gebhart/patrepeval huggingface dataset:
Recovery of stereopsis in adults through training in a virtual reality task (2012)

Impediments to binocularity coupled with a lack of early-life intervention often lead to impaired binocular disparity processing (stereopsis). A visuomotor task was developed to simultaneously train stereopsis and assess the degree to which subjects rely on disparity cues (relative to monocular depth cues) to estimate surface orientation. We asked whether repeated practice on this naturalistic task, akin to object placement on a surface, could aid in recovering stereopsis in stereo-anomalous subjects. Subjects viewed virtual images of planar texture patterns at a range of 3D slants and were required to squash a virtual bug by placing a cylinder flush onto a real, but optically hidden, slanted surface that was co-aligned optically with the virtual surface. One anisometropic amblyopic subject and three strabismic subjects with impaired stereopsis, aged 18-56, participated in this pilot training study. A range of visual functions (visual acuity, contrast sensitivity, vernier, and stereopsis) was measured pre- and post-training both clinically and psychophysically. Subjects completed at least thirty, 360 trial sessions lasting ~75 minutes each. Image contrast to the dominant eye was adjusted to match the non-dominant eye regularly. Stereopsis recovered in three of four subjects as evidenced by (a) increased weights given to disparity cues in the visuomotor task, (b) improved sensitivity in low spatial frequency edge disparity tests, and (c) decreased clinical Randot stereo-thresholds. We conclude that our paradigm successfully restored stereopsis in some adult subjects. Our results add to the growing body of literature documenting residual neural plasticity beyond the sensitive period for damage recovery. Meeting abstract presented at OSA Fall Vision 2012
<title>Optimal clustered-dot color screen design based on a human visual system model</title> (2000)

We address the periodic clustered tool dot color screen design problem. In traditional clustered dot color screening, the screen for each colorant is rotated to a different angle relative to the others. If the angles are not carefully chosen, visible moire and rosette artifacts may appear. These artifacts primarily result from the interaction of the periodic structures associated with the halftone screens of different colorants. Registration errors can also introduce unwanted artifacts in the screened images. Using lattice theory and a model for the perceived rendered halftone, we present a systematic method for designing moire and rosette free clustered dot color screens for discrete-raster color systems. We also investigate strategies for making the resulting screen robust to registration errors.
Nanoscale Characterization of Thin Film Coatings Using Annular Dark Field Scanning Transmission Electron Microscopy (2008)

When considering the optical performance of thin films in the Extreme Ultraviolet (EUV), developing an accurate physical description of a thin film coating is necessary to be able to successfully model optical performance. With the short wavelengths of the EUV, film interfaces and sample roughness warrant special attention and care. The surfaces of thin film samples are routinely measured by Atomic Force Microscopy, from which roughness can be determined. However, characterizing the quality of interfaces below the surface is much more challenging. In a recent study of scandium oxide thin films, High Resolution Transmission Electron Microscopy and Annular Dark Field Scanning Transmission Electron Microscopy (ADF STEM) were used to study the cross section of the samples. ADF STEM data analyzed along a path into the volume of the sample (normal to the interfaces) reveals information of sample density versus depth. This density-depth profile reflects the presence of subsurface film interfaces in the volume of the sample. Additionally, information from the ADF STEM profile can be used to gauge the roughness of the subsurface interfaces, which is used to refine the sample description during modeling. We believe this is the first use of ADF STEM in this capacity. This characterization technique may provide key insight to subsurface interface quality, which is particularly important when optimizing the performance of multilayer coatings in the EUV.
Efficient optoelectronic de-embedding for VCSEL intrinsic response extraction (2009)

In this present work, we propose a new method to remove the parasitics contribution to the VCSEL chip response,in order to obtain the intrinsic transmission behavior. It has been observed that the S11 reflection coefficient of the chip is only due to the electrical access to the chip composed by the transmission line and cavity contacts. This allows us to decompose the chip into two cascaded subsystems representing the electrical access and the optical cavity respectively. An equivalent electrical circuit is developed for the electrical access behavior and, combined with the transfer matrix formalism, it becomes possible to remove the parasitics contribution from the measured S21 response. In this way, the intrinsic 3-dB bandwidth of the VCSEL can be determined.
Mechanisms of beneficial colonisation of barley by fungal root endophytes. (2013)

Pathogenic fungal infections of barley can lead to costly crop losses. However, not all fungal infections are detrimental, and some are even beneficial. Beneficial root infections often involve symbiotic endophytic fungi. Benefits to barley and other plants infected with endophytic root fungi include an increase in seed yield, enhanced resistance to pathogens and improved stress tolerance. Here, we examine the mechanisms and outcomes of fungal endophyte colonisation of barley roots and briefly discuss reported benefits for the host. The most important factors that determine the nature of the relationship are the specific combination of partner genotypes and developmental stage, and the ecological and environmental setting. The full potential of these organisms is still to be determined and further studies are urgently required to develop specific beneficial root-endophyte associations, or combination of them, that are tailored to barley cultivars for maximum impact in agriculture.
Structure and spin polarization of outermost surface of theCo2FeAl0.5Si0.5full-Heusler alloy studied by spin-polarized ion-scattering spectroscopy (2009)

The outermost surfaces of epitaxial full-Heusler ${\text{Co}}_{2}{\text{FeAl}}_{0.5}{\text{Si}}_{0.5}$ (CFAS) films on MgO (001) substrates were investigated using spin-polarized ion-scattering spectroscopy. It was found that the CFAS surface was terminated by an Fe-Al-Si layer with substitution of Fe with Al and/or Si. The spin polarization of the outermost surface was detected for the first time among Heusler alloys. It was found that the spin polarization of Al and/or Si atoms in the topmost layer was significantly lower than that of Co atoms in the second layer. It was also found that the polarity of the spin polarization at the Fermi level on the outermost surface was opposite to majority spins. A possible application of SP-ISS in the development of magnetoresistance materials is suggested.
Biochemical changes and cytotoxicity associated with methionine depletion in paediatric central nervous system tumour cell lines. (2009)

Daoy and D54 cells are methionine dependent; the degree and duration of methionine depletion is related to cell death. The associated biochemical changes in MGMT and glutathione may be expected to modulate chemosensitivity and this will be investigated in future studies.
A method for deriving a 4D-interpolated balanced planning target for mobile tumor radiotherapy (2011)

The authors have developed a simple and systematic approach to generate a 4D-interpolated balanced planning target volume that implicitly incorporates the dynamics of respiratory-organ motion without requiring 4D-dose computation or optimization. Preliminary results based on 4D-CT data of five previously treated lung patients showed that this new planning target approach may improve normal tissue sparing without sacrificing tumor coverage.
UDP-glucuronosyltransferase activity and bilirubin conjugation in the bullfrog (1983)

Bile pigments of bile and serum of Rana catesbeiana were investigated by means of high-pressure liquid chromatography. The major pigment in both bile and serum was bilirubin IX alpha. Bilirubin UDP-glucuronosyltransferase activity was found in the livers of all animals examined, but no conjugated bilirubin was detectable in the bile. Frog bile was found to contain large amounts of beta-glucuronidase. When the beta-glucuronidase inhibitor saccharo-1,4-lactone was introduced into the gall bladder followed by an exogenous bilirubin load, bilirubin glucuronide appeared in the bile.
Movement of Bull Spermatozoa in Cervical Mucus1 (1981)

The movement characteristics of bull spermatozoa in fresh estrous bovine cervical mucus were studied using high-speed cinemicrography. Preparations consisted of capillary tubes of rectangular cross section (400 µm deep), exposed to semen at one end. Spermatozoa were studied while swimming in the interior midplane of the tube, and also in a plane just below the upper surface of the tube. In both these planes, the initial or “vanguard” spermatozoa that arrived at a station 2 cm from the semen-mucus interface were studied in comparison with the subsequent or “following” spermatozoa that arrived 10 min later. It was found that the vanguard spermatozoa swam more rapidly than their followers, although the flagellar beat frequencies and shapes of these two groups were not significantly different. This difference in propulsive efficiency appears to due an alteration in local mucus properties resulting from sustained permeation by spermatozoa. Spermatozoa swam more rapidly near the tube wall than in the midplane. Flagellar beat frequencies were lower near the wall, and beat shapes were also qualitatively different. This latter distinction appears to result from altered mucus properties near the wall as well as the direct hydrodynamic effect of the wall itself.
Vinyl azides in heterocyclic synthesis. Part 2. Selectivity in the decomposition of azidocinnamates with olefinic ortho-substituents (1986)

Thermolysis of azidocinnamates with an olefinic o-substituent gives products (isoquinolines, azepines, aziridines) formed by selective interaction of the azide, and the derived nitrene, with the olefinic substituent, cyclisation onto the unsubstituted aromatic ortho position now being a minor reaction. However when this interaction is removed by epoxidation of the alkene, cyclisation occurs exclusively to the aromatic ring to give 4-substituted indoles in high yield. Thus o-vinyl azidocinnamate (1a) gives isoquinoline (5a), and (1b) gives isoquinoline (5b) together with the 3-benzazepine (7); o-allyl azidocinnamate (2a) gives indole (12), the 3-benzazepine (13), and the tricyclic aziridines (14) and (15), and (2b) gives an analogous mixture of products from which only the indole (19) was isolated. A mechanism is proposed (Scheme 2) in which the azide partitions itself between intramolecular cycloaddition to the double bond and loss of nitrogen to give the azirine-nitrene equilibrium. This rationalises the formation of the 4 temperature-dependent products from azidocinnamate (2a), the aziridine (15) involving an intramolecular ene reaction of the imine bond. Thermolysis of the epoxy-azidocinnamates (3) and (4) gives indoles (20) and (21) respectively in high yield; treatment of (3) with triethyl phosphite gives the aziridine (8), presumably by formation of an iminophosphorane and intramolecular nucleophilic attack by this on the epoxide, the counterpart of a known intermolecular reaction.
Survey of Ixodes pacificus Ticks in California Reveals a Diversity of Microorganisms and a Novel and Widespread Anaplasmataceae Species (2015)

Ixodes pacificus ticks can harbor a wide range of human and animal pathogens. To survey the prevalence of tick-borne known and putative pathogens, we tested 982 individual adult and nymphal I. pacificus ticks collected throughout California between 2007 and 2009 using a broad-range PCR and electrospray ionization mass spectrometry (PCR/ESI-MS) assay designed to detect a wide range of tick-borne microorganisms. Overall, 1.4% of the ticks were found to be infected with Borrelia burgdorferi, 2.0% were infected with Borrelia miyamotoi and 0.3% were infected with Anaplasma phagocytophilum. In addition, 3.0% were infected with Babesia odocoilei. About 1.2% of the ticks were co-infected with more than one pathogen or putative pathogen. In addition, we identified a novel Anaplasmataceae species that we characterized by sequencing of its 16S rRNA, groEL, gltA, and rpoB genes. Sequence analysis indicated that this organism is phylogenetically distinct from known Anaplasma species with its closest genetic near neighbors coming from Asia. The prevalence of this novel Anaplasmataceae species was as high as 21% at one site, and it was detected in 4.9% of ticks tested statewide. Based upon this genetic characterization we propose that this organism be called 'Candidatus Cryptoplasma californiense'. Knowledge of this novel microbe will provide awareness for the community about the breadth of the I. pacificus microbiome, the concept that this bacterium could be more widely spread; and an opportunity to explore whether this bacterium also contributes to human or animal disease burden.
Pharmacological Characterization of Phospholipid Growth‐Factor Receptors (2000)

The phospholipid growth-factor (PLGE) terminology is proposed to describe a group of endogenous glycerol- and sphingolipid mediators that regulate cell proliferation through plasma membrane receptors. In addition to LPA and SPP, multiple PLGFs are present in blood plasma and serum. PLGF activity is regulated by its stimulus-coupled production and by endogenous inhibitors. In addition to LPA and SPP, alkenyl-glycerophosphate, cyclic-phosphatidic acid, and sphingosylphosphorylcholine were detected in biological fluids using mass spectrometry. Heterologous desensitization studies indicate the expression of multiple LPA-activated receptors in a variety of cell types, which are differentially activated by the different PLGFs. Northern blot and RT-PCR results reinforce the coexpression of PSP24 alpha and different members of the EDG1-7 receptors in the same cell. Stable heterologous expression of the PSP24 alpha, EDG2, and EDG4 receptors in HEK293 cells show distinct PLGF specificities and dose-response properties for each receptor subtype. Thus, both the controlled availability of the different agonists/inhibitors and the regulated expression of their receptors regulate the biological effects of PLGFs.
Structural significance of the amino-terminal residues of sperm whale myoglobin (1980)

Following the development of a nondestructive synthetic procedure for rapid production of des-Val1-myoglobin in large quantities, the synthesis of a series of myoglobin derivatives varying in structure and charge in the NH2-terminal region was accomplished. In comparison to the untreated myoglobin, the des-Val1-myoglobin was found to possess at low pH a decreased stability and an increased net positive charge in the pH range 5.5-8.5. While the elevated net positive charge was no longer apparent after removal of the second residue, the instability of the molecule was found to be sharply increased. Substitutions of the first residue, directed toward elucidating its structural importance, included glutamic acid, lysine, and glycine. Addition of any of the three amino acids to the des-Val1-myoglobin was found to restore much of the acid stability, with the [Gly1]myoglobin appearing nearly identical with the native molecule. All three semisynthetic myoglobins showed potentiometric titration curves characteristic of their respective, substituted residue. Carbamylation of the NH2 terminal of myoglobin and des-Val1-myoglobin yielded two nearly identical molecules in terms of all physical properties examined. Consequently, it was concluded that the first residue primarily serves the function of maintaining the positively charged NH2 terminus a certain distance away from the beginning of the A helix and from the charge pair interaction of Lys-133 with Glu-6. In addition, through physical measurements of the des-Val1,Leu2-myoglobin prior and subsequent to carbamylation of the NH2 terminus, it was apparent that the stabilization conferred on the des-Val1-myoglobin by the second residue was dependent to a large degree upon the hydrophobic interactions of its side chain.
Plasma and cerebrospinal fluid progesterone concentrations in pregnant and nonpregnant women. (1986)

Pregnancy is associated with a wider dermatomal spread of local anesthetics after epidural and spinal anesthesia. This phenomenon also exists in the immediate postpartum period. The mechanism of this observation is unresolved. However, an increase in progesterone concentration in pregnancy has been implicated as one of the factors. Although plasma progesterone concentrations in humans have been well-documented, the cerebrospinal fluid (CSF) progesterone levels, which may also be important in this regard, have not been determined. Therefore, this study was undertaken to measure plasma and CSF progesterone in the nonpregnant, term parturient and in the immediate postpartum patient and also to determine the relationship between the CSF progesterone concentration and the intrathecal spread of lidocaine used for spinal anesthesia. The plasma progesterone concentrations in 12 nonpregnant, 21 term and eight postpartum patients were 2.3 +/- 61 (SEM) ng/ml, 122 +/- 8 ng/ml and 16 +/- 2.2 ng/ml, respectively. The CSF progesterone concentrations in term parturients (3 +/- 0.28 (SEM) ng/ml) and postpartum patients (1.03 +/- 0.16 ng/ml) were eight and three times greater than that of nonpregnant women (0.39 +/- 0.01 ng/ml). Significantly less lidocaine was needed (P less than 0.05) for comparable segmental levels of spinal anesthesia in term and postpartum patients than in nonpregnant individuals. These data suggest that high CSF, plasma progesterone concentrations, or both may augment the anesthetic spread of lidocaine.
The Cortical Topography of Tonal Structures Underlying Western Music (2002)

Western tonal music relies on a formal geometric structure that determines distance relationships within a harmonic or tonal space. In functional magnetic resonance imaging experiments, we identified an area in the rostromedial prefrontal cortex that tracks activation in tonal space. Different voxels in this area exhibited selectivity for different keys. Within the same set of consistently activated voxels, the topography of tonality selectivity rearranged itself across scanning sessions. The tonality structure was thus maintained as a dynamic topography in cortical areas known to be at a nexus of cognitive, affective, and mnemonic processing.
Cholesteric liquid crystals: Image contrast in the TEM (1994)

Abstract Bright-field image contrast of thermotropic cholesteric liquid crystalline materials in the transmission electron microscope (TEM) is investigated. Possible sources of contrast for these systems are discussed in terms of their molecular anisotropy. A cholesteric side-chain liquid crystalline compound was investigated with TEM, low voltage high resolution scanning electron microscopy (LVHRSEM), and atomic force microscopy (AFM) to determine the origin of the strong contrast observed in these systems using bright-field transmission electron microscopy. Initial contrast of thin microtomed sections, as viewed with TEM low dose techniques and an image intensifier, was much weaker than observed under normal viewing conditions. The periodic steady state contrast typically observed for these materials is the result of beam damage. Furthermore, the surface of microtomed samples (parallel to the cholesteric helical axis) is corrugated with a periodicity of 1/2 the pitch due to a preferred fracture path in the glassy cholesteric state. AFM profile analysis shows an average peak to valley height of approximately 20–25 nm. AFM of free surfaces from aligned films also indicates a corrugation with a periodicity equal to 1/2 the pitch with substantially smaller average corrugation depths. TEM indicates a series of +1/2 and −1/2 disclination lines at the surface due to a rotation of the preferred helix direction parallel to the surface, consistent with previously reported models.
Peritoneal sepsis: patient characteristics relaparotomized. (2004)

Los pacientes con sepsis severa de origen abdomino- peritoneal requieren frecuentemente reintervenciones, persistiendo con una elevada morbimortalidad. Su manejo terapéutico es dificultoso y controvertido, con estudios que consideran poblaciones poco homogéneas. Se realizó un análisis retrospectivo durante un período de cinco años. Se estudiaron un total de 55 pacientes con sepsis abdominal severa que requirieron al menos una relaparotomía. Analizamos la incidencia, las manifestaciones clínicas que orientan a una relaparotomía positiva, la mortalidad y los factores pronósticos. La ausencia de disfunción multiorgánica (OMO) constituyó un criterio de exclusión.
Dynamic satellite system QoS architecture integrated with IP Multimedia Subsystem core network (2014)

Summary Convergence is one of the most important challenges for Next Generation Networks (NGN). This includes service convergence as well as fixed‐mobile convergence. The integration of satellite telecommunication system into NGN is a key to increasing the coverage of future networks and opening satellite access networks to a wider range of terrestrial solutions. Digital Video Broadcast (DVB) Return Channel via Satellite system (DVB‐RCS) and its evolution (DVB‐RCS2) are widely used European standards that are specified for broadband satellite systems using dynamic capacity assignment and multifrequency TDMA. This paper introduces a new QoS architecture derived from terrestrial IP Multimedia Subsystem solutions to provide advanced end‐to‐end QoS support, and defines cross‐layer optimization paths suited to the satellite context and in particular using DVB standards. Copyright © 2014 John Wiley &amp; Sons, Ltd.
A staircase transform coding scheme for screen content video coding (2016)

Demand for screen content videos that contain computer generated text and graphics is growing. They are very different from natural videos, because they include much sharper edge transitions and very repetitive patterns. On this type of material, the efficacy of the conventional discrete cosine transform (DCT) is questionable because it relies on the assumption that a Gauss-Markov model leads to a base-band signal. However, the assumption may not hold true for screen content material. This work exploits a class of staircase transforms. Unlike the DCT whose bases are samplings of sinusoidal functions, the staircase transforms have their bases sampled from staircase functions, which better approximate the sharp transitions often encountered in the context of screen content. The staircase transform is integrated into a hybrid transform coding scheme, in conjunction with DCT. It is experimentally shown that the proposed approach provides an average of 2.9% compression performance gains in terms of BD-rate reduction. A perceptual comparison further demonstrates that the use of staircase transform achieves substantial reduction in ringing artifact due to the Gibbs phenomenon.
HERMES: a molecular formula-oriented method to target the metabolome - Dataset (2021)

This dataset contains all raw LC-MS1 and LC-MS2 data from river <em>s</em>urface water, <em>Escherichia coli, </em> and human plasma used in the paper <em>HERMES: a molecular formula-oriented method to target the metabolome, </em>as well as the RMarkdown vignettes generating the results and base figures. Please refer to the README file for more information about the data organization and script reproducibility. A collection of ready-to-use molecular formula databases can be found in this Zenodo dataset.