gebhart/patrepeval huggingface dataset:
Study of the Photoconductive and Optical Limiting Processes in Organic Nanostructures (2007)

Among other areas of application of materials doped with fullerenes or carbon nanotubes (CNTs), the special aspect is being made to investigate these nanostructures in the near and middle infrared. In the present paper, the infrared nonlinear transmission processes in fullerene- and nanotubes- containing organic systems based on polyimide, polyvinyl alcohol, prolinol, pyridine, and polyaniline have been considered. The thin films, gels, solution, and dispersed liquid crystal compounds have been studied at wavelengths of 805, 1047, 1080, 1315, and 2940 nm. Optical limiting properties and photoconductive peculiarities have been found. The possible limiting mechanisms have been discussed. It should be mentioned that the photoconductivity of nanostructure-doped systems varies in the range of 5–6 orders of magnitude. Additionally, the study with a microscope has been made. The quasi-photonic organic system has been obtained. Thus, the diffraction of a laser beam passing through this structure would be considered as one of the mechanisms to attenuate the laser beam.
Geometric algorithms for the conformational analysis of long protein loops (2004)

The efficient filtering of unfeasible conformations would considerably benefit the exploration of the conformational space when searching for minimum energy structures or during molecular simulation. The most important conditions for filtering are the maintenance of molecular chain integrity and the avoidance of steric clashes. These conditions can be seen as geometric constraints on a molecular model. In this article, we discuss how techniques issued from recent research in robotics can be applied to this filtering. Two complementary techniques are presented: one for conformational sampling and another for computing conformational changes satisfying such geometric constraints. The main interest of the proposed techniques is their application to the structural analysis of long protein loops. First experimental results demonstrate the efficacy of the approach for studying the mobility of loop 7 in amylosucrase from Neisseria polysaccharea. The supposed motions of this 17-residue loop would play an important role in the activity of this enzyme.
Abolition and Reversal of Strain Differences in Behavioral Responses to Drugs of Abuse After a Brief Experience (2000)

Inbred strains of mice are largely used to identify the genetic basis of normal and pathological behaviors. This report demonstrates that a moderate period of food shortage, an ecologically common experience, can reverse or abolish strain differences in behavioral responses to the abused psychostimulant amphetamine. The period of food shortage occurred when the animals were mature and was terminated before the administration of amphetamine. Strain differences in behavior appear highly dependent on environmental experiences. Consequently, to identify biological determinants of behavior, an integrated approach considering the interaction between environmental and genetic factors needs to be used.
Experimental and Theoretical Optimization of Combustion Chamber and Fuel Distribution for the Low Emission Direct-Injection Diesel Engine (2002)

Effects of combustion chamber geometry and initial mixture distribution on the combustion process were investigated in a direct-injection diesel engine. In the engine experiment, a high squish combustion chamber with a squish lip could reduce both NOx and particulate emissions with retarded injection timing. According to the results of CFD computation and phenomenological modeling, the high squish combustion chamber with a central pip is effective to keep the combusting mixture under the squish lip until the end of combustion and the combustion region forms rich and highly turbulent atmosphere. This kind of mixture distribution tends to reduce initial burning, resulting in restraint of NOx emission while keeping low particulate emission.
Bony and Soft Tissue Reconstruction and Rehabilitation Following Traumatic Hemipelvectomy, Exsanguination and Cardiac Arrest (1988)

Survival following traumatic hemipelvectomy in the child with subsequent local flap coverage of wounds has been previously described. The use of axial skin flaps and thigh and rectus abdominis musculocutaneous flaps for coverage of hemipelvectomy defects following tumor extirpation has also been noted in the literature. The use of muscle flaps to salvage otherwise nonvital bone and to eradicate osteomyelitis with subsequent wound closure has also been thoroughly demonstrated both clinically and experimentally. The use of musculocutaneous flaps to revascularize otherwise nonviable bone of the pelvis and thus maintain the pelvic girdle integrity, however, has not to our knowledge been previously reported. We recently had an opportunity to treat such a case, which we herein describe.
No Association between <i>TERT-CLPTM1L</i> Single Nucleotide Polymorphism rs401681 and Mean Telomere Length or Cancer Risk (2010)

Our results indicate that the observed associations between rs401681 and several cancer types might be weaker than previously described. The lack of an association in our study between this SNP and mean telomere length suggests that any association with cancer risk at this locus is not mediated through TERT.
In vitro adherence of lymphocytes to dermal endothelium under shear stress: implications in pathobiology and steroid therapy of acute cutaneous GVHD (2002)

The extravasation of leukocytes at sites of inflammation critically depends on initial shear-resistant adhesive interactions between leukocytes in blood flow and target tissue endothelium. Dermal lymphocytic infiltrates are a hallmark feature of acute cutaneous graft-versus-host disease (acGVHD) following allogeneic hematopoietic stem cell (allo-HSC) transplantation. These infiltrates occur commonly during periods of profound lymphopenia, suggesting that the dermal endothelial adhesive mechanism(s) promoting lymphocyte emigration in acGVHD are highly efficient. To examine this issue, we performed Stamper-Woodruff assays on frozen sections of biopsy specimens of cutaneous lesions occurring within 100 days of HSC transplantation in 22 autologous hematopoietic stem cell transplant (auto-HSCT) and 25 allo-HSCT recipients. By using this shear-based assay, we observed lymphocyte adherence to papillary dermal vascular structures in all punch biopsy specimens of allo-HSCT recipients who had clinicohistologic evidence of acGVHD and who were not receiving steroids, whereas no lymphocyte adherence was observed within skin specimens from allo-HSCT recipients who did not develop acGVHD. Within the group of auto-HSCT recipients, 2 of 22 skin biopsies demonstrated lymphocyte binding to dermal vessels. Among allo-HSCT patients receiving steroid therapy for acGVHD, lymphocyte binding to dermal endothelium was abrogated prior to resolution of rash in those who responded, yet binding was persistent in skin from one patient whose rash did not respond to steroid therapy. Collectively, these data indicate that the papillary endothelium of skin in acGVHD displays heightened capacity to support lymphocyte adhesion under shear stress conditions and suggest that down-modulation of this endothelial adhesive capability may be one mechanism by which steroids abrogate acGVHD reactions.
Engineering Hot Channel Factors for Nuclear Reactor Design (1956)

AbstractIn the thermal design of nuclear power reactors having parallel coolant channels, engineering hot channel factors have been established to account for small dimensional deviations from the nominal design of the reactor fuel elements resulting from manufacturing tolerances, and for departures from ideal flow conditions. A description of the various deviations from nominal likely to be encountered in a practical reactor design is presented, together with methods for estimating the magnitude of the effect of each on channel enthalpy rise, film temperature difference, and maximum heat flux. Examples are given for a geometry consisting of parallel plate type fuel elements separated by rectangular coolant channels.
Irradiation Damage in Lipids (1969)

Irradiation off-flavors in food fats are distinct and differ from other off-flavors. The degradation products of lipids due to irradiation damage are found by analysis employing gas chromatography and rapid scanning mass spectrometry. Studies show identification of compounds produced by irradiation, and the products formed in several animal fats and meats are compared as well as basic lipid substances such as fatty acid esters and triglycerides. The contribution of hydrocarbon compounds to irradiation off-odor is demonstrated, and the mechanism of their formation is discussed.
The analogy between multiply-connected slices and slabs (1946)

The analogy between
Teaching cybersecurity through games: a cloud-based approach (2013)

Incorporating information security into the undergraduate curriculum seems to be a topic of growing interest to CCSC-NW attendees. In addition, it is receiving increased attention nationally in the proposed ACM/IEEE CS2013 Curricula Guidelines [1]. This area will be one of the new core requirements. The goal of this workshop is to provide faculty who have little experience in this area with some of our most recent tools and resources that would facilitate their incorporating this knowledge area into their curriculum. It builds on previous similar workshops in this area. In this tutorial, we will describe the use of cloud-based environments for developing and disseminating hands-on security exercises. We present one security game that we have developed on Amazon's AWS cloud environment and an exercise that was developed on The RAVE. Participants will learn about the framework we have developed for providing instructors with competitive, interactive exercises through the system EDURange[2]. EDURange is a new framework for creating exercises and games in a variety of environments including remotely hosted web services, i.e. cloud computing. They will learn about these exercises from two viewpoints. As players, they will learn about network security. As instructors, they will learn how to use these security exercises in the classroom, and they will learn about the scenario description language, which they can use to create games for their classes.
Direct and indirect modulation of neuropeptide Y gene expression in response to hypoglycemia in rat arcuate nucleus (2008)

Expression of neuropeptide Y (Npy) heteronuclear (hn) RNA, an indicator of gene transcription, was significantly increased in the arcuate nucleus of rats 30min after insulin injection. Npy hnRNA levels were also increased significantly in response to hypoglycemia in rats in which the hypothalamus was deafferentated, although the absolute levels were significantly lower than in sham-operated rats. Direct effects of lowering glucose levels on Npy gene expression were also confirmed in hypothalamic organotypic cultures. Thus, Npy gene transcription in the arcuate nucleus increases rapidly in response to hypoglycemia, and both direct and indirect inputs are involved in the rapid upregulation.
Quantitative <sup>1</sup>H–<sup>1</sup>H Distances in Protonated Solids by Frequency-Selective Recoupling at Fast Magic Angle Spinning NMR (2018)

Nuclear magnetic resonance (NMR) spectroscopy of protons in protonated solids is challenging. Fast magic angle spinning (MAS) and homonuclear decoupling schemes, in conjunction, with high magnetic fields have improved the proton resolution. However, experiments to quantitatively measure <sup>1</sup>H-<sup>1</sup>H distances still remain elusive due to the dense proton-proton dipolar coupling network. A novel MAS solid-state NMR pulse sequence is proposed to selectively recouple and measure interproton distances in protonated samples. The phase-modulated sequence combined with a judicious choice of transmitter frequency is used to measure quantitative <sup>1</sup>H-<sup>1</sup>H distances on the order of 3 Å in l-histidine·HCl·H<sub>2</sub>O, despite the presence of other strongly coupled protons. This method provides a major boost to NMR crystallography approaches for structural determination of pharmaceutical molecules by directly measuring <sup>1</sup>H-<sup>1</sup>H distances. The band-selective nature of the sequence also enables observation of selective <sup>1</sup>H-<sup>1</sup>H correlations (e.g., H<sup>N</sup>-H<sup>N</sup>/H<sup>N</sup>-H<sup>α</sup>/Η<sup>Ν</sup>-Η<sup>Methyl</sup>) in peptides and proteins, which should serve as useful restraints in structure determination.
Regulatory crosstalk between type I and type II toxin-antitoxin systems in the human pathogen <i>Enterococcus faecalis</i> (2015)

We discovered a chromosomal locus containing 2 toxin-antitoxin modules (TAs) with an antisense transcriptional organization in the E. faecalis clinical isolate V583. These TAs are homologous to the type I txpA-ratA system and the type II mazEF, respectively. We have shown that the putative MazF is toxic for E. coli and triggers RNA degradation, and its cognate antitoxin MazE counteracts toxicity. The second module, adjacent to mazEF, expresses a toxin predicted to belong to the TxpA type I family found in Firmicutes, and the antisense RNA antidote, RatA. Genomic analysis indicates that the cis-association of mazEF and txpA-ratA modules has been favored during evolution, suggesting a selective advantage for this TA organization in the E. faecalis species. We showed regulatory interplays between the 2 modules, involving transcription control and RNA stability. Remarkably, our data reveal that MazE and MazEF have a dual transcriptional activity: they act as autorepressors and activate ratA transcription, most likely in a direct manner. RatA controls txpA RNA levels through stability. Our data suggest a pivotal role of MazEF in the coordinated expression of mazEF and txpA-ratA modules in V583. To our knowledge, this is the first report describing a crosstalk between type I and II TAs.
Characterization of Randomly Branched Polymers Formed by End-Linking Linear Polystyrene Using Controlled Free Radical Polymerization (2001)

Randomly branched polystyrene (PS) was synthesized by end-linking monodisperse linear PS chains with divinylbenzene using controlled free radical polymerization. Samples obtained at different reaction extents were characterized using size exclusion chromatography and static and dynamic light scattering. The results are compared with those obtained on randomly branched poly(methyl methacrylate) (PMMA). The overal structure of branched PS was found to be the same as that of branched PMMA despite the very different local structure. The results strongly support the idea that the formation of polymeric gels is a universal process that may be described by the percolation model.
Ultrabroadband fiber optical parametric amplifiers pumped by chirped pulses Part 1: analytical model (2015)

An analytical model has been developed to fully understand the concept of fiber optical parametric amplifiers pumped by broadband chirped pulses. Our model is in good agreement with the numerical resolution of the nonlinear Schrödinger equation and was used to tailor the gain bandwidth. In particular, we showed that the group delay difference between the pump and the signal can play a crucial role in the spectral extension of the gain. This exciting amplification concept should pave the way toward high gain ultrashort (<30  fs) pulse amplification in fiber.
Clinical evaluation of five portable tonometers. (1995)

All portable tonometers were able to accurately predict Goldmann IOPs. While three of the tonometers were found to underestimate Goldmann IOP on average, these results can be corrected by either adding the underestimation or by using the best fitting regression equation.
Reconstruction of buildings from multiple high resolution images (2002)

This paper presents an algorithm to reconstruct buildings in an urban scene from a large number of aerial images. We start with a digital elevation model (DEM) obtained with our multiple baseline stereomatching method. This algorithm is very efficient in removing matching ambiguities and in improving the precision of the elevation estimates. The approach to building reconstruction is based on a segmentation of the DEM into homogeneous regions and a classification of these regions to separate the buildings from the ground. In addition, a second stage extrapolate missing data and performs surface reconstruction. To demonstrate the performance of the algorithm, we present results using several aerial images.
Variations in Humanized and Defined Culture Conditions Supporting Derivation of New Human Embryonic Stem Cell Lines (2006)

The evolution of "humanized" (i.e., free of animal sourced reagents) and ultimately chemically defined culture systems for human embryo stem cell (hESC) isolation and culture is of importance to improving their efficacy and safety in research and therapeutic applications. This can be achieved by integration of a multitude of individual approaches to replace or eliminate specific animal sourced reagents into a single comprehensive protocol. In the present study our objective was to integrate strategies obviating reliance on some of the most poorly defined and path-critical factors associated with hESC derivation, namely the use of animal immune compliment to isolate embryo inner cell mass, and animal sourced serum products and feeder cells to sustain hESC growth and attachment. As a result we report the derivation of six new hESC lines isolated by outgrowth from whole blastocysts on an extracellular matrix substrate of purified human laminin (Ln) with transitional reliance on mitotically inactivated human fibroblast (HDF) feeder cells. With this integrated system hESC lines were isolated using either HDF conditioned medium supplemented with a bovine-sourced serum replacement (bSRM), or a defined serum-free medium (SFM) containing only human sourced and recombinant protein. Further, outgrowth of embryonic cells from whole blastocysts in both media could be achieved for up to 1 week without reliance on feeder cells. All variant conditions sustained undifferentiated cell status, a stable karyotype and the potential to form cells representative of all three germinal lineages in vitro and in vivo, when transitioned off of feeders onto Laminin or Matrigel. Our study thus demonstrates the capacity to integrate derivation strategies eliminating a requirement for animal immune compliment and serum products, with a transitional requirement for human feeder cells. This represents another sequential step in the generation of therapeutic grade stem cells with reduced risk of zoonotic pathogen transmission.
Heuristics for Vector Bin Packing (2011)

Inspired by virtual machine placement problems, we study heuristics for the Vector Bin Packing problem, where we are required to pack n items represented by d-dimensional vectors, into as few bins of size 1 each as possible. We systematically study variants of the First Fit Decreasing (FFD) algorithm that have been proposed for this problem. Inspired by bad instances for FFD-type algorithms, we propose new geometric heuristics that run nearly as fast as FFD for reasonable values of n and d. We report on empirical evaluations of the FFD-based, as well as the new heuristics on large families of distributions. We identify which FFD variants work best in most cases and show that our new heuristics usually outperform FFD-based heuristics and can sometimes reduce the number of bins used by up to ten percent. Further, in all cases where we were able to compute the optimal solution we found our new heuristics within few percent of optimal. We conclude that these new heuristics are an excellent alternative to FFD-based heuristics and are prime candidates to be used in practice.
Advanced modulation formats and digital signal processing for next generation fiber optics networks (2011)

Advanced modulation formats are proposed and analysed for next generation optical networks. The new evolving optical networks data rates of 100G and above require real time analog-to-digital conversion followed by real time digital signal processing. This is in order to allow increased spectral efficiency and full compensation of amplitude and phase distortion imposed by the optical channel in such high bitrates. Various approaches are presented, including discrete multi-tone and optical OFDM.
Quantifying inorganic fouling in a membrane bioreactor treating nitrate-contaminated groundwater using hydrogen as energy source (2006)

A hydrogenotrophic denitrification system, which consisted of a sequencing batch membrane bioreactor, was evaluated for removal of nitrate from a synthetic groundwater feed. A hollow fiber microporous membrane diffuser was used for bubble-less diffusion of hydrogen into the bioreactor, and a membrane filter was used for separating the biomass from treated water. The nitrate loading of 0.328 kg N m−3 d−1 was completely denitrified to below detectable levels; however, inorganic fouling of both membrane filter and diffuser occurred. The increase in pH during denitrification caused inorganic precipitation and clogging of the membranes. The foulant material was quantified as beta three calcium phosphate βCa3 (PO4)2.
Statistical-Based Tracking Technique for Linear Structures Detection: Application to Vessel Segmentation in Medical Images (2010)

Linear structures such as blood vessels in medical images are important features for computer-aided diagnosis and follow-up of many diseases. In this letter a new tracking-based segmentation method is proposed to detect blood vessels in retinal images. Bayesian segmentation with the Maximum <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">a posteriori</i> (MAP) Probability criterion is used for that purpose. Tests on simulated and retinal images are presented and compared with a vessel detection technique. Our method performs better results.
Structural change of biomimetic hydroxyapatite coatings due to heat treatment. (2012)

Biomimetic deposition of hydroxyapatite (HA) coatings on implants could be done for two reasons, one is to study their possible bioactivity, and one is to generate bioactive coatings on implants before implantation surgery to improve the osseointegration. Heat treatment of coated implants can be performed for several reasons, for example, to ensure coating sterility and to increase the adhesion. This paper describes the morphology and crystalline structure changes occurring due to the heat treatment of biomimetic HA coatings on rutile TiO2. Rutile TiO2 surfaces were produced on titanium (Ti) plates by heating at 800 degrees C. Afterwards, these samples were immersed in a phosphate buffer saline solution for 7 days at 37 degrees C in order to deposit HA coatings on their surfaces. These HA coatings were then either untreated or heat treated at 600 or 800 degrees C for 1 hr. The coatings microstructural changes were studied using X-ray diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Cross-sectional TEM samples were produced using a sample preparation method based on focused ion beam microscopy (FIB). Rutile was found to be bioactive due to HA formation on the surface. The 600 degrees C heat treatment of the HA coating changed its morphology, increased its grain size and also increased the porosity. At 800 degrees C the coating was completely transformed to beta-TCP according to XRD. Sample preparation using FIB and TEM analysis proved to be a useful method for high-resolution analysis of biomimetic coatings in cross-section.