gebhart/patrepeval huggingface dataset:
The Efficacy of Radiotherapy Relies upon Induction of Type I Interferon–Dependent Innate and Adaptive Immunity (2011)

The most widely held explanation for the efficacy of local radiotherapy (RT) is based on direct cytotoxicity to cancer cells through the induction of lethal DNA damage. Recent studies have shown that local ablative radiation of established tumors can lead to increased T-cell priming and T-cell-dependent tumor regression, but the underlying mechanism remains unclear. Here, we describe an essential role for type I IFN in local RT-mediated tumor control. We show that ablative RT increases intratumoral production of IFN-β and, more surprisingly, the antitumor effect of RT is abolished in type I IFN nonresponsive hosts. Furthermore, the major target of RT-induced type I IFN is the hematopoietic compartment. RT drastically enhances the cross-priming capacity of tumor-infiltrating dendritic cells (TIDC) from wild-type mice but not type I IFN receptor-deficient mice. The enhanced cross-priming ability of TIDCs after RT was dependent on autocrine production of type I IFNs. By using adenoviral-mediated expression of IFN-β, we show that delivery of exogenous IFN-β into the tumor tissue in the absence of RT is also sufficient to selectively expand antigen-specific T cells leading to complete tumor regression. Our study reveals that local high-dose RT can trigger production of type I IFN that initiates a cascading innate and adaptive immune attack on the tumor.
Intel's FLEXlogic FPGA architecture (2002)

Intel's FLEXlogic field-programmable gate array family is a segmented architecture, SRAM (static random-access memory)-based family with on-chip nonvolatile memory. The architecture is quick to learn and easy to use for designers with standard PLD experience. Devices are organized into configurable function blocks (CFBs). Each CFB can be configured as a PLD block or as a bank of SRAMs. CFBs configured as PLD blocks include advanced features that provide significant design flexibility and high integration. Truly predictable timing simplifies the design and simulation process. The inherent speed of the FLEXlogic FPGA family, together with its selectable 3.3-V or 5-V I/O, allows it to be used in areas where previous FPGA architectures cannot operate. The iFX780, the first member of the family, illustrates the architecture.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Sealed Bacterial Ghosts--Novel Targeting Vehicles for Advanced Drug Delivery of Water-soluble Substances (2003)

The purpose of the present study was to develop a drug delivery model for water soluble drug substances using the bacterial ghost platform technology. Bacterial ghosts are non-denatured bacterial cell envelopes that are produced by the plasmid encoded gene E mediated lysis. We present a novel method to fill and seal bacterial ghosts for the application as a drug delivery system for fluid, non-anchored substances. E. coli ghosts were filled with the reporter substance calcein and sealed by fusion with membrane vesicles. By flow cytometry and fluorescence microscopy it was shown that bacterial ghosts can be filled with calcein, and that the bacterial ghosts can be sealed by restoring the membranes integrity. The adherence and uptake studies showed that almost all murine macrophages and a lower proportion of human colorectal adenocarcinoma cells took up fluorescence labeled bacterial ghosts. Moreover, these cells also took up effectively sealed E. coli ghosts filled with calcein, which then was released within the cells. Therefore, we propose bacterial ghosts as alternative drug delivery and release vehicles for advanced cell targeting.
LeoXSS: An Efficient XML Stream System for Processing Complex XPaths (2006)

Stream-based continuous query processing fits a large class of new applications, such as sensor networks, location tracking, network management and financial data analysis. In this paper, we propose an efficient system called LeoXSS that processes complex twig patterns with OR-predicates and AND-predicates over XML document streams. In LeoXSS, a set of twig patterns is processed in a single document-order pass over the input document stream avoiding the post-processing of nested paths.
Antialiasing for automultiscopic 3D displays (2006)

No abstract available.
The DNA Binding Domain of the Rat Liver Nuclear Protein C/EBP Is Bipartite (1989)

C/EBP is a rat liver nuclear protein capable of sequence-specific interaction with DNA. The DNA sequences to which C/EBP binds in vitro have been implicated in the control of messenger RNA synthesis. It has therefore been predicted that C/EBP will play a role in regulating gene expression in mammalian cells. The region of the C/EBP polypeptide required for direct interaction with DNA has been identified and shown to bear amino acid sequence relatedness with the product of the myc, fos, and jun proto-oncogenes. The arrangement of these related amino acid sequences led to the prediction of a new structural motif, termed the "leucine zipper," that plays a role in facilitating sequence-specific interaction between protein and DNA. Experimental tests now provide support for the leucine zipper hypothesis.
A stable trimeric influenza hemagglutinin stem as a broadly protective immunogen (2015)

The identification of human broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem revitalized hopes of developing a universal influenza vaccine. Using a rational design and library approach, we engineered stable HA stem antigens ("mini-HAs") based on an H1 subtype sequence. Our most advanced candidate exhibits structural and bnAb binding properties comparable to those of full-length HA, completely protects mice in lethal heterologous and heterosubtypic challenge models, and reduces fever after sublethal challenge in cynomolgus monkeys. Antibodies elicited by this mini-HA in mice and nonhuman primates bound a wide range of HAs, competed with human bnAbs for HA stem binding, neutralized H5N1 viruses, and mediated antibody-dependent effector activity. These results represent a proof of concept for the design of HA stem mimics that elicit bnAbs against influenza A group 1 viruses.
Orphan G‐protein‐coupled receptors: the next generation of drug targets? (1998)

The pharmaceutical industry has readily embraced genomics to provide it with new targets for drug discovery. Large scale DNA sequencing has allowed the identification of a plethora of DNA sequences distantly related to known G protein-coupled receptors (GPCRs), a superfamily of receptors that have a proven history of being excellent therapeutic targets. In most cases the extent of sequence homology is insufficient to assign these 'orphan' receptors to a particular receptor subfamily. Consequently, reverse molecular pharmacological and functional genomic strategies are being employed to identify the activating ligands of the cloned receptors. Briefly, the reverse molecular pharmacological methodology includes cloning and expression of orphan GPCRs in mammalian cells and screening these cells for a functional response to cognate or surrogate agonists present in biological extract preparations, peptide libraries, and complex compound collections. The functional genomics approach involves the use of 'humanized yeast cells, where the yeast GPCR transduction system is engineered to permit functional expression and coupling of human GPCRs to the endogenous signalling machinery. Both systems provide an excellent platform for identifying novel receptor ligands. Once activating ligands are identified they can be used as pharmacological tools to explore receptor function and relationship to disease.
Evernimicin Binds Exclusively to the 50S Ribosomal Subunit and Inhibits Translation in Cell-Free Systems Derived from both Gram-Positive and Gram-Negative Bacteria (2000)

Evernimicin (SCH 27899) is a new antibiotic with activity against a wide spectrum of gram-positive bacteria and activity against some gram-negative bacteria. Previous metabolic labeling studies indicated that evernimicin specifically inhibited protein synthesis in Staphylococcus aureus. Using a susceptible Escherichia coli strain, we demonstrated that evernimicin also inhibited protein synthesis in E. coli. In cell-free translation assays with extracts from either E. coli or S. aureus, evernimicin had a 50% inhibitory concentration of approximately 125 nM. In contrast, cell-free systems derived from wheat germ and rabbit reticulocytes were inhibited only by very high levels of evernimicin. Evernimicin did not promote transcript misreading. [(14)C]evernimicin specifically bound to the 50S subunit from E. coli. Nonlinear regression analysis of binding data generated with 70S ribosomes from E. coli and S. aureus and 50S subunits from E. coli returned dissociation constants of 84, 86, and 160 nM, respectively. In binding experiments, performed in the presence of excess quantities of a selection of antibiotics known to bind to the 50S subunit, only the structurally similar drug avilamycin blocked binding of [(14)C]evernimicin to ribosomes.
The Effect of Fuel Composition, Equivalence Ratio, and Mixture Temperature on Exhaust Emissions (1971)

&lt;div class="htmlview paragraph"&gt;A single-cylinder research engine was operated on pure hydrocarbons (HC) and simple mixtures of pure hydrocarbons to study the effect of fuel composition, equivalence ratio, and mixture temperature on exhaust emissions. Used as fuel components were hydrocarbons-&lt;u&gt;n&lt;/u&gt;-pentane, 2-methyl-2-butene, isooctane, and &lt;u&gt;m&lt;/u&gt;-xylene.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Total hydrocarbon emission in terms of moles of exhaust HC/mole of fuel input was lowered by increasing the amount of xylene in the fuel when operating on the fuel-rich side of stoichiometric; total hydrocarbon emission was higher for higher aromatic fuels when air-fuel ratios approached the lean misfire limit; the effect of mixture temperature on hydrocarbon emission was insignificant.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;1-Methyl-3-ethylbenzene was observed as a synthesis product of combustion in the exhaust from fuels containing &lt;u&gt;m&lt;/u&gt;-xylene. With increasing &lt;u&gt;m&lt;/u&gt;-xylene concentration in the fuel, the yield of 1-methyl-3-ethylbenzene increases, reaches a maximum, and then decreases. The effect of equivalence ratio is to shift this maximum point toward lower aromatic fuels as the fuel-air mixture is leaned out.&lt;/div&gt;
<title>Fractal-based image coding with polyphase decomposition</title> (1993)

A new method for fractal image compression by applying Jacquin's algorithm to a polyphase decomposed image is proposed to increase the encoding efficiency in this research. By using a (P X P) : (1 X 1) polyphase decomposition with P equals 2<SUP>n</SUP>, we divide an image into P X P subimages and then apply the Jacquin compression algorithm to these subimages independently. We show that the resulting scheme can improve the coding speed by a factor of P<SUP>2</SUP> at the sacrifice of the decompressed image quality. Besides, since the subimages are very similar to each other, we may focus on a small subset of subimages, seek the appropriate domain block for their range blocks, and record the information of address mapping, scaling and offset. To encode the remaining subimages, we simply determine the scaling and the offset based on the same set of addressing mapping previously found. A set of numerical experiments with various parameters, including the polyphase decimation factor P, the size D (or R) of domain (or range) blocks, and the size s of search step, are performed to illustrate the tradeoff between the speed, image quality, and compression rate.
Extracellular matrix remodeling after balloon angioplasty injury in a rabbit model of restenosis. (1994)

Remodeling of the vessel wall after balloon angioplasty injury is incompletely understood, and in particular, the role of extracellular matrix synthesis in restenosis has received little attention. The objective of the present study was to determine the sequence of changes in collagen, elastin, and proteoglycan synthesis and content after balloon injury and to relate these changes to growth of the intimal lesions and extent of cell proliferation. In a double-injury non-cholesterol-fed model, right iliac arterial lesions in 43 rabbits were treated with balloon angioplasty, and the rabbits were killed at five time points ranging from immediate to 12 weeks. Vessel wall collagen and elastin content and synthesis were measured after incubation with 14C-proline and separation with a cyanogen bromide extraction procedure. Sulfated glycosaminoglycan synthesis was measured after incubation with [35S]sulfate, papain digestion, and ethanol precipitation. Continuous in vivo infusion of bromodeoxyuridine (96 hours) was used to assess cell proliferation. The intimal area significantly increased from 0.27 +/- 0.08 to 0.73 +/- 0.11 mm2 between 0 and 12 weeks. Intimal and medial cell proliferation were modest and peaked at 1 week (labeling indexes of 4.8% and 3.0%, respectively) and then markedly declined by 2 weeks. Significant increases in collagen, elastin, and proteoglycan synthesis, up to 4 to 10 times above control nondamaged contralateral iliac arteries, were noted at 1, 2, and 4 weeks. These increases in synthesis were accompanied by significant increases in collagen and elastin content (by approximately 35%) that coincided with the temporal increase in cross-sectional area.(ABSTRACT TRUNCATED AT 250 WORDS)
Potential anticonvulsants. IX. Some isatin hydrazones and related compounds (1984)

Abstract A number of hydrazines, hydrazides, and related compounds have been condensed with isatin and substituted isatins. The anticonvulsant activity of these compounds is reported.
Interactions between Lipids and Human Anti-HIV Antibody 4E10 Can Be Reduced without Ablating Neutralizing Activity (2009)

Human 4E10 is one of the broadest-specificity, HIV-1-neutralizing monoclonal antibodies known, recognizing a membrane-proximal linear epitope on gp41. The lipid cross-reactivity of 4E10 has been alternately suggested either to contribute to the apparent rarity of 4E10-like antibody responses in HIV infections, through elimination by B-cell tolerance mechanisms to self-antigens, or to contribute to neutralization potency by virus-specific membrane binding outside of the membrane-proximal external region (MPER). To investigate how 4E10 interacts with membrane and protein components, and whether such interactions contribute to neutralization mechanisms, we introduced two mutations into 4E10 Fv constructs, Trp to Ala at position 100 in the heavy chain [W(H100)A] and Gly to Glu at position 50 in the light chain [G(L50)E], selected to disrupt potential lipid interactions via different mechanisms. Wild-type and mutant Fvs all bound with the same affinity to peptides and monomeric and trimeric gp140s, but the affinities for gp140s were uniformly 10-fold weaker than to peptides. 4E10 Fv binding responses to liposomes in the presence or absence of MPER peptides were weak in absolute terms, consistent with prior observations, and both mutations attenuated interactions even further, as predicted. The W(H100)A mutation reduced neutralization efficiency against four HIV-1 isolates, but the G(L50)E mutation increased potency across the same panel. Electron paramagnetic resonance experiments showed that the W(H100)A mutation, but not the G(L50)E mutation, reduced the ability of 4E10 to extract MPER peptides from membranes. These results show that 4E10 nonspecific membrane binding is separable from neutralization, which is achieved through specific peptide/lipid orientation changes.
Hierarchical pattern matching for knowledge based news categorization (1994)

In this paper we describe how we have combined the use of pattern matching with the exploitation of relation links between objects of a knowledge base, in order to perform a first-level broad categorization (shallow categorization) of natural language texts (agency news). This work has been done in the context of the COBALT system, a text categorization shell which we are developing in the framework of the CEC funded COBALT project (LRE, Linguistic Research and Engineering project n° 61-011). In the COBALT system, concepts are defined as frame like objects organized in a hierarchy for which properties, relations and patterns may be defined. The patterns associated to the concepts' definitions are aimed at identifying the concepts within the text through pattern matching whilst the properties and relations may be used in order to perform categorization according to their specific values in the knowledge base. An inheritance mechanism has been implemented for concept matching inheritance and a rule language has been defined which allows to exploit this inheritance mechanism besides allowing to navigate within the knowledge base structure.
Signal Correlation Prediction Using Convolutional Neural Networks (2015)

This paper focuses on analysing multiple time series relationships such as correlations between them. We develop a solution for the Connectiomics contest dataset of fluorescence imaging of neural activity recordings - the aim is reconstruction of the wiring between brain neurons. The model is implemented to achieve high evaluation score. Our model took the fourth place in this contest. The performance is similar to the other leading solutions, thus we showed that deep learning methods for time series processing are comparable to the other approaches and have wide opportunities for further improvement. We discuss a range of methods and code optimisations applied for the convolutional neural network for the time series domain.
Specific nutrient supplementation of defined serum-free medium for the improvement of CHO cells growth and t-PA production (2006)

Recombinant CHO TF70R cells are able to grow and produce t-PA on serum-free medium BIOPRO1 (BioWhitaker Europe, Belgium). The purpose of the present study was to determine the effect of medium supplementation with vitamins, lipids, and specific amino acids on cell growth, t-PA production and biological functionality. Among vitamins, only biotin, folic acid, cobalamine and benzoic acid were required for improving growth and t-PA production. Lipid supplement allowed a significant increase cell concentration and t-PA specific activity and concentration, though its specific production rate decreased slightly. Medium supplementation with proline, serine and asparagine had also positive effects on cell growth. Besides, the addition of asparagine (even in the presence of glutamine) was essential for the production and biological quality of the t-PA. This systematic approach for media supplementation produced an increase in cell concentration around 100% and in t-PA production around 80%, with no detrimental effect on its biological activity. The effect of asparagine on t-PA production was unexpected and needs to be further studied. The above modifications of the production medium did not produce a significant effect on the metabolism of the main carbon and energy sources (glucose and glutamine) and the level of by-product formation (lactate and ammonia).
Total internal reflection mirrors with ultra-low losses in 3 µm thick SOI waveguides (2015)

Total internal reflection (TIR) mirrors represent an ultra-compact and flexible method to turn light in a photonic integrated circuit (PIC). These can also have very broadband and polarisation independent operation. This paper presents results from 90 degree strip waveguide turning mirrors with novel geometry on a 3 μm SOI waveguide platform. The new TIR mirrors have record-low insertion loss of 0.08 dB/mirror. They are compared with previous designs that have demonstrated insertion losses down to 0.15 dB/mirror. The test structures consisted of up to 96 consecutive mirrors and were fabricated in a multi-project wafer run. The multi-moded test devices only propagate light in the fundamental mode. The mirrors can be used in single-mode PICs that combine low losses, small polarisation dependency, wide bandwidth and small footprint.
Initial clinical experience with the ADAPT technique: A direct aspiration first pass technique for stroke thrombectomy (2013)

This initial experience highlights the fact that the importance of the technique with which new stroke thrombectomy devices are used may be as crucial as the device itself. The ADAPT technique is a simple and effective approach to acute ischemic stroke thrombectomy. Utilizing the latest generation of large bore aspiration catheters in this fashion has allowed us to achieve excellent clinical and angiographic outcomes.
Safety, tumor trafficking and immunogenicity of chimeric antigen receptor (CAR)-T cells specific for TAG-72 in colorectal cancer (2017)

These findings demonstrate the relative safety of CART72 cells. The limited persistence supports the incorporation of co-stimulatory domains in the CAR design and the use of fully human CAR constructs to mitigate immunogenicity.
Proinflammatory Response of Immature Human Dendritic Cells is Mediated by Dectin‐1 after Exposure toAspergillus fumigatusGerm Tubes (2008)

Dectin-1 was identified as an important receptor for A. fumigatus and C. albicans on human iDCs and was found to be involved in the induction of a proinflammatory cytokine response.
Optimal Electrode Implantation Site for Asynchronous Dipolar Cardiac Pacing (1968)

From the Department of Surgery and the Harrison Department of Surgical Research, University of Pennsylvania School of Medicine, Philadelphia, Pa. * Instructor in Surgery, University of Pennsylvania.
NextGen eXtreme porting (2005)

"Maintenance is really the normal state of an XP project" - Beck. Thus porting is a natural candidate for eXtreme Programming and we present a novel tool-based XP methodology for porting C/C++ programs. The structure provided by our tooling is designed for scalability, to enable XP on large projects porting enterprise-scale codebases. Overall planning and iteration planning of the methodology are assisted by a novel, first-of-its-kind migration orchestrator tool. Automated test, debugging, and audit function are provided as unified support by our refactoring tool framework. We focus on the orchestrator tool and offer preliminary benchmarks with encouraging results.
Self-assembly of random copolymers (2014)

Self-assembly of random copolymers has attracted considerable attention recently. In this feature article, we highlight the use of random copolymers to prepare nanostructures with different morphologies and to prepare nanomaterials that are responsive to single or multiple stimuli. The synthesis of single-chain nanoparticles from random copolymers and their potential applications are also discussed in some detail. We aim to draw more attention to these easily accessible copolymers, which are likely to play an important role in translational polymer research.