gebhart/patrepeval huggingface dataset:
Amplification of chromosome 8q22 and metastasis of breast cancers (2006)

4297 Introduction. Metastasis is the major cause of the deaths of patients with breast cancer. However, the detailed mechanism and genetic basis for tumor recurrence and metastasis is still not completely understood. Gene amplification is a common mechanism for oncogenic activation causing tumor initiation and progression. The present study is to search for gene amplification associated with metastasis potential of primary breast cancers. Methods. A cohort of 121 unselected primary tumors with at least 24 months clinical follow-up (median 48 months) were examined for gene expression on Affymetrix U133 plus 2.0 arrays. A subset of 39 high-grade cases were further studied for DNA copy number changes on Affymetrix 10K SNP arrays. Supervised analyses compared cases with metastatic recurrence within 24 months, to cases with no recurrence for at least 24 months. Amplification was confirmed by fluorescence in situhybridization (FISH) on fixed tissue sections. Results. SNP array analysis of 39 high-grade tumors revealed frequent copy number gains on 8q, with a minimum 6MB amplified region on 8q22.1-q22.2. The 8q22 amplification was verified by FISH analysis using a BAC probe to this region. examination of gene expression array data highlighted several genes in this region with positive correlation between copy number gain and increased gene expression including, but not limited to, Cyclin E2, Metadherin, and LAPTM4B. By analysis of gene expression array dataset of 121 cases, we find the 8q22 amplification/gene over-expression is present in 10% of unselected breast cancers, and is particularly associated with high tumor grade (11/69 grade III, 16% vs. 1/52 grade I or II, 2%; p= 0.012) and estrogen receptor negativity (10/51 ER-, 20% vs.2/70 ER+, 3%; p= 0.0038). Cases with 8q22 amplification were significantly more likely to have distant metastatic recurrence within 24 mo. than cases without the 8q22 amplification (7/13, 54% vs.8/108, 7%; p= 0.0001). The association with metastasis was also significant among the smaller subset of high-grade tumors (7/12, 58% vs.5/57, 9%; p= 0.0004) and among ER-negative tumors (6/11, 55% vs. 5/40, 13%; p= 0.007). Conclusions: Our results suggest that 8q22 amplification and over-expression is associated with high tumor grade, estrogen receptor negativity and with increased distant metastasis potential. Possible target genes of this amplification include Cyclin E2, Metadherin, LAPTM4B, and others.
Gas chromatographic analysis of cyclopropenoid acids in cottonseed oils (1981)

Abstract A gas chromatographic method of analysis for cyclopropenoid acids in cottonseed oil, as the methyl esters, is described. With a glass column packed with a methyl silicone substrate on an inert support, methyl sterculate and methyl malvalate can be chromatographed without decomposition. Although methyl malvalate was not well resolved from methyl linoleate, it could be quantitated accurately at concentrations as low as 0.03% by a peak‐height method. Quantitation can be done manually with an internal standard, or with a data system without an internal standard. The method does not require calibration with a cyclopropenoid acid standard, i.e., it is a primary method. Results compare favorably with those obtained by HBr titration. Less than 1 mg of oil is required for an analysis.
Dendritic homopolymers and block copolymers: Tuning the morphology and properties (2004)

Abstract The synthesis and characterization of dendritic homopolymers and block copolymers of ϵ‐caprolactone and lactide ( L ‐lactide and racemic lactide) were performed with multifunctional initiators in combination with living polymerization and the selective placement of branching junctures in a divergent growth strategy. A hexahydroxy‐functional 2,2‐bis(hydroxymethyl) propionic acid derivative was used as an initiator for the stannous‐2‐ethylhexanoate‐catalyzed living ring‐opening polymerization of ϵ‐caprolactone, L ‐lactide, and racemic L , D ‐lactide. Branching junctions at the chain ends were introduced with benzylidene‐protected 2,2‐bis(hydroxymethyl) propionic acid. Subsequent generations were then polymerized, after deprotection, from these star‐shaped macroinitiators. Successive chain end capping and initiation produced three generations of polymers with molecular weights in excess of 130,000 g/mol and narrow polydispersities (&lt;1.20). It was possible to prepare diblock and triblock copolymers with phase‐separated morphologies, and with L ‐lactide or D , L ‐lactide, semicrystalline and amorphous morphologies were demonstrated. The polymers were characterized by 1 H NMR, 13 C NMR, size exclusion chromatography, and differential scanning calorimetry. The compositions of the block copolymers and the conformational structures of the optically active polymers were also confirmed by optical rotation measurements. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 1174–1188, 2004
Haemostatic derangements associated with arenavirus infection in the guinea-pig (1993)

Pichinde virus infection of inbred guinea-pigs is a model for arenaviral infections in humans. Infected animals experience reduced levels of multiple coagulation factors caused by either consumption coagulopathy or impaired factor synthesis. A radioimmunoassay (RIA) of guinea-pig fibrinopeptide A (gFPA) has been developed to measure the degree of thrombin action in vivo. gFPA was synthesized via the solid-phase method and conjugated to bovine serum albumin (BSA). A double antibody RIA was established employing goat anti-rabbit IgG to precipitate the primary complex composed of either 125I-5-Tyr-gFPA or 125I-12-Tyr-gFPA and rabbit anti-gFPA-BSA. The crossreacting material was removed by mixing the plasma with 3 vol of ethanol. The supernatant was filtered through a hollow fibre apparatus by centrifugation. Plasma gFPA immunoreactivities of outbred guinea-pigs averaged 6.56 ng/ml. The gFPA-RIA was validated by determining the quantity of gFPA released from thrombin-degraded fibrinogen. A transient elevation of gFPA levels was detected in Pichinde-infected animals by the gFPA-RIA using 125I-12-Tyr-gFPA as a tracer. The pathogenic mechanism by which the increased gFPA levels may lead to the lethality of Pichinde virus infection remains to be elucidated. It is possible that the coagulopathy triggers changes in immune and inflammatory pathways that induces high cytokine concentrations, with deleterious effects on organs such as the heart and lungs.
A novel 4 x 8 single-mode independently addressable oxide-isolated VCSEL array (1997)

We report a novel process to fabricate single-mode independently addressable oxide-isolated vertical-cavity surface-emitting laser (VCSEL) arrays. The array is fabricated with a novel simple two-mask process where a single oxidation layer is used to define the laser aperture and to isolate the interconnects. The 4/spl times/8 VCSEL array has very uniform electrical, modal and geometrical characteristics that make it ideal for two-dimensional (2-D) array applications.
Complex Actions of 2-Aminoethyldiphenyl Borate on Store-operated Calcium Entry (2008)

Store-operated Ca2+ entry (SOCE) is likely the most common mode of regulated influx of Ca2+ into cells. However, only a limited number of pharmacological agents have been shown to modulate this process. 2-Aminoethyldiphenyl borate (2-APB) is a widely used experimental tool that activates and then inhibits SOCE and the underlying calcium release-activated Ca2+ current (I CRAC). The mechanism by which depleted stores activates SOCE involves complex cellular movements of an endoplasmic reticulum Ca2+ sensor, STIM1, which redistributes to puncta near the plasma membrane and, in some manner, activates plasma membrane channels comprising Orai1, -2, and -3 subunits. We show here that 2-APB blocks puncta formation of fluorescently tagged STIM1 in HEK293 cells. Accordingly, 2-APB also inhibited SOCE and I(CRAC)-like currents in cells co-expressing STIM1 with the CRAC channel subunit, Orai1, with similar potency. However, 2-APB inhibited STIM1 puncta formation less well in cells co-expressing Orai1, indicating that the inhibitory effects of 2-APB are not solely dependent upon STIM1 reversal. Further, 2-APB only partially inhibited SOCE and current in cells co-expressing STIM1 and Orai2 and activated sustained currents in HEK293 cells expressing Orai3 and STIM1. Interestingly, the Orai3-dependent currents activated by 2-APB showed large outward currents at potentials greater than +50 mV. Finally, Orai3, and to a lesser extent Orai1, could be directly activated by 2-APB, independently of internal Ca2+ stores and STIM1. These data reveal novel and complex actions of 2-APB effects on SOCE that can be attributed to effects on both STIM1 as well as Orai channel subunits.
New serological markers for the differential diagnosis of autoimmune limbic encephalitis1) (2012)

Abstract Recently, several novel autoantibodies have been identified which are closely associated with different subtypes of autoimmune encephalitis. These antibodies are directed against structures located on the neuronal cell surface: glutamate receptors (types NMDA and AMPA), GABA B receptors, as well as the voltage-gated potassium channel-associated proteins LGI1 and CASPR2. They are much more common than the classical paraneoplastic antibodies (anti-Hu, -Yo, -Ri, -Ma, -CV2, -amphiphysin), less frequently associated with a tumor, and the corresponding clinical syndromes respond significantly better to immunotherapy. Monospecific detection of these autoantibodies in the serum or cerebrospinal fluid of patients is primarily performed by indirect immunofluorescence using transfected HEK293 cell lines recombinantly expressing the membrane-associated target antigens. Owing to the symptom overlap of the respective disorders, it is highly appropriate to determine these parameters in parallel for each patient (autoantibody profiles). Early diagnosis (substantially supported by the serological laboratory), the immediate initiation of immunotherapeutic intervention and, in cases of paraneoplastic etiology, tumor resection are crucial for prognosis. In our own investigations, antibodies against glutamate receptors (type NMDA) are most frequently found among the newly identified forms of autoimmune encephalitis, accounting for 42% of cases. In laboratory practice, one-third of positive reactions were caused by an autoantibody whose determination was not requested by the clinician. Considering the urgency for therapeutic measures in positive cases, these findings substantiate the need to implement multiparametric serological test systems in this diagnostic area.
Elastolytic and Collagenolytic Studies of Arteries (1984)

Studies were performed in vitro on cylindrical segments of 56 canine common carotid arteries, 32 human external iliac arteries, nine internal iliac arteries, and ten common iliac arteries, using purified elastase and purified collagenase. Treatment with elastase caused the canine vessels to dilate but to remain intact. Similar results were obtained with the human vessels, except that treatment with elastase caused only slight dilation. All canine and human vessels treated with collagenase ruptured. We concluded that wall integrity depends on intact collagen rather than elastin. Comparison between external iliac arteries and internal and common iliac arteries showed that the latter vessels exhibited dramatically greater dilatation and compliance changes after treatment with collagenase. This finding corresponds to the greater tendency of aneurysms to develop in internal and common iliac arteries.
Incidence of Autoantibodies Against Type I and Type II Interferons in a Cohort of Systemic Lupus Erythematosus Patients in Slovakia (2003)

Autoantibodies against interferon (IFN) can be found in patients with systemic lupus erythematosus (SLE). However, detailed information about the occurrence of type-specific antihuman IFN antibodies is not available. In this study, we investigated the incidence of autoantibodies specifically recognizing various type I IFNs (alpha1, alpha2, beta, omega) and type II IFN (gamma). Sera from 100 SLE patients were screened for the presence of IFN-binding antibodies by ELISA, using various types of recombinant IFNs as antigen. On the whole, autoantibodies against type I or type II or both IFNs were detected in 45% (45 of 100) of the serum samples investigated. More than half (56%) of the positive samples (25 of 45) contained antibodies specific only for type I IFNs, and 36% of positive sera (16 of 45) had autoantibodies only against type II IFN. Antibodies against both type I and type II IFNs were detected in 8% (4 of 45) of the positive samples. Among autoantibodies to type I IFNs, the most abundant were those against the type IFN-omega (15%) and the subtype IFN-alpha2 (11%). Autoantibodies binding subtype IFN-alpha1 and type IFN-beta were detected at a relatively lower incidence of about 3%-4%. The highest occurrence (20%) showed autoantibodies to the proinflammatory cytokine, IFN-gamma. We did not find any correlation between the production of autoantibodies against particular IFN species and an antibody response to other IFN species. We further observed that 84% (38 of 45) of the positive sera bound only one IFN species, and 13% (6 of 45) of positive samples contained antibodies against two IFN species of five different combinations (alpha1/beta, alpha1/omega, alpha2/omega, alpha2/gamma, omega/gamma). One sample uniquely showed reactivity with three IFN species (alpha2/omega/gamma). Our findings suggest that formation of autoantibodies could reflect humoral immune responses to increased spontaneous production of the respective IFN species in SLE patients.
Insulin analogues (1997)

For years, it has been recognized that "reasonable" control of blood glucose levels reduces the acute complications of diabetes mellitus. Recent studies have conclusively shown that strict glycemic control reduces the appearance and progression of chronic complications. Thus, strict glycemic control is the most salient goal of insulin therapy. Insulin regimens that closely mimic physiologic insulin secretory patterns have been inadequate because of limitations imposed by the pharmacokinetic profiles of commercially available preparations. The newer insulin analogues, both rapid-acting and long-acting, have more appropriate pharmacokinetic profiles. Lispro (Humalog) is the first human insulin analogue to be approved in the United States. Its pharmacokinetic and pharmacodynamic profile makes it amenable for use before meals. The search for long-acting and hepatospecific analogues continues.
Photonic bandgap with an index step of one percent (2005)

Early work suggested that very large refractive index contrasts would be needed to create photonic bandgaps in two or three dimensionally periodic photonic crystals. It was then shown that in two-dimensionally periodic structures (such as photonic crystal fibres) a non-zero wavevector component in the axial direction permits photonic bandgaps for much smaller index contrasts. Here we experimentally demonstrate a photonic bandgap fibre made from two glasses with a relative index step of only 1%.
Total chemical synthesis of proteins (2008)

This tutorial review outlines the modern ligation methods that enable the efficient total chemical synthesis of enzymes and other protein molecules. Key to this success is the chemoselective reaction of unprotected synthetic peptides ('chemical ligation'). Notably, native chemical ligation enables the reaction of two unprotected peptides in aqueous solution at neutral pH to form a single product in near quantitative yield. Full-length synthetic polypeptides are folded to form the defined tertiary structure of the target protein molecule, which is characterized by mass spectrometry, NMR, and X-ray crystallography, in addition to biochemical and/or biological activity.
Candida Infections of Medical Devices (2004)

The number of indwelling medical devices is escalating, and an increasing proportion of device-related infections are being caused by Candida spp. Candida spp. produce biofilms on synthetic materials, which facilitates adhesion of the organisms to devices and renders them relatively refractory to medical therapy. Management of device-related Candida infections can be challenging. Removal of the infected device is generally needed to establish cure of Candida infections of medical devices. However, since the pathogenesis of Candida bloodstream infection is complicated, more studies are necessary to determine the role of catheter exchange in patients with both gastrointestinal tract mucositis and indwelling catheters. The medical and economic impact of these infections is enormous.
Thiazolidine Diones, Specific Ligands of the Nuclear Receptor Retinoid Z Receptor/Retinoid Acid Receptor-related Orphan Receptor α with Potent Antiarthritic Activity (1996)

Rat adjuvant arthritis is a chronic T cell-dependent autoimmune disease with many similarities to rheumatoid arthritis. We have identified a class of thiazolidine diones with high potency in suppressing chronic inflammation and joint destruction in this experimental model. The lead compound CGP 52608 (1-(3-allyl-4-oxothiazolidine-2-ylidene)-4-methylthiosemicarbazone) exhibits antiarthritic activity at daily oral doses between 0.01 and 1 mg/kg and was shown to specifically activate the retinoid Z receptor/retinoid acid receptor-related orphan receptor alpha (RZR/RORalpha) in low nanomolar concentrations. This receptor is a novel member of the superfamily of ligand-inducible transcription factors, and we have recently identified the pineal gland hormone melatonin as a natural ligand. Structure-activity relationship studies with 13 closely related analogues of CGP 52608 revealed a striking correlation between RZR/RORalpha activation and antiarthritic activity. We therefore suggest that nuclear signaling via RZR/RORalpha is a key mechanism in mediating the antiarthritic effects of these thiazolidine diones and may open a novel therapeutic approach for the treatment of rheumatoid arthritis and other autoimmune diseases. The existence of a nuclear melatonin receptor may lead to a better understanding of the immunomodulatory actions of melatonin.
Generating Ambiguous Figure-Ground Images (2016)

Ambiguous figure-ground images, mostly represented as binary images, are fascinating as they present viewers a visual phenomena of perceiving multiple interpretations from a single image. In one possible interpretation, the white region is seen as a foreground figure while the black region is treated as shapeless background. Such perception can reverse instantly at any moment. In this paper, we investigate the theory behind this ambiguous perception and present an automatic algorithm to generate such images. We model the problem as a binary image composition using two object contours and approach it through a three-stage pipeline. The algorithm first performs a partial shape matching to find a good partial contour matching between objects. This matching is based on a content-aware shape matching metric, which captures features of ambiguous figure-ground images. Then we combine matched contours into a compound contour using an adaptive contour deformation, followed by computing an optimal cropping window and image binarization for the compound contour that maximize the completeness of object contours in the final composition. We have tested our system using a wide range of input objects and generated a large number of convincing examples with or without user guidance. The efficiency of our system and quality of results are verified through an extensive experimental study.
Molecular Actions of Insulin on Glucose Transport (1995)

Low basal glucose uptake by insulin-sensitive muscle and adipose cells reflects rapid endocytic retrieval of GLUT4 glucose transporters from the cell surface and their retention in intracellular membranes. Both GLUT4 endocytosis and its intracellular retention are governed by a dileucine motif in its COOH-terminal region. Acute stimulation of sugar uptake by insulin results from GLUT4 redistribution to the plasma membrane and may reflect disruption of dileucine motif function as well as enhanced bulk membrane exocytosis. Candidate signaling elements for these postulated actions of insulin are PI 3-kinase and p21ras, both acutely activated by the hormone. Recent work in our laboratory and others demonstrates the localization of PI 3-kinase to intracellular membranes via its docking to the insulin receptor substrate-1 (IRS-1). An important hypothesis for future testing is that 3' phosphoinositides generated in the endosomal tubulovesicular system in response to insulin cause budding or movements of GLUT4-containing membranes to the cell surface.
Intraperitoneal delivery of hrR3 and ganciclovir prolongs survival in mice with disseminated pancreatic cancer (1999)

Intraperitoneal delivery of hrR3 and ganciclovir improves survival in this murine model of peritoneal dissemination of pancreatic cancer. The ability of hrR3 to replicate only in rapidly dividing cells makes this virus an attractive vector for gene therapy of cancer.
Trans-Oceanic Radio Communication (1920)

The possible limitation in the number of long distance radio stations simultaneously in operation is considered. It is shown how high-speed transmission, improved directional selectivity, and better frequency selectivity would greatly increase the number of feasible co-existent stations, The utilization of a wave length band as a result of high-speed transmission is discussed in connection with frequency selectivity. The 200-kilowatt alternator station at New Brunswick is described, special mention being made of the constant speed regulation system for the induction motor drive, the functioning of the magnetic amplifier, and the operation of the multiple antenna. In this latter connection, the possibilities of effective directional radiation are considered.
The Design Space of Augmented and Virtual Reality Applications for Assistive Environments in Manufacturing (2017)

Research on how to take advantage of Augmented Reality and Virtual Reality applications and technologies in the domain of manufacturing has brought forward a great number of concepts, prototypes, and working systems. Although comprehensive surveys have taken account of the state of the art, the design space of industrial augmented and virtual reality keeps diversifying. We propose a visual approach towards assessing this space and present an interactive, community-driven tool which supports interested researchers and practitioners in gaining an overview of the aforementioned design space. Using such a framework we collected and classified relevant publications in terms of application areas and technology platforms. This tool shall facilitate initial research activities as well as the identification of research opportunities. Thus, we lay the groundwork, forthcoming workshops and discussions shall address the refinement.
Magnetically tunable Nanocomposites for microwave applications (2010)

In this work, tunability of the microwave properties of Magneto-Dielectric Polymer Nanocomposites (MDPNCs) has been demonstrated for the first time. Particularly, permeability, permittivity and loss factor were tuned by an externally applied DC magnetic field with strength achievable by commercial permanent magnets. The considerable tunability, ease of manufacturing, compatibility with multilayer RF laminates and substrate implementation make this material well-suited for use in tunable microwave circuits. Two custom-built microstrip test fixtures using multi-layer substrates were employed to extract the permeability, permittivity and loss tangent of MDPNCs using S-parameter measurements.