gebhart/patrepeval huggingface dataset:
Inhibition of the Complement Alternative Pathway by Chemically Modified DNA Aptamers That Bind with Picomolar Affinity to Factor B (2021)

The complement system is a conserved component of innate immunity that fulfills diverse roles in defense and homeostasis. Inappropriate activation of complement contributes to many inflammatory diseases, however, which has led to a renewed emphasis on development of therapeutic complement inhibitors. Activation of complement component C3 is required for amplification of complement and is achieved through two multisubunit proteases called C3 convertases. Of these, the alternative pathway (AP) C3 convertase is responsible for a majority of the C3 activation products in vivo, which renders it an attractive target for inhibitor discovery. In this study, we report the identification and characterization of two related slow off-rate modified DNA aptamers (SOMAmer) reagents that inhibit formation of the AP C3 convertase by binding to the proprotease, factor B (FB). These aptamers, known as SL1102 (31 bases) and SL1103 (29 bases), contain uniform substitutions of 5-(<i>N</i>-2-naphthylethylcarboxyamide)-2'-deoxyuridine for deoxythymidine. SL1102 and SL1103 bind FB with <i>K</i> <sub>d</sub> values of 49 and 88 pM, respectively, and inhibit activation of C3 and lysis of rabbit erythrocytes under AP-specific conditions. Cocrystal structures of SL1102 (3.4 Å) and SL1103 (3.1 Å) bound to human FB revealed that SL1102 and SL1103 recognize a site at the juncture of the CCP1, CCP3, and vWF domains of FB. Consistent with these structures and previously published information, these aptamers inhibited FB binding to C3b and blocked formation of the AP C3 convertase. Together, these results demonstrate potent AP inhibition by modified DNA aptamers and expand the pipeline of FB-binding molecules with favorable pharmacologic properties.
Deep sub-micron static timing analysis in presence of crosstalk (2002)

A complete and accurate method for static timing analysis of deep sub-micron devices in presence of crosstalk is introduced. This scheme provides an efficient platform for fast and accurate static timing verification of large scale transistor and cell level netlists, with coupled interconnects and high switching speeds. This paper presents the solution to the crosstalk problem implemented in the static timing tool PathMill as its crosstalk extension (CTX). A comparison of simulation results between this approach and SPICE is also provided.
Acoustics of Suction Mufflers with Multiple Chambers (2006)

In recent years there has been a growing focus on reducing the suction noise from hermetic household compressors. One approach is to reduce the transmitted sound power through the suction muffler at particular frequencies. In order to better control the acoustic performance of the muffler, a large variety of muffler designs have emerged. Most notably is the appearance of mufflers with two or more chambers which are often connected in series. In this study, the acoustic effects of introducing multiple chambers in series are investigated by use of boundary element and transfer matrix methods. General conclusions are given on the acoustic performance of mufflers with identical and different chambers in series.
Ohmic Contacts to Gallium Aluminum Arsenide for High Temperature Applications (1988)

A new approach for fabricating nonalloyed ohmic contacts to gallium arsenide was developed. The approach uses ultrathin layers of heavily doped germanium or silicon in contact with gallium arsenide to alter the Schottky barrier height(phi B) at the gallium arsenide interface. For n-type gallium arsenide phi B could be varied from about 0.3 to 1.0 eV. The low barriers are useful for tunneling ohmic contacts to n-gallium arsenide while the high barriers should be useful for p-gallium arsenide ohmic contacts and for Field Effect Transistor (FET) gate applications. In some instances it was necessary to interpose a thin nonmetallic electrically conducting barrier between the contact metal and the thin germanium or silicon layer to preserve optimum contact properties. Specific contact resistivity measurements indicated that contact resistivity < 10 to the -6 ohms/sq.cm should be obtainable in practical contacts to heavily doped material. It is generally observed that phi B at most gallium arsenide interfaces is confined to a relatively narrow range presumably due to a large concentration of acceptor and donor states closely spaced in energy near midgap. The new approach for normalized ohmic contact fabrication suggests that these states can be saturated with carriers from the heavily doped germanium silicon so as to substantially modify phi B. The resulting contact phi B is virtually independent of contact metallization; the heterojunction band alignment characteristics at the germanium or silicon interface with gallium arsenide determine the phi B of the contact.
Formalizing Application Integration Patterns (2018)

Enterprise Integration Patterns (EIPs) and their extensions denote the informally described building blocks of current Enterprise Application Integration (EAI) systems. Although a recent approach strives to provide an EIP formalization based on Coloured Petri Nets (CPNs), it does not completely consider EAI requirements, such as complex data, transacted resources and time. In the absence of a comprehensive formal definition, the patterns cannot be verified, and thus a formal foundation of EAI is missing. In this work, we leverage the novel db-net approach that finds a better balance between the data and process-related aspects than CPNs and we extend it according to the EAI requirements that we systematically collect on a pattern level. Then we discuss pattern realizations, and evaluate our approach for comprehensiveness, test correctness, and show its applicability.
An integrated hardware-software approach to flexible transactional memory (2007)

There has been considerable recent interest in both hardware andsoftware transactional memory (TM). We present an intermediateapproach, in which hardware serves to accelerate a TM implementation controlled fundamentally by software. Specifically, we describe an alert on update mechanism (AOU) that allows a thread to receive fast, asynchronous notification when previously-identified lines are written by other threads, and a programmable data isolation mechanism (PDI) that allows a thread to hide its speculative writes from other threads, ignoring conflicts, until software decides to make them visible. These mechanisms reduce bookkeeping, validation, and copying overheads without constraining software policy on a host of design decisions.We have used AOU and PDI to implement a hardwareacceleratedsoftware transactional memory system we call RTM. We have also used AOU alone to create a simpler RTM-Lite. Across a range of microbenchmarks, RTM outperforms RSTM, a publicly available software transactional memory system, by as much as 8.7x (geometric mean of 3.5x) in single-thread mode. At 16 threads, it outperforms RSTM by as much as 5x, with an average speedup of 2x. Performance degrades gracefully when transactions overflow hardware structures. RTM-Lite is slightly faster than RTM for transactions that modify only small objects; full RTM is significantly faster when objects are large. In a strongargument for policy flexibility, we find that the choice between eager (first-access) and lazy (commit-time) conflict detection can lead to significant performance differences in both directions, depending on application characteristics.
A Spectral Framework for Detecting Inconsistency across Multi-source Object Relationships (2011)

In this paper, we propose to conduct anomaly detection across multiple sources to identify objects that have inconsistent behavior across these sources. We assume that a set of objects can be described from various perspectives (multiple information sources). The underlying clustering structure of normal objects is usually shared by multiple sources. However, anomalous objects belong to different clusters when considering different aspects. For example, there exist movies that are expected to be liked by kids by genre, but are liked by grown-ups based on user viewing history. To identify such objects, we propose to compute the distance between different eigen decomposition results of the same object with respect to different sources as its anomalous score. We also give interpretations from the perspectives of constrained spectral clustering and random walks over graph. Experimental results on several UCI as well as DBLP and Movie Lens datasets demonstrate the effectiveness of the proposed approach.
Association Between the 21-Gene Recurrence Score Assay and Risk of Locoregional Recurrence in Node-Negative, Estrogen Receptor–Positive Breast Cancer: Results From NSABP B-14 and NSABP B-20 (2010)

Similar to the association between RS and risk for distant recurrence, a significant association exists between RS and risk for LRR. This information has biologic consequences and potential clinical implications relative to locoregional therapy decisions for patients with node-negative and ER-positive breast cancer.
Towards Pooled-Speaker Concatenative Text-to-Speech (2006)

In this paper we explore the merging of data from various speakers in building a concatenative text-to-speech system. First, we investigate the pooling of data from multiple speakers for building statistical models to predict pitch and duration, and present listening test results which show that the expressiveness of our TTS system is improved using these techniques. Additionally, we describe an experiment in which we merged databases from several speakers to form an enlarged database from which our concatenative text-to-speech system draws segments. We present listening test results which show that pooling data from several speakers yields higher quality synthetic speech in general domains than restricting ourselves to the data from just one speaker in our repertoire
Effects of temperature sensor placement on performance of temperature-controlled ablation [cardiac arrhythmias application] (2002)

The significant changes in power with tissue-electrode angle suggested that the lesions were more predictable when ablating with temperature-based RF generators, rather than non-temperature systems. The maximal tissue temperature was reached at locations within the tissue a fraction of a millimeter away from the ablation electrode surface. The errors in tissue temperature prediction introduced by temperature sensors placed inside the electrode changed with blood flow rate and tissue-electrode angle. This study shows that to reduce tissue temperature prediction errors, during temperature-controlled ablation it was better to use a temperature sensor placed at the tip rather than at the center of the ablation electrode.
Implementation of 60V tolerant dual direction ESD protection in 5V BiCMOS process for automotive application (2004)

A dual-direction ESD protection approach is applied to the problem of 60 V tolerant on-chip protection of the thin film resistors in automotive application circuits realized in 5 V BiCMOS process. A novel method for increasing the breakdown voltage of a blocked N-isolation layer is proposed and validated using process and device numerical simulation followed by experimental measurements.
Comparison of a new specific blood test and the skin test in Tuberculosis contacts (2004)

Abstract The Tuberculin skin test, used to detect latent Mycobacterium tuberculosis infection, has many drawbacks and a new diagnostic test for latent tuberculosis (QuantiFERON ? -TB) has recently been introduced. This test measures the production of interferon-? in whole blood upon stimulation with Purified Protein Derivative. The QuantiFERON ? -TB test addresses the operational problems with the tuberculin skin test, but as the test is based on Purified Protein Derivative it still has a low specificity in populations vaccinated with the BCG vaccine. We have modified the test to include the antigens ESAT-6 and CFP-10 not present in BCG vaccine strains and the vast majority of non-tuberculous mycobacteria. This test was used to detect infection in contacts in a tuberculosis outbreak at a Danish high school. The majority of the contacts were BCG-unvaccinated which allowed a direct comparison of the skin test and the novel blood test in individuals whose skin test was not confounded by vaccination. An excellent agreement between the two tests was found (94%, kappa value 0.866) and in contrast to the blood test based on Purified Protein Derivative the novel blood test was not in fluenced by the vaccination status of the subjects tested. Word count: 192 Keywords: TB, Latent infection, whole blood diagnostic, BCG, TST
<title>Organic light-emitting devices for ultralightweight color flat panel displays</title> (1997)

We review recent progress in small molecule organic light emitting devices (OLEDs) with emphasis on their potential application to lightweight, head-up displays. We discuss OLEDs grown on thin, flexible, plastic substrates which may be bent over a radius of curvature of as little as 0.7 cm without damage and exhibit operating voltages and efficiencies similar to OLEDs grown on conventional glass substrates. Transparent OLEDs grown on such substrates create the potential for a new type of lightweight, full- color, OLED pixel in which the R, G and B emission layers are vertically stacked to provide a simple fabrication process, minimum pixel size, and maximum fill factor.
<title>Data embedding method</title> (1996)

Data embedding is a new steganographic method for combining digital information sets. This paper describes the data embedding method and gives examples of its application using software written in the C-programming language. Sandford and Handel produced a computer program (BMPEMBED, Ver. 1.51 written for IBM PC/AT or compatible, MS/DOS Ver. 3.3 or later) that implements data embedding in an application for digital imagery. Information is embedded into, and extracted from, Truecolor or color-pallet images in Microsoft<SUP>TM</SUP> bitmap (BMP) format. Hiding data in the noise component of a host, by means of an algorithm that modifies or replaces the noise bits, is termed `steganography.' Data embedding differs markedly from conventional steganography, because it uses the noise component of the host to insert information with few or no modifications to the host data values or their statistical properties. Consequently, the entropy of the host data is affected little by using data embedding to add information. The data embedding method applies to host data compressed with transform, or `lossy' compression algorithms, as for example ones based on discrete cosine transform and wavelet functions. Analysis of the host noise generates a key required for embedding and extracting the auxiliary data from the combined data. The key is stored easily in the combined data. Images without the key cannot be processed to extract the embedded information. To provide security for the embedded data, one can remove the key from the combined data and manage it separately. The image key can be encrypted and stored in the combined data or transmitted separately as a ciphertext much smaller in size than the embedded data. The key size is typically ten to one-hundred bytes, and it is derived from the original host data by an analysis algorithm.
Influences of Trabecular Structure on Ultrasonic Wave Propagation in Bovine Cancellous Bone (1997)

Ultrasonic wave propagation in water-saturated bovine cancellous (spongy) bone has been experimentally studied in vitro by a pulse transmission technique. The propagation of fast and slow longitudinal waves in bovine cancellous bone [rf:1] is examined in relation to porosity using Biot's and Wyllie's equations to estimate the measured speeds versus porosity. In the high porosity range, the trabecular structure influences the propagation of the fast and slow waves in cancellous bone.
Structure-Activity Study of Tripeptide Thrombin Inhibitors Using .alpha.-Alkyl Amino Acids and Other Conformationally Constrained Amino Acid Substitutions (1995)

In our continuing effort to design novel thrombin inhibitors, a series of conformationally constrained amino acids (e.g. alpha-alkyl, N-alkyl cyclic, etc.) were utilized in a systematic structure-activity study of the P3, P2, and P1 positions of tripeptide arginal thrombin inhibitors. Early examples of this effort include: D-MePhe-Pro-Arg-H (15), Boc-D-Phg-Pro-Arg-H (18), D-1-Tiq-Pro-Arg-H (23, D-1-Tiq = D-1,2,3,4-tetrahydroisoquinolin-1-ylcarbonyl), and Boc-D-Phe-Pro-Arg-H (25).10a,20 The current work clarifies the contribution of each residue of the tripeptide arginals toward the potent and selective inhibition of thrombin relative to that of t-PA and plasmin. The alpha-methylarginal modification in the P1 residue resulted in analogs 30 (D-MePhe at P3) and 32 (D-1-Tiq at P3) which had lower potency toward thrombin while exhibiting improved selectivity. Analogs modified at the P2 site were found to be very sensitive to the conformational changes induced by variations in side chain ring size with the flexible pipecolinic acid 31 being 2 orders of magnitude less potent at thrombin inhibition than the conformationally constrained azetidine analog 20. Examination of the P3 binding region indicated that alpha-alkylphenylglycine residues resulted in a tendency to exhibit substantial improvements in selectivity over the nonalkylated residues. Combinations of optimal P3 and P2 changes led to compounds TFA-D-Phg(alpha Et)-Azt-Arg-H (16), TFA-D-Phg(alpha Me)-Azt-Arg-H (17), Ac-D-Phg(alpha Me)-Azt-Arg-H (21), TFA-D-Phg(alpha Me)-Pro-Arg-H (27), 30, and 32, which are clearly more selective for thrombin versus plasmin than the nonconformationally constrained compounds.
Epitopes for human CD4<sup>+</sup> cells on diphtheria toxin: Structural features of sequence segments forming epitopes recognized by most subjects (1995)

The sequence regions of diphtheria toxin (DTX) recognized by CD4+ T cells of seven healthy humans of different major histocompatibility complex haplotypes were identified. Overlapping synthetic peptides, screening the DTX sequence, were used to test in proliferation assays unselected blood CD4+ cells, or DTX-specific CD4+ lines propagated by stimulation with DTX of blood mononuclear cells. Blood CD4+ cells and DTX-specific CD4+ lines gave consistent results. Although each subject had an individual pattern of peptide recognition, six peptide sequences (residues 271-290, 321-340, 331-350, 351-370, 411-430 and 431-450) were recognized by all subjects. In the native DTX molecule, these sequence regions are flanked by sequence loops exposed on the DTX surface. They overlap uncharged segments of the DTX sequence. These structural properties may be general requirements for immunodominance in CD4+ cell sensitization in humans.
An approach to proteomic analysis of human tumors (2000)

A strategy for proteomic analysis of microdissected cells derived from human tumor specimens is described and demonstrated by using esophageal cancer as an example. Normal squamous epithelium and corresponding tumor cells from two patients were procured by laser-capture microdissection and studied by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Fifty thousand cells resolved approximately 675 distinct proteins (or isoforms) with molecular weights ranging between 10 and 200 kDa and isoelectric points of pH 3–10. Comparison of the microdissected protein profiles showed a high degree of similarity between the matched normal-tumor samples (98% identical). However, 17 proteins showed tumor-specific alterations, including 10 that were uniquely present in the tumors and seven that were observed only in the normal epithelium. Two of the altered proteins were characterized by mass spectrometry and immunoblot analysis and were identified as cytokeratin 1 and annexin I. Acquisition of 2D-PAGE protein profiles, visualization of disregulated proteins, and subsequent determination of the identity of selected proteins through high-sensitivity MS-MS microsequencing are possible from microdissected cell populations. These separation and analytical techniques are uniquely capable of detecting tumor-specific alterations. Continued refinement of techniques and methodologies to determine the abundance and status of proteins in vivo holds great promise for future study of normal cells and associated neoplasms. Mol. Carcinog. 27:158–165, 2000. Published by Wiley-Liss Inc.
Nanostructured polyaniline decorated graphene sheets for reversible CO2 capture (2012)

The current scientific community is extensively involved in developing novel materials for energy and environmental applications. Capture of CO2 to remove it from the atmosphere is one of the most important applications among them. In the present work, we have demonstrated for the first time, to the best of our knowledge, a polyaniline–graphene nanocomposite as a CO2 capture candidate. Graphene was prepared by hydrogen induced thermal exfoliation of graphite oxide and was further coated with polyaniline using a chemical method. The nanocomposite was characterized by different techniques and the capture capacity was measured using a high pressure Sievert’s apparatus. FTIR spectroscopy was used to confirm the possible CO2 capture mechanism in the nanocomposite. CO2 adsorption capacities at a pressure of 11 bar and different temperatures of 25, 50 and 100 °C were experimentally found to be 75, 47 and 31 mmol g−1, respectively. This nanocomposite shows much higher CO2 capture capacity compared to pure graphene and shows a high degree of recyclability.
Quantizer design for exploiting common information in layered coding (2016)

Today's diverse data consumption devices and heterogeneous network conditions require content to be coded at different quality levels. Conventional scalable coding, which generates hierarchical layers that refine quality incrementally, introduces a performance penalty, as most sources are not successively refinable at finite delays for the distortion measure employed and the combination of rates at each layer. On the other hand encoding different copies at required quality levels is clearly wasteful in resources. We previously proposed a common information based framework with a relaxed hierarchical structure to generate common and individuals bit-streams for different quality levels, to provide the flexibility of operating at points between conventional scalable coding and independent coding. In this paper we propose a quantizer design technique for this layered coding framework, which enables extracting common information between two quality levels with negligible performance penalty. Experimental results for Laplacian sources, which are prevalent in practical multimedia systems, substantiate the effectiveness of our proposed technique.