gebhart/patrepeval huggingface dataset:
Isozyme-dependent Sensitivity of Adenylyl Cyclases to P-site-mediated Inhibition by Adenine Nucleosides and Nucleoside 3′-Polyphosphates (1997)

Recombinant adenylyl cyclase isozyme Types I, II, VI, VII, and three splice variants of Type VIII were compared for their sensitivity to P-site-mediated inhibition by several adenine nucleoside derivatives and by the family of recently synthesized adenine nucleoside 3'-polyphosphates (Désaubry, L., Shoshani, I., and Johnson, R. A. (1996) J. Biol. Chem. 271, 14028-14034). Inhibitory potencies were dependent on isozyme type, the mode of activation of the respective isozymes, and on P-site ligand. For the nucleoside derivatives potency typically followed the order 2',5'-dideoxyadenosine (2',5'-ddAdo) > beta-adenosine > 9-(cyclopentyl)-adenine (9-CP-Ade) >/= 9-(tetrahydrofuryl)-adenine (9-THF-Ade; SQ 22,536), with the exception of Type II adenylyl cyclase, which was essentially insensitive to inhibition by 9-CP-Ade. For the adenine nucleoside 3'-polyphosphates inhibitory potency followed the order Ado < 2'-dAdo < 2',5'-ddAdo and 3'-mono- < 3'-di- < 3'-triphosphate. Differences in potency of these ligands were noted between isozymes. The most potent ligand was 2',5'-dd-3'-ATP with IC50 values of 40-300 nM. The data demonstrate isozyme selectivity for some ligands, suggesting the possibility of isozyme-selective inhibitors to take advantage of differences in P-site domains among adenylyl cyclase isozymes. Differential expression of adenylyl cyclase isozymes may dictate the physiological sensitivity and hence importance of this regulatory mechanism in different cells or tissues.
Towards data mining benchmarking (2000)

Performance benchmarking has played an important role in the research and development in relational DBMS, object-relational DBMS, data warehouse systems, etc. We believe that benchmarking data mining algorithms is a long overdue task, and it will play an important role in the research and development of data mining systems as well. Frequent pattern mining forms a core component in mining associations, correlations, sequential patterns, partial periodicity, etc., which are of great potential value in applications. There have been a lot of methods proposed and developed for efficient frequent pattern mining in various kinds of databases, including transaction databases, time-series databases, etc. However, so far there is no serious performance benchmarking study of different frequent pattern mining methods. To facilitate an analytical comparison of different frequent mining methods, we have constructed an open test bed for performance study of a set of recently developed, popularly used methods for mining frequent patterns in transaction databases and mining sequential patterns in sequence databases, with different data characteristics. The testbed consists of the following components. A synthetic data generator, which can generate large sets of synthetic data in various kinds of data distributions. A few large data sets from real world applications will also be provided. A good set of typical frequent pattern mining methods, ranging from classical algorithms to recent studies. The method are grouped into three classes: frequent pattern mining, max-pattern mining , and sequential pattern mining . For frequent pattern mining, we will demonstrate Apriori, hashing, partitioning, sampling, TreeProjection, and FP-growth. For maximal pattern mining, we will demonstrate MaxMiner, TreeProjection, and FP-growth-max. For sequential pattern mining, we will demonstrate GSP and FreeSpan. A set of performance curves. These algorithms their running speeds, scalabilities, bottlenecks, and performance on different data distributions, will be compared and demonstrated upon request. Some performance curves from our pre-conference experimental evaluations will also be shown. An open testbed. Our goal is to construct an extensible test bed which integrates the above components and supports an open-ended testing service. Researchers can upload the object codes of their mining algorithms, and run them in the test bed using these data sets. The architecture is shown in Figure 1. This testbed is our first step towards benchmarking data mining algorithms. By doing so, performance of different algorithms can be reported consistently, on the same platform, and in the same environment. After the demo, we plan to make the testbed available on the WWW so that it may, hopefully, benefit further research and development of efficient data mining methods.
Antineoplastic agents. 193. Isolation and structure of the cyclic peptide hymenistatin 1 (1990)

The Western Pacific Ocean sponge Hymeniacidon sp. was found to contain a cyclo-octapeptide designated hymenistatin 1 (1) active against the P388 leukemia cell line (ED 50 3.5 μg/mL). Structural determination was accomplished utilizing high field NMR (400 MHz) and mass spectral techniques (FAB MS/MS) followed by chiral gas chromatographic analysis to establish the absolute configuration (all S-amino acids). Keywords: cytostatic, Hymeniacidon, hymenistatin, cyclo-octapeptide, P388 leukemia.
Growth of CZT using additionally zone-refined raw materials (2012)

Results will be presented for the growth of CdZnTe by the low pressure Bridgman growth technique. To decrease deeplevel trapping and improve detector performance, high purity commercial raw materials will be further zone refined to reduce impurities. The purified materials will then be compounded into a charge for crystal growth. The crystals will be grown in the programmable multi-zone furnace (PMZF), which was designed and built at Northrop Grumman‟s Bethpage facility to grow CZT on Space Shuttle missions. Results of the purification and crystal growth will be presented as well as characterization of crystal quality and detector performance.
An Improved Ultra-High Temperature Microscope and Its Functional Features (1977)

An ultra-high temperature microscope was newly designed and constructed, and it has three noticeable advantages as follows. First, the maximum temperature of specimens is available more than 2500°C by electron beam heating. Secondly, the exchange procedures of specimens become more easy by using an air-lock mechanism, so-called the side-entry goniostage. Thirdly, the image contrast even under high temperatures is kept as high as that at room temperature, as the direct radiation from the heating specimen is cut off from the imaging ray by means of narrow band pass filters.In addition, an infrared pyrometer was ready to use any programming of heating and cooling of specimens, in combination with the electron beam gun. The expected functional features were attained very successfully and some preliminary applications were also obtained.
ESD protection solutions for high voltage technologies (2004)

There is a trend to revive mature technologies while including high voltage options. ESD protection in those technologies is challenging due to narrow ESD design windows, NMOS degradation issues and the creation of unexpectedly weak parasitic devices. Different case studies are presented for ESD protection based on latch-up immune SCR devices.
Speech Dereverberation Based on Maximum-Likelihood Estimation With Time-Varying Gaussian Source Model (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Distant acquisition of acoustic signals in an enclosed space often produces reverberant components due to acoustic reflections in the room. Speech dereverberation is in general desirable when the signal is acquired through distant microphones in such applications as hands-free speech recognition, teleconferencing, and meeting recording. This paper proposes a new speech dereverberation approach based on a statistical speech model. A time-varying Gaussian source model (TVGSM) is introduced as a model that represents the dynamic short time characteristics of nonreverberant speech segments, including the time and frequency structures of the speech spectrum. With this model, dereverberation of the speech signal is formulated as a maximum-likelihood (ML) problem based on multichannel linear prediction, in which the speech signal is recovered by transforming the observed signal into one that is probabilistically more like nonreverberant speech. We first present a general ML solution based on TVGSM, and derive several dereverberation algorithms based on various source models. Specifically, we present a source model consisting of a finite number of states, each of which is manifested by a short time speech spectrum, defined by a corresponding autocorrelation (AC) vector. The dereverberation algorithm based on this model involves a finite collection of spectral patterns that form a codebook. We confirm experimentally that both the time and frequency characteristics represented in the source models are very important for speech dereverberation, and that the prior knowledge represented by the codebook allows us to further improve the dereverberated speech quality. We also confirm that the quality of reverberant speech signals can be greatly improved in terms of the spectral shape and energy time-pattern distortions from simply a short speech signal using a speaker-independent codebook. </para>
NKT cells induce IgG1 class switch against <i>C. difficile</i> carbohydrate antigens and enhance immunity against a live pathogen challenge (2019)

Abstract All clinical Clostridioides difficile strains identified to date express a surface capsule-like polysaccharide structure known as polysaccharide II (PSII). The PSII antigen is immunogenic and when conjugated to a protein carrier and induces a protective antibody response in animal models. Given that CD1d-restricted Natural Killer T (NKT) cells promote antibody responses, including those against carbohydrates, we tested the hypothesis that immunization with PSII and a CD1d-binding glycolipid adjuvant could lead to enhanced protection against a live C. difficile challenge. We purified PSII from a clinical isolate of C. difficile and immunized B6 mice with PSII alone or PSII plus the CD1d-binding glycolipid α-galactosylceramide (α-GC). PSII-specific IgM and IgG3 titers were evident in sera from immunized mice, but the inclusion of α-GC led to additional isotype switch and production of IgG1. Enhanced protection against C. difficile disease was achieved by inclusion of the α-GC ligand and was associated with reduced bacterial numbers in fecal pellets. In contrast, NKT-deficient Traj18−/− mice were not protected by the PSII/α-GC immunization modality. These results indicate that α-GC-driven NKT cells stimulate a protective IgG1 response directed at the C. difficile PSII antigen. This study suggests that NKT activation represents a pathway for additional B cell help that could be used to supplement existing efforts to develop a C. difficile vaccine.
Preparation and Properties of Poly(2,2′-bipyridine-5,5′-diyl) (1990)

Abstract A reaction of 5,5′-dibromo-2,2′-bipyridine with a zero-valent nickel complex affords poly(2,2′-bipyridine-5,5′-diyl), which has physical and electrically conducting properties similar to those of poly(2,5-pyridinediyl) and forms complexes with Fe2+ and Ru2+.
Ultraviolet light emission from self-organized p–n domains in cubic boron nitride bulk single crystals grown under high pressure (2002)

Ultraviolet light emission at a wavelength of 250 nm was observed from Be-doped single crystals of cubic boron nitride (cBN) grown at high pressure and high temperatures. We found that dopants of Be were localized in the grown crystals when a small amount of Be was added to the crystals. The crystals had boundaries of blue-colored Be-rich regions and amber-colored ones. These colored regions were divided by the boundaries of growth sectors. When a direct current was induced across the boundaries, UV light emission was clearly observed. The crystals may include self-organized p–n regions along the growth sectors. Although some crystalline imperfections still prevent the crystals from exhibiting properties of materials that can emit UV light with a wide band gap (6.3 eV), it is noticeable that bulk single crystals have been synthesized that contain self-organized p–n boundaries and show UV light emission.
Sintered silicon carbide molded body and method for its production (1984)

Sintered silicon carbide shapes are described. They are produced by using a composition containing an oxide of at least one element chosen from the group: Li, Be, Mg, Si, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Zn, Nb, Mo, Ba, Tc, Ta, W and Th as a supplement to known sintering aids.
Cover Picture: Fine‐Tuning Covalent Inhibition of Bacterial Quorum Sensing (ChemBioChem 9/2016) (2016)

The cover picture shows schematically how the important quorum-sensing regulator LasR of the human pathogen Pseudomonas aeruginosa can be targeted with tailor-made covalent probes. A diverse array of electrophile-containing N-acylated homoserine lactones was prepared and evaluated for their ability to covalently modify LasR. Striking differences in activity were observed between the halogenated isothiocyanates. More information can be found in the full paper by M. M. Meijler et al on page 825 in Issue 9, 2016 l. (DOI: 10.1002/cbic.201500676).
Depth-dependent giant lattice expansion of up to 5% in ionic liquid-gated 90 nm thick VO2 (001)/Al2O3 (101¯) films (2015)

We have previously shown that ionic liquid gating suppresses the metal to insulator transition (MIT) from near room temperature to low temperatures in epitaxial VO2 films grown on TiO2(001) and (101), and Al2O3 (101¯0), for thicknesses up to ∼40 nm. We also showed that for 10 nm VO2 films grown on TiO2 (001), the suppression of the MIT is preceded by a structural phase transition in which the films expand nearly uniformly out-of-plane by as much as 3%. Here, we report that the MIT of much thicker VO2 films, grown on Al2O3 (101¯0), even as thick as 90 nm, is suppressed throughout the thickness of the film by ionic liquid gating, and that these films also show a significant lattice expansion. This lattice expansion is non-uniform with a near surface region that is expanded by up to 5%, with the bulk of the film exhibiting a depth-dependent expansion that decreases from the top to the bottom of the film.
[Photodynamic therapy in cardiac and vascular surgery]. (2003)

One of the major drawbacks to therapeutic cardiovascular intervention is intimal hyperplasia and constrictive remodeling, which result in vascular restenosis. Neointimal hyperplasia is characterized by proliferation and migration of smooth muscle cells. These cells also produce new extracellular matrix, leading to narrowing of vessels. Photodynamic therapy (PDT) represents one of the most promising approaches to the inhibition of intimal hyperplasia. PDT requires the interaction among 3 factors: a source of light, usually a laser, a photosensitizer and oxygen. When the inert photosensitizer absorbs light of a specific wavelength, it is activated to an excited triplet state, generating reactive oxygen species. These free radicals are able to induce apoptosis of the smooth muscle cells that had absorbed the photosensitizer; they also induce changes in the extracellular matrix, reducing cell migration. Because of continued success of PDT in inhibiting intimal hyperplasia in experimental animal models, it is now being tested in clinical trials for vascular diseases. PDT offers many advantages to the surgeon since it can act on numerous factors responsible for vascular lesions. In the future PDT could be used in helping to overcome the inherent failures associated to vascular reconstruction. This treatment modality is emerging as an encouraging therapeutic option, either alone or as an adjunct to conventional treatment. However, more detailed clinical investigation are necessary to determine its full potential.
Mapping Capacitive Coupling Among Pixels in a Sensor Array (2010)

An improved method of mapping the capacitive contribution to cross-talk among pixels in an imaging array of sensors (typically, an imaging photodetector array) has been devised for use in calibrating and/or characterizing such an array. The method involves a sequence of resets of subarrays of pixels to specified voltages and measurement of the voltage responses of neighboring non-reset pixels.
Study to Determine Degree of Partial Blending of Reclaimed Asphalt Pavement Binder for High-RAP Hot-Mix Asphalt (2010)

The objective of this paper is to present the process of determining the degree of partial blending occurring in the hot mix asphalt consisting of 30 % RAP by total weight of the mixture and to provide a methodology on how to determine the degree of partial blending in high RAP mixtures. Several state agencies limit the amount of RAP that can be placed in the different layers of pavement. One of the primary reasons the RAP usage is limited because the interaction between the RAP and the virgin materials remains largely unknown. The question of whether the RAP binder blends completely with the virgin binder or none of the RAP binder is available for blending, supporting the “black rock” theory, is still unanswered. Therefore, there is a need to determine a process for quantifying the degree of partial blending that occurs in high RAP mixtures. The methodology proposed in this paper provides a systematic approach for determining the degree of partial blending in the RAP mixture. The ability to accurately determine the degree of partial blending will help in precisely determining the virgin binder content to be added in the mixture. It will also help in developing a blending chart (to determine the property of the final binder grade or the virgin binder grade, or the percentage of RAP) based on the degree of partial blending measured from this procedure.
Adaptive, analog, continuous-time time-domain equalization for sampled channels in digital magnetic recording (1997)

A practical, low-cost, adaptive, analog, continuous time time-domain equalizer has been implemented in integrated sampled read/write channels. The equalizer is an IIR filter and is the generalization of a conventional analog transversal equalizer. Active frequency-domain filters are used as delay elements and filtration is completed before sampling. The equalizer has more degrees of freedom than DSP FIR filters and outperforms them. Theory of the generalized transversal equalization is presented.
Detection of Hepatitis C Core Antigen in the Antibody Negative ‘Window’ Phase of Hepatitis C Infection (2000)

Abstract Background and Objectives: Despite improvements in assays for anti–HCV, there remains a significant delay before the appearance of antibodies following infection, during which, circulating viral RNA is present. We have evaluated a prototype assay for the serological detection of hepatitis C virus (HCV) core antigen with specimens derived from the early phase of HCV infection. Materials and Methods: Serial specimens from 24 individuals undergoing HCV seroconversion were tested for the presence of anti–HCV, HCV RNA and HCV core antigen. Results: HCV antigen was detected at the same time as HCV RNA in 83% (20/24) cases. The mean time to the first detection of HCV antigen was approximately 1 day later than HCV RNA. Overall, 87% of HCV–RNA–positive specimens contained detectable HCV core antigen. Conclusion: These results indicate that HCV core antigen can be identified by routine serological ELISA in specimens from the early antibody–negative phase of HCV infection. A test for HCV core antigen may be a useful test for identifying window phase blood donations from antibody negative donors infected with HCV.
Effect of mixer phase distortions on the DOA tracking algorithm for an adaptive antenna array (2002)

The effect of the mixer phase distortions on the adaptive direction-of-arrival (DOA) tracking algorithm is investigated. The study shows that the DOA tracking algorithm is not sensitive to the mixer phase distortions. Hence the mixer phase calibration is not required for a system applying the DOA tracking algorithm. The equivalent DOA tracking error due to the mixer phase distortions is derived. Also the performance of the system applying the DOA tracking algorithm is compared with that of the system applying other algorithms in terms of the bit error rate (BER) under additive white Gaussian noise (AWGN) and Rayleigh fading environments. Simulation results are given to support the conclusions.
Antivirulence Properties of an Antifreeze Protein (2014)

As microbial drug-resistance increases, there is a critical need for new classes of compounds to combat infectious diseases. The Ixodes scapularis tick antifreeze glycoprotein, IAFGP, functions as an antivirulence agent against diverse bacteria, including methicillin-resistant Staphylococcus aureus. Recombinant IAFGP and a peptide, P1, derived from this protein bind to microbes and alter biofilm formation. Transgenic iafgp-expressing flies and mice challenged with bacteria, as well as wild-type animals administered P1, were resistant to infection, septic shock, or biofilm development on implanted catheter tubing. These data show that an antifreeze protein facilitates host control of bacterial infections and suggest therapeutic strategies for countering pathogens.
Nodal Analysis for a Transient Production System—Principles and Application (2014)

Abstract Nodal analysis is the standard technique used to evaluate the performance of integrated production systems. Two curves represent the capacities of the inflow and of the outflow, and the intersection of the two curves gives the solution operating point. Limitations of traditional nodal analysis include that results are offered only at a snapshot, not as a function of timeinflow performance relationship (IPR) models are limited, with none available for shale gas wellsanalysis is performed on a well-by-well basis, with no account of multiwell interference. We propose a new nodal-analysis method that enables the study of transient production systems in a multiwell context and at different timesteps, with IPR models generated from a high-speed semianalytical reservoir simulator and outflow curves output from a steady-state pipeline simulator. The use of analytical reservoir simulation allows accurate, reliable modeling of the real inflow system, including deepwater and unconventional wells. The new approach studies the time-lapse behavior of the system, with consideration of production history and neighboring well interference. This new method enables the study of transient deliverability at the wellhead, where the measurement is usually available, and shows the time-lapse relationship between wellhead pressure and production rate. We provide examples of wellhead deliverability and choke management and explain advantages of the method with case studies involving tight and shale wells. The method is also applied to design and optimize artificial lift in unconventional wells and to study the method's validity over time. In addition, we discuss an example of operational well dynamics using time-lapse nodal analysis. Additionally, this new method generates discussion about some concepts that are often taken for granted. For example, what should be the definition of IPR in a transient production system? On the IPR curve, is the zero-rate pressure the reservoir pressure? Can IPR curves at two different timesteps cross each other? Finding the answers to these questions will help us better understand production systems. The commonly used productivity index (PI) method is reviewed and compared with the new method. Results show that the PI method should not be used when well operational conditions change.
HemaApp IR (2017)

We propose a standalone demo prototype of HemaApp, a smartphone application that noninvasively monitors the hemoglobin concentration in the blood. A previous version HemaApp using a supplemental light attachment combined with an unmodified camera has been presented at Ubicomp 2016, however the current version is an improvement from the 2016 system demonstrating no external attachments. In this paper, we present the newest version of HemaApp, which combines the unmodified smartphone's camera, white LED flash, and IR sensor on the phone's laser autofocus system.