gebhart/patrepeval huggingface dataset:
Focusing of electric fields in the active site of Cu‐Zn superoxide dismutase: Effects of ionic strength and amino‐acid modification (1986)

In this paper we report the implementation of a finite-difference algorithm which solves the linearized Poisson-Boltzmann equation for molecules of arbitrary shape and charge distribution and which includes the screening effects of electrolytes. The microcoding of the algorithm on an ST-100 array processor allows us to obtain electrostatic potential maps in and around a protein, including the effects of ionic strength, in about 30 minutes. We have applied the algorithm to a dimer of the protein Cu-Zn superoxide dismutase (SOD) and compared our results to those obtained from uniform dielectric models based on coulombic potentials. We find that both the shape of the protein-solvent boundary and the ionic strength of the solvent have a profound effect on the potentials in the solvent. For the case of SOD, the cluster of positive charge at the bottom of the active site channel produces a strongly enhanced positive potential due to the focusing of field lines in the channel-a result that cannot be obtained with any uniform dielectric model. The remainder of the protein is surrounded by a weak negative potential. The electrostatic potential of the enzyme seems designed to provide a large cross-sectional area for productive collisions. Based on the ionic strength dependence of the size of the positive potential region emanating from the active site and the repulsive negative potential barrier surrounding the protein, we are able to suggest an explanation for the ionic strength dependence of the activity of the native and chemically modified forms of the enzyme.
An iterative algorithm for the mixed H<inf>2</inf>/H<inf>∞</inf> control problem using H<inf>2</inf> norm decreasing controller sets (2003)

This paper is concerned with the mixed H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> /H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</inf> control problem. The purpose of this paper is to give an iterative algorithm for finding a sub-optimal static state feedback controller for the mixed H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> /H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</inf> control problem. The key idea of our algorithm is to construct two “controller sets”: one is a set of controllers that improve the H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> norm of the closed loop map for a given controller and the other is a set of controllers whose elements satisfy the H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</inf> norm constraint. Using two controller sets, we propose an iterative algorithm. The obtained controller is either the global optimal solution if the H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</inf> norm constraint is satisfied until the H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> norm of the objective closed loop map converges to the H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> optimal value or a sub-optimal solution on the boundary of the H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</inf> norm constraint.
Cumulative group metrics: a new and efficient method to measure the scientific impact of research groups (2023)

The presented cumulative group metrics are an effective tool to assess the scientific impact of a research group. The cumulative submetrics can further evaluate research groups compared with other departments due to field normalization. Department leadership and funding agencies can utilize these metrics to evaluate research output quantitatively and qualitatively.
Imprint of spatial curvature on inflation power spectrum (2008)

If the Universe had a large curvature before inflation there is a deviation from the scale invariant perturbations of the inflaton at the beginning of inflation. This may have some effect on the cosmic microwave background anisotropy at large angular scales. We calculate the density perturbations for both open and closed universe cases using the Bunch-Davies vacuum condition on the initial state. We use our power spectrum to calculate the temperature anisotropy spectrum and compare the results with the Wilkinson microwave anisotropy map five year data. We find that our power spectrum gives a lower quadrupole anisotropy when $\ensuremath{\Omega}\ensuremath{-}1&gt;0$, but matches the temperature anisotropy calculated from the standard Ratra-Peebles power spectrum at large $l$. The determination of spatial curvature from temperature anisotropy data is not much affected by the different power spectra which arise from the choice of different boundary conditions for the inflaton perturbation.
Structural Essentials of Ser-1 in Tethered Peptide Ligand of Human Thrombin Receptor for Phosphoinositide Hydrolysis (1994)

Abstract In order to inspect the structural elements of Ser-1 in receptor activation by SFLLRNP (one-letter amino acid code), a ligand peptide tethered to the thrombin receptor, a series of analogs with such replacements as d-Ser, Ala, Thr, and Ac-Ser have been synthesized. These analogs were evaluated for their ability to hydrolyze the phosphoinositide in human neuroblastoma SH-EP cells. It was found that the α-amino group and l-configuration of Ser-1 are very important in the activation of receptors. N-Acetylation or deletion of Ser-1 completely eliminated the activity of SFLLRNP (a half-maximal effective concentration, EC50 = 0.89 μM (1 M = 1 mol dm−3)), and these modifications induced no antagonist activity. Incorporation of d-Ser also drastically diminished the activity, but retained about 50% activity of the maximal response by 100 μM SFLLRNP. The Ser/Ala substitution sustained 30% of the activity of SFLLRNP to elicit a full stimulation. The Ser/Thr substitution, however, enhanced the activity (20%) in spite of its decreased activity (60%) reported for platelet aggregation. These results indicated that the β-hydroxyl group of Ser-1 is important to receptor activation, but not essential. The effect of chemical modifications on the receptor activities of the tethered ligand is discussed with regard to the efficacy between phosphoinositide hydrolysis and biological activities.
The Role of Water for the Phase‐Selective Preparation of Hexagonal and Cubic Cobalt Oxide Nanoparticles (2011)

A selective preparation and the formation mechanism of hexagonal and cubic CoO nanoparticles from the reaction of [Co(acac)(2)] (acac=acetylacetonate) and amine have been investigated. CoO nanoparticles with a hexagonal pyramidal shape were yielded under decomposition conditions with amine. Importantly, the addition of water altered the final phase to cubic and comprehensively changed the reaction mechanism. The average sizes of the hexagonal and cubic CoO nanoparticles could be controlled either by changing the amine concentration or by using different reaction temperatures. Detailed formation mechanisms are proposed on the basis of gas chromatography-mass spectrometry data and color changes of the reaction mixture. The hexagonal CoO phase is obtained through two distinct pathways: solvolysis with C-C bond cleavage and direct condensation by amine. On the other hand, the cubic CoO nanoparticles were synthesized by strong nucleophilic attack of hydroxide ions from water and subsequent C-C bond breaking. The resulting caboxylate ligand can stabilize a cobalt hydroxide intermediate, leading to the generation of a thermodynamically stable CoO phase.
Bedside insertion of the inferior vena cava filter in the intensive care unit. (2003)

Historically, inferior vena cava (IVC) filters have been inserted in the Radiology Department or the Operating Room. When initially designed, vena cava filters required surgical cut down of the internal jugular vein to insert a large (24 French) introducer and it was therefore necessary to perform this procedure in the operating room. Percutaneous methods (e.g., the Seldinger technique) with smaller profile sheath-dilator devices (6 to 12 French) have made IVC filter insertion a much easier procedure. Furthermore, the remaining equipment is simple, portable, and readily available throughout most hospitals (e.g., C-arm, contrast, sterile drapes, gowns, gloves, catheters, etc.). These factors have made it easy to "bring the procedure to the patient." This is particularly advantageous in critically ill ICU patients. Complication rates of "road trips" for critically ill patients from the ICU to other parts of the hospital (i.e., radiology department or operating room) can result in a mishap rate of 5-30. Secondary benefits of bedside insertion of vena cava filters include cost-effectiveness.
Water diffusion in a rat glioma during ganciclovir‐thymidine kinase gene therapy‐induced programmed cell death in vivo: Correlation with cell density (2004)

The present results show that reduced cell density and increased water content, leading to altered water microenvironment, are associated with increased water diffusion coefficient in eradicating gliomas as a result of PCD.
Inconsistency of Template Estimation with the Fr{é}chet mean in Quotient Space (2017)

We tackle the problem of template estimation when data have been randomly transformed under an isometric group action in the presence of noise. In order to estimate the template, one often minimizes the variance when the influence of the transformations have been removed (computation of the Fr{é}chet mean in quotient space). The consistency bias is defined as the distance (possibly zero) between the orbit of the template and the orbit of one element which minimizes the variance. In this article we establish an asymptotic behavior of the consistency bias with respect to the noise level. This behavior is linear with respect to the noise level. As a result the inconsistency is unavoidable as soon as the noise is large enough. In practice, the template estimation with a finite sample is often done with an algorithm called max-max. We show the convergence of this algorithm to an empirical Karcher mean. Finally, our numerical experiments show that the bias observed in practice cannot be attributed to the small sample size or to a convergence problem but is indeed due to the previously studied inconsistency.
Ditopic Complexation and Release of Neutral Guest Molecules by a Hydrogen‐Bonded “Endo–Exo” Receptor (2005)

A complex situation: Two different types of neutral guest molecules are recognized through a combination of noncovalent interactions by a hydrogen-bonded receptor which displays two different modes of complexation: nonselective-exo and selective-endo complexation (see schematic representation). Furthermore, the hydrogen-bonded trimer can be selectively released.
Changes of Erythrocyte Fatty Acids after Supplementation with Highly Concentrated Docosahexaenoic Acid (DHA) in Pediatric Cystic Fibrosis: A Randomized Double-Blind Controlled Trial (2023)

We characterized the fatty acid profiles in the erythrocyte membrane of pediatric patients with cystic fibrosis (CF) receiving highly concentrated docosahexaenoic acid (DHA) supplementation (Tridocosahexanoin-AOX<sup>®</sup> 70%) at 50 mg/kg/day (<i>n</i> = 11) or matching placebo (<i>n</i> = 11) for 12 months. The mean age was 11.7 years. The DHA group showed a statistically significant improvement in n-3 polyunsaturated fatty acids (PUFAs), which was observed as early as 6 months and further increased at 12 months. Among the n-3 PUFAs, there was a significant increase in DHA and eicosapentaenoic acid (EPA). Additionally, a statistically significant decrease in n-6 PUFAs was found, primarily due to a decrease in arachidonic acid (AA) levels and elongase 5 activity. However, we did not observe any changes in linoleic acid levels. The long-term administration of DHA over one year was safe and well tolerated. In summary, the administration of a high-rich DHA supplement at a dose of 50 mg/kg/day for one year can correct erythrocyte AA/DHA imbalance and reduce fatty acid inflammatory markers. However, it is important to note that essential fatty acid alterations cannot be fully normalized with this treatment. These data provide timely information of essential fatty acid profile for future comparative research.
A Procedure for 3-D Contact Stress Analysis of Spiral Bevel Gears (1994)

Contact stress distribution of spiral bevel gears using nonlinear finite element static analysis is presented. Procedures have been developed to solve the nonlinear equations that identify the gear and pinion surface coordinates based on the kinematics of the cutting process and orientate the pinion and the gear in space to mesh with each other. Contact is simulated by connecting GAP elements along the intersection of a line from each pinion point (parallel to the normal at the contact point) with the gear surface. A three dimensional model with four gear teeth and three pinion teeth is used to determine the contact stresses at two different contact positions in a spiral bevel gearset. A summary of the elliptical contact stress distribution is given. This information will be helpful to helicopter and aircraft transmission designers who need to minimize weight of the transmission and maximize reliability.
Safety of Foslevodopa/Foscarbidopa During Optimization and Maintenance Treatment: Post Hoc Analysis of a Phase 3 Trial (S32.004) (2023)

To characterize the time course of adverse events (AEs) in patients with Parkinson’s disease (PD) and motor fluctuation treated with foslevodopa/foscarbidopa.
Numerical modeling of the Alboran sea circulation (1984)

Se examina la circulacion del Mar de Alboran usando modelos numericos hidrodinamicos estratificados. El rasgo mas intenso y persistente, el giro anticiclonico de Alboran, aparece consistentemente al sur del flujo Atlantico. El tamano y la forma del giro varia con cambios en el angulo, magnitud y cizalla horizontal del flujo entrante. Los efectos geometricos mas notables son la proximidad del Estrecho de Gibraltar al limite norte, y el efecto deflector del Cabo Tres Forcas sobre el flujo atlantico. Los efectos topograficos conducen el flujo de la capa inferior hacia el limite sur del mar de Alboran. Esto altera las soluciones en la plataforma de la region sur y distorsiona la forma simetrica del giro aparente en las soluciones de gravedad reducida y fondo plano. Uno de los efectos topograficos mas importantes es la inclusion de una isla de Alboran idealizada. La isla desvia el flujo Atlantico, hacia el norte de ella, si la magnitud del mismo es mayor que 40 cm/s y si entra con un angulo en una direccion ligeramente al Norte del Este.
Extending matrix‐assisted laser desorption/ionization triple quadrupole mass spectrometry enzyme screening assays to targets with small molecule substrates (2009)

Mass spectrometry (MS)-based high-throughput screening (HTS) has tremendous potential as an alternative to current screening methods due to its speed, sensitivity, reproducibility and label-free readout. We recently reported that a new generation matrix-assisted laser desorption/ionization triple quadrupole (MALDI-QqQ) mass spectrometer is ideally suited for a variety of enzyme assays and screening protocols. However, all the targets measured to date had peptide substrates that were easily monitored by selected ion monitoring (SIM) without interference from the MALDI matrix. To further extend the application to enzymes with small molecule, non-peptide substrates, we evaluated this method for measuring enzyme activity and inhibition of acetylcholinesterase (AChE). Due to the potential of MALDI matrix interference, multiple reaction monitoring (MRM) was investigated for selective MS/MS transitions and to accurately measure the conversion of acetylcholine into choline. Importantly, ionization, detection and MRM transition efficiency differences between the substrate and product can be overcome by pre-balancing the MRM transitions during method development, thus allowing for a direct readout of the enzyme activity using the ratio of the substrate and product signals. Further validation of the assay showed accurate concentration-dependent inhibition measurements of AChE with several known inhibitors. Finally, a small library of 1008 drug-like compounds was screened at a single dose (10 microM) and the top 10 inhibitors from this primary screen were validated in a secondary screen to determine the rank order of inhibitory potency for each compound. Collectively, these data demonstrate that a MALDI-QqQMS-based readout platform is amenable to measuring small molecule substrates and products and offers significant advantages over current HTS methods in terms of speed, sensitivity, reproducibility and reagent costs.
3D-printing of transparent bio-microfluidic devices in PEG-DA (2016)

The vast majority of microfluidic systems are molded in poly(dimethylsiloxane) (PDMS) by soft lithography due to the favorable properties of PDMS: biocompatible, elastomeric, transparent, gas-permeable, inexpensive, and copyright-free. However, PDMS molding involves tedious manual labor, which makes PDMS devices prone to assembly failures and difficult to disseminate to research and clinical settings. Furthermore, the fabrication procedures limit the 3D complexity of the devices to layered designs. Stereolithography (SL), a form of 3D-printing, has recently attracted attention as a way to customize the fabrication of biomedical devices due to its automated, assembly-free 3D fabrication, rapidly decreasing costs, and fast-improving resolution and throughput. However, existing SL resins are not biocompatible and patterning transparent resins at high resolution remains difficult. Here we report procedures for the preparation and patterning of a transparent resin based on low-MW poly(ethylene glycol) diacrylate (MW 250) (PEG-DA-250). The 3D-printed devices are highly transparent and cells can be cultured on PEG-DA-250 prints for several days. This biocompatible SL resin and printing process solves some of the main drawbacks of 3D-printed microfluidic devices: biocompatibility and transparency. In addition, it should also enable the production of non-microfluidic biomedical devices.
Emended description of Rickettsia felis (Bouyer et al. 2001), a temperature-dependent cultured bacterium (2002)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Processor acceleration through automated instruction set customization (2004)

Application-specific extensions to the computational capabilities of a processor provide an efficient mechanism to meet the growing performance and power demands of embedded applications. Hardware, in the form of new function units (or co-processors), and the corresponding instructions, are added to a baseline processor to meet the critical computational demands of a target application. The central challenge with this approach is the large degree of human effort required to identify and create the custom hardware units, as well as porting the application to the extended processor. In this paper, we present the design of a system to automate the instruction set customization process. A dataflow graph design space exploration engine efficiently identifies profitable computation subgraphs from which to create custom hardware, without artificially constraining their size or shape. The system also contains a compiler subgraph matching framework that identifies opportunities to exploit and generalize the hardware to support more computation graphs. We demonstrate the effectiveness of this system across a range of application domains and study the applicability of the custom hardware across the domain.
Increasing weaning age improves pig performance in a multisite production system1 (2004)

Two trials were conducted to determine the effects of weaning age on pig performance in a multisite production system. The second trial also evaluated the effects of modifying the nursery feeding program according to weaning age. In Trial 1 (2,272 pigs), treatments included weaning litters at 12, 15, 18, or 21 d of age. In Trial 2 (3,456 pigs), litters were weaned at 15, 16, 18, 19, 21, or 22 d of age and categorized into three treatments (15.5, 18.5, or 21.5 d of age). In Trial 2, pigs in each age group were fed one of two nursery feeding programs. Nursery feeding programs varied in both diet formulation and in the quantity of diets fed containing increased levels of whey and spray-dried animal plasma. Each trial was conducted as a randomized complete block design with four blocks of nursery and finishing sites. All weaning-age treatments were weaned from a 7,300-sow farm on the same day into the same nursery. Each block remained intact as pigs moved from nursery to finishing site. Increasing weaning age (12, 15, 18, or 21 d in Trials 1; and 15.5, 18.5, or 21.5 d in Trial 2) increased (linear, P < 0.001) ADG (299, 368, 409, 474 +/- 7 g/d; 435, 482, 525 +/- 13 g/d) and tended to decrease (linear, P < 0.09) mortality (5.25, 2.82, 2.11, 0.54 +/- 0.76%; 2.17, 1.56, 1.30 +/- 0.36%) in the initial 42 d after weaning. Finishing ADG (722, 728, 736, 768 +/- 11 g/d; 783, 790, 805 +/- 11 g/d) also improved (linear, P < 0.01) with increasing weaning age. Overall, increasing weaning age increased (linear, P < 0.001) wean-to-finish ADG (580, 616, 637, 687 +/- 8 g/d; 676, 697, 722 +/- 6 g/d), weight sold per pig weaned (94.1, 100.5, 104.4, 113.1 +/- 1.3 kg; 107.6, 111.6, 116.2 +/- 1.1 kg), and decreased (linear, P < 0.03) mortality rate (9.4, 7.9, 6.8, 3.6 +/- 0.95%; 3.9, 3.4, 2.5 +/- 0.5%). Altering the nursery feeding program did not affect wean-to-finish growth performance. In this multisite production system, increasing weaning age from 12 to 21.5 d of age increased weight sold per pig weaned by 1.80 +/- 0.12 kg for each day increase in weaning age. These studies suggest increasing weaning age up to 21.5 d can be an effective management strategy to improve wean-to-finish growth performance in multisite pig production.
Application of object-oriented design to Knowledge Amplification by Structured Expert Randomization (KASER) (2003)

This paper presents research results of a project that produced a progressively dependable knowledge amplifier. A knowledge amplifier can acquire a virtual-rule space automatically that is exponentially larger than the actual, declared-rule space and with a decreasing non-zero likelihood of error. A Knowledge Amplifier by Systematic Expert Randomization (KASER) overcomes the knowledge-acquisition bottleneck in intelligent systems by amplifying user-supplied knowledge. This enables the construction of an intelligent, creative system that fails softly, learns over a network and has enormous potential for automated decision making. The system achieves creative reasoning through the use of declarative object trees. A KASER computes with words and phrases and presents a capability for analogical explanation. We implemented the KASER with an object-oriented design.