gebhart/patrepeval huggingface dataset:
Why multiple b-values are required for multi-tensor models. evaluation with a constrained log-euclidean model (2010)

Multi-tensor models have been proposed to assess multiple fiber orientations but are known to be numerically challenging. We show that the estimation cannot be performed with a single-shell HARDI acquisition because the fitting procedure leads to an infinite number of solutions ; multiple-shell HARDI acquisitions are required. Additionally, we propose a new log-euclidean constrained two-tensor model capable of assessing crossing fibers configurations with a relative limited number of DW acquisitions. We provide numerical experiments with this model to verify experimentally the necessity of multiple-shell HARDI acquisitions schemes for multitensor models.
Phosphatidylserine-Positive Erythrocytes Modulate Tissue Factor Activity In Vivo and In Vitro in Sickle Cell Disease. (2004)

Abstract Evaluation of fluid phase markers reveals activated blood coagulation in sickle cell disease (SCD), with enhanced in vivo thrombin generation. Studies have shown that whole blood tissue factor (WTBF) activity is elevated, and that both monocytes and endothelial cells (ECs) contribute to WBTF. In a recent preliminary study, we have found an unexpected and interesting positive correlation between WBTF and the levels of both reticulocytes (R=0.6) and phosphatidylserine (PS)-positive red cells (R=0.4) in SCD and an inverse correlation with hemoglobin (R=-0.4). We have therefore evaluated potential mechanisms for erythroid modulation of WBTF. Reticulocytes being PS-positive, we initially evaluated the effects of PS-positive red cells on endothelial TF using human lung microvascular ECs and ionophore-treated PS-exposing control erythrocytes, since sickle erythrocytes also express other adhesion markers. Following incubation with appropriate treatments for 24 hours, ECs were analyzed for TF expression (with E-selectin as a positive control for EC activation). Co-incubation of PS-positive red cells (15% ±) with ECs increased endothelial expression of TF in a hematocrit-dependent manner. PS-positive cells increased TF expression by 140, 200, 260 and 320% at hematocrits of 2, 5, 10 and 20%, respectively, compared to media controls. Results similar to those observed with TF were also noted with E-selectin. PS-positive sickle erythrocytes have been classified as either type I or type II cells. Type I express low levels of PS (reticulocytes), while type II are highly PS-positive and include sickle dense cells. We next evaluated whether both type I and type II PS-positive red cells triggered endothelial TF expression. Type II cells were prepared by incubating control erythrocytes with calcium ionophore, and type I cells were generated by incubating type II cells with predetermined amounts of annexin V (100 μg annexin V per 25X106 PS-positive cells). FACS analyses demonstrated appropriate PS levels in each PS positive category. We show that type I cells had no effect. TF expression occurred following incubation of ECs with type II erythrocytes (0.21±0.06 units TF with type II vs 0.10±0.06 with PS-negative cells at a 2% hematocrit, n=5, P&lt;0.01). In final patient related studies we have observed a marked correlation between WBTF and type II PS-positive red cells (R=0.5, P&lt;0.00001, n=81). No such correlation was noted with type I. We conclude that while the reticulocyte component of the hemolytic anemia does not appear to affect WBTF, type II PS cells (including potentially dense cells) modulate WBTF activity in SCD with implications for both the thrombophilic and adhesive pathophysiologic complications of this disease entity. These studies in addition have potential implications for other disease states where erythrocyte PS exposure occurs.
Uniform wavelength spacing Mach-Zehnder interferometer using phase-generating couplers (2006)

A theoretical and experimental study of an optical interferometer circuit with a uniform wavelength spacing is presented. The operating principle of the filter and a phase-generating coupler (PGC) that can transform a conventional filter into a uniform-wavelength-spaced optical filter is described. As an example, a transformation method is applied to a conventional Mach-Zehnder interferometer (MZI), and the PGC variables are optimized to obtain an MZI with a constant channel spacing of 20 nm. Furthermore, the designed MZI is fabricated using 1.5%-Delta silica-based planar lightwave circuit technology and a 20-nm-spaced MZI is realized with a wavelength displacement that was less than plusmn1.2% of the wavelength period. The fabrication tolerance of the MZI in relation to the PGC design variables is discussed. It is shown that a certain PGC design can increase the fabrication tolerance
Generalised Elmore delay expression for distributed RC tree networks (1993)

A generalised Elmore delay (GED) expression is proposed which can be applied directly to distributed RC tree networks. Using this expression, the signal delay caused by interconnects such as those in LSIs can be estimated more simply and accurately than using the conventional Elmore delay model.
Far from superficial: microbial diversity associated with the skin and mucus of fish (2011)

During horizontal or water-borne infection involving an obligate pathogen (e.g. – Aeromonas salmonicida, cause of furunculosis), the pathogen interacted with and influenced the microbial diversity of the dermal mucus of fish. Prior to infection, the prevalent bacterial flora cultured from juvenile Atlantic salmon (Salmo salar) included Pseudomonas fluorescens, Comomonas terrigenia, Acinetobacter sp., Moraxella sp., Pseudomonas dimunita, Alcaligenes denitrificans, Pseudomonas pseudoalcaligenes, and Pseudomonas
Multiplicity and stability analysis of microorganisms in continuous culture: Effects of metabolic overflow and growth inhibition (1998)

Metabolic overflow (enhanced uptake of substrate and secretion of intermediates) is a phenomenon often observed for cells grown under substrate excess. Growth inhibition by substrate and/or product is also normally found for this kind of culture. An effort is made in this work to analyze the dynamic behavior of a continuous culture subject to metabolic overflow and growth inhibition by substrate and/or product. Analysis of a model system shows that in a certain range of operating conditions three nonwashout steady state solutions are possible. Local stability analysis indicates that only two of them are stable thus leading to multiplicity and hysteresis. Further analysis of the intrinsic effects of different terms describing the metabolic overflow and growth inhibitions reveals that for the model system and the parameters considered, the combined effects of product inhibition and an enhanced formation rate of product under substrate excess cause the multiplicity and hysteresis. Growth inhibition by substrate and/or an enhanced substrate uptake appear not to be necessary conditions. The combined effects of enhanced product formation and product inhibition can also lead to unusual dynamic behavior such as a prolonged time period to reach a steady state, oscillatory transition from one steady state to another, and sustained oscillations. Using the occurrence of multiplicity and oscillation as criteria, the operating regime of a continuous culture can be divided into four domains: one with multiplicity and oscillation, one with unique steady state but possible oscillatory behavior, the other two with unique and stable steady state. The model predictions are in accordance with recent experimental results. The results presented in this work may be used as guidelines for choosing proper operating conditions of similar culture systems to avoid undesired instability and multiplicity. Copyright 1998 John Wiley & Sons, Inc.
Evaluation of a luminescent ruthenium complex immobilized inside Nafion as optical pH sensor (1998)

The development of an optical pH sensor based on immobilization of a luminescent ruthenium complex, [Ru(bpy)2(dhphen)]2+ (bpy = 2,2′-bipyridine, dhphen = 4,7-dihydroxy-1,10-phenanthroline) in Nafion film is described. The sensor has a useful pH range of 1–8. The typical response time of the sensing film is 2–5 min. The polyanionic nature of the Nafion film eliminates interference from anions. The sensor also shows minimal interference effects from alkali metal and divalent cations and has good photostability and reproducibility.
Parallel mixed-technology simulation (2000)

Circuit simulation has proven to be one of the most important computer aided design (CAD) methods for the analysis and validation of integrated circuit designs. A popular approach to describing circuits for simulation purposes is to use a hardware description language such as VHDL. Similar efforts have also been carried out in the analog domain that has led to tools such as SPICE. However, with the growing trend of hardware designs that contain both analog and digital components, design environments that seamlessly integrate analog and digital circuitry are needed. Simulation of such circuit is however, exacerbated by the higher resource (CPU and memory) demands that arise when analog and digital models are integrated in a mixed-mode (analog and digital) simulation. One solution to this problem is to use PDES algorithms on a distributed platform. However, a synchronization interface between the analog and digital simulation environment is required to achieve integrated mixed-mode simulation. In this paper, we present the issues involved in the construction of synchronization protocols which support mixed-mode simulation in a distributed simulation environment. The proposed synchronization protocols provide an interface between an optimistic (Time Warp based) discrete-event simulation kernel and any continuous time simulation kernel. Empirical and formal analyses were conducted to ensure correctness and completeness of the protocols and the results of these analyses are also presented.
Advanced chemical strategies for lithium–sulfur batteries: A review (2017)

Lithium–sulfur (LiS) battery has been considered as one of the most promising rechargeable batteries among various energy storage devices owing to the attractive ultrahigh theoretical capacity and low cost. However, the performance of LiS batteries is still far from theoretical prediction because of the inherent insulation of sulfur, shuttling of soluble polysulfides, swelling of cathode volume and the formation of lithium dendrites. Significant efforts have been made to trap polysulfides via physical strategies using carbon based materials, but the interactions between polysulfides and carbon are so weak that the device performance is limited. Chemical strategies provide the relatively complemented routes for improving the batteries' electrochemical properties by introducing strong interactions between functional groups and lithium polysulfides. Therefore, this review mainly discusses the recent advances in chemical absorption for improving the performance of LiS batteries by introducing functional groups (oxygen, nitrogen, and boron, etc.) and chemical additives (metal, polymers, etc.) to the carbon structures, and how these foreign guests immobilize the dissolved polysulfides.
Effects of La Addition and Preparation Methods on Catalytic Activities for Methane Partial Oxidation Catalysts (2010)

Synthesis gas was produced by the partial oxidation of methane. For the preparation of catalysts, Ni, known to be active in this reaction and cheap, was used as the active component and , having high oxygen storage capability and high redox ability, was used as the support. The catalysts were prepared by the impregnation and urea methods. The catalyst prepared by the urea method showed about 11 times higher surface area and finer particle size than that prepared by the impregnation method. The catalysts prepared by the urea method showed higher methane conversion and synthesis gas selectivity than that prepared by the impregnation method. In this reaction, carbon deposition is a problem to be solved, so La was added to the catalyst system to reduce the carbon deposition. TGA analysis results showed that there was 2% carbon deposition with La-added catalysts and 16% with La-free catalysts. It was found that the addition of La decreases the amount of carbon deposition and prevents catalyst deactivation.
Flux-grown PZN-PT Single Crystals for High-performance Piezo Devices (2007)

Large-size Pb(Zn <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1/3</sub> Nb <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2/3</sub> )O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> -PbTiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> (PZN-PT) single crystals of different PT contents were successfully grown using an improved flux growth technique. Measurements made from samples of different orientation cuts revealed that PZN-(6-7)%PT single crystals exhibit exceptional dielectric and electromechanical properties. When poled in [001] direction, these crystals yield K <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sup> ap 7000, d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">33</sub> ap 2800 pC/N and k <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">33</sub> ges 0.92. For [011]-cut crystals, optimally poled PZN-7%PT single crystal exhibits very high transverse piezoelectric properties with d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">32</sub> ap -3800 pC/N, k32 > 0.90 and K <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sup> ges 5000, while PZN-6%PT has d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">32</sub> ap -3000 pC/N and comparable k <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">32</sub> and K <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sup> values but a high overpoling field of >2.0 kV/mm. In comparison with melt-grown PMN-PT single crystals, flux-grown PZN-PT single crystals show good compositional homogeneity, superior and consistent dielectric and electromechanical properties, and higher depolarisation temperatures.
Unreliability of Results of PCR Detection of <i>Helicobacter pylori</i> in Clinical or Environmental Samples (2009)

The aim of this study was to compare published Helicobacter pylori primer pairs for their ability to reliably detect H. pylori in gastric biopsy specimens and salivary samples. Detection limits of the 26 PCR primer pairs previously described for detection of H. pylori DNA in clinical samples were determined. Sensitivity and specificity were determined using primers with detection limits of <100 CFU/ml using 50 H. pylori-positive and -negative (by concordance by culture and histology) coded gastric biopsy specimens. These results were then confirmed with gastric biopsy specimens and saliva from patients with confirmed H. pylori status. Five of the twenty-six previously reported primer pairs (HP64-f/HP64-r, HP1/HP2, EHC-U/EHC-L, VAG-F/VAG-R, and ICT37/ICT38) had detection limits of <100 CFU/ml in the presence of gastric tissue. None had 100% specificity or sensitivity; all produced false-positive results. The HP64-f/HP64-r for ureA and HP1/HP2 for 16S rRNA individually had sensitivities and specificities of >90% with gastric biopsy specimens. No combinations of primer pairs improved the results. Using these five primer pairs, 54% of the positive saliva samples were determined to be false positive; both the HP64-f/HP64-r and the HP1/HP2 sets produced false positives with saliva. We conclude that clinicians should not rely on results using current PCR primers alone to decide the H. pylori status of an individual patient or as a basis for treatment decisions. The results of studies based on PCR identification of H. pylori in environmental samples should be viewed with caution. Possibly, specific primers sets can be identified based on the presence of multiple putative virulence factor genes.
Multimodal mechanism of action of allosteric HIV-1 integrase inhibitors (2013)

Integrase (IN) is required for lentivirus replication and is a proven drug target for the prevention of AIDS in HIV-1-infected patients. While clinical strand transfer inhibitors disarm the IN active site, allosteric inhibition of enzyme activity through the disruption of IN-IN protein interfaces holds great therapeutic potential. A promising class of allosteric IN inhibitors (ALLINIs), 2-(quinolin-3-yl) acetic acid derivatives, engage the IN catalytic core domain dimerisation interface at the binding site for the host integration co-factor LEDGF/p75. ALLINIs promote IN multimerisation and, independent of LEDGF/p75 protein, block the formation of the active IN-DNA complex, as well as inhibit the IN-LEDGF/p75 interaction in vitro. Yet, rather unexpectedly, the full inhibitory effect of these compounds is exerted during the late phase of HIV-1 replication. ALLINIs impair particle core maturation as well as reverse transcription and integration during the subsequent round of virus infection. Recapitulating the pleiotropic phenotypes observed with numerous IN mutant viruses, ALLINIs provide insight into underlying aspects of IN biology that extend beyond its catalytic activity. Therefore, in addition to the potential to expand our repertoire of HIV-1 antiretrovirals, ALLINIs afford important structural probes to dissect the multifaceted nature of the IN protein throughout the course of HIV-1 replication.
Mass–length ratio of fibrin fibers from gel permeation and light scattering (1977)

Abstract Mass–length ratios of fibers in fibrin gels were obtained from measurements of the angular dependence of the intensity of light scattered by dilute gels and from the permeability of more concentrated gels. The permeability was determined by measuring the forced flow of buffer through a short column of gel held in a glass tube. The results obtained with the two methods are consistent. At high pH and high ionic strength the mass–length ratio is found to be that calculated for a protofibril, i.e., a double strand of fibrin molecules laid end to end at a separation of 450 Å. This same value is found under conditions where the polymerized fibrin is not gelled (pH 10.25) and where it is just gelled (pH 10.0). At pH 7.4, ionic strength 0.35, the fibers are found to have a higher mass–length ratio, the average fiber consisting of some three protofibrils associated laterally. At pH 7.4 and low ionic strength (0.10 M ) the fibers are up to a hundred times more massive.
Geochemical modeling of radioactive waste glass dissolution using EQ3/6: Preliminary results and data needs (1990)

A kinetic model for the dissolution of borosilicate glass has been incorporated into the EQ3/6 geochemical modeling code. The model consists of three main parts; (1) a kinetic rate law based on thermodynamics and the principle of detailed balancing for predicting the rate of glass dissolution; (2) a modified version of the hydration theory of Plodinec and Jantzen for calculating glass dissolution affinity; and (3) secondary phase precipitation. The model predicts the solution composition including pH and Eh as a function of time, and the amounts and types of secondary phases that form during glass dissolution. Steady state conditions are assumed where an early-formed leached layer develops on the glass surface and maintains a constant thickness as the glass dissolves. The model has been used to predict the performance of SRL-165 glasses in static leach tests performed for the Yucca Mountain Project at Argonne National Laboratory.
Study of Novel Self-Humidifying PEMFC with Nano-TiO<sub>2</sub>-Based Membrane (2007)

We propose self-humidifying polymer electrolyte membranes with highly dispersed nanometer-sized Titanium dioxides for proton exchange membrane fuel cells operated with dry H2 and O2. The nanosized TiO2 particles that have hygroscopic property are expected to adsorb the water produced from the cathode reaction and to release the water once the proton exchange membrane needs water. The preparation technology of nano-TiO2 particles in a commercial Nafion 112 membrane via novel in situ sol-gel reactions was developed, resulting in a semitransparent membrane with uniform distribution of TiO2 in the proton exchange membrane. It is found that Proton conductivity increases observably by dispersing 3 wt % nano-TiO2 in the Proton exchange membrane at low humidity condition, and the newly prepared TiO2-PEM improve the self-humidifying performance of Proton exchange membrane fuel cell.
A grammar-based system for the participatory design of urban structures (2009)

We propose a three-step participatory design cycle for the early urban design phase that can be integrated into the digital design chain. Step one involves a visualization method that is implemented as an interactive card-based interview technique for the collaborative requirement specification of urban designs. In step two these specifications are a) translated into simplified GIS data and then b) implemented into a grammar-based system together with the corresponding design regulations. The final outcome is a generative and iterative urban model, which includes buildings, building blocks, transportation networks and open spaces that visually communicates spatial impacts of urban design proposals.
Single molecule localization microscopy of the distribution of chromatin using Hoechst and DAPI fluorescent probes (2014)

Several approaches have been described to fluorescently label and image DNA and chromatin in situ on the single-molecule level. These superresolution microscopy techniques are based on detecting optically isolated, fluorescently tagged anti-histone antibodies, fluorescently labeled DNA precursor analogs, or fluorescent dyes bound to DNA. Presently they suffer from various drawbacks such as low labeling efficiency or interference with DNA structure. In this report, we demonstrate that DNA minor groove binding dyes, such as Hoechst 33258, Hoechst 33342, and DAPI, can be effectively employed in single molecule localization microscopy (SMLM) with high optical and structural resolution. Upon illumination with low intensity 405 nm light, a small subpopulation of these molecules stochastically undergoes photoconversion from the original blue-emitting form to a green-emitting form. Using a 491 nm laser excitation, fluorescence of these green-emitting, optically isolated molecules was registered until “bleached”. This procedure facilitated substantially the optical isolation and localization of large numbers of individual dye molecules bound to DNA in situ, in nuclei of fixed mammalian cells, or in mitotic chromosomes, and enabled the reconstruction of high-quality DNA density maps. We anticipate that this approach will provide new insights into DNA replication, DNA repair, gene transcription, and other nuclear processes.