gebhart/patrepeval huggingface dataset:
202 Omeprazole and Fluticasone Inhibit IL-13-Stimulated Eotaxin-3 Expression by Esophageal Epithelial Cells Through Different Mechanisms and With Additive Effects: Rationale for Combining PPIs With Topical Steroids for EoE Patients (2015)

Introduction: Eosinophilic esophagitis (EoE) often presents with symptoms that are considered to relate to esophageal dysfunctions. Our previous study demonstrated that TRPA1 plays important role in tissue mast cell activation-induced increase in the excitability of esophageal vagal nodose C fibers. The present study aims to determine whether prolonged antigen exposure in vivo sensitizes TRPA1 in esophageal vagal afferents in a guinea pig model of EoE. Method: Antigen challenge-induced responses in esophageal mucosa were first studied by histological assessments and Ussing chamber methods. TRPA1 functions in vagal sensory neurons were then studied by calcium imaging and by whole-cell patch clamp recordings in DiI-labeled esophageal nodose and jugular neurons. Extracellular single-fiber recordings were performed in nodose and jugular C-fiber neurons using ex vivo esophagealvagal preparations with intact nerve endings in the esophagus. Results: (1) Prolonged antigen challenge (0.1% Ovalbumin, 30-second/day for 2-week) in antigen-sensitized guinea pigs increased inflammation scores from 2.0±0.47 (naive) to 4.33±0.27 (OVA-2w) in the esophagus (p<0.05). OVA challenge also increased the infiltrations of both mast cells (from 8.2±2.1 to 63.5±4.5 in mucosa, and from 14.0±2.4 to 43.1±4.5 in muscle layers, both p<0.05) and eosinophils (from 2.6±0.9 to 63.5±20.0 in mucosa, and from 0 to 5.2±2.55/ in muscle layers, both p<0.05) in the cross-sections of the esophagus. (2) Antigen challenge decreased the transepithelial resistance in esophageal epithelium from 564.7±63.4 V·cm2 to 356.0±45.5V·cm2 (p<0.05). (3) Antigen challenge increased TRPA1 agonist AITC-induced calcium influx in both nodose (from 43.5% to 66.7%) and jugular neurons (from 38.9% to 51.9%)(both p<0.05). (4) Antigen challenge increased current density elicited by TRPA1 agonist AITC in DiI-labeled esophageal nodose neurons (naive vs OVA-2w: 24.3±5.4 vs 59.7 ±4.7 pA/pF, p<0.05) and jugular neurons (naive vs OVA-2w: 31.5±5.3 vs 65.8 ±6.2 pA/pF, p<0.05). (5) In naive animals, intra-esophageal infusion of TRPA1 agonist AITC did not evoke action potential discharge in either esophageal nodose or jugular C fibers. After OVA challenge, intra-esophageal infusion of AITC was able to evoke action potential discharges in both nodose C fibers (baseline vs AITC: 0.75±0.25 Hz vs 4.63±1.03 Hz, p<0.01, n=8) and Jugular C fibers (baseline vs AITC: 0.88±0.25 Hz vs 2.5±0.38Hz, p<0.01, n=8). Conclusion: These results demonstrated that prolonged antigen challenge induced allergic inflammation, decreased epithelial barrier resistance, and sensitized TRPA1 in vagal nociceptive neurons and afferent C fibers in the esophagus. These changes enabled intra-esophageal noxious chemical to activate esophageal nociceptor. This novel finding may help to better understand esophageal dysfunction in EoE.
Reduced peptide bond cyclic somatostatin based opioid octapeptides Synthesis, conformational properties and pharmacological characterization (1992)

The conformational and pharmacological properties that result from peptide bond reduction as well as the use of secondary amino acids in a series of cyclic peptides related to the mu opioid receptor selective antagonist D-Phe1-Cys2-Tyr3-D-Trp4-Orn5-Thr6-Pen7+ ++-Thr8-NH2 (IV), have been investigated. Peptide analogues that contain [CH2NH] and [CH2N] pseudo-peptide bonds (in primary and secondary amino acids, respectively) were synthesized on a solid support. Substitution of Tyr3 in IV by the cyclic, secondary amino acid 1,2,3,4-tetrahydroisoquinoline carboxylate (Tic) and of D-Trp4 with D-1,2,3,4-tetrahydro-beta-carboline(D-Tca4), gave peptides 4 and 1, respectively. Both analogues displayed reduced affinities for mu opioid receptors. Conformational analysis based on extensive NMR investigations demonstrated that the backbone conformations of 1 and 4 are similar to those of the potent and selective analogue D-Phe-Cys-Tyr-D-Trp-Lys-Thr-Pen-Thr-NH2 (I), while the conformational properties of the side chains of Tic3 (4) and D-Tca4 (1) resulted in topographical properties that were not well recognized by the mu opioid receptor. Peptide bond modifications were made including (Tyr3-psi[CH2NH]-D-Trp4), 3; (Tyr3-psi[CH2N]-D-Tca4), 2; and (Cys2-psi[CH2N]-Tic3), 6. These analogues showed decreases in their mu opioid receptor affinities relative to the parent compounds IV, 1, and 4, respectively. 1H NMR based conformational analysis in conjunction with receptor binding data led to the conclusion that the reduced peptide bonds in 2, 3, 5, and 6 do not contribute to the process of discrimination between mu and delta opioid receptors, and in spite of their different dynamic behaviors (relative to 1 and 4), they are still capable of attaining similar receptor bound conformations, possibly due to their increased flexibility.
Effect of Pulse Duration on Size and Character of the Lesion in Retinal Photocoagulation (2008)

Pulse durations of approximately 20 milliseconds represent an optimal compromise between the favorable impact of speed, higher spatial localization, and reduced collateral damage on one hand, and sufficient width of the therapeutic window (> 3) on the other.
Outcomes and risk factors for cancer patients undergoing endoscopic intervention of malignant biliary obstruction (2015)

Outcome in tumor patients with malignant bile obstruction is associated with the type of microbial biliary colonization. The proof of multiresistant pathogens or Candida, as well as the level of inflammation markers, have an impact on the prognosis of the underlying tumor disease.
Synthesis and fluorescence study of conjugated polymers based on 2,4,6-triphenylpyridine moieties (2016)

Three novel 2,4,6-triphenylpyridine-based conjugated polymers showed strong fluorescence emission with large Stokes' shifts, tunable band gaps and high quantum yields.
Exoplasmic cysteine Cys384 of the HDL receptor SR-BI is critical for its sensitivity to a small-molecule inhibitor and normal lipid transport activity (2011)

The HDL receptor, scavenger receptor, class B, type I (SR-BI), is a homooligomeric cell surface glycoprotein that controls HDL structure and metabolism by mediating the cellular selective uptake of lipids, mainly cholesteryl esters, from HDL. The mechanism underlying SR-BI-mediated lipid transfer, which differs from classic receptor-mediated endocytosis, involves a two-step process (binding followed by lipid transport) that is poorly understood. Our previous structure/activity analysis of the small-molecule inhibitor blocker of lipid transport 1 (BLT-1), which potently (IC(50) ∼ 50 nM) blocks SR-BI-mediated lipid transport, established that the sulfur in BLT-1's thiosemicarbazone moiety was essential for activity. Here we show that BLT-1 is an irreversible inhibitor of SR-BI, raising the possibility that cysteine(s) in SR-BI interact with BLT-1. Mass spectrometric analysis of purified SR-BI showed two of its six exoplasmic cysteines have free thiol groups (Cys251 and Cys384). Converting Cys384 (but not Cys251) to serine resulted in complete BLT-1 insensitivity, establishing that the unique molecular target of BLT-1 inhibition of cellular SR-BI dependent lipid transport is SR-BI itself. The C384S substitution reduced the receptor's intrinsic lipid uptake activity by approximately 60% without dramatically altering its surface expression, homooligomerization, or HDL binding. Thus, a small-molecule screening approach identified a key residue in SR-BI involved in lipid transport, providing a powerful springboard into the analyses of the structure and mechanism of SR-BI, and highlighting the power of this approach for such analyses.
Sodium Ion Interactions with Aqueous Glucose: Insights from Quantum Mechanics, Molecular Dynamics, and Experiment (2013)

In the last several decades, significant efforts have been conducted to understand the fundamental reactivity of glucose derived from plant biomass in various chemical environments for conversion to renewable fuels and chemicals. For reactions of glucose in water, it is known that inorganic salts naturally present in biomass alter the product distribution in various deconstruction processes. However, the molecular-level interactions of alkali metal ions and glucose are unknown. These interactions are of physiological interest as well, for example, as they relate to cation-glucose cotransport. Here, we employ quantum mechanics (QM) to understand the interaction of a prevalent alkali metal, sodium, with glucose from a structural and thermodynamic perspective. The effect on β-glucose is subtle: a sodium ion perturbs bond lengths and atomic partial charges less than rotating a hydroxymethyl group. In contrast, the presence of a sodium ion significantly perturbs the partial charges of α-glucose anomeric and ring oxygens. Molecular dynamics (MD) simulations provide dynamic sampling in explicit water, and both the QM and the MD results show that sodium ions associate at many positions with respect to glucose with reasonably equivalent propensity. This promiscuous binding nature of Na(+) suggests that computational studies of glucose reactions in the presence of inorganic salts need to ensure thorough sampling of the cation positions, in addition to sampling glucose rotamers. The effect of NaCl on the relative populations of the anomers is experimentally quantified with light polarimetry. These results support the computational findings that Na(+) interacts similarly with α- and β-glucose.
Legends for Supplementary Figures 1-6 from Genomic Profiling of MicroRNA and Messenger RNA Reveals Deregulated MicroRNA Expression in Prostate Cancer (2023)

Legends for Supplementary Figures 1-6 from Genomic Profiling of MicroRNA and Messenger RNA Reveals Deregulated MicroRNA Expression in Prostate Cancer
A Stack-Free Traversal Algorithm for Left-Balanced k-d Trees (2022)

We present an algorithm that allows for find-closest-point and kNN-style traversals of left-balanced k-d trees, without the need for either recursion or software-managed stacks; instead using only current and last previously traversed node to compute which node to traverse next.
Synthetically Trained 3D Visual Tracker of Underwater Vehicles (2018)

We present a method for visually detecting and tracking the 3D pose of autonomous underwater vehicles, which aims to enable robust multi-robot convoying. We follow the approach of tracking-by-detection, which combines the robust, drift-free nature of object detection with the temporal consistency of tracking algorithms. Central to our method is a multi-output convolutional network that jointly predicts whether the target robot is present in the image (classification), the 2D bounding box around the target in the image plane, and the 3D orientation of the target. This, combined with camera intrinsic parameters and prior knowledge of the robot's absolute scale, allows us to recover the full 6-degree-of-freedom pose (translation and orientation) of the target robot. To train our network, we use only synthetic images rendered using the Unreal game engine, which is a cost-effective way to produce a large training set without the need for laborious manual annotations. Our evaluation analyzes the impact of orientation offset on 3D detection accuracy, and demonstrates successful generalization of the learned model to real underwater photographs of the target robot.
Intrinsic Raman Spectroscopy Improves Analyte Concentration Measurements in Turbid Media (2006)

We present a new technique, intrinsic Raman spectroscopy, which utilizes diffuse reflectance to correct sample turbidity-induced distortions in Raman spectra. This technique allows for improved analyte concentration measurements in turbid media.
Towards grasping in unstructured environments: optimization of grasper compliance and configuration (2004)

This paper examines the role of grasper compliance and kinematic configuration in unstructured environments, where object size and location may not be well known. A grasper consisting of two two-link planar fingers with compliant revolute joints was simulated as it passively deflects during contact with a target object. The kinematic configuration and joint stiffness values of the grasper were varied in order to maximize grasper workspace for a wide range of target object size. The results show a near-optimal result around the spring-rest angles of 25 and 45 degrees for the base and intermediate joints, respectively, when the joint stiffness ratio (base/intermediate) was small.
A Journey Through the Landscapes of Small Particles in Binary Colloidal Assemblies: Unveiling Structural Transitions from Isolated Particles to Clusters upon Variation in Composition (2019)

Two-dimensional (2D) amorphous binary colloidal assemblies composed of particles of two different sizes are characterized by the loss of hexagonal close-packing for larger particles, occurring when the size ratio between small (S) and large (L) particles dSdL exceeds a certain threshold value. For moderately low particle number ratios NSNL large particles still retain a denser arrangement with transitions from hexagonal symmetry to the coexistence of different types of symmetries as NSNL progressively departs from 0 to higher values. On the other hand, small particles reveal sparser arrangements: shape identification and quantification of structural transitions in small particle arrangements appear particularly challenging. In this article, we investigate their shapes and transitions for amorphous binary colloidal particles assembled at the air/water interface. For the quantitative characterization of the evolution in particle arrangements for NSNL variable between 0.5 and 2, we develop an innovative procedure for morphological analysis, combining Minkowski functionals, Voronoi diagrams and ad hoc techniques to recognize and classify specific features. Such a powerful approach has revealed a wide variety of landscapes featuring isolated particles, dimers, chains, small clusters evolving with the colloidal suspension composition. Our method can be applied to the analysis of spatial configurations of sparse colloidal patterns obtained in different conditions.
On the multiple unicast capacity of 3-source, 3-terminal directed acyclic networks (2013)

We consider the multiple unicast problem with three source-terminal pairs over directed acyclic networks with unit-capacity edges. The three $s_i-t_i$ pairs wish to communicate at unit-rate via network coding. The connectivity between the $s_i - t_i$ pairs is quantified by means of a connectivity level vector, $[k_1 k_2 k_3]$ such that there exist $k_i$ edge-disjoint paths between $s_i$ and $t_i$. In this work we attempt to classify networks based on the connectivity level. It can be observed that unit-rate transmission can be supported by routing if $k_i \geq 3$, for all $i = 1, \dots, 3$. In this work, we consider, connectivity level vectors such that $\min_{i = 1, \dots, 3} k_i &lt; 3$. We present either a constructive linear network coding scheme or an instance of a network that cannot support the desired unit-rate requirement, for all such connectivity level vectors except the vector $[1~2~4]$ (and its permutations). The benefits of our schemes extend to networks with higher and potentially different edge capacities. Specifically, our experimental results indicate that for networks where the different source-terminal paths have a significant overlap, our constructive unit-rate schemes can be packed along with routing to provide higher throughput as compared to a pure routing approach.
Demonstration of high data density recording on direct overwrite magneto-optical disk (1992)

Next generation Magneto-Optical (MO) disks must support high density recording; 0.5 μm/bit to 0.6 μm/bit which is twice the first generation recording density. They should also support direct overwrite (DOW). With this in mind, we have previously demonstrated that by adding a GdFeCo Readout layer which has no effect on the DOW function, the C/N of DOW-MO disks has been improved by 3 dB and it could be several dB higher than the C/N of first generation MO disks. Using this improved DOW-MO disk, we have achieved 21 % window margin at 0.54 μm/bit recording density using pulse width modulation.
Can CPUs Match GPUs on Performance with Productivity?: Experiences with Optimizing a FLOP-intensive Application on CPUs and GPU (2010)

In this work, we evaluate performance of a real-world image processing application that uses a cross-correlation algorithm to compare a given image with a reference one.The algorithm processes individual images represented as 2-dimensional matrices of single-precision floating-point values using (n 4 ) operations involving dot-products and additions.We implement this algorithm on a NVIDIA Fermi GPU (Tesla 2050) using CUDA, and also manually parallelize it for the Intel Xeon X5680 (Westmere) and IBM Power7 multi-core processors.Pthreads and OpenMP with SSE and VSX vector intrinsics are used for the manually parallelized version on the multi-core CPUs.A number of optimizations were performed for the GPU implementation on the Fermi, including blocking for Fermi's configurable on-chip memory architecture.Experimental results illustrate that on a single multi-core processor, the manually parallelized versions of the correlation application perform only a small order of factor slower than the CUDA version executing on the Fermi -1.005s on Power7, 3.49s on Intel X5680, and 465ms on Fermi.On a two-processor Power7 system, performance approaches that of the Fermi (650ms), while the Intel version runs in 1.78s.These results conclusively demonstrate that performance of the GPU memory subsystem is critical to effectively harness its computational capabilities.For the correlation application, a significantly higher amount of effort was put into developing the GPU version when compared to the CPU ones (several days against few hours).Our experience presents compelling evidence that performance comparable to that of GPUs can be achieved with much greater productivity on modern multi-core CPUs.
Solar heated beehives (1985)

A new translucent plastic cover for bee hives is described which will serve as a passive solar collector and insulator. Scientists at the USDA-ARS designed the cover to maintain bees in cold weather. It should be of interest to beekeepers in northern states who have had to destroy colonies to avoid overwintering costs.
Direct Determination of Grain Boundary Atomic Structure in SrTiO 3 (1994)

An atomic structure model for a 25 degrees [001] symmetric tilt grain boundary in SrTiO(3) has been determined directly from experimental data with the use of high-resolution Z-contrast imaging coupled with electron energy loss spectroscopy. The derived model of the grain boundary was refined by bond-valence sum calculations and reveals candidate sites for dopant atoms in the boundary plane. These results show how the combined techniques can be used to deduce the atomic structure of defects and interfaces without recourse to preconceived structural models or image simulations.
Atomic layer deposition for fabricating capacitive micromachined ultrasonic transducers: initial characterization (2005)

In this paper, we examine the utility of a new method for fabricating capacitive micromachined ultrasonic transducers (CMUTs). The method is based on atomic layer deposition (ALD) technology, which uses a self-limiting binary reaction process to produce ultra-thin membranes. Advantages of ALD include precise control of dimensions including gap-width between the capacitor plates, membrane thickness and radius, lower cost due to a reduction in the number of fabrication steps, the potential to use a large variety of materials, and increased reliability due to the enhanced surface quality of the membranes. These capabilities promise fabrication of transducers with superior operating characteristics. However, no study has yet documented sensitivity and power requirements for CMUTs created using ALD. We present here a first-order mechanical and equivalent circuit analysis along with a fabrication process to create and characterize CMUTs using ALD. Results show that these systems have the potential for excellent sensitivity and decreased power requirements. Work to test the fabricated elements is currently underway.
ChemInform Abstract: Room‐Temperature Pd‐Catalyzed Amidation of Aryl Bromides Using tert‐Butyl Carbamate. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A General Method of Synthesis of Regiospecifically N-Oxidized or N-Quaternized Polyazines by Palladium-Catalyzed Cross-Coupling of N-Oxidized or N-Quaternized Hetaryl Stannanes (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA General Method of Synthesis of Regiospecifically N-Oxidized or N-Quaternized Polyazines by Palladium-Catalyzed Cross-Coupling of N-Oxidized or N-Quaternized Hetaryl StannanesJohn A. Zoltewicz and Michael P. Cruskie Jr.Cite this: J. Org. Chem. 1995, 60, 11, 3487–3493Publication Date (Print):June 1, 1995Publication History Published online1 May 2002Published inissue 1 June 1995https://pubs.acs.org/doi/10.1021/jo00116a040https://doi.org/10.1021/jo00116a040research-articleACS PublicationsRequest reuse permissionsArticle Views361Altmetric-Citations17LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts