gebhart/patrepeval huggingface dataset:
Visible light-curable water-soluble chitosan derivative, chitosan hydrogel, and preparation method: a patent evaluation of US2019202998A1 (2021)

<b>Introduction</b>: Water soluble polysaccharides are versatile structural materials that can be used for the design of biocompatible hydrogels and wet dressings in wound healing applications. Glycol chitosan (GC) is an example of a multifunctional water-soluble chitosan derivative that has inherent wound healing properties and reactive sites for chemical modification.<b>Areas covered</b>: United States (US) patent US2019202998A1 describes the preparation of a novel wound healing technology based on a three-dimensional (3D) crosslinked GC hydrogel (GCH) wet dressing, prepared via the synthesis of PEG1K-biscarboxylic acid-<i>g</i>-Glycol Chitosan-<i>g</i>-methacrylate using visible light induced photocrosslinking. The selected polymeric network enables the encapsulation of additional growth factors or bioactives on reactive sites. Wet dressings in US2019202998A1 were evaluated against a commercially available control for <i>in vitro</i> release, cytotoxicity, and <i>in vivo</i> wound healing ability in a preliminary mouse model, with the overall wound healing performance consistent with related GC-based hydrogels.<b>Expert opinion</b>: Comprehensive biocompatibility and antimicrobial testing of the hydrogel is not reported in US2019202998A1, and is recommended as further work to enable clinical applicability. The invention disclosed in US2019202998A1 can potentially be integrated with 3D bioprinting and sensor technology for the preparation of 'smart' hydrogel wound dressings, and is a potential area for future research.
Kaolinite Nanocomposite Platelets Synthesized by Intercalation and Imidization of Poly(styrene-co-maleic anhydride) (2015)

A synthesis route is presented for the subsequent intercalation, exfoliation and surface modification of kaolinite (Kln) by an imidization reaction of high-molecular weight poly(styrene-<i>co</i>-maleic anhydride) or SMA in the presence of ammonium hydroxide. In a first step, the intercalation of ammonolyzed SMA by guest displacement of intercalated dimethylsulfoxide has been proven. In a second step, the imidization of ammonolyzed SMA at 160 °C results in exfoliation of the kaolinite layers and deposition of poly(styrene-co-maleimide) or SMI nanoparticles onto the kaolinite surfaces. Compared with a physical mixture of Kln/SMI, the chemically reacted Kln/SMI provides more efficient exfoliation and hydrogen bonding between the nanoparticles and the kaolinite. The kaolinite nanocomposite particles are synthesized in aqueous dispersion with solid content of 65 wt %. The intercalation and exfoliation are optimized for a concentration ratio of Kln/SMI = 70:30, resulting in maximum intercalation and interlayer distance in combination with highest imide content. After thermal curing at 135 °C, the imidization proceeds towards a maximum conversion of the intermediate amic acid moieties. The changes in O-H stretching and kaolinite lattice vibrations have been illustrated by infrared and FT-Raman spectroscopy, which allow for a good quantification of concentration and imidization effects.
Weighted Graph-Based Signal Temporal Logic Inference Using Neural Networks (2021)

Extracting spatial-temporal knowledge from data is useful in many applications. It is important that the obtained knowledge is human-interpretable and amenable to formal analysis. In this letter, we propose a method that trains neural networks to learn spatial-temporal properties in the form of <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">weighted graph-based signal temporal logic</i> (w-GSTL) formulas. For learning w-GSTL formulas, we introduce a <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">flexible</i> w-GSTL <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">formula structure</i> in which the user’s preference can be applied in the inferred w-GSTL formulas. In the proposed framework, each neuron of the neural networks corresponds to a subformula in a <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">flexible</i> w-GSTL <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">formula structure</i> . We initially train a neural network to learn the w-GSTL operators, and then train a second neural network to learn the parameters in a <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">flexible</i> w-GSTL <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">formula structure</i> . We use a COVID-19 dataset and a rain prediction dataset to evaluate the performance of the proposed framework and algorithms. We compare the performance of the proposed framework with three baseline classification methods including K-nearest neighbors, decision trees, support vector machine, and artificial neural networks. The classification accuracy obtained by the proposed framework is comparable with the baseline classification methods.
A coding approach to localization using landmarks (2020)

Fully autonomous vehicles need the ability to localize without external help, for instance by using visual sensors together with a pre-loaded map of landmarks. In this paper we connect self-localization using landmarks with coding theory. This connection enables to translate Hamming distance properties to probabilistic localization guarantees given a certain number of errors in landmark identification; it also enables to leverage existing polynomial time decoding algorithms for localization. We present promising numerical evaluation results by simulating vehicle traveling paths along a road network generated from real data of a region in Washington D.C.
Mitral valve leaflet response to ischaemic mitral regurgitation: from gene expression to tissue remodelling (2020)

Ischaemic mitral regurgitation (IMR), a frequent complication following myocardial infarction (MI), leads to higher mortality and poor clinical prognosis if untreated. Accumulating evidence suggests that mitral valve (MV) leaflets actively remodel post MI, and this remodelling increases both the severity of IMR and the occurrence of MV repair failures. However, the mechanisms of extracellular matrix maintenance and modulation by MV interstitial cells (MVICs) and their impact on MV leaflet tissue integrity and repair failure remain largely unknown. Herein, we sought to elucidate the multiscale behaviour of IMR-induced MV remodelling using an established ovine model. Leaflet tissue at eight weeks post MI exhibited significant permanent plastic radial deformation, eliminating mechanical anisotropy, accompanied by altered leaflet composition. Interestingly, no changes in effective collagen fibre modulus were observed, with MVICs slightly rounder, at eight weeks post MI. RNA sequencing indicated that YAP-induced genes were elevated at four weeks post MI, indicating elevated mechanotransduction. Genes related to extracellular matrix organization were downregulated at four weeks post MI when IMR occurred. Transcriptomic changes returned to baseline by eight weeks post MI. This multiscale study suggests that IMR induces plastic deformation of the MV with no functional damage to the collagen fibres, providing crucial information for computational simulations of the MV in IMR.
Chemical and spatial analysis of protein loaded PLGA microspheres for drug delivery applications (2012)

Polymer microspheres for controlled release of therapeutic protein from within an implantable scaffold were produced and analysed using complimentary techniques to probe the surface and bulk chemistry of the microspheres. Time of Flight - Secondary Ion Mass Spectrometry (ToF-SIMS) surface analysis revealed a thin discontinuous film of polyvinyl alcohol (PVA) surfactant (circa 4.5 nm thick) at the surface which was readily removed under sputtering with C(60). Atomic Force Microscopy (AFM) imaging of microspheres before and after sputtering confirmed that the PVA layer was removed after sputtering revealing poly(lactic-co-glycolic) acid(PLGA). Scanning electron microscopy showed the spheres to be smooth with some shallow and generally circular depressions, often with pores in their central region. The occurrence of the protein at the surface was limited to areas surrounding these surface pores. This surface protein distribution is believed to be related to a burst release of the protein on dissolution. Analysis of the bulk properties of the microspheres by confocal Raman mapping revealed the 3D distribution of the protein showing large voids within the pores. Protein was found to be adsorbed at the interface with the PLGA oil phase following deposition on evaporation of the solvent. Protein was also observed concentrated within pores measuring approximately 2 μm across. The presence of protein in large voids and concentrated pores was further scrutinised by ToF-SIMS of sectioned microspheres. This paper demonstrates that important information for optimisation of such complex bioformulations, including an understanding of the release profile can be revealed by complementary surface and bulk analysis allowing optimisation of the therapeutic effect of such formulations.
Intestinal tuft cells regulate the ATM mediated DNA Damage response via Dclk1 dependent mechanism for crypt restitution following radiation injury (2016)

Crypt epithelial survival and regeneration after injury require highly coordinated complex interplay between resident stem cells and diverse cell types. The function of Dclk1 expressing tuft cells regulating intestinal epithelial DNA damage response for cell survival/self-renewal after radiation-induced injury is unclear. Intestinal epithelial cells (IECs) were isolated and purified and utilized for experimental analysis. We found that small intestinal crypts of Villin<sup>Cre</sup>;Dclk1<sup>f/f</sup> mice were hypoplastic and more apoptotic 24 h post-total body irradiation, a time when stem cell survival is p53-independent. Injury-induced ATM mediated DNA damage response, pro-survival genes, stem cell markers, and self-renewal ability for survival and restitution were reduced in the isolated intestinal epithelial cells. An even greater reduction in these signaling pathways was observed 3.5 days post-TBI, when peak crypt regeneration occurs. We found that interaction with Dclk1 is critical for ATM and COX2 activation in response to injury. We determined that Dclk1 expressing tuft cells regulate the whole intestinal epithelial cells following injury through paracrine mechanism. These findings suggest that intestinal tuft cells play an important role in regulating the ATM mediated DNA damage response, for epithelial cell survival/self-renewal via a Dclk1 dependent mechanism, and these processes are indispensable for restitution and function after severe radiation-induced injury.
Neutralization of hepatitis B virus by a novel DNA-encoded monoclonal antibody (2020)

Hepatitis B virus (HBV) causes a potentially life-threatening liver infection that frequently results in life-long chronic infection. HBV is responsible for 887,000 deaths each year, most resulting from chronic liver diseases and hepatocellular carcinoma. Presently, there are 250 million chronic HBV carriers worldwide who are at a high risk for developing cirrhosis and hepatocellular carcinoma (HCC). HCC is the most common type of liver cancer with a strong association with HBV infection. HBV transmission through blood transfusions and perinatal transfer from infected mother to child have been common routes of infection. In the present study, we describe the development of a synthetic DNA plasmid encoding an anti-HBV human monoclonal antibody specific for the common "a determinant region" of HBsAg of hepatitis B virus and demonstrate the ability of this platform at directing <i>in vivo</i> antibody expression. <i>In vivo</i> delivery of this DNA encoded monoclonal antibody (DMAb) plasmid in mice resulted in expression of human IgG over a period of one month following a single injection. Serum antibody was found to recognize the relevant conformational epitope from plasma purified native HBsAg as well as bound HBV in HepG2.2.15 cells. The serum DMAb efficiently neutralized HBV and prevented infection of HepaRG cells <i>in vitro</i>. Additional study of these HBV-DMAb as a possible therapy or immunoprophylaxis for HBV infection is warranted.
Direct Observation of the Femtosecond Excited-State cis - trans Isomerization in Bacteriorhodopsin (1988)

Femtosecond optical measurement techniques have been used to study the primary photoprocesses in the light-driven transmembrane proton pump bacteriorhodopsin. Light-adapted bacteriorhodopsin was excited with a 60-femtosecond pump pulse at 618 nanometers, and the transient absorption spectra from 560 to 710 nanometers were recorded from -50 to 1000 femtoseconds by means of 6-femtosecond probe pulses. By 60 femtoseconds, a broad transient hole appeared in the absorption spectrum whose amplitude remained constant for about 200 femtoseconds. Stimulated emission in the 660- to 710-nanometer region and excited-state absorption in the 560- to 580-nanometer region appeared promptly and then shifted and decayed from 0 to approximately 150 femtoseconds. These spectral features provide a direct observation of the 13-trans to 13-cis torsional isomerization of the retinal chromophore on the excited-state potential surface. Absorption due to the primary ground-state photoproduct J appears with a time constant of approximately 500 femtoseconds.
1723 Observation of Droplet Evaporation Process and Watermark Formation on Si Wafer (2012)

In order to investigate the evaporation phenomena of small droplet which arises by spin drying process of Si wafer after CMP processing, a minute droplet was dropped on the various Si wafer The evaporation behavior was captured by the microscope camera. From the photograph, the contact angle and the contact area of droplet were estimated The difference m the evaporation process by time progress was observed. The droplet evaporation process was mainly categorized into two types, i.e. constant contact angle and constant contact area types. The residual area of the watermark which appears after constant contact area evaporation was larger than that of constant contact angle evaporation.
Controlling the interparticle distance in a 2D molecule–nanoparticle network (2011)

Mechanically controllable break junctions allow for an impressive level of control over the distance between two electrodes, but lack stability at room temperature. On the other hand, two-dimensional (2D) networks of nanoparticles bridged by molecules form a stable device structure for investigating molecular conductance properties. Here, we combine both techniques to create a robust platform for molecular charge transport with control over the inter-electrode distance on the picometer scale. The resistance change due to bending of our structures is dependent on the molecular species present between the nanoparticles.
NEXT GENERATION ENERGY EFFICIENT FLUORESCENT LIGHTING PRODUCT (2003)

This is the Final Report of the Next-Generation Energy Efficient Fluorescent Lighting Products program, Department of Energy (DOE). The overall goal of this three-year program was to develop novel phosphors to improve the color rendition and efficiency of compact and linear fluorescent lamps. The prime technical approach was the development of quantum-splitting phosphor (QSP) to further increase the efficiency of conventional linear fluorescent lamps and the development of new high color rendering phosphor blends for compact fluorescent lamps (CFLs) as potential replacements for the energy-hungry and short-lived incandescent lamps in market segments that demand high color rendering light sources. We determined early in the project that the previously developed oxide QSP, SrAl{sub 12}O{sub 19}:Pr{sup 3+}, did not exhibit an quantum efficiency higher than unity under excitation by 185 nm radiation, and we therefore worked to determine the physical reasons for this observation. From our investigations we concluded that the achievement of quantum efficiency exceeding unity in SrAl{sub 12}O{sub 19}:Pr{sup 3+} was not possible due to interaction of the Pr{sup 3+} 5d level with the conduction band of the solid. The interaction which gives rise to an additional nonradiative decay path for the excitation energy is responsible for the low quantum efficiency of the phosphor. Our work has led to the development of a novel spectroscopic method for determining photoionzation threshold of luminescent centers in solids. This has resulted in further quantification of the requirements for host phosphor lattice materials to optimize quantum efficiency. Because of the low quantum efficiency of the QSP, we were unable to demonstrate a linear fluorescent lamp with overall performance exceeding that of existing mercury-based fluorescent lamps. Our work on the high color rendering CFLs has been very successful. We have demonstrated CFLs that satisfies the EnergyStar requirement with color rendering index (CRI) greater than 90; the CRI of current commercial CFLs are in the low 80s. In this report we summarize the technical work completed under the Program, summarize our findings about the performance limits of the various technologies we investigated, and outline promising paths for future work.
Nonischemic myocardial damage induced by nonocclusive constriction of coronary artery in rats (1991)

To determine whether reduction in coronary vessel diameter leads to alterations in cardiac function, coronary perfusion, and tissue integrity, the left coronary artery of rats was narrowed and ventricular hemodynamics measured at 3 and 5 days after surgery. Coronary artery narrowing averaged 62% and end-diastolic pressure was increased, whereas peak systolic pressure, positive change in pressure over time, stroke volume, and total peripheral resistance were decreased. However, this impairment of function was accompanied by a preservation of resting coronary blood flow (CBF), although a 43% decrease in maximal CBF was detected. Foci of reparative fibrosis and myocytolytic necrosis were found primarily in the endomyocardium and midmyocardium. These lesions were temporally distinct, corresponding to 5 days and 12- to 24-h-old forms of myocardial damage, respectively. The changes in maximal CBF correlated with the degree of stenosis, whereas the volume fraction, average cross-sectional area, and number of foci of reparative fibrosis lesions per unit area of myocardium correlated exclusively with end-diastolic pressure. In conclusion, reductions in luminal diameter of a major coronary artery not affecting resting coronary perfusion have a profound detrimental impact on cardiac performance and initiate immediate myocyte cell loss that is ongoing. Thus tissue and cellular damage may not be ischemic in nature but rather mediated by other mechanisms such as unbearable mechanical stress.
VLSI architecture of a high-performance neural spiking activity simulator based on generalized Volterra kernel (2014)

It is well known that information is represented and transmitted among neuronal units by a series of all-or-none “neural codes”. In neuroinformatics study, this coding process, also termed as “spiking activity”, is not straightforward for prediction. It is owing to the high nonlinearity and dynamic property involved in generation of the neuronal spikes. In this paper, a novel generalized Volterra kernel-based neural spiking activity simulator is introduced for prediction of the neural codes in mammalian hippocampal region. High-performance VLSI architecture is established for the simulator based on high-order Volterra kernels involving cross terms. The effectiveness and efficiency of the simulator are proven in experimental settings. This simulator has the potential to serve as a core functional unit in future hippocampal cognitive neural prosthesis.
Data from An Epithelial–Mesenchymal Transition Gene Signature Predicts Resistance to EGFR and PI3K Inhibitors and Identifies Axl as a Therapeutic Target for Overcoming EGFR Inhibitor Resistance (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Epithelial–mesenchymal transition (EMT) has been associated with metastatic spread and EGF receptor (EGFR) inhibitor resistance. We developed and validated a robust 76-gene EMT signature using gene expression profiles from four platforms using non–small cell lung carcinoma (NSCLC) cell lines and patients treated in the Biomarker-Integrated Approaches of Targeted Therapy for Lung Cancer Elimination (BATTLE) study.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We conducted an integrated gene expression, proteomic, and drug response analysis using cell lines and tumors from patients with NSCLC. A 76-gene EMT signature was developed and validated using gene expression profiles from four microarray platforms of NSCLC cell lines and patients treated in the BATTLE study, and potential therapeutic targets associated with EMT were identified.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Compared with epithelial cells, mesenchymal cells showed significantly greater resistance to EGFR and PI3K/Akt pathway inhibitors, independent of EGFR mutation status, but more sensitivity to certain chemotherapies. Mesenchymal cells also expressed increased levels of the receptor tyrosine kinase Axl and showed a trend toward greater sensitivity to the Axl inhibitor SGI-7079, whereas the combination of SGI-7079 with erlotinib reversed erlotinib resistance in mesenchymal lines expressing Axl and in a xenograft model of mesenchymal NSCLC. In patients with NSCLC, the EMT signature predicted 8-week disease control in patients receiving erlotinib but not other therapies.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; We have developed a robust EMT signature that predicts resistance to EGFR and PI3K/Akt inhibitors, highlights different patterns of drug responsiveness for epithelial and mesenchymal cells, and identifies Axl as a potential therapeutic target for overcoming EGFR inhibitor resistance associated with the mesenchymal phenotype. &lt;i&gt;Clin Cancer Res; 19(1); 279–90. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Heat Shock Response of Archaeoglobus fulgidus (2005)

The heat shock response of the hyperthermophilic archaeon Archaeoglobus fulgidus strain VC-16 was studied using whole-genome microarrays. On the basis of the resulting expression profiles, approximately 350 of the 2,410 open reading frames (ORFs) (ca. 14%) exhibited increased or decreased transcript abundance. These span a range of cell functions, including energy production, amino acid metabolism, and signal transduction, where the majority are uncharacterized. One ORF called AF1298 was identified that contains a putative helix-turn-helix DNA binding motif. The gene product, HSR1, was expressed and purified from Escherichia coli and was used to characterize specific DNA recognition regions upstream of two A. fulgidus genes, AF1298 and AF1971. The results indicate that AF1298 is autoregulated and is part of an operon with two downstream genes that encode a small heat shock protein, Hsp20, and cdc48, an AAA+ ATPase. The DNase I footprints using HSR1 suggest the presence of a cis-binding motif upstream of AF1298 consisting of CTAAC-N5-GTTAG. Since AF1298 is negatively regulated in response to heat shock and encodes a protein only distantly related to the N-terminal DNA binding domain of Phr of Pyrococcus furiosus, these results suggest that HSR1 and Phr may belong to an evolutionarily diverse protein family involved in heat shock regulation in hyperthermophilic and mesophilic Archaea organisms.