gebhart/patrepeval huggingface dataset:
Analysis of class II (hydrolytic) and class I (β-lyase) apurinic/apyrimidinic endonucleases with a synthetic DNA substrate (1990)

We have developed simple and sensitive assays that distinguish the main classes of apurinic/apyrimidinic (AP) endonucleases: Class I enzymes that cleave on the 3' side of AP sites by beta-elimination, and Class II enzymes that cleave by hydrolysis on the 5' side. The distinction of the two types depends on the use of a synthetic DNA polymer that contains AP sites with 5'-[32P]phosphate residues. Using this approach, we now show directly that Escherichia coli endonuclease IV and human AP endonuclease are Class II enzymes, as inferred previously on the basis of indirect assays. The assay method does not exhibit significant interference by nonspecific nucleases or primary amines, which allows the ready determination of different AP endonuclease activities in crude cell extracts. In this way, we show that virtually all of the Class II AP endonuclease activity in E. coli can be accounted for by two enzymes: exonuclease III and endonuclease IV. In the yeast Saccharomyces cerevisiae, the Class II AP endonuclease activity is totally dependent on a single enzyme, the Apn1 protein, but there are probably multiple Class I enzymes. The versatility and ease of our approach should be useful for characterizing this important class of DNA repair enzymes in diverse systems.
Comparison of Synthetic Antiferromagnets and Hard Ferromagnets as Reference Layer in Magnetic Tunnel Junctions With Perpendicular Magnetic Anisotropy (2010)

In magnetic tunnel junctions (MTJ), synthetic antiferromagnets (SAF) are usually used as reference layer to minimize dipolar interactions induced between this layer and the free layer (FL). We show here that the use of SAF allows us to reduce the asymmetry of the FL reversal due to stray fields in nanosized MTJs with perpendicular magnetic anisotropy.
The Australian Imaging, Biomarkers and Lifestyle (AIBL) study of aging: methodology and baseline characteristics of 1112 individuals recruited for a longitudinal study of Alzheimer's disease (2009)

The participants comprising the AIBL cohort represent a group of highly motivated and well-characterized individuals who represent a unique resource for the study of AD. They will be reassessed at 18-month intervals in order to determine the predictive utility of various biomarkers, cognitive parameters and lifestyle factors as indicators of AD, and as predictors of future cognitive decline.
Green Fluorescent Protein (GFP):  Applications, Structure, and Related Photophysical Behavior (2002)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGreen Fluorescent Protein (GFP): Applications, Structure, and Related Photophysical BehaviorMarc ZimmerView Author Information Department of Chemistry, Connecticut College, New London, Connecticut 06320 Cite this: Chem. Rev. 2002, 102, 3, 759–782Publication Date (Web):February 2, 2002Publication History Received21 June 2001Published online2 February 2002Published inissue 1 March 2002https://pubs.acs.org/doi/10.1021/cr010142rhttps://doi.org/10.1021/cr010142rresearch-articleACS PublicationsCopyright © 2002 American Chemical SocietyRequest reuse permissionsArticle Views42821Altmetric-Citations979LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Chromophores,Fluorescence,Fluorescence resonance energy transfer,Imaging probes,Peptides and proteins Get e-Alerts
Impact of pH on the Kinetics of Acrylamide Formation/Elimination Reactions in Model Systems (2006)

The effect of pH on acrylamide formation and elimination kinetics was studied in an equimolar (0.1 M) asparagine-glucose model system in phosphate or citrate buffer, heated at temperatures between 120 and 200 degrees C. To describe the experimental data, a simplified kinetic model was proposed and kinetic parameters were estimated by combined nonlinear regression and numerical integration on the data obtained under nonisothermal conditions. The model was subsequently validated in a more realistic potato-based matrix with varying pH. By increasing acidity, the reaction rate constants at T(ref) (160 degrees C) for both acrylamide formation and elimination can significantly be reduced, whereas the temperature dependence of both reaction rate constants increases. The introduction of a lyophilized potato matrix (20%) did not affect the acrylamide formation reaction rate constant at reference temperature (160 degrees C) as compared to the asparagine-glucose model system; the elimination rate constant at T(ref), on the contrary, was almost doubled.
Photodynamic therapy of viral contaminants with potential for blood banking applications (1988)

A photodynamic method has been evaluated as a means of eradicating viral contaminants with the potential for rendering blood safe for transfusion. Herpes simplex virus type 1 (HSV-1) was tested under flowing conditions in culture media or in blood supplemented with the virus. Hematoporphyrin derivative was used as the sensitizer and was photoactivated with visible light at 630 nm and 5 J/cm2. HSV-1 in suspension both in culture medium as well as in blood was shown to be killed. The human immunodeficiency virus was also found to be photoinactivated in flowing cell culture medium and, thus, potentially may be inactivated in blood. These findings extend our previous studies which demonstrated that enveloped viruses can be photoinactivated with hematoporphyrin derivative in a static fluid system. Analysis of blood cell number, red cell lysis, plasma proteins, and other standard hematological tests showed no significant change. The possibility that transfusion-associated acquired immunodeficiency syndrome (AIDS) may result from a blood unit infected with human immunodeficiency virus that tested negative makes it imperative that a safe and effective means of viral killing be developed. The system reported here offers promise as an effective approach to this problem.
Motion Adaptive Deinterlacing With Modular Neural Networks (2011)

In this letter, a motion adaptive deinterlacing algorithm based on modular neural networks is proposed. The proposed method uses different neural networks based on the amount of motion. Modular neural networks were selectively used depending on the differences between the adjacent fields. We also used motion vectors to select optimal input pixels from the adjacent fields. Motion estimation was used to find input blocks for the neural networks with minimum errors. Intra/inter-mode switching was employed to address inaccurate motion estimation problems.
N- and C-terminal residues combine in the fusion-pH influenza hemagglutinin HA 2 subunit to form an N cap that terminates the triple-stranded coiled coil (1999)

The structure of a stable recombinant ectodomain of influenza hemagglutinin HA(2) subunit, EHA(2) (23-185), defined by proteolysis studies of the intact bacterial-expressed ectodomain, was determined to 1.9-A resolution by using x-ray crystallography. The structure reveals a domain composed of N- and C-terminal residues that form an N cap terminating both the N-terminal alpha-helix and the central coiled coil. The N cap is formed by a conserved sequence, and part of it is found in the neutral pH conformation of HA. The C-terminal 23 residues of the ectodomain form a 72-A long nonhelical structure ordered to within 7 residues of the transmembrane anchor. The structure implies that continuous alpha helices are not required for membrane fusion at either the N or C termini. The difference in stability between recombinant molecules with and without the N cap sequences suggests that additional free energy for membrane fusion may become available after the formation of the central triple-stranded coiled coil and insertion of the fusion peptide into the target membrane.
Characterization of H4: a mouse T lymphocyte activation molecule functionally associated with the CD3/T cell receptor (1996)

The monoclonal antibody C398.4A was produced by immunizing Armenian hamsters with the mouse T cell clone D10.G4.1. It recognizes a molecule selectively expressed by activated mouse T cells and was named H4. H4 is expressed on the T cell surface about 24 h after activation and peaks at day 7. By contrast, it is not expressed by resting or activated B cells, macrophages, or fibroblasts. It is also expressed by CD4 or CD8 single-positive mature thymocytes. Immunoprecipitation showed that H4 is a disulfide-linked dimer, precipitating as a broad band at about 50-65 kDa under nonreducing conditions and at 25 and 29 kDa under reducing conditions. Deglycosylation of the reduced H4 by N-glycanase gave rise to a single band of about 21 kDa, suggesting that the two chains may be differentially glycosylated forms of the same protein. The H4 expression pattern and biochemical features, together with cross-blocking, co-capping, co-modulation, and immunoprecipitation preclearing experiments showed that H4 is different from other known co-stimulatory molecules such as CD69, CD2, Ly-6, CD25, OX-40, Mac-1 and LFA-1. By in vitro kinase assay, H4 was found to co-precipitate a tyrosine kinase activity that phosphorylated substrates of about 29 and 25 kDa. Co-modulation and co-capping experiments showed that H4 is physically associated with the CD3/T cell receptor. These data suggest that H4 may function as a T cell-specific co-stimulatory molecule and play a role in the T cell response when the activation stimulus is limited either because the antigen is only available in low concentration or has a low agonistic activity.
Assisting Users in a World Full of Cameras: A Privacy-Aware Infrastructure for Computer Vision Applications (2017)

Computer vision based technologies have seen widespread adoption over the recent years. This use is not limited to the rapid adoption of facial recognition technology but extends to facial expression recognition, scene recognition and more. These developments raise privacy concerns and call for novel solutions to ensure adequate user awareness, and ideally, control over the resulting collection and use of potentially sensitive data. While cameras have become ubiquitous, most of the time users are not even aware of their presence. In this paper we introduce a novel distributed privacy infrastructure for the Internet-of-Things and discuss in particular how it can help enhance user's awareness of and control over the collection and use of video data about them. The infrastructure, which has undergone early deployment and evaluation on two campuses, supports the automated discovery of IoT resources and the selective notification of users. This includes the presence of computer vision applications that collect data about users. In particular, we describe an implementation of functionality that helps users discover nearby cameras and choose whether or not they want their faces to be denatured in the video streams.
Seed dormancy and the control of germination (2006)

Seed dormancy is an innate seed property that defines the environmental conditions in which the seed is able to germinate. It is determined by genetics with a substantial environmental influence which is mediated, at least in part, by the plant hormones abscisic acid and gibberellins. Not only is the dormancy status influenced by the seed maturation environment, it is also continuously changing with time following shedding in a manner determined by the ambient environment. As dormancy is present throughout the higher plants in all major climatic regions, adaptation has resulted in divergent responses to the environment. Through this adaptation, germination is timed to avoid unfavourable weather for subsequent plant establishment and reproductive growth. In this review, we present an integrated view of the evolution, molecular genetics, physiology, biochemistry, ecology and modelling of seed dormancy mechanisms and their control of germination. We argue that adaptation has taken place on a theme rather than via fundamentally different paths and identify similarities underlying the extensive diversity in the dormancy response to the environment that controls germination.
A Simple Technique for Determining the pH of Whole Cigarette Smoke (2000)

Abstract A new technique has been developed to determine the pH of whole cigarette smoke. In this technique, whole smoke from ten cigarettes was trapped in 300 mL water containing 1% (w/v) sodium chloride and the pH was determined on the resulting aqueous suspension of cigarette smoke. Two impingers with an extra coarse porosity fritted disc were used to dispense the smoke in the aqueous trapping medium. Cigarettes were smoked on a 20-port Borgwaldt RM 20/CS smoking machine using modified FTC (Federal Trade Commission) conditions. The puff volume was adjusted to take a 35 mL puff as measured through the cigarette and the collection traps. This new technique accounts for the contributions to smoke pH from both the vapor phase and the particulate phase of smoke. The repeatability of this new technique was determined on eighteen replicates of a commercially available non-menthol, filter cigarette. Each measurement was done on a different day to check for a possible drift in pH with time. The mean pH value for the chosen sample was found to be 4.97 with a standard deviation of 0.07 pH units. The smoke pH values for over 150 commercially available cigarette brands with a variety of “tar” levels were determined. The smoke pH values had a range from 4.6 to 5.5, with an average of 4.79 and a maximum standard deviation of 0.10 pH units. An experimental flue cured cigarette had a smoke pH of around 5.0, while an experimental Burley cigarette had a smoke pH of 5.4. No correlation between smoke pH and “tar” or total particulate matter (TPM) and between pH and nicotine levels was found. The purpose of the present study was to develop a practical, relatively simple laboratory method to measure the pH of a water solution of whole smoke, and was not intended to reflect, or have direct relevance for any biochemical or biological phenomena such as inhalability of smoke, flavor perception, nicotine ab-sorption, etc.”
High-performance densely packed vertical-cavity photonic integrated emitter arrays for direct-coupled WDM applications (1998)

High-performance multiple-wavelength photonic integrated InGaAs-GaAs MQW DBR VCSEL laser emitter arrays with a manufacturable planar scheme are demonstrated for low-cost multimode wavelength-division-multiplexing (WDM) local-area networks. Each array consists of eight pie-shaped bottom-emitting vertical-cavity lasers (VCL's) enclosed within a 60-μm-diameter circle for direct-coupling into a single multimode fiber. The arrays exhibit a wide 32.9-nm lasing wavelength span and relatively high 7.3-mW single-channel output. In particular, we have achieved a differential efficiency as high as 50.2% and a maximum wall-plug efficiency of 11.8%. These devices operate with multilateral modes and have a wide 3-dB spectral bandwidth of 1.7 nm in average, which makes them especially suitable for multimode fiber systems.
Optimization of Enzymatic Biochemical Logic for Noise Reduction and Scalability: How Many Biocomputing Gates Can Be Interconnected in a Circuit? (2008)

We report an experimental evaluation of the "input-output surface" for a biochemical AND gate. The obtained data are modeled within the rate-equation approach, with the aim to map out the gate function and cast it in the language of logic variables appropriate for analysis of Boolean logic for scalability. In order to minimize "analog" noise, we consider a theoretical approach for determining an optimal set for the process parameters to minimize "analog" noise amplification for gate concatenation. We establish that under optimized conditions, presently studied biochemical gates can be concatenated for up to order 10 processing steps. Beyond that, new paradigms for avoiding noise buildup will have to be developed. We offer a general discussion of the ideas and possible future challenges for both experimental and theoretical research for advancing scalable biochemical computing.
Blockade of the Platelet P2Y 12 Receptor by AR-C69931MX Sustains Coronary Artery Recanalization and Improves the Myocardial Tissue Perfusion in a Canine Thrombosis Model (2003)

The adjunctive administration of AR-C69931MX blocked ADP-mediated platelet aggregation and recruitment and prevented platelet-mediated thrombosis, resulting in prolongation of reperfusion time and a decrease in reocclusion and cyclic flow variations. Importantly, myocardial tissue perfusion was significantly improved in the P2Y(12) antagonist group.
Dynamical Resetting of the Human Brain at Epileptic Seizures: Application of Nonlinear Dynamics and Global Optimization Techniques (2004)

Epileptic seizures occur intermittently as a result of complex dynamical interactions among many regions of the brain. By applying signal processing techniques from the theory of nonlinear dynamics and global optimization to the analysis of long-term (3.6 to 12 days) continuous multichannel electroencephalographic recordings from four epileptic patients, we present evidence that epileptic seizures appear to serve as dynamical resetting mechanisms of the brain, that is the dynamically entrained brain areas before seizures disentrain faster and more frequently (p < 0.05) at epileptic seizures than any other periods. We expect these results to shed light into the mechanisms of epileptogenesis, seizure intervention and control, as well as into investigations of intermittent spatiotemporal state transitions in other complex biological and physical systems.
Fast adaptive interferometer in a GaP crystal using a near-infrared laser diode (2001)

We describe an adaptive interferometer for linear detection of small out-of-plane vibrations of optically rough surfaces. The interferometer is based on the polarization self-modulation effect in a GaP crystal and it uses a laser diode at 807 nm as a light source. The achieved response time of 1.9 ms is the fastest among known adaptive interferometers in the near infrared.
The Effects of a Monoclonal Antibody Directed against Tumor Necrosis Factor-α in Asthma (2006)

Treatment with infliximab was well tolerated and caused a decrease in the number of patients with exacerbations in symptomatic moderate asthma. The promising preliminary findings underscore the need to evaluate therapy directed against TNF-alpha in larger trials enrolling patients with more severe asthma.
Iron and Cobalt Ethylene Polymerization Catalysts Bearing 2,6-Bis(Imino)Pyridyl Ligands:  Synthesis, Structures, and Polymerization Studies (1999)

The synthesis, characterization, and ethylene polymerization behavior of a series of iron and cobalt halide complexes, LMXn (M = Fe, X = Cl, n = 2, 3, X = Br, n = 2; M = Co, X = Cl, n = 2), bearing chelating 2,6-bis(imino)pyridyl ligands L [L = 2,6-(ArNCR1)2C5H3N] is reported. X-ray diffraction studies show the geometry at the metal centers to be either distorted square pyramidal or distorted trigonal bipyramidal. Treatment of the complexes LMXn with methylaluminoxane (MAO) leads to highly active ethylene polymerization catalysts converting ethylene to highly linear polyethylene (PE). LFeX2 precatalysts with ketimine ligands (R1 = Me) are approximately an order of magnitude more active than precatalysts with aldimine ligands (R1 = H). Catalyst productivities in the range 3750−20600 g/mmol·h·bar are observed for Fe-based ketimine catalysts, while Co ketimine systems display activities of 450−1740 g/mmol·h·bar. Molecular weights (Mw) of the polymers produced are in the range 14000−611000. Changing reaction conditions also affects productivity and molecular weight; in some systems, a bimodal molecular weight distribution is observed. On the basis of evidence gathered to date, the lower molecular weight fraction is a result of chain transfer to aluminum while the higher molecular weight fraction is produced by a combination of mainly β-H transfer and some chain transfer to aluminum.
Recombinant Adenoviral Vectors Can Induce Expression of p73 via the E4-orf6/7 Protein (2006)

Despite the utility of recombinant adenoviral vectors in basic research, their therapeutic promise remains unfulfilled. Most engineered adenoviral vectors use a heterologous promoter to transcribe a foreign gene. We show that adenoviruses containing the cytomegalovirus immediate-early promoter induce the expression of the proapoptotic cellular protein TAp73 via the cyclin-dependent kinase-retinoblastoma protein-E2F pathway in murine embryonic fibroblasts. Cells transduced with these vectors also expressed high levels of the adenoviral E4-orf6/7 and E2A proteins. By contrast, adenoviruses containing the ubiquitin C promoter failed to elicit these effects. E4-orf6/7 is necessary and sufficient for increased TAp73 expression, as shown by using retrovirus-mediated E4-orf6/7 expression and adenovirus with the E4-orf6/7 gene deleted. Activation of TAp73 likely occurs via E4-orf6/7-induced dimerization of E2F and subsequent binding to the inverted E2F-responsive elements within the TAp73 promoter. In addition, adenoviral vectors containing the cytomegalovirus immediate-early promoter, but not the ubiquitin C promoter, cooperated with chemotherapeutic agents to decrease cellularity in vitro. In contrast to murine embryonic fibroblasts, adenoviruses containing the ubiquitin C promoter, but not the cytomegalovirus immediate-early promoter, induced both E4-orf6/7 and TAp73 in human foreskin fibroblasts, emphasizing the importance of cellular context for promoter-dependent effects. Because TAp73 is important for the efficacy of chemotherapy, adenoviruses that increase TAp73 expression may enhance cancer therapies by promoting apoptosis. However, such adenoviruses may impair the long-term survival of transduced cells during gene replacement therapies. Our findings reveal previously unknown effects of foreign promoters in recombinant adenoviral vectors and suggest means to improve the utility of engineered adenoviruses by better controlling their impact on viral and cellular gene expression.
Data Stream Query Processing (2005)

This tutorial provides a comprehensive and cohesive overview of the key research results in the area of data stream query processing, both for SQL-like and XML query languages.
In vivo Target Modulation and Biological Activity of CHIR-258, a Multitargeted Growth Factor Receptor Kinase Inhibitor, in Colon Cancer Models (2005)

These studies provide evidence that biological activity of CHIR-258 in tumors correlates with efficacy and aids in the identification of potential biomarkers of this multitargeted receptor tyrosine kinase inhibitor. CHIR-258 exhibits properties that make it a promising candidate for clinical development in a variety of solid and hematologic malignancies.