gebhart/patrepeval huggingface dataset:
Characterisation of the structure of ocr, the gene 0.3 protein of bacteriophage T7 (2001)

The product of gene 0.3 of bacteriophage T7, ocr, is a potent inhibitor of type I DNA restriction and modification enzymes. We have used biophysical methods to examine the mass, stability, shape and surface charge distribution of ocr. Ocr is a dimeric protein with hydrodynamic behaviour equivalent to a prolate ellipsoid of axial ratio 4.3 +/- 0.7:1 and mass of 27 kDa. The protein is resistant to denaturation but removal of the C-terminal region reduces stability substantially. Six amino acids, N4, D25, N43, D62, S68 and W94, are all located on the surface of the protein and N4 and S68 are also located at the interface between the two 116 amino acid monomers. Negatively charged amino acid side chains surround W94 but these side chains are not part of the highly acidic C-terminus after W94. Ocr is able to displace a short DNA duplex from the binding site of a type I enzyme with a dissociation constant of the order of 100 pM or better. These results suggest that ocr is of a suitable size and shape to effectively block the DNA binding site of a type I enzyme and has a large negatively charged patch on its surface. This charge distribution may be complementary to the charge distribution within the DNA binding site of type I DNA restriction and modification enzymes.
Photonic crystal high-efficiency multispectral thermal emitters (2008)

We demonstrate through numerical simulation the modification of the thermal emission spectrum by a metallic photonic crystal (PhC). Here the radiation is funneled into a narrow emission band in contrast to the broad spectrum associated with a Planckian-distribution. A detailed quantitative evaluation of the spectral, power, and angular efficiencies of a PhC thermal emitter and its portability across IR spectral bands is provided. We show that an optimized tungsten PhC possesses a predominant narrow-band forward emission profile with an emitter efficiency that is more than double that of an ideal blackbody and ∼65–75% more power-efficient across the IR spectrum.
From Ideal to Realisable Real-Time Specifications (1999)

. Formally refining a real-time specification to an implementation is only possible when the specification allows for all physical limitations, and timing and signal errors inherent in the implementation. Allowing for such implementation-specific details in a top-level specification can, however, obscure the desired functionality and complicate analysis. Furthermore, such an approach assumes the specifier has an understanding of the physical limitations and errors of the implementation which may not yet have been developed. As an alternative, we propose introducing a notion of realisation into the formal development process. Realisation is an approach to specification development which allows errors and physical limitations to be introduced. It also allows properties of the new specification to be derived from those proved for the original. 1 Introduction Several formal notations have been developed for the specification and refinement of real-time systems [19, 15, 16, 3, 13, 12]. To ...
In vitro regeneration of plantlets from mature embryos of Pinus ayacahuite (1997)

A plantlet regeneration protocol was developed for Pinus ayacahuite var. ayacahuite (Ehrenb.). Embryos from mature seeds from ten provenances were cultured in a 16-h photoperiod for 3 days on a medium containing 30 mM sucrose and 0.7% agar. Cotyledons from these embryos were subcultured onto MCM medium (Bornman 1983) supplemented with 50 micro M N(6)-benzyladenine and 90 mM sucrose for 2 weeks. Bud development and shoot elongation were maximized by subculturing the explants on half strength AE medium (von Arnold and Ericksson 1981), supplemented with 60 mM sucrose and 0.05% activated charcoal every 30 days. Seed source had a significant effect on the responses of the embryos to the bud induction protocol. For the provenance with the best response to bud induction, about 79% of the cultured cotyledons formed buds, and each cotyledon formed a mean of 9.1 buds, so that about 70 shoots could be induced from each seed. The best rooting response (40% rooting) was obtained by treating the shoots for 8 h with 100 micro M naphthalene acetic acid.
FPGA Implementation of a Single Pass Real-Time Blob Analysis Using Run Length Encoding (2008)

In the fields of machine vision and image processing applications the blob analysis became a well known method to detect objects in a digital image. Together with the increasing resolutions and frame rates of recent digital video cameras the requirements on the hardware to perform the blob analysis are very high. Software implementations may not be able to accomplish a satisfying performance. Furthermore, existing hardware solutions require a processing of the picture in multiple passes. This paper describes the development of a novel FPGA algorithm, performing a high speed real-time blob analysis using only one single pass. The input data are compressed using run length encoding. This allows the use of a full configuration camera link interface with data rates of up to 680MByte/s. Furthermore, object properties are passed to the host PC on-the-fly which reduces the latency to a minimum while at the same time allows the reuse of object labels thus achieving a memory efficient implementation. 1.
SI Engine Control in the Cold-Fast-Idle Period for Low HC Emissions and Fast Catalyst Light Off (2014)

<div class="section abstract"><div class="htmlview paragraph">The engine and its exhaust flow behaviors are investigated in a turbo-charged gasoline direct injection engine under simulated cold-fast-idle condition. The metrics of interest are the exhaust sensible and chemical enthalpy flows, and the exhaust temperature, all of which affect catalyst light off time. The exhaust sensible enthalpy flow is mainly a function of combustion phasing; the exhaust chemical enthalpy flow is mainly a function of equivalence ratio. High sensible and chemical enthalpy flow with acceptable engine stability could be obtained with retarded combustion and enrichment. When split injection is employed with one early and one later and smaller fuel pulse, combustion retards with early secondary injection in the compression stroke but advances with late secondary injection. Comparing gasoline to E85, the latter produces a lower exhaust temperature because of charge cooling effect and because of a faster combustion.</div></div>
Technologies used in wireless sensor networks (2008)

In recent years, a demand for remote measuring, automation and control in various branches of industry, agriculture, environmental engineering, and many other areas is rapidly growing. Therefore, many systems are emerging and evolving. Such systems utilize small autonomous devices (nodes) and it is obvious that all these devices need to communicate with each other as well as with the system administrator. In most cases the communication is wireless. Devices form networks, each of which requires specific approach because of different conditions and needs. Thus, there are many various methods, protocols and algorithms, most of them still under development. However, a few standards already exist. Such networks are called wireless sensor networks (WSN) and this paper will bring the overview of technologies used in WSNs, differences, constraints and corresponding recommendations and standards. The recent areas of research and future perspectives will also be mentioned.
The PY Motif of ENaC, Mutated in Liddle Syndrome, Regulates Channel Internalization, Sorting and Mobilization from Subapical Pool (2007)

The epithelial-Na(+)-channel (alphabetagammaENaC) regulates kidney salt-transport and blood pressure. Each ENaC subunit contains a PY motif (PPxY) and its mutation in beta/gammaENaC causes Liddle syndrome, a hereditary hypertension. These (extended) PY motifs (PP(616)xY(618)xxL(621)) serve as binding sites for the ubiquitin ligase Nedd4-2, which decreases cell-surface expression of ENaC by unknown route(s). Using polarized kidney epithelia [Madin-Darby canine kidney I (MDCK-I)] cells stably expressing extracellularly myc-tagged wild type (WT) or PY-motif mutants of betaENaC (P616A, Y618A or L621A, with WT-alphagammaENaC), and live-imaging plus enzyme-linked immunosorbent assay (ELISA)-type assays to analyze routes/rates of ENaC internalization/recycling, we show here that cell-surface half-life of all PY mutants was fourfold longer than WT-ENaC (approximately 120 versus 30 minutes), reflecting primarily reduced channel internalization but also attenuated replenishment of cell-surface ENaC from a large subapical pool. The Y618A mutant revealed more severe internalization and replenishment defects than the other PY mutants. Internalized WT-ENaC was detected in sorting/recycling and late endosomes/lysosomes, while the Y618A mutant accumulated in the former. Nedd4-2 ubiquitinated ENaC at the apical membrane causing channel internalization and degradation. Cyclic AMP (cAMP) accelerated mobilization of subapical ENaC to the cell surface and long-term ENaC recycling, but only mobilization, not recycling, was inhibited in the PY mutants. These results suggest that the ENaC PY motifs (and Nedd4-2) primarily regulate channel internalization but also affect cAMP-dependent replenishment, providing important insight into the Liddle syndrome defects.
Bent tritopic carboxylates for coordination networks: clues to the origin of self-penetration (2014)

We suggest in this paper that the combinative use of bent tritopic carboxylate, linear dipyridyl and adaptable Cu<sup>2+</sup> ion leads to a higher probability of self-penetrated polymeric networks.
Hyperbaric oxygen and chemical oxidants stimulate CO<sub>2</sub>/H<sup>+</sup>-sensitive neurons in rat brain stem slices (2003)

Hyperoxia, a model of oxidative stress, can disrupt brain stem function, presumably by an increase in O2 free radicals. Breathing hyperbaric oxygen (HBO2) initially causes hyperoxic hyperventilation, whereas extended exposure to HBO2 disrupts cardiorespiratory control. Presently, it is unknown how hyperoxia affects brain stem neurons. We have tested the hypothesis that hyperoxia increases excitability of neurons of the solitary complex neurons, which is an important region for cardiorespiratory control and central CO2/H+ chemoreception. Intracellular recordings were made in rat medullary slices during exposure to 2-3 atm of HBO2, HBO2 plus antioxidant (Trolox C), and chemical oxidants (N-chlorosuccinimide, chloramine-T). HBO2 increased input resistance and stimulated firing rate in 38% of neurons; both effects of HBO2 were blocked by antioxidant and mimicked by chemical oxidants. Hypercapnia stimulated 32 of 60 (53%) neurons. Remarkably, these CO2/H+-chemosensitive neurons were preferentially sensitive to HBO2; 90% of neurons sensitive to HBO2 and/or chemical oxidants were also CO2/H+ chemosensitive. Conversely, only 19% of HBO2-insensitive neurons were CO2/H+ chemosensitive. We conclude that hyperoxia decreases membrane conductance and stimulates firing of putative central CO2/H+-chemoreceptor neurons by an O2 free radical mechanism. These findings may explain why hyperoxia, paradoxically, stimulates ventilation.
Trust Management in Fog Computing (2017)

With the rise of fog computing, computation is moved away from a purely centralized approach. In the centralized approach devices have direct contact with the cloud servers. In fog computing allows for processing data along the path from the edge to the core of the network. The introduction of fog will have several benefits, such as reduced latency and increased reliability. The network topology changes continually in a fog computing network. New objects will join and leave. Since fog computing is a new field of study, there exists several open issues, one of them is how to establish trust. Trust is the level of assurance that an object will behave in a satisfactory manner. Trust can also be used to form autonomous collaboration. \n\nThis thesis explores the need for trust management in fog computing. Through a literature review, specific tasks for trust management in fog computing have been identified. Trust can provide assistance in the decision making, and allow autonomous connections to be established between fog nodes and resource constrained IoT devices, called fog clients. Requirements for the trust in fog computing has also been defined. Additionally, misbehaving nodes can be detected in a network as well. By surveying existing solutions in other domains, requirements for trust is fog computing were defined. Based on these requirements a trust management solution for fog computing has been devised. Finally, two main open issues are identified and discussed.
Implant-retained prostheses for facial defects: an up to 14-year follow-up report on the survival rates of implants at UCLA. (2002)

It is possible to achieve high survival rates of implants in the auricular and piriform/nasal sites through careful presurgical and radiographic planning. The less favorable long-term survival of implants in the orbital rim, especially at irradiated sites, requires further study.
Design of cyclic fixed‐bed adsorption processes. Part I: Phenol adsorption on polymeric adsorbents (1985)

Abstract A model for the adsorption of phenol in a fixed bed of a polymeric adsorbent is developed. Model parameters (equilibrium parameters, capacity factor, axial dispersion, film mass transfer coefficient, and intraparticle effective diffusivity) are experimentally determined from independent experiments. Numerical solution of the model equations uses the method of lines with double orthogonal collocation in finite elements. The model is used for the prediction of breakthrough curves and is part of a package for the design of cyclic processes.
Cluster adaptive training of hidden Markov models (2000)

When performing speaker adaptation, there are two conflicting requirements. First, the speaker transform must be powerful enough to represent the speaker. Second, the transform must be quickly and easily estimated for any particular speaker. The most popular adaptation schemes have used many parameters to adapt the models to be representative of an individual speaker. This limits how rapidly the models may be adapted to a new speaker or the acoustic environment. This paper examines an adaptation scheme requiring very few parameters, cluster adaptive training (CAT). CAT may be viewed as a simple extension to speaker clustering. Rather than selecting a single cluster as representative of a particular speaker, a linear interpolation of all the cluster means is used as the mean of the particular speaker. This scheme naturally falls into an adaptive training framework. Maximum likelihood estimates of the interpolation weights are given. Furthermore, simple re-estimation formulae for cluster means, represented both explicitly and by sets of transforms of some canonical mean, are given. On a speaker-independent task CAT reduced the word error rate using very little adaptation data. In addition when combined with other adaptation schemes it gave a 5% reduction in word error rate over adapting a speaker-independent model set.
Macromolecular dynamic contrast‐enhanced (DCE)‐MRI detects reduced vascular permeability in a prostate cancer bone metastasis model following anti–platelet‐derived growth factor receptor (PDGFR) therapy, indicating a drop in vascular endothelial growth factor receptor (VEGFR) activation (2008)

The antivascular function of the platelet-derived growth factor receptor (PDGFR) inhibitor imatinib combined with paclitaxel has been demonstrated by invasive immunohistochemistry. The purpose of this study was to 1) noninvasively monitor the response to anti-PDGFR treatment, and 2) understand the underlying mechanism of this response. Thus, response to treatment was studied in a prostate cancer bone metastasis model using macromolecular (biotin-bovine serum albumin [BSA]-Gd-diethylene triamine pentaacetic acid [GdDTPA]) dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). Human prostate cancer (PC-3MM2) bone metastases that caused osteolysis and grew in neighboring muscle showed a high blood-volume fraction (fBV) and vascular permeability (PS) at the tumor periphery compared to muscle tissue and intraosseous tumor. Imatinib alone or with paclitaxel significantly reduced PS by 35% (one-tailed paired t-test, P = 0.045) and 40% (P = 0.0003), respectively, whereas paclitaxel alone or no treatment had no effect. Based on changes in PS, we hypothesized that imatinib interferes with the signaling pathway of vascular endothelial growth factor (VEGF). This mechanism was verified by immunohistochemistry. It demonstrated reduced activation of both PDGFR-beta and VEGF receptor 2 (VEGFR2) in imatinib-treated mice. Our study therefore demonstrates that macromolecular DCE-MRI can be used to detect early vascular effects associated with response to therapy targeted to PDGFR, and provides insight into the role played by VEGF in anti-PDGFR therapy.
First accuracy evaluation of the NPL-CsF2 primary frequency standard (2010)

An accuracy evaluation of the caesium fountain NPL-CsF2 as a primary frequency standard is reported. The device operates with a simple one-stage magneto-optical trap as the source of cold atoms. Both the uncertainty in and magnitude of the cold collision frequency shift are reduced by taking advantage of the dependence of the cross section on the effective collision energy in an expanding atomic cloud. The combined type B uncertainty (typically 4 × 10−16) is dominated by an estimate of the frequency shift due to the distributed cavity phase. When operated at single density, the short-term fractional frequency instability of NPL-CsF2 is 1.7 × 10−13 at 1 s and limited by the noise of the room temperature quartz-based local oscillator. During a typical frequency measurement campaign, the fountain is operated in an alternating mode at high and low density in order to measure and correct for a residual collision shift. This increases the effective fractional frequency instability to 5.4 × 10−13 at 1 s; consequently the averaging time required for the type A uncertainty level to match that of the type B is 20 days.
Surgical Management of the Newborn with Congenital Diaphragmatic Hernia (2010)

Despite advances in the surgical treatment and medical management over the last 20 years, neonates with congenital diaphragmatic hernia (CDH) remain one of the most challenging patient groups for all clinicians. Treatment strategies have shifted from emergent surgical repair and maximum ventilatory support to delayed repair and preoperative hemodynamic stabilization with lung-sparing ventilation strategies and extracorporeal membrane oxygenation. Subsequently, overall survival has improved to as high as 80% in some centers. However, specific treatment criteria are vague and highly variable amongst centers. This lack of consensus of these treatment modalities remains elusive due to the heterogeneity in disease severity as well as heterogeneity in patient care amongst centers. As a result of the rare incidence of disease and limited experience of individual centers, the evidence for CDH is typically reported as a homogenous disease largely supported by case series and networked-based studies. To better evaluate the data and compare treatment strategies, a classification and stratification of disease and centers is needed.
[Manual method of assaying plasma hemoglobin by tetramethylbenzidine and deferoxamine]. (1984)

We describe a manual method to determine very low concentrations of hemoglobin in plasma (0,25 to 37,3 mumol/l). We use peroxidase properties of hemoglobin which decomposes hydrogen peroxide releasing oxygen. This released oxygen will oxidize tetramethylbenzidine. The original feature of the proposed method lies in the stabilization of the obtained colour by a complexing agent, the deferoxamine. The technique is quick, reliable, cheap and does not need specialized equipment. It is possible to use the method for urines.
Smart Tissue Culture: in Situ Monitoring of the Activity of Protease Enzymes Secreted from Live Cells Using Nanostructured Photonic Crystals (2009)

Monitoring enzyme secretion in tissue culture has proved challenging because to date the activity cannot be continuously measured in situ. In this Letter, we present a solution using biopolymer loaded photonic crystals of anodized silicon. Shifts in the optical response by proteolytic degradation of the biopolymer provide label-free sensing with unprecedented low detection limits (1 pg) and calculation of kinetic parameters. The enhancement in sensitivity relative to previous photonic crystal sensors constitutes a change in the sensing paradigm because here the entire pore space is responsive to the secreted enzyme rather than just the pore walls. In situ monitoring is demonstrated by detecting secretion of matrix metalloprotease 9 from stimulated human macrophages.
Fully Integrated Switch-LNA Front-End IC Design in CMOS: A Systematic Approach for WLAN (2011)

A fully integrated front-end IC is demonstrated for 802.11b/g transceivers with integrated power amplifiers. The SP3T-LNA architecture integrates Bluetooth® functionality with transmit and receive for wireless LAN. The transmit switch achieves a P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1dB</sub> greater than 33.0 dBm at 2.5 GHz by employing a cross-biasing approach, transistor stacking and deep n-well process. Power handling techniques used for the switches and the associated performance tradeoffs are discussed. The measured noise figure of the LNA and the receive chain comprising both an LNA and a switch is 1.5 dB and 3.0 dB, respectively. The LNA achieves an IIP3 of 7.0 dBm while consuming 7.0 mA of current. The measured switching times are less than 350 ns. The front-end IC employs a 3.3 V supply and occupies 0.64 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> in 0.18 μm bulk CMOS technology.
A Low Level Environmental Radiation Monitor with High Sensitivity, Stability, and Dynamic Range (1969)

An environmental radiation monitor is described which records gamma radiation levels with a logarithmic response over a dynamic range of four decades (.01 mR/hr to 100 mR/hr achievable without range switching). Constant temperature accuracy is greater than ±10% of indicated reading throughout 3.5 decades of the four decade range. A high degree of temperature stability is achieved (error due to temperature change is less than ±20% of reading over an ambient temperature range of -10°C to + 55°C). Solid-state electronic circuitry is utilized exclusively for increased reliability and long term stability.