gebhart/patrepeval huggingface dataset:
JSmol and the Next‐Generation Web‐Based Representation of 3D Molecular Structure as Applied to <i>Proteopedia</i> (2013)

Abstract Although Java does not run on some handheld devices, e.g., iPads and iPhones, JavaScript does. The development of JSmol, a JavaScript‐only version of Jmol, is described, and its use in Proteopedia is demonstrated. A key aspect of JSmol is that it includes the full implementation of the entire set of Jmol functionalities, including file reading and writing, scripting, and rendering. The relative performances of Java‐based Jmol and JavaScript‐only JSmol are discussed. We can now confirm that the guiding principles of Java programming can be completely and relatively straightforwardly transformed directly into JavaScript, requiring no Java applet, and producing identical graphical results. JSmol is thus the first full‐featured molecular viewer, and the first ever viewer for proteins, which can be utilized with an internet browser on handheld devices lacking Java. Since the MediaWiki features of Proteopedia have been modified to optionally use JSmol, the wealth of crowd‐sourced content in Proteopedia is now directly available on such devices, without the need to download any additional applet.
56 Gb/s transmission over 100m OM3 using 25G-class VCSEL and discrete multi-tone modulation (2014)

We report experimental data demonstrating 56 Gb/s VCSEL transmission over 100m OM3, and 40 Gb/s transmission over 200m OM3 using discrete multi-tone modulation. This result is achieved with a conventional 850nm 25G-class VCSEL.
An autocrine loop directed by the vascular endothelial growth factor promotes invasiveness of human melanoma cells. (2005)

The vascular endothelial growth factor-A (VEGF-A) is a cytokine that promotes angiogenesis through the activation of two tyrosine kinase receptors, VEGFR-1 and VEGFR-2, on vascular endothelial cells. Moreover, several experimental evidences indicate that VEGF-A may also play a role in tumor progression by acting on neoplastic cells expressing VEGFRs. In this study we show that human melanoma cells that simultaneously produce VEGF-A and express VEGFRs exhibit a higher spontaneous ability to invade the extracellular matrix (ECM) than melanoma cells not expressing either VEGF-A or VEGFRs. Exposure of VEGFR expressing melanoma cells to exogenous VEGF-A further increases their ability to invade the ECM. Moreover, an inhibitor of VEGFR tyrosine kinase activity is able to abrogate VEGF-A-induced stimulation of ECM invasion. A cell clone (13443/N2) derived from a VEGF-A responsive melanoma cell line and expressing high levels of VEGFR-2 invades the ECM eight-fold more efficiently than a cell clone derived from the same cell line and expressing extremely low levels of the receptor. Exposure of 13443/N2 cells to VEGF-E, which selectively binds and activates VEGFR-2, increases their ability to invade the ECM. Finally, the expression of the VEGF-A mRNA antisense sequence in 13443/N2 cells markedly reduces the release of VEGF-A and ECM invasion. In conclusion, our data show for the first time that a VEGF-A-driven autocrine loop promotes human melanoma cell ability to invade the ECM, and strongly support the hypothesis that activation of VEGFR-2 plays a primary role in this process.
New Formula of Pollen Supplemental Diets to Study Honey Bee (Apis mellifera carnica) Attractiveness (2014)

The present work aimed to examine the attractiveness of ten new pollen supplemental diets to honey bees (Apis mellifera) through evaluating the consumption rate, besides their efficiency in supporting the colony through measuring colony growth (sealed workers brood area). Twelve materials were used and mixed with honey bee in different proportions forming diets taking numbers from 1 to 10. These materials were flours of: gram seeds, beans seeds, pea seeds, fenugreek seeds, coriander seeds, cumin seeds, anise seeds, white kidney beans seeds, caraway seeds, rice seeds, fennel seeds and oats. Diets were consumed at rates that were comparable to the control (sugar candy). Generally differences among consumption rates of supplemental pollen diets were highly significant. The highest consumed amounts were recorded in colonies fed on diet (1); 47.42gm/ colony in average, mix. (2); 43.35 gm/ colony in each week. While the lowest consumption rate (27.3 gm/ colony) in each week was recorded for diet no. 10 in average. There was a significant relationship between the amount of diet consumed and the increase in workers sealed brood area. Where colonies fed with mixture diets from gram seeds (Diet 2), dried pea with rice, fennel and fenugreek (Diet 3), dried beans seeds with fennel seeds (Diet 4) and oats, rice, anise seeds (Diet 1), showed 53.71%, 38.44%, 35.98% and 5.85% more brood area than control ones.
Phase III Randomized Trial of FOLFIRI Versus FOLFOX4 in the Treatment of Advanced Colorectal Cancer: A Multicenter Study of the Gruppo Oncologico Dell’Italia Meridionale (2005)

There is no difference in ORR, TTP, and OS for patients treated with the FOLFIRI or FOLFOX4 regimen. Both therapies seemed effective as first-line treatment in these patients. The difference between these two combination therapies is mainly in the toxicity profile.
An active position sensing tag for sports visualization in American football (2013)

Remote experience and visualization in sporting events can be significantly improved by providing accurate tracking information of the players and objects in the event. Sporting events such as American football or rugby have proved difficult for camera- and radio-based tracking due to blockage of the line-of-sight, or proximity of the ball to groups of players. Magnetoquasistatic fields have been shown to enable accurate position and orientation sensing in these environments [1]-[3]. In this work, we introduce a magnetoquasistatic tag developed for tracking an American football during game-play. We describe its integration into an American football and demonstrate its use in game-play during a collegiate American football practice.
Computer-aided modeling and evaluation of reconfigurable VLSI processor arrays with VHDL (1992)

The authors present an integrated computer-aided design environment, the VAR (VHDL-based array reconfiguration) system, for the tasks of design, reconfiguration, simulation, and evaluation in an architecture modeled by VHDL. An easily diagnosable and reconfigurable two-dimensional defect-tolerant processing element (PE) switch lattice array is used as an example to illustrate the methodology of VAR. VAR allows the designers study and evaluate fault diagnosis and reconfiguration algorithms by inserting faults, which are generated based on manufacturing yield data, into the array and then locating the fault PEs as well as simulating the reconfiguration process. Thus, VAR can assist the designers in evaluating the different combinations of fault patterns, fault diagnosis algorithms, and reconfigurable architectures through a complete set of figures of merit which aim at architectural improvements. Extensive simulation and evaluation have been performed to demonstrate and support the effectiveness of VAR.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
SHIVA: Simulated Highways for Intelligent Vehicle Algorithms (2002)

SHIVA (Simulated Highways for Intelligent Vehicle Algorithms) addresses deficiencies present in existing microscopic traffic simulators with: realistic sensor modeling; support for communicating vehicles; a variety of driver models; and efficient integration with real robots. SHIVA runs on Sun Sparcstations (under X) and SGI workstations (using Inventor). Class hierarchies for vehicles, sensors and displays allow users to develop algorithms for specific vehicle/sensor configurations and to debug them with graphical viewing tools. Simulated scenarios can be interactively displayed online in 3-D. Off-line execution is also available if only statistics (such as throughput) are desired.
Predicting effectiveness of cardiac resynchronization therapy based on QRS decomposition using the Meyer orthogonal wavelet transformation (2010)

Cardiac resynchronization therapy (CRT) has shown clinical benefit for patients with heart failure (HF). However, up to one third of these patients do not respond to CRT. The aim of this study is to determine if specific conduction abnormalities are common to patients who respond to CRT and if these can be identified and quantified on the surface ECG. A signal averaging algorithm was developed to enhance the QRS features and decrease the noise level. Then, a Meyer orthogonal wavelet transformation was applied to the ECG to decompose the QRS. The receiver operating characteristic curve (ROC) showed that a combination of wavelet coefficients with clinical factors allowed 80% of sensitivity and specificity using the signal from either lead X or Z. Our preliminary results indicate that time-scale decomposition of the high-resolution QRS signal contains information on predicting individuals' response to CRT.
Atomic structure and electronic properties of single-wall carbon nanotubes probed by scanning tunneling microscope at room temperature (1998)

A detailed three-dimensional structural analysis of single-walled carbon nanotubes was carried out using a scanning tunneling microscope (STM) operated at room temperature in ambient conditions. On a microscopic scale, the images show tubes condensed in ropes as well as tubes which are separated from each other. For a single-wall nanotube rope, the outer portion is composed of highly oriented nanotubes with nearly uniform diameter and chirality. On separated nanotubes, atomically resolved images show variable chirality ranges between 0°–30°, and variable diameter (1–3 nm), with no one type dominant. From STM and scanning tunneling spectroscopy measurements we confirmed the correlation between chirality and the electronic properties, namely the tuning from metallic to semiconducting. We also observed a rectifying behavior correlated with the chiral angle of 25°, an important observation for nanodevices application.
A unique lateral displacement of a Gaussian beam transmitted through a slab with negative permittivity and permeability (2002)

Abstract This Letter demonstrates a unique negative lateral shift of a Gaussian beam transmitted through a slab with both negative permittivity and permeability, which is distinctly different from a shift caused by a regular dielectric slab. The incident beam is modeled as a tapered wave with a Gaussian spectrum. The waves inside and outside the slab are solved analytically from Maxwell's equations by matching the boundary conditions at the interfaces. It is shown that the field values in all regions can be unambiguously determined. Numerical simulations are presented and the field values as well as the power densities are computed for all regions. A dramatic negative lateral shift is observed when both ε and μ are negative. © 2002 Wiley Periodicals, Inc. Microwave Opt Technol Lett 33: 136–139, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10255
Comparison of Hexagonal and Square Dot Centers for EP Halftones. (2000)

Hexagonal dot packing seems to offer benefits for halftone printing compared to conventional square dot packing, but little practical experience has been reported. Taking advantage of recent refinements in digital electrophotographic (EP) printer technology, the authors conducted experiments on a commercially deployable system to assess whether the potential advantages of hexagonal dot packing are economically exploitable. Keywords: hexagonal, halftone, spot function, spectrogram Introduction Digital printing has nearly always been accomplished by round dots organized on rectangular grids. It is understood that the improved packing efficiency of hexagonal grids for round dots would be more easily achieved than rectangular dots for rectangular grids, but evidently neither hexagonal grids nor rectangular dots have generally been considered worthwhile. Ulichney [1] addressed halftone theory for hexagonal grids. Average dot overlap can be reduced, since smaller dots can ensure 100 perce...
Shared Resource for Collaborative Editing over a Wireless Network (2011)

Today hand-held consumer devices such as Smartphones and Mobile Internet Devices\nare getting more and more powerful and feature rich. They are no longer only built with\nnetwork capabilities through a cellular network such as GSM or 3G, but also high\nspeed Wireless Local Area Networks which opens up more possibilities.<br>\nWhile Internet based applications, such as Web browsers, E-mail clients, and Multimedia\nbased applications have been the major part of the market, programs using\nproperties of a distributed system are sparse.<br>\nThis Thesis report describes the background, design choices and development of an\napplication using distributed group communication techniques to create a collaborative\nwork space on a typical Smartphone. It also shows how to use this to implementation\na Whiteboard application. It explores the possibilites of using well known protocols,\nstandards as well as Free Software for solving the various problems associated with these\nfunctions, such as presence discovery, group communication and whiteboarding.<br><br>\nDagens bärbara handdatorer såsom Smartphones och mobila internetenheter blir hela\ntiden kraftigare och mer funktionsrika. De är inte längre endast byggda med nätverksmöjligheter via ett mobiltelefonnätet som till exempel GSM eller 3G, utan även också\nmed lokala trådlösa höghastighetsnätverk vilket öppnar upp nya möjligheter.<br>\nDå internetbaserade applikationer, såsom webläsare och e-mailklienter, samt multimediabaserade\napplikationer har varit en stor del av marknaden, program som använder\negenskaper hos ett distribuerat nätverk är mer ovanligt.<br>\nDet här examensarbetet beskriver bakgrunden, designval samt utveckling av en applikation\nsom använder distribuerad gruppkommunikationstekniker för att skapa en kollaborativ\narbetsyta på en typisk Smartphone. Det visas också hur detta går att använda\nför att implementera en Whiteboard-applikation. Möjligheterna att använda välkända protokoll, standarder samt fri mjukvara för att lösa de problem anknytna till funktionerna,\nsåsom upptäcka närliggande enheter, gruppkommunikation och whiteboarding, utforskas\ni den här rapporten.
Synthesis of Highly Substituted Pyrroles via a Multimetal-Catalyzed Rearrangement−Condensation−Cyclization Domino Approach (2006)

[reaction: see text] In a convenient one-pot process, easily accessed propargyl vinyl ethers and aromatic amines are effectively converted into tetra- and pentasubstituted 5-methylpyrroles which can further be transformed into 5-formylpyrroles via IBX-mediated oxidation. The cascade reaction proceeds through a silver(I)-catalyzed propargyl-Claisen rearrangement, an amine condensation, and a gold(I)-catalyzed 5-exo-dig heterocyclization.
Phase Behavior and Polymorphism of Organic Crystals Confined within Nanoscale Chambers (2009)

Controlling polymorphism, the ability of a compound to adopt more than one solid-state structure, often relies on empirical manipulations of conditions such as solvent, temperature, and mode of crystallization. Despite a growing interest in nanocrystalline formulations, however, the influence of crystal size on polymorph formation and stability is largely unexplored. Nanocrystals of pimelic acid, HO2C(CH2)n-2CO2H (n = 7), glutaric acid (n = 5), suberic acid (n = 8), and coumarin (1,2-benzopyrone) in nanometer-scale pores of controlled pore glass (CPG) beads and hexagonally ordered cylindrical pores of poly(cyclohexylethylene) (p-PCHE) monoliths exhibit size-dependent polymorphism and thermotropic behavior because of the physical constraints imposed by the dimensions of the pores. Pimelic acid, suberic acid, and coumarin also exhibit heretofore unknown polymorphs, denoted δ-pimelic acid, β-suberic acid, and β-coumarin, in CPG with pore sizes <23 nm and p-PCHE with pore diameters <40 nm. The melting points of the confined crystals decrease monotonically with decreasing pore size, and the enantiotropic phase behavior of bulk glutaric acid and suberic acid switches to monotropic when confined within the nanoscale pores of CPG and p-PCHE. Collectively, these results reveal that nanometer-scale size confinement can alter crystallization outcomes and affect polymorph stability compared with bulk crystallization. Moreover, crystallization in very small pores can lead to the discovery of new polymorphs that otherwise would not be detected using conventional screening methods.
High-content screening identifies a role for Na <sup>+</sup> channels in insulin production (2015)

Insulin production is the central feature of functionally mature and differentiated pancreatic β-cells. Reduced insulin transcription and dedifferentiation have been implicated in type 2 diabetes, making drugs that could reverse these processes potentially useful. We have previously established ratiometric live-cell imaging tools to identify factors that increase insulin promoter activity and promote β-cell differentiation. Here, we present a single vector imaging tool with eGFP and mRFP, driven by the Pdx1 and Ins1 promoters, respectively, targeted to the nucleus to enhance identification of individual cells in a high-throughput manner. Using this new approach, we screened 1120 off-patent drugs for factors that regulate Ins1 and Pdx1 promoter activity in MIN6 β-cells. We identified a number of compounds that positively modulate Ins1 promoter activity, including several drugs known to modulate ion channels. Carbamazepine was selected for extended follow-up, as our previous screen also identified this use-dependent sodium channel inhibitor as a positive modulator of β-cell survival. Indeed, carbamazepine increased Ins1 and Ins2 mRNA in primary mouse islets at lower doses than were required to protect β-cells. We validated the role of sodium channels in insulin production by examining Nav1.7 (Scn9a) knockout mice and remarkably islets from these animals had dramatically elevated insulin content relative to wild-type controls. Collectively, our experiments provide a starting point for additional studies aimed to identify drugs and molecular pathways that control insulin production and β-cell differentiation status. In particular, our unbiased screen identified a novel role for a β-cell sodium channel gene in insulin production.
Altered surface trafficking of presynaptic cannabinoid type 1 receptor in and out synaptic terminals parallels receptor desensitization (2008)

Presynaptic cannabinoid type 1 receptors (CB1Rs) are major mediators of retrograde synaptic plasticity at both excitatory and inhibitory synapses and participate in a plethora of physiological functions. Whether presynaptic receptors, such as CB1R, display functionally relevant movements at the surface of neuronal membranes is not known. We analyzed the lateral mobility of native CB1Rs in cortical neurons by using single-quantum dot imaging. We found that CB1Rs are highly mobile and rapidly diffuse in and out of presynapses. Agonist-induced desensitization correlated with a reduction in the fraction of surface CB1Rs and a drastic decrease in the membrane dynamic of the CB1Rs that remained at the presynaptic surface. Desensitization specifically excluded CB1Rs from synapses and increased the fraction of immobile receptors in the extrasynaptic compartment. The results suggest that decrease of mobility may be one of the core mechanisms underlying the desensitization of CB1R, the most abundant G protein-coupled receptor in the brain.
Source Identification Using Acoustic Array Techniques (1995)

<div class="htmlview paragraph">Acoustic array techniques are presented as alternatives to intensity measurements for source identification in automotive and industrial environments. With an understanding of the advantages and limitations described here for each of the available methods, a technique which is best suited to the application at hand may be selected. The basic theory of array procedures for Nearfield Acoustical Holography, temporal array techniques, and an Inverse Frequency Response Function technique is given. Implementation for various applications is discussed. Experimental evaluation is provided for tire noise identification.</div>
Ribosomal Incorporation of Consecutive β-Amino Acids (2018)

Due to their unique characteristics, which are not shared by canonical α-peptides, peptides that contain stretches of consecutive β-amino acids are attractive scaffolds for novel peptide drugs and nanomaterials. Although ribosomal incorporation of single or nonconsecutive β-amino acids into peptides has previously been reported, the incorporation of consecutive β-amino acids has not yet been accomplished. This is primarily due to their incompatibility with the ribosomal translation system. Here, we took advantage of engineered β-aminoacyl-tRNAs bearing optimized T-stem and D-arm motifs for enhancing binding affinity to EF-Tu and EF-P, respectively. Combined with a reconstituted E. coli translation system and optimized translation factor concentrations, up to seven consecutive β-amino acids could be incorporated into a model peptide. Furthermore, the synthesis of macrocyclic β-peptides closed by a thioether bond between two d-α-amino acids is also demonstrated. This represents the first example of the ribosomal synthesis of peptides containing stretches of consecutive β-amino acids.
Delayed Nogo receptor therapy improves recovery from spinal cord contusion (2006)

NgR(310)ecto-Fc treatment improves outcome in a rodent model that closely mimicked human spinal cord injury.
Effects of Escherichia coli Shiga-like toxins (verotoxins) in pigs. (1989)

Escherichia coli K12 strains TB1(pCG5), with the genes for Shiga-like toxin IIv from an edema disease isolate of E. coli and TB1(pCG5-1), with the toxin genes inactivated by transposon mutagenesis, were used to test the hypothesis that Shiga-like toxin IIv was the same as edema disease principle. Ammonium sulfate precipitated culture supernatants from the pair of E. coli K12 strains and from a wild edema disease isolate of E. coli (E145) were tested for their ability to induce signs and lesions of edema disease in intravenously inoculated weaned pigs. Similar preparations from E. coli which produce Shiga-like toxins I and II were also tested. Preparations from E. coli TB1 (pCG5) and E145 contained high levels of Shiga-like toxin IIv and induced signs and lesions similar to those seen in edema disease, whereas preparations from E. coli TB1 (pCG5-1) failed to induce signs or lesions of edema disease. All Shiga-like toxin preparations produced delayed neurological signs, fibrinoid necrosis of arterioles and hemorrhages in the cerebellum of pigs. High doses of Shiga-like toxin IIv were associated with superficial necrosis of the colonic epithelium and vasculitis. Shiga-like toxins I and II resulted in kidney lesions but no enteric pathology. Shiga-like toxin II preparations had the lowest median lethal dose for pigs, Shiga-like toxin IIv was intermediate and Shiga-like toxin I was the least toxic.
Water sorption in cellulose-based hydrogels (1996)

Sorption of distilled water in a cellulose-based hydrogel is presented. The examined system is based on a mixture of sodium salt of carboxymethylcellulose and hydroxyethylcellulose, crosslinked with divinilsulphone. The effect of chemical composition, manufacturing procedures, as well as desiccation protocols on equilibrium water uptake was investigated. Experimental results were interpreted in terms of crosslinking density, presence of ionic groups on the backbone, as well as macroscopic sample morphology detected by electron scanning microscopy. The reported results evidence the possibility to bias the process parameters in order to obtain hydrogels characterized by the desired water sorption levels. © 1996 John Wiley & Sons, Inc.