gebhart/patrepeval huggingface dataset:
A Simple Method to Measure Dermatan Sulfate at Sub-Microgram Concentrations in Plasma (1988)

A simple method for biological assay of dermatan sulfate (DS) in plasma is described. DS accelerates thrombin inhibition by heparin cofactor II (HC II). The principle of the assay is to measure the residual amidolytic thrombin activity after a short period of incubation with HC II in defibrinated plasma at low ionic strength. For this method we take advantage of two observations. Firstly, at fixed concentrations of DS and of HC II, the rate of thrombin inhibition increases when the ionic strength of the medium decreases. Secondly, defibrination by bentonite absorption also removes antithrombin III, HC II and for a large part alpha-2 macroglobulin from the plasma, so that no other thrombin inhibitor competes with HC II added as a reagent in a second step. In the conditions described, there is a linear relationship between DS concentrations in plasma from 0 to 2 micrograms/ml and the log of residual thrombin activity. The limit of sensitivity is 0.1 micrograms/ml. The assay displays an acceptable reproducibility in intra-assay, inter-assay and inter-individual experiments. It can be used to measure DS in human, rabbit and rat plasmas. The assay is also sensitive to other HC II activators such as heparin and pentosan polysulfate. DS is effective in experimental thrombosis without any detectable anticoagulant effect ex vivo. Pharmacological concentrations of DS in plasma fall into the range of sensitivity of this assay, which would be helpful in experimental or clinical studies of DS and related glycosaminoglycans.
Sfrp5 Is an Anti-Inflammatory Adipokine That Modulates Metabolic Dysfunction in Obesity (2010)

Adipose tissue secretes proteins referred to as adipokines, many of which promote inflammation and disrupt glucose homeostasis. Here we show that secreted frizzled-related protein 5 (Sfrp5), a protein previously linked to the Wnt signaling pathway, is an anti-inflammatory adipokine whose expression is perturbed in models of obesity and type 2 diabetes. Sfrp5-deficient mice fed a high-calorie diet developed severe glucose intolerance and hepatic steatosis, and their adipose tissue showed an accumulation of activated macrophages that was associated with activation of the c-Jun N-terminal kinase signaling pathway. Adenovirus-mediated delivery of Sfrp5 to mouse models of obesity ameliorated glucose intolerance and hepatic steatosis. Thus, in the setting of obesity, Sfrp5 secretion by adipocytes exerts salutary effects on metabolic dysfunction by controlling inflammatory cells within adipose tissue.
Prognostic biomarkers in osteoarthritis (2012)

Prognostic biomarkers may be used in clinical knee osteoarthritis to identify subgroups in whom the disease progresses at different rates. This could facilitate our understanding of the pathogenesis and allow us to differentiate phenotypes within a heterogeneous knee osteoarthritis population. Ultimately, such findings may help facilitate the development of disease-modifying osteoarthritis drugs (DMOADs).
Current induced modifications of domain wall (2005)

In this paper, current-induced domain wall displacement experiments that are combined with high resolution imaging of the domain walls are reported. A spin-polarized scanning electron microscope is used to determine topography and magnetization distribution of Fe/sub 20/Ni/sub 80/ sub-micron wires with a zigzag geometry. Injection of a single 10 /spl mu/s current pulse through the wire induces the displacement of both head-to-head and tail-to-tail walls in the same direction, which is the direction of the electron flow. The current density of 3 /spl times/10/sup 12/ A/m/sup 2/ is about 10% higher than the threshold current density at which domain wall motion sets in for these structures. This observation confirms unambiguously that the spin-torque effect is the driving force for the domain wall motion. The variation of the domain-wall velocity is correlated with the domain-wall configuration induced by the current. The evolution of domain wall velocities has been determined after consecutive current injections with the same current density. Additional experiments on wires with different dimensions show that the wall velocity depends on the wire width and hence on the domain wall width for constant current density. Simple 1-D models of the domain walls are not sufficient for an adequate description of current-induced domain-wall motion and spin-structure distortion. Thus, the domain walls have to be treated as 2-D objects.
Vaccines for Pandemic Influenza. The History of our Current Vaccines, their Limitations and the Requirements to Deal with a Pandemic Threat (2008)

Fears of a potential pandemic due to A(H5N1) viruses have focussed new attention on our current vaccines, their shortcomings, and concerns regarding global vaccine supply in a pandemic. The bulk of current vaccines are inactivated split virus vaccines produced from egg-grown virus and have only modest improvements compared with those first introduced over 60 years ago. Splitting, which was introduced some years ago to reduce reactogenicity, also reduces the immunogenicity of vaccines in immunologically naïve recipients. The A(H5N1) viruses have been found poorly immunogenic and present other challenges for vaccine producers which further exacerbate an already limited global production capacity. There have been some recent improvements in vaccine production methods and improvements to immunogenicity by the development of new adjuvants, however, these still fall short of providing timely supplies of vaccine for all in the face of a pandemic. New approaches to influenza vaccines which might fulfil the demands of a pandemic situation are under evaluation, however, these remain some distance from clinical reality and face significant regulatory hurdles.
Vascular Smooth Muscle Cell-derived, Gla-containing Growth-potentiating Factor for Ca2+-mobilizing Growth Factors (1995)

Proliferation of vascular smooth muscle cells (VSMC) is triggered by two types of growth factors. One activates tyrosine kinase-type receptors and the other activates G-protein-coupled receptors. We found that a conditioned medium of rat VSMC contained a growth-potentiating activity for the latter type of growth factor, and we purified a 70-kDa growth-potentiating factor (GPF) from the conditioned medium. Analyses of GPF and its cDNA revealed GPF to be a gamma-carboxyglutamic acid-containing protein encoded by a growth arrest-specific gene, gas6, which related to protein S. GPF specifically potentiated cell proliferation mediated by Ca(2+)-mobilizing receptors. The presence of a specific binding site suggests that the effect of GPF is mediated by a receptor. Thus, GPF may be a new type of extracellular factor regulating VSMC proliferation.
Optical trapping and fluorescence detection in laminar flow streams (1995)

An optical laser trap with fluorescence excitation/emission capability has been integrated in a flow cytometric geometry for the study of microparticle confinement and off-axis fluorescence detection in laminar flow streams. Measurements of particle escape velocity, trapping efficiency, and fluorescence intensity are presented for 2 μm diameter dye-tagged latex microspheres in laminar flow streams having velocities of up to 12 mm/s. Experimental results are compared with theoretical values for flow velocity and fluorescence intensity and found to be in excellent agreement.
A Ray tracing algorithm for progressive radiosity (1989)

A new method for computing form-factors within a progressive radiosity approach is presented. Previously, the progressive radiosity approach has depended on the use of the hemi-cube algorithm to determine form-factors. However, sampling problems inherent in the hemi-cube algorithm limit its usefulness for complex images. A more robust approach is described in which ray tracing is used to perform the numerical integration of the form-factor equation. The approach is tailored to provide good, approximate results for a low number of rays, while still providing a smooth continuum of increasing accuracy for higher numbers of rays. Quantitative comparisons between analytically derived form-factors and ray traced form-factors are presented.
D2P2: database of disordered protein predictions (2012)

We present the Database of Disordered Protein Prediction (D(2)P(2)), available at http://d2p2.pro (including website source code). A battery of disorder predictors and their variants, VL-XT, VSL2b, PrDOS, PV2, Espritz and IUPred, were run on all protein sequences from 1765 complete proteomes (to be updated as more genomes are completed). Integrated with these results are all of the predicted (mostly structured) SCOP domains using the SUPERFAMILY predictor. These disorder/structure annotations together enable comparison of the disorder predictors with each other and examination of the overlap between disordered predictions and SCOP domains on a large scale. D(2)P(2) will increase our understanding of the interplay between disorder and structure, the genomic distribution of disorder, and its evolutionary history. The parsed data are made available in a unified format for download as flat files or SQL tables either by genome, by predictor, or for the complete set. An interactive website provides a graphical view of each protein annotated with the SCOP domains and disordered regions from all predictors overlaid (or shown as a consensus). There are statistics and tools for browsing and comparing genomes and their disorder within the context of their position on the tree of life.
Amplification at chromosome 11q13 in transitional cell tumours of the bladder. (1991)

Amplification of several markers which map to chromosome 11q13 was detected by Southern blotting in transitional cell tumours of the urinary bladder. The oncogenes INT2 and HST and the BCL1 locus were co-amplified in 20/97 (20.6%) tumours and the locus-specific minisatellite probe pMS51 (D11S97) detected amplification in 17/97 (17.5%) tumours. The high frequency of heterozygosity (greater than 70%) detected by this latter probe on HaeIII-digested DNAs provided a sensitive means to measure low levels of gene amplification (2-fold) by comparing signals obtained from each allele. A number of probes which map to 11q were used in an attempt to map the region of amplification more precisely. PGA, PGR, STMY, D11Z1 and D11S149 were not amplified in any tumours studied. SEA was amplified in 1/59 tumours and D11S146 in 12/89 tumours. A comparison of the patterns of co-amplification of individual markers in this series of tumours revealed that of the 23 tumours with amplification at this site, 11 had co-amplification of D11S97, D11S146, BCL1, INT2 and HST, 3 had co-amplification of D11S97, BCL1, INT2 and HST, 6 had co-amplification of BCL1, INT2 and HST, 1 had co-amplification of D11S97 and D11S146 and 2 had amplification of D11S97 alone. Based on available linkage data for these markers, this suggests that a putative target gene within this amplicon lies centromeric to BCL1. Amplification at 11q13 showed no correlation with tumour grade or with HER2 amplification.
The Production of Mullerian Inhibiting Substance by the Fetal, Neonatal and Adult Rat1 (1976)

The secretory pattern of Mullerian Inhibiting Substance in the rat was documented by a graded organ culture assay on each day of the perinatal period and at more widely spaced intervals in the adult period. The influence of placenta and pituitary on Mullerian Inhibiting Substance production was studied. Fetal testicular fragments were displaced from target Mullerian ducts to determine if Mullerian Inhibiting Substance would act at a distance. Rat testes produced Mullerian Inhibiting Substance throughout the latter third of gestation. Its production continued during the first three weeks of extrauterine life, after which it disappeared, coincident with weaning. Hypophysectomy carried out after 20 days of age was ineffective in restoring Mullerian Inhibiting Substance activity to the adult rat testis. Placental fragments neither prolonged nor enhanced the Mullerian Inhibiting Substance activity of perinatal testes in organ culture. Mullerian Inhibiting Substance exerted its regressive effect on Mullerian ducts placed at a distance from a testicular source.
Chemistry of phosphodiesters, DNA, and models. 2. The hydrolysis of bis(8-hydroxyquinoline) phosphate in the absence and presence of metal ions (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemistry of phosphodiesters, DNA, and models. 2. The hydrolysis of bis(8-hydroxyquinoline) phosphate in the absence and presence of metal ionsKenneth A. Browne and Thomas C. BruiceCite this: J. Am. Chem. Soc. 1992, 114, 13, 4951–4958Publication Date (Print):June 1, 1992Publication History Published online1 May 2002Published inissue 1 June 1992https://pubs.acs.org/doi/10.1021/ja00039a001https://doi.org/10.1021/ja00039a001research-articleACS PublicationsRequest reuse permissionsArticle Views282Altmetric-Citations37LEARN 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
Mesoporous Silica Nanoparticles for Drug Delivery and Biosensing Applications (2007)

Abstract Recent advancements in morphology control and surface functionalization of mesoporous silica nanoparticles (MSNs) have enhanced the biocompatibility of these materials with high surface areas and pore volumes. Several recent reports have demonstrated that the MSNs can be efficiently internalized by animal and plant cells. The functionalization of MSNs with organic moieties or other nanostructures brings controlled release and molecular recognition capabilities to these mesoporous materials for drug/gene delivery and sensing applications, respectively. Herein, we review recent research progress on the design of functional MSN materials with various mechanisms of controlled release, along with the ability to achieve zero release in the absence of stimuli, and the introduction of new characteristics to enable the use of nonselective molecules as screens for the construction of highly selective sensor systems.
Bioactive Conformation of Luteinizing Hormone-Releasing Hormone: Evidence from a Conformationally Constrained Analog (1980)

An analog of luteinizing hormone-releasing hormone containing a gamma-lactam as a conformational constraint has been prepared with the use of a novel cyclization of a methionine sulfonium salt. The analog is more active as a luteinizing hormone-releasing hormone agonist that the parent hormone, and provides evidence for a bioactive conformation containing a beta-turn.
Macrocyclic lactones in antiparasitic therapy (2002)

<title>Abstract</title> This book contains 14 chapters on macrocyclic lactones (MLs). Chapter 1 covers chemistry, pharmacology and drug safety and chapter 2 deals with pharmacokinetics. New information on the mode of action emphasizing glutamate-gated chloride ion channels are reviewed in chapter 3. The impact of MLs on dung fauna is described in chapter 4. Chapter 5 reviews resistance mechanisms and field resistance. The use of MLs to control parasites of cattle is discussed in several sections in chapter 6. The next seven chapters deal with ML use in sheep and goats, horses, pigs, dogs and cats, wild ruminants, exotic pets and man, respectively. Finally, chapter 14 examines scientific, social, political and economic issues that control the future of MLs. The likely readership is composed of researchers and veterinarians.
Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications (1999)

From the Publisher:
Finding patterns in biomolecular data, particularly in DNA and RNA, is at the center of modern biological research. These data are complex and growing rapidly, so the search for patterns requires increasingly sophisticated computer methods. Pattern Discovery in Biomolecular Data provides a clear, up-to-date summary of the principal techniques. Since pattern searches often benefit from multiple approaches, the book presents methods in their purest form so that readers can best choose the method or combination that fits their needs. This volume will be invaluable for all workers in genomics and genetic analysis, and others whose research requires biocomputing.
Mechanisms and implications of phosphoinositide 3-kinase δ in promoting neutrophil trafficking into inflamed tissue (2004)

The phosphoinositide 3-kinase (PI3K) catalytic subunit p110 delta is expressed in neutrophils and is thought to play a role in their accumulation at sites of inflammation by contributing to chemoattractant-directed migration. We report here that p110 delta is present in endothelial cells and participates in neutrophil trafficking by modulating the proadhesive state of these cells in response to tumor necrosis factor alpha (TNF alpha). Specifically, administration of the selective inhibitor of PI3K delta, IC87114, to animals reduced neutrophil tethering to and increased rolling velocities on cytokine-activated microvessels in a manner similar to that observed in mice deficient in p110 delta. These results were confirmed in vitro as inhibition of this isoform in endothelium, but not neutrophils, diminished cell attachment in flow. A role for PI3K delta in TNF alpha-induced signaling is demonstrated by a reduction in Akt-phosphorylation and phosphatidylinositol-dependent kinase 1 (PDK1) enzyme activity upon treatment of this cell type with IC87114. p110 delta expressed in neutrophils also contributes to trafficking as demonstrated by the impaired movement of these cells across inflamed venules in animals in which this catalytic subunit was blocked or genetically deleted, results corroborated in transwell migration assays. Thus, PI3K delta may be a reasonable therapeutic target in specific inflammatory conditions as blockade of its activity reduces neutrophil influx into tissues by diminishing their attachment to and migration across vascular endothelium.
A Unique Common Fixed Point Theorem for Four Maps With Asymptotic Regularity Condition in Cone Metric Spaces (2011)

In this paper, we obtain a unique common fixed point theorem for four self maps with asymptotic regularity condition and satisfying Ciric type weak contractive condition in cone metric spaces. Our result generalizes and improves some recent results in cone metric spaces.
Immunosuppressive and Nonimmunosuppressive Cyclosporine Analogs Are Toxic to the Opportunistic Fungal PathogenCryptococcus neoformansvia Cyclophilin-Dependent Inhibition of Calcineurin (2000)

Cyclosporine (CsA) is an immunosuppressive and antimicrobial drug which, in complex with cyclophilin A, inhibits the protein phosphatase calcineurin. We recently found that Cryptococcus neoformans growth is resistant to CsA at 24 degrees C but sensitive at 37 degrees C and that calcineurin is required for growth at 37 degrees C and pathogenicity. Here CsA analogs were screened for toxicity against C. neoformans in vitro. In most cases, antifungal activity was correlated with cyclophilin A binding in vitro and inhibition of the mixed-lymphocyte reaction and interleukin 2 production in cell culture. Two unusual nonimmunosuppressive CsA derivatives, (gamma-OH) MeLeu(4)-Cs (211-810) and D-Sar (alpha-SMe)(3) Val(2)-DH-Cs (209-825), which are also toxic to C. neoformans were identified. These CsA analogs inhibit C. neoformans via fungal cyclophilin A and calcineurin homologs. Our findings identify calcineurin as a novel antifungal drug target and suggest nonimmunosuppressive CsA analogs warrant investigation as antifungal agents.
Insertion of sequences at the original provirus integration site of mouseROSA26 locus using the CRISPR/Cas9 system (2015)

Targeted transgenic mouse models, where an exogenous gene is inserted into a specified genomic locus to achieve its stable and reliable expression, have been widely used in biomedical research. However, the available methodologies for targeted insertion of sequences require many laborious steps that involve the use of embryonic stem (ES) cells. We recently developed Pronuclear Injection-based Targeted Transgenesis (PITT), a method that uses a recombinase-mediated cassette exchange (RMCE) to enable insertion of sequences at a predetermined genomic locus, such as ROSA26. The PITT technique uses fertilized eggs (instead of ES cells) collected from 'seed mice' that contain the RMCE landing pad. The PITT method can rapidly generate reliable targeted transgenic mice; it requires a seed mouse, which in our previous study was generated using ES cell targeting approaches. Here, we demonstrate that seed mice containing the RMCE landing pad can be developed rapidly by using the CRISPR/Cas9 system. One of the CRISPR targets tested in this study enabled the insertion of sequences precisely at the original ROSA26 provirus integration site. We anticipate that using a similar approach, PITT landing pad sequences can be rapidly and precisely inserted at other genomic loci to develop an array of PITT tools. This two-step strategy combines the best features of the two newer technologies-rapid creation of PITT landing pads using the CRISPR/Cas9 system and efficient and precise insertion of larger cassettes at the landing pads using PITT. This study also revealed that anomalous and mosaic sequence insertions can occur with the CRISPR/Cas9 system.
Interleukin-36–Receptor Antagonist Deficiency and Generalized Pustular Psoriasis (2011)

Aberrant interleukin-36Ra structure and function lead to unregulated secretion of inflammatory cytokines and generalized pustular psoriasis. (Funded by Agence Nationale de la Recherche and Société Française de Dermatologie.).
Ultrahigh-resolution optical coherence tomography (2004)

In the past two decades, optical coherence tomography (OCT) has been established as an adjunct diagnostic technique for noninvasive, high-resolution, cross-sectional imaging in a variety of medical fields. The rapid development of ultrabroad bandwidth light sources has recently enabled a significant improvement in OCT imaging resolution, demonstrating the potential of OCT to accomplish its original goal of performing noninvasive optical biopsies, i.e., the in vivo visualization of microstructural morphology in situ, which had previously only been possible with histopathology. In addition, these novel light sources might also enable the use of spectroscopic OCT, an extension of ultrahigh-resolution OCT, for enhancing image contrast as well as detecting spatially resolved functional, biochemical tissue information. State-of-the-art-light sources that now permit ultrahigh-resolution OCT covering the whole wavelength region from 500 to 1600 nm are reviewed and fundamental limitations of OCT image resolution are discussed. Ex vivo ultrahigh-resolution OCT tomograms are compared with histological results; first clinical in vivo ultrahigh-resolution OCT and preliminary spectroscopic OCT results are presented and their impact for future clinical and research applications is discussed.