gebhart/patrepeval huggingface dataset:
A triggered-suicide system designed as a defense against bacteriophages (1997)

A novel bacteriophage protection system for Lactococcus lactis based on a genetic trap, in which a strictly phage-inducible promoter isolated from the lytic phage phi31 is used to activate a bacterial suicide system after infection, was developed. The lethal gene of the suicide system consists of the three-gene restriction cassette LlaIR+, which is lethal across a wide range of gram-positive bacteria. The phage-inducible trigger promoter (phi31P) and the LlaIR+ restriction cassette were cloned in Escherichia coli on a high-copy-number replicon to generate pTRK414H. Restriction activity was not apparent in E. coli or L. lactis prior to phage infection. In phage challenges of L. lactis(pTRK414H) with phi31, the efficiency of plaquing was lowered to 10(-4) and accompanied by a fourfold reduction in burst size. Center-of-infection assays revealed that only 15% of infected cells released progeny phage. In addition to phage phi31, the phi31P/LlaIR+ suicide cassette also inhibited four phi31-derived recombinant phages at levels at least 10-fold greater than that of phi31. The phi31P/LlaIR+-based suicide system is a genetically engineered form of abortive infection that traps and eliminates phages potentially evolving in fermentation environments by destroying the phage genome and killing the propagation host. This type of phage-triggered suicide system could be designed for any bacterium-phage combination, given a universal lethal gene and an inducible promoter which is triggered by the infecting bacteriophage.
<i>N</i>-[3-(2-Dimethylaminoethyl)-2-methyl-1<i>H</i>- indol-5-yl]-4-fluorobenzamide:  A Potent, Selective, and Orally Active 5-HT<sub>1F</sub> Receptor Agonist Potentially Useful for Migraine Therapy (2001)

Recent studies have demonstrated that selective 5-HT(1F) receptor agonists inhibit neurogenic dural inflammation, a model of migraine headache, indicating that these compounds may be effective therapies for the treatment of migraine pain. This communication describes the synthesis and discovery of a novel compound, N-[3-(2-(dimethylamino)ethyl)-2-methyl-1H-indol-5-yl]-4-fluorobenzamide (4), which possesses high binding affinity and selectivity at the 5-HT(1F) receptor relative to more than 40 other serotonergic and nonserotonergic receptors examined.
Low-jitter single-photon detector arrays integrated with silicon and aluminum nitride photonic chips (2015)

We present progress on a scalable scheme for integration of single-photon detectors with silicon and aluminum nitride photonic circuits. We assemble arrays of low-jitter waveguide-integrated single-photon detectors and show up to 24% system detection efficiency.
Technique for absolute measurement of noise power at all radio frequencies (1975)

A method and system for absolute measurement of noise power is described. The method is valid at all radio frequencies but is particularly useful above 65 GHz where no other means for making such measurements currently exists. In addition, it has the important advantages of relative simplicity and reliability.
On-Demand Bot Detection and Archival System (2017)

Unusually high correlation in activities among users in social media is an indicator of bot behavior. We have developed a system, called DeBot, that identifies such bots in Twitter network. Our system reports and archives thousands of bot accounts every day. DeBot is an unsupervised method capable of detecting bots in a parameter-free fashion. In February 2017, DeBot has collected over 710K unique bots since August 2015. Since we are detecting and archiving Twitter bots on a daily basis, we have the ability to offer two different services based on our bot detection system. The first one is a bot archive API that makes it easy for researchers to query the DeBot's archive. This API can be used to answer various queries: Is a given Twitter account a bot? When was this bot active in the past? Which twitter accounts were detected as bots on a specific date? The second service that we offer is an on-demand bot detection platform which can detect bots that are related to a given topic or geographical location, and report them to the user in few hours. This paper explains all the details of the services we offer on top of the DeBot's bot detection engine.
Judgement of Color Difference of Fabrics (1997)

The purpose of this paper is to develop a color difference judging method, in which we introduce the standard region of color difference judgement by an expert who engages in the color inspection on woven fabrics.In our color judging method by Fuzzy inference, we construct standard value, limited value and tilt angle for every element region into which CIELAB color space is divided.The membership functions used in Fuzzy inference rules are designed in correspondence to color discriminating region of an expert which defines standard values and limited values for judgement. The optimization coefficient ki (I=1-4) which optimizes membership functions is used to apply color difference judgement to whole color space. Therefore this method enables us to carry out the color difference judgement by Fuzzy inference whenever the reference color value exists in CIELAB.As the result of the computer simulation using fabric samples, we pointed out that the present method is useful in constructing the color difference judgement system which is equivalent to the visual judgement by an expert.
Increased intrathecal inflammation in progressive multiple sclerosis (S12.001) (2015)

OBJECTIVE: To assess the presence of intrathecal inflammation by combining immunophenotyping of cerebrospinal fluid (CSF) cells with measurements of immune-cell specific soluble biomarkers. BACKGROUND: The lack of therapeutic efficacy of immunomodulatory therapies in progressive multiple sclerosis (MS) has been interpreted as evidence that neurodegeneration, rather than immunopathology, drives central nervous system (CNS) tissue destruction. METHODS: The CSF of 386 subjects, including relapsing-remitting (RRMS), secondary-progressive (SPMS), primary-progressive MS (PPMS), non-inflammatory neurological disorders (NIND), other inflammatory neurological disorders (OIND), and healthy donors (HD) was processed in a blinded fashion using standardized protocol. An electroluminescent assay was optimized to quantify soluble CD14 (sCD14), sCD163, sCD21 and sCD27 in the CSF. The cellular origin of these biomarkers was assessed from purified immune cell subtypes. Absolute numbers of each cell subtype were quantified by flow cytometry in 50-fold concentrated CSF. The ratio of specific soluble biomarker per number of CSF cells that secrete it was used to assess mobile (i.e. present in the CSF) versus stationary (i.e. embedded in CNS tissue) pool of immune cells in different patients. RESULTS: All MS groups had elevated levels of B cell-specific (sCD21) and T cell-specific (sCD27) biomarkers as compared to NIND and HD. Monocyte/microglial biomarkers sCD14 and sCD163 levels were elevated in SPMS and PPMS compared to RRMS and NIND. Patients with progressive MS subtypes had also significantly elevated sCD27/T cell ratios in comparison to RRMS. CONCLUSIONS: Our results indicate that the numbers of intrathecal T and B cells in progressive MS is comparable to RRMS. Instead, the major difference is that in RRMS the immune cells are mobile, while in progressive MS they are predominantly embedded in CNS tissue. This compartmentalization of the adaptive immune responses in both subtypes of progressive MS may be the major reason for the failure of current immunomodulatory treatments.
Combined Cardioprotectant and Antithrombotic Actions of Platelet P2Y12 Receptor Antagonists in Acute Coronary Syndrome (2013)

Since the P2Y12 receptor antagonists were first introduced, they have been extensively tested in patients with acute coronary syndrome and are now standard of care. These antiplatelet drugs are very effective in reducing subsequent cardiovascular events, stent thromboses, and mortality in patients with acute myocardial infarction undergoing reperfusion therapy. Although the prevailing view is that their benefit derives from their antithrombotic properties, other unrelated pleiotropic effects appear to be equally beneficial. Accumulating clinical and animal evidence indicates that, if present at the time of reperfusion, these drugs have a direct anti-infarct effect similar to that of ischemic postconditioning. Four oral antagonists have been developed in rapid succession: ticlopidine, clopidogrel, prasugrel, and ticagrelor. Each agent had a more consistent and rapid onset of action than the previous one, and this has correlated with improved clinical outcomes when given early in treatment. Unfortunately, gut absorption causes an appreciable delay in the onset of effect, especially when morphine is used, and the constant push to minimize the door-to-balloon time has made it difficult to achieve adequate platelet inhibition at the time of percutaneous coronary intervention with an oral agent. An intravenous P2Y12 antagonist such as cangrelor may optimize treatment because it produces nearly maximal inhibition of platelet aggregation within minutes. If antiplatelet agents do protect through postconditioning's mechanism, then they would render any other intervention that protects through that mechanism redundant. Indeed, animals treated with cangrelor cannot be further protected by pre- or postconditioning. However, interventions that use a different mechanism such as mild hypothermia or cariporide, a Na(+)-H(+) exchange blocker, do add to cangrelor's protection. Future research should be directed toward identifying interventions that can augment the protection from antiplatelet therapy and finding a way to optimize P2Y12 inhibition at reperfusion in all patients.
A study on hourglass-worm gearings with arcuate tooth profiles. The curvature effects on the constitution of the surface of contact. (1990)

The most conventional hourglass-worm gear has a tooth profile of a straight type. This paper introduces an arcuate profile in the hourglass-worm gearing. The worm gear tooth surface is treated as being generated by a torus-shaped grinding wheel that has a circular axial section, and the effects of the radius of the axial section on the constitution of the surface of contact of the tooth surfaces are investigated. Consequently, the followings were clarified : (1) In the region spreading from the central section to the end section of the tooth meshing, the angle between the contact line and the realative velocity of gears can be designed virtually on a right angle. (2) The limit normal point curve can be set on the end-meshing section of the worm thread.
Air-coupled acoustic radiation force for non-contact generation of broadband mechanical waves in soft media (2016)

A non-contact method for efficient, non-invasive excitation of mechanical waves in soft media is proposed, in which we focus an ultrasound (US) signal through air onto the surface of a medium under study. The US wave reflected from the air/medium interface provides radiation force to the medium surface that launches a transient mechanical wave in the transverse (lateral) direction. The type of mechanical wave is determined by boundary conditions. To prove this concept, a home-made 1 MHz piezo-ceramic transducer with a matching layer to air sends a chirped US signal centered at 1 MHz to a 1.6 mm thick gelatin phantom mimicking soft biological tissue. A phase-sensitive (PhS)-optical coherence tomography system is used to track/image the mechanical wave. The reconstructed transient displacement of the mechanical wave in space and time demonstrates highly efficient generation, thus offering great promise for non-contact, non-invasive characterization of soft media, in general, and for elasticity measurements in delicate soft tissues and organs in bio-medicine, in particular.
MaP Peptides:  Programming the Self-Assembly of Peptide-Based Mesoscopic Matrices (2005)

We describe an approach that utilizes nonlinear peptides to direct the assembly of previously reported Self-Assembling Fibers (SAFs). The SAF system comprises two complementary linear peptides, SAF-p1 and SAF-p2a, which combine to form exclusively linear, nonbranched fibers. The Matrix-Programming (MaP) peptides described herein are based on these peptides: they comprise two or three half-peptide blocks derived from the SAF peptides, which are conjugated via dendritic hubs. Different MaP peptides coassembled with the standard SAF peptides to form specific structures, such as hyperbranched networks, polygonal matrices, and regularly segmented and terminated fibers. The role of each half-peptide block in dictating the different features has been elucidated. This provides a strong basis for designing new peptide-based nanostructured materials from the bottom up.
Introducing industrial-grade MEMS sensors to the seismic industry (2015)

Summary The scale and complexity of seismic acquisition systems have increased by orders of magnitude over the last 30 years. Efficiency and economy of operation is facilitated by the evolution of miniature, high-reliability electronics, but conventional seismic sensors have now become a limiting factor in new system design. The solution is to utilize silicon wafer processing technology to manufacture a new generation of seismic sensors. Although geophones built on microelectro-mechanical system (MEMS) technology have been used for more than a decade, a new effort was needed to develop a generation of highly integrated 3C accelerometers that could meet the combined requirements of cost, size, power, and reliability. Aimed at utilizing proven MEMS technology, a novel electronics solution was developed to achieve uncompromised performance with small, low-cost sensor elements. The architecture embeds the sensor in a force-feedback loop that suppresses all effects of resonances and tolerance variations in the sensor elements. A fully integrated digital 3C sensor is built by combining one application-specific integrated circuit (ASIC) and three MEMS elements in a lightweight multichip module. Small size and low power consumption permit the use of 20,000 three-axis sensors in a single marine seismic streamer. This MEMS geophone has been in commercial use since 2012, and we have never had to replace a streamer section due to MEMS-related problems.
High Frequency Wobbles: A Write Clock Generation Method for Rewritable Digital Versatile Disk (DVD) That Enables Near Drop-In Compatibility with DVD-Read Only Memories (DVD-ROMs) (2000)

This paper describes a write clock generation scheme for rewritable digital versatile disk (DVD) which eliminates a major issue for drop-in compatibility with DVD-read only memories (DVD-ROMs). The method used is to co-locate a high frequency clock reference next to the data using a wobble groove. This enables bit accurate edits on rewritable DVD media.
Work in progress: temporal energy hybrid subtraction in intravenous digital subtraction angiography. (1983)

A preliminary investigation of the feasibility and practical clinical utility of combined temporal energy (hybrid) subtraction for intravenous digital subtraction angiography (DSA) was performed in 19 selected patients. Studies of carotid, aortic arch, pulmonary, and aortorenal vessels were obtained. Soft-tissue misregistration artifacts were effectively removed with hybrid subtraction. Image integration was used to produce a signal-to-noise ratio equivalent to that of single frame temporal subtraction. Diagnostic improvements were produced in 20% of the examinations. Hybrid subtraction techniques resulted in an average increase of incident radiation dose to the skin of 15%.
Incremental Self-Evolving Framework for Agent-Based Simulation (2016)

This paper presents a self-evolving scheme of an agent-based simulation to improve agent simulation models to fit real world data in an incremental way without human intervention by machine learning techniques. The proposed method can solve problems of traditional optimization methods of the agent-based simulation by the incremental optimization of agent simulation models. In this paper, we introduce requirements, the structure and internal functions of the self-evolving agent-based simulation framework for social simulation.
Deploying Intrusion-Tolerant SCADA for the Power Grid (2019)

While there has been considerable research on making power grid Supervisory Control and Data Acquisition (SCADA) systems resilient to attacks, the problem of transitioning these technologies into deployed SCADA systems remains largely unaddressed. We describe our experience and lessons learned in deploying an intrusion-tolerant SCADA system in two realistic environments: a red team experiment in 2017 and a power plant test deployment in 2018. These experiences resulted in technical lessons related to developing an intrusion-tolerant system with a real deployable application, preparing a system for deployment in a hostile environment, and supporting protocol assumptions in that hostile environment. We also discuss some meta-lessons regarding the cultural aspects of transitioning academic research into practice in the power industry.
Distributed recovery with K-optimistic logging (2002)

Fault-tolerance techniques based on checkpointing and message logging have been increasingly used in real-world applications to reduce service downtime. Most industrial applications have chosen pessimistic logging because it allows fast and localized recovery. The price that they must pay, however, is the higher failure-free overhead. In this paper, we introduce the concept of K-optimistic logging where K is the degree of optimism that can be used to fine-tune the tradeoff between failure-free overhead and recovery efficiency. Traditional pessimistic logging and optimistic logging then become the two extremes in the entire spectrum spanned by K-optimistic logging. Our approach is to prove that only dependencies on those states that may be lost upon a failure need to be tracked on-line, and so transitive dependency tracking can be performed with a variable-size vector. The size of the vector piggybacked on a message then indicates the number of processes whose failures may revoke the message, and K corresponds to the system-imposed upper bound on the vector size.
Temporally adaptive filtering of noisy image sequences using a robust motion estimation algorithm (1991)

A motion-compensated noise suppression algorithm that employs temporally adaptive filtering along motion trajectories is proposed for image sequences. Filtering is performed via linear minimum mean square error (LMMSE) point estimation. Motion trajectories are determined using a recent motion estimation algorithm, which is capable of performing very well at low signal-to-noise ratios (SNRs). The results suggest that the proposed method is far superior to methods that incorporate implicit or explicit motion compensation, especially in cases of low SNR and/or significant interframe motion.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Interaction of Cyclin-dependent Kinase 5 (Cdk5) and Neuronal Cdk5 Activator in Bovine Brain (1996)

Neuronal cdc2-like kinase (Nclk) purified from bovine brain is a heterodimer of Cdk5 and an essential 25-kDa regulatory subunit (Lew, J., and Wang, J. H. (1995) Trends Biochem. Sci. 20, 33-37). The regulatory subunit is an N-terminal truncated derivative of a 35-kDa protein expressed specifically in brain, hence the name neuronal Cdk5 activator, p25/p35nck5a. In this study, we probe the relationship between the two different forms of Nck5a and their interaction with and activation of Cdk5 in bovine brain extract. Using protein fractionation procedures in combination with Western blot analysis and protein kinase assay, three forms of Cdk5 have been detected in bovine brain: a monomeric Cdk5 that can be activated by bacterially expressed GST-p21nck5a, a heterodimer of Cdk5 and p25nck5a that displays high kinase activity, and a Cdk5.p35nck5a complex that is inactive and refractory to GST-p21nck5a activation. Analysis of the Cdk5.p35nck5a complex by gel filtration chromatography indicated that the complex was part of a macromolecular structure with a molecular mass of approximately 670 kDa. When the macromolecular complex was subjected to gel filtration chromatography in the presence of 10% ethylene glycol, the fractions containing both p35nck5a and Cdk5, although eluting at the same position as control, displayed high kinase activity. The result is compatible with the suggestion that the macromolecular complex contained a kinase inhibitory factor that dissociated from the complex in 10% ethylene glycol.
Remote infrared radiation detection using piezoresistive microcantilevers (1996)

A novel micromechanical infrared (IR) radiation sensor has been developed using commercially available piezoresistive microcantilevers. Microcantilevers coated with a heat absorbing layer undergo bending due to the differential stress between the top layer (coating) and the substrate. The bending causes a change in the piezoresistance and is proportional to the amount of heat absorbed. The microcantilever IR sensor exhibits two distinct thermal responses: a fast one (&lt;ms) and a slower one (∼10 ms). A noise equivalent power (at a modulation frequency of 30 Hz) was estimated to be ∼70 nW/Hz1/2. This value can be further reduced by designing microcantilevers with better thermal isolation that can allow microcantilevers to be used as uncooled IR radiation detectors.
Cover Picture: Bicyclic Peptides with Optimized Ring Size Inhibit Human Plasma Kallikrein and its Orthologues While Sparing Paralogous Proteases (ChemMedChem 7/2012) (2012)

The cover picture shows a novel bicyclic peptide inhibitor of the serine protease plasma kallikrein identified by phage display. By modulating the loop size of the peptide macrocycles, inhibitors with sub-nanomolar potency and an optimal specificity profile could be generated. For more details, see the Communication by Greg Winter, John Tite, Christian Heinis et al. on p. 1173 ff.
Formal Verification of Smart Contracts Using Interface Automata (2019)

Emerging distributed ledger technologies - also known as blockchains - have recently become a hot research topic across a wide variety of industries due to their immutability, availability, security, and more importantly, their ability to execute multi-party agreements or business rules in the form of smart contracts. Smart contracts provide the means to automate and enforce contractual terms between the parties entering the agreement. It is important to guarantee the correctness of such contracts in order to avoid catastrophic events that may require human intervention. This paper presents a method that builds on the interface automata model of computation as a semantic domain to formalize smart contracts. The formal model of computation assigns a precise and unambiguous meaning to smart contracts. Loyalty points are discounts and bonuses provided by companies with the purpose of retaining their loyal customers. The proposed method is evaluated in the context of a loyalty points marketplace. The decentralized, distributed and immutable nature of blockchain provides an appealing platform for the implementation of a loyalty points marketplace, and the formal semantics based on interface automata ensure that violations of the agreement can be detected, and contractual clauses can be enforced by all parties involved in loyalty points transactions.
Modulator design for x‐ray scatter correction using primary modulation: Material selection (2010)

The spatial variation in the effective transmission factor of the modulator blocker due to beam hardening caused by the modulator itself reaches a minimum when the K-edge of the modulator material is near the mean energy of the spectrum. An optimal modulator material selection using the K-edge discontinuity is therefore proposed.