, 2011) and Particle Tracking Velocimetry (PTV) (Maas, Gruen and Papantoniou, 1993) use multi-camera projections of tracer particle motion to resolve three-dimensional flow structures. A key step in the measurement chain involves reconstructing the 3D intensity field (PIV) or particle positions (PTV) given the projected images and known camera correspondence. Due to limited number of camera-views the projected particle images are non-unique making the inverse problem of volumetric reconstruction underdetermined. Moreover, higher particle concentration (&gt;0.05 ppp) increases erroneous reconstructions or “ghost” particles and decreases reconstruction accuracy. Current reconstruction methods either use voxel-based representation for intensity reconstruction (e.g. MART (Elsinga et al., 2006)) or a particle-based approach (e.g. IPR (Wieneke, 2013)) for 3D position estimation. The former method is computationally intensive and has a lesser positional accuracy due to stretched shape of the reconstructed particle along the line of sight. The latter compromises triangulation accuracy (Maas, Gruen and Papantoniou, 1993) due to overlapping particle images for higher particle concentrations. Thus, each method has its own challenges and the error in 3D reconstruction significantly affects the accuracy of the velocity measurement. Though, other methods like maximum-a-posteriori (MAP) estimation have been previously developed (Levitan and Herman, 1987; Bouman and Sauer, 1996) for computed Tomography data, it has not been explored for PIV/ PTV 3D reconstruction. Here, we use a MAP estimation framework to model and solve the inverse problem. The cost function is optimized using a stochastic gradient ascent (SGA) algorithm. Such an optimization can converge to a better local maximum and also use smaller image patches for efficient iterations.
Prediction of HLA genotypes from single-cell transcriptome data (2022)

ABSTRACT The human leukocyte antigen (HLA) locus plays a central role in adaptive immune function and has significant clinical implications for tissue transplant compatibility and allelic disease associations. Studies using bulk-cell RNA sequencing have demonstrated that HLA transcription may be regulated in an allele-specific manner and single-cell RNA sequencing (scRNA-seq) has the potential to better characterize these expression patterns. However, quantification of allele-specific expression (ASE) for HLA loci requires sample-specific reference genotyping due to extensive polymorphism. While genotype prediction from bulk RNA sequencing is well described, the feasibility of predicting HLA genotypes directly from single-cell data is unknown. Here we evaluate and expand upon several computational HLA genotyping tools by comparing predictions from human single-cell data to gold-standard, molecular genotyping. The highest 2-field accuracy averaged across all loci was 76% by arcasHLA and increased to 86% using a composite model of multiple genotyping tools. We also developed a highly accurate model (AUC 0.93) for predicting HLA-DRB345 copy number in order to improve genotyping accuracy of the HLA-DRB locus. Genotyping accuracy improved with read depth and was reproducible at repeat sampling. Using a metanalytic approach, we also show that HLA genotypes from PHLAT and OptiType can generate ASE ratios that are highly correlated (R 2 = 0.8 and 0.94, respectively) with those derived from gold-standard genotyping. Highlights - Benchmarking of HLA genotype prediction accuracy from 5’- and 3’-based single-cell RNA-seq data compared to molecular HLA genotyping - Quantification of transcript coverage by 5’- and 3’-based single cell sequencing methods - Accurate prediction of complex HLA-DRB345 copy numbers using supervised learning - Balancing accuracy and performance through composite HLA genotyping - Meta-analytic approach to summarizing allele-specific expression of HLA genotypes at single-cell level
Heterogeneity of TMPRSS2 Gene Rearrangements in Multifocal Prostate Adenocarcinoma: Molecular Evidence for an Independent Group of Diseases (2007)

Abstract Recurrent gene fusions between the androgen-regulated gene TMPRSS2 and the ETS family transcription factors ERG, ETV1, and ETV4 have been identified in the majority of prostate adenocarcinomas (PCA). PCA is often multifocal with histologic heterogeneity of different tumor foci. As TMPRSS2 is a common 5′ partner of ETS gene fusions, we monitored TMPRSS2 rearrangement by fluorescence in situ hybridization (FISH) to study the origin and molecular basis of multifocal PCA heterogeneity. TMPRSS2 rearrangement was evaluated by FISH on a tissue microarray representing 93 multifocal PCAs from 43 radical prostatectomy resections. Overall, 70% (30 of 43) of the cases showed TMPRSS2 rearrangement, including 63% through deletion (loss of the 3′ TMPRSS2 signal), 27% through translocation (split of 5′ and 3′ TMPRSS2 signals), and 10% through both mechanisms in different tumor foci. Of the 30 TMPRSS2 rearranged cases, 30% showed concordance in all tumor foci, whereas 70% were discordant in at least one focus. In TMPRSS2 rearranged cases, the largest (index) tumor was rearranged 83% of the time. Pathologic stage, size, or Gleason grade of the multifocal PCA did not correlate with overall TMPRSS2 rearrangement. Our results suggest that multifocal PCA is a heterogeneous group of diseases arising from multiple, independent clonal expansions. Understanding this molecular heterogeneity is critical to the future development and utility of diagnostic and prognostic PCA biomarkers. [Cancer Res 2007;67(17):7991–5]
Extended bioreactor conditioning of mononuclear cell–seeded heart valve scaffolds (2018)

The tissue-engineered heart valve may be the ideal valve replacement option but still must overcome challenges in leaflet recellularization. This study sought to investigate the potential for leaflet matrix restoration and repopulation following mononuclear cell seeding and extended periods of bioreactor conditioning. Human aortic heart valves were seeded with mononuclear cells and conditioned in a pulsatile bioreactor for 3 days, 3 weeks, or 6 weeks. The results of this study determined that a mononuclear cell population can be readily localized within the leaflet tissue in as little as 3 days. Furthermore, as extended bioreactor condition continued to the 3- and 6-week time points, the mesenchymal stem cell subfraction proliferated and appeared to become the predominant cell phenotype. This was evident through positive expression of mesenchymal stem cell markers and no expression of mononuclear cell markers observed by immunohistochemistry in the 3- and 6-week groups. In addition, cells in the 3- and 6-week groups exhibited an up-regulation of mesenchymal stem cell-associated genes (<i>THY1, NT5E</i>, and <i>ITGB1</i>) and a down-regulation of mononuclear cell-associated genes (<i>CD14, ICAM1</i>, and <i>PECAM1</i>) compared to the initial seeded cell population. However, repopulation of the leaflet interstitium was less extensive than anticipated. Valves in the 6-week time point also exhibited retracted leaflets. Thus, while the 3-week bioreactor-conditioning period used in this study may hold some promise, a bioreactor-conditioning period of 6 weeks is not a viable option for clinical translation due to the negative impact on valve performance.
Characterization of Human Liver Cytochrome P-450 Enzymes Involved in theO-demethylation of a New P-glycoprotein Inhibitor HM-30181∗ (2007)

HM-30181, 4-oxo-4H-chromene-2-carboxylic acid [2-(2-{4-[2-(6,7-dimethoxy-3,4-dihydro-1H-isoquinolin-2-yl)-ethyl]-phenyl}-2H-tetrazol-5-yl)-4,5-dimethoxy-phenyl]-amide, is a new P-glycoprotein inhibitor with the potential to increase the cytotoxic activity of orally coadministered paclitaxel. This study was performed to characterize human cytochrome P-450 (CYP) enzymes involved in the metabolism of HM-30181 to 4- or 5-O-desmethyl-HM-30181 (M2) and 6- or 7-O-desmethyl-HM-30181 (M3) and to investigate the inhibitory potential of HM-30181 on CYP enzymes in human liver microsomes. CYP3A4 was identified as the major isozyme responsible for the O-demethylation of HM-30181 to M2 and M3 based on the correlation analysis, chemical inhibition and immuno-inhibition study and metabolism in cDNA-expressed human CYP isozymes. HM-30181 itself had no inhibitory effects on CYPs 1A2, 2A6, 2C8, 2C9, 2C19, 2D6, and 3A4 in human liver microsomes, suggesting the possibility that the pharmacokinetics of HM-30181 could be changed with coadministration of known CYP3A4 inducers or inhibitors.
Thermal Warp Simulation in Substrate with Properties Change of Curing Resin (2019)

Thermal warp of a printed circuit board（PCB）is largely influenced by the cure shrinkage reaction of thermosetting resins, as well as the mismatch in the residual copper rate of conductive layers and the coefficient of thermal expansion（CTE）of substrate materials. In this study, the thermal warp in a substrate consisting of only resin was simulated under the manufacturing process condition of the resin substrate. As a result of reflecting the viscoelastic properties and the CTE of the incompletely cured resins in the warp simulation, the warp behavior of the resin substrate was accurately predicted.
Pixel-based averaging predictor for HEVC lossless coding (2013)

This paper presents an intra-frame prediction scheme designed for lossless coding using HEVC. The proposed coding method comprises a pixel-wise prediction based on original samples. It is realized as a separate intra prediction mode, which replaces the PLANAR mode. In order to perform the prediction, a four-sample template around the pixel that is to be predicted is compared to the respective template of a four-pixel neighborhood. For each reference template, the sum of absolute differences (SAD) is determined. A table look-up of the SAD value gives the respective weighting factor for each neighborhood pixel. The predictor for the current pixel is calculated as the weighted average of the neighborhood pixels. In comparison to the unmodified HEVC Test Model HM-9.1 configured for lossless coding by disabling/bypassing transformation, quantization, and in-loop filters, the proposed method provides average bitrate savings up to 10.88% for intra-only coding at similar computational complexity.