gebhart/patrepeval huggingface dataset:
Plasmonic-Enhanced Photodetectors for Focal Plane Arrays (2011)

Plasmonic enhancement of a quantum-dot infrared photodetector (QDIP) using a corrugated metal surface (CMS) that is fully compatible with conventional focal plane array manufacturing is demonstrated. A CMS consisting of a 2.5-μm period, 2-D square array of 1.1-μ m-high GaAs circular posts passivated with a thick Au film is fabricated into the heavily doped, top GaAs contact layer of an InAs QDIP. For substrate-side illumination, the CMS exhibits strong coupling to surface plasma waves bound to the Au/GaAs interface providing enhancement of the QDIP. At 77 K, the CMS-processed QDIP exhibits up to ~15-fold detectivity enhancement compared with the original detector.
Point‐of‐care testing in haemostasis (2010)

Point-of-care testing (POCT) in haematology has seen a significant increase in both the spectrum of tests available and the number of tests performed annually. POCT is frequently undertaken with the belief that this will reduce the turnaround time for results and so improve patient care. The most obvious example of POCT in haemostasis is the out-of-hospital monitoring of the International Normalized Ratio in patients receiving a vitamin K antagonist, such as warfarin. Other areas include the use of the Activated Clotting Time to monitor anticoagulation for patients on cardio-pulmonary bypass, platelet function testing to identify patients with apparent aspirin or clopidogrel resistance and thrombelastography to guide blood product replacement during cardiac and hepatic surgery. In contrast to laboratory testing, POCT is frequently undertaken by untrained or semi-trained individuals and in many cases is not subject to the same strict quality control programmes that exist in the central laboratory. Although external quality assessment programmes do exist for some POCT assays these are still relatively few. The use of POCT in haematology, particularly in the field of haemostasis, is likely to expand and it is important that systems are in place to ensure that the generated results are accurate and precise.
Identification of Protein-disulfide Isomerase Activity in Fibronectin (1999)

Assembly and degradation of fibronectin-containing extracellular matrices are dynamic processes that are up-regulated during wound healing, embryogenesis, and metastasis. Although several of the early steps leading to fibronectin deposition have been identified, the mechanisms leading to the accumulation of fibronectin in disulfide-stabilized multimers are largely unknown. Disulfide-stabilized fibronectin multimers are thought to arise through intra- or intermolecular disulfide exchange. Several proteins involved in disulfide exchange reactions contain the sequence Cys-X-X-Cys in their active sites, including thioredoxin and protein-disulfide isomerase. The twelfth type I module of fibronectin (I12) contains a Cys-X-X-Cys motif, suggesting that fibronectin may have the intrinsic ability to catalyze disulfide bond rearrangement. Using an established protein refolding assay, we demonstrate here that fibronectin has protein-disulfide isomerase activity and that this activity is localized to the carboxyl-terminal type I module I12. I12 was as active on an equal molar basis as intact fibronectin, indicating that most of the protein-disulfide isomerase activity of fibronectin is localized to I12. Moreover, the protein-disulfide isomerase activity of fibronectin appears to be partially cryptic since limited proteolysis of I10-I12 increased its isomerase activity and dramatically enhanced the rate of RNase refolding. This is the first demonstration that fibronectin contains protein-disulfide isomerase activity and suggests that cross-linking of fibronectin in the extracellular matrix may be catalyzed by a disulfide isomerase activity contained within the fibronectin molecule.
POWER4 system microarchitecture (2002)

The IBM POWER4 is a new microprocessor organized in a system structure that includes new technology to form systems. The name POWER4 as used in this context refers not only to a chip, but also to the structure used to interconnect chips to form systems. In this paper we describe the processor microarchitecture as well as the interconnection architecture employed to form systems up to a 32-way symmetric multiprocessor.
Effect of Microwaves on Escherichia coli and Bacillus subtilis (1967)

Suspensions of Escherichia coli and Bacillus subtilis spores were exposed to conventional thermal and microwave energy at 2,450 MHz. The degrees of inactivation by the different energy sources were compared quantitatively. During the transient heating period by microwave energy, approximately a 6 log cycle reduction in viability was encountered for E. coli. This reduction was nearly identical to what is expected for the same time-temperature exposure to conventional heating. Heating of B. subtilis spores by conventional and microwave energy was also carried out at 100 C, in ice and for transient heating. The degree of inactivation by microwave energy was again identical to that by conventional heating. In conclusion, inactivation of E. coli and B. subtilis by exposure to microwaves is solely due to the thermal energy, and there is no per se effect of microwaves.
Concise Review: Bone Morphogenetic Protein Pleiotropism in Neural Stem Cells and Their Derivatives—Alternative Pathways, Convergent Signals (2006)

Bone morphogenetic proteins (BMPs) are a class of morphogens that are critical regulators of the central nervous system (CNS), peripheral nervous system, and craniofacial development. Modulation of BMP signaling also appears to be an important component of the postnatal stem cell niche. However, describing a comprehensive model of BMP actions is complicated by their paradoxical effects in precursor cells, which include dorsal specification, promoting proliferation or mitotic arrest, cell survival or death, and neuronal or glial fate. In addition, in postmitotic neurons BMPs can promote dendritic growth, act as axonal chemorepellants, and stabilize synapses. Although many of these responses depend on interactions with other incoming signals, some reflect the recruitment of distinct BMP signal transduction pathways. In this review, we classify the diverse effects of BMPs on neural cells, focus on the known mechanisms that specify distinct responses, and discuss the remaining challenges in identifying the cellular basis of BMP pleiotropism. Addressing these issues may have importance for stem cell mobilization, differentiation, and cell integration/survival in reparative therapies.
Enhanced sequencing coverage with digital droplet multiple displacement amplification (2015)

Sequencing small quantities of DNA is important for applications ranging from the assembly of uncultivable microbial genomes to the identification of cancer-associated mutations. To obtain sufficient quantities of DNA for sequencing, the small amount of starting material must be amplified significantly. However, existing methods often yield errors or non-uniform coverage, reducing sequencing data quality. Here, we describe digital droplet multiple displacement amplification, a method that enables massive amplification of low-input material while maintaining sequence accuracy and uniformity. The low-input material is compartmentalized as single molecules in millions of picoliter droplets. Because the molecules are isolated in compartments, they amplify to saturation without competing for resources; this yields uniform representation of all sequences in the final product and, in turn, enhances the quality of the sequence data. We demonstrate the ability to uniformly amplify the genomes of single Escherichia coli cells, comprising just 4.7 fg of starting DNA, and obtain sequencing coverage distributions that rival that of unamplified material. Digital droplet multiple displacement amplification provides a simple and effective method for amplifying minute amounts of DNA for accurate and uniform sequencing.
Design and Synthesis of Phenylpyrrolidine Phenylglycinamides As Highly Potent and Selective TF-FVIIa Inhibitors (2013)

Inhibitors of the Tissue Factor/Factor VIIa (TF-FVIIa) complex are promising novel anticoagulants that show excellent efficacy and minimal bleeding in preclinical models. On the basis of a zwitterionic phenylglycine acylsulfonamide 1, a phenylglycine benzylamide 2 was shown to possess improved permeability and oral bioavailability. Optimization of the benzylamide, guided by X-ray crystallography, led to a potent TF-FVIIa inhibitor 18i with promising oral bioavailability, but promiscuous activity in an in vitro safety panel of receptors and enzymes. Introducing an acid on the pyrrolidine ring, guided by molecular modeling, resulted in highly potent, selective, and efficacious TF-FVIIa inhibitors with clean in vitro safety profile. The pyrrolidine acid 20 showed a moderate clearance, low volume of distribution, and a short t 1/2 in dog PK studies.
A Potent Adjuvant Monophosphoryl Lipid A Triggers Various Immune Responses, but Not Secretion of IL-1β or Activation of Caspase-1 (2006)

Lipid A, the membrane anchor portion of LPS, is responsible for the endotoxin activity of LPS and induces many inflammatory responses in macrophages. Monophosphoryl lipid A (MPL), a lipid A derivative lacking a phosphate residue, induces potent immune responses with low toxicity. To elucidate the mechanism underlying the low toxicity of MPL, we examined the effects of MPL on the secretion of proinflammatory cytokines by mouse peritoneal macrophages, a murine macrophage-like cell line (RAW 264.7), and a human macrophage-like cell line (THP-1). MPL enhanced the secretion of TNF-alpha, but not that of IL-1beta, whereas Escherichia coli-type lipid A (natural source-derived and chemically synthesized lipid A) enhanced the secretion of both cytokines. Although MPL enhanced the levels of IL-1beta mRNA and IL-1beta precursor protein to levels similar to those induced by lipid A, IL-1beta precursor processing in MPL-treated cells was much lower than that in E. coli-type lipid A-treated ones. Moreover, MPL, unlike E. coli-type lipid A, failed to induce activation of caspase-1, which catalyzes IL-1beta precursor processing. These results suggest that an immune response without activation of caspase-1 or secretion of IL-1beta results in the low toxicity of this adjuvant.
<title>LaneLok: robust line and curve fitting of lane boundaries</title> (1993)

The LaneLok function estimates the location of lane boundaries by a least squares approximation. This estimation can be affected by vehicles close to the lane markers in adjacent lanes. A hybrid method which combines the least squares approximation with median filtering for improving the estimation was developed and tested successfully on real-highway scenes.
Bioluminescence of cellular ATP: a new method for evaluating cytotoxic agents in vitro. (1984)

Rat Walker 256 carcinosarcoma, human MCF-7 cell line and a specimen of ovarian serous cystadenocarcinoma were cultured in vitro and exposed to different cytostatic drugs. The drug effects were evaluated by bioluminescence, i.e., by measuring the levels of adenosine triphosphate (ATP), the basic energy source of the living cells. The intracellular ATP was released by TCA or NRS -reagent, and the ATP levels were measured directly from an aliquot of the growth medium without any extraction or precipitation steps. ATP level was significantly correlated with cell number, viability, [3H]-thymidine incorporation and stem cell assay. The most important advantages of bioluminescence method was speed, technical simplicity and good sensitivity (about 500 cells/sample easily quantitated, the results are seen directly within a few seconds) and flexibility (any cell line and drug may be studied by many different test designs). ATP method obviously describes the "well- being" of the cultured cells. According to our experience, the ATP-bioluminescence method is a powerful alternative to any other cell growth estimation method in vitro. It can be used especially in primary screening of the cytostatic activity of any known or unknown substance as well as in attempts to select an individual drug therapy for patients with cancer.
Nonpsychotropic Plant Cannabinoids, Cannabidivarin (CBDV) and Cannabidiol (CBD), Activate and Desensitize Transient Receptor Potential Vanilloid 1 (TRPV1) Channels in Vitro: Potential for the Treatment of Neuronal Hyperexcitability (2014)

Epilepsy is the most common neurological disorder, with over 50 million people worldwide affected. Recent evidence suggests that the transient receptor potential cation channel subfamily V member 1 (TRPV1) may contribute to the onset and progression of some forms of epilepsy. Since the two nonpsychotropic cannabinoids cannabidivarin (CBDV) and cannabidiol (CBD) exert anticonvulsant activity in vivo and produce TRPV1-mediated intracellular calcium elevation in vitro, we evaluated the effects of these two compounds on TRPV1 channel activation and desensitization and in an in vitro model of epileptiform activity. Patch clamp analysis in transfected HEK293 cells demonstrated that CBD and CBDV dose-dependently activate and rapidly desensitize TRPV1, as well as TRP channels of subfamily V type 2 (TRPV2) and subfamily A type 1 (TRPA1). TRPV1 and TRPV2 transcripts were shown to be expressed in rat hippocampal tissue. When tested on epileptiform neuronal spike activity in hippocampal brain slices exposed to a Mg(2+)-free solution using multielectrode arrays (MEAs), CBDV reduced both epileptiform burst amplitude and duration. The prototypical TRPV1 agonist, capsaicin, produced similar, although not identical effects. Capsaicin, but not CBDV, effects on burst amplitude were reversed by IRTX, a selective TRPV1 antagonist. These data suggest that CBDV antiepileptiform effects in the Mg(2+)-free model are not uniquely mediated via activation of TRPV1. However, TRPV1 was strongly phosphorylated (and hence likely sensitized) in Mg(2+)-free solution-treated hippocampal tissue, and both capsaicin and CBDV caused TRPV1 dephosphorylation, consistent with TRPV1 desensitization. We propose that CBDV effects on TRP channels should be studied further in different in vitro and in vivo models of epilepsy.
Inherently Safe Nuclear-Driven Internal Combustion Engines (1991)

A family of nuclear driven engines is described in which nuclear energy released by fissioning of uranium or plutonium in a prompt critical assembly is used to heat a working gas. Engine performance is modeled using a code that calculates hydrodynamics, fission energy production, and neutron transport self-consistently. Results are given demonstrating a large negative temperature coefficient that produces self-shutoff of energy production. Reduced fission product inventory and the self-shutoff provide inherent nuclear safety. It is expected that nuclear engine reactor units could be scaled from 100 MW on up.
Three-Dimensional RNA Structure of the Major HIV-1 Packaging Signal Region (2013)

HIV-1 genomic RNA has a noncoding 5' region containing sequential conserved structural motifs that control many parts of the life cycle. Very limited data exist on their three-dimensional (3D) conformation and, hence, how they work structurally. To assemble a working model, we experimentally reassessed secondary structure elements of a 240-nt region and used single-molecule distances, derived from fluorescence resonance energy transfer, between defined locations in these elements as restraints to drive folding of the secondary structure into a 3D model with an estimated resolution below 10 Å. The folded 3D model satisfying the data is consensual with short nuclear-magnetic-resonance-solved regions and reveals previously unpredicted motifs, offering insight into earlier functional assays. It is a 3D representation of this entire region, with implications for RNA dimerization and protein binding during regulatory steps. The structural information of this highly conserved region of the virus has the potential to reveal promising therapeutic targets.
Overview of the 1994 ARPA human language technology workshop (1994)

This volume presents papers, session summaries, and project summaries from the Second ARPA Human Language Technology Workshop, which was held at the Merrill Lynch Conference Center in Plainsboro, NJ, March 8-11, 1994. The Workshop was actually the seventh in a series of ARPA workshops which began in 1988; the first five were called the DARPA Speech and Natural Language Workshops, and the name was changed to the ARPA Human Language Technology (HLT) Workshop in 1993 to reflect the broadened focus and increasing unification of ARPA-sponsored research in spoken and written language. In addition, the "D" was dropped from DARPA in 1993, reflecting a broadening of its charter. The Proceedings of the seven Workshops, all of which have been published by Morgan-Kaufmann, represent a rich source of information on the rapid progress in spoken and written language technology which has been achieved over the past decade, due in no small measure to the leadership of the ARPA Program Managers.
Kinetic analysis of California oil shale by programmed temperature micropyrolysis. Revision 1 (1991)

Three oil shales from California were examined by micropyrolysis for evolution behavior and pyrolysis kinetic parameters to understand hydrocarbon evolution. The samples consisted of one from the Los Angeles basin, and two from the Monterey formation. The two Monterey shales were distinguished by low and high S contents of the kerogen. The measurements were performed by a Pyromat II micropyrolyzer operating at nominal constant heating rates of 1, 7, and 50 {degrees}C/min, between 250 and 700{degrees}C. The evolution profiles at 50{degrees}C/min heating rate of Los Angeles and the low S Monterey sample were similar, having the same temperature of maximum evolution (T{sub max}) (460{degrees}C) and similar peak widths ({delta}W{sub {1/2}} approximately 70{degrees}C). The high S Monterey shale was much different having a much lower T{sub max} (441{degrees}C) and a much broader profile ({delta}W{sub {1/2}} 119{degrees}C). The derived kinetic parameters of all three shales were different. The principal energy of activation from the discrete method (principal E{sub discrete}) and the energy of activation by the approximate method (E{sub approx}) were (in kcal/mol): 57 and 57 and 54; 52 and 50.6; 57 and 65.2; for Los Angeles, low S Monterey, and high S Monterey, respectively. These values agree with literature values formore » type II kerogens except for the high S Monterey sample, which appears to be anomalously high. 8 refs., 3 figs., 3 tabs.« less
The Location of the Active Site of Blood Coagulation Factor VIIa above the Membrane Surface and Its Reorientation upon Association with Tissue Factor (1996)

The topography of membrane-bound blood coagulation factor VIIa (fVIIa) was examined by positioning a fluorescein dye in the active site of fVIIa via a tripeptide tether to yield fluorescein-D-phenylalanyl-L-prolyl-L-arginyl-fVIIa (Fl-FPR-fVIIa). The location of the active-site probe relative to the membrane surface was determined, both in the presence and absence of tissue factor (TF), using fluorescence energy transfer between the fluorescein dye and octadecylrhodamine (OR) at the phospholipid vesicle surface. When Fl-FPR-fVIIa was titrated with phospholipid vesicles containing OR, the magnitude of OR-, calcium ion-, and phosphatidylserine-dependent fluorescence energy transfer revealed that the average distance of closest approach between fluorescein in the active site of fVIIa and OR at the vesicle surface is 82 A assuming a random orientation of donor and acceptor dyes (kappa2 = 2/3; the orientational uncertainty totals approximately 10%). The active site of fVIIa is therefore located far above the membrane surface, and the elongated fVIIa molecule must bind at one end to the membrane and project approximately perpendicularly out of the membrane. When Fl-FPR-fVIIa was titrated with vesicles that contained TF, the efficiency of energy transfer was increased by a TF-dependent translational and/or rotational movement of the fVIIa protease domain relative to the membrane surface. If this movement was solely translational, the height of the active site of fVIIa was lowered by an average of 6 A after binding to TF. The association of fVIIa with TF on the membrane surface therefore causes a significant reorientation of the active site relative to the membrane surface. This cofactor-dependent realignment of the active-site groove presumably facilitates and optimizes fVIIa cleavage of its membrane-bound substrates.
Compression and transmission of depth maps for image-based rendering (2002)

We consider applications using depth-based image-based rendering (IBR), where the synthesis of arbitrary views occur at a remote location, necessitating the compression and transmission of depth maps. Traditional image compression has been designed to provide maximum perceived visual quality, and a direct application is sub-optimal for depth-map compression, since depth-maps are not directly viewed. In other words, the sensitivity of the rendering error depends on the image content as well as on the depth map, we propose two improvements to take this into account. Firstly, we consider region-of-interest (ROI) coding, where we identify those regions of the image where accurate depth is most crucial. Secondly, we reshape the dynamic range of the depth map. Our experiments show a significant improvement in coding gain (1.1 dB) and rendering quality when we integrated these two improvements into a standard JPEG-2000 coder.
Effect of variations in peptide sequence on anti-human milk fat globule membrane antibody reactions. (1991)

Monoclonal anti-mucine antibodies BC1, BC2 and BC3 produced using human milk fat globule membrane react with a synthetic peptide p1-24 (PDTRPAPGSTAPPAHGVTSAPDTR) representing the repeating amino acid sequence of the mucin core protein. The minimum epitope recognized by these three monoclonal antibodies (mAb) in p1-24 was contained in the five amino acids APDTR. To analyse the variation of position of the epitope, various modifications of the APDTR sequence were made by synthesizing peptides and testing by direct binding and inhibition enzyme-linked immunosorbent assays. Firstly, peptides p13-32 and C-p13-32, in which the epitope APDTR was placed in the middle instead of the C-terminal as in p1-24, were examined. These peptides had a greater reaction with mAb BC1, BC2 and BC3 compared with the reaction with p1-24. Secondly, A-p1-24 and TSA-p1-24 were made wherein two APDTR epitopes were present--these peptides were shown to bind two IgG antibody molecules. Finally, the contribution of each amino acid in the APDTR epitope was studied using the pepscan polyethylene rods, making all 20 of the amino acid substitutions in each position for SAPDTR (the minimum epitope APDTR with an adjacent amino acid S). In the 120 peptides examined there were some 'permissible' substitutions in A, D and T but not in P or R for BC1 and BC2; there were more 'permissible' substitutions for BC3; different substitution patterns were found with each antibody and some substitutions gave an increased reaction compared with the native peptide SAPDTR. The studies are of value in analysing the reaction of antibodies with epitopes expressed in breast cancer and in determining the antigenicity of synthetic peptides.