gebhart/patrepeval huggingface dataset:
Characterisation of adducts of the lipid peroxidation product 4‐hydroxy‐2‐nonenal and amyloid β‐peptides by liquid chromatography/electrospray ionisation mass spectrometry (2002)

Alzheimer's disease is characterised by brain neuritic plaques composed of a 39-44 amino acid peptide (Abeta). Lipid peroxidation is an early event induced by these amyloid beta-peptides, leading to the formation of 4-hydroxy-2-nonenal (HNE), which is one of the major end products of this process. HNE has been reported to form adducts via a stable covalent binding to proteins through a Michael addition to amino acid residues with a nucleophilic side chain. The present study reports an investigation of the conditions for formation of Abeta-HNE (Abeta 1-28 and Abeta 1-42) adducts, and their characterisation by liquid chromatography/electrospray ionisation mass spectrometry (LC/ESI-MS). The results suggest that one or more HNE moieties are localised in the 6-16 region of these adducts, while Asp-1, Lys-16 and Lys-28 are not modified under the described reaction conditions.
Involvement of Peripheral-Type Benzodiazepine Receptors in the Intracellular Transport of Heme and Porphyrins1 (1995)

To investigate the involvement of peripheral-type benzodiazepine receptors (PBR) in heme metabolism, we examined the interaction of [55Fe]heme with PBR. Transfection of the cloned mouse PBR-isoquinoline carboxamide-binding protein (PBR/IBP) cDNA into monkey kidney Cos-1 cells resulted in a 2.5-fold increase in [55Fe]hemin binding sites, concomitant with the increase in [3H]PK11195 binding sites, as compared with those seen in antisense PBR/IBP cDNA-transfected cells. The binding of hemin to the transfected receptors exhibited a relatively high affinity with a Kd of 12 nM, and was inhibited by several benzodiazepine ligands, including PK11195, Ro 5-4864, diazepam and protoporphyrin IX. When mouse liver mitochondria were incubated with [55Fe]hemin, the binding to PBR had a Kd of 15 +/- 1.8 nM. The Bmax of [55Fe]hemin binding to the mitochondria was 6.88 +/- 0.76 pmol/mg of protein, a value consistent with that of [3H]PK11195 binding, with a lower affinity. Coproporphyrinogen III, a precursor porphyrin produced in the cytosol, is translocated into mitochondria, then is converted to protoporphyrinogen IX; this conversion decreased in the presence of benzodiazepine ligands. To examine whether this decrease was related to a decrease in the binding of coproporphyrinogen to the mitochondria, the effects of benzodiazepines on the binding of coproporphyrinogen were examined. As the binding was dose-dependently inhibited by PK11195, Ro 5-4864, and diazepam, porphyrins are likely to be endogenous ligands for PBR. We propose that PBR play a role in the intracellular transport of porphyrins and heme.
A new quadrature sampling and processing approach (1989)

A quadrature sampling and array signal processing technique that differs from earlier approaches in that is processes the data before the Hilbert transformation is presented. A fast Fourier transformation (FFT) technique that performs the discrete Fourier transformation (DFT) on the sampled data directly without Hilbert transformation is proposed for frequency-domain signal processing. For array signal processing, the proposed approach does not perform Hilbert transformation prior to signal combining. It features high processing speed, low distortion, and hardware simplicity. Error analyses, performance evaluation, and computer simulation results are included.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Biofunctional Subwavelength Optical Waveguides for Biodetection (2008)

We report a versatile biofunctional subwavelength photonic device platform for real-time detection of biological molecules. Our devices contain lipid bilayer membranes fused onto metal oxide nanowire waveguides stretched across polymeric flow channels. The lipid bilayers incorporating target receptors are submersed in the propagating evanescent field of the optical cavity. We show that the lipid bilayers in our devices are continuous, have very high mobile fraction, and are resistant to fouling. We also demonstrate that our platform allows rapid membrane exchange. Finally, we use this device to detect the hybridization of specific DNA target sequences in solution to complementary probe DNA strands anchored to the lipid bilayer. This evanescent wave sensing architecture holds great potential for portable, all-optical detection systems.
Design, Synthesis, and Biological Evaluation of Novel Cyclic Adenosine–Inosine Monophosphate (cAIMP) Analogs That Activate Stimulator of Interferon Genes (STING) (2016)

We describe novel STING-activating cyclic dinucleotides whose constituent nucleosides are adenosine and inosine and that vary by ribose substitution, internucleotide linkage position, and phosphate modification. In mammalian cells in vitro, some of these cAIMP analogs induce greater STING-dependent IRF and NF-κB pathway signaling than do the reference agonists for murine (DMXAA) or human (2',3'-cGAMP) STING. In human blood ex vivo, they induce type I interferons (IFNs) and proinflammatory cytokines: for the former, 3',3'-cAIMP (9; EC<sub>50</sub> of 6.4 μM) and analogs 52-56 (EC<sub>50</sub> of 0.4-4.7 μM), which contain one or two 2'-fluoro-2'-deoxyriboses and/or bis-phosphorothioate linkages, are more potent than 2',3'-cGAMP (EC<sub>50</sub> of 19.6 μM). Interestingly, 9 induces type I IFNs more strongly than do its linkage isomers 2',3'-cAIMP (10), 3',2'-cAIMP (23), and 2',2'-cAIMP (27). Lastly, some of the cAIMP analogs are more resistant than 2',3'-cGAMP to enzymatic cleavage in vitro. We hope to exploit our findings to develop STING-targeted immunotherapies.
Regulation of Actinobacillus actinomycetemcomitans leukotoxin expression: analysis of the promoter regions of leukotoxic and minimally leukotoxic strains (1994)

The leukotoxin of Actinobacillus actinomycetemcomitans has been implicated as a virulence determinant in various human infections and is encoded by a multigene operon consisting of four known genes, designated ltxC, ltxA, ltxB, and ltxD. The ltx operon appears to be present in all A. actinomycetemcomitans strains, but levels of toxin expression vary greatly among strains. Thus, to gain a better understanding of the expression and regulation of the ltx operon, we have analyzed the ltx promoters of a highly toxic (JP2) and a minimally toxic (652) strain of A. actinomycetemcomitans. The nucleotide sequence of the JP2 ltx promoter contains -10 and -35 elements situated 350 bases upstream of ltxC, and primer extension of JP2 RNA confirmed that they are functional in vivo. However, a second primer extension product of 40 bases was present, and analysis of a series of truncated JP2 promoters fused to lacZ suggested that the region immediately upstream of ltxC also promotes transcription in Escherichia coli. These results suggest that two promoters may direct ltx expression in JP2. In addition, a small open reading frame capable of encoding a peptide of 78 amino acids was identified upstream of ltxC. Northern blots showed that this open reading frame is transcribed as part of a 4.2-kb mRNA, a transcript not previously identified as being derived from the ltx operon. In contrast, strain 652 expresses low steady-state levels of ltx mRNA, and its intact ltx promoter was inefficient in transcribing lacZ in E. coli. The nucleotide sequence of the 652 promoter is similar to that of the JP2 promoter but contains a region of 530 bp that is not present in JP2. Of 15 additional strains of A. actinomycetemcomitans that were analyzed, 13 contained promoters resembling the 652 sequence and 2 possessed JP2-like promoters. Both strains possessing the JP2-like promoter expressed 10- to 20-fold-higher levels of leukotoxin than did the strains possessing promoters resembling the 652 promoter. These results suggest that high levels of leukotoxin expression may correlate with the presence of the JP2-like promoter.
Optical properties of zero mode waveguides (2005)

Single molecule fluorescence techniques have contributed considerably to our understanding of a variety of biological systems. Unfortunately, single molecule techniques are fundamentally limited by the concentration of fluorescent species and volume being observed. Nanofabricated structures have emerged as ideal tools for volume confinement in fluorescence spectroscopy. This has allowed the extension of single molecule techniques to high concentration regimes. Zero Mode Waveguides, nanometer scale holes in a thin metal film produce observation volumes in the attoliter to zeptoliter range. These structures have been used to measure protein kinetics in the micro molar concentration range as well as for observations of polymerase incorporating single nucleotide bases. We have investigated the optical properties of these structures using a combination of fluorescence spectroscopy, scanning electron microscopy and optical transmission measurements in an effort to accurately model the optical properties of these structures. These measurements have allowed a detailed characterization of the optical behavior of sub-wavelength apertures in a thin metal film.
Multicast over wireless networks (2002)

How to ensure the participation of mobile users (no matter how disruptive the circumstances), especially for mobile commerce applications distributed over multiple networks.
Wavefront control of UV narrow bandpass filters prepared by plasma ion-assisted deposition (2006)

Metal oxide layers produced by plasma ion-assisted deposition are extensively used for complex optical coatings due to the availability of materials, the high packing density of films, and the smooth surfaces. Stringent optical surface figure specifications necessary for both laser optics and precision optics require film stress to be well controlled and surface deformation to be corrected or compensated. In this paper, SiO<sub>2</sub> based single cavity UV narrow bandpass filters were prepared by plasma ion-assisted deposition. The correlation between film stress, refractive index, deposition parameters, and post deposition annealing was established. The film stress was calculated based on interferometric surface deformation. The refractive index and film thickness were determined by means of variable angle spectroscopic ellipsometry. The center wavelength of the filters was obtained through spectral transmission measurement. The results suggest that the wavefront distortion of the multilayer coatings is dominated by the compressive stress of the SiO<sub>2</sub> layers, and can be controlled and corrected by the amount of plasma ion momentum transfer, substrate temperature, post deposition annealing, and stress compensation via backside SiO<sub>2</sub> coating. Based on the understanding of the mechanical and optical properties, the wavefront correction technique enables us to satisfy stringent surface figure specifications.
Reading 'Rewriting...' (2002)

This note welcomes and supports Peterson's analysis and develops a critical engagement with her arguments. Particular attention is paid to the methodological framing she develops and the issues arising fromthis. The need to include a critical political economy of knowledge production is argued.
The structure of porin from <i>Rhodobacter capsulatus</i> at 1.8 Å resolution (1991)

The structure of the porin from Rhodobacter capsulatus was determined at a resolution of 1.8 A. The analysis started from a closely related crystal structure that had been solved at a medium resolution of 3 A using multiple isomorphous replacement and solvent flattening. The new structure contains the complete sequence of 301 amino acid residues. Refinement of the model is under way; the present R-factor is 22% with good geometry. Except for the lengths of several loops, the resulting chain fold corresponds to the medium resolution model. The membrane channel is lined by a large number of ionogenic side chains with characteristic segregation of differently charged groups.
ARMAX-Based Transfer Function Model Identification Using Wide-Area Measurement for Adaptive and Coordinated Damping Control (2015)

One of the main drawbacks of the existing oscillation damping controllers that are designed based on offline dynamic models is adaptivity to the power system operating condition. With the increasing availability of wide-area measurements and the rapid development of system identification techniques, it is possible to identify a measurement-based transfer function model online that can be used to tune the oscillation damping controller. Such a model could capture all dominant oscillation modes for adaptive and coordinated oscillation damping control. This paper describes a comprehensive approach to identify a low-order transfer function model of a power system using a multi-input multi-output (MIMO) autoregressive moving average exogenous (ARMAX) model. This methodology consists of five steps: 1) input selection; 2) output selection; 3) identification trigger; 4) model estimation; and 5) model validation. The proposed method is validated by using ambient data and ring-down data in the 16-machine 68-bus Northeast Power Coordinating Council system. The results demonstrate that the measurement-based model using MIMO ARMAX can capture all the dominant oscillation modes. Compared with the MIMO subspace state space model, the MIMO ARMAX model has equivalent accuracy but lower order and improved computational efficiency. The proposed model can be applied for adaptive and coordinated oscillation damping control.
Antibiotika aus Gleitenden Bakterien, XXIV. Corallopyronin A, B und C – drei neue Antibiotika aus <i>Corallococcus coralloides</i> Cc c127 (Myxobacterales) (1985)

Abstract Aus dem Kulturmedium von Corallococcus coralloides , Stamm Cc c127 (DSM 2550), wurden drei neue Antibiotika, die Corallopyronine A ( 1 ), B ( 2 ) und C ( 4 ) durch Phasenverteilung und Chromatographie isoliert. Die Corallopyronine sind mit den Myxopyroninen A ( 5 ) und B ( 6 ), zwei homologen 3‐Acyl‐4‐hydroxy‐α‐pyronen mit α,β‐ungesättigter Methylcarbamatfunktion, nahe verwandt. Die neuen Antibiotika unterscheiden sich strukturell von den Myxopyroninen durch einen verlängerten 3‐Acylrest mit zwei zusätzlichen Doppelbindungen und einer Hydroxyfunktion in Corallopyronin A ( 1 ) und B ( 2 ) oder durch einen 3‐Acylrest mit einem Tetrahydrofuranring in der Komponente C ( 4 ).
SCAR Markers for Correct Identification of <i>Phyllanthus amarus, P. fraternus, P. debilis</i> and <i>P. urinaria</i> used in Scientific Investigations and Dry Leaf Bulk Herb Trade (2008)

The trade in Phyllanthus material as bulk herb is rampant and mainly involves herbaceous species such as Phyllanthus amarus, P. fraternus, P . debilis and P. urinaria. These species are very important in herbal medicines and have varied activities. In India these species grow sympatrically and there are chances of deliberate or ignorant adulteration of crude drugs, lowering the efficiency of the medication for its intended purpose. Secondly, incorrect identification may also lead to erroneous reports on activities/molecules. To overcome this problem in crude drug (dry leaf powder) and compliment morphological identification in live plant, we have developed SCAR markers for all four species. In each species, we selected one fragment as being monomorphic between accessions but differing in size between species. These species-specific fragments were selected, cloned and sequenced. Based on the sequences, primer pairs were designed and amplification conditions standardized. SCAR markers were isolated from population DNA amplification profiles and validated by sequencing. The species-specific SCAR primers could retrieve the same size and sequence of fragments as in the RAPD profile. These fragments are 1150 bp, 317 bp, 980 bp and 550 bp in size for P. amarus, P. fraternus, P. debilis and P. urinaria, respectively. Additional fragments in P. debilis and P. urinaria indicate different alleles. The retrieval of same size and sequence of species-specific unique SCAR markers from the respective accessions (mixed DNA sample of same accessions) indicates the usefulness to study natural hybridization between the species in addition to adulteration.
The Design of a Dynamic Positioning System (1979)

The hydrodynamic problem of a dynamically positioned vessel is formulated by a double time scale expansion. Simplified models are derived and then used to design a control device to keep the vessel within a permissible radius. Physical concepts lead the design while using the theory for multivariable systems in frequency domain. Simulation results validate the design.
Tree structured hybrid intra prediction (2005)

This paper proposes a new method to generate intra prediction images in intra coding, tree structured hybrid intra prediction. When generating intra prediction images, the proposed method selects the most suitable one from intra prediction images generated using two methods, pixel-based and block-based intra prediction. This selection is performed on macroblock or sub macroblock level based on a rate distortion optimization scheme. In addition, information indicating which prediction method is selected is described in the bitstream using a tree structure. The proposed method is initially described, and then the results of evaluation experiments are shown by comparison to conventional methods. Evaluation is carried out by implementing the proposed method in an H.264-based intra picture codec. The results of evaluation confirm that the proposed method improves PSNR by up to nearly 0.7 dB compared to conventional methods over a wide range of bit rates.
Vietnamese agriculture in a centrally planned economy and in the transition to a market economy (1995)

agricultural development; planned economy; market economy; collective farming; agrarian reform; Viet Nam;
Fate and transport of zoonotic, bacterial, viral, and parasitic pathogens during swine manure treatment, storage, and land application1 (2010)

Members of the public are always somewhat aware of foodborne and other zoonotic pathogens; however, recent illnesses traced to produce and the emergence of pandemic H1N1 influenza virus have increased the scrutiny on all areas of food production. The Council for Agricultural Science and Technology has recently published a comprehensive review of the fate and transport of zoonotic pathogens that can be associated with swine manure. The majority of microbes in swine manure are not zoonotic, but several bacterial, viral, and parasitic pathogens have been detected. Awareness of the potential zoonotic pathogens in swine manure and how treatment, storage, and handling affect their survival and their potential to persist in the environment is critical to ensure that producers and consumers are not at risk. This review discusses the primary zoonotic pathogens associated with swine manure, including bacteria, viruses, and parasites, as well as their fate and transport. Because the ecology of microbes in swine waste is still poorly described, several recommendations for future research are made to better understand and reduce human health risks. These recommendations include examination of environmental and ecological conditions that contribute to off-farm transport and development of quantitative risk assessments.
Modeling control and dynamic data-parallelism in object-oriented languages (1996)

Object-oriented paradigms are becoming widely accepted and are being used in a number of areas of computing. A large number of algorithms have components that interact in complex ways. These components may have structural and computational similarities. The realization that object-oriented facilities can be used to provide abstractions for these complex structures and for interaction between these structures has led to a number of research projects for designing and implementing object-oriented parallel runtime systems and languages.
Multithreading has been used in several areas of computing like operating systems, graphic window systems, and data-base systems, to mask computation with communication, synchronization, and interaction with external agents like devices, remote machines, etc.
This dissertation couples multithreading and object-oriented paradigms and proposes a model for control-parallelism and dynamic data-parallelism that addresses symmetric shared-memory, hierarchical shared memory, and distributed-memory architectures. The model, called Coir, abstracts parallelism at a level much higher than that of physical processors and provides a mechanism for overlapping computation with communication, synchronization, and I/O. Data-parallel operations are defined specific to data-parallel active objects called ropes. Coir provides support for load-balancing and locality through migration. Nested parallelism is natural to this model.
Coir is implemented in C++ on shared and distributed memory systems. The active control-parallel and data-parallel objects can be customized in interesting ways in a serial or a parallel manner. Regular and adaptive algorithms are implemented in the model and mechanisms for building collection-oriented parallel languages are discussed.
Relationship between Plasma Volume, Carotid Baroreceptor Sensitivity and Orthostatic Tolerance (1995)

1. Studies were carried out on 43 otherwise healthy patients referred for investigation for attacks of syncope of unknown cause and on six healthy volunteers. 2. Plasma volume was determined by Evans Blue dye dilution and blood volume was estimated using haematocrit. Carotid baroreceptor sensitivity was determined from the changes in pulse interval in response to subatmospheric pressures applied to the neck overlying the carotid sinuses, and orthostatic tolerance was assessed as the time to presyncope in a test of head-up tilt, followed by the addition of graded lower body suction. 3. Eight patients and one volunteer fainted during head-up tilt alone, 23 patients and two volunteers fainted during tilt with lower body suction at -20 mmHg and 12 patients and three volunteers either fainted during suction at -40 mmHg or tolerated the entire procedure. 4. Although plasma and blood volumes were higher in males than females, the values normalized for either body weight or for calculated lean body mass were not different between male and female patients and asymptomatic volunteers. The subjects showing the greatest resistance to syncope were found to have significantly larger plasma and blood volumes (P < 0.0001) and significantly smaller baroreceptor sensitivities (P < 0.0002) than those who fainted earlier.(ABSTRACT TRUNCATED AT 250 WORDS)
A new source extraction algorithm for optical space debris observation (2013)

Specific challenges arise in the task of real-time automatic data reduction of optical space debris observations. Here we present an automatic technique that optimally detects and measures the sources from images of optical space debris observations. We show that highly reliable and accurate results can be obtained on most images produced by our specific sensors, and due to optimizations, the whole pipeline works fast and efficiently. Tests demonstrate that the technique performs better than SExtractor from the point of view of fast and accurate detection, therefore it is well suited for data reduction of optical space debris observations.
Based on Feature Points Transform (2008)

Mapping the raw time series data to a modality space effectively is a critical problem in time series similarity search.This paper puts forward a method of Feature Points Transform Symbolization(FPTS) for time series,which combines ideology of symbolic time series and piecewise linear representation.It can extract the shape modality of time series,hold the speciality of extreme value points under dimensionality reduction and noises removing,and support the similarity measure based on Dynamic Time Warping(DTW) distance,which overcomes the limitation of precise matching of traditional symbolization method.Experiments prove the accuracy and efficiency of the method.