gebhart/patrepeval huggingface dataset:
The χψ Subunits of DNA Polymerase III Holoenzyme Bind to Single-stranded DNA-binding Protein (SSB) and Facilitate Replication of an SSB-coated Template (1998)

A complex of the chi and psi proteins is required to confer resistance to high levels of glutamate on the DNA polymerase III holoenzyme-catalyzed reaction (Olson, M., Dallmann, H. G., and McHenry, C. (1995) J. Biol. Chem. 270, 29570-29577). We demonstrate that this salt resistance also requires templates to be coated with the Escherichia coli single-stranded DNA-binding protein (SSB). We show that this is the result of a direct chipsi-SSB interaction that is strengthened approximately 1000-fold when SSB is bound to DNA. On model oligonucleotide templates, DNA polymerase III core is inhibited by SSB. We show that the minimal polymerase assembly that will synthesize DNA on SSB-coated templates is polymerase III-tau-psi chi. gamma, the alternative product of the dnaX gene, will not replace tau in this reaction, indicating that tau's unique ability to bind to DNA polymerase III holding chipsi in the same complex is essential. All of our findings are consistent with chipsi strengthening DNA polymerase III holoenzyme interactions with the SSB-coated lagging strand at the replication fork, facilitating complex assembly and elongation.
Tolvaptan in Autosomal Dominant Polycystic Kidney Disease (2011)

ADPKD cyst growth progresses more slowly with tolvaptan than in historical controls, but AEs are common.
Transport of Quantum Noise through Random Media (2005)

We present an experimental study of the propagation of quantum noise in a multiple scattering random medium. Both static and dynamic scattering measurements are performed: the total transmission of noise is related to the mean free path for scattering, while the noise frequency correlation function determines the diffusion constant. The quantum noise observables are found to scale markedly differently with scattering parameters compared to classical noise observables. The measurements are explained with a full quantum model of multiple scattering.
Physics and applications of positron beams in an integrated PET/MR (2013)

In PET/MR systems having the PET component within the uniform magnetic field interior to the MR, positron beams can be injected into the PET field of view (FOV) from unshielded emission sources external to it, as a consequence of the action of the Lorentz force on the transverse components of the positron's velocity. Such beams may be as small as a few millimeters in diameter, but extend 50 cm or more axially without appreciable divergence. Larger beams form 'phantoms' of annihilations in air that can be easily imaged, and that are essentially free of γ-ray attenuation and scatter effects, providing a unique tool for characterizing PET systems and reconstruction algorithms. Thin targets intersecting these beams can produce intense annihilation sources having the thickness of a sheet of paper, which are very useful for high resolution measurements, and difficult to achieve with conventional sources. Targeted beams can provide other point, line and surface sources for various applications, all without the need to have radioactivity within the FOV. In this paper we discuss the physical characteristics of positron beams in air and present examples of their applications.
Sliding Mode Control of a Shape Memory Alloy Actuated Manipulator (2003)

This paper presents a two-pan controller that uses a state variable estimator for control of a single degree of freedom rotary manipulator acutated by Shape Memory Alloy (SMA) wire. A model for the SMA actuated manipulator is presented. The model includes nonlinear dynamics of the manipulation a constitutive model of the Shape Memory Alloy. and the electrical and heat transfer behavior of SMA wire. The estimator predicts the state vector at each time step and corrects its prediction based on the angular position measurements. The transformation temperatures of the SMA wire are stress dependent: this adds to complexity of the control of the position of the arm for certain angular positions. To overcome this problem a sliding mode controller is designed to calculate the desired stress of the wire based on the desired angular position of the arm. A classical feedback controller maintains this desired stress by regulating the input voltage to the SMA wire. The stress of the wire is a better set-point for the controller since the transformation temperatures and hence the Martensite traction are frictions of the wire's stress. The stabilization and tracking performance of this two-pan controller is presented and compared with a PID controller.
Architecture in global socialism: Eastern Europe, West Africa, and the Middle East in the Cold War (2020)

"Architecture in global socialism: Eastern Europe, West Africa, and the Middle East in the Cold War." Eurasian Geography and Economics, 63(1), pp. 142–143
A Method for Lowering Turbo Code Error Flare using Correction Impulses and Repeated Decoding (2006)

Turbo codes exhibit an “error floor ” or “flare ” making it difficult to further improve the error performance without a significant increase in the signal-to-noise ratio (SNR). The error flare is mainly characterized by the distance properties of the code. The conventional way to lower the error flare is to increase the minimum distance, which is mainly determined by the interleaver. Unfortunately, the design of interleavers that yield high minimum distances is not a simple task. In fact, the design of such interleavers for applications requiring very low frame error rates (FERs) can be a real challenge. This paper introduces a new method that significantly lowers the error flare while leaving the interleaver unchanged. It also improves the error performance in the waterfall region. The key element of this method is the insertion of correction impulses in the received codeword and the use of repeated decoding. The effectiveness of this method is demonstrated by its ability to reduce the error rate by one order of magnitude in the waterfall region and more than three orders of magnitude in the flare region for 8-state single- and double-binary turbo codes of code rate 1/3 and 1/2 that use high-spread random (HSR) interleavers and packets of 1504 bits. 1
6‐Hydroxymellein synthetase as a multifunctional enzyme complex in elicitor‐treated carrot root extract (1991)

Synthetic activity of a polyketide compound 6-hydroxymellein was induced in elicitor-treated carrot root tissues. The activity was significantly inhibited by an antiserum raised against the acyl carrier protein (ACP) of fatty acid synthetase, suggesting that the enzyme(s) for 6-hydroxymellein synthesis require(s) a functional unit similar to ACP. However, the synthetic activity was not stimulated by the addition of ACP purified from Escherichia coli and was not lost even after fractionation by gel-filtration chromatography. The active fraction obtained by gel-filtration (136 kDa) was subjected to immunoblot analysis, and a 128 kDa polypeptide in the fraction was found to cross-react with anti-ACP serum. These observations suggest that the biosynthesis of 6-hydroxymellein in carrot cells is catalyzed by an enzyme consisting of a single peptide chain.
Chemokines and asthma. (2003)

Asthma is a complex disease resulting from a combination of factors including genetics, environmental exposure to allergens and prior infection with respiratory viruses. Worldwide, asthma is considered to be one of the leading causes of chronic childhood illness with young children living in poverty in urban environments being particularly severely affected. A common feature of the response to allergen challenge in asthmatic individuals is pattern of intense inflammation in the airways and a group of chemotactic cytokines, also known as chemokines, are believed to play a central role at multiple stages of this inflammatory response. Identification of the role of individual chemokines in the allergic response has been complicated by the diversity of chemokine production and the promiscuous pattern of chemokine-chemokine receptor interactions. However, chemokines have been shown to mediate the differential recruitment of leukocytes to the airways and regulate activation of both recruited and resident cells in the lungs. As the role of chemokines and their receptors at each stage of allergic inflammation become more clearly defined, it becomes increasingly likely that novel anti-inflammatory agents which modulate chemokine-chemokine receptor interactions will be developed and prove to be therapeutically beneficial.
Uptake and metabolism of retinol in cultured Sertoli cells: evidence for a kinetic model (1987)

When cultured Sertoli cells derived from 20-day-old weanling rats were supplied [3H]retinol bound to serum retinol binding protein-transthyretin complex, [3H]retinol was rapidly incorporated and [3H]retinyl esters were synthesized. Within 28 h after administration, 83% of the labeled retinoids were accounted for as retinyl esters (64% as retinyl palmitate). Sertoli cells derived from vitamin A deficient rats and supplied [3H]retinol in culture under identical conditions likewise incorporated [3H]retinol and synthesized retinyl esters. In contrast to normal Sertoli cells, vitamin A deficient Sertoli cells eventually metabolized virtually all of the cellular [3H]retinol to retinyl esters. The primary metabolic fate of retinol administered to Sertoli cell cultures was the synthesis of retinyl esters under all conditions tested. However, administration of [3H]retinol bound to serum retinol binding protein gave metabolic profiles having a higher proportion of retinyl esters and lower proportions of unresolved polar material than administration of [3H]retinol alone. The kinetics of retinol uptake and intracellular retinyl ester synthesis in cultured Sertoli cells was complex. An initial, rapid phase of [3H]retinol incorporation lasting 30 min was followed by a slower rate of incorporation and a concomitant decrease in the intracellular concentration of [3H]retinol. During the time course the specific activity of [3H]retinyl palmitate eventually exceeded that of intracellular [3H]retinol. These observations suggest that two intracellular pools of retinol may exist in Sertoli cells.
Homeotic transformations and limb defects in Hox A11 mutant mice. (1993)

Hox All is one of the expanded set of vertebrate homeo box (Hox) genes with similarities to the Drosophila homeotic gene, Abdominal-B (Abd-B). These Abd-B-type Hox genes have been shown to be expressed in the most caudal regions of the developing vertebrate embryo and in overlapping domains within the developing limbs, suggesting that these genes play important roles in pattern formation in both appendicular and axial regions of the body. In this report whole-mount in situ hybridization in mouse embryos gave a precise description of Hox All gene expression in the developing limbs and in the axial domain of the developing body. In addition, we generated a targeted mutation in Hox All and characterized the resulting phenotype to begin to dissect developmental functions of the Abd-B subfamily of Hox genes. Hox All mutant mice exhibited double homeotic transformations, with the thirteenth thoracic segment posteriorized to form an additional first lumbar vertebra and with the sacral region anteriorized, generating yet another lumbar segment. Furthermore, skeletal malformations were observed in both forelimbs and hindlimbs. In mutant forelimbs, the ulna and radius were misshapen, the pisiform and triangular carpal bones were fused, and abnormal sesamoid bone development occurred. In mutant hindlimbs the tibia and fibula were joined incorrectly and malformed at their distal ends. Also, an enlarged sesamoid developed ventral to the tibiale bone. Both heterozygous and homozygous mice displayed mutant phenotypes adding an additional level of complexity to the Hox code hypothesis.
SU‐FF‐T‐378: Radiation Transport Software for Medical Physics Studies (2006)

Purpose: To present a summary of radiation transport software for medical physics applications. Method and Materials: The Radiation Safety Information Computational Center (RSICC), a center at Oak Ridge National Laboratory (ORNL), is the Department of Energy software center for radiation transport and safety software. The center houses over 1600 software packages and nuclear cross section data of importance to nuclear science applications. The different software packages have been applied to the following topics: • Dosimetry calculations for radiation therapy • Treatment planning in radiation oncology • Design of photon and secondary neutron shielding for therapy rooms • Evaluating and estimating patient and staff radiation dose • Electron beam transport and energy deposition • Secondary neutron and gamma transport and energy deposition • Cancer brachytherapy dosimetry • Medical diagnostic imaging applications, including SPECT, PET, and x‐ray imaging • Error evaluations for accelerator particle delivery systems • Modalities of treatment and exploration of alternatives • Licensing and safety analysis for medical radiation facilities • Medical diagnostics and therapy Examples of software in the RSICC collection include MCNP/MCNPX, ITS, ANISN, TORT, EGS4, PARTISN, SERA, and PENELOPE. There are other software packages (not available through RSICC), which have been applied to the above topics ‐ for example, PENTRAN, A3MCNP, ATTILA, COMET, EGSnrc, TransMED, EVENT, FLUKA, PEREGRINE. Results: Studies on selected software is presented, particularly on the above applications. Conclusion: As the field of medical physics advances, computer software technology continues on the road to improvement and efficiency. Conflict of Interest: Work was supported by the Department of Energy under contract DE‐AC05‐00OR22725.
Bottom-up nanoarchitectonics of two-dimensional freestanding metal doped carbon nanosheet (2014)

Fabrication of freestanding carbon–metal-sulfide nanosheet from a self-assembled monolayer.
A geometrical inverse problem (1986)

A simple solution is given to the problem of finding the unknown boundary from the extra boundary condition.
Photoconductive pulse power switches: a review (1985)

This paper reviews the state of development and discusses the operational considerations of photoconductive power switch (PCPS) technology that has recently been used to generate very fast rising, high-power pulses. The rationale for using PCPSs is discussed along with the advantages of this type of switch in high-power pulse systems. The operational considerations are discussed, and the resultant operational characteristics that are dependent on the material parameters of several photoconductive materials are presented and compared. Areas for additional research and development of PCPSs are also presented.
An Unpredictable Chronic Mild Stress Protocol for Instigating Depressive Symptoms, Behavioral Changes and Negative Health Outcomes in Rodents (2015)

Chronic, unresolved stress is a major risk factor for the development of clinical depression. While many preclinical models of stress-induced depression have been reported, the unpredictable chronic mild stress (UCMS) protocol is an established translationally-relevant model for inducing behavioral symptoms commonly associated with clinical depression, such as anhedonia, altered grooming behavior, and learned helplessness in rodents. The UCMS protocol also induces physiological (e.g., hypercortisolemia, hypertension) and neurological (e.g., anhedonia, learned helplessness) changes that are clinically associated with depression. Importantly, UCMS-induced depressive symptoms can be ameliorated through chronic, but not acute, treatment with common SSRIs. As such, the UCMS protocol offers many advantages over acute stress protocols or protocols that utilize more extreme stressors. Our protocol involves randomized, daily exposures to 7 distinct stressors: damp bedding, removal of bedding, cage tilt, alteration of light/dark cycles, social stresses, shallow water bath, and predator sounds/smells. By subjecting rodents 3-4 hr daily to these mild stressors for 8 weeks, we demonstrate both significant behavioral changes and poor health outcomes to the cardiovascular system. This approach allows for in-depth interrogation of the neurological, behavioral, and physiological alterations associated with chronic stress-induced depression, as well as for testing of new potential therapeutic agents or intervention strategies.
The <i>Xenopus</i> Egg Wnt/β-catenin Pathway (2003)

In embryonic development in vertebrates, β-catenin signaling promotes polarization of the embryo to establish the dorsoventral axis and it is this process that is highlighted by the Xenopus Egg Wnt/β-catenin Pathway. In the amphibian Xenopus , fertilization of the egg results in the establishment of a parallel array of microtubules with the plus end pointing away from the sperm entry point. Concurrent with a process of cortical rotation, in which the cortex of the egg utilizes these microtubules to rotate relative to the inner cytoplasm, there is a movement of small vesicles toward the plus end of the microtubules. Cells inheriting these vesicles are destined to give rise to dorsal and anterior structures of the embryo. Two components of the Wnt/β-catenin pathway, Dishevelled and β-catenin, accumulate on the side of the egg and early embryo that receive these small vesicles. It is likely that Dishevelled is associated with the vesicles that move along the microtubules, and that it promotes the stabilization and dorsal accumulation of β-catenin. Although Wnts and Frizzled are present in the egg, their roles in axis specification remain unclear. Dorsal β-catenin then activates direct target genes, including the homeobox genes siamois and twinned . Activation of these genes on the prospective dorsal side is necessary and sufficient for formation of the gastrula organizer, which organizes the embryonic germ layers and axes. Science Viewpoint R. T. Moon, B. Bowerman, M. Boutros, and N. Perrimon, The promise and perils of Wnt signaling through β-catenin. Science 296 , 1644-1646 (2002). [ Abstract ] [ Full Text ]
A Rapid and Simple High-Performance Liquid Chromatography Assay for the Leflunomide Metabolite, Teriflunomide (A77 1726), in Renal Transplant Recipients (2010)

Leflunomide (Arava), a drug with immunosuppressive and antiviral effects, is being used in renal transplant recipients, primarily for its action against BK polyomavirus (BKV), which affects 1% to 10% of renal transplant recipients and often causes failure of grafted kidneys. Leflunomide effects are solely due to an active metabolite, teriflunomide (formerly A77 1726). Trough blood concentrations of teriflunomide exceeding 40 microg/mL (148 micromol/L) are associated with progressive clearance of BKV. Toxic effects become increasingly apparent at higher concentrations. We have developed a rapid, simple, and robust high-performance liquid chromatography (HPLC) method for therapeutic monitoring of teriflunomide in renal transplant recipients. Sample preparation is rapid, and each HPLC separation takes about 7 minutes. Intraday and interday coefficients of variation were 1.5% or less and 5.6% or less, respectively. The method was linear to 200 microg/mL (740 micromol/L), which is well above teriflunomide concentrations that are likely to be observed.
Activated protein C: biased for translation (2015)

The homeostatic blood protease, activated protein C (APC), can function as (1) an antithrombotic on the basis of inactivation of clotting factors Va and VIIIa; (2) a cytoprotective on the basis of endothelial barrier stabilization and anti-inflammatory and antiapoptotic actions; and (3) a regenerative on the basis of stimulation of neurogenesis, angiogenesis, and wound healing. Pharmacologic therapies using recombinant human and murine APCs indicate that APC provides effective acute or chronic therapies for a strikingly diverse range of preclinical injury models. APC reduces the damage caused by the following: ischemia/reperfusion in brain, heart, and kidney; pulmonary, kidney, and gastrointestinal inflammation; sepsis; Ebola virus; diabetes; and total lethal body radiation. For these beneficial effects, APC alters cell signaling networks and gene expression profiles by activating protease-activated receptors 1 and 3. APC's activation of these G protein-coupled receptors differs completely from thrombin's activation mechanism due to biased signaling via either G proteins or β-arrestin-2. To reduce APC-associated bleeding risk, APC variants were engineered to lack >90% anticoagulant activity but retain normal cell signaling. Such a neuroprotective variant, 3K3A-APC (Lys191-193Ala), has advanced to clinical trials for ischemic stroke. A rich data set of preclinical knowledge provides a solid foundation for potential translation of APC variants to future novel therapies.
Auctions: online auctions (2019)

This chapter describes the phenomenon of auctions which take place via the internet, ranging from ‘virtual’ auctions which take place entirely online to physical auctions via the internet in which bidders may participate.
Evolution of hematopoiesis: Three members of the PU.1 transcription factor family in a cartilaginous fish, <i>Raja eglanteria</i> (2001)

T lymphocytes and B lymphocytes are present in jawed vertebrates, including cartilaginous fishes, but not in jawless vertebrates or invertebrates. The origins of these lineages may be understood in terms of evolutionary changes in the structure and regulation of transcription factors that control lymphocyte development, such as PU.1. The identification and characterization of three members of the PU.1 family of transcription factors in a cartilaginous fish, Raja eglanteria, are described here. Two of these genes are orthologs of mammalian PU.1 and Spi-C, respectively, whereas the third gene, Spi-D, is a different family member. In addition, a PU.1-like gene has been identified in a jawless vertebrate, Petromyzon marinus (sea lamprey). Both DNA-binding and transactivation domains are highly conserved between mammalian and skate PU.1, in marked contrast to lamprey Spi, in which similarity is evident only in the DNA-binding domain. Phylogenetic analysis of sequence data suggests that the appearance of Spi-C may predate the divergence of the jawed and jawless vertebrates and that Spi-D arose before the divergence of the cartilaginous fish from the lineage leading to the mammals. The tissue-specific expression patterns of skate PU.1 and Spi-C suggest that these genes share regulatory as well as structural properties with their mammalian orthologs.
Real-Time Job Monitoring and Performance Control of Primary Cementing Operations as a Way to Total Quality Management (1995)

Summary A high-accuracy wellsite mud-logging system was developed and implemented to compare standpipe pressures and annular flow rates during primary cementing operations with real-time predictions from a hydraulic simulation model. This paper investigates the development of possible cementing job execution problems, such as low (laminar) flow rates in the annulus at critical job stages, resulting in unsatisfactory mud displacement and ultimately inadequate zonal isolation. Ways to eliminate or at least control free-fall-induced problems through hydraulic simulation at the rigsite and comparison with real-time job parameters, such as pump rates, standpipe pressures, and annular return rates, are presented with detailed descriptions of tested flowmeter equipment and logging experience gained during field testing. Several case studies are presented that compare predictions from job simulation with recorded data (flow-in/-out and standpipe pressure) highlighting special trends, such as fracturing formations, caused by excessive equivalent circulating densities (ECD's) during free-fall conditions.
An Ultrafast Fault Sensor for a Fault Current Limiting Device (1979)

A power system fault current limiting device must act quickly if it is to limit the initial fault current.