gebhart/patrepeval huggingface dataset:
Abstract 5757: Preclinical development and testing of a therapeutic antibody against LRG1 (2018)

Abstract Introduction: The purpose of this study was to generate a therapeutic function-blocking antibody against leucine-rich alpha-2-glycoprotein 1 (LRG1), a novel regulator of pathological angiogenesis that is up-regulated in many cancers, and demonstrate efficacy in proof of principle experiments in mouse models. Experimental Procedures: Mice were immunized with recombinant human LRG1 and hybridomas generated. More than 100 monoclonal antibodies (mAbs) were first screened by surface plasmon resonance (SPR) to measure affinity for target, and then in a co-culture angiogenesis assay to evaluate functional activity. The most promising candidates were then tested in vivo in the mouse model of laser-induced choroidal neovascularization, and from this study a lead was humanized and deimmunized. The resulting antibody is a hinge-stabilized IgG4 that is now undergoing manufacturing and pre-clinical safety and toxicology testing. Results: Of the original set of mouse mAbs, an initial screen to eliminate low affinity (KD greater than 1nM) binders resulted in 25 progressing to functional testing in angiogenesis assays. The seven most effective blocking mAbs were then tested in vivo in the mouse model of laser-induced choroidal neovascularization. Intraocular injections of mAb yielded two that exhibited equivalent inhibition of neovascularization to a therapeutic VEGF-blocker, and of these, the higher affinity mAb (15C4) was selected for humanization. Epitope mapping identified an amino-acid sequence within human LRG1, that in the form of a synthetic peptide was able to compete the binding of 15C4 to LRG1. Multiple species sequence alignment revealed the epitope to be partially conserved with the corresponding mouse sequence, and SPR analysis showed that 15C4 binding to recombinant mouse LRG1 was several orders of magnitude lower than to human LRG1. Nevertheless, administration of 15C4 to tumor-bearing mice significantly inhibited tumor growth in a range of subcutaneous and genetic models. Furthermore, due to the vessel normalizing effects of 15C4, combinations of mAb with both immunotherapy and cytotoxics were significantly more effective at restricting tumor growth than either monotherapy. Conclusions: We have generated and characterized a novel vessel-normalizing, fully humanized function-blocking mAb against LRG1 that shows efficacy in mouse tumor models. GMP manufacture is on-going, and early stage clinical trials are planned in 2019. Financial Support: The work was supported by the Medical Research Council, the Rosetrees Trust and UCL Business. Citation Format: Stephen Moss, David Kallenberg, Vineeta Tripathi, Sterenn Davis, Jestin George, Marie O'Connor, Laura Dowsett, John Greenwood. Preclinical development and testing of a therapeutic antibody against LRG1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5757.
Robust and steerable kronecker product differential beamforming With rectangular microphone arrays (2020)

Differential microphone arrays (DMAs), a class of welldesigned small-size arrays combined with differential beamforming, are very useful for processing broadband acoustic, audio, and speech signals in a wide range of applications. However, most efforts in the literature so far have been devoted to linear, circular, and spherical arrays. In this paper, we consider rectangular shapes of planar microphone arrays. Instead of adopting the traditional differential beamforming methods developed in the literature, we present a differential beamforming method based on the so-called Kronecker product. We first decompose the entire rectangular array into two virtual rectangular sub-arrays so that the steering vector of the entire array is the Kronecker product of the steering vectors of the two smaller virtual rectangular sub-arrays. We use the first virtual rectangular array, which is much smaller in size than the entire array but well satisfies the basic requirements for differential beamforming, to design a steerable differential beamformer. For the second virtual rectangular array, we can design either the delay-and-sum (DS) beamformer, which helps to improve the robustness of the global differential beamformer, or an adaptive beamformer, which makes the global differential beamformer adaptive. This method has many interesting properties, particularly the designed beamformer is fully steerable, and its robustness and the array gain can be easily controlled.
ChemInform Abstract: Crystal Structure of La<sub>2</sub>Mo<sub>2</sub>O<sub>9</sub>, a New Fast Oxide‐Ion Conductor. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Fabrication of Thin Graphene Layers on a Stacked 6H-SiC Surface in a Graphite Enclosure (2013)

Thin and homogeneous epitaxial graphene (EG) layers on a 6H-SiC (000) substrate are fabricated and they cover the whole substrate (10 × 10 mm2). The sample surface is capped by another 6H-SiC (000) wafer in a graphite enclosure to form a relatively high Si partial pressure between them, which significantly reduces the extremely high growth rate of EG. The structure and morphology of the EG layers are investigated by Raman spectroscopy, atomic force microscopy and field-emission scanning electronic microscopy. The results are compared with an uncapped sample surface, and reveal the obvious existence of ridges on the surface of the EG, and show that capping is indeed beneficial to obtain homogeneous graphene.
The Low Conductivity of Geobacter uraniireducens Pili Suggests a Diversity of Extracellular Electron Transfer Mechanisms in the Genus Geobacter (2016)

Studies on the mechanisms for extracellular electron transfer in Geobacter species have primarily focused on Geobacter sulfurreducens, but the poor conservation of genes for some electron transfer components within the Geobacter genus suggests that there may be a diversity of extracellular electron transport strategies among Geobacter species. Examination of the gene sequences for PilA, the type IV pilus monomer, in Geobacter species revealed that the PilA sequence of Geobacter uraniireducens was much longer than that of G. sulfurreducens. This is of interest because it has been proposed that the relatively short PilA sequence of G. sulfurreducens is an important feature conferring conductivity to G. sulfurreducens pili. In order to investigate the properties of the G. uraniireducens pili in more detail, a strain of G. sulfurreducens that expressed pili comprised the PilA of G. uraniireducens was constructed. This strain, designated strain GUP, produced abundant pili, but generated low current densities and reduced Fe(III) very poorly. At pH 7, the conductivity of the G. uraniireducens pili was 3 × 10(-4) S/cm, much lower than the previously reported 5 × 10(-2) S/cm conductivity of G. sulfurreducens pili at the same pH. Consideration of the likely voltage difference across pili during Fe(III) oxide reduction suggested that G. sulfurreducens pili can readily accommodate maximum reported rates of respiration, but that G. uraniireducens pili are not sufficiently conductive to be an effective mediator of long-range electron transfer. In contrast to G. sulfurreducens and G. metallireducens, which require direct contact with Fe(III) oxides in order to reduce them, G. uraniireducens reduced Fe(III) oxides occluded within microporous beads, demonstrating that G. uraniireducens produces a soluble electron shuttle to facilitate Fe(III) oxide reduction. The results demonstrate that Geobacter species may differ substantially in their mechanisms for long-range electron transport and that it is important to have information beyond a phylogenetic affiliation in order to make conclusions about the mechanisms by which Geobacter species are transferring electrons to extracellular electron acceptors.
Simple MAP decoding of first order Reed-Muller and Hamming codes (2003)

In this paper we are interested in MAP decoding of first order Reed-Muller and Hamming codes. A MAP decoder of a linear code computes a-posteriori probabilities for all values of each transmitted symbol and chooses the maximum one. The standard way of doing this is the BCJR algorithm. This algorithm is based on a trellis representation of a code. Such a representation allows one to reduce the complexity of MAP decoding, though it still remains exponential. The BCJR algorithm for binary first order Reed-Muller and Hamming codes has complexity proportional to n/sup 2/, where n is the code length. In this paper we propose a new MAP decoding algorithm for both RM-1 and Hamming codes with complexity proportional to nlog/sub 2/n.
Analytic study of compensation of nonlinear phase shift by third-order dispersion in chirped-pulse amplification (2006)

An analytic model of chirped-pulse amplification is presented. The model is used to optimize the peak power in fiber chirped-pulse amplification, in which the interplay of nonlinearity and third-order dispersion plays a major role.
Molecular haplotyping of genomic DNA for multiple single-nucleotide polymorphisms located kilobases apart using long-range polymerase chain reaction and intramolecular ligation (2002)

Genetic polymorphisms are well-recognized causes of interindividual differences in disease risk and treatment response in humans. For genes containing multiple single-nucleotide polymorphisms (SNPs), haplotype structure is often the principal determinant of phenotypic consequences, and haplotype distribution represents the best approach for assessing patterns of linkage disequilibrium. To permit more widespread molecular determination of haplotypes, we developed a simple yet robust method to determine haplotype structure for multiple SNPs located up to 30 kb apart in genomic DNA using long-range polymerase chain reaction (LR-PCR) and intramolecular ligation. Complete concordance was shown between the new method and conventional approaches, such as family pedigree analysis or cloning and sequencing. The availability of a simple method to directly determine haplotype structure using genomic DNA, without family pedigree analysis, cloning or complex instrumentation, provides an important new tool for elucidating the genetic determinants of drug disposition and effects, disease risk, and molecular evolution.
De Novo Synthesis of Phosphorylated Triblock Copolymers with Pathogen Virulence-Suppressing Properties That Prevent Infection-Related Mortality (2017)

Phosphate is a key and universal "cue" in response to which bacteria either enhance their virulence when local phosphate is scarce or downregulate it when phosphate is adundant. Phosphate becomes depleted in the mammalian gut following physiologic stress and serves as a major trigger for colonizing bacteria to express virulence. This process cannot be reversed with oral supplementation of inorganic phosphate because it is nearly completely absorbed in the proximal small intestine. In the present study, we describe the de novo synthesis of phosphorylated polyethylene glycol compounds with three defined ABA (hydrophilic/-phobic/-philic) structures, ABA-PEG10k-Pi10, ABA-PEG16k-Pi14, and ABA-PEG20k-Pi20, and linear polymer PEG20k-Pi20 absent of the hydrophobic block. The 10k, 16k, and 20k demonstrate the molecular weights of the poly(ethylene glycol) block, and Pi10, Pi14, and Pi20 represent the repeating units of phosphate. Polymers were tested for their efficacy against <i>Pseudomonas aeruginosa</i> virulence in vitro and in vivo by assessing the expression of the phosphate sensing protein PstS, the production of key virulence factor pyocyanin, and <i>Caenorhabditis elegans</i> killing assays. Results indicate that all phosphorylated polymers suppressed phosphate sensing, virulence expression, and lethality in <i>P. aeruginosa</i>. Among all of the phosphorylated polymers, ABA-PEG20k-Pi20 displayed the greatest degree of protection against <i>P. aeruginosa</i>. To define the role of the hydrophobic core in ABA-PEG20k-Pi20 in the above response, we synthesized PEG20k-Pi20 in which the hydrophobic core is absent. Results indicate that the hypdrophobic core of ABA-PEG20k-Pi20 is a key structure in its protective effect against <i>P. aeruginosa</i>, in part due to its ability to coat the surface of bacteria. Taken together, the synthesis of novel polymers with defined structures and levels of phosphorylation may elucidate their antivirulence action against clinically important and lethal pathogens such as <i>P. aeruginosa</i>.
Catalytic Upgrading of Biomass Pyrolysis Oxygenates with Vacuum Gas Oil Using a Davison Circulating Riser Reactor (2018)

We investigate and quantitate the changes in hydrocarbon product composition while evaluating the performance and operability of the National Renewable Energy Laboratory’s Davison Circulating Riser (DCR) reactor system when biomass model compounds are cofed with traditional fluid catalyst cracking (FCC) feeds and catalyst: vacuum gas oil (VGO) and equilibrium zeolite catalyst (E-Cat). Three compounds (acetic acid, guaiacol, and sorbitan monooleate) were selected to represent the major classes of oxygenates present in biomass pyrolysis vapors. These vapors can contain 30–50% oxygen as oxygenates, which create conversion complications (increased reactivity and coking) when integrating biomass vapors and liquids into fuel and chemical processes long dominated by petroleum feedstocks. We used these model compounds to determine the appropriate conditions for coprocessing with petroleum and ultimately pure pyrolysis vapors only as compared with standard baseline conditions obtained with VGO and E-Cat only in the DCR. Model compound addition decreased the DCR catalyst circulation rate, which controls reactor temperature and measures reaction heat demand, while increasing catalyst coking rates. Liquid product analyses included 2-dimensional gas chromatography time-of-flight mass spectroscopy (2D GC×GC TOFS), simulated distillation (SIM DIST), 13C NMR, and carbonyl content. Aggregated results indicated that the model compounds were converted during reaction, and despite functional group differences, product distributions for each model compound were very similar. In addition, we determined that adding model compounds to the VGO feed did not significantly affect the DCR’s operability or performance. Future work will assess catalytic upgrading of biomass pyrolysis vapor to fungible hydrocarbon products using upgrading catalysts currently being developed at NREL and at Johnson Matthey.
Seamless Producer Mobility as a Service in Information Centric Networks (2016)

In this paper, we present a service-driven mobility support architecture for Information Centric Networks that provides seamless mobility as an on-demand network service, which can be enabled/disabled based on network capabilities or resource availability. Proposed architecture relies on the ID/Locator split on ICN namespaces to support the use of persistent names and avoids name reconfiguration due to mobility. We implemented the proposed solution over a service-centric CCN platform, with multiple end-hosts running a video conferencing application acting as Consumers and Producers, and observed its capability to support seamless handover.
Multi-view 3D estimation and applications to match move (2003)

Multiple views of a rigid 3D scene captured from a moving camera can be used to estimate the 3D poses (rotations and translations) and the 3D structure of the unmodeled scene. In this problem domain, there are two key problems addressed in this paper: automatic Euclidean pose estimation in extended sequences even when views of the scene rapidly change, that is features come in and go out of view relatively rapidly; and insertion of synthetic 3D objects in the real scene and their authentic projection into the given real views (also called match move). The paper presents a number of examples of different camera motions to highlight the versatility of 3D estimation. Examples of match move are also presented.
Electric‐Field‐Induced Resistive Switching in a Family of Mott Insulators: Towards a New Class of RRAM Memories (2010)

Flash memories (USB portable drives) are close to their miniaturization limits. The ultimate evolution of such devices is believed to exploit different concepts such as electronic phase transitions. Here we show that an electric field can trigger fast resistive switching in the fragile Mott insulators AM4X8 (A= Ga, Ge ; M = V, Nb, Ta; X = S, Se). This new type of resistive switching could lead to a new class of resistive random access memory (RRAM) with fast writing/erasing times (down to 50 ns) and resistance ratios ΔR/R of the order of 25% at room temperature. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Fine-grained layered multicast (2002)

Traditional approaches to receiver-driven layered multicast have advocated the benefits of cumulative layering, which can enable coarse-grained congestion control that complies with TCP-friendliness equations over large time scales. In this paper, we quantify the costs and benefits of using non-cumulative layering and present a new, scalable multicast congestion control scheme which provides a fine-grained approximation to the behavior of TCP additive increase/multiplicative decrease (AIMD). In contrast to the conventional wisdom, we demonstrate that fine-grained rate adjustment can be achieved with only modest increases in the number of layers and aggregate bandwidth consumption, while using only a small constant number of control messages to perform either additive increase or multiplicative decrease.
T‐Cell inactivation and immunosuppressive activity induced by HIV gp41 via novel interacting motif (2006)

Fusion peptide (FP) of the HIV gp41 molecule inserts into the T cell membrane during virus-cell fusion. FP also blocks the TCR/CD3 interaction needed for antigen-triggered T cell activation. Here we used in vitro (fluorescence and immunoprecipitation), in vivo (T cell mediated autoimmune disease adjuvant arthritis), and in silico methods to identify the FP-TCR novel interaction motif: the alpha-helical transmembrane domain (TMD) of the TCR alpha chain, and the beta-sheet 5-13 region of the 16 N-terminal aa of FP (FP(1-16)). Deciphering the molecular mechanism of the immunosuppressive activity of FP provides a new potential target to overcome the immunosuppressant activity of HIV, and in addition a tool for down-regulating immune mediated inflammation.
Database query generation from spoken sentences (2002)

In the context of our spoken language inquiry system, we present the component which extracts the values needed for a database query from the textual representation of an utterance in the form of a word graph. A stochastic attributed grammar is used as a language model, to identify the relevant parts of the sentence, and to compute their meaning. High understanding rates, low computational costs and practically no restrictions of the usable language are important features of our system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The transcriptional control region of the human carcinoembryonic antigen gene: DNA sequence and homology studies (1993)

Phage clones containing human carcinoembryonic antigen (CEA) 5' flanking sequences were isolated from a chromosome 19 genomic library. The clones were confirmed to contain CEA sequences flanking the CEA transcriptional start site by restriction endonuclease mapping, PCR analysis, and sequence determination. Restriction endonuclease mapping determined that the clones spanned approximately 26 kbp of contiguous sequence from 14 kbp 5' to 12 kbp 3' of the CEA transcriptional start. The DNA sequence of a 11,288 bp Hind III/Sau 3A restriction endonuclease fragment was determined. This sequence extends from 10.7 kbp 5' to 0.6 kbp 3' of the transcriptional start. This sequence was analyzed for the presence of consensus transcriptional regulatory sequences, repetitive sequences, and other features. Several transcriptional regulatory consensus sequences were identified. These consensus sequences may have significance for the transcriptional regulation of CEA.
Radio frequency wireless power transfer to chip-scale apparatuses (2016)

This paper reports a design methodology for a tri-coil system that can wirelessly transfer power from a macro-scale probe to a chipscale apparatus over a long distance and with a high efficacy. Such systems can be employed for enabling the wireless charging and communication between implanted body sensors and smart phones as well as between hardware roots of trust and their interrogation probes. A design example has been offered and subsequently validated by an experimental testbed consisting of micro-fabricated coils on both sides of a Silicon substrate. As predicted by the analytical models, the measured power transfer efficacy (PTEF) of the designed system is as high as -27 dB at the resonance, confirming an orders-of-magnitude higher PTEF than that of prior WPT systems over a distance greater than 5 times the coil diameter.
Novel architectures for the lifting-based discrete wavelet transform (2003)

In this paper, we propose two modular and highly efficient architectures, the recursive architecture and the double scan architecture, for implementing the lifting-based discrete wavelet transform. The recursive architecture simultaneously processes all stages of the transform, while the double scan architecture processes two independent signals at the same time. Compared to other known architectures, both new architectures significantly improve the efficiency and hardware utilization. Compared to other published lifting-based architectures, the new architectures speed up the computational time by up to 100% with either simpler or comparable hardware complexity.
Hardware Design and Analysis for Generalized Receive Space Modulation Techniques (2019)

Receive space modulation techniques (RSMTs) have recently been introduced as efficient implementations of multiple input multiple output (MIMO) receivers. RSMTs achieve these implementations assuming knowledge of the channel state information (CSI) at the transmitter through a feedback link. RSMTs, however, encounter the limitation that the number of receive antennas has to always be a power of two. In this letter, two new generalized additions to RSMTs are introduced where an arbitrary number of antennas can be deployed. The two techniques are named generalized receive space shift keying (GRSSK) and generalized receive spatial modulation (GRSM). The hardware models for both techniques are defined and compared with each other and to existing models of non-generalized techniques. The bit error rate performance, power consumption, and required hardware cost for practical deployments of both systems are presented and thoroughly discussed.