gebhart/patrepeval huggingface dataset:
Hyperspectral imaging using electro-optic Fourier transform spectrometer (2004)

JPL and BNS Inc. are jointly developing a compact, low mass, Electro-Optic Imaging Fourier Transform Spectrometer (E-O IFTS) for hyperspectral imaging applications. The spectral region of this spectrometer will be 1 - 2.5 &mu;m (1000 - 4000 cm<sup>-1</sup>) to allow high-resolution, high-speed hyperspectral imaging applications. The specific applications for NASA's missions will focus on the measurement of a large number of different atmospheric gases simultaneously in the same airmass. Due to the use of a combination of birefringent phase retarders and multiple achromatic phase switches to achieve phase delay, this spectrometer is capable of hyperspectral measurements similar to that of the conventional Fourier transform spectrometer but without any moving parts. In this paper, the principle of operations, system architecture and recent experimental progress will be presented.
Imaging Human Cerebral Pain Modulation by Dose-dependent Opioid Analgesia (2007)

Remifentanil induced regional cerebral blood flow increases in the cingulofrontal cortex and periaqueductal gray during pain stimulation, indicating that mu-opioidergic activation modulates activity in pain inhibitory circuitries. This provides direct evidence that opioidergic analgesia is mediated by activation of established descending antinociceptive pathways.
Insight into the Self-Assembling Properties of Peptergents: A Molecular Dynamics Simulation Study (2018)

By manipulating the various physicochemical properties of amino acids, the design of peptides with specific self-assembling properties has been emerging for more than a decade. In this context, short peptides possessing detergent properties (so-called "peptergents") have been developed to self-assemble into well-ordered nanostructures that can stabilize membrane proteins for crystallization. In this study, the peptide with "peptergency" properties, called ADA8 and extensively described by Tao et al., is studied by molecular dynamic simulations for its self-assembling properties in different conditions. In water, it spontaneously forms beta sheets with a β barrel-like structure. We next simulated the interaction of this peptide with a membrane protein, the bacteriorhodopsin, in the presence or absence of a micelle of dodecylphosphocholine. According to the literature, the peptergent ADA8 is thought to generate a belt of β structures around the hydrophobic helical domain that could help stabilize purified membrane proteins. Molecular dynamic simulations are here used to image this mechanism and provide further molecular details for the replacement of detergent molecules around the protein. In addition, we generalized this behavior by designing an amphipathic peptide with beta propensity, which was called ABZ12. Both peptides are able to surround the membrane protein and displace surfactant molecules. To our best knowledge, this is the first molecular mechanism proposed for "peptergency".
Subthalamic nucleus deep brain stimulation changesvelopharyngeal control in Parkinson’s disease (2011)

Purpose Adequate velopharyngeal control is essential for speech, but may be impaired in Parkinson’s disease (PD). Bilateral subthalamic nucleus deep brain stimulation (STN DBS) improves limb function in PD, but the effects on velopharyngeal control remain unknown. We tested whether STN DBS would change aerodynamic measures of velopharyngeal control, and whether these changes were correlated with limb function and stimulation settings. Methods Seventeen PD participants with bilateral STN DBS were tested within a morning session after a minimum of 12 h since their most recent dose of anti-PD medication. Testing occurred when STN DBS was on, and again 1 h after STN DBS was turned off, and included aerodynamic measures during syllable production, and standard neurological ratings of limb function. Results We found that PD participants exhibited changes with STN DBS, primarily consistent with increased intraoral pressure (n = 7) and increased velopharyngeal closure (n = 5). These changes were modestly correlated with measures of limb function, and were correlated with stimulation frequency. Conclusion Our findings suggest that STN DBS may change velopharyngeal control during syllable production in PD, with greater benefit associated with low frequency stimulation. However, DBS demonstrates a more subtle influence on speech-related velopharyngeal control than limb motor control. This distinction and its underlying mechanisms are important to consider when assessing the impact of STN DBS on PD.
&lt;title&gt;New urea sensor based on a metal island coated ion sensitive swelling polymer device&lt;/title&gt; (1995)

An optical reflectivity change induced by a change of the micro environment around metal island is used to construct various sensors and biosensors. To obtain a sensitive micro sensor either the island density at the surface of the sensor device or the distance of an island layer film to a solid metal surface or to another island film can be varied. Polyvinylpyrrolidone crosslinked with sulfonated bisazidostilbenes shows chaotropic ion dependent nanometric shrinking and swelling which can be observed by using this polymer as interlayer in a metal island device. This volume change of the sensing polymer is transduced to an optical signal using a metal island film, followed by a thin layer of an optically transparent welling polymer and a further metal island film as the topmost layer, exposed to the analyte. This new set-up enables the spectroscopic monitoring of the reflectance change from the backside of the sensor chip not exposed to the analyte solution. For the construction of a biosensor the device was either covered by a photo-structured polyvinylpyrrolidone membrane incorporating the desired enzymes or combined with a micro enzyme reactor. The fully reversible response of the sensor is induced by carbonate and ammonium ions liberated from urea by immobilized urease.
Direct visualization of aqueous tear secretion from lacrimal gland (2016)

This visualization method allowed us to directly observe tear secretion from the palpebral lobe of the main lacrimal glands and Wolfring glands, and to quantitatively measure the tear flow rate from the lacrimal glands.
Low-Latency Communications in LTE Using Spatial Diversity and Encoding Redundancy (2016)

Control of data delivery latency in wireless mobile networks is an open problem due to the inherently unreliable and stochastic nature of wireless channels. This paper explores how the current best-effort throughput-oriented wireless services could be evolved into latency-sensitive enablers of new mobile applications such as remote 3D graphical rendering for interactive virtual/augmented-reality overlay. Assuming that the signal propagation delay and achievable throughput meet the basic latency requirements of the user application, we examine the idea of trading excess/federated bandwidth for the elimination of non-negligible data re-ordering delays, caused by temporal transmission failures and buffer overflows. The general system design is based on (i) spatially diverse delivery of data over multiple paths with uncorrelated outage likelihoods, and (ii) forward packet protection based on encoding redundancy that enables proactive recovery of lost or intolerably delayed data without end-to-end re-transmissions. Our analysis is based on traces of real-life traffic in live carrier-grade LTE networks.
The present and future of event correlation: A need for end-to-end service fault localization (2001)

the observable malfunctioning of the managed system. Until recently, fault localization efforts concentrated mostly on diagnosing faults related to the availability of network resources in the lowest layers of the protocol stack. Modern enterprise environments require that fault diagnosis be performed in integrated fashion in multiple layers of the protocol stack and that it include diagnosing performance problems. This paper reviews the existing approaches to fault localization and presents its new facets revealed by the demands of modern enterprise systems. We also present end-to-end service failure diagnosis as a critical step towards multi-layer fault localization in an enterprise environment.
Streamlines, ray tracing and production tomography: generalization to compressible flow (2000)

We exploit an analogy between streamlines and seismic ray tracing to develop an efficient formalism for integrating dynamic data into high-resolution reservoir models. Utilizing concepts from asymptotic ray theory in seismic and diffusive electromagnetic imaging, we generalize the streamline approach to com- pressible flow. A 'diffusive' streamline time-of-flight is introduced for transient pressure calculations. Production data integration is carried out in a manner analogous to seismic tomography and waveform imaging. The power and versatility of our approach is illustrated using synthetic examples that utilize transient pressure, tracer and multiphase production history. A field example from a heterogeneous carbonate reservoir demonstrates the practical feasibility of our approach.
Urban slum structure: integrating socioeconomic and land cover data to model slum evolution in Salvador, Brazil (2013)

Our approach captures the socioeconomic and land cover heterogeneity within and between slum settlements and identifies the most marginalized communities in a large, complex urban setting. These findings indicate that changes in the canonical scores for slum areas can be used to track their evolution and to monitor the impact of development programs such as slum upgrading.
Frequency Stability and Noise Characteristics of Ultra-High Frequency (UHF) Nanoelectromechanical Resonators (2005)

Nanoelectromechanical silicon carbide doubly-clamped beam vibrating resonators operating in the ultra-high frequency (UHF) band, with resonance frequencies of 395MHz, 411MHz, 428MHz, and 482MH, and quality factors (Q’s) of 2000~3000, have been demonstrated. The readout of electromechanical resonances from the nanodevices is integrated with a low-noise phase-locked loop to implement real-time resonance frequency locking and tracking, with which the frequency stability and phase noise of the resonators are measured. The measured frequency stability shows typical crystal resonator behavior, and represents unprecedented mass sensitivity (in 10 -20 g ~ 10 -21 g scale) achieved by nanoelectromechanical resonant mass sensors. The achievable lowest phase noise of the system is ultimately determined by the thermomechanical noise of the resonator device, but presently limited by the thermal noise and other noise processes of the measurement electronic system.
The neural correlates of learned motor acuity (2014)

We recently defined a component of motor skill learning as "motor acuity," quantified as a shift in the speed-accuracy trade-off function for a task. These shifts are primarily driven by reductions in movement variability. To determine the neural correlates of improvement in motor acuity, we devised a motor task compatible with magnetic resonance brain imaging that required subjects to make finely controlled wrist movements under visual guidance. Subjects were imaged on day 1 and day 5 while they performed this task and were trained outside the scanner on intervening days 2, 3, and 4. The potential confound of performance changes between days 1 and 5 was avoided by constraining movement time to a fixed duration. After training, subjects showed a marked increase in success rate and a reduction in trial-by-trial variability for the trained task but not for an untrained control task, without changes in mean trajectory. The decrease in variability for the trained task was associated with increased activation in contralateral primary motor and premotor cortical areas and in ipsilateral cerebellum. A global nonlocalizing multivariate analysis confirmed that learning was associated with increased overall brain activation. We suggest that motor acuity is acquired through increases in the number of neurons recruited in contralateral motor cortical areas and in ipsilateral cerebellum, which could reflect increased signal-to-noise ratio in motor output and improved state estimation for feedback corrections, respectively.
Quasi-phase-matched second-harmonic generation at vacuum ultraviolet 193 nm (2011)

By successful fabrication of fine twin structure, QPM SHG at 193 nm is achieved in crystalline quartz. Mechanical module suppressing switch back of twins enables stable wavelength conversion for all-solid-state compact vacuum-ultraviolet laser.
Toward Homosuccinate Fermentation: Metabolic Engineering of Corynebacterium glutamicum for Anaerobic Production of Succinate from Glucose and Formate (2012)

Previous studies have demonstrated the capability of Corynebacterium glutamicum for anaerobic succinate production from glucose under nongrowing conditions. In this work, we have addressed two shortfalls of this process, the formation of significant amounts of by-products and the limitation of the yield by the redox balance. To eliminate acetate formation, a derivative of the type strain ATCC 13032 (strain BOL-1), which lacked all known pathways for acetate and lactate synthesis (Δcat Δpqo Δpta-ackA ΔldhA), was constructed. Chromosomal integration of the pyruvate carboxylase gene pyc(P458S) into BOL-1 resulted in strain BOL-2, which catalyzed fast succinate production from glucose with a yield of 1 mol/mol and showed only little acetate formation. In order to provide additional reducing equivalents derived from the cosubstrate formate, the fdh gene from Mycobacterium vaccae, coding for an NAD(+)-coupled formate dehydrogenase (FDH), was chromosomally integrated into BOL-2, leading to strain BOL-3. In an anaerobic batch process with strain BOL-3, a 20% higher succinate yield from glucose was obtained in the presence of formate. A temporary metabolic blockage of strain BOL-3 was prevented by plasmid-borne overexpression of the glyceraldehyde 3-phosphate dehydrogenase gene gapA. In an anaerobic fed-batch process with glucose and formate, strain BOL-3/pAN6-gap accumulated 1,134 mM succinate in 53 h with an average succinate production rate of 1.59 mmol per g cells (dry weight) (cdw) per h. The succinate yield of 1.67 mol/mol glucose is one of the highest currently described for anaerobic succinate producers and was accompanied by a very low level of by-products (0.10 mol/mol glucose).
Supplementary Fig S1 from Genomic Amplification of &lt;i&gt;CD274&lt;/i&gt; (PD-L1) in Small-Cell Lung Cancer (2023)

&lt;p&gt;SNP chip analysis of three tumors from cohort 1.&lt;/p&gt;
Global distribution and diversity of coral‐associated <i>Archaea</i> and their possible role in the coral holobiont nitrogen cycle (2008)

Diversity, distribution and genetic comparison of Archaea associated with the surface mucus of corals from three genera, namely Acanthastrea sp., Favia sp. and Fungia sp., from the Gulf of Eilat, Israel and from Heron Island, Australia were studied. Sequencing of the 16S rRNA gene of the coral-associated Archaea revealed dominance of Crenarchaeota (79%, on average). In this phylum, 87% of the sequences were similar (>or= 97%) to the Thermoprotei, with 76% of these being similar (>or= 97%) to the ammonium oxidizer, Nitrosopumilus maritimus. Most of the coral-associated euryarchaeotal sequences (69%) were related to marine group II, while other euryarchaeotal clades were found to be related to anaerobic methanotrophs (8%), anaerobic nitrate reducers (i.e. denitrification, 15%) and marine group III (8%). Most of the crenarchaeotal and euryarchaeotal coral-associated 16S rRNA gene sequences from Heron Island (61%) and from the Gulf of Eilat (71%) were closely related (>or= 97%) to sequences previously derived from corals from the Virgin Islands. Analysis of archaeal amoA sequences obtained from the fungiid coral, Fungia granulosa, divided into three clades, all related to archaeal sequences previously obtained from the marine environment. These sequences were distantly related to amoA sequences previously found in association with other coral species. Preliminary experiments suggest that there is active oxidation of ammonia to nitrite in the mucus of F. granulosa. Thus, coral-associated Archaea may contribute to nitrogen recycling in the holobiont, presumably by acting as a nutritional sink for excess ammonium trapped in the mucus layer, through nitrification and denitrification processes.
Supplementary Figure S2 from Chromatin Regulators as a Guide for Cancer Treatment Choice (2023)

&lt;p&gt;A chromatin regulator gene panel distinguishes docetaxel high-responders and poor-responders&lt;/p&gt;
Modeling Dioxygen Reduction at Multicopper Oxidase Cathodes (2014)

We report a general kinetics model for catalytic dioxygen reduction on multicopper oxidase (MCO) cathodes. Our rate equation combines Butler-Volmer (BV) electrode kinetics and the Michaelis-Menten (MM) formalism for enzymatic catalysis, with the BV model accounting for interfacial electron transfer (ET) between the electrode surface and the MCO type 1 copper site. Extending the principles of MM kinetics to this system produced an analytical expression incorporating the effects of subsequent intramolecular ET and dioxygen binding to the trinuclear copper cluster into the cumulative model. We employed experimental electrochemical data on Thermus thermophilus laccase as benchmarks to validate our model, which we suggest will aid in the design of more efficient MCO cathodes. In addition, we demonstrate the model's utility in determining estimates for both the electronic coupling and average distance between the laccase type-1 active site and the cathode substrate.
The role of interleukin 17 in Crohn’s disease-associated intestinal fibrosis (2013)

Our results suggest that IL-17A, but not IL-17E, is pro-fibrotic in CD. Further studies are needed to clarify whether the therapeutic blockade of IL-17A through the anti-IL-17A monoclonal antibody secukinumab is able to counteract the fibrogenic process in CD.
Spo5/Mug12, a Putative Meiosis-Specific RNA-Binding Protein, Is Essential for Meiotic Progression and Forms Mei2 Dot-Like Nuclear Foci (2006)

We report here a functional analysis of spo5(+)(mug12(+)) of Schizosaccharomyces pombe, which encodes a putative RNA-binding protein. The disruption of spo5(+) caused abnormal sporulation, generating inviable spores due to failed forespore membrane formation and the absence of a spore wall, as determined by electron microscopy. Spo5 regulates the progression of meiosis I because spo5 mutant cells display normal premeiotic DNA synthesis and the timely initiation of meiosis I but they show a delay in the peaking of cells with two nuclei, abnormal tyrosine 15 dephosphorylation of Cdc2, incomplete degradation of Cdc13, retarded formation and repair of double strand breaks, and a reduced frequency of intragenic recombination. Immunostaining showed that Spo5-green fluorescent protein (GFP) appeared in the cytoplasm at the horsetail phase, peaked around the metaphase I to anaphase I transition, and suddenly disappeared after anaphase II. Images of Spo5-GFP in living cells revealed that Spo5 forms a dot in the nucleus at prophase I that colocalized with the Mei2 dot. Unlike the Mei2 dot, however, the Spo5 dot was observed even in sme2Delta cells. Taken together, we conclude that Spo5 is a novel regulator of meiosis I and that it may function in the vicinity of the Mei2 dot.
Correlating the local magnetic properties of the magnetic phase transition in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mi>Gd</mml:mi><mml:mn>5</mml:mn></mml:msub><mml:msub><mml:mi>Ge</mml:mi><mml:mn>4</mml:mn></mml:msub></mml:mrow></mml:math>using scanning Hall probe imaging (2006)

We present a study of scanning Hall probe imaging on a bulk sample of the prototype giant magnetocaloric material ${\mathrm{Gd}}_{5}{\mathrm{Ge}}_{4}$ across the magnetic field-induced antiferromagnetic to ferromagnetic and the reverse ferromagnetic to antiferromagnetic transitions at $35\phantom{\rule{0.3em}{0ex}}\mathrm{K}$. We confirm that the sample presents phase coexistence of both antiferromagnetic and ferromagnetic phases through the crossover region in the field-temperature plane indicative of the first order nature of the phase transition. By studying the features of the local magnetization-field loops corresponding to the pixel size of $30\phantom{\rule{0.3em}{0ex}}\mathrm{\ensuremath{\mu}}\mathrm{m}\ifmmode\times\else\texttimes\fi{}30\phantom{\rule{0.3em}{0ex}}\mathrm{\ensuremath{\mu}}\mathrm{m}$ across the entire image region we show that the two magnetic transitions are not spatially symmetric and, therefore, are not governed entirely by static inhomogeneity. Our work adds further support to the idea that random strain fields play a considerable role in defining the magnetic behavior across the field driven transition.
Gold Nanoparticle Satellite Nanostructures on a Glass Substrate for Dual-responsive Optical Sensing of Organic Liquids (2014)

Abstract Core–satellite nanostructures made of gold nanoparticles were fabricated on glass substrates by controlled immobilization of the nanoparticles and VUV irradiation. Coupled SPR absorption between core and satellite nanoparticles was observed, depending on the length of the dithiol linkers. These satellite nanostructures provide an improved selectivity for distinguishing various liquids using single and coupled SPR absorption in a dual-responsive manner.
Segmentation of Optic Disc and Optic Cup in Retinal Fundus Images Using Coupled Shape Regression (2016)

Accurate segmentation of optic cup and disc in retinal fundus images is required to derive the cup-to-disc ratio (CDR) parameter which is the main indicator for Glaucoma assessment. In this paper, we propose a coupled regression method for accurate segmentation of optic cup and disc in retinal colour fundus image. The proposed coupled regression framework consists of a parameter regressor which directly predicts CDR from a given image, as well as an ensemble shape regressor which iteratively estimates the OD-OC boundary by taking into account the CDR estimated by the parameter regressor. The parameter regressor and the shape regressor are then coupled together within a feedback loop so that estimation of one reinforces the other. Both parameter regressor and the ensemble shape regressor are modeled using Boosted Regression Trees. The proposed optic cup and disc segmentation method is applied on an image set of 50 patients and demonstrates high segmentation accuracy. A comparative study shows that our proposed method outperforms state of the art methods for cup segmentation.
Growth and fluorination of CaSi<sub>2</sub> thin film (2019)

journal article
Increased [<sup>32</sup>P]‐phosphorylation of tryptic peptides of erythrocyte spectrin in duchenne muscular dystrophy (1981)

Increased [32P]-incorporation in tryptic peptides of the erythrocyte membrane protein spectrin Band 2 in Duchenne muscular dystrophy (DMD) was studied in a consecutive series of 10 matched DMD/control pairs. Spectrin was [32P]-phosphorylated by cyclic AMP-independent endogenous membrane protein kinase in the presence of [gamma-32P]ATP. [32P]-labeled spectrin was isolated, purified, and subjected to tryptic cleavage with excess trypsin. The resulting peptides were separated on a high-resolution 5%/15% stacking SDS--polyacrylamide gel electrophoresis system. Liquid scintillation counting was performed on sequential slices of unstained gels. A broad [32P]-labeled band containing a number of [32P]-polypeptides was found to be more highly [32P]-phosphorylated in DMD patients than in their matched controls. This band migrated with an apparent molecular mass of 4.8-5.2 kilodaltons and contained approximately 55% of total [32P] radioactivity covalently bound to spectrin peptides. These data demonstrated an increased [32P]-phosphorylation of an identifiable tryptic peptide fraction in DMD that is consistent with previous reports of increased spectrin Band 2 [32P]-phosphorylation in DMD.