gebhart/patrepeval huggingface dataset:
Effect of Laponite and a Nonionic Polymer on the Absorption Character of Cationic Dye Solutions (2005)

The effect of Laponite and an amphiphilic triblock copolymer of poly(ethylene oxide) (PEO)-poly(propylene oxide) (PPO)-poly(ethylene oxide) (PEO) (PEO(99)-PPO(65)-PEO(99), and labeled F127) on the absorption character of two cationic dyes, methylene blue and toluidine blue O, was studied and interpreted in terms of the changing state of aggregation of the dye molecules. The combined effect of the polymer and Laponite on dye absorption was significantly different from their individual influences. Specifically, the presence of Laponite resulted in an increase in monomer population by dispersing the dye on the silicate surface. The presence of F127 also resulted in an increase in the dye monomer population, although to a smaller extent. The combined effect of the polymer and Laponite was an increase in the dimer or aggregate populations attributed to the competition of F127 with the dye molecules for the silicate surface.
Anisotropy of the upper critical field and its thickness dependence in superconducting FeSe electric-double-layer transistors (2018)

High-temperature superconductivity in FeSe thin films has attracted keen interest owing to the counterintuitive enhancement of the superconducting critical parameters in the monolayer-thin limit. Here, the authors apply an electrochemical etching technique to the FeSe-based electric-double-layer transistor (FeSe-EDLT) to investigate systematically the thickness and angular dependence of the upper critical magnetic field (H${}_{c2}$) below 10 nm. Compared with the isotropic H${}_{c2}$ in low-T${}_{c}$ bulk FeSe, the high-${T}_{c}$ FeSe-EDLT exhibits highly anisotropic and three-dimensional behavior, with a much smaller out-of-plane coherence length than the interlayer distance between FeSe sheets. The authors consider this to be the reason for the robust high-${T}_{c}$ superconductivity of monolayer FeSe.
Boundary Matting for View Synthesis (2005)

In the last few years, new view synthesis has emerged as an important application of 3D stereo reconstruction. While the quality of stereo has improved, it is still imperfect, and a unique depth is typically assigned to every pixel. This is problematic at object boundaries, where the pixel colors are mixtures of foreground and background colors. Interpolating views without explicitly accounting for this effect results in objects with a "cut-out" appearance. To produce seamless view interpolation, we propose a method called boundary matting, which represents each occlusion boundary as a 3D curve. We show how this method exploits multiple views to perform fully automatic alpha matting and to simultaneously refine stereo depths at the boundaries. The key to our approach is the unifying 3D representation of occlusion boundaries estimated to sub-pixel accuracy. Starting from an initial estimate derived from stereo, we optimize the curve parameters and the foreground colors near the boundaries. Our objective function maximizes consistency with the input images, favors boundaries aligned with strong edges, and damps large perturbations of the curves. Experimental results suggest that this method enables high-quality view synthesis with reduced matting artifacts.
Computerized self-assessment of automated lesion segmentation in breast ultrasound: implication for CADx applied to findings in the axilla (2008)

We developed a self-assessment method in which the CADx system provided a confidence level for its lesion segmentations. The self-assessment was performed by a fuzzy-inference system based on 4 computer-extracted features of the computer-segmented lesions in a leave-one-case-out evaluation protocol. In instances where the initial segmentation received a low assessment rating, lesions were re-segmented using the same segmentation method but based on a user-defined region-of-interest. A total of 542 cases with 1133 lesions were collected in this study, and we focused here on the 97 normal lymph nodes in this dataset since these pose challenges for automated segmentation due to their inhomogeneous appearance. The percentage of all lesions with satisfactory segmentation (i.e., normalized overlap with the radiologist-delineated lesion >=0.3) was 85%. For normal lymph nodes, however, this percentage was only 36%. Of the lymph nodes, 53 received a low confidence rating (<0.3) for their initial segmentation. When those lymph nodes were re-segmented, the percentage with a satisfactory segmentation improved to 80.0%. Computerassessed confidence levels demonstrated potential to 1) help radiologists decide whether to use or disregard CADx output, and 2) provide a guide for improvement of lesion segmentation.
Chemokines and Targeted Migration of Neural Stem Cells Towards Ischemic Lesions (2006)

s of Oral Proceedings: 2006 Joint Annual Meeting of the AANS/CNS Cerebrovascular Section and the American Society of Interventional & Therapeutic Neuroradiology Caribe Royale Orlando—Orlando, Florida February 17–20, 2006: Anatomy: Cerebrovascular
Protein Surface Recognition by Synthetic Receptors:  A Route to Novel Submicromolar Inhibitors for α-Chymotrypsin (1998)

A family of synthetic receptors for protein surface recognition has been prepared. The receptors are based on a design in which four peptide loops are arrayed around a central calilx[4]arene core. By varying the sequence of the loop regions a range of differently functionalized receptor surfaces approximately 450 Å2 in area can be prepared. From this family we have identified potent inhibitors of chymotrypsin that function by binding to the surface of the protein. The most potent of these (1) shows slow binding kinetics in an analogous manner to several of the natural protein proteinase inhibitors. Detailed kinetic analysis showed 1 to be a competitive inhibitor with Ki and Ki* values of 0.81 and 0.11 μM, respectively.
Sparsity-aware estimation of CDMA system parameters (2009)

The number of active users, their timing offsets, and their (possibly dispersive) channels with the access point are decisive parameters for wireless code division multiple access (CDMA). Estimating them as accurately as possible using as short as possible training sequences can markedly improve error performance as well as the capacity of CDMA systems. The fresh look advocated here permeates benefits from recent advances in variable selection (VS) and compressive sampling (CS) approaches to multiuser communications by casting estimation of these parameters as a sparse linear regression problem. Novel estimators are developed by exploiting two forms of sparsity present: the first emerging from user (in) activity, and the second because the actual nonzero parameters are very few relative to the number of candidate user delays and channel taps. Simulations demonstrate an order of magnitude gains in performance when sparsity-aware estimators of CDMA parameters are compared to sparsity-agnostic standard least-squares based alternatives.
Identification of Protein‐Phosphatase‐1‐Binding Domains on the Glycogen and Myofibrillar Targetting Subunits (1996)

The specificity of the catalytic subunit of protein phosphatase-1 (PP1c) is modified by regulatory subunits that target it to particular subcellular locations. Here, we identify PP1c-binding domains on GL and GM, the subunits that target PP1c to hepatic and muscle glycogen, respectively, and on M110, the subunit that targets PP1c to smooth muscle myosin. GM-(G63-T93) interacted with PP1c and prevented GL from suppressing the dephosphorylation of glycogen phosphorylase, but it did not dissociate GL from PP1c or affect other characteristic properties of the PP1GL complex. These results indicate that GL contains two PP1c-binding sites, the region which suppresses the dephosphorylation of glycogen phosphorylase being distinct from that which enhances the dephosphorylation of glycogen synthase. At higher concentrations, GM-(G63-N75) had the same effect as GM-(G63-T93), but not if Ser67 was phosphorylated by cyclic-AMP-dependent protein kinase. Thus, phosphorylation of Ser67 dissociates GM from PP1c because phosphate is inserted into the PP1c-binding domain of GM. M110-(M1-E309) and M110-(M1-F38), but not M110-(D39-E309), mimicked the M110 subunit in stimulating dephosphorylation of the smooth muscle myosin P-light chain and heavy meromyosin in vitro. However, in contrast to the M110 subunit and M110-(M1-E309), neither M110-(M1-F38) nor M110-(D39-E309) suppressed the PP1c-catalysed dephosphorylation of glycogen phosphorylase. These observations suggest that the region which stimulates the dephosphorylation of myosin is situated within the N-terminal 38 residues of the M110 subunit, while the region which suppresses the dephosphorylation of glycogen phosphorylase requires the presence of at least part of the region 39-309 which contains seven ankyrin repeats. M110-(M1-F38) displaced GL from PP1c, while GM-(G63-T93) displaced M110 from PP1c in vitro. These observations indicate that the region(s) of PP1c that interact with GM/GL and M110 overlap, explaining why different forms of PP1c contain just a single targetting subunit.
Microbial threat lists: obstacles in the quest for biosecurity? (2010)

Anxiety about threats from the microbial world and about the deliberate misuse of microorganisms has led to efforts to define and control these dangers using lists and regulations. One list with tremendous legal implications and a potentially huge impact on research is the Select Agents and Toxins List, which was created by the US Government to limit the possession of and access to particular microorganisms and toxins. In this article, in addition to highlighting general problems with taxonomy-based, microorganism-centric lists, we discuss our view that such lists may have the paradoxical effect of increasing the societal vulnerability to biological attack and natural epidemics by interfering with the sharing of microbial samples and hindering research on vaccines and therapeutics.
ChemInform Abstract: CLEMMENSEN REDUCTION. PART 5. CHIRAL Γ‐HYDROXY‐KETONES (1978)

Abstract Die Clemmensen‐Reduktion von chiralen γ‐Hydroxyketonen (I) bzw. (IXb) verläuft unter Retention der 7‐ Hydroxygruppe [Bildung der Produkte (II), (IIIa)+(IIIb) bzw. (X)]; damit wird ein früher postulierter Mechanismus für die Clemmensen‐Reduktion teilweise widerlegt.
Interaction of thymidylate synthase with pyridoxal 5'-phosphate as studied by UV/visible difference spectroscopy and molecular modeling (1993)

Pyridoxal 5'-phosphate (PLP) is an effective inhibitor of Lactobacillus casei thymidylate synthase (TS), competitive with respect to the nucleotide substrate dUMP (Chen et al., 1989). The UV/vis difference spectra of TS-PLP complexes show lambda max at 328 nm due to the specific interaction between Cys 198 of TS and PLP to form a thiohemiacetal, and lambda min at 388 nm due to depletion of free PLP. At high concentrations of PLP a new absorbance at 430 nm forms due to nonspecific Schiff base formation between PLP and lysine residues of the enzyme. Using spectral titration at 328 nm, the binding constant of the specific TS-PLP complex was determined to be 0.5 microM, and the stoichiometry was 2 mol of PLP/mol of TS dimer. The 328-nm absorbance of the TS-PLP complex can be competitively and completely eliminated by addition of dUMP or dTMP; this serves as a convenient binding assay for molecules which bind to the active site of TS. Analogs of PLP which do not contain the phosphate or the aldehyde moieties of PLP bound poorly to the enzyme, thus demonstrating the importance of these functional groups for binding. When treated with PLP, C244T TS, which contains the active site Cys 198 as the sole cysteine residue, showed the same properties as the wild-type enzyme. Treatment of the C198A and C198S mutants with PLP did not produce the absorbance at 328 nm assigned to thiohemiacetal formation.(ABSTRACT TRUNCATED AT 250 WORDS)
[Preparation and property of platinum microcoil modified by a copolymer-VEGF conjugate]. (2009)

The use of P(DLLA-co-TMC) copolymer allows immobilization of VEGF on the platinum coils for controlled VEGF release, and improves the biological property of the coils.
Inside Cover: “Conformational” Solvatochromism: Spatial Discrimination of Nonpolar Solvents by Using a Supramolecular Box of a π‐Conjugated Zinc Bisporphyrin Rotamer (Angew. Chem. Int. Ed. 28/2008) (2008)

Conformational solvatochromism has been used to discriminate nonpolar solvents by using a self-assembled chromophoric molecule. A. Tsuda, T. Aida, and co-workers describe in their Communication on page 5153 ff. the self-assembly of a bis(zinc pyridylporphyrin) rotamer with a π-conjugated linker to give a mixture of supramolecular boxes composed of planar and perpendicular conformers. The ratio of the two boxes changes depending on the solvent, and leads to a solvatochromic response.
Video-rate high-precision time-frequency multiplexed 3D surface imaging (2020)

Recently, there has been growing interest and effort in developing high-speed high-precision 3D imaging technologies for a wide range of industrial, automotive and biomedical applications. Optical frequency-modulated continuous wave (FMCW) light detection and ranging (LiDAR), which shares the same working principle as swept-source optical coherence tomography (SSOCT), is an emerging 3D surface imaging technology that offers higher sensitivity and resolution than conventional time-of-flight (ToF) ranging. Recently, with the development of high-performance swept sources with meter-scale instantaneous coherence lengths, the imaging range of both OCT and FMCW has been significantly improved. However, due to the limited bandwidth of current generation digitizers and the speed limitations of beam steering using mechanical scanners, long range OCT and FMCW typically suffer from a low 3D frame rate (<1Hz), which greatly restricts their applications in imaging dynamic or moving objects. In this work, we report a high-speed FMCW based 3D surface imaging system, combining a grating for beam steering with a compressed time-frequency analysis approach for depth retrieval. We thoroughly investigate the localization accuracy and precision of our system both theoretically and experimentally. Finally, we demonstrate 3D surface imaging results of multiple static and moving objects, including a flexing human hand. The demonstrated technique performs 3D surface imaging with submillimeter localization accuracy over a tens-of-centimeter imaging range with an overall depth voxel acquisition rate of 7.6 MHz, enabling densely sampled 3D surface imaging at video rate.
Physico-Chemical and Catalytic Properties of Mesoporous CuO-ZrO2 Catalysts (2016)

Mesoporous CuO-ZrO2 catalysts were prepared and calcined at 500 °C. The performance of the synthesized catalysts for benzylation of benzene using benzyl chloride was studied. The bare support (macroporous ZrO2) offered 45% benzyl chloride conversion after reaction time of 10 h at 75 °C. Significant increase in benzyl chloride conversion (98%) was observed after CuO loading (10 wt. %) on porous ZrO2 support. The conversion was decreased to 80% with increase of CuO loading to 20 wt. %. Different characterization techniques (XRD, Raman, diffuse reflectance UV-vis, N2-physisorption, H2-TPR, XPS and acidity measurements) were used to evaluate physico-chemical properties of CuO-ZrO2 catalysts; the results showed that the surface and structural characteristics of the ZrO2 phase as well as the interaction between CuO-ZrO2 species depend strongly on the CuO content. The results also indicated that ZrO2 support was comprised of monoclinic and tetragonal phases with macropores. An increase of the volume of monoclinic ZrO2 phase was observed after impregnation of 10 wt. % of CuO; however, stabilization of tetragonal ZrO2 phase was noticed after loading of 20 wt. % CuO. The presence of low-angle XRD peaks indicates that mesoscopic order is preserved in the calcined CuO-ZrO2 catalysts. XRD reflections due to CuO phase were not observed in case of 10 wt. % CuO supported ZrO2 sample; in contrast, the presence of crystalline CuO phase was observed in 20 wt. % CuO supported ZrO2 sample. The mesoporous 10 wt. % CuO supported ZrO2 catalyst showed stable catalytic activity for several reaction cycles. The observed high catalytic activity of this catalyst could be attributed to the presence of a higher number of dispersed interactive CuO (Cu2+-O-Zr4+) species, easy reducibility, and greater degree of accessible surface Lewis acid sites.
ChemInform Abstract: MECHANISM OF ISOMERIZATION OF A β‐KETO SULFIDE (1982)

Abstract In Gegenwart von Natriummercaptiden und ‐thiophenolaten wird jeweils das Gleichgewicht zwischen den Isomeren (I) und (II) eingestellt.
Extending the Clapper–Yule model to rough printing supports (2005)

The Clapper-Yule model is the only classical spectral reflection model for halftone prints that takes explicitly into account both the multiple internal reflections between the print-air interface and the paper substrate and the lateral propagation of light within the paper bulk. However, the Clapper-Yule model assumes a planar interface and does not take into account the roughness of the print surface. In order to extend the Clapper-Yule model to rough printing supports (e.g., matte coated papers or calendered papers), we model the print surface as a set of randomly oriented microfacets. The influence of the shadowing effect is evaluated and incorporated into the model. By integrating over all incident angles and facet orientations, we are able to express the internal reflectance of the rough interface as a function of the rms facet slope. By considering also the rough interface transmittances both for the incident light and for the emerging light, we obtain a generalization of the Clapper-Yule model for rough interfaces. The comparison between the classical Clapper-Yule model and the model extended to rough surfaces shows that the influence of the surface roughness on the predicted reflectance factor is small. For high-quality papers such as coated and calendered papers, as well as for low-quality papers such as newsprint or copy papers, the influence of surface roughness is negligible, and the classical Clapper-Yule model can be used to predict the halftone-print reflectance factors. The influence of roughness becomes significant only for very rough and thick nondiffusing coatings.
Automated Method for Identification and Artery-Venous Classification of Vessel Trees in Retinal Vessel Networks (2014)

The separation of the retinal vessel network into distinct arterial and venous vessel trees is of high interest. We propose an automated method for identification and separation of retinal vessel trees in a retinal color image by converting a vessel segmentation image into a vessel segment map and identifying the individual vessel trees by graph search. Orientation, width, and intensity of each vessel segment are utilized to find the optimal graph of vessel segments. The separated vessel trees are labeled as primary vessel or branches. We utilize the separated vessel trees for arterial-venous (AV) classification, based on the color properties of the vessels in each tree graph. We applied our approach to a dataset of 50 fundus images from 50 subjects. The proposed method resulted in an accuracy of 91.44% correctly classified vessel pixels as either artery or vein. The accuracy of correctly classified major vessel segments was 96.42%.
Hf-based high-k dielectrics for p-Ge MOS gate stacks (2013)

The physical and electrical properties of the gate stack high-k/Al2O3/GeO2/p-Ge were studied in detail, where the high-k is either HfO2 or alloyed HfO2 (HfZrOy, HfGdOx, or HfAlOx). Electrical measurements combined with x-ray photoelectron spectroscopy chemical bonding analysis and band alignment determination were conducted in order to assess the suitability of hafnium-based high-k for this kind of gate stacks, with emphasis on low density of interface states and border traps. HfAlOx was found to be the most promising high-k from those studied. The authors have also found that the current- voltage trends for the various systems studied can be explained by the band alignment of the samples obtained by our x-ray photoelectron spectroscopy analysis.
How Close Is Too Close? Polymerization Behavior and Monomer-Dependent Reorganization of a Bimetallic Salphen Organotitanium Catalyst (2018)

The binuclear salphen Ti polymerization catalyst N,N′-1,2-phenylene[(salicylideneaminato)Ti(Cp*)Me2)]2 (2) is synthesized by reaction of salphen-H2 with Cp*TiMe3. Mononuclear [N-(2,6-diisopropyl)phenyl(salicylideneaminato)]Ti(Cp*)Me2 (1) serves as a control. Activation studies of 2 with cocatalyst Ph3C+B(C6F5)4– yield the cationic polymerization-inactive complex [N,N′-1,2-phenylene(salicylideneaminato)Ti(Cp*)]+B(C6F5)4– (4) and polymerization-active Cp*TiMe2+B(C6F5)4–. Polymerization studies comparing 2 with Cp*TiMe3 suggest that, within the catalytic time frame, while 2 retains bimetallic character under an ethylene atmosphere, it rapidly decomposes to 4 and Cp*TiMe2+ in the presence of 1-hexene. These monomer-dependent reorganization results highlight the importance of olefin polymerization activation mechanistic studies while providing insight for improved bimetallic catalyst design.
The Development of the “Vertical Shape Line-Beam Headlamp” (2001)

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Figure S5 from TRK Fusions Are Enriched in Cancers with Uncommon Histologies and the Absence of Canonical Driver Mutations (2023)

&lt;p&gt;Supplemental Figure 5. Timeline for Patients with Emergent or Lost TRK Fusions.&lt;/p&gt;
Synergies between centralized and federated approaches to data quality: a report from the national COVID cohort collaborative (2021)

By combining rapid, continual assessment of DQ with a large volume of multisite data, it is possible to support more nuanced scientific questions with the scale and rigor that they require.
Treatment of infection-induced vascular pathologies is protective against persistent rough morphotype Mycobacterium abscessus infection in zebrafish (2021)

Abstract Mycobacterium abscessus infections are of increasing global prevalence and are often difficult to treat due to complex antibiotic resistance profiles. While there are similarities between the pathogenesis of M. abscessus and tuberculous mycobacteria, including granuloma formation and stromal remodeling, there are distinct molecular differences at the host-pathogen interface. Here we have used a zebrafish- M. abscessus model and host-directed therapies that were previously identified in the zebrafish- M. marinum model to identify potential host-directed therapies against M. abscessus infection. We find efficacy of anti-angiogenic and vascular normalizing therapies against rough M. abscessus infection, but no effect of anti-platelet drugs.