gebhart/patrepeval huggingface dataset:
Simulation of electromagnetic induction scattering from targets with negligible to moderate penetration by primary fields (2002)

The problem of numerical modeling of electromagnetic induction (EMI) responses by metallic objects is complicated by the fact that transmitted fields may penetrate the target, but will often only do so slightly. The effect cannot be ignored, yet it is often grossly impractical to discretize the entire surface or volume of a target in space increments only on the order of a fraction of the skin depth. To deal with this problem, we retain a simple integral equation formulation in scalar potential for the region outside the target, where magnetic fields are quasi-static and irrotational. Within the target we apply only the divergence relation, /spl nabla//spl middot/H = 0. When the skin depth is small relative to the radius of curvature of the target (e.g., <0.1), we use the thin skin depth approximation (TSA), /spl part/H/sub n///spl part/n as /spl sim/-ikH/sub n/, just inside the target's surface, where k is the electromagnetic wavenumber inside the metal and n is the normal direction on the surface and pointing inside of metallic object. Examination of analytical solutions for the sphere suggests the parameter range in which this approximation might perform well and suggests ways of improving accuracy over an extended range. The fundamental TSA formulation appears to be relatively robust. Analysis indicates that it is insensitive to variation over the target's surface of primary field orientation relative to that surface, and that it is only dependent on the target's magnetic permeability through induction number. Implementing the TSA numerically, within the above divergence relation, allows us to express all quantities in terms of tangential magnetic field components and their tangential derivatives over the target surface. In principle, this closes the system completely in terms of the exterior scalar potential. Broad-band numerical simulations based on the TSA compare favorably with analytical and other numerical solutions.
Prevalence of Anti‐HCV Antibody in Blood Donors in the Tokyo Area (1990)

Prospective studies of posttransfusion hepatitis carried out in the past decade showed that 18.1% of the blood transfusions resulted in non-A non-B hepatitis in Japan. As an approach to the prevention of posttransfusion non-A non-B hepatitis (PTNANB), anti-hepatitis C virus (HCV) positivity was measured in 2,970 blood donations in the Tokyo area, and in 200 children aged between 6 and 15 years. Thirty-four cases were anti-HCV-positive, showing an overall positivity of 1.14%. None of the 200 children younger than 15 years old were positive. Correlation of anti-HCV positivity with the serum ALT levels was observed, but by reducing the accepted ALT levels from 35 Karmen Units (KU) down to 25 KU, it is estimated that 62.5% of the observed PTNANB would still have occurred, and 5.1% of the donated blood could not be used for transfusion. On the other hand, it is estimated that the majority of PTNANB could be prevented, with the loss of 1.14% of donated blood units, using the anti-HCV screening test.
Triggers for delayed intervention in patients with small renal masses undergoing active surveillance: a systematic review (2020)

The available evidence shows that both tumor-related and patient-related factors are ultimate triggers for DI in patients with SRMs undergoing AS. However, the level of evidence is still low and further research is needed to individualize AS strategies according to both tumor biology and patient-related characteristics and values.
Anti-HIV Pronucleotides: SATE Versus Phenyl as a Protecting Group of AZT Phosphoramidate Derivatives (1999)

We comparatively studied the decomposition pathways in CEM cell extract of several PHENYL phosphoramidate diesters of AZT. A correlation between anti-HIV activities in TK- cell lines and pharmacokinetic data has been observed. This study would help to design corresponding SATE phosphoramidate diesters which revealed potent anti-HIV properties.
James Wyant's contributions to polarization aberration theory (2021)

James Wyant’s contributions to the foundations of polarization aberration theory are reviewed and the simplifications it provided relative to polarization ray tracing are emphasized.
Femtosecond Time-Resolved Stimulated Raman Spectroscopy:  Application to the Ultrafast Internal Conversion in β-Carotene (2003)

We have developed the technique of femtosecond stimulated Raman spectroscopy (FSRS), which allows the rapid collection of high-resolution vibrational spectra on the femtosecond time scale. FSRS combines a sub-50 fs actinic pump pulse with a two-pulse stimulated Raman probe to obtain vibrational spectra whose frequency resolution limits are uncoupled from the time resolution. This allows the acquisition of spectra with <100 fs time resolution and <30 cm(-1) frequency resolution. Additionally, FSRS is unaffected by background fluorescence, provides rapid (100 ms) acquisition times, and exhibits traditional spontaneous Raman line shapes. FSRS is used here to study the relaxation dynamics of beta-carotene. Following optical excitation to S(2) (1B(u) (+)) the molecule relaxes in 160 fs to S(1) (2A(g) (-)) and then undergoes two distinct stages of intramolecular vibrational energy redistribution (IVR) with 200 and 450 fs time constants. These processes are attributed to rapid (200 fs) distribution of the internal conversion energy from the S(1) C=C modes into a restricted bath of anharmonically coupled modes followed by complete IVR in 450 fs. FSRS is a valuable new technique for studying the vibrational structure of chemical reaction intermediates and transition states.
Capsular Polysaccharide Cross-Regulation Modulates Bacteroides thetaiotaomicron Biofilm Formation (2020)

<i>Bacteroides thetaiotaomicron</i> is one of the most abundant gut symbiont species, whose contribution to host health through its ability to degrade dietary polysaccharides and mature the immune system is under intense scrutiny. In contrast, adhesion and biofilm formation, which are potentially involved in gut colonization and microbiota structure and stability, have hardly been investigated in this intestinal bacterium. To uncover <i>B. thetaiotaomicron</i> biofilm-related functions, we performed a transposon mutagenesis in the poorly biofilm-forming reference strain VPI-5482 and showed that capsule 4, one of the eight <i>B. thetaiotaomicron</i> capsules, hinders biofilm formation. We then showed that the production of capsules 1, 2, 3, 5, and 6 also inhibits biofilm formation and that decreased capsulation of the population correlated with increased biofilm formation, suggesting that capsules could be masking adhesive surface structures. In contrast, we showed that capsule 8 displayed intrinsic adhesive properties. Finally, we demonstrated that <i>BT2934</i>, the <i>wzx</i> homolog of the <i>B. thetaiotaomicron</i> glycosylation locus, competes with capsule production and impacts its adhesion capacity. This study therefore establishes <i>B. thetaiotaomicron</i> capsule regulation as a major determinant of <i>B. thetaiotaomicron</i> biofilm formation, providing new insights into how modulation of different <i>B. thetaiotaomicron</i> surface structures affects <i>in vitro</i> biofilm formation.<b>IMPORTANCE</b> The human gut harbors a complex bacterial community that plays important roles in host health and disease, including nutrient acquisition, maturation of the immune system, and resistance to infections. The capacity to adhere to surfaces and form communities called biofilms is believed to be important for niche colonization and maintenance of gut bacteria. However, little is known about the adhesion capacity of most gut bacteria. In this study, we investigated biofilm formation in <i>Bacteroides thetaiotaomicron</i>, one of the most abundant bacteria of the normal mammalian intestine. We identified that <i>B. thetaiotaomicron</i> capsules, a group of eight surface-exposed polysaccharidic layers mediating important interactions with the gut environment, are also major determinants of biofilm formation that mask or unmask adhesion factors. Studying how <i>B. thetaiotaomicron</i> regulates its adhesion properties will allow us to better understand the physiology and specific properties of this important gut symbiont within anaerobic biofilms.
Proceedings of the 1st Workshop on Deep Learning for Recommender Systems (2016)

The advent of deep learning has made it possible to extract high-level information from perceptual signals without having to specify manually and explicitly how to obtain it; instead, this can be learned from examples. This creates opportunities for ...
Real-Time and Post-reaction Microscopic Structural Analysis of Biomass Undergoing Pyrolysis (2009)

The structural complexity of unprocessed plant tissues used for thermochemical conversion of biomass to fuels and energy impedes heat and mass transfer and may increase the occurrence of tar-forming secondary chemical reactions. At industrial scales, gas and liquid products trapped within large biomass particles may reduce net fuel yields and increase tars, impacting industrial operations and increasing overall costs. Real-time microscopic analysis of poplar (Populus sp.) wood samples undergoing anoxic, pyrolytic heat treatment has revealed a pattern of tissue and macropore expansion and collapse. Post-reaction structural analyses of biomass char (biochar) by light and transmission electron microscopy have provided direct structural evidence of pyrolysis product mass-transfer issues, including trapped pyrolysis products and cell wall compression, and have demonstrated the impact of heat-transfer problems on biomass particles. Finally, microscopic imaging has revealed that pyrolyzed/gasified biochars recovered from a fluidized bed reactor retain a similar pre-reaction basic plant tissue structure as the samples used in this study, suggesting that the phenomena observed here are representative of those that occur in larger scale reactors.
Variability in the Size of Individual Airways Over the Course of One Year (1995)

Several studies have examined the reproducibility over time of standard clinical measurements of pulmonary airways parameters, such as FEV1 and FVC. These studies indicate fairly consistent reproducibility of such measurements over periods of months and years. Although such traditional pulmonary function tests can provide quantitative measures of lung function, they do not provide any insight into the local or regional variation of individual airways. Therefore, in a longitudinal study in dogs, we directly measured the baseline size (cross-sectional area) of the same individual canine airways multiple times over a 1-yr period, using high-resolution computed tomography (HRCT). We compared the variability of individual airway size both within and between subjects to the various sizes of airways and to seasonal differences in size. Five anesthetized, intubated, and ventilated dogs were studied between five and eight times over a 15-mo period. HRCT scans were acquired at end expiration with the dogs at FRC on all occasions. All individual airways showed considerable variability in size over time as measured by the coefficient of variation (CV) (range: 9.2 to 69.3). The sizes of individual airways within a dog were seen to change by as much as twofold over time. Some dogs also showed significantly greater overall variability in airway size than did other dogs (p < 0.01), but this variability was related neither to the size of the airway (p = 0.34) nor to the season. These findings indicate a substantial local and regional variability in airway caliber that would not be detectable with conventional pulmonary function tests. This variability in airway size could contribute to the local pathogenesis of lung disease.
Extraordinary Properties of Epsilon-Near-Zero and Low-Index Chalcogenide Metamaterials (2018)

‘Laminar flow’ transmission, suppression of plasmonic powerflow vortices, and absorption decreasing with increasing Joule losses can be observed in metamaterials combining plasmonic nanostructures with chalcogenide inclusions exhibiting epsilon-near-zero and sub-unitary refractive index behaviors.
Spinal Reconstruction (2007)

With an ever-expanding array of biomaterials and implant devices appearing in the field, Spinal Reconstruction: Clinical Examples of Applied Basic Science, Biomechanics and Engineering helps surgeons assess and utilize the latest technologies to improve the reconstruction of the spine and enhance the reconstitution of diseased spinal segments. With
Abstract P6-10-08: Preliminary results of a first in human Phase 1 clinical trial to demonstrate safety and feasibility of chimeric antigen receptor T (CART) cells directed against c-Met in the treatment of breast cancer (2017)

Abstract This abstract was withdrawn by the authors.
Influence of the Hydroxylation of γ-Al2O3Surfaces on the Stability and Diffusion of Single Pd Atoms:  A DFT Study (2006)

Using recent well-defined models of gamma-Al2O3 surfaces, we study the interaction of single Pd atoms with gamma-Al2O3 surfaces corresponding to realistic pretreatment conditions by means of density functional theory periodic calculations. For relevant hydroxylation states of the surface, we determine potential energy surfaces (PES) that depict the relationship between structure and interaction at the metal-oxide interface. This approach enables the determination of the low-energy diffusion paths of the adsorbed Pd species. We applied classical transition-state theory to derive the temperature-dependent hopping rate of Pd on gamma-Al2O3 surfaces. Our work provides new insight into the chemisorption and diffusion process of single Pd atoms on alumina and show that the binding energy and hopping rate of Pd atoms decrease as the surface OH coverage increases. These results offer new highlights on Pd cluster formation at the initial nucleation steps on gamma-Al2O3 surfaces.
Supplementary Data from Neutrophil Conversion to a Tumor-Killing Phenotype Underpins Effective Microbial Therapy (2023)

&lt;p&gt;SUPPLEMENTARY FIGURES 1-10; SUPPLEMENTARY TABLE and VIDEO LEGENDS; EXTENDED MATERIALS AND METHODS&lt;/p&gt;
Ultrasonic transducers for imaging and therapy based on time-reversal principles (2008)

Focusing of ultrasonic waves is a fundamental aspect of most of the medical applications of ultrasound. There are three approaches in focusing acoustic energy: geometrical, using concave transducers and acoustic lenses, electronic, using phased arrays, and time-reversal (TR), which allows both spatial and temporal concentration of acoustic energy. The aim of this talk is to make comparative analysis of advantages and disadvantages of ultrasound focusing techniques, demonstrate unique capabilities of TR focusing in medical imaging, surgery and therapy. Examples of embodiments of ultrasonic focusing transducers utilizing TR method for various biomedical applications will be presented. TR ultrasonic transducers are comprised of a reverberation chamber, which could be either an aluminum block or a water filled volume of irregular shape, and one or several piezotransducers attached to or incorporated in the reverberator. Optimization of the TR transducers for a particular application is considered, including the geometry of the TR reverberator, shape, type and dimensions of the piezotransducers. Unique abilities of TR transducers to steer the focal spot in 3D, produce pulses with arbitrary waveforms in a wide frequency band and generate focal regions of arbitrary predefined shapes using simple means such as single channel system with one piezoelement will be demonstrated.
Phosphanilic acid inhibits dihydropteroate synthase (1989)

Intact cells of Pseudomonas aeruginosa were more susceptible to phosphanilic acid (PA) than cells of Escherichia coli. In cell extracts, the dihydropteroate synthases of P. aeruginosa and E. coli were about equally susceptible to inhibition by PA. These results suggest that cells of P. aeruginosa are more permeable to PA than cells of E. coli. Although a weak inhibitor, PA acted on dihydropteroate synthase in the same manner as the sulfonamides with which PA is structurally related. Inhibition of E. coli by PA in a basal salts-glucose medium was prevented by p-aminobenzoic acid (pABA). However, pABA did not protect P. aeruginosa from PA under these conditions, possibly because pABA itself exhibited an inhibitory effect. PA also appeared to have a second mode of action. The mechanism was not elucidated.
A study of the?-NLMS algorithm with application to stereophonic acoustic echo cancellation (2000)

In stereophonic acoustic echo cancellation (SAEC), one of the fundamental problems lies in the misalignment in the filter coefficients due to the two strongly correlated channel inputs. In this paper, we study the effect of the normalization factor, ϵ, upon the convergence properties of the two-channel normalized least-mean-square (ϵ-NLMS) algorithm, through analysis and simulation studies with real speech datasets. We then show that the optimal choice for ϵ may be close to the variance of the channel-input data. Finally, a subband stereo echo canceller structure which uses a combination of the two-channel ϵ-NLMS and the fast least-squares (FLS) algorithms is proposed as a practical and promising solution to SAEC. Copyright © 2000 John Wiley & Sons, Ltd.
An Unusual “OR” Gate for Allosteric Regulation of Mammalian Transglutaminase 2 in the Extracellular Matrix (2021)

Transglutaminase 2 (TG2) is a highly expressed mammalian enzyme whose biological function is unclear, although its catalytic activity in the small intestine appears necessary for celiac disease (CeD) pathogenesis. While TG2 activity is reversibly regulated by multiple allosteric mechanisms, their roles under fluctuating physiological conditions are not well understood. Here, we demonstrate that extracellular TG2 activity is competitively controlled by the mutually exclusive binding of a high-affinity Ca<sup>2+</sup> ion or the formation of a strained disulfide bond. Binding of Ca<sup>2+</sup> at the high-affinity site does not activate TG2 <i>per se</i>, but it protects against oxidative enzyme deactivation while preserving the ability of Ca<sup>2+</sup> ions to occupy weaker binding sites capable of allosteric TG2 activation. In contrast, disulfide bond formation competitively occludes the high-affinity Ca<sup>2+</sup> site while resulting in complete TG2 inactivation. Because both outcomes are comparably favorable under typical extracellular conditions, subtle changes in the availability of redox catalysts or promoters in the extracellular matrix can dramatically alter steady-state TG2 activity. Thus, TG2 harbors a molecular "OR" gate that determines its catalytic fate upon export from cells.
Essential role of heat shock protein 90 in direct and cross-presentation (93.13) (2007)

Abstract Direct antigen presentation involves the generation of peptides by proteasomes, ferrying of peptides from cytosol to endoplasmic reticulum and finally, formation and transport of peptide-MHC I complexes. Chaperones hsp90, hsp70, gp96 and TriC have previously been shown to associate with MHC class I epitopes and their precursors. Here, we have treated cells with hsp90 inhibitors Radicicol, 17-AAG or geldanamycin and observe that (i) treatment of cells with such inhibitors leads, in a dose-and time- dependent fashion, to a decrease in the levels of peptide-bound but not total cell surface MHC I; (ii) Radicicol does not affect transport of non-MHC I, control proteins to the cell surface; (iii) Radicicol does not impair MHC I synthesis; and (iv) the reduction in surface MHC I expression caused by Radicicol, is restored by pulsing cells with exogenous peptides. These results indicate an essential role for hsp90 in peptide-transport during endogenous (direct) presentation. During indirect or cross-presentation, antigen presenting cells acquire, process and present exogenous antigen onto the MHC I. Our previous studies (Binder and Srivastava, 2005, Nature Immunology 6, 593) have shown an essential role for HSP-chaperoned peptides in this process. In that study, cell lysates replete with or depleted of one or several HSP-peptide complexes were used to study cross-priming. We have now examined cross-priming by intact cells instead of cell lysates and we observe that hsp90 plays a unique, essential and non-redundant role in cross-priming as well. Data that bear on the mechanism of post-proteasomal transport of peptides, shall be presented.
GaInN light-emitting diodes with omnidirectional reflectors (2003)

A high-reflectivity omni directional reflector (ODR) has been incorporated into a GaInN light-emitting diode (LED) structure. The ODR comprises a transparent, electrically conductive quarter-wave layer of indium tin oxide clad by silver and serves as an ohmic contact to p-type GaN. It is shown that ODR-LEDs have low optical losses and high extraction efficiency. Mesa-structure GaInN/GaN ODR-LEDs emitting in the blue wavelength range are demonstrated and compared to GaInN/GaN LEDs with semitransparent Ni/Au top contacts. The extraction efficiency of ODR-LEDs is higher as compared to conventional LEDs with Ni/Au contacts.
Word-Level Sequential Memory Abstraction for Model Checking (2008)

Many designs intermingle large memories with wide data paths and nontrivial control. Verifying such systems is challenging, and users often get little traction when applying model checking to decide full or partial end-to-end correctness of such designs. Interestingly, a subclass of these systems can be proven correct by reasoning only about a small number of the memory entries at a limited number of time points. In this paper, we leverage this fact to abstract certain memories in a sound way, and we demonstrate how our memory abstraction coupled with an abstraction refinement algorithm can be used to prove correctness properties for three challenging designs from industry and academia. Key features of our approach are that we operate on standard safety property verification problems, that we proceed completely automatically without any need for abstraction hints, that we can use any bit-level model checker as a back-end decision procedure, and that our algorithms fit seamlessly into a standard transformational verification paradigm.
Error behaviours in an unreliable in-air gesture recognizer (2014)

This article presents results of two pilot studies that investigated error behaviours with an unreliable in-air gesture recognizer. During the studies, users performed a small set of simple in-air gestures. In the first study, these gestures were abstract. The second study associated concrete tasks with each gesture. The error patterns in the two studies were substantially different.