gebhart/patrepeval huggingface dataset:
Common structural features of nucleic acid polymerases (2002)

Structures of multisubunit RNA polymerases strongly differ from the many known structures of single subunit DNA and RNA polymerases. However, in functional complexes of these diverse enzymes, nucleic acids take a similar course through the active center. This finding allows superposition of diverse polymerases and reveals features that are functionally equivalent. The entering DNA duplex is bent by almost 90 degrees with respect to the exiting template-product duplex. At the point of bending, a dramatic twist between subsequent DNA template bases aligns the "coding" base with the binding site for the incoming nucleoside triphosphate (NTP). The NTP enters through an opening that is found in all polymerases, and, in most cases, binds between an alpha-helix and two catalytic metal ions. Subsequent phosphodiester bond formation adds a new base pair to the exiting template-product duplex, which is always bound from the minor groove side. All polymerases may undergo "induced fit" upon nucleic acid binding, but the underlying conformational changes differ.
Fast visualization, manipulation, and analysis of binary volumetric objects (1991)

A set of algorithms for interactive visualization, manipulation, and measurement of large 3-D objects on general-purpose workstations is described. They are based on a method of representing digital structures called a semiboundary. This data structure stores boundary and interior information. The use of these algorithms for visualizing medical data is addressed. Examples of their use are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
T Cell Responses and Regulation and the Impact of <i>In Vitro </i><scp>IL</scp>‐10 and <scp>TGF</scp>‐<i>β</i> Modulation During Treatment of Active Tuberculosis (2016)

Mycobacterium tuberculosis (Mtb) is particularly challenging for the immune system being an intracellular pathogen, and a variety of T cell subpopulations are activated by the host defence mechanism. In this study, we investigated T cell responses and regulation in active TB patients with drug-sensitive Mtb (N = 18) during 24 weeks of efficient anti-TB therapy. T cell activation, differentiation, regulatory T cell (Treg) subsets, Mtb-induced T cell proliferation and in vitro IL-10 and TGF-β modulation were analysed by flow cytometry at baseline and after 8 and 24 weeks of therapy, while soluble cytokines in culture supernatants were analysed by a 9-plex Luminex assay. Successful treatment resulted in significantly reduced co-expression of HLA-DR/CD38 and PD-1/CD38 on both CD4<sup>+</sup> and CD8<sup>+</sup> T cells, while the fraction of CD4<sup>+</sup> CD25<sup>high</sup> CD127<sup>low</sup> Tregs (P = 0.017) and CD4<sup>+</sup> CD25<sup>high</sup> CD127<sup>low</sup> CD147<sup>+</sup> Tregs (P = 0.029) showed significant transient increase at week 8. In vitro blockade of IL-10/TGF-β upon Mtb antigen stimulation significantly lowered the fraction of ESAT-6-specific CD4<sup>+</sup> CD25<sup>high</sup> CD127<sup>low</sup> Tregs at baseline (P = 0.047), while T cell proliferation and cytokine production were unaffected. Phenotypical and Mtb-specific T cell signatures may serve as markers of effective therapy, while the IL-10/TGF-β pathway could be a target for early inhibition to facilitate Mtb clearance. However, larger clinical studies are needed for verification before concluding.
Primate restraint system for studies of metabolic responses during recumbency. (1971)

Primate restraint harness of nylon jacket and cotton cot on aluminum frame padded seat for bone resorption and calcium metabolism studies
The synthesis of 3‐bromo‐2,4,5‐trifluorobenzoic acid and its conversion to 8‐bromoquinolonecarboxylic acids (1996)

Abstract A series of 8‐bromo‐4‐oxo‐3‐quinolinecarboxylic acids was prepared via the borate ester, 8 . The key intermediate in the synthesis of the final products 10a‐10d was 3‐bromo‐2,4,5‐trifluorobenzoic acid ( 3 ), conveniently prepared in two steps from the known oxazoline, 1 . The preparation of 10a‐10d is a significant improvement of the literature procedure currently available for the synthesis of these compounds.
The Effect of a Carbohydrate-Arginine Supplement on Postexercise Carbohydrate Metabolism (1999)

The effect of a carbohydrate-arginine supplement on postexercise muscle glycogen storage was investigated. Twelve well-trained cyclists rode for 2 hr on two separate occasions to deplete their muscle glycogen stores. At 0, 1, 2, and 3 hr after each exercise bout, the subjects ingested either a carbohydrate (CHO) supplement (1 g carbohydrate/kg body weight) or a carbohydrate-arginine (CHO/AA) supplement (1 g carbohydrate/kg body mass and 0.08 g arginine-hydrochloride/kg body weight). No difference in rate of glycogen storage was found between the CHO/AA and CHO treatments, although significance was approached. There were also no differences in plasma glucose, insulin, or blood lactate responses between treatments. Postexercise carbohydrate oxidation during the CHO/AA treatment was significantly reduced compared to the CHO treatment. These results suggest that the addition of arginine to a CHO supplement reduces the rate of CHO oxidation postexercise and therefore may increase the availability of glucose for muscle glycogen storage during recovery.
Phospholipase D: a Downstream Effector of ARF in Granulocytes (1994)

Activation of the phospholipase D (PLD) pathway is a widespread response when cells are activated by agonists that bind receptors on the cell surface. A 16-kD cytosolic component can reconstitute guanosine triphosphate (GTP)-mediated activation of phospholipase D in HL60 cells depleted of their cytosol by permeabilization. This factor was purified and identified as two small GTP-binding proteins, ARF1 and ARF3. Recombinant ARF1 substituted for purified ARF proteins in the reconstitution assay. These results indicate that phospholipase D is a downstream effector of ARF1 and ARF3. The well-established role of ARF in vesicular traffic would suggest that alterations in lipid content by PLD are an important determinant in vesicular dynamics.
Coupled-Wave Theory for Square-Lattice Photonic Crystal Lasers With TE Polarization (2010)

We present a coupled-wave analysis for square-lattice photonic crystal lasers with transverse electric polarization. A model consisting of eight plane waves coupled by Bragg diffraction is used to describe two-dimensional optical coupling. The resonant frequencies and threshold criteria for the modes of oscillation have been determined for the case of index periodicity with a lattice of circular holes. The spatial intensity distributions of these resonant modes have also been calculated. For the fundamental modes, we have investigated how the intensity distribution varies as a function of coupling strength. The dependence of the threshold gain of these modes on hole size has also been elucidated. This semianalytical approach provides a comprehensive understanding of square-lattice photonic crystal lasers and allows more effective optimization of their cavity design.
Determination of the Nonlinearity Parameter <i>B/A</i> for Water and <i>m</i>-Xylene (1962)

The rate at which harmonics are developed during the propagation of an initially sinusoidal ultrasonic wave of finite amplitude depends on the nonlinearity of the compressibility of the medium. Thus, determinations of the harmonics as a function of propagation distance may be used to determine the parameter B/A (describing nonlinearity). A method which circumvents the effects of absorption in the medium is developed and used to determine the parameter B/A for water and m-xylene. This method utilizes optical determinations of the second harmonic component of a distorted 3.0 Mc ultrasonic wave at various distances and initial pressure amplitudes. The second harmonic was isolated by use of a calibrated acoustic filter plate. The values obtained for the nonlinearity parameter are B/A = 6.2±0.6 for water and B/A = 9.6±1 for m-xylene.
A low power discrete-time receiver for triple-band FM/T-DMB/DAB system-on-chip (2011)

This paper presents a low power discrete-time receiver supporting three broadcast services FM, T-DMB and DAB. To meet the requirement of sensitivity, three LNAs are implemented to cover each band. The proposed mixer core is terminated by a common-gate current buffer to improve linearity and merged with a switched-capacitor sampled filter in current mode for low power and low complexity. The filter performs the second-order low-pass filtering with anti-aliasing ratio up to 70 dB at 1.6 MHz bandwidth. The chip is fabricated in a 90 nm CMOS technology and dissipates 11 mA current from 1.2 V supply. The receiver shows 48 dB maximum gain, 60 dB gain control range, 2.7 dB noise figure, and -22/0 dBm IIP3 in LNA high/low gain mode.
A Synthesis of dl-C17-Cecropia Juvenile Hormone (1972)

A novel synthesis of dl-C17-Cecropia juvenile hormone (I) was accomplished.
Optimal probe geometry for near-infrared spectroscopy of biological tissue (1997)

The results of this study clarify the influence of probe geometry on spectroscopic measurements obtained from the surface of a turbid biological tissue. We show that the transition between the measurement of the predominantly backward-propagating and the predominantly forward-propagating photon fluxes is marked by the separation between the source probe and the detector probes at which the dependence of the fluence on small changes in scattering coefficient vanishes. This is the probe separation at which a variable scattering background has the least influence on the measurement of optical absorption in turbid materials. Estimates of the optimum probe spacing for typical values of absorption and scattering coefficients of soft tissue in the near-infrared spectral region (800-2500 nm) are derived from an analytical solution of the diffusion equation. The estimates were verified by Monte Carlo simulations and experiments on particle suspensions with optical properties similar to those of skin tissue.
Molecular weight changes in irradiated polypropylene (1967)

Abstract We have shown by two separate measurements that polypropylene when melted after irradiation undergoes crosslinking from the inception of irradiation. The first proof was an immediate increase in the solution viscosity of a narrow molecular weight fraction of polypropylene. The second proof was the marked change in melt‐flow properties on irradiation of a broad molecular weight distribution polypropylene. These findings tend to support one of the two currently held views on the action of radiation on polypropylene. In addition we have confirmed previous reports that melting after irradiation contributes to the overall crosslinking reaction.
Reaction of Superoxide and Nitric Oxide with Peroxynitrite (2001)

Peroxynitrite (ONOO(-)/ONOOH), the product of the diffusion-limited reaction of nitric oxide (*NO) with superoxide (O(-*)(2)), has been implicated as an important mediator of tissue injury during conditions associated with enhanced *NO and O(-*)(2) production. Although several groups of investigators have demonstrated substantial oxidizing and cytotoxic activities of chemically synthesized peroxynitrite, others have proposed that the relative rates of *NO and production may be critical in determining the reactivity of peroxynitrite formed in situ (Miles, A. M., Bohle, D. S., Glassbrenner, P. A., Hansert, B., Wink, D. A., and Grisham, M. B. (1996) J. Biol. Chem. 271, 40-47). In the present study, we examined the mechanisms by which excess O(-*)(2) or *NO production inhibits peroxynitrite-mediated oxidation reactions. Peroxynitrite was generated in situ by the co-addition of a chemical source of *NO, spermineNONOate, and an enzymatic source of O(-*)(2), xanthine oxidase, with either hypoxanthine or lumazine as a substrate. We found that the oxidation of the model compound dihydrorhodamine by peroxynitrite occurred via the free radical intermediates OH and NO(2), formed during the spontaneous decomposition of peroxynitrite and not via direct reaction with peroxynitrite. The inhibitory effect of excess O(-*)(2) on the oxidation of dihydrorhodamine could not be ascribed to the accumulation of the peroxynitrite scavenger urate produced from the oxidation of hypoxanthine by xanthine oxidase. A biphasic oxidation profile was also observed upon oxidation of NADH by the simultaneous generation of *NO and O(-*)(2). Conversely, the oxidation of glutathione, which occurs via direct reaction with peroxynitrite, was not affected by excess production of *NO. We conclude that the oxidative processes initiated by the free radical intermediates formed from the decomposition of peroxynitrite are inhibited by excess production of *NO or O(-*)(2), whereas oxidative pathways involving a direct reaction with peroxynitrite are not altered. The physiological implications of these findings are discussed.
Perfect reconstruction modulated filter banks with sum of powers-of-two coefficients (2002)

In this paper, a new family of multiplier-less modulated filter banks, called the SOPOT MFB, is presented. The coefficients of the proposed filter banks consist of sum of powers-of-two coefficients (SOPOT), which require only simple shifts and additions for implementation. The modulation matrix and the prototype filter are derived from the fast DCT-IV algorithm of Wang (1984) and a lattice structure. The design of the SOPOT MFB is performed using the genetic algorithm (GA). An 16-channel SOPOT MFB with 34 dB stopband attenuation is given as an example, and its average number of terms per SOPOT coefficient is only 2.6.
Executable object modeling with statecharts (1996)

This paper reports on an effort to develop an integrated set of diagrammatic languages for modeling object-oriented systems, and to construct a supporting tool. The goal is for models to be intuitive and well-structured, yet fully executable and analyzable, enabling automatic synthesis of usable and efficient code in object-oriented languages such as C++. At the heart of the modeling method is the language of statecharts for specifying object behavior, and a hierarchical OMT-like language for describing the structure of classes and their inter-relationships, that we call O-charts. Objects can interact by event generation, or by direct invocation of operations. In the interest of keeping the exposition manageable, we leave out some technically involved topics, such as multiple-thread concurrency and active objects.
Photophysical Properties of Substituted Homoleptic and Heteroleptic Phenylimidazolinato Ir(III) Complexes as a Blue Phosphorescent Material (2013)

Iridium complexes are one of the most important materials for fabrication of organic light emitting diodes (OLEDs). There are difficulties in the preparation of blue phosphorescent complexes with respect to chromaticity, emission efficiency, and stability of the material, compared with green and red phosphorescent complexes. Control of the frontier orbital energy level (HOMO-LUMO) is the sole method to achieve better blue phosphorescent iridium complexes by appropriate ligand selection and the introduction of adequate substituents. Homoleptic and heteroleptic iridium(III) tris(phenylimidazolinate) complexes were synthesized, and the effect of the substituents on their nature in the excited state was examined. Density functional theory calculation showed that the imidazolinato complexes have the HOMO localized at the iridium d- and phenyl π-orbitals. The LUMO is also localized on the phenyl moiety with a much higher population than HOMO. This LUMO is quite different from other complexes, such as iridium(III) tris(phenylpyridinate) and tris(phenylpyrazolinate) complexes. Therefore, substitution with π-electron donating groups and electron withdrawing groups induces blue and red spectral shifts, respectively, which is the reverse shift exhibited by other complexes. The ancillary ligand (acetylacetone) acts as a path for nonradiative deactivation in the blue phosphorescent complexes.
Imidazoline Receptors (1995)

Journal of Cardiovascular Pharmacology™ is a peer reviewed, multidisciplinary journal that publishes original articles and pertinent review articles on basic and clinical aspects of cardiovascular pharmacology. Appropriate subjects include new drug development and evaluation, physiological and pharmacological bases of drug action, metabolism, drug interactions and side effects, clinical results with new and established agents and novel methods. The focus is on pharmacology in its broadest applications, incorporating not only traditional approaches, but new approaches to the development of pharmacological agents and the prevention and treatment of cardiovascular diseases.
Hematopoietic stem cell transplantation for patients with AML in first complete remission (2015)

Postremission therapy in patients with acute myeloid leukemia (AML) may consist of continuing chemotherapy or transplantation using either autologous or allogeneic stem cells. Patients with favorable subtypes of AML generally receive chemotherapeutic consolidation, although recent studies have also suggested favorable outcome after hematopoietic stem cell transplantation (HSCT). Although allogeneic HSCT (alloHSCT) is considered the preferred type of postremission therapy in poor- and very-poor-risk AML, the place of alloHSCT in intermediate-risk AML is being debated, and autologous HSCT is considered a valuable alternative that may be preferred in patients without minimal residual disease after induction chemotherapy. Here, we review postremission transplantation strategies using either autologous or allogeneic stem cells. Recent developments in the field of alternative donors, including cord blood and haploidentical donors, are highlighted, and we discuss reduced-intensity alloHSCT in older AML recipients who represent the predominant category of patients with AML who have a high risk of relapse in first remission.
Blind Separation of Image Sources via Adaptive Dictionary Learning (2012)

Sparsity has been shown to be very useful in source separation of multichannel observations. However, in most cases, the sources of interest are not sparse in their current domain and one needs to sparsify them using a known transform or dictionary. If such a priori about the underlying sparse domain of the sources is not available, then the current algorithms will fail to successfully recover the sources. In this paper, we address this problem and attempt to give a solution via fusing the dictionary learning into the source separation. We first define a cost function based on this idea and propose an extension of the denoising method in the work of Elad and Aharon to minimize it. Due to impracticality of such direct extension, we then propose a feasible approach. In the proposed hierarchical method, a local dictionary is adaptively learned for each source along with separation. This process improves the quality of source separation even in noisy situations. In another part of this paper, we explore the possibility of adding global priors to the proposed method. The results of our experiments are promising and confirm the strength of the proposed approach.
Recombinant human alpha lymphotoxin (tumor necrosis factor-beta) induces peripheral neutrophilia and lymphopenia in the rat. (1987)

Recombinant human alpha lymphotoxin (rLT) administered intravenously to Lewis rats induces peripheral neutrophilia and lymphopenia in a dose-response dependent fashion. A dose of 30,000 units of rLT induced a neutrophilia (1589 +/- 326 to 5554 +/- 1050 neutrophils/cu mm) and lymphopenia (10,368 +/- 992 to 4636 +/- 878 lymphocytes/cu mm) at 2 hours after injection that was highly significant (P less than 0.001 and P less than 0.001, respectively) in comparison with vehicle controls. The kinetics of the neutrophilia that peaked at 2 hours as well as of the lymphopenia were highly reminiscent of the neutrophilia and lymphopenia following intravenous administration of either recombinant human interleukin-1 (IL-1) alpha or beta to rats. The peripheral neutrophilia was accompanied by a significant depletion of bone marrow neutrophils (P less than 0.001), as is also known to occur after administration of IL-1. Systemic blood pressure was not affected by rLT, which suggested that the changes in circulating leukocyte subsets were not attributable to hemodynamic changes nor to the hemodynamic-change-related release of adrenal hormones. Adrenalectomy did not alter the rLT-induced neutrophilia or lymphopenia, which suggested that rLT does not mediate its hematologic effects on peripheral blood leukocytes via the release of adrenal hormones. Pretreatment of rats with dexamethasone, indomethacin, or aspirin also did not alter rLT-induced neutrophilia or lymphopenia, which suggested that rLT-induced hematologic effects were not mediated via arachidonic acid metabolites, in stark contrast to IL-1 induced neutrophilia, which is inhibited by both dexamethasone and indomethacin.
Auctioning Data for Learning (2015)

In this paper we advocate that market mechanisms inspired by economics in conjunction with intelligent data selection is the key to fulfilling learning tasks in the presence of big data subject to privacy concerns of users. We design a market of private data that are gathered towards building a classifier. Each data owner has a private cost that quantifies his discomfort for providing data to the learner. Also, at each stage of the learning process, each data owner is characterized by a utility score, which expresses the utility of his data for the learner. The learner initiates a call for buying data, and interested owners respond by declaring their costs. The learner computes the utility score of each data owner. It then selects one owner to buy data from and associated payment. For the goals of minimizing the expected privacy cost of users and of minimizing the expected payment by the learner, we propose a variation of a Vickrey-Clarke-Groves (VCG) auction and an optimal auction respectively. For the case where the data arrive in a streaming fashion, we formulate the multi-round sequential decision version of the problem of learning the classifier. At each round the learner decides whether it will stop the learning process given the current classifier accuracy or perform one more auction. The problem amounts to weighing the current cost of classifier inaccuracy against the expected (privacy or reimbursement) costs incurred through the auction, plus the expected cost of the new classifier accuracy, we cast this problem as an optimal stopping one. The complexity of our framework scales only linearly with the size of the data set and fits in a broad range of private-data scenarios and data attributes.
AsAP: An Asynchronous Array of Simple Processors (2008)

An array of simple programmable processors is implemented in 0.18 mum CMOS and contains 36 asynchronously clocked independent processors. Each processor occupies 0.66 and is fully functional at a clock rate of 520-540 MHz at 1.8 V and over 600 MHz at 2.0 V. Processors dissipate an average of 32 mW under typical conditions at 1.8 V and 475 MHz, and 2.4 mW at 0.9 V and 116 MHz while executing applications such as a JPEG encoder core and a fully compliant IEEE 802.11 a/g wireless LAN baseband transmitter.
SCREW-PRESSURE CODPLER AND MODE CONVERTER (1984)

Abstract Fine-pitch threads are used to pressure-couple extensional mode ultrasonic pulses at frequencies on the order of 50 to 100 kHz between four stainless steel lead wires of 1.6 mm diameter and a density or liquid level sensor of rectangular cross section (2.5 × 6.4 mm). Two of the lead wires are orthogonal to the plane of the sensor and are tightly screwed into its ends off-axis to generate and detect, by mode conversion, torsional waves in the sensor. Use of this screw-pressure coupling technique in acoustic emission and moduli studies, and in temperature and corrosion monitoring, is suggested.