gebhart/patrepeval huggingface dataset:
Plasminogen activators augment endothelial cell organization in vitro by two distinct pathways (1995)

Endothelial cell differentiation into capillary structures is a complex process that requires the concerted effects of several extracellular matrix proteases, including plasminogen activators. Here, the role of tissue-type plasminogen activator (tPA) and urokinase-type plasminogen activator (uPA) was evaluated in an in vitro model of endothelial morphogenesis involving organization of human umbilical vein endothelial cells into tubular structures when they are cultured on the basement membrane preparation, Matrigel. Both uPA and tPA were detected in HUVEC cultures on Matrigel, and inhibitors of plasminogen activators or of serine proteases decreased the extent of the tube network formed by the cells. The decrease resulting from serine protease inhibitors was additive to that from matrix metalloproteinase inhibitors which have previously been shown to decrease tube formation in this model, suggesting that the two classes of proteases modulate tube formation by distinct mechanisms. Plasminogen activator inhibitor (PAI)-1 decreased tube formation by 50% when added up to 4.5 h after the initiation of an 18 h assay and caused 25% inhibition when added 9.5 h after culture initiation, indicating that the effects of plasminogen activators are not limited to an early event in the differentiation process. Steady-state expression of mRNA for uPA increased during the first several hours of culture on Matrigel, further supporting a role for PA activity throughout the process of tube formation. These findings suggested that PAs may affect multiple events during tube-forming activity. A fucosylated peptide comprising the amino-terminal domain of uPA that binds to the uPA receptor (uPAR) but lacking proteolytic activity enhanced tube formation. In contrast, a defucosylated form of the same peptide had no effect. Since fucosylation of this fragment has been shown to be essential in other models of cell stimulation by uPA-uPAR interaction, these data support the hypothesis that uPA enhances endothelial morphogenesis both through proteolytic activity and via uPAR occupancy. Plasminogen activators could facilitate angiogenesis in vivo.
Therapeutic arterial embolisation in children. (1984)

Arterial embolisation was performed in five paediatric patients. Indications were hypersplenism in two, gastrointestinal bleeding in two and treatment of an aneurysmal bone cyst in one. Embolisation provided definitive treatment in each case with no complications.
Tubular Graphite Cones (2003)

We report the synthesis of tubular graphite cones using a chemical vapor deposition method. The cones have nanometer-sized tips, micrometer-sized roots, and hollow interiors with a diameter ranging from about 2 to several tens of nanometers. The cones are composed of cylindrical graphite sheets; a continuous shortening of the graphite layers from the interior to the exterior makes them cone-shaped. All of the tubular graphite cones have a faceted morphology. The constituent graphite sheets have identical chiralities of a zigzag type across the entire diameter, imparting structural control to tubular-based carbon structures. The tubular graphite cones have potential for use as tips for scanning probe microscopy, but with greater rigidity and easier mounting than currently used carbon nanotubes.
Fast Point Feature Histograms (FPFH) for 3D registration (2009)

In our recent work [1], [2], we proposed Point Feature Histograms (PFH) as robust multi-dimensional features which describe the local geometry around a point p for 3D point cloud datasets. In this paper, we modify their mathematical expressions and perform a rigorous analysis on their robustness and complexity for the problem of 3D registration for overlapping point cloud views. More concretely, we present several optimizations that reduce their computation times drastically by either caching previously computed values or by revising their theoretical formulations. The latter results in a new type of local features, called Fast Point Feature Histograms (FPFH), which retain most of the discriminative power of the PFH. Moreover, we propose an algorithm for the online computation of FPFH features for realtime applications. To validate our results we demonstrate their efficiency for 3D registration and propose a new sample consensus based method for bringing two datasets into the convergence basin of a local non-linear optimizer: SAC-IA (SAmple Consensus Initial Alignment).
Comparison of the Effect of Different Inhibitors on the Non-Enzymatic Glycation of Rat Tail Tendons and Bovine Serum Albumin (1996)

The biomechanical and biochemical properties of collagen are changed by non-enzymatic glycation culminating in increased cross-linking. We have previously shown that dibasic amino acids such as L-arginine inhibit in vitro the non-enzymatic glycation of soluble proteins and insoluble connective tissue macromolecules. In the present in vitro study we obtained evidence that the nucleophilic hydrazine derivative aminoguanidine and the non-steroidal anti-rheumatic drug ibuprofen inhibit the formation of fluorescent advanced glycation end products (AGEs) to a comparable extent, while arginine is ineffective as a consequence of its tendency to form AGEs itself. Periodic replacement of glycated arginine in the rat tail tendon system, however, engendered an inhibition of fluorescence similar to that obtained by the other inhibitors. Long-term glycation of rat tail tendons caused a significant increase in Young's modulus, which could also be inhibited by periodically renewed arginine. In contrast to ibuprofen, aminoguanidine and arginine-lysine inhibited the marked increase in maximum contraction force of long-term glycated rat tail tendons. As opposed to other inhibitors, aminoguanidine also reduced the thermal contraction force of native tendons, shifted the maximum contraction temperature to markedly lower values and solubilized a significant part of the rat tail tendon collagen. These findings indicate that the in vitro alterations of rat tail tendon collagen induced by non-enzymatic glycation can be prevented by arginine, arginine-lysine and aminoguanidine. However, collagen structure is seriously affected by aminoguanidine.
Bioinformatics for Next Generation Sequencing Data (2010)

The emergence of next-generation sequencing (NGS) platforms imposes increasing demands on statistical methods and bioinformatic tools for the analysis and the management of the huge amounts of data generated by these technologies. Even at the early stages of their commercial availability, a large number of softwares already exist for analyzing NGS data. These tools can be fit into many general categories including alignment of sequence reads to a reference, base-calling and/or polymorphism detection, de novo assembly from paired or unpaired reads, structural variant detection and genome browsing. This manuscript aims to guide readers in the choice of the available computational tools that can be used to face the several steps of the data analysis workflow.
Development of Interpretive Breakpoints for Antifungal Susceptibility Testing: Conceptual Framework and Analysis of In Vitro-In Vivo Correlation Data for Fluconazole, Itraconazole, and Candida Infections (1997)

The availability of reproducible antifungal susceptibility testing methods now permits analysis of data correlating susceptibility in vitro with outcome in vivo in order to define interpretive breakpoints. In this paper, we have examined the conceptual framework underlying interpretation of antimicrobial susceptibility testing results and then used these ideas to drive analysis of data packages developed by the respective manufacturers that correlate fluconazole and itraconazole MICs with outcome of candidal infections. Tentative fluconazole interpretive breakpoints for MICs determined by the National Committee for Clinical Laboratory Standards' M27-T broth macrodilution methodology are proposed: isolates for which MICs are < or = 8 microg/mL are susceptible to fluconazole, whereas those for which MICs are > or = 64 microg/mL appear resistant. Isolates for which the MIC of fluconazole is 16-32 microg/mL are considered susceptible dependent upon dose (S-DD), on the basis of data indicating clinical response when > 100 mg of fluconazole per day is given. These breakpoints do not, however, apply to Candida krusei, as it is considered inherently resistant to fluconazole. Tentative interpretive MIC breakpoints for itraconazole apply only to mucosal candidal infections and are as follows: susceptible, < or = 0.125 microg/mL; S-DD, 0.25-0.5 microg/mL; and resistant, > or = 1.0 microg/mL. These tentative breakpoints are now open for public commentary.
A Fibril-Network-Reinforced Biphasic Model of Cartilage in Unconfined Compression (1999)

Cartilage mechanical function relies on a composite structure of a collagen fibrillar network entrapping a proteoglycan matrix. Previous biphasic or poroelastic models of this tissue, which have approximated its composite structure using a homogeneous solid phase, have experienced difficulties in describing measured material responses. Progress to date in resolving these difficulties has demonstrated that a constitutive low that is successful for one test geometry (confined compression) is not necessarily successful for another (unconfined compression). In this study, we hypothesize that an alternative fibril-reinforced composite biphasic representation of cartilage can predict measured material responses and explore this hypothesis by developing and solving analytically a fibril-reinforced biphasic model for the case of uniaxial unconfined compression with frictionless compressing platens. The fibrils were considered to provide stiffness in tension only. The lateral stiffening provided by the fibril network dramatically increased the frequency dependence of disk rigidity in dynamic sinusoidal compression and the magnitude of the stress relaxation transient, in qualitative agreement with previously published data. Fitting newly obtained experimental stress relaxation data to the composite model allowed extraction of mechanical parameters from these tests, such as the rigidity of the fibril network, in addition to the elastic constants and the hydraulic permeability of the remaining matrix. Model calculations further highlight a potentially important difference between homogeneous and fibril-reinforced composite models. In the latter type of model, the stresses carried by different constituents can be dissimilar, even in sign (compression versus tension) even though strains can be identical. Such behavior, resulting only from a structurally physiological description, could have consequences in the efforts to understand the mechanical signals that determine cellular and extracellular biological responses to mechanical loads in cartilage.
No loss spectral phase correction and arbitrary phase shaping of regeneratively amplified femtosecond pulses using MIIPS (2006)

Automated pulse compression through adaptive phase distortion compensation and compensation of gain narrowing of femtosecond regeneratively amplified pulses (2.5 mJ, 27.6 fs, transform limited) using a MIIPS-enabled pre-amplification pulse shaper is demonstrated. Rigorous characterization of the shaped pulses is presented.
New Currents in Electrical Stimulation of Excitable Tissues (2000)

Electric fields can stimulate excitable tissue by a number of mechanisms. A uniform long, straight peripheral axon is activated by the gradient of the electric field that is oriented parallel to the fiber axis. Cortical neurons in the brain are excited when the electric field, which is applied along the axon-dendrite axis, reaches a particular threshold value. Cardiac tissue is thought to be depolarized in a uniform electric field by the curved trajectories of its fiber tracts. The bidomain model provides a coherent conceptual framework for analyzing and understanding these apparently disparate phenomena. Concepts such as the activating function and virtual anode and cathode, as well as anode and cathode break and make stimulation, are presented to help explain these excitation events in a unified manner. This modeling approach can also be used to describe the response of excitable tissues to electric fields that arise from charge redistribution (electrical stimulation) and from time-varying magnetic fields (magnetic stimulation) in a self-consistent manner. It has also proved useful to predict the behavior of excitable tissues, to test hypotheses about possible excitation mechanisms, to design novel electrophysiological experiments, and to interpret their findings.
Expression of connexin43 in the developing rat heart. (1991)

Connexin43 is the predominant gap junction protein expressed in the heart. To determine the relation between cardiac maturation and gap junction gene expression, the developmental profiles of connexin43 mRNA and protein were examined in the rat heart. Connexin43 mRNA levels accumulate progressively (eightfold) during embryonic and early neonatal stages, accompanied by a parallel, but temporally delayed, accumulation of connexin43 protein (15-fold). As the heart matures further, both mRNA and protein levels subsequently decline, to about 50% and 30% of their maximum levels, respectively. These observations suggest that increases in intercellular coupling that characterize cardiac development do not depend solely on modulation of connexin43 gene expression, but rather are likely to involve organization of gap junction channels into the intercalated disc.
Microencapsulated Islets as Bioartificial Endocrine Pancreas (1980)

Single implantation of microencapsulated islets into rats with streptozotocin-induced diabetes corrected the diabetic state for 2 to 3 weeks. The microencapsulated islets remained morphologically and functionally intact throughout long-term culture studies lasting over 15 weeks.
MSM ameliorates HIV-1 Tat induced neuronal oxidative stress via rebalance of the glutathione cycle. (2015)

HIV-1 Tat protein is a key neuropathological element in HIV associated neurogcognitive disorders (HAND); a type of cognitive syndrome thought to be at least partially mediated by increased levels of brain reactive oxygen species (ROS) and nitric oxide (NO). Methylsulfonylmethane (MSM) is a sulfur-containing compound known to reduce oxidative stress. This study was conducted to determine whether administration of MSM attenuates HIV-1 Tat induced oxidative stress in mouse neuronal cells. MSM treatment significantly decreased neuronal cell NO and ROS secretion. Further, MSM significantly reversed HIV-1 Tat mediated reductions in reduced glutathione (GSH) as well as HIV-1 Tat mediated increases in oxidized glutathione (GSSG). In addition, Tat reduced nuclear translocation of nuclear factor-erythroid 2 p45-related factor 2 (Nrf2), a key nuclear promoter of antioxidant activity, while MSM increased its translocation to the nucleus in the presence of Tat. These results suggest that HIV-1 Tat reduces the resiliency of neuron cells to oxidative stress which can be reversed by MSM. Given the clinical safety of MSM, future preclinical in vivo studies will be required to further confirm these results in effort to validate MSM as a neuroprotectant in patients at risk of, or who are already diagnosed with, HAND.
Pollen- and anther-specific chi promoters from petunia: tandem promoter regulation of the chiA gene. (1990)

We have analyzed the spatial and temporal activities of chalcone flavanone isomerase (chi) A and B gene promoters from petunia. To study the tandem promoter regulation of chiA, various chiA promoter fragments were fused with the beta-glucuronidase (GUS) reporter gene. Analysis of transgenic plants containing these chimeric genes provided definitive proof that the chiA coding region is regulated by two distinct promoters (designated PA1 and PA2). We also showed that both promoters can function independently and that the chiA PA1 promoter is expressed in limb (epidermal and parenchyma cells), tube (inner epidermal and parenchyma cells), seed (seed coat, endosperm, and embryo), sepal, leaf, and stem. The use of chiA and chiB promoters in the regulation of anther- and pollen-specific gene expression has been studied. By analyzing transgenic plants containing chimeric genes consisting of chiA and B promoter fragments and the GUS reporter gene, we were able to identify a 0.44-kilobase chiA PA2 promoter fragment that drives pollen-specific gene expression and a 1.75-kilobase chiB PB promoter fragment that confers anther-specific (pollen and tapetum cells) expression to the GUS gene.
Activated B-RAF Is an Hsp90 Client Protein That Is Targeted by the Anticancer Drug 17-Allylamino-17-Demethoxygeldanamycin (2005)

Hsp90 is a ubiquitously expressed molecular chaperone that folds, stabilizes, and functionally regulates many cellular proteins. The benzoquinone ansamysin 17-allylamino-17-demethoxygeldanamycin (17-AAG) is an anticancer drug that disrupts Hsp90 binding to its clients, causing their degradation through the ubiquitin-dependent proteasomal pathway. The protein kinase B-RAF is mutated in approximately 7% of human cancers. The most common mutation (approximately 90%) is (V600E)B-RAF, which has constitutively elevated kinase activity, stimulates cancer cell proliferation, and promotes survival. Here, we show that (V600E)B-RAF is an Hsp90 client protein that requires Hsp90 for its folding and stability. (V600E)BRAF is more sensitive to degradation by 17-AAG treatment than (WT)B-RAF and we show that the majority of the other mutant forms of B-RAF are also sensitive to 17-AAG-mediated proteasomal degradation. Our data show that B-RAF is an important target for 17-AAG in human cancer.
The effect of initial morphology on the mechanical properties of ultra‐high molecular weight polyethylene (1986)

Abstract Studies of the physical and mechanical properties of melt crystallized ultra‐high molecular weight polyethylene morphologies from melts with different thermal histories indicate that their properties depend on the degree of fusion of the powder particles during their processing and can be enhanced by heating the polymer above 220°C. The degree of cohesion of the powder particles and their initial morphology also have a significant effect on the deformability of the polymer in the solid state forming methods used to prepare high modulus and strength products.
New insights into the P‐glycoprotein‐mediated effluxes of rhodamines (2003)

Multidrug resistance (MDR) in tumour cells is often caused by the overexpression of the plasma drug transporter P-glycoprotein (P-gp). This protein is an active efflux pump for chemotherapeutic drugs, natural products and hydrophobic peptides. Despite the advances of recent years, we still have an unclear view of the molecular mechanism by which P-gp transports such a wide diversity of compounds across the membrane. Measurement of the kinetic characteristics of substrate transport is a powerful approach to enhancing our understanding of their function and mechanism. The aim of the present study was to further characterize the transport of several rhodamine analogues, either positively charged or zwitterionic. We took advantage of the intrinsic fluorescence of rhodamines and performed a flow-cytometric analysis of dye accumulation in the wild-type drug sensitive K562 that do not express P-gp and its MDR subline that display high levels of MDR. The measurements were made in real time using intact cells. The kinetic parameter, ka = VM/km, which is a measure of the efficiency of the P-gp-mediated efflux of a substrate was similar for almost all the rhodamine analogues tested. In addition these values were compared with those determined previously for the P-gp-mediated efflux of anthracycline. Our conclusion is that the compounds of these two classes of molecules, anthracyclines and rhodamines, are substrates of P-gp and that their pumping rates at limiting low substrate concentration are similar. The findings presented here are the first to show quantitative information about the kinetic parameters for P-gp-mediated efflux of rhodamine analogues in intact cells.
The nature of the silica cage as reflected by spectral changes and enhanced photostability of trapped Rhodamine 6G (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe nature of the silica cage as reflected by spectral changes and enhanced photostability of trapped Rhodamine 6GDavid Avnir, David Levy, and Renata ReisfeldCite this: J. Phys. Chem. 1984, 88, 24, 5956–5959Publication Date (Print):November 1, 1984Publication History Published online1 May 2002Published inissue 1 November 1984https://doi.org/10.1021/j150668a042RIGHTS & PERMISSIONSArticle Views2408Altmetric-Citations814LEARN 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 (560 KB) Get e-Alerts
Orthogonal frequency CDMA for broadband communications (2003)

A general scheme called orthogonal frequency CDMA (OFCDMA) to describe CDMA using orthogonal carriers is proposed. Three well-known multicarrier CDMA schemes can be derived as special cases of the proposed OFCDMA if we appropriately define the signature waveforms and separation between adjacent carriers. We proceed with a unified analysis of OFCDMA to systematically understand the performance of these three schemes. Five types of interference can exist in a OFCDMA system under a multi-ray multipath fading channel. We compare the three schemes for each type of interference and discuss their pros and cons to help in designing effective OFCDMA receivers in interference-limited environments.
A precursor—product relationship exists between oval cells and hepatocytes in rat liver (1987)

Oval cell proliferation was induced in twelve male Fischer rats by administration of 2-acetylaminofluorene (2-AAF) for 2 weeks and by performing partial hepatectomy one week after the beginning of 2-AAF administration. Albumin expression in liver was studied by using in situ hybridization of 3H-labeled rat albumin riboprobe. Radiolabeled thymidine was administered to a group of animals at day 6 after partial hepatectomy. The animals were killed at 0, 3, 7, 9, 11 and 13 days after partial hepatectomy. Both oval cells and basophilic hepatocytes showed a prominent expression of albumin, whereas albumin expression in acidophilic pre-existing hepatocytes was decreased. Oval cell nuclei were exclusively labeled one day after administration of [3H]thymidine. At day 9, 11 and 13 basophilic hepatocytes became labeled and the area occupied by these cells increased. This is the first demonstration of the transfer of radiolabeled thymidine from oval cells to newly formed hepatocytes in vivo. Thus the precursor-product relationship between oval cells and basophilic hepatocytes has been established.