gebhart/patrepeval huggingface dataset:
Four Distinct Cyclin-Dependent Kinases Phosphorylate Histone H1 at All of Its Growth-Related Phosphorylation Sites (1997)

In mammalian cells, up to six serines and threonines in histone H1 are phosphorylated in vivo in a cell cycle dependent manner that has long been linked with chromatin condensation. Growth-associated H1 kinases, now known as cyclin-dependent kinases (CDKs), are thought to be the enzymes responsible for this process. This paper describes the phosphorylation of histone H1 by four different purified CDKs. The four CDKs phosphorylate only the cell cycle specific phosphorylation sites of H1, indicating that they belong to the kinase class responsible for growth-related H1 phosphorylation in vivo. All four CDKs phosphorylate all of the interphase and mitotic-specific H1 sites. In addition to the (S/T)PXK consensus phosphorylation sites, these four CDKs also phosphorylate a mitotic-specific in vivo H1 phosphorylation site that lacks this sequence. There is no site selectivity among the growth-related phosphorylation sites by any of the four CDKs because all four CDKs phosphorylate all relevant sites. The results imply that the cell cycle dependent H1 phosphorylations observed in vivo must involve differential accessibility of H1 sites at different stages of the cell cycle.
Critical assessment of the transport of intensity equation as a phase recovery technique in optical lithography (2014)

Photomasks are expected to have phase effects near edges due to their 3D topography, which can be modeled as imaginary boundary layers in thin mask simulations. We apply a modified transport of intensity (TIE) phase imaging technique to through-focus aerial images of photomasks in order to recover polarization-dependent edge effects. We use AIMS measurements with 193nm light to study the dependence of recovered phase on mask type and geometry. The TIE is an intensity conservation equation that quantitatively relates phase in the wafer plane to intensity through-focus. Here, we develop a modified version of the TIE for strongly absorbing objects, and apply it to recover wafer plane phase of attenuating masks. The projection printer blurs the fields at the wafer plane by its point spread function, hence an effective deconvolution is used to predict the boundary layers at the mask that best approximate the measured thick mask edge effects. Computation required for the inverse problem is fast and independent of mask geometry, unlike FDTD computations.
Extraction of a Murine Tumor-Specific Transplantation Antigen With 1-Butanol. I. Partial Purification by Isoelectric Focusing<xref ref-type="fn" rid="FN2">2</xref><xref ref-type="fn" rid="FN3">3</xref> (1980)

Treatment of whole viable MCA-F murine sarcoma cells from syngeneic female C3H/HeJ mice with a single-phase solution of 2.5% (vol/vol) 1-butanol yielded a crude membrane protein extract without loss of cell viability. 1-Butanol-extracted cells were capable of in vitro proliferation. Variations in extraction conditions significantly influenced not only protein yield but also viability. The crude butanol extract (CBE) contained a tumor-specific transplantation antigen (TSTA) more potent than that obtained by 3-M KCl extraction of MCA-F cells: a specific activity of 40 TSTA U/mg protein in the former and 2 U/mg in the latter. The antigen was specific and protected host against challenge with MCA-F cells but not the antigenically different MCA-D cells. The growth of MCA-F cells was not reduced by pretreatment with equivalent doses of CBE obtained from MCA-D cells. Partial purification of the antigenic activity by preparative isoelectric focusing revealed that most activity focused in the pH 6.4 fraction, which increased the specific activity to 1,000 TSTA U/mg protein. Thus 1-butanol was an effective agent for the extraction of certain membrane polypeptides, including an immunogenic TSTA, from whole cells.
Systolic-Time Intervals (1977)

Despite the early introduction of the measurement of the phases of the cardiac cycle, their clinical application received little attention until recent years. In large part, this delay can be attributed to the fact that the physiologic implications of the systolic-time intervals could not be validated until comparisons with direct measures of cardiac function could be made. It was only in the modern era of clinical physiology, when the technics of cardiac catheterization and ventriculography became clinically available, that the importance of these measurements could be appreciated. On the basis of studies in recent years, a new understanding of the . . .
Joint source-channel coding for wireless object-based video communications utilizing data hiding (2006)

In recent years, joint source-channel coding for multimedia communications has gained increased popularity. However, very limited work has been conducted to address the problem of joint source-channel coding for object-based video. In this paper, we propose a data hiding scheme that improves the error resilience of object-based video by adaptively embedding the shape and motion information into the texture data. Within a rate-distortion theoretical framework, the source coding, channel coding, data embedding, and decoder error concealment are jointly optimized based on knowledge of the transmission channel conditions. Our goal is to achieve the best video quality as expressed by the minimum total expected distortion. The optimization problem is solved using Lagrangian relaxation and dynamic programming. The performance of the proposed scheme is tested using simulations of a Rayleigh-fading wireless channel, and the algorithm is implemented based on the MPEG-4 verification model. Experimental results indicate that the proposed hybrid source-channel coding scheme significantly outperforms methods without data hiding or unequal error protection.
A 15-Channel Digital Active Electrode System for Multi-Parameter Biopotential Measurement (2015)

This paper presents a digital active electrode (DAE) system for multi-parameter biopotential signal acquisition in portable and wearable devices. It is built around an IC that performs analog signal processing and digitization with the help of on-chip instrumentation amplifiers, a 12 bit ADC and a digital interface. Via a standard <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">${\rm I}^{{2}}{\rm C}$</tex> </formula> bus, up to 16 digital active electrodes (15-channels) can be connected to a commercially available microcontroller, thus significantly reducing system complexity and cost. In addition, the DAE utilizes an innovative functionally DC-coupled amplifier to preserve input DC signal, while still achieving state-of-the-art performance: 60 nV/sqrt(Hz) input-referred noise and <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">${\pm} $</tex></formula> 350 mV electrode-offset tolerance. A common-mode feedforward scheme improves the CMRR of an AE pair from 40 dB to maximum 102 dB.
Preparation and Maintenance of Dorsal Root Ganglia Neurons in Compartmented Cultures (2008)

Neurons extend axonal processes that are far removed from the cell body to innervate target tissues, where target-derived growth factors are required for neuronal survival and function. Neurotrophins are specifically required to maintain the survival and differentiation of innervating sensory neurons but the question of how these target-derived neurotrophins communicate to the cell body of innervating neurons has been an area of active research for over 30 years. The most commonly accepted model of how neurotrophin signals reach the cell body proposes that signaling endosomes carry this signal retrogradely along the axon. In order to study retrograde transport, a culture system was originally devised by Robert Campenot, in which cell bodies are isolated from their axons. The technique of preparing these compartmented chambers for culturing sensory neurons recapitulates the selective stimulation of neuron terminals that occurs in vivo following release of target-derived neurotrophins. Retrograde signaling events that require long-range microtubule dependent retrograde transport have important implications for the treatment of neurodegenerative disorders.
Pyrophosphatase of the Roundworm<i>Ascaris suum</i>Plays an Essential Role in the Worm's Molting and Development (2005)

Previous studies indicated that inorganic pyrophosphatase of Ascaris suum (AsPPase) plays an important role in larval survival in the host. Here we describe a precise role for AsPPase in larval molting and development and also describe the potential role of recombinant AsPPase (rAsPPase) in protective immunity to A. suum infection. Using reverse transcriptase PCR analysis, we found that disruption of AsPPase gene function by RNA interference resulted in suppression of AsPPase mRNA levels. RNA interference also caused inhibition of molting of third-stage larvae (31%) and suppression of native protein expression, as demonstrated by a 56% reduction in enzyme activity and quantified by immunoblot and immunofluorescence analyses, suggesting that AsPPase has a role in the molting process. The anatomic location of the AsPPase native enzyme in the hypodermis of larvae along with its elevated expression prior to and during the molting process supports such a role. Anti-rAsPPase immunoglobulin G (IgG) also resulted in 57% inhibition of molting of A. suum lung-stage third-stage larvae to fourth-stage larvae in vitro with developmental arrest. Antigenic epitopes of AsPPase overlapped the enzyme active sites. Mice immunized with rAsPPase exhibited high antigen-specific IgG antibody responses and were protected (>70%) against a challenge A. suum migratory-phase infection. Splenic T cells from rAsPPase-immunized mice produced low levels of T helper 1-type cytokines (gamma interferon and interleukin-2) in vitro but exhibited an elevated interleukin-10 response. A significantly high level of IgG1 subclass antibodies was found in immunized mice. Our results establish that AsPPase has a critical role in the molting and development of Ascaris roundworms and suggest the potential of AsPPase for use as a candidate vaccine against ascariasis.
Are global wind power resource estimates overstated? (2013)

Estimates of the global wind power resource over land range from 56 to 400 TW. Most estimates have implicitly assumed that extraction of wind energy does not alter large-scale winds enough to significantly limit wind power production. Estimates that ignore the effect of wind turbine drag on local winds have assumed that wind power production of 2–4 W m ^−2 can be sustained over large areas. New results from a mesoscale model suggest that wind power production is limited to about 1 W m ^−2 at wind farm scales larger than about 100 km ^2 . We find that the mesoscale model results are quantitatively consistent with results from global models that simulated the climate response to much larger wind power capacities. Wind resource estimates that ignore the effect of wind turbines in slowing large-scale winds may therefore substantially overestimate the wind power resource.
Most Patients with Abdominal Aortic Aneurysm Are Not Suitable for Endovascular Repair Using Currently Approved Bifurcated Stent-Grafts (2004)

Strict morphologic criteria must be used for patient selection to achieve durable success with endovascular aortic aneurysm repair (EVAR). The goal of this study was to assess morphologic suitability (MS) of abdominal aortic aneurysms (AAAs) for 2 currently approved bifurcated stent grafts and identify reasons for exclusion from EVAR. The authors reviewed the electronic charts of 1,795 consecutive patients who were diagnosed as having AAA between January 1999 and July 2001 at their institution. Three hundred and twenty patients had an AAA with a diameter of > or = 5.0 cm, measured on computed tomography (CT). The records of 301 patients, 254 men, 47 women, with a mean age of 74 years were available for review, and these patients constituted the study cohort. Criteria used for MS included a proximal neck length > or = 15 mm; neck diameter between 18 and 26 mm; neck angulation < or = 60 degrees ; common or external iliac artery (CIA or EIA) diameters of 7-16 mm and 8-13 mm, respectively, for AneuRx (Medtronic Ave, Santa Rosa, CA) and Ancure (Guidant Cardiac and Vascular Division, Menlo Park, CA) bifurcated grafts. AAAs were suitable for AneuRx device in 14% of patients (43 of 301; 95% CI = 11-19%) and for Ancure in 5% (16 of 301; 95% CI = 3.1-9%). The main reason for exclusion was an inadequate proximal aortic neck (73%). The neck was too short in 49.5%, too wide in 64% and badly angulated in 12% of the patients. Iliac artery morphology precluded EVAR with AneuRx and Ancure devices in 52% and 80%. Both CIAs were too wide for EVAR in 43% and 77%, respectively. When iliac artery diameter < or = 20 mm was accepted, iliac suitability for AneuRx increased from 49% to 70% and overall suitability increased from 14% to 20%. When more permissive criteria were used for MS (neck length > or = 10 mm, neck diameter < or = 30 mm, CIA < or = 20), 39% of patients became candidates for EVAR. More than three fourths of the patients with an AAA > or = 5.0 cm in size, seen in a tertiary referral center, are morphologically not suitable for EVAR using 2 currently approved bifurcated endografts. The main reasons for exclusion are a short or wide proximal aortic neck. Considerable changes in size of the devices and in proximal attachment techniques have to occur before most AAAs will be suitable for EVAR.
Estimation of metabolizable energy and utilization of fly larvae (Musca domestica L.) in the feeding of broilers (1999)

Larvae of the domestic fly (Musca domestica L.) seem to be a viable alternative for
use in animal feeding. Thus, in this study the appparent and true metabolic energy
contents, corrected for nitrogen balance, of dry larvae, were estimated by the method of Sibbald, as 4 071 ± 133 and 4 252 ± 218 kcal kg-1, respectively. For evaluation of dry fly larvae as a protein and energy source for broilers, an experiment of 7 weeks duration was conducted, using 70 female day-old chicks of the Ross strain, divided into five experimental units of 7 chicks each assigned to each of two treatments. The experimental design was completely randomized with repeated measurements. All chicks were housed in wire floor, electrically heated batteries until 4 weeks of age, and then moved to grower batteries. The treatments were: T1, diet with dry fly larvae; and T2, diet with soybean meal and soybean oil; both diets in mash form and supplemented with sorghum, minerals, and vitamins, were offered ad libtium. Experimental data were recorded weekly. No differences (P>.05) were found between T1 and T2 in bodyweight gain (2 107 vs 2 148 g), feed intake (4 064 vs 4 158g), and in feed conversion ratio (1.93 vs 1.94), respectively. Three birds on each treatment died from ascites syndrome. The results show that the protein and energy supplied by the dry fly larvae support animal performance similar to that of chicks fed a conventional diet of sorghum-soybean.
Atmospheric Pressure Chemical Vapor Deposition: An Alternative Route to Large‐Scale MoS<sub>2</sub> and WS<sub>2</sub> Inorganic Fullerene‐like Nanostructures and Nanoflowers (2004)

Large-scale MoS2 and WS2 inorganic fullerene-like (IF) nanostructures (onionlike nanoparticles, nanotubes) and elegant three-dimensional nanoflowers (NF) have been selectively prepared through an atmospheric pressure chemical vapor deposition (APCVD) process with the reaction of chlorides and sulfur. The morphologies were controlled by adjusting the deposition position, the deposition temperature, and the flux of the carrier gas. All of the nanostructures have been characterized by X-ray powder diffraction (XRD), transmission electron microscopy (TEM), and scanning electron microscopy (SEM). A reaction mechanism is proposed based on the experimental results. The surface area of MoS2 IF nanoparticles and the field-emission effect of as-prepared WS2 nanoflowers is reported.
Analysis of Airplane Boarding Times (2009)

We model and analyze the process of passengers boarding an airplane. We show how the model yields closed-form estimates for the expected boarding time in many cases of interest. Comparison of our computations with previous work, based on discrete-event simulations, shows a high degree of agreement. Analysis of the model reveals a clear link between the efficiency of various airline boarding policies and a congestion parameter that is related to interior airplane design parameters, such as distance between rows. In particular, as congestion increases, random boarding becomes more attractive among row-based policies.
Radio resource allocation for OFDMA-based cognitive systems (2011)

This paper addresses the problem of wireless resource allocation in OFDMA-based cognitive radio cooperative systems. The objective is maximizing the total throughput and minimizing the transmission power of cognitive transmissions while guaranteeing fairness between the different cognitive users queues. The proposed radio resource allocation algorithm is based on maximizing the rate to power ratio. We also investigate the conflict resolution problem by suggesting a Conflict Resolution rate-based procedure to allocate conflicted subcarriers. Moreover, to secure cognitive transmissions we propose a double reservation procedure based on rate to power ratio margin RPRM, and thus to allocate secondary subcarriers. We propose to serve urgent transmissions, based on a fairness indicator. Simulations show the performance and the efficiency of the proposed algorithm.
Using simulation for option pricing (2002)

Monte Carlo simulation is a popular method for pricing financial options and other derivative securities because of the availability of powerful workstations and recent advances in applying the tool. The existence of easy-to-use software makes simulation accessible to many users who would otherwise avoid programming the algorithms necessary to value derivative securities. This paper presents examples of option pricing and variance reduction, and demonstrates their implementation with Crystal Ball 2000, a spreadsheet simulation add-in program.
Effect of Electron Beam Irradiation on Biomechanical Properties of Patellar Tendon Allografts in Anterior Cruciate Ligament Reconstruction (2010)

Terminal sterilization of patellar tendon allografts with electron beam irradiation can ensure higher safety of transplanted grafts and hence improve patient safety and acceptance.
A Cross-Layering and Autonomic Approach to Optimized Seamless Handover (2006)

Abstract — Performing global node mobility requires to support seamless vertical and horizontal handovers between different network providers and technologies. The optimization of the handover processes requires not only continuous network services, but also continuous service performance. In this paper we present a novel design approach based on autonomic components and cross-layer monitoring and control to optimize the performance of the WiOptiMo system, which provides seamless internetwork roaming by handling mobility at the application layer. We also distinguish from past work, in that we pragmatically followed the approach to rely only on existing technologies, deployed protocols and lightweight calculations, such that our system can be straightforwardly implemented as it is on most of the currently available mobile network devices. We report results from some simple real-world experiments showing the benefits of using a cross-layering approach. We also describe a first version of the new WiOptiMo based on the innovative design. Results from preliminary tests in real-world scenarios indicate the effectivness of our pragmatic approach. The system is still under development and testing, and we plan to integrate in it several autonomic components, which are presented and discussed in the paper. 1 I.
Cleavage of denatured natural collagen type II by neutrophil gelatinase B reveals enzyme specificity, post‐translational modifications in the substrate, and the formation of remnant epitopes in rheumatoid arthritis (2002)

During acute inflammation, leukocytes release proteolytic enzymes including matrix metalloproteinases (MMPs), but the physiopathological mechanisms and consequences of this process are not yet fully understood. Neutrophils, the predominant leukocyte type, produce neutrophil collagenase (MMP-8) and gelatinase B (MMP-9) but not the tissue inhibitors of MMPs. After stimulation, these cells also activate MMPs chemically. In arthritic diseases, neutrophils undergo great chemoattraction to the synovium, are activated by interleukin-8, and are stimulated to release gelatinase B in vivo. Production levels and net activities of gelatinase B were found to be absent in degenerative osteoarthritis but significantly increased in rheumatoid arthritis. The cleavage sites in cartilage type II collagen by gelatinase B were determined by a combination of reverse phase high-performance liquid chromatography, Edman degradation, and mass spectrometry analysis. The analysis revealed the site specificity of proline and lysine hydroxylations and O-linked glycosylation, the cleavage specificities by gelatinase B, and the preferential absence and presence of post-translational modifications at P2' and P5', respectively. Furthermore, gelatinase B leaves the immunodominant peptides intact, which are known from studies with (autoreactive) T cells. Lysine hydroxylation was detected at a critical position for T-cell activation. These data lend support to the thesis that extracellular proteolysis and other post-translational modifications of antigenic peptides may be critical in the establishment and perpetuation of autoimmune processes.
<title>Development of particle standards for testing explosive detection systems: characterization of the adhesion forces between composition 4 particles and polyethylene</title> (1994)

A method has been developed to study the adhesion of particles on a surface and the gas velocity needed to overcome the adhesion and dislodge the particle from the surface. Experiments have been performed to determine the minimum detachment velocity for particles deposited on a surface by gravitational settling and by finger print transfer. Particles of Arizona road dust and SiO<SUB>2</SUB> were deposited on smooth, and frosted glass for the study. In addition, composition-4 particles transferred via finger print onto polyethylene films were also studied. Results indicate that gas velocities in the 1 - 100 m/s range were needed to detach particles in the 10 - 300 micrometers range from these surfaces. Generally, the larger the particle size, the lower is the detachment velocity. Particles transferred via finger print were found to adhere to surfaces more tightly than similar particles deposited by gravitational settling, and surface roughness tend to decrease the detachment velocity.
Gold nanoparticles in micellar poly(styrene)‐b‐poly(ethylene oxide) films—size and interparticle distance control in monoparticulate films (1996)

Block copolymer micelles have been employed as nanosized reactors in which single gold particles were formed. Films can be produced by a process consisting of four steps. Monolayers of hexagonally assembled micelles (see Figure and this month's cover) can be prepared with rather regularly arranged, size‐controlled Au nanoparticles. The method of preparation and the factors influencing control of the process are presented. magnified image