gebhart/patrepeval huggingface dataset:
Supplementary Material for: Gingipains: Critical Factors in the Development of Aspiration Pneumonia Caused by Porphyromonas gingivalis (2016)

<br>Aspiration pneumonia is a life-threatening infectious disease often caused by oral anaerobic and periodontal pathogens such as <i>Porphyromonas gingivalis.</i> This organism produces proteolytic enzymes, known as gingipains, which manipulate innate immune responses and promote chronic inflammation. Here, we challenged mice with <i>P. gingivalis</i> W83 and examined the role of gingipains in bronchopneumonia, lung abscess formation, and inflammatory responses. Although gingipains were not required for <i>P. gingivalis</i> colonization and survival in the lungs, they were essential for manifestation of clinical symptoms and infection-related mortality. Pathologies caused by wild-type (WT) <i>P. gingivalis</i> W83, including hemorrhage, necrosis, and neutrophil infiltration, were absent from lungs infected with gingipain-null isogenic strains or WT bacteria preincubated with gingipain-specific inhibitors. Damage to lung tissue correlated with systemic inflammatory responses, as manifested by elevated levels of TNF, IL-6, IL-17, and C-reactive protein. These effects were unequivocally dependent on gingipain activity. Gingipain activity was also implicated in the observed increase in IL-17 in lung tissues. Furthermore, gingipains increased platelet counts in the blood and activated platelets in the lungs. Arginine-specific gingipains made a greater contribution to <i>P. gingivalis-</i>related morbidity and mortality than lysine-specific gingipains. Thus, inhibition of gingipain may be a useful adjunct treatment for <i>P. gingivalis-</i>mediated aspiration pneumonia.
Ferroelectricity-free lead halide perovskites (2019)

We employ direct piezoelectric force microscopy to examine the ferroelectric response of halide perovskites and prove that halide perovskites are ferroelectricity free.
Printing a Pacinian Corpuscle: Modeling and Performance (2021)

The Pacinian corpuscle is a highly sensitive mammalian sensor cell that exhibits a unique band-pass sensitivity to vibrations. The cell achieves this band-pass response through the use of 20 to 70 elastic layers entrapping layers of viscous fluid. This paper develops and explores a scalable mechanical model of the Pacinian corpuscle and uses the model to predict the response of synthetic corpuscles, which could be the basis for future vibration sensors. The -3dB point of the biological cell is accurately mimicked using the geometries and materials available with off-the-shelf 3D printers. The artificial corpuscles here are constructed using uncured photoresist within structures printed in a commercial stereolithography (SLA) 3D printer, allowing the creation of trapped fluid layers analogous to the biological cell. Multi-layer artificial Pacinian corpuscles are vibration tested over the range of 20-3000 Hz and the response is in good agreement with the model.
Rap1 relocalization contributes to the chromatin-mediated gene expression profile and pace of cell senescence (2013)

Cellular senescence is accompanied by dramatic changes in chromatin structure and gene expression. Using Saccharomyces cerevisiae mutants lacking telomerase (tlc1Δ) to model senescence, we found that with critical telomere shortening, the telomere-binding protein Rap1 (repressor activator protein 1) relocalizes to the upstream promoter regions of hundreds of new target genes. The set of new Rap1 targets at senescence (NRTS) is preferentially activated at senescence, and experimental manipulations of Rap1 levels indicate that it contributes directly to NRTS activation. A notable subset of NRTS includes the core histone-encoding genes; we found that Rap1 contributes to their repression and that histone protein levels decline at senescence. Rap1 and histones also display a target site-specific antagonism that leads to diminished nucleosome occupancy at the promoters of up-regulated NRTS. This antagonism apparently impacts the rate of senescence because underexpression of Rap1 or overexpression of the core histones delays senescence. Rap1 relocalization is not a simple consequence of lost telomere-binding sites, but rather depends on the Mec1 checkpoint kinase. Rap1 relocalization is thus a novel mechanism connecting DNA damage responses (DDRs) at telomeres to global changes in chromatin and gene expression while driving the pace of senescence.
Empirical analysis of compressive sensing reconstruction using the curvelet transform: SEAM Barrett model (2021)

In this paper, we study one of the key elements of seismic compressive sensing (CS) – the sparse transform. CS reconstruction properties of the 2D curvelet transform are considered with application to the SEAM Barrett model data. We considered two CS reconstruction tests: (i) when a sampling scheme has a maximum gap smaller than the size of the key curvelet basis functions, and (ii) when a sampling scheme has a gap size on the order of the key curvelet basis function. In the first test, we observe a typical behavior of reconstructed coefficients: coefficients with larger initial energy were reconstructed better. For the second case, coefficient reconstruction error depends on the decimation level of the curvelet basis functions. The curvelet coefficients are not reconstructed when the curvelet basis functions are entirely missed due to the gap. We plan to apply this analysis in an inverse manner: assessing curvelet coefficient reconstruction based on the decimation level of corresponding basis functions. This will be helpful in situations when the initial signal is not known.
ChemInform Abstract: Polymer Supported Transition Metal Complexes for Catalytic Epoxidation of Olefins. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Nonlinear quantum logic with colliding graphene plasmons (2023)

Graphene has emerged as a promising platform to bring nonlinear quantum optics to the nanoscale, where a large intrinsic optical nonlinearity enables long-lived and actively tunable plasmon polaritons to strongly interact. Here we theoretically study the collision between two counter-propagating plasmons in a graphene nanoribbon, where transversal subwavelength confinement endows propagating plasmons with a flat band dispersion that enhances their interaction. This scenario presents interesting possibilities towards the implementation of multimode polaritonic gates that circumvent limitations imposed by the Shapiro no-go theorem for photonic gates in nonlinear optical fibers. As a paradigmatic example we demonstrate the feasibility of a high-fidelity conditional $\ensuremath{\pi}$ phase shift (CZ), where the gate performance is fundamentally limited only by the single-plasmon lifetime. These results open exciting avenues towards quantum information and many-body applications with strongly interacting polaritons.
Highly-reliable, low-resistivity bcc-Ta gate MOS technology using low-damage Xe-plasma sputtering and Si-encapsulated silicidation process (2002)

We present for the first time highly reliable metal-gate MOS technology with low-resistivity bcc-Ta. Low sheet resistance of 1.7 /spl Omega//sq. has been obtained by precisely controlling the ion bombardment conditions during Ta sputtering process, and by employing Si-encapsulation technique to suppress oxidation or hydrogen-accumulation in Ta thin film. By comparing Ta-gate and poly-Si gate MOS devices, it is confirmed that Ta-gate structure does not induce significant degradation in the gate-oxide reliability by using low-damage Xe-plasma sputtering and the Si encapsulation technique. It is also demonstrated that carrier mobility/velocity in the inversion layer of Ta gate SOI MOSFET is slightly higher than that of poly-Si gate SOI MOSFET because of higher thermal-conductivity of the metal gate.
Comparative Genomic Hybridization and Copy Number Abnormalities in Breast Cancer (2020)

In most cases, array comparative genomic hybridization (CGH) is the method of choice for their discovery and may be used in some setting for clinical assessments of these abnormalities. Accordingly, authors review several of the current array CGH technologies available and the considerations needed when determining the technology most applicable to a given study. Several recurrent high-level genome copy number abnormalities (CNAs) are associated with clinical endpoints, including reduced survival duration and response to aberration-targeted therapies. CGH is the primary technology used for assessment of genome copy number. Typically, analysis proceeds by hybridizing differentially labeled tumor and normal DNA to a representation of the normal genome, although some platforms perform tumor and normal reference hybridization in separate representations. Array CGH technologies are becoming increasingly powerful tools for the identification of recurrent genome CNAs that are associated with outcome or response to therapy in breast and other cancers.
Laser Beam Analysis, Propagation, and Spatial Shaping Techniques (2021)

The propagation and focusing properties of real laser beams are greatly influenced by beam shape, phase distortions, degree of coherence, and aperture truncation effects. The ability to understand, predict, and correct these real-world effects is essential in optical engineering. This short course develops the analytical tools for measuring and quantifying the important characteristics of a real laser beam, allowing the optical engineer to calculate the performance of the beam in a given optical system. In addition, the intensity, phase, and polarization of laser beams can often be engineered to enhance system performance. The course explores a wide variety of engineering approaches to beam optimization using intuitive design methods coupled with a rigorous mathematical treatment of fundamental limits.
Observing monomer - dimer transitions of neurotensin receptors 1 in\n single SMALPs by homoFRET and in an ABELtrap (2019)

G protein-coupled receptors (GPCRs) are a large superfamily of membrane\nproteins that are activated by extracellular small molecules or photons.\nNeurotensin receptor 1 (NTSR1) is a GPCR that is activated by neurotensin, i.e.\na 13 amino acid peptide. Binding of neurotensin induces conformational changes\nin the receptor that trigger the intracellular signaling processes. While\nrecent single-molecule studies have reported a dynamic monomer - dimer\nequilibrium of NTSR1 in vitro, a biophysical characterization of the\noligomerization status of NTSR1 in living mammalian cells is complicated. Here\nwe report on the oligomerization state of the human NTSR1 tagged with mRuby3 by\ndissolving the plasma membranes of living HEK293T cells into 10 nm-sized\nsoluble lipid nanoparticles by addition of styrene-maleic acid copolymers\n(SMALPs). Single SMALPs were analyzed one after another in solution by\nmulti-parameter single molecule spectroscopy including brightness, fluorescence\nlifetime and anisotropy for homoFRET. Brightness analysis was improved using\nsingle SMALP detection in a confocal ABELtrap for extended observation times in\nsolution. A bimodal brightness distribution indicated a significant fraction of\ndimeric NTSR1 in SMALPs or in the plasma membrane, respectively, before\naddition of neurotensin.\n
Finite Element Modeling Methodology for Monotonic Bend Test of Flip-Chip BGA Package (2020)

This paper presents a finite element modeling methodology to predict failure during four-point monotonic bend test of flip-chip ball grid array (FCBGA) packages mounted on printed circuit boards (PCBs). Monotonic bend tests are conducted to failure at approximately 4 mm/sec according to IPC/JEDEC-9702 and the strain is monitored by mounted strain gauges. Test conditions are specified through displacement boundary conditions. Models are validated with displacement and strain. We propose a failure criterion based on the typical failure location and assume it to be a material property. Three test vehicles, one single die FCBGA package and two chip-on-wafer-on-substrate (CoWoS) FCBGA packages are used for validation; all test vehicles are exposed die with stiffener ring packages. From these test vehicles, failure occurs most by cratering the board side pad. Using the proposed methodology, the failure strain for a 3.175mm thick Megtron6 board is calculated to be 5975 μstrain without via-in- pad plated over (VIPPO) and 8130 with VIPPO. The failure criterion is then used to study the effect of design parameters on monotonic bend performance. A parametric study finds when the PCB is thick, board parameters are the most important, BGA parameters are next most important, and most package level parameters have little impact.
ChemInform Abstract: Improved Deprotection Procedure for DPSE Protected Phosphorothioates. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Process window discovery, expansion and control of design hotspots susceptible to overlay failures (2017)

The latest design nodes have seen development and use of multi-patterning techniques like SAQP and LELELE for density multiplication in semiconductor industry below 28nm processes. Traditional lithography process window studies have centered on focus and dose latitudes and are typically evaluated with inspection and CD measurements on a focus dose modulated wafer. However, on sub 14 nm design nodes, overlay has become an important litho parameter acting as a source of new systematic defects on an otherwise centered process.
Incorporating Beauveria bassiana Into an Integrated Pest Management Plan for Coffee Berry Borer in Hawaii (2020)

Since its recent establishment in Hawaii, the coffee berry borer (CBB), Hypothenemus hampei (Coleoptera: Curculionidae), threatens yields, quality and price of coffee production. A limited number of insecticides (primarily Beauveria bassiana) is used to control CBB with minimal disruption in this agroecosystem. We evaluated two insecticide spray strategies across eight coffee farms in the Kona and Ka‘u Districts of Hawaii Island. Coffee growers sprayed insecticides approximately monthly (calendar basis) or in response to CBB field-monitoring data (threshold-based). Overall, farms adopting thresholds performed more insecticide applications early in the season (May to July), but significantly fewer overall, when compared with calendar-based strategies (i.e., 4–5 versus 7–11 seasonal sprays, respectively). Generalized linear models assessing the variability in CBB infestation rates, berry penetration, and infection by B. bassiana indicated that threshold-based sprays provided equivalent CBB-control compared with calendar ones. When corrected for yield, there was a cost saving for threshold versus calendar-based spray programs (i.e., cost 5.4% versus 11.8% of gross yield). Total defects in processed coffee after harvest were statistically similar between the two spray regimes; i.e., 8.5% ± 1.0% and 10.4% ± 1.7%, respectively. We hypothesize that B. bassiana applied early in the season is more effective, since the fungus targets initial CBB infestations when the prolonged location of founder females in the outer berry endosperm favors its infection. Our study suggests that spray timing for CBB based on field monitoring data can reduce costs, however additional measures, such as field and post-harvest sanitation, are necessary to achieve sustainable CBB control in the Islands.
Experimental Study of High Reynolds' Number Flows Between Narrow Gaps (1992)

Abstract High Reynolds' number flows between narrow gaps are very common in the reaction injection mold filling process (RIM) where low viscosity polymers are injected into thin mold cavities in relatively short time intervals. The resulting short cycle times have given RIM advantages over other manufacturing techniques in the polymer industry. In addition to the lower temperatures encountered during the RIM process, the low material viscosities enables mold filling using smaller injection pressures and mold clamping forces than in the conventional thermoplastic injection mold filling process. Considering the low viscosity of the injected fluid, short injection times and considerably large parts, such as automotive body panels, it is clear that in RIM processes inertia effects are not negligible. In fact Reynolds' numbers in such processes can reach 10 and above. This paper presents an experimental study performed on the high Reynolds' number flows between narrow gaps. First, the general equations that govern such flows are derived and written in dimensionless form. The magnitudes and influence of inertia forces, surface tension and viscous forces are analyzed in terms of Reynolds' number, capillary number and Weber number. The theoretical background is followed by a short explanation of the experimental set-up. Several experiments are shown in different mold configurations and at various mold filling speeds. The results showed that inertia greatly influences the mold filling pattern and capillary effects are a major cause of air bubble entrapment.
Theoretical Development of Cross Section Uncertainty Library for Core Simulators (2019)

Abstract The current regulatory process allows for the use of models employing realistic assumptions as opposed to conservative bounding approaches, requiring a concerted use of best-estimate modeling and comprehensive estimation of uncertainties, collectively referred to as best-estimate-plus-uncertainty methods. This necessitates access to an integrated and automated procedure for the propagation and understanding of key sources of uncertainties. Focusing on neutronic reactor core simulation, this paper lays the theoretical foundations for an uncertainty characterization framework that is comprehensive, informative, and efficient, implying its ability to propagate all sources of uncertainties and identify key contributors in a computationally efficient manner. This paper represents the overarching objective of our work to propagate multigroup (MG) cross section uncertainties through lattice physics calculations and core-wide simulation. This requires the evaluation of few-group parameters uncertainties in terms of a wide range of local conditions, e.g., burnup, fuel temperature, etc., which results in a very high dimensional uncertainty space. The first strategy employed to compress the few-group uncertainties is the physics-guided coverage mapping (PCM) methodology developed to assess the similarity between the branch and base uncertainties in lattice calculation. To further compress the uncertainty propagated, this paper employs an accuracy-preserving reduced order modeling (ROM) technique relying on the use of range finding algorithms to construct all few-group parameters variations to a very small preset tolerance. In a separate cosubmitted paper, this framework is demonstrated to thermal reactors including both light and heavy water systems using a number of computer codes, including NESTLE-C, SERPENT, SCALE's NEWT, and SAMPLER codes.
Physical Layer Control for Disaggregated Optical Systems (2018)

Disaggregating optical communication systems can impact physical layer control. Recent progress on multi-domain transmission control and machine-learning provide capabilities for adaptation and development of engineering rules in the field with potential benefits for disaggregated systems.
Mechanisms underlying global stereopsis in fovea and periphery (2013)

To better understand the pooling properties underlying global stereopsis we examined the relationship between carrier luminance spatial frequency and modulator disparity spatial frequency. Thresholds for detecting global sinusoidal disparity corrugations of spatially band-pass noise were measured as a function of modulator disparity spatial frequency for both centrally and peripherally located stimuli using a standard 2-IFC task. We found a characteristic relationship that depended on modulator disparity spatial frequency. At high modulator disparity spatial frequencies (>1c/d), there is an optimal ratio of around 2.6, whereas at low modulator disparity spatial frequencies, there is an optimal absolute carrier luminance spatial frequency (i.e., 3c/d). In the periphery, vision is restricted to modulator disparity spatial frequencies below 1c/d and, as a consequence, following the above rule, there is an optimum absolute carrier luminance spatial frequency that reduces in spatial frequency with increasing eccentricity. This finding is consistent with there being more than one channel processing global stereo that is subsequently confirmed using a 2×2 AFC detection/discrimination paradigm. Furthermore, because of the different carrier/modulator relationships in central and peripheral vision, peripheral global stereo cannot be simply related to central global stereo by a scaling factor and thus cannot be simply due to cortical magnification, as originally thought.
A Variable Step Size Normalized Least-Mean-Square Algorithm Based on Data Reuse (2022)

The principal issue in acoustic echo cancellation (AEC) is to estimate the impulse response between the loudspeaker and microphone of a hands-free communication device. This application can be addressed as a system identification problem, which can be solved by using an adaptive filter. The most common one for AEC is the normalized least-mean-square (NLMS) algorithm. It is known that the overall performance of this algorithm is controlled by the value of its normalized step size parameter. In order to obtain a proper compromise between the main performance criteria (e.g., convergence rate/tracking versus accuracy/robustness), this specific term of the NLMS algorithm can be further controlled and designed as a variable parameter. This represents the main motivation behind the development of variable step size algorithms. In this paper, we propose a variable step size NLMS (VSS-NLMS) algorithm that exploits the data reuse mechanism, which aims to improve the convergence rate/tracking of the algorithm by reusing the same set of data (i.e., the input and reference signals) several times. Nevertheless, we involved an equivalent version of the data reuse NLMS, which provides the convergence modes of the algorithm. Based on this approach, a sequence of normalized step sizes can be a priori scheduled, which is advantageous in terms of the computational complexity. The simulation results in the context of AEC supported the good performance features of the proposed VSS-NLMS algorithm.