gebhart/patrepeval huggingface dataset:
Intercalating dye as an acceptor in quantum-dot-mediated FRET (2008)

Fluorescence resonance energy transfer (FRET) is a popular tool to study intermolecular distances and characterize structural or conformational changes of biological macromolecules. We investigate a novel inorganic/organic FRET pair with quantum dots (QDs) as donors and DNA intercalating dyes, BOBO-3, as acceptors by using DNA as a linker. Typically, FRET efficiency increases with the number of stained DNA linked to a QD. However, with the use of intercalating dyes, we demonstrate that FRET efficiency at a fixed DNA:QD ratio can be further enhanced by increasing the number of dyes stained to a DNA strand through the use of an increased staining dye/bp ratio. We exploit this flexibility in the staining ratio to maintain a high FRET efficiency of >0.90 despite a sixfold decrease in DNA concentration. Having characterized this new QD-mediated FRET system, we test this system in a cellular environment using nanocomplexes generated by encapsulating DNA with commercial non-viral gene carriers. Using this novel FRET pair, we are able to monitor the configuration changes and fate of the DNA nanocomplexes during intracellular delivery, thereby providing an insight into the mechanistic study of gene delivery.
Active-flux-based, V/f-with-stabilizing-loops versus sensorless vector control of IPMSM Drives (2011)

This paper proposes two control methods for Interior Permanent Magnet Synchronous Motor (IPMSM) Drives. The first one is a V/f control with two stabilizing loops: one loop based on active flux balance for voltage magnitude correction and a second, based on speed error, with voltage phase correction. By this control strategy, a fast dynamic speed response, without steady state error and without speed or current regulators, for all AC machines is obtained. The second control method is a sensorless vector control strategy which also has been implemented and tested, just for comparison. Comprehensive simulations of both proposed V/f and sensorless vector control have been implemented by using a Matlab/Simulink package and a dSpace based platform has been built. Rather promising fast dynamic performance is obtained, both in simulations and in laboratory experiments for the proposed IPMSM Drive.
Identification of Phospholipid Scramblase 1 as a Novel Interacting Molecule with β-Secretase (β-Site Amyloid Precursor Protein (APP) Cleaving Enzyme (BACE)) (2003)

beta-Site amyloid precursor protein (APP)-cleaving enzyme (BACE) is an integral membrane aspartic proteinase responsible for beta-site processing of APP, and its cytoplasmic region composed of 24 amino acid residues has been shown to be involved in the endosomal localization of BACE. With the yeast two-hybrid screening, we found that the cytoplasmic domain of phospholipid scramblase 1 (PLSCR1), a type II integral membrane protein, interacts with the cytoplasmic region of BACE. In cultured cells, BACE and PLSCR1 were colocalized in the Golgi area and in endosomal compartments, whereas they were co-redistributed in late endosome-derived multivesicular bodies when treated with U18666A, suggesting that both proteins share a common trafficking pathway in cells. Co-immunoprecipitation analysis showed that both proteins form a protein complex at an endogenous expression level in the human neuroblastoma SH-SY5Ycells, and the dileucine residue of the BACE tail is also revealed to be essential for the physical interaction with PLSCR1 in vitro and in vivo. Moreover, both BACE and PLSCR1 were localized in a low buoyant lipid microdomain in SH-SY5Y cells. The dileucine-defective BACE mutant was also fractionated into the lipid microdomain, but much less stably than wild-type BACE. Taken together, our current study suggests the functional involvement of PLSCR1 in the intracellular distribution of BACE and/or recruitment of BACE into the detergent-insoluble lipid raft.
Angiographic Findings in Patients With Refractory Unstable Angina According to Troponin T Status (1999)

Complex lesion characteristics and visible thrombus formation at baseline were significantly linked to TnT elevation. However, TnT status was a more powerful predictor of increased cardiac risk and efficacy of treatment with abciximab than either. Relative to the angiogram, TnT can thus be considered a more sensitive marker for the underlying pathology, identifying patients with unstable angina who will particularly benefit from antiplatelet treatment.
Dexmedetomidine provides cortical neuroprotection: impact on anaesthetic‐induced neuroapoptosis in the rat developing brain (2009)

Dexmedetomidine prevents cortical apoptosis in vitro and in vivo. However, using higher doses of dexmedetomidine does not further increase protection against isoflurane injury in the cortex than previously observed.
Constrained Synthesis and Organization of Catalytically Active Metal Nanoparticles by Self‐Assembled Protein Templates (2009)

Novel geometrical architectures of hybrid nanoparticle–protein complexes are generated by chemically synthesizing monodisperse metal nanoparticles in situ in the presence of a stable, stress-related protein. The catalytic activity of the protein–particle hybrids is examined for the reduction of 4-nitrophenol, providing future biofunctional nanoparticle labels for catalytic signal amplification in optical assays.
An analysis of program and erase operation for FC-SGT flash memory cells (2002)

The floating channel type surrounding gate transistor (FC-SGT) flash memory cell realizes high-speed bipolarity program and erase operations. In this investigation, the time dependence of the surface potential in the floating channel region, which strongly affects program and erase performance, is studied during program and erase operation. By analyzing the carrier generation processes in the floating channel region, the program and erase operation for FC-SGT flash memory cells is clarified.
Monitoring of modified factor VIII and IX products (2014)

The dawning era of novel recombinant factor VIII and factor IX concentrates, many of which have been bioengineered to achieve prolonged activity, brings with it the need to consider the most appropriate clinical laboratory approaches for potency assignment, as well as the measurement of postinfusion levels. This session will highlight the known limitations and inconsistencies between existing assay methodologies with respect to currently available products, and discuss some of the early data with respect to the novel agents.
Tailoring the oxidation state of cobalt through halide functionality in sol-gel silica (2013)

The functionality or oxidation state of cobalt within a silica matrix can be tailored through the use of cationic surfactants and their halide counter ions during the sol-gel synthesis. Simply by adding surfactant we could significantly increase the amount of cobalt existing as Co3O4 within the silica from 44% to 77%, without varying the cobalt precursor concentration. However, once the surfactant to cobalt ratio exceeded 1, further addition resulted in an inhibitory mechanism whereby the altered pyrolysis of the surfactant decreased Co3O4 production. These findings have significant implications for the production of cobalt/silica composites where maximizing the functional Co3O4 phase remains the goal for a broad range of catalytic, sensing and materials applications.
An enhanced immunocytochemical method for staining bone marrow trephine sections. (1997)

The tyramide enhanced immunostaining method, while retaining specificity, is highly sensitive and enables an increased number and range of antigens to be detected than previously possible. The method could be applied to BMT sections for the routine diagnosis and classification of haematological disorders.
Rosai-Dorfman Disease of the Paranasal Sinuses: Results of Computed Tomography and Magnetic Resonance Imaging (2000)

We describe Rosai-Dorfman disease (RDD) of the paranasal sinus in a 14-year-old boy who presented with a bilateral exophthalmos. Computed tomography (CT) and magnetic resonance imaging (MRI) demonstrated a bulky abnormal soft-tissue mass filling the bilateral paranasal sinuses which extended into bilateral orbits. This resulted in remodeling of the adjacent bony structures and cervical lymphadenopathy. Recognition of the imaging features of RDD may facilitate appropriate diagnoses and management of future patients.
Helical Polyaniline Nanofibers Induced by Chiral Dopants by a Polymerization Process (2007)

Dopant-induced helical conformations of polyaniline (PANI) nanofibers are presented. Right- and left-handed helical nanofibers of conducting PANI are produced using respectively D- and L-camphorsulfonic acid as the dopant, it is reported, as proved by the mirror-image chiral dichroism spectra (see figure). The authors suggest a mechanism for the formation of nanofibrillar bundles of helical nanofibers.
A comparative evaluation of epidural and general anaesthetic technique for renal surgeries: A randomised prospective study (2014)

Epidural anaesthesia with ropivacaine and dexmedetomidine can be safely and effectively used in patients undergoing renal surgeries.
Constructing lower and upper bounded delay routing trees using linear programming (1996)

Article Constructing lower and upper bounded delay routing trees using linear programming Share on Authors: Jaewon Oh University of Southern California, Department of Electrical Engineering, Los Angeles, CA University of Southern California, Department of Electrical Engineering, Los Angeles, CAView Profile , Iksoo Pyo Intel Corporation, JF1-61, Hillsboro, OR Intel Corporation, JF1-61, Hillsboro, ORView Profile , Massoud Pedram University of Southern California, Department of Electrical Engineering, Los Angeles, CA University of Southern California, Department of Electrical Engineering, Los Angeles, CAView Profile Authors Info & Claims DAC '96: Proceedings of the 33rd annual Design Automation ConferenceJune 1996 Pages 401–404https://doi.org/10.1145/240518.240595Online:01 June 1996Publication History 7citation253DownloadsMetricsTotal Citations7Total Downloads253Last 12 Months3Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Towards Discovering Data Center Genome Using Sensor Nets (2008)

The IT industry is the fastest growing sector in US energy consumption. Improving data center energy efficiency is a pressing issue with significant economic and environmental consequences. Heat distribution is a key operational parameter that affects data center cooling and energy consumption. However, typical data centers lack effective finegrained sensing systems to monitor heat distribution at a large scale. In this paper, we motivate the use of sensor networks as a dense instrumentation technology to understand and control cooling in data centers. We present Microsoft Research Genomote sensors designed for data center monitoring, and the RACNet for reliable data acquisition. We describe lessons learned from early pilot deployments, and discuss architectural and technical challenges in developing data center sensor networks.
Aza-crown ether tethered with benzothiazole : Synthesis and optical spectral studies (2006)

Synthesis of a new fluoroionophore 2 encompassing azaphenyl-crown and benzothiazole is described. The UV-Vis spectra ol'2 are not altered with change in solvent polarity indicating the absence of solvalochromism. However, the fluorescence spectra are progressively red shifted in more polar solvents on account of increasing charge transfer character of the excited state. In the presence of trifluoroacetic acid (TFAA), protonation of benzothiazole nitrogen results in the red shift of the absorption spectra. Contrary to expectation, the emission spectra suffers blue shift in the presence of TFAA. Presumably, the emission for the case 2+H + occurs from higher vibrational energy levels which accounts for the blue shift. Unfortunately, selected alkali or alkaline earth metals ions examined for metal sensing applications have failed to induce significant perturbations either in the absorption or emission spectra. This may be attributed to poor electronic communication between the crown-bound metal ions and the benzothiazole fluorophore due to steric encumbrance between the ortho-substitutcd benzothiazole chromophore and the phenyl aza-crown moiety.
The Commelina Yellow Mottle Virus Promoter Is a Strong Promoter in Vascular and Reproductive Tissues (1992)

Scott L. Medberry, B. E. L. Lockhart, Neil E. Olszewski, The Commelina Yellow Mottle Virus Promoter Is a Strong Promoter in Vascular and Reproductive Tissues, The Plant Cell, Vol. 4, No. 2 (Feb., 1992), pp. 185-192
Rechargeable Hydrogen Storage System Based on the Dehydrogenative Coupling of Ethylenediamine with Ethanol (2015)

A novel and simple hydrogen storage system was developed, based on the dehydrogenative coupling of inexpensive ethylenediamine with ethanol to form diacetylethylenediamine. The system is rechargeable and utilizes the same ruthenium pincer catalyst for both hydrogen loading and unloading procedures. It is efficient and uses a low catalyst loading. Repetitive reversal reactions without addition of new catalyst result in excellent conversions in both the dehydrogenation and hydrogenation procedures in three cycles.
Privacy Protection for Social Networking Platforms (2008)

Social networking platforms integrate third-party content into social networking sites and give third-party developers access to user data. These open interfaces enable popular site enhancements but pose serious privacy risks by exposing user data to third-party developers. We address the privacy risks associated with social networking APIs by presenting a privacy-by-proxy design for a privacy-preserving API. Our design is motivated by an analysis of the data needs and uses of Facebook applications. We studied 150 popular Facebook applications and found that nearly all applications could maintain their functionality using a limited interface that only provides access to an anonymized social graph and placeholders for user data. Since the platform host can control the third party applications’ output, privacy-by-proxy can be accomplished by using new tags and data transformations without major changes to either the platform architecture or applications.
Arginine-glycine-aspartic acid binding leading to molecular stabilization between integrin alpha v beta 3 and its ligand. (1991)

Cell adhesion is characterized by an integrin-mediated ligand binding event followed by reorganization of the actin-cytoskeleton leading to cell spreading and/or migration. In this report we examine the role of integrin alpha v beta 3 in mediating cell attachment to vitronectin or a RGD-containing peptide in the presence of cytochalasin B to prevent actin polymerization. Under these conditions cell attachment to a RGD-containing peptide can be dissociated by excess soluble ligand whereas cells attached to vitronectin cannot. These results suggest that alpha v beta 3-mediated cell attachment to vitronectin results in a highly stabilized interaction that is independent of the actin-cytoskeleton. To investigate the molecular nature of this interaction alpha v beta 3 was purified to homogeneity, and its binding properties toward various ligands were measured in a solid-phase receptor assay. The data indicate that alpha v beta 3 binds to vitronectin or fibronectin in a nondissociable manner whereas a RGD-containing peptide derived from vitronectin binds specifically but is completely dissociable with a Kd of 9.4 x 10(-7) M. Moreover, chemical modification of alpha v beta 3 with limited glutaraldehyde treatment allowed vitronectin to bind in a RGD-dependent and dissociable manner, suggesting that receptor conformational changes or specific amino acid residues proximal to the ligand binding site(s) are involved in the stabilization event. Thus, in the absence of cytoskeletal proteins or other cellular components, integrin alpha v beta 3-ligand binding involves recognition of the RGD sequence leading to a highly stabilized protein-protein association.
Multiscale Biomimetic Topography for the Alignment of Neonatal and Embryonic Stem Cell-Derived Heart Cells (2011)

Nano- and microscale topographical cues play critical roles in the induction and maintenance of various cellular functions, including morphology, adhesion, gene regulation, and communication. Recent studies indicate that structure and function at the heart tissue level is exquisitely sensitive to mechanical cues at the nano-scale as well as at the microscale level. Although fabrication methods exist for generating topographical features for cell culture, current techniques, especially those with nanoscale resolution, are typically complex, prohibitively expensive, and not accessible to most biology laboratories. Here, we present a tunable culture platform comprised of biomimetic wrinkles that simulate the heart's complex anisotropic and multiscale architecture for facile and robust cardiac cell alignment. We demonstrate the cellular and subcellular alignment of both neonatal mouse cardiomyocytes as well as those derived from human embryonic stem cells. By mimicking the fibrillar network of the extracellular matrix, this system enables monitoring of protein localization in real time and therefore the high-resolution study of phenotypic and physiologic responses to in-vivo like topographical cues.
Recognizing contextual polarity in phrase-level sentiment analysis (2005)

This paper presents a new approach to phrase-level sentiment analysis that first determines whether an expression is neutral or polar and then disambiguates the polarity of the polar expressions. With this approach, the system is able to automatically identify the contextual polarity for a large subset of sentiment expressions, achieving results that are significantly better than baseline.
Type III secretion machines and the pathogenesis of enteric infections caused by Yersinia and Salmonella spp. (1999)

Salmonella and Yersinia spp. infect the intestinal tract of humans. Although these organisms cause fundamentally different diseases, each pathogen relies on type III secretion machines to either inject virulence factors into the cytosol of eukaryotic cells or release toxins into the extracellular milieu. Type III secretion machines are composed of many different subunits and export several polypeptides with unique substrate requirements. During Salmonella pathogenesis, the type III machine encoded by the Salmonella pathogenicity island (SPI)-1 genetic element functions to cause invasion of the intestinal epithelium, whereas another type III machine (SPI-2) is required for survival in macrophages. Yersinia enterocolitica and Yersinia pseudotuberculosis employ type III machines to resist macrophage phagocytosis and to manipulate the host's immune response, thereby colonizing intestinal lymphoid tissues. We describe what is known about the pathogenic functions of virulence factors secreted by type III machines. Furthermore, type III secretion machines may be exploited for the injection of recombinant proteins, a strategy that has already been successfully employed to elicit a cell-mediated immune response.
Functional analysis of HIV-1 reverse transcriptase amino acids involved in resistance to multiple nonnucleoside inhibitors. (1992)

Several novel, structurally distinct classes of specific human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) nonnucleoside inhibitors have been described recently. These include the pyridinone derivatives L-697,639, L-697,661, and L-696,229 as well as BI-RG-587 and the tetrahydroimidazo[4,5,1-j,k]-benzodiazepin-2(1H)-one and -thione compounds. Previous studies have implicated involvement of the RT amino acid residues at positions 103, 181, and 188 in the activity of the compounds. Accordingly, HIV-1 RT mutants containing a series of amino acid substitutions at these positions were constructed. The relative resistance of purified mutant enzymes to each of the inhibitors was assessed. This analysis established the functional equivalence of the three inhibitor classes and provided evidence for the interaction of the 103 site with the 181/188 region. Amino acid substitutions at these positions were also found to influence RT sensitivity to inhibition by phosphonoformate, thereby suggesting a close association between this pyrophosphate analog's binding site in RT and the binding site of the nonnucleoside inhibitors. In addition, aromatic stacking of the amino acid side groups at residues 181 and 188 was suggested to be required for inhibitor activity.
Analysis of chromosomal structural polymorphisms in the St, P, and Y genomes of Triticeae (Poaceae) (2010)

The St, P, and Y genomes are three important genomes in the tribe Triticeae, which includes many perennial species. To study polymorphisms within the chromosomes of the St, P, and Y genomes, a GISH-FISH method was developed that allowed them to be clearly distinguished. The karyotypes of five individuals from population Z1925 of Kengyilia grandiglumis (Keng) J.L. Yang et al. (2n = 6x = 42, StStPPYY) were analyzed. The results showed that there were structural polymorphisms in all of the chromosomes from the three individual genomes. The polymorphisms were found mainly in the terminal regions of chromosomes and infrequently near the centromeric region. Of all the chromosomes, 1P, 1St, 1Y, 2Y, 3St, and 3Y showed the most polymorphisms. The polymorphisms within the individual chromosomes suggested that more extensive and scientific conclusions regarding the origin and evolution of genomes in wild species of Triticeae would be achieved by studying a population as a sampling and analysis unit.
Generating highly ordered DNA nanostrand arrays (2005)

Highly ordered arrays of stretched DNA molecules were generated over the millimeter scale by using a modified molecular combing method and soft lithography. Topological micropatterning on polydimethyl siloxane stamps was used to mediate the dynamic assembly of DNA molecules into arranged nonostrand arrays. These arrays consisted of either short nanostrands of several micrometers with fixed length and orientation or long nanostrands up to several hundred micrometers in length. The nanostrand arrays were transferred onto flat solid surfaces by contact printing, allowing for the creation of more complex patterns. This technique has potential applications for the construction of next-generation DNA chips and functional circuits of DNA-based 1D nanostructures.
Nitric oxide synthase: Irreversible inhibition by L-N -Nitroarginine in brain and (1991)

Inhibition of nitric oxide (NO) synthase activity by L-NG-Nitroarginine (NO2Arg) in brain preparations is not reversed by dialysis and is enhanced by prolonged preincubation of NO2Arg with the enzyme. By contrast, the weaker inhibition by NO2Arg of macrophage NO synthase is fully reversible. NO2Arg inhibits NO synthase activity in the brain after i.p. administration of 5 or 50 mg/kg. This in vivo inhibition also appears to be irreversible. The potent in vivo inhibition of central NO synthase by NO2Arg may facilitate studies of the physiologic function of NO as a neuronal messenger.
Direct Detection of Volatile Metabolites Produced by Microorganisms (1993)

Volatile metabolites produced by microorganisms can be measured directly in growth media by membrane inlet mass spectrometry (MIMS). A polymer membrane, which allows volatile compounds to pass, is used as the only separation between the mass spectrometer and the liquid to be analyzed. The practical aspects of membrane inlet design are reviewed and recent innovations, e.g. the use of microporous membranes with solvent chemical ionization are discussed. In addition, applications of MIMS to the direct monitoring and identification of volatiles in microbial cultures are described.