gebhart/patrepeval huggingface dataset:
Inhibition of Allogeneic T Cell Proliferation by Indoleamine 2,3-Dioxygenase–expressing Dendritic Cells (2002)

Indoleamine 2,3-dioxygenase (IDO), an enzyme involved in the catabolism of tryptophan, is expressed in certain cells and tissues, particularly in antigen-presenting cells of lymphoid organs and in the placenta. It was shown that IDO prevents rejection of the fetus during pregnancy, probably by inhibiting alloreactive T cells, and it was suggested that IDO-expression in antigen-presenting cells may control autoreactive immune responses. Degradation of tryptophan, an essential amino acid required for cell proliferation, was reported to be the mechanism of IDO-induced T cell suppression. Because we wanted to study the action of IDO-expressing dendritic cells (DCs) on allogeneic T cells, the human IDO gene was inserted into an adenoviral vector and expressed in DCs. Transgenic DCs decreased the concentration of tryptophan, increased the concentration of kynurenine, the main tryptophan metabolite, and suppressed allogeneic T cell proliferation in vitro. Kynurenine, 3-hydroxykynurenine, and 3-hydroxyanthranilic acid, but no other IDO-induced tryptophan metabolites, suppressed the T cell response, the suppressive effects being additive. T cells, once stopped in their proliferation, could not be restimulated. Inhibition of proliferation was likely due to T cell death because suppressive tryptophan catabolites exerted a cytotoxic action on CD3(+) cells. This action preferentially affected activated T cells and increased gradually with exposure time. In addition to T cells, B and natural killer (NK) cells were also killed, whereas DCs were not affected. Our findings shed light on suppressive mechanisms mediated by DCs and provide an explanation for important biological processes in which IDO activity apparently is increased, such as protection of the fetus from rejection during pregnancy and possibly T cell death in HIV-infected patients.
Guiding optical light in air using an all-dielectric structure (1999)

The emergence of a dielectric omnidirectional multilayer structure opens new opportunities for low loss broad-band guiding of light in air. We demonstrate the effectiveness of such an approach by fabricating a broad-band, low-loss hollow waveguide in the 10-/spl mu/m region and measuring its transmission around a 300 bend. The generality of the solution enables the application of the method to many wavelengths of interest important in telecommunication applications as well as for guiding high-power lasers in medical and other fields of use.
Characterization of a nested polymerase chain reaction assay for detection of parvovirus B19 (1993)

The characterization and application of a nested polymerase chain reaction (PCR) assay for the detection of human parvovirus B19 DNA is described. The assay was evaluated with 149 diagnostic serum samples (collected up to 150 days after the onset of symptoms) previously tested by dot blot hybridization for B19 DNA and by class-specific capture radioimmunoassays for the detection of B19 immunoglobulin M (IgM) and IgG. B19 DNA was detectable by the PCR in 70% of the sera. There was a statistically significant association between the detection of B19 DNA by PCR and high B19 IgM values (P < 0.005), low B19 IgG values (P < 0.05), and a short interval between onset of symptoms and serum collection (P < 0.005). Serial serum samples, throat swabs, and peripheral blood mononuclear cells collected from 10 individuals during an outbreak of parvovirus B19 were also tested by the nested PCR. B19 DNA was detectable in the throat swabs at the time of the clinical illness and in the peripheral blood mononuclear cell fraction up to the end point of the study 6 months after infection. The location of the B19 DNA could not be determined in cytocentrifuge preparations of peripheral blood mononuclear cells with nonisotopic in situ hybridization and immunolabelling.
Sustained clinical benefits of glatiramer acetate in relapsing multiple sclerosis patients observed for 6 years (2000)

In a randomized, placebo-controlled, double-blind study, glatiramer acetate (Copaxone®) reduced the relapse rate and slowed accumulation of disability for patients with relapsing-remitting multiple sclerosis. Of the original 251 patients randomized to receive glatiramer acetate or placebo, 208 chose to continue in an open-label study with all patients receiving active drug. The majority of the original double-blind cohort continues to receive glatiramer acetate by daily subcutaneous injection and are evaluated at 6-month intervals and during suspected relapse. The data reported here are from approximately 6 years of organized evaluation, including the double-blind phase of up to 35 months and the open-label phase of over 36 months. Daily subcutaneous injections of 20 mg glatiramer acetate were well tolerated. The mean annual relapse rate of the patients who received glatiramer acetate since randomization and continued into the open-label study was 0.42 (95% confidence interval (CI), CI=0.34-0.51). The rat...
Procedure-Related Complications of Amniocentesis and Chorionic Villous Sampling (2007)

Although the risks of pregnancy loss are relatively low, lack of adequate controls tends to underestimate the true added risk of prenatal invasive procedures.
Production and characterization of four monoclonal antibodies specific for human interferon-alpha-1 and -alpha-2. (1989)

Four monoclonal antibodies against HuIFN-alpha-1 and -alpha-2 were produced by the lymphocyte hybridoma technique. The screening for monoclonal anti-IFN antibodies was performed by two different procedures permitting the detection of neutralizing and non-neutralizing antibodies. The first antibody screening in the supernatants of hybridoma clones was carried out by an immunodot ELISA using a novel chromogen, 2-bromo-1-naphthol, for the immunoperoxidase reaction. The second screening was performed with a solid-phase bioassay. The monoclonal antibodies IIG11 and IVH2 react specifically with HuIFN-alpha-1 independently of its origin, natural or recombinant. The mAb IIG11 recognizes also an epitope on a 27 kDa interferon, probably HuIFN-alpha-8. The mAb IIG7 binds to HuIFN-alpha-2 only, whereas the mAb IIB2 binds to HuIFN-alpha-2 and also to the 27 kDa interferon and to a 25 kDa interferon, not yet further characterized. These antibodies can be used successfully for immunopurification as well as for quantification of the corresponding interferons.
Gems of Chemistry and Physics: Macroporous Metal Oxides with 3D Order (2001)

Naturally occurring gem opals would seem to be the inspiration for the recent explosion of work on three-dimensionally ordered macroporous, or “3DOM” materials. Myriad techniques have been developed for the creation of 3DOM products. This work focuses on ordered metal oxides and the effects that the chemistry behind precursors and template removal have on the phase and composition of the end product. Structural features that affect the materials' photonic, optical, catalytic, and magnetic properties are discussed.
Complement activation plays a key role in the side‐effects of rituximab treatment (2001)

Treatment with rituximab, a chimaeric anti-CD20 monoclonal antibody, can be associated with moderate to severe first-dose side-effects, notably in patients with high numbers of circulating tumour cells. The aim of this study was to elucidate the mechanism of these side-effects. At multiple early time points during the first infusion of rituximab, complement activation products (C3b/c and C4b/c) and cytokines [tumour necrosis factor alpha (TNF-alpha), interleukin 6 (IL-6) and IL-8] were measured in five relapsed low-grade non-Hodgkin's lymphoma (NHL) patients. Infusion of rituximab induced rapid complement activation, preceding the release of TNF-alpha, IL-6 and IL-8. Although the study group was small, the level of complement activation appeared to be correlated both with the number of circulating B cells prior to the infusion (r = 0.85; P = 0.07) and with the severity of the side-effects. We conclude that complement plays a pivotal role in the pathogenesis of side-effects of rituximab treatment. As complement activation can not be prevented by corticosteroids, it might be relevant to study the possible role of complement inhibitors during the first administration of rituximab.
Cross-talk-limited storage capacity of volume holographic memory (1992)

We consider the storage density limited by the cross talk between stored pages during readout. We review some earlier work done in this area and present new theoretical work that characterizes the storage capacity limitations due to the cross talk. The results show that because of the presence of degeneracy noise, storage capacity does not benefit from expanding the reference points from one dimension to two dimensions. An optimum configuration that fully utilizes storage capacity and completely eliminates degeneracy noise is given for an angularly multiplexed volume holographic memory system.
Prime–boost vaccination with plasmid and adenovirus gene vaccines control HER2/neu +metastatic breast cancer in mice (2005)

We report herein that vaccination of mice with a plasmid gene vaccine and an adenovirus gene vaccine, each containing the gene for HER2/neu, prevented growth of a HER2/neu-expressing breast cancer cell line injected into the mammary fat pad or intravenously. Sequential administration of the vaccines in a prime-boost protocol was therapeutically effective when tumor cells were injected intravenously before the vaccination. The vaccines induced high levels of both cellular and humoral immunity as determined by in vitro assessment. These findings indicate that clinical evaluation of these vaccines, particularly when used sequentially in a prime-boost protocol, is justified.
Carbamate-Linked Lactose: Design of Clusters and Evidence for Selectivity to Block Binding of Human Lectins to (Neo)Glycoproteins with Increasing Degree of Branching and to Tumor Cells (2009)

Various pathogenic processes are driven by protein(lectin)-glycan interactions, especially involving beta-galactosides at branch ends of cellular glycans. These emerging insights fuel the interest to design potent inhibitors to block lectins. As a step toward this aim, we prepared a series of ten mono- to tetravalent glycocompounds with lactose as a common headgroup. To obtain activated carbonate for ensuing carbamate formation, conditions for the facile synthesis of pure isomers from anomerically unprotected lactose were identified. To probe for the often encountered intrafamily diversity of human lectins, we selected representative members from the three subgroups of adhesion/growth-regulatory galectins as receptors. Diversity of the glycan display was accounted for by using four (neo)glycoproteins with different degrees of glycan branching as matrices in solid-phase assays. Cases of increased inhibitory potency of lactose clusters compared to free lactose were revealed. Extent of relative inhibition was not directly associated with valency in the glycocompound and depended on the lectin type. Of note for screening protocols, efficacy of blocking appeared to decrease with increased degree of glycan branching in matrix glycoproteins. Binding to tumor cells was impaired with selectivity for galectins-3 and -4. Representative compounds did not impair growth of carcinoma cells up to a concentration of 5 mM of lactose moieties (valence-corrected value) per assay. The reported bioactivity and the delineation of its modulation by structural parameters of lectins and glycans set instructive examples for the further design of selective inhibitors and assay procedures.
Regularization methods for near-field acoustical holography (2001)

The reconstruction of the pressure and normal surface velocity provided by near-field acoustical holography (NAH) from pressure measurements made near a vibrating structure is a linear, ill-posed inverse problem due to the existence of strongly decaying, evanescentlike waves. Regularization provides a technique of overcoming the ill-posedness and generates a solution to the linear problem in an automated way. We present four robust methods for regularization; the standard Tikhonov procedure along with a novel improved version, Landweber iteration, and the conjugate gradient approach. Each of these approaches can be applied to all forms of interior or exterior NAH problems; planar, cylindrical, spherical, and conformal. We also study two parameter selection procedures, the Morozov discrepancy principle and the generalized cross validation, which are crucial to any regularization theory. In particular, we concentrate here on planar and cylindrical holography. These forms of NAH which rely on the discrete Fourier transform are important due to their popularity and to their tremendous computational speed. In order to use regularization theory for the separable geometry problems we reformulate the equations of planar, cylindrical, and spherical NAH into an eigenvalue problem. The resulting eigenvalues and eigenvectors couple easily to regularization theory, which can be incorporated into the NAH software with little sacrifice in computational speed. The resulting complete automation of the NAH algorithm for both separable and nonseparable geometries overcomes the last significant hurdle for NAH.
Simulation-based Defect Printability Analysis on Alternating Phase Shifting Masks for 193nm Lithography (2002)

For alternating aperture phase shift masks (AAPSM) and 193 nm (ArF) lithography, we have simulated defect printability using inspection images and software-based modeling. Masks were fabricated by DuPont Photomasks with programmed defects of known size, phase, and location. Three phase layers were used to generate defect angles 60, 120 and 180 degrees. Simulated wafer prints were performed using Numerical Technologies’ Virtual Stepper System, which takes inspection images as input and models the lithographic process. With inspection images from KLA-Tencor’s SLF27 system, our critical-dimension measurements show good agreement with those from wafers printed on an ASML PAS 5500/900 scanner.
Layered representations for human activity recognition (2003)

We present the use of layered probabilistic representations using hidden Markov models for performing sensing, learning, and inference at multiple levels of temporal granularity We describe the use of representation in a system that diagnoses states of a user's activity based on real-time streams of evidence from video, acoustic, and computer interactions. We review the representation, present an implementation, and report on experiments with the layered representation in an office-awareness application.
Allelic Imbalance of 12q22–23 Associated with APAF-1 Locus Correlates with Poor Disease Outcome in Cutaneous Melanoma (2004)

Cutaneous melanoma is a highly aggressive tumor that is relatively resistant to chemotherapy and radiotherapy. This resistance may be in part due to inhibition of apoptosis. Apoptotic protease activating factor-1(APAF-1), a candidate tumor suppressor gene, mediates p53-induced apoptosis, and its loss promotes oncogenic transformation. To determine whether loss of the APAF-1 locus influences tumor progression, we assessed loss of heterozygosity microsatellites on the APAF-1 locus (12q22-23) in 62 primary and 112 metastatic melanomas. We discovered that frequency of allelic imbalance was significantly higher in metastatic tumors (n = 36 of 98; 37%) than in primary melanomas (n = 10 of 54; 19%; P = 0.02). In metastatic melanomas, APAF-1 loss significantly correlated with a worse prognosis (P < 0.05) in the patients, and its loss during melanoma tumor progression suggests that APAF-1 is a tumor suppressor gene. Furthermore, loss of heterozygosity was frequent in the 12q22-23 chromosome region centromeric to the APAF-1 locus suggesting that other tumor-related genes may be present in the 12q22-23 region. In summary, the study demonstrates that allelic imbalance in the 12q22-23 region is a genomic surrogate of poor disease outcome for cutaneous melanoma patients.
Optical Properties of Metal Nanoparticles with Arbitrary Shapes (2003)

We have studied the optical properties of metallic nanoparticles with arbitrary shape. We performed theoretical calculations of the absorption, extinction, and scattering efficiencies, which can be directly compared with experiments, using the discrete dipole approximation (DDA). In this work, the main features in the optical spectra have been investigated depending of the geometry and size of the nanoparticles. The origin of the optical spectra are discussed in terms of the size, shape, and material properties of each nanoparticle, showing that a nanoparticle can be distinguish by its optical signature.
The role of catecholamines in cocaine toxicity: A model for cocaine “sudden death” (1996)

Sudden death associated with cocaine abuse is preceded by a state of agitated delirium. We postulated that release of catecholamines associated with this stress enhanced toxicity from cocaine. Thus we investigated the effect of catecholamine infusion [(epinephrine (7.25 ugml-1), norepinephrine (4.4 ugml-1) and dopamine (8.0 ugml-1), infused at 6 ml h-1] on the toxicity from concomitant infusion of cocaine (1 mg-kg-1 min-1). Two groups of rats were studied in order to isolate distinct toxicity endpoints: convulsions and respiratory arrest in conscious, and, circulatory arrest in anesthetized and ventilated rats. Catecholamines were administered at either full or 1/2 strength to establish a dose response effect on cocaine toxicity. Catecholamine infusion in a dose dependent fashion provoked earlier convulsions and respiratory arrest in conscious rats and circulatory arrest in anesthetized and ventilated rats. Despite lower cocaine cumulative dose administration, rats receiving catecholamines had similar plasma cocaine concentrations at the onset of convulsions and respiratory arrest compared to those with cocaine infusion alone. The data suggest that catecholamines enhance the convulsive, respiratory and circulatory toxicity of cocaine by a pharmacokinetic interaction.
[The construction of rapid amplification of cDNA ends cDNA libraries from human fetal bone and joint]. (2001)

The protocol of RACE cDNA library construction from limited materials proved to be simple and efficient and the library was suitable for RACE to isolate tissue-specific genes.
Inflammatory Bowel Disease: Current Therapeutic Options (2006)

Medical management of inflammatory bowel diseases (IBD) includes two treatment strategies: induction and maintenance of remission. 5-Aminosalicylates are mostly used for mild active IBD and for maintenance treatment in ulcerative colitis (UC). Glucocorticoids remain, despite their frequent (and occasionally severe) side effects, as the mainstay for induction of remission in moderate to severe active IBD, both UC and Crohn's disease (CD). Cyclosporine and infliximab have emerged as the main, rapid-acting, alternatives in steroid-refractory UC and CD, respectively. Thiopurines (azathioprine and 6-mercaptopurine) are the most efficient and used immunomodulators in IBD; steroid refractoriness, steroid dependency, and long-term maintenance of remission for both UC and CD are their main indications. Methotrexate and infliximab may be used in the same clinical settings as thiopurines in CD, but not in UC; however, these drugs are a second-line treatment because of safety profile and economic costs.
Tissue-specific Alterations of Glucose Transport and Molecular Mechanisms of Intertissue Communication in Obesity and Type 2 Diabetes (2007)

Insulin resistance plays a major role in the pathogenesis of type 2 diabetes. Insulin regulates blood glucose levels primarily by promoting glucose uptake from the blood into multiple tissues and by suppressing glucose production from the liver. The glucose transporter, GLUT4, mediates insulin-stimulated glucose uptake in muscle and adipose tissue. Decreased GLUT4 expression in adipose tissue is a common feature of many insulin resistant states. GLUT4 expression is preserved in skeletal muscle in many insulin resistant states. However, functional defects in the intracellular trafficking and plasma membrane translocation of GLUT4 result in impaired insulin-stimulated glucose uptake in muscle. Tissue-specific genetic knockout of GLUT4 expression in adipose tissue or muscle of mice has provided new insights into the pathogenesis of insulin resistance. We recently determined that the expression of serum retinol binding protein (RBP4) is induced in adipose tissue as a consequence of decreased GLUT4 expression. We found that RBP4 is elevated in the serum of insulin resistant humans and mice. Furthermore, we found that increasing serum RBP4 levels by transgenic overexpression or by injection of purified RBP4 protein into normal mice causes insulin resistance. Therefore, RBP4 appears to play an important role in mediating adipose tissue communication with other insulin target tissues in insulin resistant states.
Chemical modification of erythromycins. I. Synthesis and antibacterial activity of 6-O-methylerythromycins A. (1984)

The in vitro and in vivo antibacterial activities of 6-O-methylerythromycin A (TE-031, A-56268, or clarithromycin) and 6, 11-di-O-methylerythromycin A (TE-032) have been compared with those of erythromycin A (EM) and josamycin (JM). TE-031 and TE-032, having the same antibacterial spectra as EM, are active against aerobic Gram-positive bacteria, some Gram-negative bacteria, anaerobic bacteria, L-form bacteria and Mycoplasmapneumoniae. The activity of TE-031 against clinical isolates is equal to or two times more potent than that of EM, whereas TE-032 is slightly less active than EM. The activities of TE-031 and TE-032 are pH dependent (more active at pH 8 than at 5) and are increased by adding serum to medium. TE-031 and TE-032 show dose-related bactericidal activities against Haemophilus influenzae. The therapeutic efficacies of TE-031 and TE-032 against systemic and subcutaneous infections provoked by Gram-positive bacteria in mice are 4- to 35-fold superior to those of EM and JM. TE-031 and TE-032 have demonstrated higher and longer-lasting plasma levels than EM when administered orally to mice, rats or dogs.