gebhart/patrepeval huggingface dataset:
Multiple WASP-interacting Protein Recognition Motifs Are Required for a Functional Interaction with N-WASP (2007)

The WASP-interacting protein (WIP) targets WASP/WAVE proteins through a constitutive interaction with an amino-terminal enabled/VASP homology (EVH1) domain. Parallel investigations had previously identified two distinct N-WASP binding motifs corresponding to WIP residues 451-461 and 461-485, and we determined the structure of a complex between WIP-(461-485) and the N-WASP EVH1 domain (Volkman, B. F., Prehoda, K. E., Scott, J. A., Peterson, F. C., and Lim, W. A. (2002) Cell 111, 565-576). The present results show that, when combined, the WIP-(451-485) sequence wraps further around the EVH1 domain, extending the interface observed previously. Specific contacts with three WIP epitopes corresponded to regions of high sequence conservation in the verprolin family. A central polyproline motif occupied the canonical binding site but in a reversed orientation relative to other EVH1 complexes. This interaction was augmented in the amino- and carboxyl-terminal directions by additional hydrophobic contacts involving WIP residues 454-459 and 475-478, respectively. Disruption of any of the three WIP epitopes reduced N-WASP binding in cells, demonstrating a functional requirement for the entire binding domain, which is significantly longer than the polyproline motifs recognized by other EVH1 domains.
Molecular Fingerprint of Interferon-γ Signaling in Unstable Angina (2001)

Monocytes from UA patients exhibit a molecular fingerprint of recent IFN-gamma triggering, such as nuclear translocation of STAT-1 complexes and upregulation of IFN-gamma-inducible genes CD64 and IP-10, which suggests that monocytes are activated, at least in part, by IFN-gamma. IFN-gamma may derive from stimulated T lymphocytes, which implicates specific immune responses in the pathogenesis of acute coronary syndromes.
Supplementary Table 1 from ALK1-Fc Inhibits Multiple Mediators of Angiogenesis and Suppresses Tumor Growth (2023)

Supplementary Table 1 from ALK1-Fc Inhibits Multiple Mediators of Angiogenesis and Suppresses Tumor Growth
MATRIX at the TREC 2005 robust track (2005)

In the TREC 2005 robust retrieval track, we tested our adaptive retrieval model that automatically switches between the 2-Poisson model/adaptive vector space model and our initial predictive probabilistic context-based model depending on some query characteristics. Our 2-Poisson model uses the BM11 term weighting scheme with passage retrieval and pseudo-relevance feedback. The context-based model incorporates the term locations in a document for calculating the term weights. By doing this, different term weights are assigned to the same query term depending on its context and location in the document. We also use WordNet in the term selection process when doing pseudo-rele vance feedback. The performance of our model is comparable to the median among all participants in the robust track on the whole query set including the title, descriptive and long queries.
ChemInform Abstract: A Comparison of (Chloromethyl)‐ and (Iodomethyl)zinc Cyclopropanation Reagents. (1992)

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.
Supplementary Table and Figure Legends from High-Order Drug Combinations Are Required to Effectively Kill Colorectal Cancer Cells (2023)

&lt;p&gt;Legend for Supplementary Tables S1-S6 and Supplementary Figures S1-S15.&lt;/p&gt;
<title>Coating-induced wavefront aberrations</title> (1992)

The coatings which are used on telescope mirrors and other optical interfaces can have a profound effect on the image quality formed by an optical system. This paper evaluates the defocus and astigmatism which are caused by the s- and p-phase shifts of coatings. These coating-induced wavefront aberrations are usually insignificant, but can, under certain circumstances, overshadow the geometric wavefront aberrations of the system. The wavefront aberrations induced by reflection-enhanced coatings on an f/1.5 Cassegrain telescope are numerically evaluated as an example.
A genomic and evolutionary approach reveals non-genetic drug resistance in malaria (2014)

We provide a three-step model for multi-locus evolution of halofuginone drug resistance in P. falciparum. Informed by genomic approaches, our results provide the first comprehensive view of the evolutionary trajectory malaria parasites take to achieve drug resistance. Our understanding of the multiple genetic and non-genetic mechanisms of drug resistance informs how we will design and pair future anti-malarials for clinical use.
Positron annihilation at proton-induced defects in6H−SiC/SiCand6H−SiC/SiO2/Sistructures (2000)

Positron annihilation is used to detect vacancy-related defects in proton-implanted and Smart Cut $6H\ensuremath{-}\mathrm{SiC}.$ The measurement of positron-electron pair momentum distribution as a function of depth shows that vacancy-related defects produced along the proton track and cavities formed in the region of the hydrogen peak survive in smart cut $6H\ensuremath{-}\mathrm{SiC}$ even after 1300 \ifmmode^\circ\else\textdegree\fi{}C annealing.
Unified approach to the formation of phase holograms in ferroelectric crystals (1975)

The description of the formation of thick-phase holograms over the entire range of exposures has been accomplished using numerical methods. The internal electric field distributions (and thus the refractive-index profiles for linear electro-optic crystals) generated through diffusion and through drift of charge carriers are calculated. The treatment allows for the presence of an effective electric field due to the photovoltaic effect and an externally applied electric field. The results of this approach reduce to the existing analytic expressions for the limiting cases of the initial and the steady-state stages of hologram formation. This approach establishes the limits of validity for the analytic expressions in terms of exposure and material parameters.
10 Gb/s Monolithically Integrated, Photocurrent Driven Wavelength Converter with Widely Tunable SGDBR Laser and Optical Receiver (2006)

A monolithically integrated photocurrent driven wavelength converter is fabricated and characterized. Bit-Error-Rate measurements at 10Gb/s show 1dB power penalties over 32nm with extinction ratios between 8.5-9.5dB. Input power is-11dBm and conversion efficiency is +13dB.
Supplemental Table S2 from The Distinctive Mutational Spectra of Polyomavirus-Negative Merkel Cell Carcinoma (2023)

&lt;p&gt;Supplemental Table S2. Quality metrics for sequencing libraries&lt;/p&gt;
Molecular Dynamics Simulations of Polyelectrolyte Brushes:  From Single Chains to Bundles of Chains (2007)

Using molecular dynamics simulations in combination with scaling analysis, we have studied the effects of the solvent quality and the strength of the electrostatic interactions on the conformations of spherical polyelectrolyte brushes in salt-free solutions. The spherical polyelectrolyte brush could be in one of four conformations: (1) a star-like conformation, (2) a "star of bundles" conformation in which the polyelectrolyte chains self-assemble into pinned cylindrical micelles, (3) a micelle-like conformation with a dense core and charged corona, or (4) a conformation in which there is a thin polymeric layer uniformly covering the particle surface. These different brush conformations appear as a result of the fine interplay between electrostatic and monomer-monomer interactions. The brush thickness depends nonmonotonically on the value of the Bjerrum length. This dependence of the brush thickness is due to counterion condensation inside the brush volume. We have also established that bundle formation in poor solvent conditions for the polymer backbone can also occur in a planar polyelectrolyte brush. In this case, the grafted polyelectrolyte chains form hemispherical aggregates at low polymer grafting densities, cylindrical aggregates at an intermediate range of the grafting densities, and vertically oriented ribbon-like aggregates at high grafting densities.
A Wearable Vibratory Device (The Emma Watch) to Address Action Tremor in Parkinson Disease: Pilot Feasibility Study (2023)

There were visually depicted and subjectively reported improvements in handwriting for a small subset of individuals. This pilot study was limited by a small sample size, and this should be taken into consideration with the interpretation of the quantitative results. Combining vibratory devices, such as the Emma Watch, with task specific training, or personalizing the frequency to one's individual tremor may be important steps to consider when evaluating the effect of vibratory devices on hand function or writing ability in future studies. While the Emma Watch may help attenuate action tremor, its efficacy in improving fine motor or handwriting skills as a stand-alone tool remains to be demonstrated.
Low-Cost Processing of Fine Grained Transparent Yttrium Aluminum Garnet (2008)

Transparent polycrystalline yttrium aluminum garnet (YAG) with a fine grain size (1∼2 μm) was produced via a sinter-HIP process using highly reactive nano-sized powders that were synthesized by partial and full combustion processes at 200° — 240°C. the primary particle size was estimated to be between 30 — 50 nm, and the powders appeared to be weakly agglomerated. the densities after sintering at 1550° — 1650°C were 95.0 — 99.0 % of the theoretical density and the samples appeared translucent. Further HIPing at temperatures between 1500° and 1550°C resulted in completely dense polycrystalline YAG that showed a visibly higher transparency that was comparable to a single crystal YAG. the details of microstrucrural characterization (SEM), phase identification (XRD), and visible and IR transmittance (Spectrophotometer) are presented.
Throughput enhancement strategy of maskless electron beam direct writing for logic device (2002)

A pattern design method for semiconductor circuits in logic device was developed, which realized an electron beam (EB) exposure with sufficient throughput. The number of EB shots can be decreased by repeating logic synthesis and P and R (place and route) by removing usable standard cells (SCs). By using the design method, a functional block with about 140 kGates could be generated with only 17 SCs, and the minimum number of EB shots was attained with 24 SCs. The increase in the total area of SCs and the consumed power of the chip was only 10%.
The Past, Present, and Future of Patient-Reported Outcomes in Oncology (2015)

Patient-reported outcomes capture a unique and important perspective of oncology therapy. Surveys to properly capture patient-reported outcome measures have been under development for more than 2 decades. More recent efforts to understand the clinical significance of patient-reported outcomes, called performance measures, are underway. Patient-reported outcomes can be used in a variety of ways, including therapy decisions for an individual patient, payment for treatment, research into disease progression, or new drug development. Technology has already enabled electronic systems to capture and search patient-reported outcomes and in the future will assist in capturing everyday activities, which, in combination with improved informatics to sort the meaningful and actionable information, will reduce the time commitment for both patients and providers.
Performance measures for satellite-to-land-mobile communication systems using spread spectrum (2002)

A direct-sequence spread-spectrum satellite-to-land-mobile communications system is analyzed with respect to fading/multipath effects in Rayleigh or Rayleigh faded multiple-access environment with an unfaded, Rayleigh, and Rician faded desired user. Numerical results employing Gold codes of lengths 31 and 127 for all three fading cases of the desired user are presented in terms of tight lower and upper bounds of the bit error probability as well as user capacity. The latter performance measure is represented by the minimum required SNR for a specified acceptable bit error probability versus the number off users in the system. Conclusions on the fading/multipath effect on the number of simultaneous users of the satellite-to-land-mobile communications system are drawn from the numerical results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Hyperlapse generation of omnidirectional videos by adaptive sampling based on 3D camera positions (2017)

Capturing a city with an omnidirectional camera can produce a continuous motion street view and provides the view of the moving person. However, watching such a video is not necessarily pleasant because the videos are often excessively lengthy. In this paper, we propose a method for shortening an omnidirectional video. Subsampling a video captured by a hand-held camera displays a significant amount of destabilization resulting from shaking. This prompted us to propose an adaptive subsampling scheme that selects optimal frames by minimizing our cost function based on 3D camera positions. This optimal selection suppresses only the translational camera instabilities. The rotational instabilities are initially ignored and later compensated for. This approach allowed us to successfully generate a subsampled and stable omnidirectional video. In addition, we propose an alternative measure of translational instability to evaluate our frame selection.
Neutralization of wafer charging in nitrogen gas (1992)

In an attempt to prevent wafers from getting charged in the N/sub 2/ gas sealed semiconductor manufacturing process, the authors have developed a neutralization method employing ultraviolet (UV) irradiation. This method depends on the fact that the N/sub 2/ molecule is ionized when it absorbs ultraviolet light. This method is superior to the neutralization method employing corona discharge in terms of neutralization capability in the inert gas ambient. The neutralization rate is very high; the residual potential caused by the unbalanced ion distribution is always 0 V after the neutralization. Neutralization is rapid. The neutralization capability is enhanced by decreasing the ambient pressure. The neutralization capability is further enhanced by replacing the N/sub 2/ gas ambient with the Ar gas ambient.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
ChemInform Abstract: PHENYLTETRAFLUORPHOSPHORAN ALS FLUORIERUNGSMITTEL FUER ALKOHOLE (1973)

Abstract Aus den Alkoholen (I) werden mit Chlortrimethylsilan (II) unter Stickstoff bei ‐50°C die entsprechenden Silyläther dargestellt, die bei der Umsetzung mit dem Phosphoran (III) die intermediären Alkoxytrifluorplhosphorane (IV) bilden, die in die Fluoride (V) und (VI) sowie Sekundärprodukte, wie z.B. die Olefine (VII), zerfallen , wobei die Zerfallstemperatur stark von der Struktur des Alkohols abhängt.
Frequency Conversion in a Dielectric Time-Variant Metasurface via Optical Pumping. (2021)

Abstract not provided.
TWO-PHOTON ABSORPTION INDUCED EFFECTS IN CRYSTALLINE POLYSILANE FILMS (1988)

The new class of polysilane polymers has recently attracted interest as a medium for nonlinear optical interactions. These materials consist of a long (>1000 atoms) σ-bonded silicon backbone with two organic substituent groups attached to each Si atom. As nonlinear materials, these have several advantages over their π-bonded carbon analogs, the polydiacetylenes. First, polysilanes have been extensively investigated as possible photoresists,1 so thin (≤4 μm) films of excellent optical quality can be easily prepared using conventional photoresist technology. Second, the σ-σ* absorption edge is typically in the ultraviolet, so the material is transparent at all visible wavelengths. Finally, this absorption band edge can be shifted by changing the molecular weight, conformation of the Si backbone, or the substituent groups, making resonant enhancement of nonlinear effects at particular wavelengths possible.
Statistical mapping of zones of focused groundwater/surface-water exchange using fiber-optic distributed temperature sensing (2013)

[1] Fiber-optic distributed temperature sensing (FO-DTS) increasingly is used to map zones of focused groundwater/surface-water exchange (GWSWE). Previous studies of GWSWE using FO-DTS involved identification of zones of focused GWSWE based on arbitrary cutoffs of FO-DTS time-series statistics (e.g., variance, cross-correlation between temperature and stage, or spectral power). New approaches are needed to extract more quantitative information from large, complex FO-DTS data sets while concurrently providing an assessment of uncertainty associated with mapping zones of focused GSWSE. Toward this end, we present a strategy combining discriminant analysis (DA) and spectral analysis (SA). We demonstrate the approach using field experimental data from a reach of the Columbia River adjacent to the Hanford 300 Area site. Results of the combined SA/DA approach are shown to be superior to previous results from qualitative interpretation of FO-DTS spectra alone.
Mechanistic studies of ultrasonically enhanced transdermal drug delivery (1998)

The transdermal route of drug delivery offers a noninvasive and painless alternative to more traditional routes such as injections. However, its applicability is limited to only a handful of drugs due to the low permeability of the skin. It has been demonstrated that low-frequency ultrasound significantly enhances transdermal transport of a variety of drugs (sonophoresis). There is strong experimental evidence to suggest that cavitation plays a key role in this enhancement, although it is not clear which cavitational effects are primarily responsible for the transport. Cavitation can affect transdermal transport in at least two ways: It can induce changes in skin structure, creating pathways or channels for molecules to diffuse across and/or it can induce convective transport across the skin. An experimental system has been developed to assess contributions due to each of these phenomena individually. Although the data are insufficient to eliminate a role for convective processes, these experiments clearly indicate that stuctural changes in the skin play an important, and probably primary, role in enhanced transport.
Design and fabrication of a preclinical adaptive SPECT imaging system : AdaptiSPECT (2014)

This item is part of the GPSC Student Showcase collection. For more information about the Student Showcase, please email the GPSC (Graduate and Professional Student Council) at gpsc@email.arizona.edu.
Synthetic transmit aperture imaging using orthogonal Golay coded excitation (2002)

The frame rate in medical ultrasound imaging may be increased significantly by reducing the number of transmits per image frame. Cooley et al. (1994) and Lockwood et al. (1995) have described synthetic transmit aperture (STA) systems where each frame is imaged using data obtained from a small number of point sources fired in succession. These systems have potential for very high frame rates, but they also suffer from low SNR. In this paper we present a computationally efficient method to increase the SNR of STA systems by using spatio-temporal encoding which increases SNR by 101og(ML) dB, where M is the number of active phase centers or transmits and L is the temporal code length. By using an orthogonal Golay set for the spatio-temporal encoding, the received data can be sorted by each transmit phase center and pulse-compressed for subsequent synthetic aperture beamforming. Computer simulations are used to demonstrate the method.
Effect of clay concentration on the oxygen permeability and optical properties of a modified poly(vinyl alcohol) (2004)

Abstract The effect of clay concentration on the oxygen permeability and optical properties of a modified poly(vinyl alcohol) (PVOH) was studied. Sodium montmorrilonite (MMT‐Na + ), at a concentration of 10 wt %, was found to decrease the oxygen permeability of the PVOH below 0.001 cc · mil/m 2 /day at 55% relative humidity. This low permeability is attributed to the strong interaction between PVOH and clay, as evidenced by an increase of more than 10°C in the glass transition temperature at this concentration. Transmission electron microscopy images show the high level of clay exfoliation that results from the strong affinity to PVOH. Haze and clarity were optical properties that changed significantly with increasing clay concentration. These values were 0.4 and 100%, respectively, in the absence of clay, but became 80 and 23% with 10 wt % MMT‐Na + . Transmission did not change as considerably, reaching a low of 73% with a clay concentration of 10 wt %. The ability to reduce the oxygen permeability of PVOH‐based systems at elevated humidity may prove advantageous for applications in food and flexible electronics packaging, where moisture sensitivity currently prevents them from being used. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 93: 1102–1109, 2004
Structure of a protective epitope of group BStreptococcustype III capsular polysaccharide (2017)

Despite substantial progress in the prevention of group B <i>Streptococcus</i> (GBS) disease with the introduction of intrapartum antibiotic prophylaxis, this pathogen remains a leading cause of neonatal infection. Capsular polysaccharide conjugate vaccines have been tested in phase I/II clinical studies, showing promise for further development. Mapping of epitopes recognized by protective antibodies is crucial for understanding the mechanism of action of vaccines and for enabling antigen design. In this study, we report the structure of the epitope recognized by a monoclonal antibody with opsonophagocytic activity and representative of the protective response against type III GBS polysaccharide. The structure and the atomic-level interactions were determined by saturation transfer difference (STD)-NMR and X-ray crystallography using oligosaccharides obtained by synthetic and depolymerization procedures. The GBS PSIII epitope is made by six sugars. Four of them derive from two adjacent repeating units of the PSIII backbone and two of them from the branched galactose-sialic acid disaccharide contained in this sequence. The sialic acid residue establishes direct binding interactions with the functional antibody. The crystal structure provides insight into the molecular basis of antibody-carbohydrate interactions and confirms that the conformational epitope is not required for antigen recognition. Understanding the structural basis of immune recognition of capsular polysaccharide epitopes can aid in the design of novel glycoconjugate vaccines.
ChemInform Abstract: Fungal Biotransformation of 1,3‐Oxathiolanes. (1989)

Abstract Incubation of the oxathiolanes (I) with the fungus Mortierella isabellina leads to sulfoxidation yielding the products (II) as single diastereomers, whose relative stereochemistry is assigned by 1 H NMR analysis.