gebhart/patrepeval huggingface dataset:
Bioresponsive Copolymers of Poly(N-isopropylacrylamide) with Enzyme-Dependent Lower Critical Solution Temperatures (2010)

Novel thermoreversible copolymers of N-isopropylacrylamide (NIPAAm) with collagenase-sensitive solubility behavior were synthesized by radical polymerization of poly(NIPAAm-co-NASI) and nucleophilic substitution of custom peptides GAPGL-NH(2) and GAPGLF-NH(2). The materials were characterized by nuclear magnetic resonance spectroscopy (NMR), gel permeation chromatography in conjunction with static light scattering, differential scanning calorimetry (DSC), and cloud point determination. Successful synthesis and specific degradation by collagenase above and below the material LCST was confirmed by NMR. The LCST behavior of the polymers was affected by collagenase. The LCST of the copolymers, as measured by cloud point determination, increased by 1 and 9 degrees C, respectively, after enzymatic degradation. DSC thermographs indicated increased polymer solubility after enzymatic degradation because of a reduced energy of gelation. These results demonstrate the significant impact of a single amino acid on the LCST behavior of thermosensitive copolymers. Furthermore, the results suggest that comonomers in similar systems could be designed to elicit phase transitions or conformation changes in response to a variety of enzymes for which the substrate structure is known.
Detection of Differences in the Nucleotide and Amino Acid Sequences of Diphtheria Toxin fromCorynebacterium diphtheriaeandCorynebacterium ulceransCausing Extrapharyngeal Infections (2003)

While Corynebacterium ulcerans can mimic classical diphtheria, extrapharyngeal infections are extremely rare. Sequencing of the diphtheria toxin (DT)-encoding tox gene of two C. ulcerans isolates from extrapharyngeal infections revealed differences from C. diphtheriae DT sequences, mainly in the translocation and receptor-binding domains. C. ulcerans supernatants were much less potent than supernatant from C. diphtheriae. A C. ulcerans DT-specific PCR is described below.
The Evolution: From Car Audio to Digital Mobile Multimedia (1997)

&lt;div class="htmlview paragraph"&gt;New advances in wireless and digital communication technologies are causing the traditional car audio system to undergo a radical transformation. The historic function of providing high-quality music and sound reproduction to the consumer will continue; however, additional data and information services will soon be available to consumers using ancillary high-speed data channels available in the new Digital Audio Broadcasting (DAB) systems.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The European developed EUREKA/147 DAB system represents leading-edge technology and has already been introduced in several global markets. This proven system has demonstrated the capability for providing excellent quality music, along with significant data-casting capabilities. Potential benefits to the consumer include the ability to receive traffic management information, digital news and weather services, slow-speed video images, and even subscription services such as personal paging and messages. The traditional “audio” system will soon become an integral part of the wireless-link to the many information and data-services which are currently available.&lt;/div&gt;
SOSIMPLE: A Serverless, Standards-based, P2P SIP Communication System (2006)

Voice over IP (VoIP) and instant messaging (IM) systems to date have either followed a client-server model or have required the use of clients that do not follow any VoIP or IM standard. We present SOSIMPLE - a fully decentralized, P2P, standards-based approach to communications. By building on the existing SIP/SIMPLE infrastructure for VoIP and IM, we support reuse of clients, network infrastructure, and open-source protocol stacks designed using current standards. By avoiding traditional centralized architectures, SOSIMPLE addresses corporate privacy concerns, eliminates dependency on constant Internet connectivity, and supports ad hoc groups. SOSIMPLE implements a DHT overlay based on Chord (Stoicha et al., 2001) using SIP messages, replicating location information for reliability. The DHT is used only for lookups, with actual communication passing directly between clients. We discuss important issues for security and authentication, as well as adaptations of conventional P2P routing for the social networks typical of personal communications. We are testing a prototype implementation of SOSIMPLE and anticipate a public release in the near future
Global health risks: progress and challenges (2009)

WHO's upcoming report Global health risks will identify the global and regional mortality and disease burden associated with 24 health risks. These risk factors range from environmental risks such as exposure to smoke from indoor solid fuel use, to metabolic risks such as high blood pressure. The report finds that five leading risk factors (childhood underweight, unsafe sex, alcohol use, unsafe water and sanitation, and high blood pressure) are responsible for one-quarter of all deaths in the world and one-fifth of all disability-adjusted life years (DALYs). Success in reducing exposure to these five risk factors alone would increase global life expectancy by nearly 5 years.
Regulation of Immunoglobulin Expression in Mouse Myeloma Cells (1977)

Recent experimental evidence suggests that all the somatic cells of a given individual have considerable genetic potential and may be genetically identical (Gurdon 1974; Illmensee and Mintz 1976). In addition, the vertebrate cell contains a number of genes which encode the constant regions of the different classes and subclasses of immunoglobulin heavy (H) and light (L) polypeptide chains, as well as the genes for some, if not all, of the heavy- and light-chain variable regions that the individual can express. Furthermore, the cells of a heterozygous individual contain the information to synthesize two different allelic products of each gene (Cebra 1969). In spite of this large genetic potential, most somatic cells never express any immunoglobulin (Ig) genes at all, and the fully differentiated plasma cell usually produces large amounts of only one class or subclass of H and L chain and one set of variable regions. The molecular mechanisms responsible
On certificate-based security protocols for wireless mobile communication systems (1997)

Mutual authentication and session key exchange protocols based on certificates for the wireless mobile communication/computing system are proposed. First, two improved versions for the conventional certificate-based systems are proposed, and an offline authentication mechanism based on the dynamic certificate is introduced. Then, an end-to-end internetwork-authenticated session key exchange protocol, which preserves a private communication between two mobile users, is finally proposed. In designing the security protocols proposed, the low computational power of the mobile stations and the low bandwidth of the wireless networks are considered.
Inhibition of Src Impairs the Growth of Met-Addicted Gastric Tumors (2010)

Src is as a key downstream transducer of Met-driven tumor growth. Targeting Src might provide therapeutic benefit in Met-addicted tumors.
Mammalian In Vitro Splicing Assays (2003)

Splicing reactions are typically carried out using nuclear extracts, S100 extracts complemented with SR proteins, or partially purified fractions derived from the crude extracts. The extract preparation procedures are described in Chapter 24 . Extracts derived from HeLa cells are used most commonly (see Note 1). The pre-mRNA substrates are usually prepared by in vitro runoff transcription with a bacteriophage polymerase (see Chapter 1 ). The intermediates and products of splicing are most conveniently visualized by urea/polyacrylamide gel electrophoresis (urea-PAGE) and autoradiography, which requires the use of labeled pre-mRNA substrate. The protocols provided here are based on ref. 1, with modifications introduced in refs. 2,3, and have been routinely used in our laboratory for many years.
The Stanford CoreNLP Natural Language Processing Toolkit (2014)

Christopher Manning, Mihai Surdeanu, John Bauer, Jenny Finkel, Steven Bethard, David McClosky. Proceedings of 52nd Annual Meeting of the Association for Computational Linguistics: System Demonstrations. 2014.
Anchoring of Silyl Donors on a N‐Heterocyclic Carbene through the Cobalt‐Mediated Silylation of Benzylic CH Bonds (2013)

Pep up your carbene catalyst: A sequential cobalt-mediated CH activation and silylation protocol has been developed for the preparation of novel silyl-donor-functionalized NHC complexes (see scheme; Mes=mesityl; R=H, Me, Ph). The resulting cobalt complexes exhibited high activity and selectivity as catalysts for the hydrosilylation of olefins.
Approximation of three dimensional mask effects with two dimensional features (2005)

As an important resolution enhancement technique (RET), alternating aperture phase shift masks (AAPSM) has been widely adopted in 90 nm technology node and beyond. Mask topographical effect due to the 3D nature of the shifter features is becoming an increasingly important factor in lithography modeling. Rigorous 3D modeling of PSM is very computationally demanding thus impractical for full chip optical proximity correction (OPC). Here we introduce an alternative approach employing boundary layers to effectively approximate the 3D mask effect. We will present the model calibration versus real wafer data using the boundary layers and the corresponding OPC correction flow.
Meta‐analysis of Genome‐Wide Association Studies Identifies Novel Loci Associated With Optic Disc Morphology (2015)

Primary open-angle glaucoma is the most common optic neuropathy and an important cause of irreversible blindness worldwide. The optic nerve head or optic disc is divided in two parts: a central cup (without nerve fibers) surrounded by the neuroretinal rim (containing axons of the retinal ganglion cells). The International Glaucoma Genetics Consortium conducted a meta-analysis of genome-wide association studies consisting of 17,248 individuals of European ancestry and 6,841 individuals of Asian ancestry. The outcomes of the genome-wide association studies were disc area and cup area. These specific measurements describe optic nerve morphology in another way than the vertical cup-disc ratio, which is a clinically used measurement, and may shed light on new glaucoma mechanisms. We identified 10 new loci associated with disc area (CDC42BPA, F5, DIRC3, RARB, ABI3BP, DCAF4L2, ELP4, TMTC2, NR2F2, and HORMAD2) and another 10 new loci associated with cup area (DHRS3, TRIB2, EFEMP1, FLNB, FAM101, DDHD1, ASB7, KPNB1, BCAS3, and TRIOBP). The new genes participate in a number of pathways and future work is likely to identify more functions related to the pathogenesis of glaucoma.
Disruption of Anthrax Toxin Binding with the Use of Human Antibodies and Competitive Inhibitors (1999)

The protective antigen (PA83) of Bacillus anthracis is integral to the mechanism of anthrax toxicity. We have isolated a human single-chain Fv antibody fragment (scFv) that blocks binding of a fluorescently tagged protective antigen (PA) moiety to cell surface receptors. Several phage-displayed scFv were isolated from a naive library biopanned against PA83. Soluble, monomeric scFv were characterized for affinity and screened for their capacity to disrupt receptor-mediated binding of PA. Four unique scFv bound to PA83, as determined by surface plasmon resonance, the tightest binder exhibiting a Kd of 50 nM. Two scFv had similar affinities for natural PA83 and a novel, recombinant, 32-kDa carboxy-terminal PA fragment (PA32). Binding of scFv to green fluorescent protein fused to the amino-terminal 32-kDa fragment of B. anthracis edema factor, EGFP-EF32, was used to confirm specificity. Fusion of EGFP to PA32 facilitated development of a novel flow cytometric assay that showed that one of the scFv disrupted PA receptor binding. This method can now be used as a rapid assay for small molecule inhibitors of PA binding to cell receptors. The combined data presented suggest the potential utility of human scFv as prophylactics against anthrax poisoning. Moreover, recombinant PA32 may also be useful as a therapeutic agent to compete with anthrax toxins for cellular receptors during active infection.
IMMU-130, a unique antibody-drug conjugate (ADC) of SN-38 targeting CEACAM5 antigen: Preclinical basis for clinical activity in metastatic colorectal cancer (mCRC). (2015)

625 Background: IMMU-130 is a CEACAM5-targeted ADC, labetuzumab-SN-38, with the drug being the active form of the topoisomerase I inhibitor, CPT-11, and substituted at 7-8 moles/mole of IgG. This agent is in phase I/II clinical trials in patients with relapsed mCRC (NCT01270698; NCT01605318). Methods: Therapy experiments were conducted in female athymic nude mice (n=5-10 per group), 4-6 weeks of age, bearing s.c. LS174T human colon carcinoma xenografts of ~0.2 cm 3 size, or 2 weeks after lung metastases were generated by i.v. injection of GW-39 human colon carcinoma cells. Untreated controls, including a non-targeting ADC, were included. Biodistribution was examined in the s.c model using a single 12.5-mg/kg dose of the ADC or unconjugated labetuzumab, each spiked with 111 In-labeled substrate. Tolerability studies were conducted in white New Zealand rabbits. Results: In the metastatic model, fractionated dosing of a total of 50 mg/kg of ADC showed that 2 × the schedules of twice-weekly × 2 weeks with 1 week off and once-weekly × 2 weeks with 1 week off doubled the median survival vs. untreated mice, and were better than a 25-mg/kg dose given on days 1 and 15 (p &lt; 0.0474; log-rank). Pre-dosing with as much as twice the dose of labetuzumab as the ADC dose in the metastatic model did not affect median survival (p &gt; 0.15). Therapy experiments in the s.c. model revealed that IMMU-130, with 50% of drug released in ~20 h, was superior to the conjugate with an ultrastable linker, that the ADC was better than an MTD of 5FU/leucovorin chemotherapy (p &lt; 0.0001), and that the ADC could be combined with bevacizumab for improved efficacy (p &lt; 0.031). Significantly better efficacy for the specific ADC vs. nonspecific ADC was observed. Pharmacokinetics in mice indicated ~25% longer half-life for the unconjugated MAb vs. ADC, but with minimal impact on tumor uptake. A tolerability study in rabbits showed the NOAEL to be the human equivalent dose of 40-60 mg/kg, given as two doses. Conclusions: Preclinical data show an excellent therapeutic window for IMMU-130, which appears to be translated into the clinical experience thus far. The potential for combination therapy is also indicated.
PixelNet: Towards a General Pixel-level Architecture (2016)

We explore architectures for general pixel-level prediction problems, from low-level edge detection to mid-level surface normal estimation to high-level semantic segmentation. Convolutional predictors, such as the fully-convolutional network (FCN), have achieved remarkable success by exploiting the spatial redundancy of neighboring pixels through convolutional processing. Though computationally efficient, we point out that such approaches are not statistically efficient during learning precisely because spatial redundancy limits the information learned from neighboring pixels. We demonstrate that (1) stratified sampling allows us to add diversity during batch updates and (2) sampled multi-scale features allow us to explore more nonlinear predictors (multiple fully-connected layers followed by ReLU) that improve overall accuracy. Finally, our objective is to show how a architecture can get performance better than (or comparable to) the architectures designed for a particular task. Interestingly, our single architecture produces state-of-the-art results for semantic segmentation on PASCAL-Context, surface normal estimation on NYUDv2 dataset, and edge detection on BSDS without contextual post-processing.
Prólogo Vol.2(2) (2011)

Este número contiene 9 artículos inéditos.
Color image quantization for frame buffer display (1982)

Algorithms for adaptive, tapered quantization of color images are described. The research is motivated by the desire to display high-quality reproductions of color images with small frame buffers. It is demonstrated that many color images which would normally require a frame buffer having 15 bits per pixel can be quantized to 8 or fewer bits per pixel with little subjective degradation. In most cases, the resulting images look significantly better than those made with uniform quantization. The color image quantization task is broken into four phases: 1) Sampling the original image for color statistics 2) Choosing a colormap based on the color statistics 3) Mapping original colors to their nearest neighbors in the colormap 4) Quantizing and redrawing the original image (with optional dither). Several algorithms for each of phases 2-4 are described, and images created by each given.
Internet resource discovery services (1993)

An overview of resource discovery services currently available on the Internet is presented. The authors concentrate on the following discovery tools: the Wide Area Information Servers (WAIS) project, Archie, Prospero, Gopher. The World-Wide Web (WWW), Netfind, the X.500 directory, Indie, the Knowbot Information Service (KIS), Alex, Semantic File Systems, and Nomenclator. The authors summarize the surveyed tools by presenting a taxonomy of their characteristics and design decisions. They also describe where to find and how to access several of the surveyed discovery services. They conclude with a discussion of future directions in the area of resource discovery and retrieval.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
F-SSCP: fluorescence-based polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) analysis. (1992)

A fluorescence-based method for polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) analysis, F-SSCP, was developed in which the target sequence is amplified by the PCR using fluorescent primers. The amplified products are then heat-denatured and applied to a water-jacket controlled gel in an automated DNA sequencer. The separated strands are detected as laser-excited fluorescence at the bottom of the gel, and mutations are detected as shifts in the position of the peaks in the fluorogram. The system does not involve radioactivity, and the conditions of electrophoresis are more strictly controlled than in the previous system, which relied on ambient air-cooling to maintain the gel at a constant temperature. The nature of the output data allows direct quantitative interpretation, and so the relative abundance of each allele in a mixture of two or more alleles can easily be estimated. The application of F-SSCP for detection of mutations and loss of heterozygosities of p53 in tumor tissues is reported.
Introduction to differential power analysis (2011)

The power consumed by a circuit varies according to the activity of its individual transistors and other components. As a result, measurements of the power used by actual computers or microchips contain information about the operations being performed and the data being processed. Cryptographic designs have traditionally assumed that secrets are manipulated in environments that expose no information beyond the specified inputs and outputs. This paper examines how information leaked through power consumption and other side channels can be analyzed to extract secret keys from a wide range of devices. The attacks are practical, non-invasive, and highly effective—even against complex and noisy systems where cryptographic computations account for only a small fraction of the overall power consumption. We also introduce approaches for preventing DPA attacks and for building cryptosystems that remain secure even when implemented in hardware that leaks.
Properties of a reversible soluble–insoluble cellulase and its application to repeated hydrolysis of crystalline cellulose (1989)

Cellulase was covalently immobilized on an enteric coating polymer, Eudragit L, that is reversibly soluble and insoluble depending on the pH of the medium. The hydrolysis of solid cellulose with the immobilized enzyme can take advantage of the soluble property of the immobilized enzyme itself at the most reactive pH value; on the other hand, recovery of the enzyme can take advantage of the insoluble property of the enzyme at other pH values. It was experimentally confirmed that 100% of immobilized enzyme activity in solution can be recovered by precipitation and by dissolving it again by alternative change of pH. After a period of hydrolysis, immobilized enzyme and unreacted cellulose were precipitated together to remove the product-the soluble sugar solution-by changing pH. Following this, a new buffer solution was added to the precipitate to dissolve it and resume the reaction. This was repeated several times. The hydrolysis rate of this process increased significantly compared with that of a batch process. Utilization of the reversible soluble-insoluble carrier for immobilizing enzyme is promising, not only for cellulose-cellulase systems, but also for other heterogeneous reaction systems.
Multiplex ligation-dependent probe amplification (MLPA) for ultrasensitive multiplexed microRNA detection using ribonucleotide-modified DNA probes (2013)

Using the ribonucleotide-modified DNA probes, multiple microRNAs can be simultaneously detected in one ligation-based PCR reaction. As low as 0.2 fM microRNA can be accurately detected with high specificity.
A Dynamic Interface for Capsaicinoid Systems Biology (2009)

Capsaicinoids are the pungent alkaloids that give hot peppers (Capsicum spp.) their spiciness. While capsaicinoids are relatively simple molecules, much is unknown about their biosynthesis, which spans diverse metabolisms of essential amino acids, phenylpropanoids, benzenoids, and fatty acids. Pepper is not a model organism, but it has access to the resources developed in model plants through comparative approaches. To aid research in this system, we have implemented a comprehensive model of capsaicinoid biosynthesis and made it publicly available within the SolCyc database at the SOL Genomics Network (http://www.sgn.cornell.edu). As a preliminary test of this model, and to build its value as a resource, targeted transcripts were cloned as candidates for nearly all of the structural genes for capsaicinoid biosynthesis. In support of the role of these transcripts in capsaicinoid biosynthesis beyond correct spatial and temporal expression, their predicted subcellular localizations were compared against the biosynthetic model and experimentally determined compartmentalization in Arabidopsis (Arabidopsis thaliana). To enable their use in a positional candidate gene approach in the Solanaceae, these genes were genetically mapped in pepper. These data were integrated into the SOL Genomics Network, a clade-oriented database that incorporates community annotation of genes, enzymes, phenotypes, mutants, and genomic loci. Here, we describe the creation and integration of these resources as a holistic and dynamic model of the characteristic specialized metabolism of pepper.
Photodiode performance and nanostructure of polythiophene/C60 blends (1997)

Highly efficient photovoltaic devices , constructed using polythiophene derivatives blended with fullerenes, are described. The photovoltaic behavior of the sandwich‐structure devices (current‐voltage characteristic, conversion efficiency) is reported and the electrical, optical (optical absorption, photoluminescence), and morphological properties of the blends are presented. The importance of the morphology of the films is pointed out: it can determine the photovoltaic properties of the devices.