gebhart/patrepeval huggingface dataset:
Extracellular Vesicles From Hyperammonemic Rats Induce Neuroinflammation in Cerebellum of Normal Rats: Role of Increased TNFα Content (2022)

Hyperammonemia plays a main role in the neurological impairment in cirrhotic patients with hepatic encephalopathy. Rats with chronic hyperammonemia reproduce the motor incoordination of patients with minimal hepatic encephalopathy, which is due to enhanced GABAergic neurotransmission in cerebellum as a consequence of neuroinflammation. Extracellular vesicles (EVs) could play a key role in the transmission of peripheral alterations to the brain to induce neuroinflammation and neurological impairment in hyperammonemia and hepatic encephalopathy. EVs from plasma of hyperammonemic rats (HA-EVs) injected to normal rats induce neuroinflammation and motor incoordination, but the underlying mechanisms remain unclear. The aim of this work was to advance in the understanding of these mechanisms. To do this we used an ex vivo system. Cerebellar slices from normal rats were treated ex vivo with HA-EVs. The aims were: 1) assess if HA-EVs induce microglia and astrocytes activation and neuroinflammation in cerebellar slices of normal rats, 2) assess if this is associated with activation of the TNFR1-NF-kB-glutaminase-GAT3 pathway, 3) assess if the TNFR1-CCL2-BDNF-TrkB pathway is activated by HA-EVs and 4) assess if the increased TNFα levels in HA-EVs are responsible for the above effects and if they are prevented by blocking the action of TNFα. Our results show that ex vivo treatment of cerebellar slices from control rats with extracellular vesicles from hyperammonemic rats induce glial activation, neuroinflammation and enhance GABAergic neurotransmission, reproducing the effects induced by hyperammonemia <i>in vivo</i>. Moreover, we identify in detail key underlying mechanisms. HA-EVs induce the activation of both the TNFR1-CCL2-BDNF-TrkB-KCC2 pathway and the TNFR1-NF-kB-glutaminase-GAT3 pathway. Activation of these pathways enhances GABAergic neurotransmission in cerebellum, which is responsible for the induction of motor incoordination by HA-EVs. The data also show that the increased levels of TNFα in HA-EVs are responsible for the above effects and that the activation of both pathways is prevented by blocking the action of TNFα. This opens new therapeutic options to improve motor incoordination in hyperammonemia and also in cirrhotic patients with hepatic encephalopathy and likely in other pathologies in which altered cargo of extracellular vesicles contribute to the propagation of the pathology.
GaInN-based light emitting diodes embedded with wire grid polarizers (2014)

The use of liquid crystal displays (LCDs) has become prevalent in our modern, technology driven society. We demonstrate a linearly polarized GaInN light-emitting diode (LED) embedded with a wire-grid polarizer (WGP). A derivation of rigorous coupled-wave analysis is given; starting from Maxwell's equations and finishing by matching the boundary conditions in the grating and other regions of interest. Simulated results are shown for various grating parameters, including different metals used for the grating and the metal-line dimensions. An LED fabrication process is developed for demonstrating WGP-LEDs. A clear polarization preference for the light coming out of the WGP-LED is experimentally demonstrated with a polarization ratio over 0.90, which is in good agreement with simulation results.
ChemInform Abstract: Chemistry in Crop Protection. Part 6. Amino Acid Chemistry in Crop Protection (2010)

Abstract Review: ca. 150 refs.
H2O vapor assisted growth of β-Ga2O3 by MOCVD (2020)

The role of water (H2O) vapor in reducing background impurity concentration in epitaxial Ga2O3 thin films grown by metalorganic chemical vapor deposition (MOCVD) was studied. Adding H2O vapor to oxygen was found to increase the surface roughness and decrease the carrier concentration but have no effect on the structural quality and RT electron mobility of both the UID and doped films. The H2O vapor promotes the growth of the stable (110) and 1¯10 facets elongated along the [001] direction. Using [H2O] of 250 ppm, the β-Ga2O3 films showed a RMS roughness of &amp;gt;13 nm, which is much higher than that measured for similar films grown without H2O (RMS = 0.8 nm). The electron mobility of the UID Ga2O3 layers grown with and without water vapor was ∼150 cm2/V s, while the carrier concentration dropped by ∼2.5× after increasing the [H2O] to 6000 ppm. Similarly, for the lightly Si doped films, the RT carrier concentration dropped from 5.4 × 1015 cm−3 ([H2O] = 0 ppm) to 3.4 × 1015 cm−3 ([H2O] = 250 ppm), leaving the mobility unaffected. The results offer a new method of using water vapor assisted growth of Ga2O3 films with low RT carrier concentration that are required for the realization of high-performance electronic power devices with high breakdown voltages.
Antigen presenting cell (APC)-targeted hCGβ vaccine for cancer therapy (2007)

3013 Background: CDX-1307 is a novel vaccine approach designed to target antigens directly into the endocytic compartments of dendritic cells (DCs) and other professional APCs. The β subunit of human chorionic gonadotropin (hCGβ) is selectively over-expressed by a number of epithelial tumors and has been reported to correlate with stage of disease and prognosis. We have coupled this tumor-associated antigen to a human monoclonal antibody (B11) that targets mannose receptors on human dendritic cells and macrophages, and have demonstrated the efficacy of this approach in preclinical models using hCGβ-expressing tumors and cell lines. Methods: In this phase I, dose-escalating study, sequential cohorts of 6 patients with relapsed epithelial tumors receive 4 biweekly intradermal injections of CDX-1307 at either 0.3, 1.0 or 2.5 mg, or 2.5 mg concurrent with GM-CSF. Objectives: safety and tolerability; DLT, humoral and cellular immune response, and clinical activity. Results: Enrollment in the first three cohorts (n=18) is complete with no DLTs. Common potential treatment-related toxicities were injection site reaction (n=5) and fatigue/malaise (n=4), and were generally mild to moderate in severity. One transient Grade 3 generalized allergic reaction in the 1.0 mg cohort was suspected possibly related to either a nut allergy or CDX-1307. One mixed response was seen, with variable effects on circulating hCGβ. CDX-1307 localized to dermal macrophages and DCs in post-treatment biopsies. Conclusions: Administration of CDX-1307 is well tolerated and results in antigen localization in APCs of the skin. Immune Response and tumor impact are under evaluation. Further development includes systemic delivery that may provide antigen targeting to a broad APC population, and combination with immunostimulants to generate optimal immune responses. No significant financial relationships to disclose.
Mechanistic Study on Deoxydehydration and Hydrogenation of Methyl Glycosides to Dideoxy Sugars over a ReOx–Pd/CeO2 Catalyst (2020)

We found that nonprotected methyl glycosides with cis-vicinal OH groups could be converted to the corresponding methyl dideoxy glycosides by deoxydehydration and consecutive hydrogenation (DODH + HG) over a ReOx–Pd/CeO2 catalyst with gaseous H2. In the study, the reactivity of the methyl glycosides in DODH was clearly lower than that of simple cyclic vicinal diols, such as cis-1,2-cyclohexanediol and cis-1,2-cyclopentanediol, and the reactivity of the methyl glycosides was also different. Herein, we investigated the reactivity difference based on kinetic studies and density-functional theory (DFT) calculations. The kinetic studies suggest that the reactivity difference between the methyl glycosides and the simple diols is derived from the OH group of methyl glycosides except the cis-vicinal diols, and that the reactivity difference among the methyl glycosides will be associated with the configuration of the substituents adjacent to the cis-vicinal diols, while the reaction mechanism of DODH is suggested to be basically similar judging from almost the same reaction orders with respect to the substrate concentration and H2 pressure in all substrates. The adsorption and transition states of methyl α -l- rhamnopyranoside and methyl α-l-fucopyranoside, which have a large reactivity difference (methyl α-l-rhamnopyranoside≫ methyl α-l-fucopyranoside), were estimated by DFT calculations with ReOx/CeO2 as the active site of the ReOx–Pd/CeO2 catalyst, showing that the main difference is the activation energy in DODH of these substrates (65 kJ mol–1 for methyl α-l-rhamnopyranoside and 77 kJ mol–1 for methyl α-l-fucopyranoside), which was also supported by the results of Arrhenius plots (63 and 73 kJ mol–1 for methyl α-l-rhamnopyranoside and methyl α-l-fucopyranoside, respectively). The activation energy was influenced by the torsional angle of the substituents adjacent to the cis-vicinal OH groups, which is derived from the interaction of the OH group adjacent to the cis-vicinal OH groups and the surface hydroxy groups on CeO2.
Phenotype-based variation as a biomarker of sensitivity to molecularly targeted therapy in melanoma (2016)

Transcriptomic phenotypes defined for melanoma have been reported to correlate with sensitivity to various drugs. In this study, we aimed to define a minimal signature that could be used to distinguish melanoma sub-types <i>in vitro</i>, and to determine suitable drugs by which these sub-types can be targeted. By using primary melanoma cell lines, as well as commercially available melanoma cell lines, we find that the evaluation of MLANA and INHBA expression is as capable as one based on a combined analysis performed with genes for stemness, EMT and invasion/proliferation, in identifying melanoma subtypes that differ in their sensitivity to molecularly targeted drugs. Using this approach, we find that 75% of melanoma cell lines can be treated with either the MEK inhibitor AZD6244 or the HSP90 inhibitor 17AAG.
Supplementary Figure 5 from A Human Breast Cell Model of Preinvasive to Invasive Transition (2023)

Supplementary Figure 5 from A Human Breast Cell Model of Preinvasive to Invasive Transition
Abstract #LB-262: A Randomized Placebo-Controlled Trial of a Selective Androgen Receptor Modulator in patients with cancer cachexia (2009)

AACR Annual Meeting-- Apr 18-22, 2009; Denver, CO

Many common malignancies, including non small cell lung cancer, colorectal cancer, pancreatic cancer and others, can lead to a wasting state termed cancer cachexia, which is a hypermetabolic state that leads to catabolism and subsequent reductions in lean body mass (LBM). Increases and/or better maintenance of LBM should result in improvements in quality of life and treatment response in cancer patients. We have developed selective androgen receptor modulators (SARMs) to investigate the effects on both LBM and physical performance. Herein we report the results of a phase II trial of Ostarine in patients with cancer cachexia. Methods: We conducted a randomized double-blind placebo controlled trial in 159 subjects with non small cell lung cancer, colorectal cancer, non-Hodgkin lymphoma, breast cancer, or chronic lymphocytic leukemia. Entry criteria included a 2% or greater weight loss within six months of screening, life expectancy of greater than 6 months, and ECOG score of less than or equal to 1. Subjects were randomized to receive either: 1mg Ostarine, 3mg Ostarine, or matching placebo daily for 16 weeks. The primary end point was total LBM measured by DEXA scan. Secondary end points included muscle performance measured by stair climb time and power, gait speed (6-meter walk) and grip strength. Results: Mean weight loss over the 6 months prior to study entry was 8.8% of total body weight. One hundred subjects were included in this MITT analysis. Subjects in both Ostarine treatment arms experienced an improvement in LBM. The change from baseline in LBM for the placebo, 1mg and 3mg treatment groups was 0.1 kg (p=0.874 compared to baseline), 1.5 kg (p=0.001) and 1.3 kg (p=0.045), respectively. Performance was assessed via a 12 step stair climb. Subjects in both treatment arms demonstrated improved muscle function measured both by stair climb time and stair climb power. The change from baseline in stair climb power in the placebo, 1mg and 3mg treatment groups respectively was 0.23 watts (p=0.666 compared to baseline), 35.2 watts (p=0.003) and 44.7 watts (p=0.003). Statistically significant decreases from baseline in stair climb time were also observed. Changes from baseline in gait speed and grip strength were not different between the Ostarine treatment arms and placebo. Conclusions: Ostarine treatment results in clinically meaningful and statistically significant improvements of LBM and muscle performance in cancer cachexia subjects that have experienced significant (mean 8.8%) weight loss.

Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr LB-262.
Semiactive control of a secondary train suspension (2007)

The topic of this paper is the design and analysis of a control system for the lateral movement of the carbody in a train. The control system is implemented via semi-active electro-hydraulic dampers located on the secondary-suspension that links the bogie to the structure of the carbody of the train. The entire design procedure is outlined: the semi-active damper is characterized; the best control strategies then are implemented and tested on a realistic laboratory test-bench, which accurately reproduces the lateral dynamics of a train. Among the tested control strategies, the most performing and efficient is a recently proposed one which requires only a single sensor located cabin-side.
Data from Identification of EZH2 as a Molecular Marker for a Precancerous State in Morphologically Normal Breast Tissues (2023)

&lt;div&gt;Abstract&lt;p&gt;The discovery of molecular markers to detect the precancerous state would have profound implications in the prevention of breast cancer. We report that the expression of the Polycomb group protein EZH2 increases in histologically normal breast epithelium with higher risk of developing cancer. We identify EZH2 as a potential marker for detecting preneoplastic lesions of the breast &lt;i&gt;in vivo&lt;/i&gt; and as a possible target for preventative intervention. (Cancer Res 2006; 66(8): 4095-9)&lt;/p&gt;&lt;/div&gt;
Pristine submucosal visibility using Texture and Color Enhancement Imaging during saline-immersion rectal endoscopic submucosal dissection (2021)

Pristine submucosal visibility using Texture and Color Enhancement Imaging during saline-immersion rectal endoscopic submucosal dissection Imaging (TXI) mode under saline immersion conditions with clear identification of the limits of the lesion. Lifting is obtained with glycerol injection into the submucosa in these conditions.
ChemInform Abstract: Synthesis and Catalytic Applications of Re(VII) and Mo(VI) Oxo Complexes (2002)

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.
Broadband transparent chiral mirrors: Design methodology and bandwidth analysis (2019)

Chiral mirrors are a class of metamaterials that reflect circularly polarized light of a certain helicity in a handedness-preserving manner, while absorbing circular polarization of the opposite handedness. However, most absorbing chiral mirrors operate only in a narrow frequency band, as limited by the causality principle. Instead of absorbing the undesired waveform, here we propose a transparent chiral mirror that allows undesired waves to pass through. In particular, the handedness-preserving band of the transparent chiral mirror is free of the causality limit, thus enabling broadband functionality. Furthermore, since electromagnetic waves outside the handedness-preserving band may transmit through the proposed chiral mirror, the reflected wave contains only circular polarization components of a certain handedness over a wide frequency range, which is favored in many applications. Moreover, the scheme is lossless and scalable. To realize the proposed transparent chiral mirror, we apply an array of helical microstructures in a two-dimensional square lattice. Traditionally, this kind of structure has been used as a circular polarizer but we apply it instead in a reflective mode. Our work provides a bandwidth analysis of chiral mirrors, and paves the way to new opportunities for creating broadband chiral metamaterials with handedness-preserving properties.
The Need for Transfer Learning in CRISPR-Cas Off-Target Scoring (2021)

Abstract Motivation The scalable design of safe guide RNA sequences for CRISPR gene editing depends on the computational “scoring” of DNA locations that may be edited. As there is no widely accepted benchmark dataset to compare scoring models, we present a curated “TrueOT” dataset that contains thoroughly validated datapoints to best reflect the properties of in vivo editing. Many existing models are trained on data from high throughput assays. We hypothesize that such models may suboptimally transfer to the low throughput data in TrueOT due to fundamental biological differences between proxy assays and in vivo behavior. We developed new Siamese convolutional neural networks, trained them on a proxy dataset, and compared their performance against existing models on TrueOT. Results Our simplest model with a single convolutional and pooling layer surprisingly exhibits state-of-the-art performance on TrueOT. Adding subsequent layers improved performance on a proxy dataset while compromising performance on TrueOT. We demonstrate improved generalization on TrueOT with a Siamese model of higher complexity when we apply transfer learning techniques. These results suggest an urgent need for the CRISPR community to agree upon a benchmark dataset such as TrueOT and highlight that various sources of CRISPR data cannot be assumed to be equivalent. Availability and Implementation Our code base and datasets are available on GitHub at github.com/baolab-rice/CRISPR_OT_scoring .
An improved stator flux estimation for speed sensorless stator flux orientation control of induction motors (2002)

This paper proposes a programmable low pass filter (LPF) to estimate stator flux for speed sensorless stator flux orientation control of induction motors. The programmable LPF is developed to solve the DC drift problem associated with a pure integrator and an analog LPF with fixed pole. The pole of the programmable LPF is located far from the origin in order to decrease the time constant as speed increases. The programmable LPF has the phase and the magnitude compensator to exactly estimate stator flux in a wide speed range. So, the drift problem is much improved and the stator flux is exactly estimated in the wide speed range. The validity of the proposed programmable LPF is verified by speed sensorless vector control of a 2.2 kW three-phase induction motor.
Multiple HIV-1-specific IgG3 responses decline during acute HIV-1: implications for detection of incident HIV infection (2020)

Different HIV-1 antigen specificities appear in sequence after HIV-1 transmission and the immunoglobulin G (IgG) subclass responses to HIV antigens are distinct from each other. The initial predominant IgG subclass response to HIV-1 infection consists of IgG1 and IgG3 antibodies with a noted decline in some IgG3 antibodies during acute HIV-1 infection. Thus, we postulate that multiple antigen-specific IgG3 responses may serve as surrogates for the relative time since HIV-1 acquisition.
Efficient second-harmonic generation in high Q-factor asymmetric lithium niobate metasurfaces (2021)

Lithium niobate (LN) has been widely used for second-harmonic generation (SHG) from bulk crystals. Recent studies have reported improved SHG efficiency in LN micro-ring resonators and hybrid waveguiding structures, as well as in LN nanostructures supporting anapole modes and plasmon-assisted dipole resonances. Here we numerically demonstrate that high <i>Q</i>-factor resonances associated with symmetry-protected bound states in the continuum can lead to highly efficient frequency doubling in LN metasurfaces. Simulations show that the radiative <i>Q</i>-factor and on-resonance field enhancement factor observed in the metasurface are closely dependent on the asymmetric parameter <i>α</i> of the system. Furthermore, high <i>Q</i>-factor resonances boost the SH conversion process in the LN nanostructures. In particular, for a LN metasurface with a <i>Q</i>-factor of ∼8×10<sup>4</sup>, a 0.49% peak SH conversion efficiency is achieved at a pump intensity of 3.3<i>k</i><i>W</i>/<i>c</i><i>m</i><sup>2</sup>. This suggests that such high <i>Q</i>-factor LN metasurfaces may be good candidates for practical blue-ultraviolet light sources. Our work provides insight into the possible implementation of metadevices based on nanoengineering of conventional nonlinear crystals.
Fusion of two distinct peptide exosite inhibitors of Factor VIIa (2002)

Highly potent bifunctional inhibitors of Factor VIIa (FVIIa) were generated by linking two distinct peptides, recently shown to bind to two discrete exosites on the FVIIa protease domain [Dennis, Eigenbrot, Skelton, Ultsch, Santell, Dwyer, O'Connell and Lazarus (2000) Nature (London) 404, 465–470; Dennis, Roberge, Quan and Lazarus (2001) Biochemistry 40, 9513–9521; Roberge, Santell, Dennis, Eigenbrot, Dwyer and Lazarus (2001) Biochemistry 40, 9522–9531]. Fusion peptides consisting of an N-terminal A-series peptide followed by flexible linkers, an E-series peptide, and the Z-domain of protein A were expressed in Escherichia coli and purified using IgG—Sepharose affinity chromatography. The fusion peptides were potent anticoagulants and had steep concentration dependence curves in tissue factor-dependent prothrombin time (PT) assays in comparison to the individual peptides or their noncovalent combination. This phenomenon was dependent on the length of the linker joining the A- and E-peptides. The fusion of the peptides increased the extent of inhibition of Factor X (FX) activation to 100% at saturating peptide concentrations, but did not improve the binding affinity for Factor VIIa (FVIIa) at the A- and E- binding sites or the IC50 for the inhibition of FX activation. Differences between the peptides in the PT fold prolongation in normal and FVII-deficient plasma, in conjunction with the inhibition of 125I-FVII activation, suggest that the enhanced effects of the fusion peptides involve the inhibition of FVII autoactivation.
Laparoscopic surgery improves pregnancy outcomes in women with suspected endometriosis with or without pathological confirmation (2016)

There is no difference in fertility outcomes in women with UI, whether or not suspected endometriosis is confirmed pathologically.
Inside Cover: Room‐Temperature Carbide‐Derived Carbon Synthesis by Electrochemical Etching of MAX Phases (Angew. Chem. Int. Ed. 19/2014) (2014)

The electrochemically induced extraction of metal atoms from the ternary layered carbides Ti3AlC2, Ti2AlC, and Ti3SiC2 (MAX phases) at room temperature results in predominantly amorphous carbon with a narrow distribution of micropores, as described by Y. Gogotsi et al. in their Communication on page 4877 ff. This approach forgoes energy-intensive thermal processing and presents a novel method for the synthesis of carbon materials that may be used as supercapacitors, battery electrodes, or for CO2 capture.