gebhart/patrepeval huggingface dataset:
Differential roles of selectins and the alpha4-integrin in acute, subacute, and chronic leukocyte recruitment in vivo (1997)

Adhesion blocking mAbs specific for rat P-, E-, and L-selectin and the alpha4-integrin were used to characterize leukocyte recruitment mechanisms in models of LTC4 (acute), LPS (subacute), and adjuvant-induced (chronic) inflammation. Intravital microscopy was employed to measure leukocyte rolling and adhesion in rat mesenteric venules. Superfusing the mesentery with 20 nM LTC4 elicited an increase in leukocyte rolling (66.8 +/- 3.8 vs 18.2 +/- 3.2 cells/min control) that was completely eliminated by an anti-rat P-selectin mAb. Superfusion with 1 microg/ml LPS induced a significant increase in leukocyte rolling within 15 min (73 +/- 8 vs 33 +/- 6 cells/min control). Rolling increased further starting at 105 min and peaked by 150 min (141 +/- 23 cells/min). LPS-induced leukocyte rolling was eliminated during the first 90 min by the P-selectin mAb. The later increase in leukocyte rolling was not prevented by a second treatment with P-selectin mAb or a function-blocking mAb against rat E-selectin. This later phase of leukocyte rolling was blocked by treatments with mAbs against either the alpha4-integrin or L-selectin. Twelve days following Mycobacterium butyricum immunization, 300 to 500 rolling cells/min were observed. This could be reduced approximately 50 to 60% by mAb against either the alpha4-integrin or L-selectin. The combination of both mAbs eliminated approximately 90% of rolling. Neither the P- nor E-selectin mAbs reduced rolling in this chronic inflammatory model. This study highlights differences in leukocyte adhesive mechanisms elicited by different stimuli and at different time points within the same vascular bed.
Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand (2015)

RosettaLigand has been successfully used to predict binding poses in protein-small molecule complexes. However, the RosettaLigand docking protocol is comparatively slow in identifying an initial starting pose for the small molecule (ligand) making it unfeasible for use in virtual High Throughput Screening (vHTS). To overcome this limitation, we developed a new sampling approach for placing the ligand in the protein binding site during the initial 'low-resolution' docking step. It combines the translational and rotational adjustments to the ligand pose in a single transformation step. The new algorithm is both more accurate and more time-efficient. The docking success rate is improved by 10-15% in a benchmark set of 43 protein/ligand complexes, reducing the number of models that typically need to be generated from 1000 to 150. The average time to generate a model is reduced from 50 seconds to 10 seconds. As a result we observe an effective 30-fold speed increase, making RosettaLigand appropriate for docking medium sized ligand libraries. We demonstrate that this improved initial placement of the ligand is critical for successful prediction of an accurate binding position in the 'high-resolution' full atom refinement step.
COHERENT ION-EXCHANGE GELS AND MEMBRANES (1950)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCOHERENT ION-EXCHANGE GELS AND MEMBRANESWalter Juda and Wayne A. McRaeCite this: J. Am. Chem. Soc. 1950, 72, 2, 1044Publication Date (Print):February 1, 1950Publication History Published online1 May 2002Published inissue 1 February 1950https://pubs.acs.org/doi/10.1021/ja01158a528https://doi.org/10.1021/ja01158a528research-articleACS PublicationsRequest reuse permissionsArticle Views496Altmetric-Citations140LEARN 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
Concentration of organics from aqueous solutions using uncoated capillary columns (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConcentration of organics from aqueous solutions using uncoated capillary columnsAlbert. Zlatkis, Ravindra P. J. Ranatunga, and Brian S. MiddleditchCite this: Anal. Chem. 1990, 62, 22, 2471–2478Publication Date (Print):November 15, 1990Publication History Published online1 May 2002Published inissue 15 November 1990https://pubs.acs.org/doi/10.1021/ac00221a012https://doi.org/10.1021/ac00221a012research-articleACS PublicationsRequest reuse permissionsArticle Views35Altmetric-Citations19LEARN 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
Sustained virologic control in SIV <sup>+</sup> macaques after antiretroviral and α <sub>4</sub> β <sub>7</sub> antibody therapy (2016)

Antiretroviral drug therapy (ART) effectively suppresses replication of both the immunodeficiency viruses, human (HIV) and simian (SIV); however, virus rebounds soon after ART is withdrawn. SIV-infected monkeys were treated with a 90-day course of ART initiated at 5 weeks post infection followed at 9 weeks post infection by infusions of a primatized monoclonal antibody against the α<sub>4</sub>β<sub>7</sub> integrin administered every 3 weeks until week 32. These animals subsequently maintained low to undetectable viral loads and normal CD4<sup>+</sup> T cell counts in plasma and gastrointestinal tissues for more than 9 months, even after all treatment was withdrawn. This combination therapy allows macaques to effectively control viremia and reconstitute their immune systems without a need for further therapy.
Expansion of Human Embryonic Stem Cells on Cellulose Microcarriers (2010)

This unit describes the routine maintenance and expansion of undifferentiated human embryonic stem cells (hESC) on cellulose microcarriers. Conventionally, hESCs have been maintained on feeder cells or extracellular matrix-coated two-dimensional tissue culture plates. The expansion of hESC on a tissue culture platform is limited by the available surface area and the requirement of repetitive subculturing to reach the required cell yield. Here, we show that expansion of hESC can be carried out in a three-dimensional suspension culture using Matrigel-coated cellulose microcarriers. hESCs from a tissue culture plate can be seeded directly onto the microcarriers; hESC microcarrier culture is passaged and expanded by mechanical dissociation of the cells without enzyme. Expansion of the culture in a 100-ml spinner flask is also described. Long-term culture of hESC on the microcarriers maintains typical pluripotent markers (OCT-4, Tra-1-60, and SSEA-4) and stable karyotype. Spontaneous differentiations of microcarrier-maintained hESCs in vitro (embryoid body formation) and in vivo (teratoma formation in SCID mouse) have demonstrated formation of the three germ layers. These protocols can also be applied equally well to human induced pluripotent stem cells.
A Century of the McNaghten Rules (1944)

The subject falls conveniently into two parts, (I) comment made during the century since McNaghten's Case in 1843 on the answers given by the judges to the questions put to them by the House of Lords, and (II) discussion of the defence of irresistible impulse. For the convenience of readers the Questions and Answers are reprinted from the tenth volume of Clark and Finnelly's Keports, 200, 209–212.
An Efficient Diamine·Copper Complex-Catalyzed Coupling of Arylboronic Acids with Imidazoles (2000)

[formula: see text] A novel diamine.copper complex-catalyzed intermolecular coupling of arylboronic acids (1) with imidazoles (3) is described. In the presence of a catalytic amount of [Cu(OH).TMEDA]2Cl2 (2), arylboronic acids (1) react smoothly with imidazoles (3) in dichloromethane at room temperature to give a variety of N-arylimidazoles (4) in good to excellent yields.
Highly efficient and chemoselective hydrogenation of α,β-unsaturated carbonyls over Pd/N-doped hierarchically porous carbon (2014)

Pd supported on N-doped hierarchically porous carbon was successfully applied in the selective hydrogenation of CC bonds.
Isolation and Structural and Genetic Analysis of the Mouse Enkephalin Gene and its d(AC/TG) <sub>n</sub> Repeats (1998)

Enkephalins, the endogenous opioids, mediate a wide variety of intercellular communications through ontogeny and their involvement has been suggested in drug addiction and alcohol abuse as well as in various neuropsychiatric disorders. In order to generate a genetic model, we have isolated the mouse enkephalin (mENK) gene, analyzed its regulatory region and compared its structure to the well characterized rat ENK (rENK) gene. We analyzed 2600 bp and found 3 highly homologous regions: The highest level (98%) of positional and sequence homology between mice and rats was in the TATA/proximal regulatory region. This region contains all the inducible regulatory elements (enkCRE1, NF1, AP-2, NFkappaB, etc.) and also an octamer-like element at -543 bp. This high homology is interrupted in both mice and rats by the typically polymorphic d(AC/TG)n and d(TC/GA)n dinucleotide repeats positioned between nucleotides -670 and -950. The position and orientation of these repetitive elements differ substantially in the two species. Genomic PCR analysis of the d(AC/TG)n repeat in various mouse strains, including aberrant behavioral or neurological phenotypes, showed lack of polymorphism at this repeat. The positional and sequence homologies between the rat and the mouse ENK genes decrease in more upstream regions due to the presence of nonhomologues repetititve DNA sequences.
MILATRAS: MIcrosimulation Learning-based Approach to TRansit ASsignment (2009)

Public transit is considered a cost-effective alternative to mitigate the effects of traffic gridlock through the implementation of innovative service designs, and deploying new smart systems for operations control and traveller information. Public transport planners use transit assignment models to predict passenger loads and levels of service.\n\nExisting transit assignment approaches have limitations in evaluating the effects of information technologies, since they are neither sensitive to the types of information that may be provided to travellers nor to the traveller’s response to that information. Moreover, they are not adequate for evaluating the impacts of Intelligent Transportation Systems (ITS) deployments on service reliability, which in turn affect passengers’ behaviour.\n\nThis dissertation presents an innovative transit assignment framework, namely the MIcrosimulation Learning-based Approach to TRansit ASsignment – MILATRAS. MILATRAS uses learning and adaptation to represent the dynamic feedback of passengers’ trip choices and their adaptation to service performance. Individual passengers adjust their behaviour (i.e. trip choices) according to their experience with the transit system performance. MILATRAS introduces the concept of ‘mental model’ to maintain and distinguish between the individual’s experience with service performance and the information provided about system conditions.\n\nA dynamic transit path choice model is developed using concepts of Markovian Decision Process (MDP) and Reinforcement Learning (RL). It addresses the departure time and path choices with and without information provision. A parameter-calibration procedure using a generic optimization technique (Genetic Algorithms) is also proposed. A proof-of-concept prototype has been implemented; it investigates the impact of different traveller information provision scenarios on departure time and path choices, and network performance. A large-scale application, including parameter calibration, is conducted for the Toronto Transit Commission (TTC) network. \n\nMILATRAS implements a microsimulation, stochastic (nonequilibrium-based) approach for modelling within-day and day-to-day variations in the transit assignment process, where aggregate travel patterns can be extracted from individual choices. MILATRAS addresses many limitations of existing transit assignment models by exploiting methodologies already established in the areas of traffic assignment and travel behaviour modeling. Such approaches include the microsimulation of transportation systems, learning-based algorithms for modelling travel behaviour, agent-based representation for travellers, and the adoption of Geographical Information Systems (GIS). \n\nThis thesis presents a significant step towards the advancement of the modelling for the transit assignment problem by providing a detailed operational specification for an integrated dynamic modelling framework – MILATRAS.
Variational Physics-Informed Neural Networks For Solving Partial Differential Equations (2019)

Physics-informed neural networks (PINNs) [31] use automatic differentiation to solve partial differential equations (PDEs) by penalizing the PDE in the loss function at a random set of points in the domain of interest. Here, we develop a Petrov-Galerkin version of PINNs based on the nonlinear approximation of deep neural networks (DNNs) by selecting the {\em trial space} to be the space of neural networks and the {\em test space} to be the space of Legendre polynomials. We formulate the \textit{variational residual} of the PDE using the DNN approximation by incorporating the variational form of the problem into the loss function of the network and construct a \textit{variational physics-informed neural network} (VPINN). By integrating by parts the integrand in the variational form, we lower the order of the differential operators represented by the neural networks, hence effectively reducing the training cost in VPINNs while increasing their accuracy compared to PINNs that essentially employ delta test functions. For shallow networks with one hidden layer, we analytically obtain explicit forms of the \textit{variational residual}. We demonstrate the performance of the new formulation for several examples that show clear advantages of VPINNs over PINNs in terms of both accuracy and speed.
MediaMill (2005)

In this technical demonstration we showcase the MediaMill system. A search engine that facilitates access to news video archives at a semantic level. The core of the system is an unprecedented lexicon of 100 automatically detected semantic concepts. Based on this lexicon we demonstrate how users can obtain highly relevant retrieval results using query-by-concept. In addition, we show how the lexicon of concepts can be exploited for novel applications using advanced semantic visualizations. Several aspects of the MediaMill system are evaluated as part of our TRECVID 2005 efforts.
Design and implementation of model predictive control using Multi-Parametric Toolbox and YALMIP (2010)

The paper introduces a new version of the Multi-Parametric Toolbox (MPT), which allows model predictive control (MPC) problems to be formulated in an intuitive and user-friendly fashion. In addition to control synthesis, the toolbox can also be employed for stability analysis, verification and simulation of MPC-based strategies. The toolbox is also capable of converting MPC controllers into real-time executable code which can be easily deployed to typical hardware control platforms. The most notable feature of the new version is its ability to formulate and solve complex MPC problems involving non-trivial requirements, like logic relations, move blocking, or contraction constraints.
Electrospun poly(d/l-lactide-co-l-lactide) hybrid matrix: a novel scaffold material for soft tissue engineering (2010)

Electrospinning is a long-known polymer processing technique that has received more interest and attention in recent years due to its versatility and potential use in the field of biomedical research. The fabrication of three-dimensional (3D) electrospun matrices for drug delivery and tissue engineering is of particular interest. In the present study, we identified optimal conditions to generate novel electrospun polymeric scaffolds composed of poly-D/L-lactide and poly-L-lactide in the ratio 50:50. Scanning electron microscopic analyses revealed that the generated poly(D/L-lactide-co-L-lactide) electrospun hybrid microfibers possessed a unique porous high surface area mimicking native extracellular matrix (ECM). To assess cytocompatibility, we isolated dermal fibroblasts from human skin biopsies. After 5 days of in vitro culture, the fibroblasts adhered, migrated and proliferated on the newly created 3D scaffolds. Our data demonstrate the applicability of electrospun poly(D/L-lactide-co-L-lactide) scaffolds to serve as substrates for regenerative medicine applications with special focus on skin tissue engineering.
Arylnitroalkenes: A New Group of Antibacterial Agents<sup>1</sup> (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTArylnitroalkenes: A New Group of Antibacterial Agents1Otto Schales and Heinz A. GraefeCite this: J. Am. Chem. Soc. 1952, 74, 18, 4486–4490Publication Date (Print):September 1, 1952Publication History Published online1 May 2002Published inissue 1 September 1952https://pubs.acs.org/doi/10.1021/ja01138a004https://doi.org/10.1021/ja01138a004research-articleACS PublicationsRequest reuse permissionsArticle Views518Altmetric-Citations76LEARN 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
Ds-echinoside A, a new triterpene glycoside derived from sea cucumber, exhibits antimetastatic activity via the inhibition of NF-κB-dependent MMP-9 and VEGF expressions (2011)

Ds-echinoside A (DSEA), a non-sulfated triterpene glycoside, was isolated from the sea cucumber Pearsonothuria graeffei. In vitro and in vivo investigations were conducted on the effects of DSEA on tumor cell adhesion, migration, invasion, and angiogenesis. In this study, we found that DSEA inhibited the proliferation of human hepatocellular liver carcinoma cells Hep G2, with a half-maximal inhibitory concentration (IC₅₀) of 2.65 μmol/L, and suppressed Hep G2 cell adhesion, migration, and invasion in a dose-dependent manner. DSEA also reduced tube formation of human endothelial cells ECV-304 on matrigel in vitro and attenuated neovascularization in the chick embryo chorioallantoic membrane (CAM) assay in vivo. Immunocytochemical analysis revealed that DSEA significantly decreased the expression of matrix metalloproteinase-9 (MMP-9), which plays an important role in the degradation of basement membrane in tumor metastasis and angiogenesis. DSEA also increased the protein expression level of tissue inhibitor of metalloproteinase-1 (TIMP-1), an important regulator of MMP-9 activation. From the results of Western blotting, the expressions of nuclear factor-kappa B (NF-κB) and vascular endothelial growth factor (VEGF) were found to be remarkably reduced by DSEA. These findings suggest that DSEA exhibits a significant anti-metastatic activity through the specific inhibition of NF-κB-dependent MMP-9 and VEGF expressions.
Autophagy flux induced by ginsenoside-Rg3 attenuates human prion protein-mediated neurotoxicity and mitochondrial dysfunction (2016)

Mitochondrial quality control is a process by which mitochondria undergo successive rounds of fusion and fission with dynamic exchange of components to segregate functional and damaged elements. Removal of mitochondrion that contains damaged components is accomplished via autophagy. In this study, we investigated whether ginsenoside Rg3, an active ingredient of the herbal medicine ginseng that is used as a tonic and restorative agent, could attenuate prion peptide, PrP (106-126)-induced neurotoxicity and mitochondrial damage. To this end, western blot and GFP-LC3B puncta assay were performed to monitor autophagy flux in neuronal cells; LC3B-II protein level was found to increase after Rg3 treatment. In addition, electron microscopy analysis showed that Rg3 enhanced autophagic vacuoles in neuronal cells. By using autophagy inhibitors wortmannin and 3-methyladenine (3MA) or autophagy protein 5 (Atg5) small interfering RNA (siRNA), we demonstrated that Rg3 could protect neurons against PrP (106-126)-induced cytotoxicity via autophagy flux. We found that Rg3 could also attenuate PrP (106-126)-induced mitochondrial damage via autophagy flux. Taken together, our results suggest that Rg3 is a possible therapeutic agent in neurodegenerative disorders, including prion diseases.