gebhart/patrepeval huggingface dataset:
Ordered and Dynamic Assembly of Single Spliceosomes (2011)

The spliceosome is the complex macromolecular machine responsible for removing introns from precursors to messenger RNAs (pre-mRNAs). We combined yeast genetic engineering, chemical biology, and multiwavelength fluorescence microscopy to follow assembly of single spliceosomes in real time in whole-cell extracts. We find that individual spliceosomal subcomplexes associate with pre-mRNA sequentially via an ordered pathway to yield functional spliceosomes and that association of every subcomplex is reversible. Further, early subcomplex binding events do not fully commit a pre-mRNA to splicing; rather, commitment increases as assembly proceeds. These findings have important implications for the regulation of alternative splicing. This experimental strategy should prove widely useful for mechanistic analysis of other macromolecular machines in environments approaching the complexity of living cells.
Eddy-current-based contactless speed sensing of conductive surfaces (2016)

Contactless speed sensors are used in a broad area of applications in various industries such as machining, assembly lines and transportation. Commonly used technologies are based on optics (e.g. cameras, encoders), or electromagnetic effects (e.g. variable reluctance sensors, Hall sensors). However, these sensors require a non-uniform property of the moving target that can be detected. For example, variable reluctance sensors rely on the variation of the air gap, and Hall sensors require a magnetic field whose spatial distribution is dependent on the position of the mover. A clear disadvantage of all these systems is the fact that they require modifications on the target's geometry and/or magnetic properties, since they cannot measure the speed of a smooth body/surface. Moreover, some of them are sensitive to environmental conditions; e.g. dirt in case of optical encoders and high temperature in case of permanent magnets can render these systems ineffective. Therefore, an eddy-current-based contactless speed sensor is developed in this work for measuring the speed of smooth, electrically conductive surfaces in harsh operating conditions. An injection coil is used to induce eddy currents in the mover whose speed is to be detected, and two differentially wound pick-up coils are used to detect the speed-dependent deformation of the eddy-current field. Two-dimensional finite-element method (2-D FEM) is used for modeling the system and optimizing the sensor geometry as well as the injection frequency. Measurements taken from a prototype verify the validity of the design procedure and the analyzed speed-sensing concept.
Highly Site Specific, Protease Cleavable, Hydrophobic Peptide–Polymer Nanoparticles (2011)

Here we present the synthesis of site specific, protease (trypsin) cleavable, hydrophobic peptide–polymer conjugate nanoparticles in inverse miniemulsion. Different peptide sequences were synthesized by microwave-assisted solid-phase synthesis and characterized by HPLC, NMR, and MALDI-TOF MS. The peptides were used to cross-link a hydrophobic functional polymer with standard peptide-coupling chemistry in inverse miniemulsion, thus generating the desired nanoparticulate morphology. By these means, well-defined nanoparticles in the size range of 200–300 nm were obtained. After transferring the particles into aqueous medium, they were characterized with photon cross-correlation spectroscopy (PCCS) and scanning electron microscopy (SEM). After removal of the solvent, the degree of cross-linking was determined by 15N solid-state NMR. Integration of a fluorophore/quencher system, based on fluorescence resonance energy transfer (FRET) in the peptide sequences, enabled the monitoring of site specific recognition of cross-linked polymeric nanostructures by enzymes, resulting in a fluorescence recovery upon cleavage of the peptide.
Artificial Sensing Intelligence with Silicon Nanowires for Ultraselective Detection in the Gas Phase (2014)

The use of molecularly modified Si nanowire field effect transistors (SiNW FETs) for selective detection in the liquid phase has been successfully demonstrated. In contrast, selective detection of chemical species in the gas phase has been rather limited. In this paper, we show that the application of artificial intelligence on deliberately controlled SiNW FET device parameters can provide high selectivity toward specific volatile organic compounds (VOCs). The obtained selectivity allows identifying VOCs in both single-component and multicomponent environments as well as estimating the constituent VOC concentrations. The effect of the structural properties (functional group and/or chain length) of the molecular modifications on the accuracy of VOC detection is presented and discussed. The reported results have the potential to serve as a launching pad for the use of SiNW FET sensors in real-world counteracting conditions and/or applications.
HIGH DENSITY AND HIGH BANDWIDTH CHIP-TO-CHIP CONNECTIONS WITH 20μm PITCH FLIP-CHIP ON FAN-OUT WAFER LEVEL PACKAGE (2018)

Various Fan-Out Wafer Level Packaging (FO-WLP) approaches have been developed and established over the past years to answer the increasing need for high data rates, wide I/O count and the demand for increase function integration on package. Imec has been working on a novel 300mm FO-WLP concept that enables 20μm pitch interconnect density: FlipChip on FO-WLP. Major challenges and solutions are reported in this paper. Results demonstrate die placement alignment of <;3μm, which is suitable to allow stacking for high density interconnect. Connections between the assembled dies were intact before and after molding.
<title>Single-shot measurement of duration and contrast of high-power picosecond pulses</title> (1990)

Measurement of the characteristics of high energy, high peak power laser pulses for plasma physics experiments requires detection of prepulses of intensity <i06 of the main pulse, in addition to accurate determination of the pulse duration. We describe a single shot, third order autocorrelator that is capable of measuring these prepulses, as well as showing their location.
A single amino acid substitution in HLA-A2 can alter the selection of the cytotoxic T lymphocyte repertoire that responds to influenza virus matrix peptide 55-73. (1989)

Previous studies have demonstrated that certain amino acid substitutions in the alpha two domain at positions 152 and 156 in the alpha two helix of the HLA-A2 molecule can affect presentation of the influenza virus matrix peptide M1 55-73 without abolishing binding of the M1 peptide. HLA-A2.1-restricted M1 55-73 peptide-specific CTL lines obtained from almost all HLA-A2.1+ individuals fail to recognize the M1 peptide presented by site-directed mutants of HLA-A2 that have either a Val----Ala or Val----Gln substitution at position 152 or a Leu----Trp substitution at position 156. Only one HLA-A2+ individual (donor Q66, HLA-A2,-B53,-B63) has been found who is able to generate a unique repertoire of HLA-A2-restricted M1 peptide-specific CTL that can recognize peptide presented by HLA-A2 mutants with either an Ala or Gln substitution at position 152 or a Trp substitution at position 156. These Q66 M1 peptide-specific CTL could be selected by stimulation with M1 peptide-pulsed transfectants that express the mutant HLA-A2 gene with the Trp substitution at 156. To determine if the presence of the unique CTL repertoire could be attributed to a variant HLA-A2 molecule in Q66, sequences were determined from polymerase chain reaction-amplified segments of the HLA-A2 RNA. Two different HLA-A2 genes were found expressed in Q66 cells: one is identical to HLA-A2.1 and the other is identical to HLA-A2.2F (Gln----Arg at position 43, Val----Leu at position 95, and Leu----Trp at position 156). These results demonstrate that a different CTL repertoire specific for HLA-A2 plus the M1 55-73 peptide is generated in an individual that expresses both HLA-A2.1 and HLA-A2.2F compared to individuals who express HLA-A2.1 alone, and that the unique repertoire can be selected by the presence of an HLA-A2 molecule with a single amino acid substitution at position 156.
Cystinosis in the Federal Republic of Germany. Coordination and analysis of the data (1983)

In our survey, 101 infants and children with cystinosis were registered in the Federal Republic of Germany. Ninety-five patients showed the infantile type of cystinosis, five the adolescent type and one possibly the adult type. The minimum incidence rate of infantile and adolescent cystinosis in the FRG was 1 patient per 179 000 live-births. In contrast to other countries, cystinotic patients were evenly distributed in the FRG. Patients with cystinosis originated more frequently from rural communities than from large cities. Before 1968 most patients died before reaching terminal renal failure, usually due to uncontrolled disturbances of water and electrolyte metabolism. Since 1976 the causes of death other than uraemia have been rare and most patients with terminal renal failure have entered a renal replacement program.
Synthesis of Highly Substituted 2,6‐anti‐Configured Tetrahydropyrans. First Steps Towards an Efficient Access to the Amphidinol 3 Ring System. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Towards Automatic Musical Instrument Timbre Recognition (2010)

This dissertation is comprised of two parts—focus on issues concerning research and development of an artificial system for automatic musical instrument timbre recognition and musical compositions. The technical part of the essay includes a detailed record of developed and implemented algorithms for feature extraction and pattern recognition. A review of existing literature introducing historical aspects surrounding timbre research, problems associated with a number of timbre definitions, and highlights of selected research activities that have had significant impact in this field are also included. The developed timbre recognition system follows a bottom-up, data-driven model that includes a pre-processing module, feature extraction module, and a RBF/EBF (Radial/Elliptical Basis Function) neural network-based pattern recognition module. 829 monophonic samples from 12 instruments have been chosen from the Peter Siedlaczek library (Best Service) and other samples from the Internet and personal collections. Significant emphasis has been put on feature extraction development and testing to achieve robust and consistent feature vectors that are eventually passed to the neural network module. In order to avoid a garbage-in-garbage-out (GIGO) trap and improve generality, extra care was taken in designing and testing the developed algorithms using various dynamics, different playing techniques, and a variety of pitches for each instrument with inclusion of attack and steady-state portions of a signal. Most of the research and development was conducted in Matlab. The compositional part of the essay includes brief introductions to “A d'Ess Are ,” “Aboji,” “48 13 N, 16 20 O,” and “pH-SQ.” A general outline pertaining to the ideas and concepts behind the architectural designs of the pieces including formal structures, time structures, orchestration methods, and pitch structures are also presented.
An error analysis of Helmholtz inversion for incompressible shear, vibration elastography with application to filter-design for tissue characterization (2002)

For over fifteen years there has been significant effort in elastography, which describes the general area of imaging material mechanical properties. Shear vibration elastography uses dynamic tissue displacements to infer material properties from the physics of motion. The method can be used with both magnetic resonance and ultrasound data, which can both be modeled with the time-harmonic, Helmholtz equation if the material is linear, isotropic, incompressible, and piecewise-homogeneous. In this work, we develop a unified perspective on direct Helmholtz inversion. Using the fundamental theorem of statistics and a Gaussian noise model, we present a closed form for the joint conditional probability distribution of the real and imaginary parts of the squared wavenumber given the data and an arbitrary set of weights. An approximate distribution can be used in the case of high SNR which allows a figure-of-merit to be established to objectively compare inversion approaches. Adaptively choosing the inversion weights for each subregion as the smoothed and windowed conjugate of the data results in a narrow conditional probability distribution function and, consequently, high-quality estimates of complex shear modulus. To test the results, we used experimental ultrasound data-collected using a focused 5 MHz transducer with a pulse-repetition frequency of 4 kHz in a block of 15% bovine gel. The gel was harmonically compressed using a signal containing equal amplitudes at frequencies of 200, 300, 400 and 500 Hz. Noise on the measured displacement was estimated from the magnitude of the complex (baseband) correlation function and used with the conditional probability distribution function to report error bars on single-region estimates of complex shear modulus, wave-speed and attenuation.
Session Description Protocol (SDP) Offer/Answer Procedures for Interactive Connectivity Establishment (ICE) (2021)

This document describes Session Description Protocol (SDP) Offer/
Answer procedures for carrying out Interactive Connectivity
Establishment (ICE) between the agents. This document obsoletes RFC
5245.
Supplementary Figure S1 from Broadening Specificity and Enhancing Cytotoxicity of Adoptive T Cells for Nasopharyngeal Carcinoma Immunotherapy (2023)

&lt;p&gt;Supplementary figure describing the generation of C666.1 NPC cell line stably espressing HLA-A02 and the induction of immunogenic cell death in LCLs derived from NPC patients.&lt;/p&gt;
Next generation optical fiber sensing technology (2022)

We discuss the advantages of phase sensitive distributed fiber sensing techniques enabled by a new generation of optical fibers that exhibit enhanced backscattering.
Diffusion curves (2008)

We describe a new vector-based primitive for creating smooth-shaded images, called the diffusion curve. A diffusion curve partitions the space through which it is drawn, defining different colors on either side. These colors may vary smoothly along the curve. In addition, the sharpness of the color transition from one side of the curve to the other can be controlled. Given a set of diffusion curves, the final image is constructed by solving a Poisson equation whose constraints are specified by the set of gradients across all diffusion curves. Like all vector-based primitives, diffusion curves conveniently support a variety of operations, including geometry-based editing, keyframe animation, and ready stylization. Moreover, their representation is compact and inherently resolution-independent. We describe a GPU-based implementation for rendering images defined by a set of diffusion curves in realtime. We then demonstrate an interactive drawing system for allowing artists to create artworks using diffusion curves, either by drawing the curves in a freehand style, or by tracing existing imagery. The system is simple and intuitive: we show results created by artists after just a few minutes of instruction. Furthermore, we describe a completely automatic conversion process for taking an image and turning it into a set of diffusion curves that closely approximate the original image content.
Hierarchical Gaussian Process Models for Improved Metamodeling (2020)

Simulations are often used for the design of complex systems as they allow one to explore the design space without the need to build several prototypes. Over the years, the simulation accuracy, as well as the associated computational cost, has increased significantly, limiting the overall number of simulations during the design process. Therefore, metamodeling aims to approximate the simulation response with a cheap to evaluate mathematical approximation, learned from a limited set of simulator evaluations. Kernel-based methods using stationary kernels are nowadays widely used. In many problems, the smoothness of the function varies in space, which we call nonstationary behavior [20]. However, using stationary kernels for nonstationary responses can be inappropriate and result in poor models when combined with sequential design. We present the application of two recent techniques: Deep Gaussian Processes and Gaussian Processes with nonstationary kernel, which are better able to cope with these difficulties. We evaluate the method for nonstationary regression on a series of real-world problems, showing that these recent approaches outperform the standard Gaussian Processes with stationary kernels. Results show that these techniques are suitable for the simulation community, and we outline the variational inference method for the Gaussian Process with nonstationary kernel.
Helix-Forming Carbohydrate Amino Acids (2005)

[reaction: see text] The solution-phase conformational properties of tetrameric and octameric chains of C-glycosyl alpha-d-lyxofuranose configured tetrahydrofuran amino acids (where the C-2 and C-5 substituents on the tetrahydrofuran ring are trans to each other) were examined using NMR and IR and CD in organic solvents. Studies by NMR and IR demonstrated that in chloroform solution, the tetramer 7 does not adopt a hydrogen-bonded conformation whereas the octamer 10 populates a well-defined helical secondary structure stabilized by 16-membered (i, i - 3) interresidue hydrogen bonds, similar to a pi-helix. Circular dichroism studies in trifluoroethanol are consistent with this conformation for the octamer 10, and also indicate that the tetramer 7 adopts a rigid conformation not stabilized by hydrogen bonds.
#371 RP34 (1999)

Gauger, C.; Jackson, D.; Gaillard, J. P.; Frazer, K.; Banchereau, J.; Pascual, V. Author Information
Interferenceless Coded Aperture Correlation Holography – A Way to Record Incoherent Digital Holograms from a Single Viewpoint without Wave Interference (2017)

An incoherent digital holography technique without two-wave interference is developed based on coded aperture correlation holography. The technique is used for recording and reconstructing 3D information of objects. The reconstruction results are compared with regular imaging.
Robust Decoupling Techniques to Extend Quantum Coherence in Diamond (2010)

We experimentally demonstrate over 2 orders of magnitude increase in the room-temperature coherence time of nitrogen-vacancy centers in diamond by implementing decoupling techniques. We show that equal pulse spacing decoupling performs just as well as nonperiodic Uhrig decoupling and also allows us to take advantage of revivals in the echo to explore the longest coherence times. At short times, we can extend the coherence of particular quantum states out from T2*=2.7 μs out to an effective T2>340 μs. For preserving arbitrary states we show the experimental importance of using pulse sequences that compensate the imperfections of individual pulses for all input states through judicious choice of the phase of the pulses. We use these compensated sequences to enhance the echo revivals and show a coherence time of over 1.6 ms in ultrapure natural abundance 13C diamond.
Isolated CD39 Expression on CD4+ T Cells Denotes both Regulatory and Memory Populations (2009)

Foxp3(+) regulatory T cells (Tregs) express both ectoenzymes CD39 and CD73, which in tandem hydrolyze pericellular ATP into adenosine, an immunoinhibitory molecule that contributes to Treg suppressive function. Using Foxp3GFP knockin mice, we noted that the mouse CD4(+)CD39(+) T-cell pool contains two roughly equal size Foxp3(+) and Foxp3(-) populations. While Foxp3(+)CD39(+) cells are CD73(bright) and are the bone fide Tregs, Foxp3(-)CD39(+) cells do not have suppressive activity and are CD44(+)CD62L(-)CD25(-)CD73(dim/-), exhibiting memory cell phenotype. Functionally, CD39 expression on memory and Treg cells confers protection against ATP-induced apoptosis. Compared with Foxp3(-)CD39(-) naïve T cells, Foxp3(-)CD39(+) cells freshly isolated from non-immunized mice express at rest significantly higher levels of mRNA for T-helper lineage-specific cytokines IFN-gamma (Th1), IL-4/IL-10 (Th2), IL-17A/F (Th17), as well as pro-inflammatory cytokines, and rapidly secrete these cytokines upon stimulation. Moreover, the presence of Foxp3(-)CD39(+) cells inhibits TGF-beta induction of Foxp3 in Foxp3(-)CD39(-) cells. Furthermore, when transferred in vivo, Foxp3(-)CD39(+) cells rejected MHC-mismatched skin allografts in a much faster tempo than Foxp3(-)CD39(-) cells. Thus, besides Tregs, CD39 is also expressed on pre-existing memory T cells of Th1-, Th2- and Th17-types with heightened alloreactivity.
TRECVID 2003 Experiments at Media Team Oulu and VTT. (2003)

) discard umlauts MediaTeam Oulu and VTT Technical Research Centre of Finland participated jointly in semantic feature extraction, manual search and interactive search tasks of TRECVID 2003. We participated to the semantic feature extraction by submitting results to 15 out of the 17 defined semantic categories. Our approach utilized spatio-temporal visual features based on correlations of quantized gradient edges and color values together with several physical features from the audio signal. Most recent version of our Video Browsing and Retrieval System (VIRE) contains an interactive cluster-temporal browser of video shots exploiting three semantic levels of similarity: visual, conceptual and lexical. The informativeness of the browser was enhanced by incorporating automatic speech transcription texts into the visual views based on shot key frames. The experimental results for interactive search task were obtained by conducting a user experiment of eight people with two system configurations: browsing by (I) visual features only (visual and conceptual browsing was allowed, no browsing with ASR text) or (II) visual features and ASR text (all semantic browsing levels were available and ASR-text content was visible). The interactive results using ASR-based features were better than the results using only visual features. This indicates the importance of successful integration of both visual and textual features for video browsing. In contrast to previous version of VIRE which performed early feature fusion by training unsupervised self-organizing maps, newest version capitalises on late fusion of features queries, which was evaluated in manual search task. This paper gives an overview of the developed system and summarises the results. 1
Bacterial Imprinting of the Neonatal Immune System: Lessons From Maternal Cells? (2007)

Bacterial translocation is a unique physiologic event, which is increased during pregnancy and lactation in rodents. Human breast milk cells contain a limited number of viable bacteria but a range of bacterial DNA signatures, as also found in maternal peripheral blood mononuclear cells. Those peripheral blood mononuclear cells showed greater biodiversity than did peripheral blood mononuclear cells from control women. Taken together, our results suggest that intestinally derived bacterial components are transported to the lactating breast within mononuclear cells. We speculate that this programs the neonatal immune system to recognize specific bacterial molecular patterns and to respond appropriately to pathogens and commensal organisms.