gebhart/patrepeval huggingface dataset:
Effects of Bisphosphonates on the Growth ofEntamoeba histolyticaandPlasmodiumSpecies in Vitro and in Vivo (2003)

The effects of a series of 102 bisphosphonates on the inhibition of growth of Entamoeba histolytica and Plasmodium falciparum in vitro have been determined, and selected compounds were further investigated for their in vivo activity. Forty-seven compounds tested were active (IC(50) < 200 microM) versus E. histolytica growth in vitro. The most active compounds (IC(50) approximately 4-9 microM) were nitrogen-containing bisphosphonates with relatively large aromatic side chains. Simple n-alkyl-1-hydroxy-1,1-bisphosphonates, known inhibitors of the enzyme farnesylpyrophosphate (FPP) synthase, were also active, with optimal activity being found with C9-C10 side chains. However, numerous other nitrogen-containing bisphosphonates known to be potent FPP synthase inhibitors, such as risedronate or pamidronate, had little or no activity. Several pyridine-derived bisphosphonates were quite active (IC(50) approximately 10-20 microM), and this activity was shown to correlate with the basicity of the aromatic group, with activity decreasing with increasing pK(a) values. The activities of all compounds were tested versus a human nasopharyngeal carcinoma (KB) cell line to enable an estimate of the therapeutic index (TI). Five bisphosphonates were selected and then screened for their ability to delay the development of amebic liver abscess formation in an E. histolytica infected hamster model. Two compounds were found to decrease liver abscess formation at 10 mg/kg ip with little or no effect on normal liver mass. With P. falciparum, 35 compounds had IC(50) values <200 microM in an in vitro assay. The most active compounds were also simple n-alkyl-1-hydroxy-1,1-bisphosphonates, having IC(50) values around 1 microM. Five compounds were again selected for in vivo investigation in a Plasmodium berghei ANKA BALB/c mouse suppressive test. The most active compound, a C9 n-alkyl side chain containing bisphosphonate, caused an 80% reduction in parasitemia with no overt toxicity. Taken together, these results show that bisphosphonates appear to be useful lead compounds for the development of novel antiamebic and antimalarial drugs.
Human monoclonal antibodies to the V3 loop of HIV-1 with intra- and interclade cross-reactivity (1997)

Five human anti-V3 mAbs were generated from Ab-producing cells derived from the blood of HIV-1-infected individuals from North America and selected using the V3 peptide of a divergent clade B isolate, HIV(RF). The anti-V3(RF) mAbs were mapped to a cluster of three overlapping epitopes present in the KSITKGP sequence located in the hypervariable region on the N-terminal side of the V3 loop. Broad immunochemical cross-reactivity was noted when the mAbs were tested for binding to V3 peptides derived from four clade A viruses, nine clade B viruses, and two clade C viruses. These results demonstrate antigenic relatedness in the V3 regions of these three HIV-1 clades. Affinities determined by surface plasmon resonance were higher for recombinant gp120 than for V3 peptides, suggesting that these mAbs recognize both linear and conformationally dependent epitopes of the V3 loop. Two of the mAbs neutralized four clade B T cell line-adapted and primary isolates with varying degrees of potency. The two neutralizing mAbs were the most cross-reactive with V3 peptides from several clades, had the highest affinity for V3(RF) and V3(MN), and stained HIV-infected cells. The data suggest that cross-reactivity, affinity, cell surface staining, and neutralizing activity are characteristics that describe an optimal fit between Ag and Ab. The results also demonstrate that the V3 peptides representing the sequence of several clade A, B, and C viruses share antigenic features that are recognized by the human immune response, a finding that suggests that cross-clade immunity to HIV-1 may be inducible by HIV-1 vaccines.
Minimizing Back Exchange in the Hydrogen Exchange-Mass Spectrometry Experiment (2012)

The addition of mass spectrometry (MS) analysis to the hydrogen exchange (HX) proteolytic fragmentation experiment extends powerful HX methodology to the study of large biologically important proteins. A persistent problem is the degradation of HX information due to back exchange of deuterium label during the fragmentation-separation process needed to prepare samples for MS measurement. This paper reports a systematic analysis of the factors that influence back exchange (solution pH, ionic strength, desolvation temperature, LC column interaction, flow rates, system volume). The many peptides exhibit a range of back exchange due to intrinsic amino acid HX rate differences. Accordingly, large back exchange leads to large variability in D-recovery from one residue to another as well as one peptide to another that cannot be corrected for by reference to any single peptide-level measurement. The usual effort to limit back exchange by limiting LC time provides little gain. Shortening the LC elution gradient by 3-fold only reduced back exchange by ~2%, while sacrificing S/N and peptide count. An unexpected dependence of back exchange on ionic strength as well as pH suggests a strategy in which solution conditions are changed during sample preparation. Higher salt should be used in the first stage of sample preparation (proteolysis and trapping) and lower salt (<20 mM) and pH in the second stage before electrospray injection. Adjustment of these and other factors together with recent advances in peptide fragment detection yields hundreds of peptide fragments with D-label recovery of 90% ± 5%.
Human Milk Kills Giardia lamblia by Generating Toxic Lipolytic Products (1986)

This study supports our previous hypotheses that normal human milk kills Giardia lamblia trophozoites in vitro and that this killing is due to the release of free fatty acids (FFAs) from milk triglycerides by action of the bile salt-stimulated lipase (BSL) of human milk. Heat-stable killing of G. lamblia was generated when normal human milk was preincubated with sodium cholate, which activates BSL. Moreover, both the skim-milk (containing BSL) and cream (containing mainly triglycerides) fractions were required to kill G. lamblia. We measured the toxicity of FFA and other products of lipolysis to G. lamblia. cis-Unsaturated FFAs (LD50 less than 12 microM), three of four monoglycerides, and four of five lysophosphatidylcholines were toxic to the parasites (LD50 less than 100 microM). In contrast, the parasites were not harmed by the corresponding diglycerides, phosphatidylcholines, triolein, or glycerol. Thus, products of lipid hydrolysis in the normal digestive tract are toxic to G. lamblia. We also demonstrated that albumin and conjugated bile salts, which bind FFA, partially protected trophozoites from killing by oleic acid.
Formation of large monodisperse copolymer particles by dispersion polymerization (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFormation of large monodisperse copolymer particles by dispersion polymerizationChristopher K. Ober and Kar P. LokCite this: Macromolecules 1987, 20, 2, 268–273Publication Date (Print):February 1, 1987Publication History Published online1 May 2002Published inissue 1 February 1987https://pubs.acs.org/doi/10.1021/ma00168a007https://doi.org/10.1021/ma00168a007research-articleACS PublicationsRequest reuse permissionsArticle Views1024Altmetric-Citations180LEARN 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
Cartography of complex networks: modules and universal roles (2005)

Integrative approaches to the study of complex systems demand that one knows the manner in which the parts comprising the system are connected. The structure of the complex network defining the interactions provides insight into the function and evolution of the components of the system. Unfortunately, the large size and intricacy of these networks implies that such insight is usually difficult to extract. Here, we propose a method that allows one to systematically extract and display information contained in complex networks. Specifically, we demonstrate that one can (i) find modules in complex networks and (ii) classify nodes into universal roles according to their pattern of within- and between-module connections. The method thus yields a 'cartographic representation' of complex networks.
Cell-based imaging of sodium iodide symporter activity with the yellow fluorescent protein variant YFP-H148Q/I152L (2006)

The sodium iodide symporter (NIS) mediates iodide (I(-)) transport in the thyroid gland and other tissues and is of increasing importance as a therapeutic target and nuclear imaging reporter. NIS activity in vitro is currently measured with radiotracers and electrophysiological techniques. We report on the development of a novel live cell imaging assay of NIS activity using the I(-)-sensitive and genetically encodable yellow fluorescent protein (YFP) variant YFP-H148Q/I152L. In FRTL-5 thyrocytes stably expressing YFP-H148Q/I152L, I(-) induced a rapid and reversible decrease in cellular fluorescence characterized by 1) high affinity for extracellular I(-) (35 muM), 2) inhibition by the NIS inhibitor perchlorate, 3) extracellular Na(+) dependence, and 4) TSH dependence, suggesting that fluorescence changes are due to I(-) influx via NIS. Individual cells within a population of FRTL-5 cells exhibited a 3.5-fold variation in the rate of NIS-mediated I(-) influx, illustrating the utility of YFP-H148Q/I152L to detect cell-to-cell difference in NIS activity. I(-) also caused a perchlorate-sensitive decrease in YFP-H148Q/I152L fluorescence in COS-7 cells expressing NIS but not in cells lacking NIS. These results demonstrate that YFP-H148Q/I152L is a sensitive biosensor of NIS-mediated I(-) uptake in thyroid cells and in nonthyroidal cells following gene transfer and suggest that fluorescence detection of cellular I(-) may be a useful tool by which to study the pathophysiology and pharmacology of NIS.
A novel method of conjugation of daunomycin with antibody with a poly(L-glutamic acid) derivative as intermediate drug carrier. An anti-.alpha.-fetoprotein antibody-daunomycin conjugate (1984)

In studies on antitumor antibody-cytotoxic drug conjugates as potential antitumor agents with improved tumor specificity, daunomycin (DM) was first linked to a poly-L-glutamic acid (PLGA) derivative having a single masked thiol group. At the thiol group, DM-linked PLGA was bound to horse anti-rat alpha-fetoprotein (AFP) antibody. The anti-AFP antibody-PLGA-DM conjugate (anti-AFP conjugate, DM/PLGA/Ig molar binding ratio, 7.5/1.2/1.0) retained most of the antigen-binding activity of the parent antibody and was more potent than either unconjugated DM, a conjugate similarity prepared with normal horse immunoglobulin (normal conjugate), or an unconjugated mixture of anti-AFP antibody and DM in an in vitro cytotoxicity assay against the AFP-producing rat ascites hepatoma cell line AH66. Anti-AFP conjugate tended to be less cytotoxic than DM against the AFP-nonproducing rat ascites hepatoma AH272 cells, and in this case there was no difference between the cytotoxicities of anti-AFP conjugate and of normal conjugate.
A Dynamic Model for Bilirubin Binding to Human Serum Albumin (2000)

Site-directed mutagenesis of human serum albumin was used to study the role of various amino acid residues in bilirubin binding. A comparison of thermodynamic, proteolytic, and x-ray crystallographic data from previous studies allowed a small number of amino acid residues in subdomain 2A to be selected as targets for substitution. The following recombinant human serum albumin species were synthesized in the yeast species Pichia pastoris: K195M, K199M, F211V, W214L, R218M, R222M, H242V, R257M, and wild type human serum albumin. The affinity of bilirubin was measured by two independent methods and found to be similar for all human serum albumin species. Examination of the absorption and circular dichroism spectra of bilirubin bound to its high affinity site revealed dramatic differences between the conformations of bilirubin bound to the above human serum albumin species. The absorption and circular dichroism spectra of bilirubin bound to the above human serum albumin species in aqueous solutions saturated with chloroform were also examined. The effect of certain amino acid substitutions on the conformation of bound bilirubin was altered by the addition of chloroform. In total, the present study suggests a dynamic, unusually flexible high affinity binding site for bilirubin on human serum albumin.
Gold Nanorod Bioconjugates (2005)

Gold nanorods have been stabilized, conjugated to antibodies, and characterized for biological applications. The stabilizing surfactant bilayer which surrounds gold nanorods was replaced by thiol terminated methoxypoly(ethylene glycol) so that the nanorods are stable in buffer solutions free of surfactant. Nanorod bioconjugation was accomplished with a heterobifunctional cross-linker, with antibody activity confirmed by a strip plate assay. Nanorod bioconjugates were characterized by independent measurements of the nanorod and antibody concentrations. The nanorod molar extinction coefficient was measured from dense yet well separated nanorod films to be 4.4 ± 0.5 × 109 M-1 cm-1, thus allowing quantitative determination of nanorod concentrations. However, a colorimetric protein assay overestimated the antibody concentration and is therefore likely perturbed by the presence of the nanorods electromagnetically and/or chemically.
Reduction of the Clutter Component in Doppler Ultrasound Signals Based on Singular Value Decomposition: A Simulation Study (1997)

In pulsed Doppler ultrasound systems, the ultrasound radiofrequency (RF) signals received can be employed to estimate noninvasively the time-dependent blood velocity distribution within and artery. The RF signals are composed of signals originating from clutter (e.g., vessel walls) and scatterers (e.g., red blood cells). The clutter, which is induced by stationary or slowly-moving structure interfaces, must be suppressed to get reliable estimates of the mean blood flow velocities. In conventional pulsed Doppler systems, this is achieved with a static temporal high-pass filter. The static cut-off frequency and the roll-off of these filters cause the culture not always to be optimally suppressed. This paper introduces a clutter removal filter that is based on Singular Value Decomposition (SVD). Unlike conventional high-pass filters, which take into account only the information of the temporal direction, the SVD filter makes use of the information of the temporal and spatial directions. The advantage of this approach is that it does not matter where the clutter is located in the RF signal. The performance of the SVD filter is examined with computer-generated Doppler RF signals. The results are compared with those of standard linear regression (SLR) filter. The performance of the SVD filter is good, especially if a large temporal window (i.e., approximately 100 RF signals) is applied, which improves the performance for low blood flow velocities, A major disadvantage of the SVD filter is its computational complexity, which increases considerably for larger temporal windows.
Cystic Tumor of the Atrioventricular Node of the Heart Appears to Be the Heart Equivalent of the Solid Cell Nests (Ultimobranchial Rests) of the Thyroid (2005)

We studied a series of 10 solid cell nests (SCNs) of the thyroid and a case of cystic tumor of the atrioventricular node (CTAVN) of the heart and reviewed the literature. The CTAVN and SCNs appeared as cystic and/or solid (squamoid) structures mainly composed of polygonal or oval cells (main cells) admixed with occasional clear cells (neuroendocrine and C cells). Main cells were immunoreactive for simple and stratified epithelial-type cytokeratins, epithelial membrane antigen, carcinoembryonic antigen, carbohydrate antigen 19.9, p63, bcl-2, and galectin-3. Neuroendocrine (and C) cells were positive for simple-type cytokeratins, carcinoembryonic antigen, calcitonin, chromogranin, synaptophysin, and thyroid transcription factor-1. Our data support the hypothesis that the CTAVN of the heart and the SCNs of the thyroid are identical structures that represent the same lesional process. The assumption that CTAVN is a ultimobranchial heterotopia fits with the known role of cardiac neural crest cells in cardiovascular development.
Light leakage in optical fibers: experimental results, modeling, and the consequences for remote lighting and solar concentrator systems (2001)

The optical performance of remote lighting systems and recent innovations in solar fiber-optic concentrators is acutely sensitive to transmission losses in their optical fibers. Typically, these multi-mode fibers are expected to incur small losses over long distances for broad-spectrum light sources. Experimental results reveal substantial light leakage within the nominal numerical aperture of optical fibers that have been deemed suitable for these applications. The same fibers exhibit negligible attenuation in their core. Of particular interest is the dependence of this leakage on: (a) incidence angle, (b) the optical properties of the core and the cladding, and (c) fiber length. We present laboratory measurements of fiber angular transmission, along with a theoretical model.
Alphavirus vectors: from protein production to gene therapy (2000)

Founded in 1683 in Leiden, the Netherlands, Brill is a leading international academic publisher in the Humanities, Social Sciences, International Law, and Biology. With offices in the Netherlands, Germany, Austria, the USA and Asia, Brill today publishes more than 360 journals and 2,000 new books and reference works each year as well as a large number of databases and primary source research collections.
The human immunodeficiency virus type 1 capsid p2 domain confers sensitivity to the cyclophilin-binding drug SDZ NIM 811 (1996)

Human immunodeficiency virus type 1 (HIV-1) specifically incorporates the host cell peptidyl-prolyl isomerase cyclophilin A into virions via contacts with the capsid (CA) domain of the Gag polyprotein Pr55gag. The immunosuppressant drug cyclosporin A and the nonimmunosuppressive cyclosporin A analog SDZ NIM 811 bind to cyclophilin A and inhibit its incorporation into HIV-1 virions. Both drugs inhibit the virion association of cyclophilin A and the replication of HIV-1 with a similar dose dependence. In contrast, these compounds are inactive against other primate lentiviruses which do not incorporate cyclophilin A, such as simian immunodeficiency virus (SIV). To locate determinants which confer sensitivity to SDZ NIM 811, we generated chimeric proviruses between HIV-1 and SIVmac. A hybrid SIVmac which has the CA-p2 domain of the Gag polyprotein replaced by the corresponding domain from HIV-1 replicated in an established CD4+ cell line and in human but not macaque peripheral blood mononuclear cells. The transfer of the HIV-1 CA-p2 domain to SIVmac led to the efficient incorporation of cyclophilin A, and SDZ NIM 811 effectively inhibited both the virion association of cyclophilin A and the spread of the hybrid virus in infected cultures. We conclude that the HIV-1 CA-p2 domain contains determinants which confer the necessity to interact with cyclophilin A for efficient virus replication. Furthermore, our data show that the CA-p2 domain can play a crucial role in species tropism.
Implications of Small Reductions in Diastolic Blood Pressure for Primary Prevention (1995)

A small reduction of 2 mm Hg in DBP in the mean of the population distribution, in addition to medical treatment, could have a great public health impact on the number of CHD and stroke events prevented. Whether such DBP reductions can be achieved in the population through lifestyle interventions, in particular through sodium reduction, depends on the results of ongoing primary prevention trials as well as the cooperation of the food industry, government agencies, and health education professionals.
Cutting Edge: Control of CD8+ T Cell Activation by CD4+CD25+ Immunoregulatory Cells (2001)

CD4(+)CD25(+) regulatory T cells inhibit organ-specific autoimmune diseases induced by CD4(+)CD25(-) T cells and are potent suppressors of CD4(+)CD25(-) T cell activation in vitro. We demonstrate that CD4(+)CD25(+) T cells also suppress both proliferation and IFN-gamma production by CD8(+) T cells induced either by polyclonal or Ag-specific stimuli. CD4(+)CD25(+) T cells inhibit the activation of CD8(+) responders by inhibiting both IL-2 production and up-regulation of IL-2Ralpha-chain (CD25) expression. Suppression is mediated via a T-T interaction as activated CD4(+)CD25(+) T cells suppress the responses of TCR-transgenic CD8(+) T cells stimulated with soluble peptide-MHC class I tetramers in the complete absence of APC. These results broaden the immunoregulatory role played by CD4(+)CD25(+) T cells in the prevention of autoimmune diseases, but also raise the possibility that they may hinder the induction of effector CD8(+) T cells to tumor or foreign Ags.
YKL-40 Is Elevated in Cerebrospinal Fluid from Patients with Purulent Meningitis (2002)

YKL-40, a member of the family 18 glycosyl hydrolases, is secreted by activated neutrophils and macrophages. It is a growth factor for connective tissue cells and a potent migration factor for endothelial cells and may function in inflammation and tissue remodeling. YKL-40 was determined in 134 cerebrospinal fluid (CSF) samples taken on admission from patients suspected of having meningitis (48 with purulent meningitis, 49 with lymphocytic meningitis, 5 with encephalitis, and 32 without evidence of meningitis). YKL-40 levels in CSF were significantly higher in patients with purulent meningitis (median, 663 microg/liter [range, 20 to 8,960]) and encephalitis (5,430 microg/liter [620 to 11,600]) than in patients with lymphocytic meningitis (137 microg/liter [41 to 1,865]) or patients without meningitis (167 microg/liter [24 to 630]) (Kruskal-Wallis and Dunn multiple comparison tests, P < 0.001). CSF YKL-40 levels were also determined for 26 patients with purulent meningitis having a repuncture, and patients who died (n = 5) had significantly higher YKL-40 levels than patients who survived (n = 21) (2,100 microg/liter [1,160 to 7,050] versus 885 microg/liter [192 to 15,400], respectively; Mann-Whitney test, P = 0.018). YKL-40 was most likely locally produced, since patients with infections of the central nervous system had CSF YKL-40 levels that were at least 10-fold higher than the corresponding levels in serum (2,033 microg/liter [470 to 11,600] versus 80 microg/liter [19 to 195]). The CSF neopterin level was the biochemical parameter in CSF and blood that correlated best with CSF YKL-40 levels, indicating that YKL-40 may be produced by activated macrophages within the central nervous system. In conclusion, high levels of YKL-40 in CSF are found in patients with purulent meningitis.