gebhart/patrepeval huggingface dataset:
Performance and Scalability of a Large-Scale N-gram Based Information Retrieval System (2000)

Information retrieval has become more and more important due to the rapid growth of all kinds of information. However, there are few suitable systems available. This paper presents a few approaches that enable large-scale information retrieval for the TELLTALE system. TELLTALE is an information retrieval environment that provides full-text search for text corpora that may be garbled by OCR (optical character recognition) or transmission errors, and that may contain multiple languages. It can find similar documents against a 1 kB query from 1 GB of text data in 45 seconds. This remarkable performance is achieved by integrating new data structures and gamma compression into the TELLTALE framework. This paper also compares several different types of query methods such as tf.idf and incremental similarity to the original technique of centroid subtraction. The new similarity techniques give better performance but less accuracy.
The organization and expression of essential transcription translation component genes in the extremely thermophilic eubacterium Thermotoga maritima (1992)

A 5789-nucleotide-long EcoRI fragment from the genome of Thermotoga maritima, identified by cross-hybridization to L11, L1, L10, and L12 ribosomal protein gene sequences from Escherichia coli, was cloned and sequenced. The fragment encodes five tRNAs (tRNA(met1), anticodon complementary to AUG; tRNA(met2), AUG; tRNA(thr), ACA; tRNA(tyr), UAC; tRNA(trp), UGG), the transcription termination-antitermination factor nusG, the four 50 S subunit ribosomal proteins L11, L1, L10, and L12, and the amino-terminal portion of the RNA polymerase beta subunit protein. The five tRNA genes, the nusG gene, and the L11, L1, L10, and L12 ribosomal protein genes form a complex transcription unit. Transcripts appear to be initiated from an upstream promoter, P1, located in front of the tRNA(met1) gene and from three internal promoters: P2 is located immediately in front of the tRNA(met2) gene; PL10 is near the beginning of the L1-L10 intergenic space, and PL12 is at the end of the L10 gene sequence. The tRNA sequences are excised from the leader regions of the P1- and P2-initiated transcripts. Three putative but potentially important regulatory sequences were identified within this operon: an L1 translational control site, a transcription attenuator, and a strong rho-independent terminator. The strong terminator located distal to the L12 gene overlaps a fifth promoter, P beta, which is used to initiate transcripts of the downstream RNA polymerase beta subunit gene. The T. maritima NusG protein exhibits 43% amino acid sequence identity when aligned to the E. coli protein; the alignment is interrupted by a large 171-amino acid-long insertion into the T. maritima protein after codon 45.
Phosphorescence quenching microrespirometry of skeletal muscle in situ (2010)

We have developed an optical method for the evaluation of the oxygen consumption (Vo(2)) in microscopic volumes of spinotrapezius muscle. Using phosphorescence quenching microscopy (PQM) for the measurement of interstitial Po(2), together with rapid pneumatic compression of the organ, we recorded the oxygen disappearance curve (ODC) in the muscle of the anesthetized rats. A 0.6-mm diameter area in the tissue, preloaded with the phosphorescent oxygen probe, was excited once a second by a 532-nm Q-switched laser with pulse duration of 15 ns. Each of the evoked phosphorescence decays was analyzed to obtain a sequence of Po(2) values that constituted the ODC. Following flow arrest and tissue compression, the interstitial Po(2) decreased rapidly and the initial slope of the ODC was used to calculate the Vo(2). Special analysis of instrumental factors affecting the ODC was performed, and the resulting model was used for evaluation of Vo(2). The calculation was based on the observation of only a small amount of residual blood in the tissue after compression. The contribution of oxygen photoconsumption by PQM and oxygen inflow from external sources was evaluated in specially designed tests. The average oxygen consumption of the rat spinotrapezius muscle was Vo(2) = 123.4 ± 13.4 (SE) nl O(2)/cm(3) · s (N = 38, within 6 muscles) at a baseline interstitial Po(2) of 50.8 ± 2.9 mmHg. This technique has opened the opportunity for monitoring respiration rates in microscopic volumes of functioning skeletal muscle.
Abnormal V(D)J Recombination of T Cell Receptor β Locus in SMAR1 Transgenic Mice (2004)

Scaffold/matrix-associated region-1-binding protein (SMAR1) specifically interacts with the MARbeta sequence, which is located 400-bp upstream of the murine TCRbeta enhancer and is highly expressed during the DP stage of thymocyte development. To further analyze the functions of SMAR1, transgenic mice were generated that express SMAR1 in a tissue-independent manner. SMAR1-overexpressing mice exhibit severely altered frequency of the T cells expressing commonly used Vbetas (Vbeta5.1/5.2 and Vbeta8.1/8.2/8.3). The rearrangements of Vbeta5.1/5.2, Vbeta8.1/8.2/8.3 loci are also reduced in SMAR1 transgenic mice. The T cells in SMAR1 transgenic mice exhibit a mild perturbation at the early DN stage. SMAR1 transgenic mice exhibit hypercellular lymph nodes and spleen accompanied with prominent architectural defects in these organs. These results indicate that SMAR1 plays an important role in the regulation of T cell development as well as V(D)J recombination besides maintaining the architecture of the lymphoid organs.
Generating 3D faces using Convolutional Mesh Autoencoders (2018)

Learned 3D representations of human faces are useful for computer vision problems such as 3D face tracking and reconstruction from images, as well as graphics applications such as character generation and animation. Traditional models learn a latent representation of a face using linear subspaces or higher-order tensor generalizations. Due to this linearity, they can not capture extreme deformations and non-linear expressions. To address this, we introduce a versatile model that learns a non-linear representation of a face using spectral convolutions on a mesh surface. We introduce mesh sampling operations that enable a hierarchical mesh representation that captures non-linear variations in shape and expression at multiple scales within the model. In a variational setting, our model samples diverse realistic 3D faces from a multivariate Gaussian distribution. Our training data consists of 20,466 meshes of extreme expressions captured over 12 different subjects. Despite limited training data, our trained model outperforms state-of-the-art face models with 50% lower reconstruction error, while using 75% fewer parameters. We also show that, replacing the expression space of an existing state-of-the-art face model with our autoencoder, achieves a lower reconstruction error. Our data, model and code are available at http://github.com/anuragranj/coma
The si<scp>RNA</scp>‐mediated downregulation of <scp>PD</scp>‐1 alone or simultaneously with <scp>CTLA</scp>‐4 shows enhanced in vitro <scp>CAR</scp>‐T‐cell functionality for further clinical development towards the potential use in immunotherapy of melanoma (2018)

Chimeric antigen receptor (CAR)-T cells have been used successfully for cancer immunotherapy. While substantial tumor regression was observed in leukaemia and lymphoma, CAR therapy of solid tumors needs further improvement. A major obstacle to the efficiency of engineered T cells is posed by triggering of inhibitory receptors, for example programmed cell death protein 1 (PD-1) and cytotoxic T lymphocyte-associated protein 4 (CTLA-4), leading to an impaired antitumor activity. To boost CAR-T-cell function, we co-electroporated T cells with both, mRNA encoding a CAR specific for chondroitin sulphate proteoglycan 4 (CSPG4) and small-interfering RNAs (siRNAs) to downregulate PD-1 (siPD-1) and CTLA-4 (siCTLA-4). Flow cytometry revealed that activation-induced upregulation of both PD-1 and CTLA-4 was suppressed when compared to CAR-T cells electroporated with negative control siRNA. The siRNA transfection showed no influence on CAR expression of engineered T cells. Functionality assays were performed using PD-L1- and CD80-transfected melanoma cells endogenously expressing CSPG4. CAR-T cells transfected with siPD-1 alone showed improvement in cytokine secretion. Additionally, CAR-T cells transfected with either siPD-1 alone or together with siCTLA-4 exhibited a significantly increased cytotoxicity. No or only little effects were observed when CAR-T cells were co-transfected with siCTLA-4 only. Taken together, it is feasible to optimize CAR-T cells by co-transfection of CAR-encoding mRNA and siRNAs to downregulate inhibitory receptors. Our in vitro data indicate an improvement of the functionality of these CAR-T cells, suggesting that this strategy could represent a novel method to enhance CAR-T-cell immunotherapy of cancer.
Oxidative Stress Inactivates Cobalamin-Independent Methionine Synthase (MetE) in Escherichia coli (2004)

In nature, Escherichia coli are exposed to harsh and non-ideal growth environments-nutrients may be limiting, and cells are often challenged by oxidative stress. For E. coli cells confronting these realities, there appears to be a link between oxidative stress, methionine availability, and the enzyme that catalyzes the final step of methionine biosynthesis, cobalamin-independent methionine synthase (MetE). We found that E. coli cells subjected to transient oxidative stress during growth in minimal medium develop a methionine auxotrophy, which can be traced to an effect on MetE. Further experiments demonstrated that the purified enzyme is inactivated by oxidized glutathione (GSSG) at a rate that correlates with protein oxidation. The unique site of oxidation was identified by selectively cleaving N-terminally to each reduced cysteine and analyzing the results by liquid chromatography mass spectrometry. Stoichiometric glutathionylation of MetE by GSSG occurs at cysteine 645, which is strategically located at the entrance to the active site. Direct evidence of MetE oxidation in vivo was obtained from thiol-trapping experiments in two different E. coli strains that contain highly oxidizing cytoplasmic environments. Moreover, MetE is completely oxidized in wild-type E. coli treated with the thiol-oxidizing agent diamide; reduced enzyme reappears just prior to the cells resuming normal growth. We argue that for E. coli experiencing oxidizing conditions in minimal medium, MetE is readily inactivated, resulting in cellular methionine limitation. Glutathionylation of the protein provides a strategy to modulate in vivo activity of the enzyme while protecting the active site from further damage, in an easily reversible manner. While glutathionylation of proteins is a fairly common mode of redox regulation in eukaryotes, very few proteins in E. coli are known to be modified in this manner. Our results are complementary to the independent findings of Leichert and Jakob presented in the accompanying paper (Leichert and Jakob 2004), which provide evidence that MetE is one of the proteins in E. coli most susceptible to oxidation. In eukaryotes, glutathionylation of key proteins involved in protein synthesis leads to inhibition of translation. Our studies suggest a simpler mechanism is employed by E. coli to achieve the same effect.
Successful Treatment of Passive Fecal Incontinence in an Animal Model Using Engineered Biosphincters: A 3-Month Follow-Up Study (2017)

Fecal incontinence (FI) is the involuntary passage of fecal material. Current treatments have limited successful outcomes. The objective of this study was to develop a large animal model of passive FI and to demonstrate sustained restoration of fecal continence using anorectal manometry in this model after implantation of engineered autologous internal anal sphincter (IAS) biosphincters. Twenty female rabbits were used in this study. The animals were divided into three groups: (a) Non-treated group: Rabbits underwent IAS injury by hemi-sphincterectomy without treatment. (b) Treated group: Rabbits underwent IAS injury by hemi-sphincterectomy followed by implantation of autologous biosphincters. (c) Sham group: Rabbits underwent IAS injury by hemi-sphincterectomy followed by re-accessing the surgical site followed by immediate closure without implantation of biosphincters. Anorectal manometry was used to measure resting anal pressure and recto-anal inhibitory reflex (RAIR) at baseline, 1 month post-sphincterectomy, up to 3 months after implantation and post-sham. Following sphincterectomy, all rabbits had decreased basal tone and loss of RAIR, indicative of FI. Anal hygiene was also lost in the rabbits. Decreases in basal tone and RAIR were sustained more than 3 months in the non-treated group. Autologous biosphincters were successfully implanted into eight donor rabbits in the treated group. Basal tone and RAIR were restored at 3 months following biosphincter implantation and were significantly higher compared with rabbits in the non-treated and sham groups. Histologically, smooth muscle reconstruction and continuity was restored in the treated group compared with the non-treated group. Results in this study provided promising outcomes for treatment of FI. Results demonstrated the feasibility of developing and validating a large animal model of passive FI. This study also showed the efficacy of the engineered biosphincters to restore fecal continence as demonstrated by manometry. Stem Cells Translational Medicine 2017;6:1795-1802.
A Cell-Based Approach for the Biosynthesis/Screening of Cyclic Peptide Libraries against Bacterial Toxins (2007)

Available methods for developing and screening small drug-like molecules able to knockout toxins or pathogenic microorganisms have some limitations. In order to be useful, these new methods must provide high-throughput analysis and identify specific binders in a short period of time. To meet this need, we are developing an approach that uses living cells to generate libraries of small biomolecules, which are then screened inside the cell for activity. Our group is using this new, combined approach to find highly specific ligands capable of disabling anthrax Lethal Factor (LF) as proof of principle. Key to our approach is the development of a method for the biosynthesis of libraries of cyclic peptides, and an efficient screening process that can be carried out inside the cell.
Physical mechanisms behind the SERS enhancement of pyramidal pit substrates (2010)

Abstract In this paper we theoretically consider the physical mechanisms behind the surface‐enhanced Raman scattering (SERS) enhancement produced by commercially available Klarite substrates, which consist of rectangular arrays of micrometre‐sized pyramidal pits in silicon with a thin gold coating. Full three‐dimensional numerical simulations of the pits are conducted for both a real gold metal coating and a perfect electrical conductor (PEC) to determine whether the SERS enhancement is due to diffraction or plasmon effects. The pit apex angle and metal coating thickness are also varied to determine whether it is possible to further enhance the SERS signal by optimising the structural parameters of these substrates. By decreasing the film thickness and adjusting the apex angle, it is possible to achieve an enhancement almost double that of a standard Klarite substrate. Copyright © 2010 John Wiley & Sons, Ltd.
The IEEE 802.17 media access protocol for high-speed metropolitan-area resilient packet rings (2004)

The resilient packet ring (RPR) IEEE 802.17 standards is under development as a new high-speed technology for metropolitan backbone networks. A key performance objective of PRP is to simultaneously achieve high utilization, spatial reuse, and fairness, an objective not achieved by current technologies such as SONET and Gigabit Ethernet or legacy ring technologies, such as FDDI. The core technical challenge for RPR is the design of a fairness algorithm that dynamically throttles traffic to achieve these properties. The difficulty is in the distributed nature of the problem, that upstream ring nodes must inject traffic at a rate according to congestion and fairness criteria downstream. This article provides an overview of the RPR protocol with a focus on medium access and fairness.
Multiband Asymmetric Transmission of Airborne Sound by Coded Metasurfaces (2017)

$A\phantom{\rule{0}{0ex}}s\phantom{\rule{0}{0ex}}y\phantom{\rule{0}{0ex}}m\phantom{\rule{0}{0ex}}m\phantom{\rule{0}{0ex}}e\phantom{\rule{0}{0ex}}t\phantom{\rule{0}{0ex}}r\phantom{\rule{0}{0ex}}i\phantom{\rule{0}{0ex}}c$ $t\phantom{\rule{0}{0ex}}r\phantom{\rule{0}{0ex}}a\phantom{\rule{0}{0ex}}n\phantom{\rule{0}{0ex}}s\phantom{\rule{0}{0ex}}m\phantom{\rule{0}{0ex}}i\phantom{\rule{0}{0ex}}s\phantom{\rule{0}{0ex}}s\phantom{\rule{0}{0ex}}i\phantom{\rule{0}{0ex}}o\phantom{\rule{0}{0ex}}n$ is an active subject in information processing, because of its utility in constructing electromagnetic and acoustic devices. The authors present a multiband, subwavelength acoustic device based on a ``coded metasurface'', an alternating arrangement of elements corresponding to bit values of 0 or 1. By assembling these building blocks to encode patterns such as 0000\dots{}, 1111\dots{}, or 0101\dots{}, asymmetric transmission can be handily controlled to select ``off'' and ``on'' states.
Web-Based Appreciation and Peer-Assessment for Visual-Art Education (2006)

This study describes the application of a Web-based portfolio for appreciation and peer assessment for visual-art education in elementary school. Besides examining the effectiveness of the proposed system in enhancing visual art education, this study also addresses how Web-based portfolios can help teachers to assess student learning progress and facilitate peer assessment. The results of questionnaires and interviews shows that the proposed portfolio system can help student learning and the peer assessment component of the proposed portfolio system can help the students’ learning in visual-art education in elementary school.
Two-Stage Optical Data Storage in Azo Polymers (2000)

We have demonstrated two-stage optical memory in a photoaddressable azo polymer. The polymer serves as a data storage medium with two recording mechanisms: photoanisotropic modulation and surface-shape modulation. We can select the recording mechanism by manipulating beam energies for recording. The characteristics can be motivated to rewritable and write-once optical memories: polarization-multiplex bit memories, surface-modulated bit memories and surface-modulated holographic memories.
1 J/pulse Q-switched 2 µm solid-state laser (2006)

Q-switched output of 1.1 J/pulse at a 2.053 microm wavelength has been achieved in a diode-pumped Ho: Tm: LuLF laser with a side-pumped rod configuration in a master-oscillator-power-amplifier (MOPA) architecture. This is the first time to our knowledge that a 2 microm laser has broken the joule per pulse barrier for Q-switched operation. The total system efficiency reaches 5% and 6.2% for single- and double-pulse operation, respectively. The system produces an excellent 1.4 times transform-limited beam quality.
Swarm Robots Long Term Autonomy Using Moveable Charger (2009)

This paper proposes an alternative docking charger station for mobile robots. One crucial task in swarm robots scenario is to find low battery robots and recover them. Overcoming this problem requires a versatile mobile charging station that is able to actively locate and charge inactive mobile robots unlike the conventional stationary docking stations. The mobile charger robot should perform independent tasks other than the swarm robots global task. It uses similar communication method with other swarm robots, however new preprogrammed instructions are required to facilitate battery charging task for swarm robots.
The impact of digital audio and video on high-speed storage (2002)

Digital audio and video are difficult to store and replay due to their real-time nature, high bandwidth, and large size. To investigate the techniques required to support audio and video, a specialized continuous media storage server, in operation since December 1991, was built at Lancaster. This server and the techniques used in its design are briefly described. The current work at Lancaster in distributed continuous media storage servers is then outlined. This work is developing a scalable multimedia storage server architecture that supports wide area multimedia storage; storage server scalability that allows the incremental addition of new nodes; high bandwidth through the use of load balancing, including node striping and file replication; and store-and-forward caching for slower and faster than real-time links. The architecture will allow tens of simultaneous users for classroom teaching and video-on-demand applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
High Energy Glass Lasers (1976)

A number of laboratories throughout the world are actively pursuing the development of pulsed high power Nd:glass lasers for use in their laser fusion and laser plasma interaction studies programs. Perhaps the most ambitious programs in this field have been undertaken by the Lawrence Livermore Laboratory where several irradiation facilities are in opera-tion and where the 4-arm ARGUS and 20-arm SHIVA lasers are currently under construction. These systems are designed to provide the energy, power and wavefront uniformity required to spherically implode nuclear fuel targets such as the deuterium-tritium (DT) solid sphere, in an effort to achieve thermonuclear fusion through inertial confinement.
Sulfur Single-wavelength Anomalous Diffraction Crystal Structure of a Pheromone-Binding Protein from the Honeybee Apis mellifera L (2004)

Pheromone binding proteins (PBPs) are small helical proteins ( approximately 13-17 kDa) present in several sensory organs from moth and other insect species. They are involved in the transport of pheromones from the sensillar lymph to the olfactory receptors. We report here the crystal structure of a PBP (Amel-ASP1) originating from the honey-bee (Apis mellifera) antennae and expressed as recombinant protein in the yeast Pichia pastoris. Crystals of Amel-ASP1 were obtained at pH 5.5 using the nano-drops technique of crystallization with a novel optimization procedure, and the structure was solved initially with the single-wavelength anomalous diffraction technique using sulfur anomalous dispersion. The structure of Amel-ASP1 has been refined at 1.6-A resolution. Its fold is roughly similar to that of other PBP/odorant binding proteins, presenting six helices and three disulfide bridges. Contrary to the PBPs from Bombyx mori (Sandler, B. H., Nikonova, L., Leal, W. S., and Clardy, J. (2000) Chem. Biol. 7, 143-151) and Leucophea maderae (Lartigue, A., Gruez, A., Spinelli, S., Riviere, S., Brossut, R., Tegoni, M., and Cambillau, C. (2003) J. Biol. Chem. 278, 30213-30218), the extended C terminus folds into the protein and forms a wall of the internal hydrophobic cavity. Its backbone groups establish two hydrogen bonds with a serendipitous ligand, n-butyl-benzene-sulfonamide, an additive used in plastics. This mode of binding might, however, mimic that used by one of the pheromonal blend components and illustrates the binding versatility of PBPs.