gebhart/patrepeval huggingface dataset:
Fixational eye movements improve visual performance at the sampling limit (2015)

Purpose: We explored whether fixational movements of the eye in the human visual system might enhance visual acuity, by effectively scanning the retinal image with its sparse receptive fields, rather than taking a static snapshot of the retinal image with a fixed sampling array. Methods: We used an adaptive optics scanning laser ophthalmoscope to test orientation discrimination performance in three normal subjects while simultaneously imaging the underlying cone photoreceptor mosaic. Imaging and psychophysics were done with 840-nm light over a 1.2 deg field at about 1 degree from the foveal center. Stimuli were AO-corrected, negative-contrast tumbling-E optotypes presented randomly at one of four orientations. Stimulus size was held constant, with a gap opening that yielded ~40% correct discrimination performance determined in a preceding acuity experiment (0.57, 0.61, 0.74 arcmin of visual angle for the subjects). At that size and retinal eccentricity, the gap opening was below the retina’s Nyquist sampling limit (0.94, 0.90, 0.85 arcmin). Stimulus presentation duration was 750 msec, trial progression was self-paced. Stimuli were presented either retinally stabilized by locking the stimulus to the underlying photoreceptor mosaic, or unstabilized, i.e. habitual retinal image motion was allowed to occur. Discrimination performance is reported based on 500 trials for each viewing condition, all pseudorandomly interleaved. Results: For all subjects, discrimination performance was significantly worse under stabilized than unstabilized conditions. Performance reductions were 33.6, 13.4, and 21.1% (p = 0.015, 0.046, 0.017, binomial z-test) for each subject. Conclusions: Performance in the finest visual acuity tasks for retinal images that are at or below the Nyquist sampling limit seem to be enhanced by the retinal image motion caused by natural fixational eye movements. These findings suggest that fixational eye movements are used to facilitate a form of ‘super-resolution’ that surpasses the photoreceptor sampling resolution. Meeting abstract presented at VSS 2015
RNA Splicing and Immune-Checkpoint Inhibition (2021)

A growing body of evidence supports aberrant splicing as both a cause and a potential Achilles’ heel of cancers, especially when it comes to the effects of immune-checkpoint inhibitors.
Characterization of PZT capacitors with SrRuO<sub>3</sub> electrodes (1998)

Abstract Pb(Zr, Ti)O3 [PZT] capacitors were prepared by CSD on sputtered electrodes of SrRuO3(SRO)/Pt on SiO2/Si wafers. The SRO/Pt bottom electrodes were deposited using two different conditions: (1) at 600°C in-situ (abbreviated HT), and (2) at low temperature followed by a post-deposition anneal at 600°C (abbreviated LTA). The PZT orientation and switching pulse polarization, i.e. HT-SRO (43 μC cm-2) and LTA-SRO (32 μC cm-2) were strongly dependent on the bottom electrodes. Yet neither capacitor showed polarization loss resulting from switching 108 times with ± 5 V pulses. These results indicate that the PZT ferroelectric properties are greatly influenced by the SRO bottom electrode processing conditions.
Evaluating Angiogenic Potential of Small Molecules Using Genetic Network Approaches (2018)

Control of microvascular network growth is critical to treatment of ischemic tissue diseases and enhancing regenerative capacity of tissue engineering implants. Conventional therapeutic strategies for inducing angiogenesis aim to deliver one or more proangiogenic cytokines or to over-express known pro-angiogenic genes, but seldom address potential compensatory or cooperative effects between signals and the overarching signaling pathways that determine successful outcomes. An emerging grand challenge is harnessing the expanding knowledge base of angiogenic signaling pathways toward development of successful new therapies. We previously performed drug optimization studies by various substitutions of a 2-(2,6-dioxo-3-piperidyl)isoindole-1,3-dione scaffold to discover novel bioactive small molecules capable of inducing growth of microvascular networks, the most potent of which we termed phthalimide neovascularization factor 1 (PNF1, formerly known as SC-3-149). We then showed that PNF-1 regulates the transcription of signaling molecules that are associated with vascular initiation and maturation in a time-dependent manner through a novel pathway compendium analysis in which transcriptional regulatory networks of PNF-1-stimulated microvascular endothelial cells are overlaid with literature-derived angiogenic pathways. In this study, we generated three analogues (SC-3-143, SC-3-263, SC-3-13) through systematic transformations to PNF1 to evaluate the effects of electronic, steric, chiral, and hydrogen bonding changes on angiogenic signaling. We then expanded our compendium analysis toward these new compounds. Variables obtained from the compendium analysis were then used to construct a PLSR model to predict endothelial cell proliferation. Our combined approach suggests mechanisms of action involving suppression of VEGF pathways through TGF-β andNR3C1 network activation.
Non-contact sheet resistance and leakage current monitoring of multi-implant, ultra-shallow junctions: Doping and damage effects for ms-anneals (2006)

Junction photo‐voltage methods are used to measure sheet resistance and recombination leakage current effects in ultra‐shallow junctions formed with low‐energy Boron implants annealed with ms‐timescale thermal cycles at ∼1300 C. The impact of sub‐junction doping and implant damage levels present before the ms‐anneal is studied.
Preussomerin D from the Endophyte Hormonema dematioides (1993)

Click to increase image sizeClick to decrease image sizeKey Words: antibioticChamaecyparis thyoidesendophyteHormonerna dematioidespreussomerin D
Involvement of autotaxin in the pathophysiology of elevated intraocular pressure in Posner-Schlossman syndrome (2020)

To examine whether autotaxin (ATX) in the aqueous humor causes elevated intraocular pressure (IOP) in patients with Posner-Schlossman syndrome (PSS). ATX and transforming growth factor beta (TGF-β) in the aqueous humor were quantified in PSS patients. The expression of ATX and TGF-β in cytomegalovirus (CMV)-infected-human trabecular meshwork (hTM) cells was examined. Biological changes in hTM cells and monkey Schlemm's canal endothelial (SCE) cells cultured in the conditioned medium of CMV-infected hTM cells were analyzed. The expression of ATX and TGF-β1 was upregulated in the aqueous humor of CMV-positive PSS patients, and the level of ATX in the aqueous humor was positively correlated with IOP. CMV infection upregulated ATX and TGF-β1 in hTM cells. The conditioned medium induced fibrotic changes in hTM cells and reduced SCE permeability, which was attenuated by an ATX inhibitor, a lysophosphatidic acid receptor antagonist, and a Rho kinase inhibitor. ATX in the aqueous humor induced by CMV infection may trigger elevated IOP. Modulating ATX activity may be a novel treatment modality for PSS.
Measurement of the W → ℓν and Z/γ * → ℓℓ production cross sections in proton-proton collisions at $ \sqrt {s} = 7\;{\text{TeV}} $ with the ATLAS detector (2010)

First measurements of the W and Z/ * ( = e, ) production cross sections in proton-proton collisions at s = 7 TeV are presented using data recorded by the ATLAS experiment at the LHC. The results are based on 2250 W and 179 Z/ * candidate events selected from a data set corresponding to an integrated luminosity of approximately 320 nb -1 . The measured total W and Z/ * -boson production cross sections times the respective leptonic branching ratios for the combined electron and muon channels are tot W BR(W ) = 9.96 0.23(stat) 0.50(syst) 1.10(lumi) nb and tot Z/ * BR(Z/ * ) = 0.82 0.06 (stat) 0.05 (syst) 0.09 (lumi) nb (within the invariant mass window 66 < m < 116 GeV). The W/Z cross-section ratio is measured to be 11.7 0.9(stat) 0.4(syst). In addition, measurements of the W + and W -production cross sections and of the lepton charge asymmetry are reported. Theoretical predictions based on NNLO QCD calculations are found to agree with the measurements.
Novel biomarker more strongly associated with tuberculosis treatment outcome than conventional or genotypic methods (2015)

<b>Introduction:</b> Development of a surrogate biomarker for treatment outcome is a critical gap in TB clinical trials and improving efficiency of drug testing. We have developed an enhanced mycobacteriophage with fluorescent reporter (Φ<sup>2</sup>GFP10), which detects metabolically active MTB and has excellent potential as a prognostic biomarker in clinical sputum. <b>Aims and objectives:</b> To compare Φ<sup>2</sup>GFP10 assay to conventional TB culture and GeneXpert MTB/RIF in serial sputum samples from TB patients on treatment to predict 6-month outcome. <b>Methods:</b> Sputum samples were collected from prospectively enrolled patients presenting to a municipal chest clinic in Durban, South Africa at baseline and weeks 1,2,3,4, and 8. For each sample, liquid TB culture measured as time to positivity (TTP) (hrs.), GeneXpert quantified as cycle threshold (CT), and Φ<sup>2</sup>GFP10 assay enumerated by flow cytometry (9gated events9) was performed. Outcome was determined at 6-months by blinded clinician with standard WHO criteria. We compared inverse TTP and inverse CT to gated events to determine which was most associated with treatment outcome. Analysis was by t-test at baseline and 8 weeks. Further longitudinal analysis is planned. <b>Results:</b> We enrolled 20 patients at treatment start. Initial median gated events 3344 declined to 362 by week 8. Week 8 gated events in clinical failures was significantly higher than cure (p=.0067). While both TTP and CT declined during treatment, the difference was not significant in clinical failure and cure at week 8 (p=.515 and p=.366, respectively). <b>Conclusions:</b> The phage biomarker accurately predicts treatment outcome compared to conventional liquid culture and GeneXpert.
Non-covalent interactions of the hydroperoxo group in crystalline adducts of organic hydroperoxides and their potassium salts (2022)

X-ray diffraction of three new stable cocrystals of potassium salts of organic hydroperoxides with molecular hydroperoxides reveals strong charge-assisted ROO − ⋯HOOR H-bonds.
¿Vanguardia socialista y masas peronistas? : Montoneros (2013)

Este trabajo intenta desbrozar si la orgánica montonera y, fundamentalmente la interpretación del peronismo que hacían sus cuadros superiores, conllevó a una deliberada dosificación de la información desde la cúspide a las bases, que hasta el día de hoy confunde, tanto a ex militantes como a historiadores. Los documentos de su conducción eran muy diferentes, en contenido, a sus publicaciones de superficie. Este trabajo se centra en analizar esos documentos entre 1971 y 1973. Su objetivo socialista aparece muy lejano de las tres banderas históricas del peronismo que tomaban como identidad política. El rol que Perón tenía en el proyecto de los primeros cuadros montoneros, aparece en un lugar muy diferente a la consigna “Perón o muerte”.
Compact and simple diversity methods for mitigating severe fading (2006)

Recently, measured channel responses for wireless links in airframes, busses and helicopter environments have demonstrated that frequency-selective fading can be more severe than predicted by the Rayleigh channel model. The work herein investigates simple diversity methods as a means to mitigate such fading which is referred to as exhibiting hyper-Rayleigh behavior. In particular, the work presents the gains achieved by utilizing selection diversity for two spatially separated antennas and by simple phasing of a two-element array. The key results are that: (1) severe fades are well-mitigated in selection diversity even if elements are spaced less than the lambda/2 typically assumed for statistically independent paths; and (2) even coarse phasing (increments of 45deg) of elements mitigates severe fades. The motivation for this work is to develop diversity strategies that are suitable for use by low-energy wireless sensor nodes that may be deployed in such severe environments; that is, the methods should be computationally simple, physically compact, and require minimum DC power to implement.
A Cooperative Evolution for QoS-driven IoT Service Composition (2013)

To facilitate the automation process in the Internet of Things, the research issue of distinguishing prospective services out of many “similar” services, and identifying needed services w.r.t the criteria of Quality of Service (QoS), becomes very important. To address this aim, we propose heuristic optimization, as a robust and efficient approach for solving complex real world problems. Accordingly, this paper devises a cooperative evolution approach for service composition under the restrictions of QoS. A series of effective strategies are presented for this problem, which include an enhanced local best first strategy and a global best strategy that introduces perturbations. Simulation traces collected from real measurements are used for evaluating the proposed algorithms under different service composition scales that indicate that the proposed cooperative evolution approach conducts highly efficient search with stability and rapid convergence. The proposed algorithm also makes a well-designed trade-off between the population diversity and the selection pressure when the service compositions occur on a large scale.
Multi-band UWB sensor networks for high density sub-surface diagnostic (2010)

Acquisition systems for sub-surface diagnostic (e.g., earthquake monitoring) require large number of sensors (geo-phones or accelerometers) to be deployed outdoor over large areas (tens of sqkm) to measure backscattered wave fields that are collected into a storage/processing unit (sink node). Aggregated data sets are analyzed to obtain an image of the sub-surface, monitor seismic activity, and declare possible alarm conditions. Cable based connectivity is the bottleneck of current systems, in terms of power consumption and degradation in accuracy. Replacing cables with wireless is now becoming attractive to improve the monitoring quality and reduce the probability of false negatives. Strict sampling synchronization constraint over large geographic areas, high precision sensor localization, high data-rate, and low delay are all topics that call for a scalable network system: Multi-Band Ultra Wide-Band radio transmissions (MB-UWB) play a key role as the only viable technology. This paper introduces the system and UWB network architecture based on ECMA-368 standard, moreover it provides a novel analytical tool to evaluate the energy consumption and delay during network set-up.
Pseudomonas azotifigens sp. nov., a novel nitrogen-fixing bacterium isolated from a compost pile (2005)

A nitrogen-fixing bacterium, designated strain 6H33b(T), was isolated from a compost pile in Japan. The nitrogenase activity of this strain was detected based on its acetylene-reducing activity under low oxygen concentrations (2-4%). An analysis of the genes responsible for nitrogen fixation in this strain, nifH and nifD, indicated a close relationship to those of Pseudomonas stutzeri A15 (A1501). Sequence similarity searches based on the 16S rRNA gene sequences showed that strain 6H33b(T) belongs within the genus Pseudomonas sensu stricto; closest similarity was with Pseudomonas indica (97.3%). A comparison of several taxonomic characteristics of 6H33b(T) with those of P. indica and some type strains of the genus Pseudomonas sensu stricto indicated that 6H33b(T) could be distinguished from P. indica based on the presence of nitrogen fixation ability, the absence of nitrate reduction and denitrification abilities and the utilization of some sugars and organic acids. Phylogenetic analyses and the results of DNA-DNA hybridization experiments also indicated that strain 6H33b(T) represents a species distinct from P. indica. From these results, it is proposed that strain 6H33b(T) (=ATCC BAA-1049(T)=JCM 12708(T)) is classified as the type strain of a novel species of the genus Pseudomonas sensu stricto under the name Pseudomonas azotifigens sp. nov.
Secretory vesicle rebound hyperacidification and increased quantal size resulting from prolonged methamphetamine exposure (2008)

Acute exposure to amphetamines (AMPHs) collapses secretory vesicle pH gradients, which increases cytosolic catecholamine levels while decreasing the quantal size of catecholamine release during fusion events. AMPH and methamphetamine (METH), however, are retained in tissues over long durations. We used optical and electron microscopic probes to measure the effects of long-term METH exposure on secretory vesicle pH, and amperometry and intracellular patch electrochemistry to observe the effects on neurosecretion and cytosolic catecholamines in cultured rat chromaffin cells. In contrast to acute METH effects, exposure to the drug for 6-48 h at 10 microM and higher concentrations produced a concentration-dependent rebound hyperacidification of secretory vesicles. At 5-10 microM levels, prolonged METH increased the quantal size and reinstated exocytotic catecholamine release, although very high (> 100 microM) levels of the drug, while continuing to produce rebound hyperacidification, did not increase quantal size. Secretory vesicle rebound hyperacidification was temperature dependent with optimal response at approximately 37 degrees C, was not blocked by the transcription inhibitor, puromycin, and appears to be a general compensatory response to prolonged exposure with membranophilic weak bases, including AMPHs, methylphenidate, cocaine, and ammonia. Thus, under some conditions of prolonged exposure, AMPHs and other weak bases can enhance, rather than deplete, the vesicular release of catecholamines via a compensatory response resulting in vesicle acidification.
Decentralized MMSE attacks in electricity grids (2016)

Decentralized data-injection attack construction with minimum mean-square-error state estimation is studied in a game-theoretic setting. Within this framework, the interaction between the network operator and the set of attackers, as well as the interactions among the attackers, are modeled by a game in normal form. A novel utility function that captures the trade-off between the maximum distortion that an attack can introduce and the probability of the attack being detected by the network operator is proposed. Under the assumption that the state variables can be modeled as a multivariate Gaussian random process, it is shown that the resulting game is a potential game. The cardinality of the corresponding set of Nash Equilibria (NEs) of the game is analyzed. It is shown that attackers can agree on a data-injection vector construction that achieves the best trade-off between distortion and detection probability by sharing only a limited number of bits offline. Interestingly, this vector construction is also shown to be an NE of the resulting game.
Spray-dried iron Fischer-Tropsch catalysts. 2. Effect of carburization on catalyst attrition resistance: (2000)

Spray drying has been recently used by this research team in the preparation of Fe Fischer−Tropsch catalysts with higher attrition resistance for use in slurry bubble column reactors. In the first paper in this series, the effects of the type, concentration, and network structure of SiO2 on the attrition resistance of two series of spray-dried Fe catalysts in their calcined state were explored and the dependence of catalyst attrition resistance on catalyst particle density was discussed. As a continuation of our previous effort, the effect of carburization on catalyst attrition resistance was studied and is presented in this paper. After carburization, the majority component of the catalysts, hematite (Fe2O3), was converted to iron carbides, mostly χ-carbide (Fe2C5). Breakage of individual catalyst particles and fines formation, which can be considered as evidence of chemical attrition, was only observed during carburization of the catalyst with low SiO2 concentration <9 wt %. With an increase in the tota...
Imaging dynamically-driven strain at the nanometer-scale using stroboscopic Scanning X-ray Diffraction Microscopy (2018)

Phononic manipulation provides a direct route to control diverse materials properties in solid state systems. In materials hosting optically-active defects, strain control near engineered structures is an important path to harnessing the potential of solid-state qubits for quantum information science and nanoscale sensing. While lattice strain can be used both statically and dynamically to tune quantum energy levels and engineer hybrid system responses, the direct, independent observation of in-situ nanoscale strain fields induced near quantum defects remains challenging. We report the development of a stroboscopic Scanning X-ray Diffraction Microscopy (s-SXDM) imaging approach for investigating dynamic strain in 4H-SiC, which hosts vacancy related spin defects for quantum sensing and information. This approach uses nano-focused X-ray photon pulses synchronized to a surface acoustic wave (SAW) launcher, in order achieve static time domain and phase sensitive Bragg diffraction imaging with nanoscale spatial resolution near an engineered acoustic-scattering object. We use this technique to simultaneously map near-surface microstructures and acoustically induced lattice curvatures generated by interdigitated transducers fabricated on 4H-SiC as well as corroborate the images with the photoluminescence response of optically-active defect in the SiC, sensitive to local piezoelectric effects. The nanofocused diffraction patterns, stroboscopically varying in time, are analyzed to reveal micro-radian dynamic curvature oscillations trapped near a model structural defect etched into the SiC. This technique yields 0.01 pm d-spacing sensitivity and an effective time resolution of 100 ps. These results demonstrate a unique route for directly studying local strain induced by acoustically manipulated structures under realistic operating conditions.
Bioactivation I: Bioactivation by Cytochrome P450s (2012)

Abstract Metabolism reactions generally result in detoxification of xenobiotics and are accompanied by the formation of chemically stable metabolites, which are devoid of pharmacological or toxicological activities. However, in some cases, these reactions can convert drugs to products that are either chemically reactive or pharmacologically active, a process that is commonly referred to as metabolic activation or bioactivation . Most, if not all, functionalization and conjugation reactions can result in bioactivation. Even though all enzymes have the propensity to catalyze the metabolic activation of compounds, cytochrome P450 (P450) enzymes, which generally dominate metabolism, play a major role in the metabolic activation of drugs. The primary objective of this chapter is to provide an overview of bioactivation by P450 to pharmacologically active and chemically reactive metabolites. The common reactions that result in bioactivation of xenobiotics and consequences of bioactivation have been discussed here.
Kernel-Based Semi-Supervised Learning Over Multilayer Graphs (2018)

Networks arise in fields such as sociology, biology, and machine learning among others, to describe complex and often interdependent systems. These increasingly complex systems call for flexible network models that allow for multiple types of interactions among the agents (nodes) known as multilayer networks. A frequently encountered task entails inference of nodal processes across the network given values on a subset of nodes. The present contribution relies on graph kernels, to put forth a novel inference approach that accounts for linear and nonlinear dependencies among nodes and leverages the layered network structure. Numerical tests with synthetic as well as real data corroborate the effectiveness of the proposed kernel-based multilayer learning scheme.