gebhart/patrepeval huggingface dataset:
Conversion of human 5‐lipoxygenase to a 15‐lipoxygenase by a point mutation to mimic phosphorylation at Serine‐663 (2012)

The enzyme 5-lipoxygenase (5-LOX) initiates biosynthesis of the proinflammatory leukotriene lipid mediators and, together with 15-LOX, is also required for synthesis of the anti-inflammatory lipoxins. The catalytic activity of 5-LOX is regulated through multiple mechanisms, including Ca(2+)-targeted membrane binding and phosphorylation at specific serine residues. To investigate the consequences of phosphorylation at S663, we mutated the residue to the phosphorylation mimic Asp, providing a homogenous preparation suitable for catalytic and structural studies. The S663D enzyme exhibits robust 15-LOX activity, as determined by spectrophotometric and HPLC analyses, with only traces of 5-LOX activity remaining; synthesis of the anti-inflammatory lipoxin A(4) from arachidonic acid is also detected. The crystal structure of the S663D mutant in the absence and presence of arachidonic acid (in the context of the previously reported Stable-5-LOX) reveals substantial remodeling of helices that define the active site so that the once fully encapsulated catalytic machinery is solvent accessible. Our results suggest that phosphorylation of 5-LOX at S663 could not only down-regulate leukotriene synthesis but also stimulate lipoxin production in inflammatory cells that do not express 15-LOX, thus redirecting lipid mediator biosynthesis to the production of proresolving mediators of inflammation.
Porosity and biological properties of polyethylene glycol-conjugated collagen materials (1995)

Collagen-based materials can be designed for use as scaffolds for connective tissue reconstruction. The goal of the present study was to evaluate the behavior of collagen materials as well as cell and tissue reactions after the conjugation of activated polyethylene glycols (PEGs) with collagen. It is known that proteins conjugated with PEGs exhibit a decrease in their biodegradation rate and their immunogenicity. Different concentrations and molecular weights of activated PEGs (PEG-750 and PEG-5000) were conjugated to collagen materials (films or sponges) which were then investigated by collagenase assay, fibroblast cell culture, and subcutaneous implantation. PEG-conjugated collagen sponge degradation by collagenase was delayed in comparison to untreated sponges. In culture, fibroblasts with a normal morphology reached confluency on PEG-conjugated collagen films. In vivo, the porous structure of non-modified sponges collapsed by day 15 with a few observable fibroblasts between the collagen fibers. In PEG-modified collagen sponges, the porous structure remained stable for 30 days. Cell infiltration was particularly enhanced in PEG-750-conjugated collagen sponges. In conclusion, PEGs conjugated onto collagen sponges stabilize the porous structure without deactivating the biological properties of collagen. These porous composite materials could function as a scaffold to organize tissue ingrowth.
Protection against Hemorrhagic Colitis in an Animal Model by Oral Immunization with Isogeneic Rabbit Enteropathogenic <i>Escherichia coli</i> Attenuated by Truncating Intimin (2005)

Strains of Shiga toxin (Stx)-producing Escherichia coli, also called enterohemorrhagic E. coli (EHEC), are important food-borne pathogens for humans. Most EHEC strains intimately adhere to the intestinal mucosa in a characteristic attaching and effacing (A/E) pattern, which is mediated by the bacterial adhesin intimin. Subsequent release of Stx1 and/or Stx2 leads to the frequent development of hemorrhagic colitis and, less commonly, to hemolytic-uremic syndrome. The aim of the present study was to develop an attenuated A/E E. coli strain for use as a vaccine against EHEC infection encoding a truncated intimin lacking adhesive capacity, but which would still express somatic antigens, other products of the locus of enterocyte effacement pathogenicity island, and an immunogenic remnant of the intimin molecule. A single-nucleotide deletion was generated in the eae gene in the prototype rabbit A/E E. coli strain RDEC-1 (O15:H-), which resulted in truncation of intimin by 81 C-terminal residues (860 to 939 amino acids) containing a disulfide loop. Inoculation of rabbits with large doses of the truncated intimin mutant (RDEC-1Deltaeae(860-939)) was well tolerated, as observed by the absence of clinical signs of disease or evidence of intestinal A/E lesions. The efficacy of RDEC-1Deltaeae(860-939) as a vaccine was evaluated by orogastric inoculation of rabbits with RDEC-1Deltaeae(860-939) followed by challenge with the virulent strain RDEC-H19A, an Stx1-producing derivative of wild-type RDEC-1 capable of inducing hemorrhagic colitis in rabbits. Following RDEC-H19A challenge, nonimmunized control rabbits exhibited characteristic weight loss with watery to bloody diarrhea and demonstrated intimate bacterial attachment, effacement of microvilli, submucosal edema, mucosal heterophile infiltrates, and Shiga toxin-induced vascular lesions. In contrast, the RDEC-1Deltaeae(860-939)-immunized rabbits showed no clinical signs of disease, maintained normal weight gain, had reduced fecal shedding of challenge organisms, and showed an absence of gross or microscopic lesions in the intestinal mucosa. Serum antibodies specific to intimin were detected among rabbits immunized with RDEC-1Deltaeae(860-939), indicating that truncation of the intimin functional domain not only attenuated bacterial virulence, but also retained at least some of the immunogenicity of native intimin. Although it is not possible to gauge the exact contribution of residual intimin immunity to protection, this attenuation strategy for A/E E. coli strains shows promise for the development of effective vaccines to prevent EHEC infection in humans and animals.
Multiple biological responses are induced by glycosylation-deficient hepatocyte growth factor (2005)

HGF (hepatocyte growth factor), a heterodimeric glycoprotein composed of alpha- and beta-chains, exerts biological activities through the c-Met receptor tyrosine kinase. The alpha-chain has three glycosylation sites, while the beta-chain has two; however, the role of sugar chains on HGF is still unknown. To address the significance of glycosylation of HGF, three different types of glycosylation-deficient HGFs, i.e. non-glycosylated in the alpha-chain, the beta-chain, and in both the alpha- and beta-chains, were respectively expressed in COS-7 cells and then purified from culture supernatants. Unexpectedly, glycosylation-deficient HGFs induced tyrosine phosphorylation of the c-Met receptor and subsequent phosphorylation of ERK (extracellular-signal-regulated kinase) and Akt in rat hepatocytes with the same potency as glycosylated HGF. Consistent with this, glycosylation-deficient HGFs strongly stimulated DNA synthesis of hepatocytes equal to glycosylated HGF. Likewise, glycosylation-deficient HGFs induced cell scattering and branching tubulogenesis in MDCK (Madin-Darby canine kidney) cells, and thus were indistinguishable from glycosylated HGF in biological activities. Glycosylation also did not affect stability, protease sensitivity and tissue distribution, although the plasma clearance of HGF was slightly prolonged by glycosylation deficiency. Glycosylation deficiency resulted in a decrease in post-transcriptional biosynthesis of HGF in the cells, whereas extracellularly secreted HGFs were efficiently activated to a two-chain form. These results indicate that glycosylation influences post-transcriptional biosynthesis of HGF, whereas biological activities and basic physicochemical characteristics are retained, even in completely non-glycosylated HGF. Hence, non-glycosylated HGF is promising as an alternative for glycosylated HGF in clinical applications.
Single-Walled Aluminosilicate Nanotube/Poly(vinyl alcohol) Nanocomposite Membranes (2012)

The fabrication, detailed characterization, and molecular transport properties of nanocomposite membranes containing high fractions (up to 40 vol %) of individually-dispersed aluminosilicate single-walled nanotubes (SWNTs) in poly(vinyl alcohol) (PVA), are reported. The microstructure, SWNT dispersion, SWNT dimensions, and intertubular distances within the composite membranes are characterized by scanning and transmission electron microscopy (SEM and TEM), energy-dispersive spectroscopy (EDS), X-ray diffraction (XRD), XRD rocking curve analysis, small-angle X-ray scattering (SAXS), and solid-state NMR. PVA/SWNT nanocomposite membranes prepared from SWNT gels allow uniform dispersion of individual SWNTs in the PVA matrix with a random distribution of orientations. SAXS analysis reveals the length (∼500 nm) and outer diameter (~2.2 nm) of the dispersed SWNTs. Electron microscopy indicates good adhesion between the SWNTs and the PVA matrix without the occurrence of defects such as voids and pinholes. The transport properties of the PVA/SWNT membranes are investigated experimentally by ethanol/water mixture pervaporation measurements, computationally by grand canonical Monte Carlo and molecular dynamics, and by a macroscopic transport model for anisotropic permeation through nanotube-polymer composite membranes. The nanocomposite membranes substantially enhance the water throughput with increasing SWNT volume fraction, which leads to a moderate reduction of the water/ethanol selectivity. The model is parameterized purely from molecular simulation data with no fitted parameters, and shows reasonably good agreement with the experimental water permeability data.
The releasable balloon technique with activated high frequency electrical current. (1980)

A new releasable balloon catheter was developed which has a soluble joint connecting the balloon and the catheter. The joint is made from a polyvinyl alcohol tube and has two electrodes. When a high frequency electrical current is activated, the resulting heat causes the joint to disappear within one second. The type of generator used in the experiment was an Aesculap GK-34. This catheter was used for embolization of carotid-jugular fistulas in dogs.
Novel applications of porous silicon (1990)

Porous silicon is best known for its applications in the oxide isolation of silicon integrated circuits. However, porous silicon is a very versatile material and its unique properties are being researched for a surprising range of applications. These include use as a substrate for epitaxial growth, for the production of ``smart'' dielectrics, for the location of defects in other silicon-on-insulator materials, for the producion of sensors, for conversion to metal and for the emission of visible light. These and others are described.
Performance Optimization Strategies for Nanophotonic Digital Fourier Transform Spectrometers (2019)

We present techniques for improving the performance of ultra-high resolution on-chip digital Fourier transform spectrometers. These methods enable perfect optical switching, broadband operation, large visibility, and filtering of narrowband signals
The multimodulus blind equalization algorithm (2002)

This paper presents a new blind equalization algorithm called the multimodulus algorithm (MMA). This algorithm is particularly well suited to applications using two-dimensional transmission schemes such as carrierless AM/PM (CAP) and quadrature amplitude modulation (QAM). The paper also discusses some of the advantages provided by MMA when compared to traditional blind equalization algorithms, such as the reduced constellation algorithm (RCA) and the constant modulus algorithm (CMA).
Role of the KIT protooncogene in normal and malignant human hematopoiesis. (1992)

The role of the KIT protooncogene in human hematopoiesis is uncertain. Therefore, we examined KIT mRNA expression in normal human bone marrow mononuclear cells (MNC) and used antisense oligodeoxynucleotides (oligomers) to disrupt KIT function. KIT mRNA was detected with certainty only in growth factor-stimulated MNC. Expression was essentially abrogated by making MNC quiescent or by inhibiting myb gene function. Oligomers blocked KIT mRNA expression in a dose-response and sequence-specific manner, thereby allowing functional examination of the KIT receptor. In experiments with either partially purified or CD34(+)-enriched MNC, neither granulocyte nor megakaryocyte colony formation was inhibited by oligomer exposure. In contrast, KIT antisense oligomers inhibited interleukin 3/erythropoietin-driven erythroid colony formation approximately 70% and "stem cell factor"/erythropoietin-driven colony formation 100%. The presence of erythroid progenitor cell subsets with differential requirements for KIT function is therefore suggested. Growth of hematopoietic colonies from chronic myeloid leukemia and polycythemia vera patients was also inhibited, while acute leukemia colony growth appeared less sensitive to KIT deprivation. These results suggest that KIT plays a predominant role in normal erythropoiesis but may be important in regulating some types of malignant hematopoietic cell growth as well. They also suggest that KIT expression is linked to cell metabolic activity and that its expression may be regulated by or coregulated with MYB.
High-efficiency white phosphorescent OLEDs for lighting (2004)

Organic light emitting devices (OLEDs) are viewed as a potential next generation lighting source. Phosphorescent OLED (PHOLED) technology, with its inherently high efficiencies, represents the best opportunity to meet the challenging requirements of lighting. We discuss the requirements of OLEDs for lighting applications and present the state-of-the-art of white PHOLEDs, which have demonstrated the luminous efficiencies exceeding 30 cd/A at CIE coordinates of (0.35, 0.33).
Adaptive Feature Abstraction for Translating Video to Text (2018)

Previous models for video captioning often use the output from a specific layer of a Convolutional Neural Network (CNN) as video features. However, the variable context-dependent semantics in the video may make it more appropriate to adaptively select features from the multiple CNN layers. We propose a new approach for generating adaptive spatiotemporal representations of videos for the captioning task. A novel attention mechanism is developed, that adaptively and sequentially focuses on different layers of CNN features (levels of feature "abstraction"), as well as local spatiotemporal regions of the feature maps at each layer. The proposed approach is evaluated on three benchmark datasets: YouTube2Text, M-VAD and MSR-VTT. Along with visualizing the results and how the model works, these experiments quantitatively demonstrate the effectiveness of the proposed adaptive spatiotemporal feature abstraction for translating videos to sentences with rich semantics.
Discrimination of Human Coronary Artery Atherosclerotic Lipid-Rich Lesions by Time-Resolved Laser-Induced Fluorescence Spectroscopy (2001)

Lesion composition plays a significant role in atherosclerotic lesion instability and rupture. Current clinical techniques cannot fully characterize lesion composition or accurately identify unstable lesions. This study investigates the use of time-resolved fluorescence spectroscopy for unstable atherosclerotic lesion diagnosis. The fluorescence of human coronary artery samples was induced with nitrogen laser and detected in the 360- to 510-nm wavelength range. The samples were sorted into 7 groups according to the AHA classification: normal wall and types I, II(a) (fatty streaks), III (preatheroma), IV (atheroma), V(a) (fibrous), and V(b) (calcified) lesions. Spectral intensities and time-dependent parameters [average lifetime tau(f); decay constants: tau(1) (fast-term), tau(2) (slow-term), A(1) (fast-term amplitude contribution)] derived from the time-resolved spectra of coronary samples were used for tissue characterization. We determined that a few intensity values at longer wavelengths (>430 nm) and time-dependent parameters at peak emission region (390 nm) discriminate between all types of arterial samples except between normal wall and type I lesions. The lipid-rich lesions (more unstable) can be discriminated from fibrous lesions (more stable) on the basis of time-dependent parameters (lifetime and fast-term decay). We inferred that features of lipid fluorescence are reflected on lipid-rich lesion emission. Our results demonstrate that analysis of the time-resolved spectra may be used to enhance the discrimination between different grades of atherosclerotic lesions and provide a means of discrimination between lipid-rich and fibrous lesions.
High performance charge-trapping flash memory with highly-scaled trapping layer (2011)

We report a novel charge-trapping (CT) flash memory device with highly scaled equivalent-Si <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> N <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</inf> -thickness (ENT) trapping layer <4 nm. This device shows a large 10-year extrapolated retention window of 3.1 V at 125°C and excellent endurance of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> cycles, under the fast 100 μs and low ±16 V program/erase. These excellent memory device performances and ultra-thin ENT trapping thickness are the enable technology to continuously downscale the flash memory.
Discovery of SY-5609: A Selective, Noncovalent Inhibitor of CDK7 (2021)

CDK7 has emerged as an exciting target in oncology due to its roles in two important processes that are misregulated in cancer cells: cell cycle and transcription. This report describes the discovery of <b>SY-5609</b>, a highly potent (sub-nM CDK7 K<sub>d</sub>) and selective, orally available inhibitor of CDK7 that entered the clinic in 2020 (ClinicalTrials.gov Identifier: NCT04247126). Structure-based design was leveraged to obtain high selectivity (>4000-times the closest off target) and slow off-rate binding kinetics desirable for potent cellular activity. Finally, incorporation of a phosphine oxide as an atypical hydrogen bond acceptor helped provide the required potency and metabolic stability. The development candidate <b>SY-5609</b> displays potent inhibition of CDK7 in cells and demonstrates strong efficacy in mouse xenograft models when dosed as low as 2 mg/kg.
Expression of human inducible nitric oxide synthase in <i>Escherichia coli</i> (1996)

We have expressed active full-length human inducible nitric oxide synthase (iNOS) in E. coli. Expression required co-expression with calmodulin, a particularly tight-binding cofactor. The extracts also required tetrahydrobiopterin to display activity. Specific activity of the purified recombinant iNOS was similar to iNOS purified from murine macrophages. This result indicates that no special processing events unique to eucaryotic cells are necessary for iNOS activity.
Traffic-responsive signal timing for system-wide traffic control (1997)

Due to the many complex aspects of a traffic system, it has been difficult to determine the optimal signal timing. Much of this difficulty has stemmed from the need to build extremely complex models of the traffic dynamics as a component of the control strategy. This paper presents a fundamentally different approach for optimal signal timing that eliminates the need for such complex models. The approach is based on a neural network serving as the basis for the control law, with the weight estimation occurring in closed-loop mode via the simultaneous perturbation stochastic approximation (SPSA) algorithm. Since the SPSA algorithm requires only loss function measurements, there is no system-wide model required for the weight estimation.
Optimal Sizing for Stand-alone Microgrid Considering Different Control Strategies (2013)

A stand-alone microgrid often contains a variety of distributed generators and energy storage devices,so the coordinated operation and control are very complex.Different control strategies have significant influences on operation conditions.This paper gives full consideration to different control strategies of a stand-alone wind-solar-diesel-battery microgrid.Taking into account the initial cost,the operation and maintenance cost,the fuel cost,and the replacement cost,the optimal sizing model for stand-alone wind-solar-diesel-battery microgrid based on different control strategies is established.With the economical and environmental benefits as the optimization objectives,the non-dominated sorting genetic algorithm(NSGA-Ⅱ) is adopted to seek the optimal sizing scheme for power source types and capacities under the optimal control strategy.The results show that the method can make comprehensive assessment of the role and influence of different control strategies on optimal sizing,as well as the economic and environmental benefits of different schemes.It can clearly serve as a useful tool for optimal microgrid design.
Shortest Paths In Unweighed Graphs (2011)

When dealing with shortest paths in weighed or unweighed graphs, one may solve one-to-one, one-to-all or all-to-all instances. But the known algorithms compute one single shortest path of the considered instance. This article describes a new algorithm (patent pending) designed to compute all the shortest paths between two vertices of a directed, strongly connected and unweighed graph G, containing v vertices and a arcs. The purpose of this article is to propose an efficient one-to-one shortest path algorithm in unweighed graphs... The technique allows for instance the computations of all shortest paths between any two vertices in a graph G containing 10, 000, 000 vertices and 500, 000, 000 arcs in a mean time of 0.3 second on an average single processor computer. This article describes the algorithm, gives the proof of the complexity and describes some experimentations.
<title>Fiber Bragg gratings for tunable compensation of chromatic dispersion and slope in broadband WDM communication systems</title> (2001)

The use of nonlinearly chirped fiber Bragg gratings (FBGs) for tunable dispersion compensation is described. It is experimentally demonstrated that wide dispersion tunability can be accomplished over multiple wavelength division multiplexed (WDM) channels simultaneously in a single device with an approximately 10 cm long nonlinearly chirped FBG. Multiple channels are generated in such a short grating by fabricating a periodic superstructure over (sampling) the FBG. Proper design of the sampling also allows one to achieve dispersion slope compensation over broad bandwidth in WDM communication systems.
Design of efficient matching networks for capacitive wireless power transfer systems (2016)

High-power large air-gap capacitive wireless power transfer (WPT) systems require matching networks that provide large voltage or current gain and reactive compensation. This paper introduces an analytical optimization approach for the design of L-section multistage matching networks for capacitive WPT systems. The proposed approach maximizes the matching network efficiency and identifies the optimal distribution of gains and compensations among the L-section stages. The results of the proposed approach are validated using an exhaustive-search based numerical optimization for a 12-cm air-gap, 6.78-MHz, 125-W capacitive WPT system. A 6.78-MHz, 15-W prototype comprising a two-stage matching network is also designed using the proposed analytical approach and the theoretical predictions are validated experimentally.