gebhart/patrepeval huggingface dataset:
Ellipsometric scatterometry for sub-0.1-μm CD measurements (1998)

Conventional scatterometry measures the intensity of a diffraction order from a periodic structure as one or more measurement parameters is changed. We have previously demonstrated conventional techniques to characterize developed photoresist linewidths as small as approximately 0.15 micrometer, with scatterometer results agreeing well with measurements performed using other techniques. For developed photoresist, the measurement sensitivity of conventional scatterometer techniques diminishes considerably for sample linewidths that are sub-0.1 micrometer, using 633 nm laser illumination. We present a modified scatterometer configuration which combines aspects of conventional scatterometry and ellipsometry that provide increased sensitivity for characterizing sub-0.1 micrometer linewidth periodic photoresist structures. The complex reflection coefficients representing the grating sample are extracted, both in magnitude and in relative phase, through intensity measurements at selected polarizer/analyzer/compensator orientations. The cross-polarization terms of the reflection coefficient matrix are shown to be equal for a symmetric photoresist grating structure with line widths approximately 0.5 micrometer. Theoretical results for nominal 70 nm photoresist lines are presented that show phase measurement sensitivity to linewidth changes on the order of 2 - 4 deg/nm and reflectance sensitivity of at least 3%/nm. This results in linewidth measurement resolutions that are sub-nm.
Inhibition of the Activities of Matrix Metalloproteinases 2, 8, and 9 by Chlorhexidine (1999)

Matrix metalloproteinases (MMPs) are a host cell-derived proteolytic enzyme family which plays a major role in tissue-destructive inflammatory diseases such as periodontitis. The aim of the present study was to evaluate the inhibitory effect of chlorhexidine (CHX) on MMP-2 (gelatinase A), MMP-9 (gelatinase B), and MMP-8 (collagenase 2) activity. Heat-denatured type I collagen (gelatin) was incubated with pure human MMP-2 or -9 activated with p-aminophenylmercuric acetate (APMA), and the proteolytic degradation of gelatin was monitored by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Coomassie blue staining. The effect of CHX on MMP-8 activity was also studied with a cellular model addressing the ability of phorbol myristate acetate (PMA)-triggered human peripheral blood neutrophils (polymorphonuclear leukocytes [PMNs]) to degrade native type I collagen. CHX inhibited the activities of both gelatinases (A and B), but MMP-2 appeared to be more sensitive than MMP-9. Adding calcium chloride to the assay mixtures almost completely prevented the inhibition of MMP-9 activity by CHX, while the inhibition of MMP-2 activity could be reversed only when CHX was used at a low concentration. This observation suggests that CHX may act via a cation-chelating mechanism. CHX dose-dependently inhibited collagenolytic activity of MMP-8 released by PMA-triggered PMNs. MMP-8 without APMA activation was inhibited clearly more efficiently than APMA-activated MMP-8. Our study suggests that the direct inhibition of the MMPs' activities by CHX may represent a new valuable effect of this antimicrobial agent and explains, at least in part, the beneficial effects of CHX in the treatment of periodontitis.
Learning 3D Scene Synthesis from Annotated RGB‐D Images (2016)

Abstract We present a data‐driven method for synthesizing 3D indoor scenes by inserting objects progressively into an initial, possibly, empty scene. Instead of relying on few hundreds of hand‐crafted 3D scenes, we take advantage of existing large‐scale annotated RGB‐D datasets, in particular, the SUN RGB‐D database consisting of 10,000+ depth images of real scenes, to form the prior knowledge for our synthesis task. Our object insertion scheme follows a co‐occurrence model and an arrangement model, both learned from the SUN dataset. The former elects a highly probable combination of object categories along with the number of instances per category while a plausible placement is defined by the latter model. Compared to previous works on probabilistic learning for object placement, we make two contributions. First, we learn various classes of higher‐order object‐object relations including symmetry, distinct orientation, and proximity from the database. These relations effectively enable considering objects in semantically formed groups rather than by individuals. Second, while our algorithm inserts objects one at a time, it attains holistic plausibility of the whole current scene while offering controllability through progressive synthesis. We conducted several user studies to compare our scene synthesis performance to results obtained by manual synthesis, state‐of‐the‐art object placement schemes, and variations of parameter settings for the arrangement model.
Comparing sequence scaffolds (2001)

The DNA sequence assembler we built for the whole genome shotgun assembly of the human genome, utilizes end-reads of inserts to order and orient assembled contigs into scaffolds for which the distances between consecutive contigs are statistically characterized. We consider the problem of comparing two such scaffolds. Applications include comparison of two distinct assemblies for mutual confirmation, and comparison of scaffold assemblies of BACs to determine a whole genome tiling of the BACs. We formalize the problem and develop efficient algorithms for a number of variations of the problem, the essential result being a sparse algorithm that refines gap estimates based on the overlap evidence.
Discovering novel systemic biomarkers in photos of the external eye (2022)

External eye photos were recently shown to reveal signs of diabetic retinal disease and elevated HbA1c. In this paper, we evaluate if external eye photos contain information about additional systemic medical conditions. We developed a deep learning system (DLS) that takes external eye photos as input and predicts multiple systemic parameters, such as those related to the liver (albumin, AST); kidney (eGFR estimated using the race-free 2021 CKD-EPI creatinine equation, the urine ACR); bone & mineral (calcium); thyroid (TSH); and blood count (Hgb, WBC, platelets). Development leveraged 151,237 images from 49,015 patients with diabetes undergoing diabetic eye screening in 11 sites across Los Angeles county, CA. Evaluation focused on 9 pre-specified systemic parameters and leveraged 3 validation sets (A, B, C) spanning 28,869 patients with and without diabetes undergoing eye screening in 3 independent sites in Los Angeles County, CA, and the greater Atlanta area, GA. We compared against baseline models incorporating available clinicodemographic variables (e.g. age, sex, race/ethnicity, years with diabetes). Relative to the baseline, the DLS achieved statistically significant superior performance at detecting AST>36, calcium<8.6, eGFR<60, Hgb<11, platelets<150, ACR>=300, and WBC<4 on validation set A (a patient population similar to the development sets), where the AUC of DLS exceeded that of the baseline by 5.2-19.4%. On validation sets B and C, with substantial patient population differences compared to the development sets, the DLS outperformed the baseline for ACR>=300 and Hgb<11 by 7.3-13.2%. Our findings provide further evidence that external eye photos contain important biomarkers of systemic health spanning multiple organ systems. Further work is needed to investigate whether and how these biomarkers can be translated into clinical impact.
High-Performance Raman-Based Distributed Fiber-Optic Sensing Under a Loop Scheme Using Anti-Stokes Light Only (2011)

A distributed fiber-optic temperature sensor technique inherently allowing for system calibration, compensating time-dependent variations of the fiber losses as well as local external perturbations, is proposed using a loop-scheme together with Raman anti-Stokes-only measurement. A temperature resolution enhancement with respect to a standard loop configuration is shown by experiments, providing a robust and reliable high-performance sensing technique for long sensing ranges.
Attenuation and dispersion of compressional waves in fluid-filled porous rocks with partial gas saturation (White model); Part II, Results (1979)

Abstract In this investigation, Biot's (1962) theory for wave propagation in porous solids is applied to study the velocity and attenuation of compressional seismic waves in partially gas-saturated porous rocks. The physical model, proposed by White (1975), is solved rigorously by using Biot's equations which describe the coupled solid-fluid motion of a porous medium in a systematic way. The quantitative results presented here are based on the theory described in Dutta and Ode (1979, this issue). We removed several of White's questioned approximations and examined their effects on the quantitative results. We studied the variation of the attenuation coefficient with frequency, gas saturation, and size of gas inclusions in an otherwise brine-filled rock. Anomalously large absorption (as large as 8 dB/cycle) at the exploration seismic frequency band is predicted by this model for young, unconsolidated sandstones. For a given size of the gas pockets and their spacing, the attenuation coefficient (in dB/cycle) increases almost linearly with frequency f to a maximum value and then decreases approximately as 1/f. A sizable velocity dispersion (of the order of 30 percent) is also predicted by this model. A low gas saturation (4-6 percent) is found to yield high absorption and dispersion.An analysis of all of the field variables (stresses and displacements) is presented in terms of Biot's type I (the classical compressional) wave and type II (the diffusion) wave. It is pointed out that the dissipation of energy in this model is mainly due to the relative fluid flow from the type II wave. From our formulation, many of White's equations can be derived as suitable approximations, and it is shown that the discontinuity in fluid pressure assumed by White at the gas-water interface is the discontinuity in the fluid pressure contribution by the type II wave.Our quantitative results are in reasonably good agreement with White's (1975) approximate theory. However, the phase velocities computed by White's approximate treatment do not approach the correct zero-frequency limit (Gassmann-Wood) when compared to the present theory. Most of these disagreements disappear if the corrections to White's theory as suggested by Dutta and Seriff (1979, this issue) are incorporated.
Slotted substrate integrated waveguide phase shifter (2016)

The slotted substrate integrated waveguide (SSIW) phase shifter with periodic loading varactors is presented. With appropriate numbers of varactors placed on the SIW's surface, the phase of two-port device could be varied with the varactors' capacitance, which is inversely proportional to the bias voltage. To prove it, a phase shifter installed seventeen varactors has been designed. There are good agreements between simulated results and experimental ones. In the frequency bandwidth of 2.5 to 3.45 GHz (about 31.9% relative bandwidth), the return loss and inserted loss are mostly better than 10 dB and 5 dB, respectively. At the center frequency of 3GHz, the maximum phase range of 80° is obtained.
Effects of Oxidative Stress on Behavior, Physiology, and the Redox Thiol Proteome of <i>Caenorhabditis elegans</i> (2010)

Accumulation of reactive oxygen species has been implicated in various diseases and aging. However, the precise physiological effects of accumulating oxidants are still largely undefined. Here, we applied a short-term peroxide stress treatment to young Caenorhabditis elegans and measured behavioral, physiological, and cellular consequences. We discovered that exposure to peroxide stress causes a number of immediate changes, including loss in mobility, decreased growth rate, and decreased cellular adenosine triphosphate levels. Many of these alterations, which are highly reminiscent of changes in aging animals, are reversible, suggesting the presence of effective antioxidant systems in young C. elegans. One of these antioxidant systems involves the highly abundant protein peroxiredoxin 2 (PRDX-2), whose gene deletion causes phenotypes symptomatic of chronic peroxide stress and shortens lifespan. Applying the quantitative redox proteomic technique OxICAT to oxidatively stressed wild-type and prdx-2 deletion worms, we identified oxidation-sensitive cysteines in 40 different proteins, including proteins involved in mobility and feeding (e.g., MYO-2 and LET-75), protein translation and homeostasis (e.g., elongation factor 1 [EFT-1] and heat shock protein 1), and adenosine triphosphate regeneration (e.g., nucleoside diphosphate kinase). The oxidative modification of some of these redox-sensitive cysteines may contribute to the physiological and behavioral changes observed in oxidatively stressed animals.
Direct effect of zinc on mitochondrial apoptogenesis in prostate cells (2002)

Exposure to zinc induces apoptosis in PC-3 and BPH cells, which accumulate high intracellular levels of zinc, but not in HPR-1 cells, which do not accumulate high levels of zinc. Once initiated, the induction of apoptosis is not reversed by the removal of zinc, i.e., it is an irreversible process. The apoptogenic effect is due to a direct effect of zinc on mitochondria that results in the release of cytochrome c. The cell specificity of zinc induction of apoptogenesis is dependent on the ability of the cells to accumulate high levels of intracellular zinc and on the ability of the mitochondria to respond to the direct effect of zinc.
Pituitary adenylate cyclase-activating polypeptide regulates prolactin promoter activity via a protein kinase A-mediated pathway that is independent of the transcriptional pathway employed by thyrotropin- releasing hormone (1996)

The hypothalamic peptide, pituitary adenylate cyclase-activating polypeptide (PACAP), can efficiently increase cAMP levels in pituitary cells and release a number of pituitary hormones, suggesting an important physiological role for this peptide in pituitary function. Exposure of GH3 rat pituitary cells to PACAP results in increases in cellular cAMP levels, PRL promoter activity, and PRL messenger RNA levels. We have employed this system to further characterize PACAP regulation of PRL gene expression. RT-PCR analysis showed that GH3 cells express transcripts for two PACAP receptors, PACAP-R-hop1 and VIP2. As the former can couple PACAP to increases in both cAMP and inositol phosphates, we investigated whether either pathway mediates PACAP action on the PRL promoter. Our observations that TRH, but not PACAP, increases the intracellular Ca2+ concentration in GH3 cell cultures and that the optimal concentrations of TRH and PACAP have additive effects on transient expression of a PRL-CAT construct imply that the inositol trisphosphate-Ca2+ pathway is not significantly involved in PACAP action on the PRL promoter. Four kinase inhibitors exhibited similar profiles of inhibition of the activity on PRL-chloramphenicol acetyltransferase (PRL-CAT) of either the adenylyl cyclase activator forskolin (FSK) or PACAP, suggesting a transcriptional role for protein kinase A (PKA). The observations that coexpression of the dominant PKA inhibitor RAB completely blocked either FSK or PACAP action on PRL-CAT and that these actions of FSK and PACAP were completely nonadditive imply that the cAMP-PKA pathway plays a dominant role in PACAP regulation of PRL gene expression. Coexpression of low levels of KCREB, a cAMP response element (CRE)-binding protein (CREB) dominant inhibitor, partially blocked regulation of PRL-CAT activity by PACAP, but not TRH, implying that PACAP action is mediated at least in part by a CREB family member that can dimerize with CREB. The PRL promoter contains an asymmetric sequence at positions -99/-92 resembling a canonical CRE and termed here the CRE-like element (CLE). Mutation of either the left or right 4 bp of the CLE yielded a strong decrease in the response to either FSK or PACAP, but not to TRH. These data imply that PACAP and TRH employ independent pathways to regulate the PRL promoter, and that PACAP action is exerted virtually entirely via a cAMP/PKA-mediated pathway that is strongly dependent upon an intact CLE sequence and at least partially dependent upon the activity of a CREB-related protein.
Metamodel-Based Optimization of a Lithium-Ion Battery Cell for Maximization of Energy Density with Evolutionary Algorithm (2019)

The demand for lithium-ion batteries is gradually increasing, not only in the field of portable electronic devices but also in high-capacity energy storage systems and electric vehicles, owing to such advantages as a high capacity and high power. Accordingly, power and capacity improvements of lithium-ion batteries are required. To achieve such improvements, it is very effective to optimize the electrode thickness, porosity, separator thickness, and active particle size. In this study, maximization of the specific energy density is achieved using metamodel-based global optimization. The capacity and power of the design variables are calculated using an electrochemical-thermal model. The sampling points for the generation of a metamodel are obtained using an optimal Latin hypercube design, and a radial basis function-based metamodel is generated. Furthermore, the global optimal solution is obtained using an evolutionary algorithm. As the results of the optimization show, unnecessary mass reduction, increased negative/positive capacity ratio, and decreased internal resistance, thereby improving the specific energy density without changing the specific power density.
Coding of Real-Number Sequences for Error Correction: A Digital Signal Processing Problem (1984)

Error-correcting codes defined over the real-number and complex-number fields are introduced. The possibility of utilizing realnumber arithmetic permits the codes to be implemented with operations normally available in standard programmable digital signal processors by methods which are discussed. Hadamard and discrete Fourier transform codes are presented for block coding, and the latter are seen to be cyclic and to include the class of BCH codes. It is shown that maximum distance separable real-number BCH ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N, K</tex> ) codes exist for all nontrivial values of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">K</tex> . A large class of block and convolutional real-number single-error-correcting codes, derived from similar codes over <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">GF(p)</tex> , are presented. Both block and convolutional codes are seen to be describable by the <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">z</tex> -transform in a manner which emphasizes their similarities to conventional digital signal processing structures such as digital filters and digital filter banks. Methods for correcting weight <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t + 1</tex> errors in a <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</tex> error-correcting code are demonstrated and interpreted; in particular, the use of a VLSI digital signal processor for implementation of an algorithm for correcting almost all double adjacent error patterns in a single-error-correcting convolutional code is discussed.
Spatial and Temporal Stability of Paneth Cell Phenotypes in Crohnʼs Disease (2014)

Accurate Paneth cell phenotypes can be assessed using biopsy materials with the caveat that sufficient well-oriented crypts exist in the specimen. This advance will extend the potential clinical application of this novel stratification platform.
Optical-fibre data collection (1981)

A new form of optical-fibre data-highway telemetry system enables a large number of separate data sources to be input anywhere along the fibre cable, without involving optical connections
A modular esterase from <i>Pseudomonas fluorescens</i> subsp. <i>cellulosa</i> contains a non-catalytic cellulose-binding domain (1993)

The 5' regions of genes xynB and xynC, coding for a xylanase and arabinofuranosidase respectively, are identical and are reiterated four times within the Pseudomonas fluorescens subsp. cellulosa genome. To isolate further copies of the reiterated xynB/C 5' region, a genomic library of Ps. fluorescens subsp. cellulosa DNA was screened with a probe constructed from the conserved region of xynB. DNA from one phage which hybridized to the probe, but not to sequences upstream or downstream of the reiterated xynB/C locus, was subcloned into pMTL22p to construct pFG1. The recombinant plasmid expressed a protein in Escherichia coli, designated esterase XYLD, of M(r) 58,500 which bound to cellulose but not to xylan. XYLD hydrolysed aryl esters, released acetate groups from acetylxylan and liberated 4-hydroxy-3-methoxycinnamic acid from destarched wheat bran. The nucleotide sequence of the XYLD-encoding gene, xynD, revealed an open reading frame of 1752 bp which directed the synthesis of a protein of M(r) 60,589. The 5' 817 bp of xynD and the amino acid sequence between residues 37 and 311 of XYLD were almost identical with the corresponding regions of xynB and xynC and their encoded proteins XYLB and XYLC. Truncated derivatives of XYLD lacking the N-terminal conserved sequence retained the capacity to hydrolyse ester linkages, but did not bind cellulose. Expression of truncated derivatives of xynD, comprising the 5' 817 bp sequence, encoded a non-catalytic polypeptide that bound cellulose. These data indicate that XYLD has a modular structure comprising of a N-terminal cellulose-binding domain and a C-terminal catalytic domain.
Topic-Enhanced Capsule Network for Multi-Label Emotion Classification (2020)

Identifying multiple emotions in a piece of text is an important research topic in the NLP community.Existing methods usually model the task as a multi-label classification problem, while these work has two issues. First, these methods fail to leverage the topic information of the text, which has been shown to be effective for sentiment analysis task. Second, different parts of the text can contribute differently to predicting different emotion labels, so the proposed model needs to capture effective features for each corresponding emotion, which is not considered by existing models. To tackle these problems, we propose a topic-enhanced capsule network, which contains two main parts: a variational autoencoder and a capsule module, for multi-label emotion detection task. Specifically, the variational autoencoder can learn the latent topic information of the text, and the capsule module can capture rich features for corresponding emotion. Experimental results on two benchmark datasets show that the proposed model achieves the current best performance, outperforming previous methods and strong baselines by a large margin.
Real-Time Evaluation of Optical Nonlinear Effects on 112Gbps PM-QPSK Signal in Dispersion Managed Links (2011)

We demonstrate the impact of nonlinear effects on dispersion managed links with a FPGA-based 112Gbps real-time receiver. We clarify that PM-RZ-QPSK provides superior robustness, whereas PM-NRZ-QPSK offers better total performance resulting from higher OSNR sensitivity.