gebhart/patrepeval huggingface dataset:
A parallel mesh generation algorithm based on the vertex label assignment scheme (1989)

Abstract In this article a new mesh generation algorithm is presented. The algorithm is based on a new approach called the vertex label assignment scheme to provide the information for the mesh generation so that parallel processing becomes possible. The algorithm generates 2D meshes of quadrilaterals on the basis of individual faces; conformity and smoothness of the resultant mesh are automatically assured. Local and selective mesh‐refinements are also supported. A regular quadrilateral network which defines the geometry of the problem and an associated subdivision level assignment which specifies mesh density data on the network are the only input information.
A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas (2005)

F-values and real TFBS occurrences calculated for human, chimp, mouse, rat, zebrafish and fugu genomes are available for free download at http://www.gmu.edu/departments/mmb/baranova/pages/bioinformatics
A one-pot reaction for biorefinery: combination of solid acid and base catalysts for direct production of 5-hydroxymethylfurfural from saccharides (2009)

5-Hydroxymethylfurfural (HMF), one of the most important intermediates derived from biomass, was directly produced from monosaccharides (fructose and glucose) and disaccharides (sucrose and cellobiose) by a simple one-pot reaction including hydrolysis, isomerization and dehydration using solid acid and base catalysts under mild conditions.
Bonding behavior of ultrahigh strength unsintered hydroxyapatite particles/poly(L‐lactide) composites to surface of tibial cortex in rabbits (1999)

Unsintered hydroxyapatite particles/poly(l-lactide) (u-HA/PLLA) composites with an initial bending strength of up to 270 MPa were developed based on the hypothesis that inclusion of u-HA particles in a PLLA matrix might enhance bone bonding. The purpose of this study was to examine the bonding strength and behavior of these u-HA/PLLA composites on the surface of the bone cortex. Composites containing 30 (u-HA30), 40 (u-HA40), or 50 wt % (u-HA50) of fine u-HA particles (3-μm average particle size) were prepared. Semicolumnar plates of these composites and control PLLA plates were fixed with metal screws to the surface of both proximal tibial cortices in 45 rabbits. The loads required to detach the plates from the bone cortex surface, defined as the bonding strengths, were measured at 4, 8, and 25 weeks after implantation. Bonding strengths in the u-HA30 group at 8 weeks and in the u-HA40 and u-HA50 groups at each postimplantation time were significantly greater than in the PLLA group (post hoc test using Fisher's protected least significant difference method). At each postimplantation time histological examinations revealed direct contact between the bone and the u-HA/PLLA composite plates without any intervening fibrous tissue. There was no evidence of any inflammatory or foreign-body response in any group throughout the follow-up periods. The results of this study suggest that the biodegradable PLLA fixation plates amended with u-HA particles could be functionally superior to PLLA plates without particles. © 1999 John Wiley & Sons, Inc. J. Biomed Mater Res, 47, 412–419, 1999.
Comparison of ion channels in multidrug-resistant and -sensitive human leukemic cells. (1988)

Tumor cell lines selected to grow in the presence of one "natural product" antineoplastic drug often develop cross-resistance to others. This multidrug resistance (MDR) is believed to be a major problem in cancer therapy. Organic Ca2+-channel blockers, such as verapamil, can reverse this resistance and render MDR cells in culture nearly as sensitive to the antineoplastic drugs as the drug-sensitive cells from which they were derived. It has therefore been suggested that Ca2+ channels may play a role in MDR. To determine directly whether there are electrophysiological correlates of MDR, we used whole-cell and single-channel patch-clamp techniques to survey the ion channels in a drug-sensitive human T-cell leukemia line, CCRF-CEM, and a MDR variant, CEM/VLB100. We found no evidence for a voltage-gated Ca2+ channel. However, we did identify three other current/channel types: a voltage-gated tetrodotoxin-sensitive inward current carried by Na+, a voltage-gated labile outward current carried by K+, and a nonselective cation channel reversing at 0 mV. Drug-sensitive and -resistant cells were the same with respect to the level of expression of these channels.
Microfibrillar network of a rigid rod polymer. 2. Small-angle x-ray scattering (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMicrofibrillar network of a rigid rod polymer. 2. Small-angle x-ray scatteringYachin Cohen and Edwin L. ThomasCite this: Macromolecules 1988, 21, 2, 436–441Publication Date (Print):February 1, 1988Publication History Published online1 May 2002Published inissue 1 February 1988https://pubs.acs.org/doi/10.1021/ma00180a026https://doi.org/10.1021/ma00180a026research-articleACS PublicationsRequest reuse permissionsArticle Views207Altmetric-Citations24LEARN 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
The Angiosperm Gibberellin-GID1-DELLA Growth Regulatory Mechanism: How an “Inhibitor of an Inhibitor” Enables Flexible Response to Fluctuating Environments (2009)

The phytohormone gibberellin (GA) has long been known to regulate the growth, development, and life cycle progression of flowering plants. However, the molecular GA-GID1-DELLA mechanism that enables plants to respond to GA has only recently been discovered. In addition, studies published in the last few years have highlighted previously unsuspected roles for the GA-GID1-DELLA mechanism in regulating growth response to environmental variables. Here, we review these advances within a general plant biology context and speculate on the answers to some remaining questions. We also discuss the hypothesis that the GA-GID1-DELLA mechanism enables flowering plants to maintain transient growth arrest, giving them the flexibility to survive periods of adversity.
C–C Bond Formation via Copper-Catalyzed Conjugate Addition Reactions to Enones in Water at Room Temperature (2012)

Conjugate addition reactions to enones can now be done in water at room temperature with in situ generated organocopper reagents. Mixing an enone, zinc powder, TMEDA, and an alkyl halide in a micellar environemnt containing catalytic amounts of Cu(I), Ag(I), and Au(III) leads to 1,4-adducts in good isolated yields: no organometallic precursor need be formed.
The case for registered routing switches in field programmable gate arrays (2001)

FPGAs are characterized by a programmable interconnect that contains highly resistive and capacitive elements. While the configurable structure of the interconnect allows for the implementation of arbitrary circuits, it has also become a significant bottleneck for high-speed circuits. Even if there are only a few signal paths that run along long stretches of interconnect, it is these paths that may determine the maximum operating frequency of the circuit.
Cellular morphogenesis in the Saccharomyces cerevisiae cell cycle: localization of the CDC3 gene product and the timing of events at the budding site. (1991)

Budding cells of the yeast Saccharomyces cerevisiae possess a ring of 10-nm-diameter filaments, of unknown biochemical nature, that lies just inside the plasma membrane in the neck connecting the mother cell to its bud. Electron microscopic observations suggest that these filaments assemble at the budding site coincident with bud emergence and disassemble shortly before cytokinesis (Byers, B. and L. Goetsch. 1976. J. Cell Biol. 69:717-721). Mutants defective in any of four genes (CDC3, CDC10, CDC11, or CDC12) lack these filaments and display a pleiotropic phenotype that involves abnormal bud growth and an inability to complete cytokinesis. We showed previously by immunofluorescence that the CDC12 gene product is probably a constituent of the ring of 10-nm filaments (Haarer, B. and J. Pringle. 1987. Mol. Cell. Biol. 7:3678-3687). We now report the use of fusion proteins to generate polyclonal antibodies specific for the CDC3 gene product. In immunofluorescence experiments, these antibodies decorated the neck regions of wild-type and mutant cells in patterns suggesting that the CDC3 gene product is also a constituent of the ring of 10-nm filaments. We also used the CDC3-specific and CDC12-specific antibodies to investigate the timing of localization of these proteins to the budding site. The results suggest that the CDC3 protein is organized into a ring at the budding site well before bud emergence and remains so organized for some time after cytokinesis. The CDC12 product appears to behave similarly, but may arrive at the budding site closer to the time of bud emergence, and disappear from that site more quickly after cytokinesis, than does the CDC3 product. Examination of mating cells and cells responding to purified mating pheromone revealed novel arrangements of the CDC3 and CDC12 products in the regions of cell wall reorganization. Both proteins were present in normal-looking ring structures at the bases of the first zygotic buds.
Deep2Full: Evaluating strategies for selecting the minimal mutational experiments for optimal computational predictions of deep mutational scan outcomes (2020)

Performing a complete deep mutational scan with all single point mutations may not be practical, and may not even be required, especially if predictive computational models can be developed. Computational models are however naive to cellular response in the myriads of assay-conditions. In a realistic paradigm of assay context-aware predictive hybrid models that combine minimal experimental data from deep mutational scans with structure, sequence information and computational models, we define and evaluate different strategies for choosing this minimal set. We evaluated the trivial strategy of a systematic reduction in the number of mutational studies from 85% to 15%, along with several others about the choice of the types of mutations such as random versus site-directed with the same 15% data completeness. Interestingly, the predictive capabilities by training on a random set of mutations and using a systematic substitution of all amino acids to alanine, asparagine and histidine (ANH) were comparable. Another strategy we explored, augmenting the training data with measurements of the same mutants at multiple assay conditions, did not improve the prediction quality. For the six proteins we analyzed, the bin-wise error in prediction is optimal when 50-100 mutations per bin are used in training the computational model, suggesting that good prediction quality may be achieved with a library of 500-1000 mutations.
Headspace Solid-Phase Microextraction Method for the Study of the Volatility of Selected Flavor Compounds (2002)

Changes in the volatility of selected flavor compounds in the presence of nonvolatile food matrix components were studied using headspace solid-phase microextraction (HS-SPME) combined with GC-MS quantification. Time-dependent adsorption profiles to the SPME fiber and the partition coefficients between different phases were obtained for several individual volatiles, showing that HS-SPME analysis with a short sampling time can be used to determine the "true" headspace concentration at equilibrium between the headspace and a sample matrix. Equilibrium dialysis followed by HS-SPME/GC-MS was carried out to confirm the ability of HS-SPME extraction for monitoring the free volatile compounds in the presence of proteins. In particular, a short sampling time (1 min) avoided additional extraction of volatiles bound to the protein. Interactions between several selected flavor compounds and nonvolatile food matrix components [beta-lactoglobulin or (+)-catechin] were also studied by means of HS-SPME/GC-MS analysis. The volatility of ethyl hexanoate, heptanone, and hexanal was significantly decreased by the addition of beta-lactoglobulin compared to that of isoamyl acetate. Catechin decreased the volatility of ethyl hexanoate and hexanal by 10-20% and increased that of 2-heptanone by approximately 15%. This study indicates that HS-SPME can be a useful tool for the study of the interactions between volatile compounds and nonvolatile matrix components provided the kinetic and thermodynamic behavior of the volatiles in relation to the fiber chosen for the studies is carefully considered.
Ultrasonic Infiltration in Alumina Fiber/Molten Aluminum System (1993)

This study was aimed to improve the wettability of a non-wetting Al2O3 fiber/molten aluminum system, so as to attain full infiltration with a low applied pressure (Pa). The threshold infiltration pressure (Pc) of this composite system with an average fiber volume fraction (Vf) of 0.17 is 139 kPa at a molten aluminum temperature of 1023 K in pressure infiltration. Then non-infiltrated defects appear at locally high Vf portions. The θ of 2.24 rad is obtained taking into consideration the effect of non-infiltrated defects. Ultrasonic infiltration, in which ultrasonic vibration was transmitted into molten aluminum through a direct contact of the step-horn and melt, was performed to compare the apparent wettability with that in pressure infiltration. When molten aluminum was subjected to ultrasonic vibration with an ultrasonic power of 500 kW/m2 (resonant frequency of 20.5 kHz), the Pc becomes zero, that is, the melt entry occurs even with a zero Pa. An infiltrated area with a semi-spherical shape is observed on the cross section close to the step-horn at the initial stage of ultrasonic infiltration, which coincides with the ultrasonic pressure (Pus) distribution obtained analytically. Then non-infiltrated defects are not observed in an incorporated region. Ultrasonic infiltration seems to have a kind of driving force giving aid to realize full infiltration, such as improvement of the apparent wettability due to a hysteresis of contact angles, the Pus acted instead of Pa and the high vibrational acceleration.
Using Imiquimod-Induced Psoriasis-Like Skin as a Model to Measure the Skin Penetration of Anti-Psoriatic Drugs (2015)

We established the topical delivery profiles of anti-psoriatic drugs via imiquimod-treated psoriasis-like skin.
Interpreting the ECFA: A New Common Market for Taiwan and Mainland China? (2011)

The ECFA was signed by Taiwan and Mainland China on June 29, 2010. It is Taiwan' s new overall national economic policy calling for rapproachment with Mainland China. A primary purpose of this Agreement is to establish a quasi national cross-strait common market within the framework of the WTO as well as to design the legal framework of bilateral economic cooperation. It is a course for the Chinese common market as the final economic integration. By its nature the current ECFA lies somewhat between a free trade agreement and a bilateral trade agreement within the framework of the WTO in the sector of trade in goods. Two parties have agreed on a new model of preferential treatment for goods exported from Taiwan to Mainland China. An agreed Early Harvest for Trade in Goods list is favourable for Taiwan, while an Early Harvest for Trade in Services list is balanced one for both parties. Other principles formulated by the ECFA are related to intellectual property rights and mutual investment. The success and failure of the ECFA will depend largely on the future cross-strait political atmosphere.
Impact of Chromatic and Polarization-Mode Dispersions on DPSK Systems Using Interferometric Demodulation and Direct Detection (2004)

We study the impact of chromatic dispersion (CD) and first-order polarization-mode dispersion (PMD) on systems using binary differential phase-shift keying (2-DPSK) or quaternary DPSK (4-DPSK) with nonreturn-to-zero (NRZ) or return-to-zero (RZ) formats. These signals are received using optical preamplification, interferometric demodulation, and direct detection. We consider the linear propagation regime and compute optical power penalties at fixed bit-error ratio (BER). In order to evaluate the BER precisely taking account amplifier noise, arbitrary pulse shapes, arbitrary optical and electrical filtering, CD, and PMD, we introduce a novel model for DPSK systems and compute the BER using a method recently proposed by Forestieri for on-off keying (OOK) systems. We show that when properly applied, the method yields highly accurate results for DPSK systems. We have found that when either the NRZ or RZ format is used, 2-DPSK exhibits lower power penalties than OOK in the presence of CD and first-order PMD. RZ-2-DPSK, as compared with NRZ-2-DPSK, incurs smaller penalties due to PMD, but offers no advantage in terms of CD. 4-DPSK, as it has twice the symbol duration of OOK or 2-DPSK for a given bit rate, incurs much lower CD and PMD power penalties than either of these techniques. RZ-4-DPSK is especially promising, as it offers CD and PMD penalties significantly smaller than all other techniques, including NRZ-4-DPSK.
Overexpression of<i>Candida albicans CDR1</i>,<i>CDR2</i>, or<i>MDR1</i>Does Not Produce Significant Changes in Echinocandin Susceptibility (2006)

The micafungin and caspofungin susceptibilities of Candida albicans laboratory and clinical isolates and of Saccharomyces cerevisiae strains stably hyperexpressing fungal ATP-binding cassette (ABC) or major facilitator superfamily (MFS) transporters involved in azole resistance were determined using three separate methods. Yeast strains hyperexpressing individual alleles of ABC transporters or an MFS transporter from C. albicans gave the expected resistance profiles for the azoles fluconazole, itraconazole, and voriconazole. The strains hyperexpressing CDR2 showed slightly decreased susceptibility to caspofungin in agar plate drug resistance assays, as previously reported, but increased susceptibility to micafungin compared with either the strains hyperexpressing CDR1 or the null parent deleted of seven ABC transporters. The strains hyperexpressing CDR1 showed slightly decreased susceptibility to micafungin in these assays. A C. albicans clinical isolate overexpressing both Cdr1p and Cdr2p relative to its azole-sensitive isogenic progenitor acquired resistance to azole drugs and showed reduced susceptibility to caspofungin and slightly increased susceptibility to micafungin in agar plate drug resistance assays. None of the strains showed significant resistance to micafungin or caspofungin in liquid microdilution susceptibility assays. The antifungal activities of micafungin and caspofungin were similar in agarose diffusion assays, although the shape and size of the caspofungin inhibitory zones were affected by medium composition. The assessment of micafungin and caspofungin potency is therefore assay dependent; the differences seen with agar plate drug resistance assays occur over narrow ranges of echinocandin concentrations and are not of clinical significance.
Use of Varicose Veins as Arterial Bypass Grafts (1993)

Varicose veins are not generally used as arterial bypass grafts despite their physiological endothelial flow surface. The large, irregular diameter and the thin wall renders these veins inadequate. Experimental studies have shown that a considerable reduction in the diameter of veins can be achieved by external wrapping without the generation of obstructing folds of the vein wall. A Dacron mesh tube surrounding varicose veins was used as a bypass graft in 13 infrainguinal arterial reconstructions. Ligated larger side branches and connections of the mesh segments caused irregularities of the otherwise smooth flow surfaces. Ten grafts were patent after a mean follow-up of 17 months. Two grafts have remained patent despite severe outflow obstruction in one and proximal occlusion in the other; both underwent successful interventions. The antithrombogenic properties of these grafts were partly due to a marked increase of the vasa vasorum. Externally constricted varicose veins may be used as arterial bypass conduits with good intermediate-term patency.
What the Victorian Internet did for us (2006)

The history of technical developments can help pupils appreciate the relationship between design and technology, science, society and the economy. This article looks at the earliest practical application of electricity – the electric telegraph.
Total Synthesis of Siomycin A: Construction of Synthetic Segments (2008)

The five practical segments for the total synthesis of siomycin A, that is, the dehydropiperidine segment A (5), the pentapeptide segment B (3), the dihydroquinoline segment C (6), and the beta-phenylselenoalanine dipeptide segments D (7) and E (4), were synthesized. Segment A (5) was constructed by the coupling of the azomethine ylide and the chiral sulfinimine, followed by the stereoselective reduction of the six-membered imine function. Segment B (3) was synthesized by the phenylselenylation of the beta-lactone, stereoselective vinylzinc addition to the chiral sulfinimine, and oxazoline-thioamide conversion. Segment C (6) was prepared by the one-pot olefination of the tetrahydroquinoline N-oxide using triflic anhydride and triethylamine, stereoselective reduction of the methyl ketone function, and regioselective Yb(OTf)(3)-catalyzed epoxide opening by the amino group. Segments D (7) and E (4) were synthesized by coupling of the properly protected beta-phenylselenoalanines.
Crystal chemistry of metal dioxides with rutile-related structures (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCrystal chemistry of metal dioxides with rutile-related structuresDonald B. Rogers, Robert D. Shannon, Arthur W. Sleight, and Joseph L. GillsonCite this: Inorg. Chem. 1969, 8, 4, 841–849Publication Date (Print):April 1, 1969Publication History Published online1 May 2002Published inissue 1 April 1969https://doi.org/10.1021/ic50074a029RIGHTS & PERMISSIONSArticle Views2296Altmetric-Citations432LEARN 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 InReddit PDF (950 KB) Get e-Alerts Get e-Alerts