gebhart/patrepeval huggingface dataset:
Recovery Strategies for Parsing Extragrammatical Language (2018)

Practical natural language interfaces must exhibit robust behaviour in the presence of extragrammatical user input. This paper classifies different types of grammatical deviations and related phenomena at the lexical, sentential and dialogue levels and presents recovery strategies tailored to specific phenomena in the classification. Such strategies constitute a tool chest of computationally tractable methods for coping with extragrammaticality in restricted domain natural language. Some of the strategies have been tested and proven viable in existing parsers.
Cloning of antibiotic-resistance genes in Streptomyces. (1983)

Antibiotic-resistance genes were shotgun cloned from antibiotic-producing Streptomyces sp. using pock-forming plasmids (pSF689 and pSF765), as cloning vectors. Streptomyces chartreusis SF1623 and S. lividans 66 were used as host strains. The ribostamycin (RSM) resistance gene was cloned from S. ribosidificus SF733 DNA (on a 2.3 Md PstI fragment) into both S. chartreusis SF1623 and S. lividans 66, using pSF689 as vector. Kanamycin (KM), novobiocin (NB), destomycin (DM) and racemomycin (RM) resistance genes were cloned from S. kanamyceticus M1164, S. spheroides M1469, S. rimofaciens M1470 and S. lavendulae A249 genomic DNA into S. lividans 66, using pSF765 as vector. Furthermore two types of KM resistance determinants derived from S. kanamyceticus M1164 were cloned using S. lividans 66, the pSF689 vector. The RSM resistance gene showed no homology to plasmid pSF733 of S. ribosidificus SF733, but hybridized to PstI or BclI digested total DNA of S. ribosidificus SF733.
Methotrexate Treatment Causes Early Onset of Disease in a Mouse Model of Ross River Virus-Induced Inflammatory Disease through Increased Monocyte Production (2013)

Part of the Togaviridae family, alphaviruses, including chikungunya virus (CHIKV), Sindbis virus (SINV) and Ross River virus (RRV), are able to cause significant inflammatory pathologies ranging from arthritis to encephalitis. Following symptomatic infection with arthritis-associated alphaviruses, patients often experience severe joint pain, affecting distal and small joints, which can last six months or longer. Recently, methotrexate (MTX), a disease modifying anti-rheumatic drug (DMARD), was used to treat patients experiencing chronic rheumatic symptoms following infection with CHIKV. Here, the effect of MTX on Ross River virus disease (RRVD) in mice was examined to better understand its therapeutic potential for alphaviral-induced musculoskeletal disease and to further our knowledge of the development of alphaviral pathologies. Using a mouse model, we analyzed the effect of MTX on RRVD. RRV disease pathogenesis in response to MTX treatment was determined by measuring levels of proinflammatory factors, cellular infiltrates, viral titer and histological analysis of infected tissues. RRV-infected mice receiving MTX treatment rapidly developed musculoskeletal disease, which correlated with a significant influx of inflammatory cell infiltrates into the skeletal muscle tissue. Although no difference was observed in the level of proinflammatory cytokines and chemokines, the viral load increased at early time points post infection in the serum and quadriceps of MTX treated mice, possibly contributing to disease pathogenesis. Results suggest that MTX treatment of acute RRVD in mice provides no therapeutic benefit and underline the importance of inflammatory monocytes in alphaviral induced arthritides.
β-Adrenergic stimulation induces cardiac ankyrin repeat protein expression: involvement of protein kinase A and calmodulin-dependent kinase (2003)

Our study provides the first evidence that overexpression of CARP, which is thought to act as a transcriptional co-repressor, may deteriorate contractile function of the heart tissue. Furthermore, beta-adrenoceptor stimulation and activation of PKA and CaMK have been identified as mechanisms that induce expression of CARP in cardiomyocytes.
Workflow management for paramedical emergency operations within a mobile-static distributed environment (2009)

In this paper we present the OMU Workflow platform and underlaying toolkit we developed based on the Triana Workflows environment, for implementing the Workflow Management of Paramedical Emergency Operations scenario within an intelligent context-aware mobile distributed Peer-to-Grid (P2G) infrastructure. The underlying OMU toolkit is a stand-alone system and the core components are independent of any workflow environment. We discuss the novel hybrid P2G architectural model we designed consolidating Peer-to-Peer and Grid computing research, providing new solutions to a dynamic distributed data-driven scenario that could radically increase the volume and timeliness of available information for decision support during the rescue operations. We also discuss the application of our workflow platform to other domain problems in our future work and the next steps in the path of testing and validation.
AC Impedance Investigations of Proton Conduction in Nafion™ (1993)

AC impedance spectroscopy has been employed to study the conduction of protons in Nafion 117 polymer electrolyte membranes. Both two‐ and four‐electrode geometries have been used to uniquely distinguish between the membrane impedance and the interfacial impedances. The results show that the impedance of Nafion for frequencies up to 100 kHz is characterized by a pure resistance, similar to conventional liquid electrolytes. The frequency dependent features observed using a two‐electrode geometry are shown to be consistent with well‐characterized interfacial impedances and do not arise from ionic conduction in the membrane. These results show that previous two‐electrode studies reported in the literature have misinterpreted the impedance of the electrode interfaces as belonging to the conduction process in the electrolyte.
A Framework for the Development of a Dynamic Adaptive Intelligent User Interface to Enhance the User Experience (2019)

The aim of this paper is to present PhD research that aims to enhance the User Experience by proposing a framework that combines the three core components of: dynamic interfaces; adaptive interfaces; and intelligent interfaces. Initial research into the field has identified a gap at the intersection of these types of interaction. A dynamic interaction understands the user, their device and their physical environment to provide a basic User Experience. An adaptive interaction understands the user's capabilities further to implement an enhanced experience via usability and accessibility whilst recognising the flow of the user and their pipeline. The intelligent interaction builds further upon this through the incorporation of Machine Learning algorithms that assist in making the interface intelligent and provide a personalised experience for each user based upon their end goal. This in turn will reduce a user's cognitive load and enhance their interactive experience with an interface.
Feel what you hear (2011)

The paper describes the creation of a mobile music player accompanied with synchronised haptic feedback to create a novel method of audio playback on a mobile device. There has been extensive research into the development of audio haptic systems to enhance user interaction on mobile devices as well as providing useful information about users' surroundings while way-finding. We investigated an alternative collaboration of haptics and audio feedback which we present here. We believe that this collaboration provides a novel and fun method of interaction with a music playback application.
Ultrafine particles in the urban air: to the respiratory tract--and beyond? (2002)

In 1994, when we introduced the ultrafine particle hypothesis stating that ambient ultrafine particles (UFP; < 0.1 m in aerodynamic diameter) may cause adverse health effects at the first Colloquium for Particulate Air Pollution and Human Mortality and Morbidity in Irvine, California, it was met with friendly skepticism as well as out-right dismissal. Arguments were that UFP are very short-lived and disappear through heterogeneous and homogeneous aggregation within seconds or minutes and therefore are toxicologically irrelevant. These arguments did not recognize that UFP are continuously generated or that ambient UFP contribute very little, if any, mass to ambient PM 10 (particles < 10 m in aerodynamic diameter) or PM 2.5 (particles < 2.5 m in aerodynamic diameter). Indeed, the mass distribution of a typical urban aerosol among the different particle sizes may support this point (Figure This attitude of skepticism has changed considerably. Research teams across the world are working now on UFP, forming multidisciplinary alliances between atmospheric scientists, engineers, epidemiologists, clinicians, and toxicologists. They investigate UFP sources, generation, physicochemical characteristics, behavior in ambient air, and potential effects and underlying mechanisms following their inhalation. Still, sound skepticism lingers, as demonstrated by the title of a presentation at the 2002 meeting of the Health Effects Institute: "Nanoparticles: Are They Real?"
Nanotechnology-enabled flexible and biocompatible energy harvesting (2010)

The development of a method for efficiently harvesting energy from the human body could enable extraordinary advances in biomedical devices and portable electronics. Being electromechanically coupled, nanopiezoelectrics represent a promising new materials paradigm for scavenging otherwise wasted energy, with the ultimate goal of replacing or augmenting batteries. Of particular interest is developing biomechanical energy nanogenerators that are highly efficient, but with flexible form factors for wearable or implantable applications. This perspective presents an overview of the opportunities, progresses, and challenges in the rapidly accelerating field of nanopiezoelectrics. The combination of new nanomaterial properties, novel assembly strategies, and breakthrough device performance metrics suggests a rich platform for a host of exciting avenues in fundamental research and novel applications.
Multiuser detection and turbo multiuser decoding for asynchronous multitone multiple access systems (2003)

We consider multicarrier multiple access architectures that are based on combining discrete multitone (DMT) or filtered multitone (FMT) modulation with multiplexing of tones across users. Communications are asynchronous, e.g., uplink cellular communications. Optimum multiuser detection is formulated for demodulation of multitone signals that experience time and frequency asynchronism and propagate through frequency selective fading channels. Channel coding is also considered and practical decoding based on iterative (turbo) multiuser detection and decoding is investigated. Simplified detection schemes are also devised.
Automatic Homographic Registration of a Pair of Images, with A Contrario Elimination of Outliers (2012)

The RANSAC algorithm (RANdom SAmple Consensus) is a robust method to estimate parameters of a model fitting the data, in presence of outliers among the data. Its random nature is due only to complexity considerations. It iteratively extracts a random sample out of all data, of minimal size sufficient to estimate the parameters. At each such trial, the number of inliers (data that fits the model within an acceptable error threshold) is counted. In the end, the set of parameters maximizing the number of inliers is accepted. The variant proposed by Moisan and Stival consists in introducing an a contrario criterion to avoid the hard thresholds for inlier/outlier discrimination. It has three consequences: The threshold for inlier/outlier discrimination is adaptive, it does not need to be fixed. It gives a decision on the adequacy of the final model: it does not provide a wrong set of parameters if it does not have enough confidence. The procedure to draw a new sample can be amended as soon as one set of parameters is deemed meaningful: the new sample can be drawn among the inliers of this model. In this particular instantiation, we apply it to the estimation of the homography registering two images of the same scene. The homography is an 8-parameter model arising in two situations when using a pinhole camera: the scene is planar (a painting, a facade, etc.) or the viewpoint location is fixed (pure rotation around the optical center). When the homography is found, it is used to stitch the images in the coordinate frame of the second image and build a panorama. The point correspondences between images are computed by the SIFT algorithm.
Occurrence and biological function of cytochrome P450 monooxygenases in the actinomycetes (1991)

Many species within the order Actinomycetales contain one or more soluble cytochrome P450 monooxygenases, often substrate-inducible and responsible for a variety of xenobiotic transformations. The individual cytochromes exhibit a relatively broad substrate specificity, and some strains have the capacity to synthesize large amounts of the protein(s) to compensate for low catalytic turnover with some substrates. All three of the Streptomyces cytochromes sequenced to date are exclusive members of one P450 family, CYP105. In several instances, monooxygenase activity arises from induction of a P450 and associated ferredoxin, or of a P450 only, suggesting that some essential electron donor proteins (reductase and ferredoxin) are not co-ordinately regulated with the cytochrome. The overall properties of these systems suggest an adaptive strategy whose twofold purpose is to maintain a competitive advantage via the production of secondary metabolites, and, whenever possible, to utilize unusual growth substrates by introducing metabolites from these reactions into the more substrate-specific primary metabolic pathways.
Digital image correlation for surface deformation measurement: historical developments, recent advances and future goals (2018)

This article is a personal review of the historical developments of digital image correlation (DIC) techniques, together with recent important advances and future goals. The historical developments of DIC techniques over the past 35 years are divided into a foundation-laying phase (1982–1999) and a boom phase (2000 to the present), and are traced by describing some of the milestones that have enabled new and/or better DIC measurements to be made. Important advances made to DIC since 2010 are reviewed, with an emphasis on new insights into the 2D-DIC system, new improvements to the correlation algorithm, and new developments in stereo-DIC systems. A summary of the current state-of-the-art DIC techniques is provided. Some further improvements that are needed and the future goals in the field are also envisioned.
Design of coupled reactions for simplification of bioluminescence analysis (1989)

Luminescence analysis may be applied to many substances by arranging a prior reaction producing a species entering the light-emitting reaction. Under favourable conditions the two consecutive reactions are carried out simultaneously as a one-step procedure. In a bioluminescence assay, luciferase stability is frequently a problem, making it desirable to develop analytical schemes where the analytical response becomes largely independent of any impaired luciferase activity. The value of maximal emission or an approached steady-state level is a convenient and usually well-defined analytical parameter. When recording this level it is important to design the participating reactions in a way that compensates for changes in luciferase activity.
SSE: a nucleotide and amino acid sequence analysis platform (2012)

There is an increasing need to develop bioinformatic tools to organise and analyse the rapidly growing amount of nucleotide and amino acid sequence data in organisms ranging from viruses to eukaryotes. A simple sequence editor (SSE) was developed to create an integrated environment where sequences can be aligned, annotated, classified and directly analysed by a number of built-in bioinformatic programs. SSE incorporates a sequence editor for the creation of sequence alignments, a process assisted by integrated CLUSTAL/MUSCLE alignment programs and automated removal of indels. Sequences can be fully annotated and classified into groups and annotated of sequences and sequence groups and access to analytical programs that analyse diversity, recombination and RNA secondary structure. Methods for analysing sequence diversity include measures of divergence and evolutionary distances, identity plots to detect regions of nucleotide or amino acid homology, reconstruction of sequence changes, mono-, di- and higher order nucleotide compositional biases and codon usage. Association Index calculations, GroupScans, Bootscanning and TreeOrder scans perform phylogenetic analyses that reconcile group membership with tree branching orders and provide powerful methods for examining segregation of alleles and detection of recombination events. Phylogeny changes across alignments and scoring of branching order differences between trees using the Robinson-Fould algorithm allow effective visualisation of the sites of recombination events. RNA secondary and tertiary structures play important roles in gene expression and RNA virus replication. For the latter, persistence of infection is additionally associated with pervasive RNA secondary structure throughout viral genomic RNA that modulates interactions with innate cell defences. SSE provides several programs to scan alignments for RNA secondary structure through folding energy thermodynamic calculations and phylogenetic methods (detection of co-variant changes, and structure conservation between divergent sequences). These analyses complement methods based on detection of sequence constraints, such as suppression of synonymous site variability. For each program, results can be plotted in real time during analysis through an integrated graphics package, providing publication quality graphs. Results can be also directed to tabulated datafiles for import into spreadsheet or database programs for further analysis. SSE combines sequence editor functions with analytical tools in a comprehensive and user-friendly package that assists considerably in bioinformatic and evolution research.
Characterization of Recombinant, Ureolytic <i>Streptococcus mutans</i> Demonstrates an Inverse Relationship between Dental Plaque Ureolytic Capacity and Cariogenicity (2000)

Dental caries results from prolonged plaque acidification that leads to the establishment of a cariogenic microflora and demineralization of the tooth. Urease enzymes of oral bacteria hydrolyze urea to ammonia, which can neutralize plaque acids. To begin to examine the relationship between plaque ureolytic activity and the incidence of dental caries, recombinant, ureolytic strains of Streptococcus mutans were constructed. Specifically, the ureABCEFGD operon from Streptococcus salivarius 57.I was integrated into the S. mutans chromosome in such a way that the operon was transcribed from a weak, cognate promoter in S. mutans ACUS4 or a stronger promoter in S. mutans ACUS6. Both strains expressed NiCl(2)-dependent urease activity, but the maximal urease levels in ACUS6 were threefold higher than those in ACUS4. In vitro pH drop experiments demonstrated that the ability of the recombinant S. mutans strains to moderate a decrease in pH during the simultaneous metabolism of glucose and urea increased proportionately with the level of urease activity expressed. Specific-pathogen-free rats that were infected with ACUS6 and fed a cariogenic diet with drinking water containing 25 mM urea and 50 microM NiCl(2) had relatively high levels of oral urease activity, as well as dramatic decreases in the prevalence of smooth-surface caries and the severity of sulcal caries, relative to controls. Urease activity appears to influence plaque biochemistry and metabolism in a manner that reduces cariogenicity, suggesting that recombinant, ureolytic bacteria may be useful to promote dental health.
IAF: Examples of Institutions Organizing on Behalf of Families (2016)

In 1997, Samsung received an $80 million tax abatement to build a plant in Austin, Texas amid the promise of “high paying jobs.” People were excited about the company coming to town and there was great buzz, but then they learned that most of the jobs would pay minimum wage. At a meeting of non-profits gathered to learn more about the Samsung jobs and to help them recruit, the company said that they also needed $1 million to train an advance group of 100 workers for six weeks. In addition to forgoing $80 million in tax revenue that this growing city needed, and creating an uneven playing field with direct competitors in the tech industry, now the city of Austin and Travis county were being asked to come up with an additional million dollars. This angered Fr. John Korcsmar, pastor of Dolores Catholic Church. He had come to the meeting in hopes of hearing how his parishioners could work one job to provide for their families instead of two or three. Angry that most jobs would pay minimum wage and that this was not what was promised, Fr. John Korcsmar stood up and said, “We will fight you on this!”
Fluorescence detection of hydroxyl radicals in water produced by atmospheric pulsed discharges (2015)

It has been proven that hydroxyl (OH) radicals can be generated by streamer discharges across water surfaces under ambient atmospheric conditions. Hydroxyl radicals have the highest oxidation capability amongst all oxygen-based reactive species, thus OH play an important role in oxidation of organic molecules and the bactericidal effects of plasma discharges. In this study, generation of hydroxyl radicals in water by pulsed streamer discharges was investigated. Terephthalic acid was used as a chemical probe as this acid is converted into 2-hydroxyterephthalic acid (HTA) by chemical reaction with OH radicals. The concentration of OH radicals was quantified by measuring the fluorescence light intensity generated by HTA molecules in water solutions. Both positive and negative pulsed discharges with different voltage levels were tested. Two different types of sample holder – non-conductive plastic dishes, and dishes lined with conductive aluminum foil – were used in order to investigate the effect of the discharge propagation path on the efficiency of OH production. The efficiency of OH production was measured as a function of: the distance between the needle electrode and the water surface; the magnitude and polarity of HV energization; and the total delivered charge. The obtained results will help in optimization of non-thermal plasma systems for chemical and biological decontamination.