gebhart/patrepeval huggingface dataset:
Photoresist defect diagnosis using a rigorous topography simulator (2002)

Defects in photoresist are often difficult to diagnose, because patterned wafer inspections can only be done after the photoresist is developed. In this paper, defect simulation is used to understand the relation between defects in the photoresist and the resulting photoresist profiles. It is shown that particles and bubbles in the photoresist translate into a wide variety of defective photoresist profiles. Knowledge of the relation between defects and photoresist profiles can assist in yield improvement efforts, since defects may be diagnosed by comparing simulated and observed photoresist profiles.
A polynomial algorithm for gateway generation from formal specifications (1993)

A systematic procedure that takes exponential time to synthesize protocol converters from formal specifications is presented. The algorithm proceeds in two steps: compute the largest common subset of services provided by the two mismatched protocols, and reduce the converter, retaining common services, without traversing the entire machine that represents the composition of the two mismatched protocols. In a number of cases, the converter can be constructed by a memoryless translation of messages from one protocol to another. Conditions under which such stateless conversion is possible are given. Two examples are presented to illustrate the techniques. In the first example, a converter that interconnects a half-duplex protocol with a full-duplex protocol from their formal specifications is computed. In the second example, the polynomial procedure is applied to computation of a converter for interconnecting the SNR and TCP protocols.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Recapitulation of HDV infection in a fully permissive hepatoma cell line allows efficient drug evaluation (2019)

Hepatitis delta virus (HDV) depends on the helper function of hepatitis B virus (HBV), which provides the envelope proteins for progeny virus secretion. Current infection-competent cell culture models do not support assembly and secretion of HDV. By stably transducing HepG2 cells with genes encoding the NTCP-receptor and the HBV envelope proteins we produce a cell line (HepNB2.7) that allows continuous secretion of infectious progeny HDV following primary infection. Evaluation of antiviral drugs shows that the entry inhibitor Myrcludex B (IC<sub>50</sub>: 1.4 nM) and interferon-α (IC<sub>50</sub>: 28 IU/ml, but max. 60-80% inhibition) interfere with primary infection. Lonafarnib inhibits virus secretion (IC<sub>50</sub>: 36 nM) but leads to a substantial intracellular accumulation of large hepatitis delta antigen and replicative intermediates, accompanied by the induction of innate immune responses. This work provides a cell line that supports the complete HDV replication cycle and presents a convenient tool for antiviral drug evaluation.
Tuberculosis Biomarker and Surrogate Endpoint Research Roadmap (2011)

The Centers for Disease Control and Prevention and National Institutes of Health convened a multidisciplinary meeting to discuss surrogate markers of treatment response in tuberculosis. The goals were to assess recent surrogate marker research and to provide specific recommendations for (1) the qualification and validation of biomarkers of treatment outcome; (2) the standardization of specimen and data collection for future clinical trials, including a minimum set of samples and collection time points; and (3) the creation ofa specimen repository to support biomarker testing. This article summarizes these recommendations and provides a roadmap for their implementation.
Phototype design and testing of two fiber-optic spectrochemical emission sensors (1988)

A unique radio frequency-induced helium plasma (RFIHP) sensor and a spark discharge (SD) sensor were designed, and prototype units were developed and tested. Both sensors use an atomic excitation source coupled to a fiber-optic cable and optical spectrometer to monitor in situ the emission intensity of selected elements of interest in the ambient air. Potential applications include vadose zone monitoring of volatile species. The RFIHP sensor was designed to measure the total chlorine concentration from carbon tetrachloride (and other volatile chlorinated hydrocarbons), and the SD sensor was designed to measure in situ concentrations of chlorine-containing compounds. The results of this research demonstrate proof of concept of the theory, but suggest further refinements are necessary to achieve detection sensitivities sufficiently low to be useful for monitoring concentrations of selected elements in vadose zone air. 9 refs., 10 figs.
Hybridly Modelocked Multiwavelength Semiconductor Diode Laser (2002)

We demonstrate a hybridly modelocked multiwavelength semiconductor laser using an intracavity saturable absorber. Intensity autocorrelations show improved interchannel phase coherence versus active modelocking. Eye diagrams illustrate the suppression of mode partition noise and the production of error-free optical pulse trains in each of the multiwavelength channels.
Coronaviruses Resistant to a 3C-Like Protease Inhibitor Are Attenuated for Replication and Pathogenesis, Revealing a Low Genetic Barrier but High Fitness Cost of Resistance (2014)

Viral protease inhibitors are remarkably effective at blocking the replication of viruses such as human immunodeficiency virus and hepatitis C virus, but they inevitably lead to the selection of inhibitor-resistant mutants, which may contribute to ongoing disease. Protease inhibitors blocking the replication of coronavirus (CoV), including the causative agents of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), provide a promising foundation for the development of anticoronaviral therapeutics. However, the selection and consequences of inhibitor-resistant CoVs are unknown. In this study, we exploited the model coronavirus, mouse hepatitis virus (MHV), to investigate the genotype and phenotype of MHV quasispecies selected for resistance to a broad-spectrum CoV 3C-like protease (3CLpro) inhibitor. Clonal sequencing identified single or double mutations within the 3CLpro coding sequence of inhibitor-resistant virus. Using reverse genetics to generate isogenic viruses with mutant 3CLpros, we found that viruses encoding double-mutant 3CLpros are fully resistant to the inhibitor and exhibit a significant delay in proteolytic processing of the viral replicase polyprotein. The inhibitor-resistant viruses also exhibited postponed and reduced production of infectious virus particles. Biochemical analysis verified double-mutant 3CLpro enzyme as impaired for protease activity and exhibiting reduced sensitivity to the inhibitor and revealed a delayed kinetics of inhibitor hydrolysis and activity restoration. Furthermore, the inhibitor-resistant virus was shown to be highly attenuated in mice. Our study provides the first insight into the pathogenicity and mechanism of 3CLpro inhibitor-resistant CoV mutants, revealing a low genetic barrier but high fitness cost of resistance. Importance: RNA viruses are infamous for their ability to evolve in response to selective pressure, such as the presence of antiviral drugs. For coronaviruses such as the causative agent of Middle East respiratory syndrome (MERS), protease inhibitors have been developed and shown to block virus replication, but the consequences of selection of inhibitor-resistant mutants have not been studied. Here, we report the low genetic barrier and relatively high deleterious consequences of CoV resistance to a 3CLpro protease inhibitor in a coronavirus model system, mouse hepatitis virus (MHV). We found that although mutations that confer resistance arise quickly, the resistant viruses replicate slowly and do not cause lethal disease in mice. Overall, our study provides the first analysis of the low barrier but high cost of resistance to a CoV 3CLpro inhibitor, which will facilitate the further development of protease inhibitors as anti-coronavirus therapeutics.
Clean-Label Backdoor Attacks on Video Recognition Models (2020)

Deep neural networks (DNNs) are vulnerable to backdoor attacks which can hide backdoor triggers in DNNs by poisoning training data. A backdoored model behaves normally on clean test images, yet consistently predicts a particular target class for any test examples that contain the trigger pattern. As such, backdoor attacks are hard to detect, and have raised severe security concerns in real-world applications. Thus far, backdoor research has mostly been conducted in the image domain with image classification models. In this paper, we show that existing image backdoor attacks are far less effective on videos, and outline 4 strict conditions where existing attacks are likely to fail: 1) scenarios with more input dimensions (eg. videos), 2) scenarios with high resolution, 3) scenarios with a large number of classes and few examples per class (a "sparse dataset"), and 4) attacks with access to correct labels (eg. clean-label attacks). We propose the use of a universal adversarial trigger as the backdoor trigger to attack video recognition models, a situation where backdoor attacks are likely to be challenged by the above 4 strict conditions. We show on benchmark video datasets that our proposed backdoor attack can manipulate state-of-the-art video models with high success rates by poisoning only a small proportion of training data (without changing the labels). We also show that our proposed backdoor attack is resistant to state-of-the-art backdoor defense/detection methods, and can even be applied to improve image backdoor attacks. Our proposed video backdoor attack not only serves as a strong baseline for improving the robustness of video models, but also provides a new perspective for more understanding more powerful backdoor attacks.
Kinetically Controlled Growth And Shape Formation Mechanism Of Platinum Nanoparticles (1998)

Abstract Many studies on colloidal nanoparticles have focused on the control of nanoparticle size and correlated this to the catalytic activity. Recently, our group has reported for the first time a technique that controlled the shape distribution of Pt nanoparticles. This was done by varying the concentration of the capping polymer and the platinum ion ratio used in the reductive synthesis of colloidal nanoparticles at room temperature. Cubic, tetrahedral and truncated octahedral (TO) particles have been prepared, making it possible to study the catalytic activities of nanoparticles with different shapes and facets. Using transmission electron microscopy (TEM), we imaged the shapes and determined the shape distribution of platinum nanoparticles at different stages of their growth as a function of time. The small nanoparticles formed during the early stages of growth or at high polymer concentration displayed distributions with a dominance of tetrahedral shapes (see Figure la).
Heparanase 2 Interacts with Heparan Sulfate with High Affinity and Inhibits Heparanase Activity (2010)

Heparanase activity is highly implicated in cell dissemination associated with tumor metastasis, angiogenesis, and inflammation. Heparanase expression is induced in many hematological and solid tumors, associated with poor prognosis. Heparanase homolog, termed heparanase 2 (Hpa2), was cloned based on sequence homology. Detailed characterization of Hpa2 at the biochemical, cellular, and clinical levels has not been so far reported, and its role in normal physiology and pathological disorders is obscure. We provide evidence that unlike heparanase, Hpa2 is not subjected to proteolytic processing and exhibits no enzymatic activity typical of heparanase. Notably, the full-length Hpa2c protein inhibits heparanase enzymatic activity, likely due to its high affinity to heparin and heparan sulfate and its ability to associate physically with heparanase. Hpa2 expression was markedly elevated in head and neck carcinoma patients, correlating with prolonged time to disease recurrence (follow-up to failure; p = 0.006) and inversely correlating with tumor cell dissemination to regional lymph nodes (N-stage; p = 0.03). Hpa2 appears to restrain tumor metastasis, likely by attenuating heparanase enzymatic activity, conferring a favorable outcome of head and neck cancer patients.
High-Affinity Mu Opioid Receptor Ligands Discovered by the Screening of an Exhaustively Stereodiversified Library of 1,5-Enediols (2002)

In this communication, we report the synthesis of an exhaustively stereodiversified library of 16 1,5-enediols (2) and the screening of these compounds for mu opioid receptor (MOR) binding. The stereochemical configuration of 2 strongly impacted the binding affinity, and (S,S,S,R)-2 exhibited a Ki of 8.8 nM for MOR, comparable to that of endomorphin-2 (Ki = 1.2 nM). Moreover, compounds 2 exhibited 5-86-fold selectivity for MOR over delta opioid receptor (DOR) and 16-150-fold selectivity for MOR over kappa opioid receptor (KOR). Additionally, analogues of 2 were synthesized which showed the importance of the trans olefin for receptor binding but that modifications of the C-terminal amino acid were well tolerated. Ligand 11 is noteworthy because it retains only one of the amide bonds present in 1, but binds MOR with an affinity of 10 nM and 110- and 600-fold selectivity for MOR over DOR and KOR. These results demonstrate the utility of stereochemical diversity in the discovery of bioactive small molecules.
A Sensitivity Model for Predicting Photonic Crystal Biosensor Performance (2008)

We present a model for predicting photonic crystal label-free biosensor performance based primarily on the spatial distribution of electromagnetic near fields at device resonance. To achieve maximum device sensitivity, the resonant fields can be shaped by careful choice of material and geometrical parameters. The effect of each property on the resonant mode profile, and consequently on sensor performance, is illustrated. A comparison of device sensitivity calculated by both the proposed model and direct rigorous coupled wave analysis simulation supports the validity of our model.
Smoke Detector (2017)

The central task of a Security Incident and Event Manager (SIEM) or Managed Security Service Provider (MSSP) is to detect security incidents on the basis of tens of thousands of event types coming from many kinds of security products. We present Smoke Detector, which processes trillions of security events with the Random Walk with Restart (RWR) algorithm, inferring high order relationships between known security incidents and imperfect secondary security events (smoke) to .nd undiscovered security incidents (fire). By finding previously undetected incidents, Smoke Detector's RWR algorithm is able to increase the MSSP's critical incident count by 19% with a 1.3% FP rate. Perhaps equally importantly, our approach offers significant benefits beyond increased incident detection: (1) It provides a robust approach for leveraging Big Data sensor nets to increase adversarial resistance of protected networks; (2) Our event-scoring techniques enable efficient discovery of primary indicators of compromise; (3) Our con.dence scores provide intuition and tuning capabilities for Smoke Detector's discovered security incidents, aiding incident display and response.
Evaluation of single-nucleotide polymorphisms in CAPN1 for association with meat tenderness in cattle1,2 (2002)

Micromolar calcium activated neutral protease (CAPN1) was evaluated as a candidate gene for a quantitative trait locus (QTL) on BTA29 affecting meat tenderness by characterization of nucleotide sequence variation in the gene. Single-nucleotide polymorphisms (SNP) were identified by sequencing all 22 exons and 19 of the 21 introns in two sires (Piedmontese × Angus located at the U.S. Meat Animal Research Center in Clay Center, NE; Jersey × Limousin located at AgResearch in New Zealand) of independent resource populations previously shown to be segregating meat tenderness QTL on BTA29. The majority of the 38 SNP were found in introns or were synonymous substitutions in the coding regions, with two exceptions. Exons 14 and 9 contained SNP that were predicted to alter the protein sequence by the substitution of isoleucine for valine in Domain III of the protein, and alanine for glycine in Domain II of the protein. The resource populations were genotyped for these two SNP in addition to six intronic polymorphisms and two silent substitutions. Analysis of genotypes and shear force values in both populations revealed a difference between paternal CAPN1 alleles in which the allele encoding isoleucine at position 530 and glycine at position 316 associated with decreased meat tenderness (increased shear force values) relative to the allele encoding valine at position 530 and alanine at position 316 (P < 0.05). The association of maternal alleles with meat tenderness phenotypes is consistent with the hypothesis of CAPN1 as the gene underlying the QTL effect in two independent resource populations and presents the possibility of using these markers for selective breeding to reduce the numbers of animals with unfavorable meat tenderness traits.
Enabling sovereign information sharing using Web Services (2004)

Sovereign information sharing allows autonomous entities to compute queries across their databases in such a way that nothing apart from the result is revealed. We describe an implementation of this model using web services infrastructure. Each site participating in sovereign sharing offers a data service that allows database operations to be applied on the tables they own. Of particular interest is the provision for binary operations such as relational joins. Applications are developed by combining these data services. We present performance measurements that show the promise of a new breed of practical applications based on the paradigm of sovereign information integration.
Thermosensitive Cyclotriphosphazenes (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTThermosensitive CyclotriphosphazenesSang Beom Lee, Soo-Chang Song, Jung-Il Jin, and Youn Soo SohnView Author Information Inorganic Chemistry Laboratory Korea Institute of Science and Technology Seoul 130-650, Korea Department of Chemistry, Korea University Seoul 136-701, Korea Cite this: J. Am. Chem. Soc. 2000, 122, 34, 8315–8316Publication Date (Web):August 15, 2000Publication History Received4 May 2000Published online15 August 2000Published inissue 1 August 2000https://pubs.acs.org/doi/10.1021/ja001542jhttps://doi.org/10.1021/ja001542jrapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views665Altmetric-Citations60LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alcohols,Molecular structure,Organic compounds,Polymers,Substituents Get e-Alerts
Hydrogenation of CO2 at ambient pressure catalyzed by a highly active thermostable biocatalyst (2018)

The discovery of the first thermostable HDCR provides a promising biological alternative for a chemically challenging reaction and might serve as model for the better understanding of catalysts able to efficiently reduce CO<sub>2</sub>. The catalytic activity for reversible CO<sub>2</sub> hydrogenation of this enzyme is the highest activity known for bio- and chemical catalysts and requiring only ambient temperatures and pressures. The thermostability provides more flexibility regarding the process parameters for a biotechnological application.
The human gene for neurotrophic tyrosine kinase receptor type 2 (NTRK2) is located on chromosome 9 but is not the familial dysautonomia gene (1995)

The neurotrophic tyrosine kinase receptor type 2 (NTRK2) gene is a member of the trk family of tyrosine protein kinases, which encode receptors for the nerve growth factor-related proteins known as neurotrophins. The neurotrophins and their receptors have long been considered candidate genes for familial dysautonomia (FD), a hereditary sensory neuropathy resulting from the congenital loss of both sensory and autonomic neurons. The DYS gene has recently been mapped to human chromosome 9q31-q33, and therefore we set out to determine the chromosomal localization of the candidate gene NTRK2. A mouse trkB probe was hybridized to both somatic cell hybrids containing human chromosome 9 and a human chromosome 9 flow-sorted cosmid library. The human homologue of trkB, NTRK2, was assigned to chromosome 9. To localize the NTRK2 gene further, a dinucleotide repeat polymorphism was identified within a cosmid that contains NTRK2 exon sequences. This marker was genotyped in the CEPH reference pedigrees and places the NTRK2 gene near D9S1 on the proximal long arm of human chromosome 9. The NTRK2 gene is located approximately 22 cm proximal to DYS and shows several recombinants in disease families. Therefore, the NTRK2 gene can now be excluded as a candidate gene for familial dysautonomia.
Queuing Network Models for Multi-Channel P2P Live Streaming Systems (2009)

In recent years there have been several large-scale deployments of P2P live video systems. Existing and future P2P live video systems will offer a large number of channels, with users switching frequently among the channels. In this paper, we develop infinite-server queueing network models to analytically study the performance of multi-channel P2P streaming systems. Our models capture essential aspects of multi-channel video systems, including peer channel switching, peer churn, peer bandwidth heterogeneity, and Zipf-like channel popularity. We apply the queueing network models to two P2P streaming designs: the isolated channel design (ISO) and the View-Upload Decoupling (VUD) design. For both of these designs, we develop efficient algorithms to calculate critical performance measures, develop an asymptotic theory to provide closed-form results when the number of peers approaches infinity, and derive near- optimal provisioning rules for assigning peers to groups in VUD. We use the analytical results to compare VUD with ISO. We show that VUD design generally performs significantly better, particularly for systems with heterogeneous channel popularities and streaming rates.