gebhart/patrepeval huggingface dataset:
Characterization of monovalent ion transport systems in an insect cell line (Manduca sexta embryonic cell line che) (1984)

The monovalent ion transport systems of an immortalized insect cell line (CHE) have been investigated. These cells are unusual in that unlike most vertebrate cells, their normal extracellular environment consists of high potassium and low sodium concentrations. CHE cells maintained high intracellular [K+] through both a furosemide-inhibitable and a vanadate-inhibitable transport system. Intracellular exchangeable [Na+] was slightly lower than the extracellular [Na+] and was maintained at this level through a vanadate-sensitive transport system. Na+ uptake was also inhibited by furosemide: however, the stoichiometry of furosemide-sensitive Na+ uptake when compared with furosemide-sensitive K+ uptake indicated that these cations are not cotransported. 4,4'-Diisothiocyano-2,2'-disulfonic acid stilbene (DIDS) inhibited Na+, K+, and Cl- uptake. Vanadate and furosemide decreased cytoplasmimic pH, while cytoplasmic pH increased in the presence of DIDS. A model is presented explaining how Na+, K+, Cl-, H+ and HCO3-fluxes are regulated in these cells.
Snapback and Postsnapback Saturation of Pseudomorphic High-Electron Mobility Transistor Subject to Transient Overstress (2010)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> The snapback and postsnapback saturation characteristics in a pseudomorphic high-electron mobility transistor (PHEMT) subject to electrostatic discharge (ESD) transient overstress are studied. This is undertaken, for the first time, via transmission line pulsing (TLP)-like 2-D device simulations and benchmarked against TLP measurements. Physical mechanisms underlying the postsnapback behavior and ESD-induced failure are identified and discussed by analyzing TLP-like simulation results rather than extrapolating dc-like numerical simulation data. </para>
The influence of gas saturation and pore pressure on the characteristics of the Frenkel-Biot P waves in partially saturated porous media (2010)

For the case of a partially saturated porous medium, analysis of the conditions is carried out under which the properties of the Frenkel-Biot P waves are similar. The condition of dynamic compatibility (with fulfillment of which a wave of the first kind is propagated without attenuation) is generalized to the case of partially saturated porous media. It is found that the wave connected with the matrix deformation possesses a high attenuation coefficient in a porous medium saturated with a weakly-compressible liquid, but it is a weakly decaying wave in a gas-saturated porous medium. Asymptotic formulas for phase wave velocities are obtained within a low-frequency and high-frequency limit for the general case of a partially saturated porous medium. It is shown that in the domain of low gas saturation, the attenuation coefficient of a wave of the first kind (i.e., a wave connected with the compressibility of phases) depends on the state of the gas in porous space. The following three cases are considered: (1) the microbubbles occluded in the saturating liquid; (2) the microbubbles adsorbed on the walls of pores; and (3) the macrobubbles that completely occupy one or several pores. This characteristic can be used as the diagnostic parameter.
Effects of oxygen concentration and exposure time on cultured human airway epithelial cells (2008)

In this model, airway epithelial cells demonstrate profound concentration and time-dependent responses to hyperoxic exposure with respect to cell physiology, viability, histology, and secretion of inflammatory mediators. This model might be a valuable tool for preliminary analysis of potentially protective therapies against hyperoxia-induced airway epithelial injury.
Value of Information in Minimum-Rate LQG Control (2017)

This study concerns fundamental limitations in control of mobile cyber-physical systems. In these systems, communication between a node and its base station due to limited power of the node is asymmetrical in terms of bandwidth and signal-to-noise ratio. The framework we develop in this paper is for partially observed linear quadratic Gaussian (LQG) control over communication networks in which the forward channel transporting measurements is modeled by a zero-delay packet-deletion channel and the feedback channel transporting control inputs is assumed ideal. Making use of dynamic programming, we characterize the optimal control and the optimal sampling policies that achieve the minimum data rate required for a guaranteed level of control performance. In particular, we prove that in the presence of event-driven sampling the adopted filter is optimal and the separation principle between control and estimation holds. We show that the optimal control policy is a certainty equivalent policy and the optimal sampling policy is a threshold policy expressed in terms of the value of information. Furthermore, we prove that the value of information is a quadratic function of the innovation.
How Does Chronic Cigarette Smoke Exposure Affect Human Skin? A Global Proteomics Study in Primary Human Keratinocytes (2016)

Cigarette smoking has been associated with multiple negative effects on human skin. Long-term physiological effects of cigarette smoke are through chronic and not acute exposure. Molecular alterations due to chronic exposure to cigarette smoke remain unclear. Primary human skin keratinocytes chronically exposed to cigarette smoke condensate (CSC) showed a decreased wound-healing capacity with an increased expression of NRF2 and MMP9. Using quantitative proteomics, we identified 4728 proteins, of which 105 proteins were overexpressed (≥2-fold) and 41 proteins were downregulated (≤2-fold) in primary skin keratinocytes chronically exposed to CSC. We observed an alteration in the expression of several proteins involved in maintenance of epithelial barrier integrity, including keratin 80 (5.3 fold, p value 2.5 × 10<sup>-7</sup>), cystatin A (3.6-fold, p value 3.2 × 10<sup>-3</sup>), and periplakin (2.4-fold, p value 1.2 × 10<sup>-8</sup>). Increased expression of proteins associated with skin hydration, including caspase 14 (2.2-fold, p value 4.7 × 10<sup>-2</sup>) and filaggrin (3.6-fold, p value 5.4 × 10<sup>-7</sup>), was also observed. In addition, we report differential expression of several proteins, including adipogenesis regulatory factor (2.5-fold, p value 1.3 × 10<sup>-3</sup>) and histone H1.0 (2.5-fold, p value 6.3 × 10<sup>-3</sup>) that have not been reported earlier. Bioinformatics analyses demonstrated that proteins differentially expressed in response to CSC are largely related to oxidative stress, maintenance of skin integrity, and anti-inflammatory responses. Importantly, treatment with vitamin E, a widely used antioxidant, could partially rescue adverse effects of CSC exposure in primary skin keratinocytes. The utility of antioxidant-based new dermatological formulations in delaying or preventing skin aging and oxidative damages caused by chronic cigarette smoke exposure warrants further clinical investigations and multi-omics research.
Method of CO and/or CO.sub.2 hydrogenation to higher hydrocarbons using doped mixed-metal oxides (2023)

A method of hydrogenation utilizing a reactant gas mixture comprising a carbon oxide and a hydrogen agent, and a hydrogenation catalyst comprising a mixed-metal oxide containing metal sites supported and/or incorporated into the lattice. The mixed-metal oxide comprises a pyrochlore, a brownmillerite, or mixtures thereof doped at the A-site or the B-site. The metal site may comprise a deposited metal, where the deposited metal is a transition metal, an alkali metal, an alkaline earth metal, or mixtures thereof. Contact between the carbon oxide, hydrogen agent, and hydrogenation catalyst under appropriate conditions of temperature, pressure and gas flow rate generate a hydrogenation reaction and produce a hydrogenated product made up of carbon from the carbon oxide and some portion of the hydrogen agent. The carbon oxide may be CO, CO.sub.2, or mixtures thereof and the hydrogen agent may be H.sub.2. In a particular embodiment, the hydrogenated product comprises olefins, paraffins, or mixtures thereof.
A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes (2006)

Our results demonstrate that jumps in our jumping profile HMM often correspond to recombination breakpoints; our approach can therefore be used to detect recombinations in genomic sequences. The recombination breakpoints identified by jpHMM were found to be significantly more accurate than breakpoints defined by traditional methods based on comparing single representative sequences.
Luminescence Properties of CaF2 Nanostructure Activated by Different Elements (2015)

Nanostructures of calcium fluoride (CaF 2 ) doped with Eu, Tb, Dy, Cu, and Ag were synthesized by the coprecipitation method and studied for their thermoluminescence (TL) and photoluminescence (PL) properties. The PL emission spectrum of pure CaF 2 nanostructure has a broad band in the 370–550 nm range. Similar spectra were observed in case of doped samples, beside extra bands related to these impurities. The maximum PL intensity was observed in Eu doped sample. The TL results of Eu, Cu, Ag, and Tb doped samples show weak glow peaks below 125°C, whereas Dy doped one is found to be highly sensitive with a prominent peak at 165°C. This sample was further exposed to a wide range of gamma rays exposures from 137 Cs source. The response curve is linear in the 100 Gy‐10 kGy range. It is also observed that the particle size of CaF 2 nanostructure was significantly reduced by increasing Dy concentration. These results showed that Dy is a proper activator in the host of CaF 2 nanostructure, providing a highly sensitive dosimeter in a wide range of exposures and also plays a role as a controlling agent for particle size growth.
Lrpap1 (RAP) Inhibits Proximal Tubule Clathrin Mediated and Clathrin Independent Endocytosis, Ameliorating Renal Aminoglycoside Nephrotoxicity (2023)

Key Points Proximal tubule endocytosis of toxins often leads to nephrotoxicity. Inhibition of endocytosis with receptor-associated protein may serve as a clinical approach to reduce or eliminate kidney damage from a potential nephrotoxin. Background Proximal tubules (PTs) are exposed to many exogenous and endogenous nephrotoxins that pass through the glomerular filter. This includes many small molecules, such as aminoglycoside and myeloma light chains. These filtered molecules are rapidly endocytosed by the PTs and lead to nephrotoxicity. Methods To investigate whether inhibition of PT uptake of filtered toxins can reduce toxicity, we evaluated the ability of Lrpap1 or receptor-associated protein (RAP) to prevent PT endocytosis. Munich Wistar Frömter rats were used since both glomerular filtration and PT uptake can be visualized and quantified. The injury model chosen was the well-established gentamicin-induced toxicity, which leads to significant reductions in GFR and serum creatinine increases. CKD was induced with a right uninephrectomy and left 40-minute pedicle clamp. Rats had 8 weeks to recover and to stabilize GFR and proteinuria. Multiphoton microscopy was used to evaluate endocytosis in vivo and serum creatinine, and 24-hour creatinine clearances were used to evaluate kidney functional changes. Results Studies showed that preadministration of RAP significantly inhibited both albumin and dextran endocytosis in outer cortical PTs. Importantly, this inhibition was found to be rapidly reversible with time. RAP was also found to be an excellent inhibitor of PT gentamicin endocytosis. Finally, gentamicin administration for 6 days resulted in significant elevation of serum creatinine in vehicle-treated rats, but not in those receiving daily infusion of RAP before gentamicin. Conclusions This study provides a model for the potential use of RAP to prevent, in a reversible manner, PT endocytosis of potential nephrotoxins, thus protecting the kidney from damage.
6LoWPAN Neighbor Discovery (2010)

This document specifies a new Neighbor Discovery mechanism suitable\nfor LoWPANs. The 6LoWPAN format allows IPv6 to be used over energy and\nbandwidth constrained wireless networks often making use of multihop\ntopologies. However, the use of classic IPv6 Neighbor Discovery with\n6LoWPAN has several problems. Classic Neighbor Discovery was not\ndesigned for non-transitive wireless links, and the traditional IPv6\nlink concept and heavy use of multicast makes it unpractical. This\ndocument specifies a simple Neighbor Discovery mechanism both\nsufficient yet minimal for LoWPAN operation.
Location-aware optical coherent tomography (OCT) tethered capsule endomicroscopy (TCE) of the small intestine (2021)

For OCT-tethered capsule endomicroscopy (TCE) to be a useful minimally invasive tool for evaluating Crohn’s disease, the capsule must be able to be localized within the terminal ileum where the disease often manifests. Here, we developed a machine learning algorithm to assign OCT images of the small intestine into their corresponding anatomical regions. We selected a convolutional neural network and trained it on a set of 2108 cross-sectional images obtained from four swine ex vivo imaging studies to classify images into duodenum, jejunum, or terminal ileum. The model achieved 93±1.72% (95% confidence interval) accuracy on a separate test set of 846 images. These results suggest machine learning may be used to automatically determine when the capsule is in the terminal ileum, enabling microscopic evaluation of this anatomical segment that exhibits pathology in Crohn’s disease.
Efficiency of low-power design techniques in multi-gate FET CMOS circuits (2007)

Energy dissipation, performance, and voltage scaling of Multi-Gate FET (MuGFET) based CMOS circuits are analyzed using product-representative test circuits composed of 10k devices. The circuits are fabricated in a low power MuGFET CMOS technology, achieve clock frequencies of 370–500MHz at V <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DD</sup> =1.2V, and operate down to the subthreshold region. Voltage scalability of MuGFET circuits is superior to sub-100nm planar CMOS circuits due to excellent short-channel effect control.
Linearization of DFB laser diode using cross gain modulation (XGM)-based light injection for RoF link (2006)

We proposed a novel linearization technique for DFB LD in Radio-over-Fiber. The proposed scheme is using light injection based on cross-gain modulation (XGM) effect. We experimentally demonstrated and evaluated the enhanced CNR performance using the proposed scheme.
ChemInform Abstract: Synthesis of (.+‐.)‐Cycloprop‐G, the Cyclopropyl Analogue of the Broad Spectrum Antiviral Agent Cyclobut‐G. (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.
THz imaging Si MOSFET system design at 215 GHz (2014)

Exelis Geospatial Systems and its CEIS partners at the University of Rochester and Rochester Institute of Technology are developing an active THz imaging focal plane for use in standoff detection, molecular spectroscopy and penetration imaging. This activity is focused on the detection of radiation centered on the atmospheric window at 215.5 GHz. The pixel consists of a direct coupled bowtie antenna utilizing a 0.35 μm CMOS technology MOSFET, where the plasmonic effect is the principle method of detection. With an active THz illumination source such as a Gunn diode, a design of catadioptric optical system is presented to achieve a resolution of 3.0 mm at a standoff distance of 1.0 m. The primary value of the initial system development is to predict the optical performance of a THz focal plane for active imaging and to study the interaction of THz radiation with various materials.
Visual Data Exploration (Tutorial). (1999)

The basic concept of tissue engineering, an actively applied technology in regenerative medicine, is the coordination between cells, scaffolds, and proliferation factors. Collagen and gelatin are materials that have mostly been used as scaffolds because of their excellent affinity for cells, they are biodegradable, and their ability to form gel. However, very few of the collagen or gelatin preparations used as tissue engineering material have been prepared with low levels of endotoxin, which may trigger fever, shock and a fall in blood pressure even in very minute quantities. Therefore we decided to decrease the content of endotoxin in gelatin so that this biomaterial is not harmful to the body but still maintains its properties, namely, bioaffinity and biodegradation for use in the fields of cell culture and regenerative medicine. In this paper, we describe a method whereby endotoxin could be removed from gelatin solution by using an ultrafiltration membrane with a molecular weight cut-off of 100 kDa and low endotoxin gelatin, endotoxin activity in 0.1% gelatin solution was below 0.03 EU/ml, was obtained as the resulting filtrate solution.
Supersensitive detection and discrimination of enantiomers by dorsal olfactory receptors: evidence for hierarchical odour coding (2015)

Enantiomeric pairs of mirror-image molecular structures are difficult to resolve by instrumental analyses. The human olfactory system, however, discriminates (-)-wine lactone from its (+)-form rapidly within seconds. To gain insight into receptor coding of enantiomers, we compared behavioural detection and discrimination thresholds of wild-type mice with those of ΔD mice in which all dorsal olfactory receptors are genetically ablated. Surprisingly, wild-type mice displayed an exquisite "supersensitivity" to enantiomeric pairs of wine lactones and carvones. They were capable of supersensitive discrimination of enantiomers, consistent with their high detection sensitivity. In contrast, ΔD mice showed selective major loss of sensitivity to the (+)-enantiomers. The resulting 10(8)-fold differential sensitivity of ΔD mice to (-)- vs. (+)-wine lactone matched that observed in humans. This suggests that humans lack highly sensitive orthologous dorsal receptors for the (+)-enantiomer, similarly to ΔD mice. Moreover, ΔD mice showed >10(10)-fold reductions in enantiomer discrimination sensitivity compared to wild-type mice. ΔD mice detected one or both of the (-)- and (+)-enantiomers over a wide concentration range, but were unable to discriminate them. This "enantiomer odour discrimination paradox" indicates that the most sensitive dorsal receptors play a critical role in hierarchical odour coding for enantiomer identification.
Pharmacological Characterization, Structural Studies, and In Vivo Activities of Anti-Chagas Disease Lead Compounds Derived from Tipifarnib (2012)

Chagas disease, caused by the protozoan pathogen Trypanosoma cruzi, remains a challenging infection due to the unavailability of safe and efficacious drugs. Inhibitors of the trypanosome sterol 14α-demethylase enzyme (CYP51), including azole antifungal drugs, are promising candidates for development as anti-Chagas disease drugs. Posaconazole is under clinical investigation for Chagas disease, although the high cost of this drug may limit its widespread use. We have previously reported that the human protein farnesyltransferase (PFT) inhibitor tipifarnib has potent anti-T. cruzi activity by inhibiting the CYP51 enzyme. Furthermore, we have developed analogs that minimize the PFT-inhibitory activity and enhance the CYP51 inhibition. In this paper, we describe the efficacy of the lead tipifarnib analog compared to that of posaconazole in a murine model of T. cruzi infection. The plasma exposure profiles for each compound following a single oral dose in mice and estimated exposure parameters after repeated twice-daily dosing for 20 days are also presented. The lead tipifarnib analog had potent suppressive activity on parasitemia in mice but was unsuccessful at curing mice, whereas posaconazole as well as benznidazole cured 3 of 5 and 4 of 6 mice, respectively. The efficacy results are consistent with posaconazole having substantially higher predicted exposure than that of the tipifarnib analog after repeat twice-daily administration. Further changes to the tipifarnib analogs to reduce plasma clearance are therefore likely to be important. A crystal structure of a trypanosomal CYP51 bound to a tipifarnib analog is reported here and provides new insights to guide structure-based drug design for further optimized compounds.
Sorting of Single Biomolecules based on Fourier Polar Representation of Surface Enhanced Raman Spectra (2016)

Surface enhanced Raman scattering (SERS) spectroscopy becomes increasingly used in biosensors for its capacity to detect and identify single molecules. In practice, a large number of SERS spectra are acquired and reliable ranking methods are thus essential for analysing all these data. Supervised classification strategies, which are the most effective methods, are usually applied but they require pre-determined models or classes. In this work, we propose to sort SERS spectra in unknown groups with an alternative strategy called Fourier polar representation. This non-fitting method based on simple Fourier sine and cosine transforms produces a fast and graphical representation for sorting SERS spectra with quantitative information. The reliability of this method was first investigated theoretically and numerically. Then, its performances were tested on two concrete biological examples: first with single amino-acid molecule (cysteine) and then with a mixture of three distinct odorous molecules. The benefits of this Fourier polar representation were highlighted and compared to the well-established statistical principal component analysis method.
Direct Installation of a Silyl Linker on Ready-Made NHC Ligands: Immobilized NHC-Pd Complex for Buchwald–Hartwig Amination (2019)

An immobilized N-heterocyclic carbene (NHC)-Pd complex was prepared via direct silyl linker installation onto the imidazole backbone of commercially available 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene (IPr) ligand. The IPr backbone was lithiated and treated with Me2SiCl2 to afford ClMe2Si-IPr, which reacted with [Pd(π-allyl)Cl]2 to yield a ClMe2Si-IPr-Pd complex, and this was immobilized on Wang resin. The immobilized NHC-Pd complex facilitated quantitative Buchwald–Hartwig amination of aryl chlorides within 10 min, even at a low Pd loading of 0.2 mol %. The catalyst could be removed from the reaction mixture by simple filtration, and Pd leaching into the reaction medium was suppressed to below 1 ppm.