gebhart/patrepeval huggingface dataset:
A sequence-specific, single-strand binding protein activates the far upstream element of c-myc and defines a new DNA-binding motif. (1994)

The far upstream element (FUSE) of the human c-myc proto-oncogene stimulates expression in undifferentiated cells. A FUSE-binding protein (FBP) is present in undifferentiated but not differentiated cells. Peptide sequences from the purified protein allowed cloning of cDNAs encoding FBP. Expression of FBP mRNA declined upon differentiation, suggesting transcriptional regulation of FBP. Features in the FBP cDNA suggest that FBP is also regulated by RNA processing, translation, and post-translational mechanisms. Both cellular and recombinant FBP form sequence-specific complexes with a single strand of FUSE. Transfection of FBP into human leukemia cells stimulated c-myc-promoter-driven expression from a reporter plasmid in a FUSE-dependent manner. Deletion and insertion mutagenesis of FBP defined a novel single-strand DNA-binding domain. Analysis of the primary and predicted secondary structure of the amino acid sequence reveals four copies of a reiterated unit comprised of a 30-residue direct repeat and an amphipathic alpha-helix separated by an 18- to 21-residue spacer. The third and fourth copies of this repeat-helix unit constitute the minimum single-stranded DNA-binding domain. To determine whether the FUSE site, in vivo, possesses single-strand conformation, and therefore could be bound by FBP, cells were treated with potassium permanganate (KMnO4) to modify unpaired bases. Modification of genomic DNA in vivo revealed hyperreactivity associated with single-stranded DNA in the FUSE sequence and protection on the strand that binds FBP in vitro. The role of single-stranded DNA and single-strand binding proteins in c-myc regulation is discussed.
A wireless intraocular pressure monitoring device with a solder-filled microchannel antenna (2014)

This paper presents the prototype of an intraocular pressure sensor as a major step toward building a device that can be permanently implanted during cataract surgery. The implantation will proceed through an incision of 2–3 mm using an injector, during which the complete device must be folded into a cross-section of 2 mm × 1 mm. The device uses radio frequency (RF) for wireless power and data transfer. The prototype includes an antenna, an RF chip and a pressure sensor assembled on a printed circuit board with several circuit components used for testing and calibration. The antenna is fabricated and integrated with the circuit using a fabrication method employing solder-filled microchannels embedded in an elastomer. The monitoring device is powered at 2.716 GHz from a distance of 1–2 cm. The prototype has undergone electrical and mechanical tests for antenna and sensor performance. The flexible antenna can withstand a stress of 33.4 kPa without any electrical disconnection. It did not show a significant increase in electrical resistance after 50 bending cycles with a maximum applied stress of 116 kPa. Transmitted pressure data shows an averaged sensitivity of 16.66 Hz (mm-Hg)–1.
<title>Navigation through fog using stereoscopic active imaging</title> (2000)

Navigation, especially in aviation, has been plagued since its inception with the hazards of poor visibility conditions. Our ground vehicles and soldiers have difficulty moving at night or in low visibility even with night vision augmentation because of the lack of contrast and depth perception. Trying to land an aircraft in fog is more difficult yet, even with radar tracking. The visible and near-infrared spectral regions have been ignored because of the problem with backscattered radiation from landing light illumination similar to that experienced when using high beam headlights when driving in fog. This paper describes the experimentation related to the development of a visible/near-infrared active hyperstereo vision system for landing an aircraft in fog. Hyperstereo vision is a binocular system with baseline separation wider than the human interocular spacing. The basic concept is to compare the imagery obtained from alternate wings of the aircraft while illuminating only from the opposite wing. This produces images with a backscatter radiation pattern that has a decreasing gradient away from the side with the illumination source. Flipping the imagery from one wing left to right and comparing it to the opposite wing imagery allows the backscattered radiation pattern to be subtracted from both sets of imagery. The use of retro-reflectors along the sides of the runway allows the human stereo fusion process to fuse the forward scatter blurred hyperstereo imagery of the array of retro-reflectors while minimizing backscatter. The appropriate amount of inverse point spread function deblurring is applied for improved resolution of scene content to aid in detection of objects on the runway. The experimental system is described and preliminary results are presented to illustrate the concept.
Video Compressive Sensing for Spatial Multiplexing Cameras using Motion-Flow Models (2015)

Spatial multiplexing cameras (SMCs) acquire a (typically static) scene through a series of coded projections using a spatial light modulator (e.g., a digital micro-mirror device) and a few optical sensors. This approach finds use in imaging applications where full-frame sensors are either too expensive (e.g., for short-wave infrared wavelengths) or unavailable. Existing SMC systems reconstruct static scenes using techniques from compressive sensing (CS). For videos, however, existing acquisition and recovery methods deliver poor quality. In this paper, we propose the CS multi-scale video (CS-MUVI) sensing and recovery framework for high-quality video acquisition and recovery using SMCs. Our framework features novel sensing matrices that enable the efficient computation of a low-resolution video preview, while enabling high-resolution video recovery using convex optimization. To further improve the quality of the reconstructed videos, we extract optical-flow estimates from the low-resolution previews and impose them as constraints in the recovery procedure. We demonstrate the efficacy of our CS-MUVI framework for a host of synthetic and real measured SMC video data, and we show that high-quality videos can be recovered at roughly $60\times$ compression.
Density-based indexing for approximate nearest-neighbor queries (1999)

We consider the problem of performing Nearest-neighbor queries efficiently over large high-dimensional databases. To avoid a full database scan, we target constructing a multidimensional index structure. It is well-accepted that traditional database indexing algorithms fail for high-dimensional data (say d > 10 or 20 depending on the scheme). Some arguments have advocated that nearest-neighbor queries do not even make sense for high-dimensional data. We show that these arguments are based on over-restrictive assumptions, and that in the general case it is meaningful and possible to build an index for such queries. Our approach, called DBIN, scales to high-dimensional databases by exploiting statistical properties of the data. The approach is based on statistically modeling the density of the content of the data table. DBIN uses the density model to derive a single index over the data table and requires physically rewriting data in a new table sorted by the newly created index (i.e. create a clustered-index).
Control of Morbillivirus replication by RNAi (2007)

The Morbillivirus genus includes measles virus (MV), peste des petits ruminants virus (PPRV) and rinderpest virus (RPV). Although preventive vaccines are available against these three viruses, efficient therapeutics for virus control under emergency situations are desirable. Inhibition of morbillivirus replication can be achieved by post-transcriptional silencing of the nucleoprotein (N) gene by RNA interference (RNAi). The viral N protein, a well conserved protein among the genus, plays a central role in the replication of the virus. Using a comprehensive siRNA-based screening of the conserved sequences of the N gene, we have identified, three common positions on the N gene, for the design of siRNA evenly effectives for PPRV, RPV and MV. siRNA silencing resulted in more than 80% decrease of the viral replication in infected Vero cell, as shown by real-time quantitative PCR, flow cytometry and virus titration. In a second step, a recombinant replication-defective human type 5 adenovirus (Ad-5) encoding one of the functional sequences directed against the N gene of PPRV was constructed and shown to reduce the PPRV replication in vitro. These results illustrate that adenovirus vector could be a promising candidate for the development of siRNA antiviral treatments against morbilliviruses.
Competition between ions in size exclusion chromatography of electrolytes on neutral microporous materials (2005)

Competition between hydrated ions for accessible porous space within particles of non-functionalised microporous sorbents (hypercrosslinked polystyrene or microporous carbonaceous materials) in the size exclusion chromatography of concentrated solutions of mineral electrolytes results in the enhancing of both the selectivity of separation and the self-concentrating effect of resolved components.
Congestion control for multimedia services (1992)

The problem of congestion control in high-speed networks for multimedia traffic, such as voice and video, is considered. It is shown that the performance requirements of high-speed networks involve delay, delay-jitter, and packet loss. A framing congestion control strategy based on a packet admission policy at the edges of the network and on a service discipline called stop-and-go queuing at the switching nodes is described. This strategy provides bounded end-to-end delay and a small and controllable delay-jitter. The strategy is applicable to packet switching networks in general, including fixed cell length asynchronous transfer mode (ATM), as well as networks with variable-size packets.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Polyoxometalates in the Design of Effective and Tunable Water Oxidation Catalysts (2011)

Abstract Water oxidation catalysts (WOCs) are of core importance in several green energy production technologies, including water splitting and water reduction of CO 2 driven by electrochemical potential and/or photons (radiant energy). General challenges in solar fuel generating structures, WOC design concepts, and some success‐limiting considerations in WOC development are described. The first class of WOCs are presented that combine the stability benefits of heterogeneous WOCs with the reactivity and other benefits of homogeneous WOCs.
Enantioselective Epoxide Polymerization Using a Bimetallic Cobalt Catalyst (2010)

A highly active enantiopure bimetallic cobalt complex was explored for the enantioselective polymerization of a variety of monosubstituted epoxides. The polymerizations were optimized for high rates and stereoselectivity, with s-factors (k(fast)/k(slow)) for most epoxides exceeding 50 and some exceeding 300, well above the threshold for preparative utility of enantiopure epoxides and isotactic polyethers. Values for mm triads of the resulting polymers are typically greater than 95%, with some even surpassing 98%. In addition, the use of a racemic catalyst allowed the preparation of isotactic polyethers in quantitative yields. The thermal properties of these isotactic polyethers are presented, with many polymers exhibiting high T(m) values. This is the first report of the rapid synthesis of a broad range of highly isotactic polyethers via the enantioselective polymerization of racemic epoxides.
327. Muscle Specific and Efficient Transgene Expression Using the Fast and Slow Troponin I Promoters in Cell Culture (2006)

Gene replacement therapy for muscular diseases, such as Duchenne muscular dystrophy, using viral vectors requires strong promoters with the ability to confer muscle specific expression of the therapeutic gene product. Because skeletal muscle consists of a mixture of slow and fast muscle fibers, an ideal promoter for such application should direct efficient expression in both muscle fiber types. The genetic elements regulating expression of the fast and slow isoforms of troponin I (TnI), an abundant muscle protein, are relatively well characterized. Theoretically, a combination of vectors expressing transgenes regulated by TnIfast and TnIslow enhancers/promoters could be used to deliver strong and muscle specific transgene expression in every skeletal muscle fiber of the body. To evaluate the usefulness of the TnIfast and TnIslow enhancers/promoters for gene therapy, we have compared their strengths with the cytomegalovirus (CMV) and with the short (1.3-kb) murine muscle creatine kinase (MCK) promoters in cell culture. Plasmids expressing β-galactosidase (β-gal) regulated by MCK, CMV or TnIfast/TnIslow enhancers/promoters were constructed. The TnIfast construct includes the minimal promoter (200-bp) of the quail TnIfast gene linked to three copies (150-bp each) of that gene’s first-intron enhancer element (IRE). The TnIslow construct includes the minimal promoter (100-bp) of the human TnIslow gene linked to that gene’s upstream enhancer element of 160-bp (USE). Except for MCK, a small intron (100-bp) derived from SV40 was inserted between the promoter and β-bal. 293A cells and C2C12 myoblasts were transfected with the different constructs and β-gal expression was compared 48 hrs later. Analyses were also performed in culture of C2C12 myotubes 10 days after serum withdrawal. In 293 cells, MCK-, TnIfast-, and TnIslow-driven expression was at least 1300 folds weaker than CMV. In non-differentiated myoblasts, TnIslow-driven expression was 3.5 and 15 times better than TnIfast- and MCK-driven expression, respectively. Both TnIfast and TnIslow enhancers/promoters provided high-level β- gal expression in myotubes (35-40 % of CMV, and at least 10 times stronger than MCK). Our data confirmed the excellent muscle specificity and strength of TnIfast and TnIslow enhancer/promoter elements. Their relative small size makes them very attractive for usage in vectors with limited insert capacity such as AAV. These excellent properties warrant further in vivo gene transfer studies using viral vectors.
Musicrainbow: A New User Interface To Discover Artists Using Audio-Based Similarity And Web-Based Labeling. (2006)

[TODO] Add abstract here.
Wide-Field Multispectral Super-Resolution Imaging Using Spin-Dependent Fluorescence in Nanodiamonds (2013)

Recent advances in fluorescence microscopy have enabled spatial resolution below the diffraction limit by localizing multiple temporally or spectrally distinguishable fluorophores. Here, we introduce a super-resolution technique that deterministically controls the brightness of uniquely addressable, photostable emitters. We modulate the fluorescence brightness of negatively charged nitrogen-vacancy (NV(-)) centers in nanodiamonds through magnetic resonance techniques. Using a CCD camera, this "deterministic emitter switch microscopy" (DESM) technique enables super-resolution imaging with localization down to 12 nm across a 35 × 35 μm(2) area. DESM is particularly well suited for biological applications such as multispectral particle tracking since fluorescent nanodiamonds are not only cytocompatible but also nonbleaching and bright. We observe fluorescence count rates exceeding 1.5 × 10(6) photons per second from single NV(-) centers at saturation. When combined with emerging NV(-)-based techniques for sensing magnetic and electric fields, DESM opens the door to rapid, super-resolution imaging for tracking and sensing applications in the life and physical sciences.
Large current modulation in novel vertical-type organic transistor using sheet metal base (2006)

High performance vertical-type organic transistors have been fabricated using a simple structure composed of organic/metal/organic layers. The modulated collector current exceeded 300 mA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for application of only several volts of the base voltage.
Synchronization of optical polarization conversion and scattering in chiral optical fibers (2005)

We find that the evolution of an optical polarization along a twisted optical fiber may be spatially synchronized with polarization-selective light scattering. We demonstrate experimentally that linearly polarized light initially oriented along the fast axis of an adiabatically twisted single-mode, polarization-maintaining optical fiber is converted into elliptically and then into circularly polarized light with the same handedness as the chiral structure. As the state of polarization is changing along the length of the fiber, the light is scattered out of the fiber core. By choosing an appropriate twist acceleration profile in custom-made, rectangular-core polarization maintaining fibers, scattering and conversion may be synchronized, allowing the orthogonal polarization to freely propagate through the fiber. When the portion of the fiber with accelerated twist is combined with another fiber segment with decelerated twist, the fiber becomes a broadband, low-insertion-loss, in-fiber, linear polarizer. In this polarizer, the passing component of the incident light oriented along the slow axis, is converted to circularly polarized light of the opposite handedness, and then converted back to linearly polarized light oriented along the same slow axis. While the polarization evolution may be calculated using 1D model of light propagation through a birefringent medium, the calculation of light scattering requires a full 3D calculation.
Novel Reconfigurable Logic Gates Using Spin Metal–Oxide–Semiconductor Field-Effect Transistors (2004)

We propose and numerically simulate novel reconfigurable logic gates employing spin metal-oxide-semiconductor field-effect transistors (spin MOSFETs). The output characteristics of the spin MOSFETs depend on the relative magnetization configuration of the ferromagnetic contacts for the source and drain, that is, high current-drive capability in parallel magnetization and low current-drive capability in antiparallel magnetization [S. Sugahara and M. Tanaka: Appl. Phys. Lett. 84 (2004) 2307]. A reconfigurable NAND/NOR logic gate can be realized by using a spin MOSFET as a driver or an active load of a complimentary MOS (CMOS) inverter with a neuron MOS input stage. Its logic function can be switched by changing the relative magnetization configuration of the ferromagnetic source and drain of the spin MOSFET. A reconfigurable logic gate for all symmetric Boolean functions can be configured using only five CMOS inverters including four spin MOSFETs. The operation of these reconfigurable logic gates was confirmed by numerical simulations using a simple device model for the spin MOSFETs.
Detection of Curvilinear Objects in Noisy Image using Feature-Adapted Beamlet Transform (2007)

This paper addresses the problem of detecting features running along lines or piecewise constant curves. Our method is adapted either for common image features like edges or ridges as well as any kind of features that can be designed by a priori knowledge. The main contribution of this paper is to unify the well-known Beamlet transform, introduced by Donoho et al, with linear filtering technique in order to define what we call the feature-adapted Beamlet transform. If the desired feature is chosen to belong to the class of steerable filters, our method can be achieved in linear time and can be easily implemented on a parallel machine. We present some experimental results both on edge- and ridge-like features that demonstrate the substantial improvement over classical feature detectors.
Anatomical-based segmentation with stenosis bridging and gap closing in atherosclerotic cardiac MSCT (2006)

In the diagnosis of coronary artery disease, 3D-multi-slice computed tomography (MSCT) has recently become more and more important. In this work, an anatomical-based method for the segmentation of atherosclerotic coronary arteries in MSCT is presented. This technique is able to bridge severe stenosis, image artifacts or even full vessel occlusions. Different anatomical structures (aorta, blood-pool of the heart chambers, coronary arteries and their orifices) are detected successively to incorporate anatomical knowledge into the algorithm. The coronary arteries are segmented by a simulated wave propagation method to be able to extract anatomically spatial relations from the result. In order to bridge segmentation breaks caused by stenosis or image artifacts, the spatial location, its anatomical relation and vessel curvature-propagation are taken into account to span a dynamic search space for vessel bridging and gap closing. This allows the prevention of vessel misidentifications and improves segmentation results significantly. The robustness of this method is proven on representative medical data sets.
Bewegingsvolgsysteem = Monitor tracking system (2006)

A motion tracking system for tracking an object composed of object parts in a three-dimensional space. The system comprises a number of magnetic field transmitters; a number of field receivers for receiving the magnetic fields of the field transmitters; a number of inertial measurement units for recording a linear acceleration; a number of angular velocity transducers for recording angular velocities. The system further comprises a processor for controlling the transmitters and receiving signals coming from the field receivers and the inertial measurement unit; which processor contains a module for deriving orientation and/or position information of the constituent object parts of the object on the basis of the received signals. The processor is configured for intermittently controlling the transmitters transmit at a predetermined frequency, wherein the position and/or orientation information is derived by periodically calibrating the motion information coming from the inertial measurement unit with the motion information coming from the magnetic field receivers.