gebhart/patrepeval huggingface dataset:
Enhancement of ribosomal frameshifting by oligonucleotides targeted to the HIVgag-polregion (1992)

The pol gene of all retroviruses is expressed as a gag-pol fusion protein which is proteolytically processed to produce all viral enzymes. In the human immunodeficiency virus (HIV), the gag and pol genes overlap by 241 nucleotides with pol in the -1 phase with respect to gag. The gag-pol fusion is produced via a -1 ribosomal frameshifting event that brings the overlapping, out-of-phase gag and pol genes into translational phase. Frameshifting occurs at a so called 'shift site' 8-10 nucleotides upstream of a hairpin loop which may play a role in the regulation of frameshifting. We have fused this region of HIV-1 to the 5' end of the firefly luciferase reporter gene in order to quantitatively measure ribosomal frameshifting both in cells and by in vitro translation. A series of 2'-O-methyl oligonucleotides was designed to specifically bind the sequences which flank the gag-pol hairpin. Ribosomal frameshifting is enhanced up to 6 fold by those oligonucleotides which bind the area just 3 to the stem. Oligonucleotides which bind 5' to the stem have no effect on frameshift efficiency. In addition, we have constructed a series of fusion genes which mimic the effect of the bound oligonucleotides with intramolecular hairpins. The results suggest that increasing RNA secondary structure downstream of the shift site increases the frequency of ribosomal frameshifting, and that this effect can be mimicked by antisense oligonucleotides.
A 1kW inductive charging system using AC processing pickups (2011)

This paper presents a 1kW inductive charging system for Electric Vehicles (EV's). The primary topology uses an LCL converter and the secondary topology uses a parallel AC processing pickup to produce a controllable current source ideal for EV battery charging applications. Standard circular pads with a diameter of 420mm were used. The system can operate over a variable charging height of 45-90mm. The measured efficiency from the AC mains socket to the DC battery is 73-83% at rated power conditions of 1kW depending on the relative height and alignment of the pads.
The Role of Inflammatory Cytokines as Intermediates in the Pathway from Increased Adiposity to Disease (2021)

Observational and MR estimates of the effect of BMI on cytokine levels were generally concordant. There was little evidence for an effect of raised levels of BMI-driven cytokines on disease. These findings illustrate the challenges of MR when applied in the context of molecular mediation.
Nonlinear optical loop mirror based on standard communication fiber (1997)

We numerically analyze the effectiveness of a nonlinear optical loop mirror (NOLM) based on standard communication fiber with randomly varying birefringence for demultiplexing streams of picosecond pulses at 100 GHz. A broad switching window of about three pulse full-width at half maximum (FWHM) can be obtained. The device performance is defined by the pulse duration, the dispersion of the fiber, and the fiber length. We show that imperfect averaging of the randomly varying birefringence causes amplitude fluctuations on the NOLM transmission curve. We also show that the Raman self-frequency shift does not affect the NOLM switching characteristics at picosecond pulse durations.
Modeling the HEVC Encoding Energy Using the Encoder Processing Time (2022)

The global significance of energy consumption of video communication renders research on the energy need of video coding an important task. To do so, usually, a dedicated setup is needed that measures the energy of the encoding and decoding system. However, such measurements are costly and complex. To this end, this paper presents the results of an exhaustive measurement series using the x265 encoder implementation of HEVC and analyzes the relation between encoding time and encoding energy. Finally, we introduce a simple encoding energy estimation model which employs the encoding time of a lightweight encoding process to estimate the encoding energy of complex encoding configurations. The proposed model reaches a mean estimation error of 11.35% when averaged over all presets. The results from this work are useful when the encoding energy estimate is required to develop new energy-efficient video compression algorithms.
Flex-Frame Timing-Critical Passive Optical Networks for Delay Sensitive Mobile and Fixed Access Services (2017)

We demonstrate a timing-critical TDM-PON compatible fiber-wireless access network with shorter frames and upstream bursts to support delay-sensitive wireless and fixed services. In comparison with conventional schemes, transmission latencies are reduced up to 70%.
Body- or Tip-Controlled Reactivity of Gold Nanorods and Their Conversion to Particles through Other Anisotropic Structures (2007)

We report the shape transformation of gold nanorods to spherical nanoparticles, assisted by cupric ions. The reaction proceeds through a series of structures and could be arrested at any stage to produce particles of desired shape. In the presence of a larger concentration of cetyltrimethylammonium bromide (CTAB), selective etching of the tips of the nanorods occurs to a greater extent. The subsequent transformation is driven by the surface reconstruction of nanorods to generate more stable surfaces. As the stability of various surfaces depends on the protecting agent used, the reactivity is modified by controlling its presence at the surface. We show that the body of the rods is more susceptible for reaction at reduced CTAB concentrations. During the conversion to particles, several anisotropic transient structures were observed and were imaged using high-resolution transmission electron microscopy (HRTEM). The transformation occurs due to the hydroxyl radicals produced by Cu2+ in the presence of ascorbic acid (AA). A mechanism has been proposed and several control experiments were conducted to test it. The cupric ion induced shape transformations can be extended to other ions, and knowing the mechanism allows the control of the process to stabilize various anisotropic structures.
On the Use of Side Information for Mining Text Data (2012)

In many text mining applications, side-information is available along with the text documents. Such side-information may be of different kinds, such as document provenance information, the links in the document, user-access behavior from web logs, or other non-textual attributes which are embedded into the text document. Such attributes may contain a tremendous amount of information for clustering purposes. However, the relative importance of this side-information may be difficult to estimate, especially when some of the information is noisy. In such cases, it can be risky to incorporate side-information into the mining process, because it can either improve the quality of the representation for the mining process, or can add noise to the process. Therefore, we need a principled way to perform the mining process, so as to maximize the advantages from using this side information. In this paper, we design an algorithm which combines classical partitioning algorithms with probabilistic models in order to create an effective clustering approach. We then show how to extend the approach to the classification problem. We present experimental results on a number of real data sets in order to illustrate the advantages of using such an approach.
Large signal linearity enhancement of AlGaN/GaN high electron mobility transistors by device-level V<inf>t</inf> engineering for transconductance compensation (2017)

This work illustrates the use of device-physics and system-level understanding to demonstrate a novel device-technique to achieve high-linearity in RF-GaN HEMTs. By eliminating access-regions and engineering device-transfer function (gm and its derivatives), a significant boost in large-signal non-linearity: 20 dB reduction in harmonics, OIP3 boost by 6 dB is shown. The full potential of this technique in providing IMD below the state-of-art is highlighted in commercial RF-devices using physical-MVSG model.
The Rat Gonadotropin-Releasing Hormone: SH Locus: Structure and Hypothalamic Expression (1989)

The rat GnRH gene as expressed in the central nervous system is comprised of four exons and three introns and spans 4.5 kilobases of genomic DNA. Recently it has been shown that the DNA strand opposite that which is transcribed to produce GnRH mRNA is transcribed in heart to produce a set of transcripts, SH RNAs, which share significant exonic sequences with the GnRH gene. The nucleotide sequence of this locus and approximately 3 kilobases on either side has been determined. Northern analysis of hypothalamic RNA probed with GnRH and SH strand specific probes demonstrate that both GnRH and SH RNAs are present within the preoptic hypothalamus. The cap sites for GnRH and SH transcripts have been localized using polymerase chain reaction technology. Results from these experiments indicate that in the preoptic hypothalamus GnRH transcription initiates from three sites. The majority of GnRH transcripts is spliced efficiently and gives rise to the major class of GnRH mRNA. A second spliced population is present in lower abundance, while a third population is not spliced. The SH gene contains at least two distinct promoters, from which two populations of transcripts are derived containing unique 5'-sequences spliced to a common 3'-region.
A CNN based neurobiology inspired approach for retinal image quality assessment (2016)

Retinal image quality assessment (IQA) algorithms use different hand crafted features for training classifiers without considering the working of the human visual system (HVS) which plays an important role in IQA. We propose a convolutional neural network (CNN) based approach that determines image quality using the underlying principles behind the working of the HVS. CNNs provide a principled approach to feature learning and hence higher accuracy in decision making. Experimental results demonstrate the superior performance of our proposed algorithm over competing methods.
Simple analytical expression for crosstalk estimation in homogeneous trench-assisted multi-core fibers (2014)

An analytical expression for the mode coupling coefficient in homogeneous trench-assisted multi-core fibers is derived, which has a simple relationship with the one in normal step-index structures. The amount of inter-core crosstalk reduction (in dB) with trench-assisted structures compared to the one with normal step-index structures can then be written by a simple expression. Comparison with numerical simulations confirms that the obtained analytical expression has very good accuracy for crosstalk estimation. The crosstalk properties in trench-assisted multi-core fibers, such as crosstalk dependence on core pitch and wavelength-dependent crosstalk, can be obtained by this simple analytical expression.
Development and Testing of an Electrically Propelled Capsule Endoscope in Man (2003)

Introduction: Electrostimulation can cause propulsion of ovoid objects in the lumen of the gastrointestinal tract. Aim: To develop and test in man a new type of endoscope with a propulsion system driven by electrostlmulation. Methods: Ovoid capsule endoscopes were modified. Four electrodes arranged in bipolar pairs were attached to the front and rear portions of the capsule. By careful attachment and subsequent polishing, it was possible to obtain unimpaired video images from tbe modified capsule endoscope without altering its geometry (11 X 27 mm). Several of these devices were constructed with wires to the front and back electrodes, which allowed an electrical stimulus to be applied to drive the capsule backwards or forwards from an external Grass stimulator which had been rendered electrically safe for use in man. Separate devices were constructed to include the circuitry necessary to drive similar devices without wires or external connectors, all these devices were tested in studies in the pig esophagus and small intestine prior to the use of identical devices in man. Ethical committee permission was given for testing these devices in a human volunteer. Results: Independent and wired devices were successfully tested in porcine experiments. It was shown that both wired and unwired devices could drive wireless capsule endoscopes backwards and forwards in the small intestine at equal rates. The same devices did not move when electrostimulation was not switched on in these anaesthetized animals. In an experiment in a human volunteer an electrostimulation capsule was swallowed. It reached the small intestine in 25 minutes. Electrostimulation was tested over a range of settings as the device travelled through the small intestine. The current used in these experiments was never enough to elicit conscious awareness or pain. At the settings used, the device was able to initiate contraction and accelerate the passage of the ovoid. The movements were analyzed using x-ray screening and capsule image analysis. At high settings, a possible vagal stimulation effect may have been detected. The device was easily introduced and worked well in stimulating propulsive and retropulsive movement. It was easy to remove under screening from the middle of the small intestine. It did not hurt. Conclusion: A new propulsion system for capsule-type endoscopy and enteroscopy was successfully tested for the first time in man
F0F1‐ATPase from Vibrio alginolyticus Subunit composition and proton pumping activity (1991)

An F0F1-ATPase was isolated from the membranes of the marine bacterium Vibrio alginolyticus. Homology between the subunits of the F0-complexes from E. coli and V. alginolyticus was found using antibodies against subunits a, b and c of the E. coli F0F1-ATPase. The F0F1-complex from V. alginolyticus was reconstituted into proteoliposomes, which were competent in ATP-dependent proton uptake. This process was inhibited by triphenyltin, DCCD, and venturicidin. Na+ did not affect proton translocation.
Dual precursor atmospheric plasma deposition of bilayer organosilicate protective coatings on plastics (2016)

We demonstrate a dual organic and inorganic precursor method to deposit transparent organosilicate protective bilayer coatings on poly methyl methacrylate (PMMA) substrates with atmospheric plasma deposition in ambient air. The bottom layer was a hybrid organosilicate adhesive layer deposited with dual organic 1, 5-cyclooctadiene (CYC) and Tetraethoxysiline (TEOS) precursors. The selection of the organic CYC precursor allowed incorporation of carbon chain in the organosilicate adhesive layer, which resulted in improved adhesion. The top layer was a dense silica coating with high Young's modulus and hardness deposited with TEOS. The deposited bilayer structure showed ∼100% transparency in the visible light wavelength region, twice the adhesion energy and five times the Young's modulus of commercial polysiloxane sol-gel coatings.
The Impact of Intentionally Added Water to the Electrolyte of Li-Ion Cells (2013)

Wound prismatic LiCoO2/Li4Ti5O12 cells with 1 M LiPF6 in ethylene carbonate (EC):ethyl methyl carbonate (EMC) (3:7 by wt) baseline electrolyte had water intentionally added to the electrolyte and were studied using the High Precision Charger at Dalhousie University, automated cycling/storage, AC impedance and extended cycling. Water was added at 200, 1000 and 2000 ppm to the control electrolyte. The control cells have been shown by the manufacturer to cycle for over four years with only about 1% capacity loss in on-going tests. Swelling during the formation cycle increased gradually when 200 and 1000 ppm water was added and substantially when 2000 ppm water was added. A corresponding increase in first cycle irreversible capacity with increasing water content was observed. Adding up to 2000 ppm water resulted in minimal change to measured coulombic efficiency, charge end point slippage, voltage drop during storage and average charge voltage increase. In fact, most measured parameters were slightly improved with the addition of up to 1000 ppm water compared to control. Measured cell impedance was reduced compared to control cells for all cells containing water. There was no detrimental effect on capacity retention due to the added water for cells tested for 400 charge-discharge cycles. At these relatively low loading levels of water in the electrolyte there were no obvious detrimental effects to cell performance and therefore it may be possible to relax water content specifications in Li-ion battery electrolyte leading to one avenue for cost reduction.
Characterization of a transposon Tn916-generated mutant of Haemophilus ducreyi 35000 defective in lipooligosaccharide biosynthesis (1997)

To define the role of the surface lipooligosaccharide (LOS) of Haemophilus ducreyi in the pathogenesis of chancroid, Tn916 mutants of H. ducreyi 35000 defective in expression of the murine monoclonal antibody (MAb) 3F11 epitope on H. ducreyi LOS were identified by immunologic screening. One mutant, designated 1381, has an LOS which lacks the MAb 3F11 epitope and migrates with an increased mobility on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The gene disrupted by the Tn916 element in strain 1381 was identified by cloning the sequences flanking the Tn916 element. The sequences were then used to probe a lambda DASHII genomic library. In strain 1381, Tn916 interrupts a gene which encodes an open reading frame (ORF) with an Mr of 40,246. This ORF has homology to the product of the rfaK gene of Escherichia coli. The major LOS glycoform produced by strain 1381 was analyzed by using a combination of mass spectrometry, linkage and composition analysis, and 1H nuclear magnetic resonance spectroscopy. The major LOS species was found to terminate in a single glucose attached to the heptose (L-glycero-D-manno-heptose, or Hep) trisaccharide core. In the wild-type strain 35000, glucose serves as the acceptor for the addition of the D-glycero-D-manno-heptose (or DDHep), which extends to form the mature branch of the H. ducreyi LOS. This mature oligosaccharide is in turn partially capped by the addition of sialic acid (NeuAc), i.e., NeuAc2 alpha-->3Gal beta1-->4GlcNAc beta1-->3Gal beta1-->4DDHep alpha1-->6Glc beta1 (W. Melaugh et al., Biochemistry 33:13070-13078, 1994). Since this LOS terminates prior to the addition of the branch DD-heptose, this gene is likely to encode the D-glycero-D-manno-heptosyltransferase. Strain 1381 exhibits a significant reduction in adherence to and invasion of primary human keratinocytes. This defect was complemented by the cloned heptosyltransferase gene, indicating that the terminal portion of the LOS oligosaccharide plays an important role in adherence to human keratinocytes.
Surface modes and loss in air-core photonic bandgap fibers (2003)

We briefly review recent progress in the fabrication and characterization of air-core photonic band-gap fibers. These are silica fibers with an hexagonal array of air holes in the cladding, and a larger air hole creating the core. Improved structural uniformity transverse to the fiber axis and down the fiber axis has yielded fibers with better transmission characteristics. We have measured a minimum loss of 13 dB/km at 1500 nm for a 100 m length of our fiber. This is a marked improvement over previous loss measurements for air-core fibers of any kind. A comparison of observed spectra and calculated gap modes suggests that coupling between surface modes and core modes may be an important contributor to the remaining loss. We present a detailed analysis of the expected losses associated with mode crossings between the fundamental core mode and surface modes, showing that Lorentzian-shaped loss peaks are predicted.
TH-E-AUD-02: Dosimetry Studies of GeneSeed Therapy (2007)

Purpose: Interstitially delivered gene therapy using GeneSeeds (small metallic containers similar in size to brachytherapy sources) may have many valuable properties for cancer treatment. We are currently pursuing both simulation and experimental work to more fully understand the dosimetry properties of GeneSeeds and their potential use as both a direct tumoricidal agent and a co-therapy for enhancing tumor radiation sensitivity. Method and Materials: Simulated GeneSeed dosimetry was based on modeling of the diffusion process using the physical properties of the GeneSeed and its potential biochemical payloads. Experimental data was drawn from pathology and immunohistochemistry performed on sectional slices of mouse xenograft tumors into which single GeneSeeds had been implanted. These data were combined into a computational model (implemented in Matlab) which computes the dose as a function of distance and orientation from the GeneSeed using cylindrical coordinates. We have also developed an interface for placing multiple GeneSeeds in a 3-D space and computing their overall effect on a regular Cartesian coordinate grid, to facilitate integration with conventional treatment planning systems. Results: GeneSeed dosimetry differs from conventional brachytherapy dosimetry by having a sigmoidally-shaped falloff as opposed to an exponential falloff. This implies that positioning of the GeneSeeds may require a higher level of precision than what is expected for conventional brachytherapy with radioactive sources. However, homogeneous coverage of larger regions can still be achieved using controlled inter-seed spacing. Image guided robotics may be of assistance in achieving the level of precision needed for this application. Conclusion: We have developed dosimetry models for single GeneSeeds based on a combination of experimental and simulation data. These models can be used to predict overall dosimetry of a larger distribution of GeneSeeds, similar to calculations for groups of brachytherapy seeds. GeneSeeds may have potential use in many organ targets.
Towards a generic model of intelligent networks and services (2007)

The next generation of intelligent networks will provide non-conventional information processing, retrieval and transfer services for the user in a transparent way. The structure and services of large networks are dynamically changing because of modifications and failures, with static or dynamic task allocation over inhomogeneous or homogeneous resource types, leading to n-dimensional demand driven network structure model. The processing nodes of the network may use any mix of the four basic information processing models: control driven, data driven, demand driven and information driven models. A knowledge based generic model is presented for such a system, having logical, temporal and topological structures together with operations on these structures. The necessary mathematical concepts are parameterised hierarchical relations, logic functions, hierarchies of variables with their hierarchical control operators, and neighbourhood/similarity structures. Introducing a model time as a partial ordered set of time instants, an evolutionary system can be considered, both its capabilities and its active structure. For the operating system the mobile agent paradigm is proposed. The main goal of the model is to provide a theoretically sound base for the development of particular design models for various problem classes.
Seven-Core Fiber with Enlarged Aeff and Full-C-band Seven-Core EDFA for 100-Tbit/s-Class Transoceanic Transmission (2013)

We report fabrication of a 45.5-km seven-core fiber with enlarged Aeff and a high-power seven-core EDFA with 5-THz bandwidth. Using them, we confirmed the feasibility of 100-Tbit/s-class transoceanic transmission.