gebhart/patrepeval huggingface dataset:
The human OX40/gp34 system directly mediates adhesion of activated T cells to vascular endothelial cells. (1996)

Fresh leukemic cells from patients with adult T cell leukemia (ATL) and some ATL-derived T cell lines show adhesion to human umbilical vein endothelial cells (HUVECs) mainly through E-selectin, but a proportion of this binding remains unaffected by the addition of combinations of antibodies against known adhesion molecules. By immunizing mice with one of such cell lines, we established monoclonal antibodies (mAbs), termed 131 and 315, that recognize a single cell surface antigen (Ag) and inhibit the remaining pathway of the adhesion. These mAbs did not react with normal resting peripheral blood mononuclear cells (PBMC) or most of the cell lines tested except for two other human T cell leukemia virus type I (HTLV-I)-infected T cell lines. After stimulation with phytohemagglutinin (PHA), PBMC expressed Ag 131/315 transiently, indicating that these mAbs define a T cell activation Ag. Western blotting and immunoprecipitation revealed that Ag 131/315 has an apparent molecular mass of 50 kD. Expression cloning was done by transient expression in COS-7 cells and immunological selection to isolate a cDNA clone encoding Ag 131/315. Sequence analysis of the cDNA indicated that it is identical to human OX40, a member of the tumor necrosis factor/nerve growth factor receptor family. We then found that gp34, the ligand of OX40, was expressed on HUVECs and other types of vascular endothelial cells. Furthermore, it was shown that the adhesion of CD4+ cells of PHA-stimulated PBMC to unstimulated HUVECs was considerably inhibited by either 131 or 315. Finally, OX40 transfectants of Kit 225, a human interleukin 2-dependent T cell line, were bound specifically to gp34 transfectants of MMCE, a mouse epithelial cell line, and this binding was blocked by either 315 or 5A8, an anti-gp34 mAb. These results indicate that the OX40/gp34 system directly mediates adhesion of activated T cells or OX40+-transformed T cells to vascular endothelial cells.
Extrinsic calibration of a vision sensor mounted on a robot (1992)

A vision sensor mounted on a robot to detect surrounding objects is discussed. Its mounting position and orientation must be identified, resulting in an extrinsic calibration problem. The author presents three classes of extrinsic calibration procedures. All use closed-form solutions. The class A calibration procedure requires a reference object at a recalibrated location. The class B calibration procedure takes advantage of robot mobility. It requires a reference frame, but not precalibration. The class C procedure, by taking full advantage of both robot mobility and dexterity, requires no reference object but the simplest one-a visible point. In simulation studies, the class A, B, and C calibration procedures have produced estimates successfully converging to true extrinsic parameter values. Results of field experiments carried out for class B and C calibration procedures are presented. For comparison, two existing B-type calibration methods have also been tested with real data.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Putting the Invader® Assay to Work: Laboratory Application and Data Management (2009)

Choosing a single nucleotide polymorphism genotyping method that suits specific research needs is not much less of a challenge than determining the genetic components underlying the disease and/or trait being investigated. This is especially true with a long list of tempting methodologies available, as summarized in this book. Here, from an end-user point of view, we discuss how a commercially available genotyping platform, the Invader assay, can be utilized to meet the needs and demands of human genomic research in a laboratory.
Phase I Trial of 90Y-DOTATOC Therapy in Children and Young Adults with Refractory Solid Tumors That Express Somatostatin Receptors (2010)

Peptide receptor radionuclide therapy with (90)Y-DOTATOC is safe in children and young adults and demonstrated a 12% partial response plus 29% minor response rate in patients with somatostatin receptor-positive tumors. No dose-limiting toxicities were observed. The recommended phase II dosing is 3 cycles of 1.85 GBq/m(2)/dose of (90)Y-DOTATOC coadministered with amino acids.
Mechanisms of Angiogenesis in the Brain (1999)

Brain angiogenesis is a tightly controlled process that is regulated by neuroectodermal derived growth factors that bind to tyrosine kinase receptors expressed on endothelial cells. In the rat brain, angiogenesis is complete around postnatal day 20, but endothelial cells can proliferate in the adult brain under pathological conditions such as hypoxia/ischemia and brain tumor growth. Current evidence suggests that physiological angiogenesis in the brain is regulated by similar mechanisms as pathological angiogenesis induced by tumors or by hypoxia/ischemia. The hypoxia-inducible endothelial cell mitogen and vascular permeability factor, vascular endothelial growth factor (VEGF) appears to play a pivotal role in most of these processes. VEGF is expressed when angiogenesis is high, as in embryonic neuroectoderm, in glioblastomas and around infarcts, but is expressed at low levels when angiogenesis is absent, as in adult neuroectoderm. Since growth factors such as VEGF and angiopoietins and their receptors appear to be necessary for angiogenesis, targeting of growth factor/receptor pathways for angiogenesis-dependent diseases such as glioblastoma might be useful for therapy. Several compounds, including anti-VEGF antibodies and VEGFR-2 inhibitors are currently in clinical trial. On the other hand, induction of angiogenesis by growth factors (pro-angiogenesis) might prove to be a rational therapy for patients with stroke.
Engineering Human Prolactin to Bind to the Human Growth Hormone Receptor (1990)

A strategy of iterative site-directed mutagenesis and binding analysis was used to incorporate the receptor-binding determinants from human growth hormone (hGH) into the nonbinding homolog, human prolactin (hPRL). The complementary DNA for hPRL was cloned, expressed in Escherichia coli, and mutated to introduce sequentially those substitutions from hGH that were predicted by alanine-scanning mutagenesis and other studies to be most critical for binding to the hGH receptor from human liver. After seven rounds of site-specific mutagenesis, a variant of hPRL was obtained containing eight mutations with an association constant for the hGH receptor that was increased more than 10,000-fold. This hPRL variant binds one-sixth as strongly as wild-type hGH, but shares only 26 percent overall sequence identity with hGH. These studies show the feasibility of recruiting receptor-binding properties from distantly related and functionally divergent hormones and show that a detailed functional database can be used to guide the design of a protein-protein interface in the absence of direct structural information.
Clostridium difficile Toxin Biology (2017)

Clostridium difficile is the cause of antibiotics-associated diarrhea and pseudomembranous colitis. The pathogen produces three protein toxins: C. difficile toxins A (TcdA) and B (TcdB), and C. difficile transferase toxin (CDT). The single-chain toxins TcdA and TcdB are the main virulence factors. They bind to cell membrane receptors and are internalized. The N-terminal glucosyltransferase and autoprotease domains of the toxins translocate from low-pH endosomes into the cytosol. After activation by inositol hexakisphosphate (InsP6), the autoprotease cleaves and releases the glucosyltransferase domain into the cytosol, where GTP-binding proteins of the Rho/Ras family are mono-O-glucosylated and, thereby, inactivated. Inactivation of Rho proteins disturbs the organization of the cytoskeleton and affects multiple Rho-dependent cellular processes, including loss of epithelial barrier functions, induction of apoptosis, and inflammation. CDT, the third C. difficile toxin, is a binary actin-ADP-ribosylating toxin that causes depolymerization of actin, thereby inducing formation of the microtubule-based protrusions. Recent progress in understanding of the toxins' actions include insights into the toxin structures, their interaction with host cells, and functional consequences of their actions.
A complete collection of single‐gene deletion mutants of Acinetobacter baylyi ADP1 (2008)

We have constructed a collection of single-gene deletion mutants for all dispensable genes of the soil bacterium Acinetobacter baylyi ADP1. A total of 2594 deletion mutants were obtained, whereas 499 (16%) were not, and are therefore candidate essential genes for life on minimal medium. This essentiality data set is 88% consistent with the Escherichia coli data set inferred from the Keio mutant collection profiled for growth on minimal medium, while 80% of the orthologous genes described as essential in Pseudomonas aeruginosa are also essential in ADP1. Several strategies were undertaken to investigate ADP1 metabolism by (1) searching for discrepancies between our essentiality data and current metabolic knowledge, (2) comparing this essentiality data set to those from other organisms, (3) systematic phenotyping of the mutant collection on a variety of carbon sources (quinate, 2-3 butanediol, glucose, etc.). This collection provides a new resource for the study of gene function by forward and reverse genetic approaches and constitutes a robust experimental data source for systems biology approaches.
A Series of Isoreticular, Highly Stable, Porous Zirconium Oxide Based Metal–Organic Frameworks (2012)

Brolly good MOFs: A new series of hydrophobic isoreticular porous Zr oxide dicarboxylate MOFs have been prepared (see picture, Zr blue polyhedra, O red, C black). They have a one-dimensional pore system, a rare combination of Lewis acidity and hydrophobic character, and a higher hydrothermal and mechanical stability than their UiO MOF polymorph counterparts.
Edge-phase-shifting lithography for sub-0.3-μm T-gates (1997)

We have developed an edge-phase-shifting (EPS) lithography for the fabrication of sub 0.3 micrometers T-gates using a 5X i-line stepper with a 0.4 numerical aperture lens. Two exposures have to be accurately aligned on each other within 150 nm. The first exposure uses EPS lithography and defines the gate length in a negative resist. The second exposure defines the cross-section of the T-gate. Using this lithography, hetero structure field effect transistors can be fabricated.
Substituted oxines inhibit endothelial cell proliferation and angiogenesis (2012)

Two substituted oxines, nitroxoline (5) and 5-chloroquinolin-8-yl phenylcarbamate (22), were identified as hits in a high-throughput screen aimed at finding new anti-angiogenic agents. In a previous study, we have elucidated the molecular mechanism of antiproliferative activity of nitroxoline in endothelial cells, which comprises of a dual inhibition of type 2 human methionine aminopeptidase (MetAP2) and sirtuin 1 (SIRT1). Structure-activity relationship study (SAR) of nitroxoline offered many surprises where minor modifications yielded oxine derivatives with increased potency against human umbilical vein endothelial cells (HUVEC), but with entirely different as yet unknown mechanisms. For example, 5-nitrosoquinolin-8-ol (33) inhibited HUVEC growth with sub-micromolar IC(50), but did not affect MetAP2 or MetAP1, and it only showed weak inhibition against SIRT1. Other sub-micromolar inhibitors were derivatives of 5-aminoquinolin-8-ol (34) and 8-sulfonamidoquinoline (32). A sulfamate derivative of nitroxoline (48) was found to be more potent than nitroxoline with the retention of activities against MetAP2 and SIRT1. The bioactivity of the second hit, micromolar HUVEC and MetAP2 inhibitor carbamate 22 was improved further with an SAR study culminating in carbamate 24 which is a nanomolar inhibitor of HUVEC and MetAP2.
The antioxidant effects of thylakoid Vitamin E (α‐tocopherol) (1992)

ABSTRACT Vitamin E (α‐tocopherol) is essential for the prevention of photo‐oxidative deterioration of biomembranes. The occurrence, relative biological activity and distribution of tocopherols in photosynthetic membranes is considered together with the possible biochemical and biophysical mechanisms by which tocopherols confer protection upon illuminated membranes. The common protective effects of Vitamin E in photo‐synthetic membranes and in medically important light‐induced diseases and conditions of the skin and eye in animal cell membranes are discussed. The importance of the Vitamin E‐Vitamin C thylakoid antioxidant system is also examined, in terms of susceptibility to photo‐oxidative damage under stress conditions including chilling, ageing and senescence, drought, atmospheric pollutants, herbicides and photosensitizing fungal toxins.
A lighting reproduction approach to live-action compositing (2002)

We describe a process for compositing a live performance of an actor into a virtual set wherein the actor is consistently illuminated by the virtual environment. The Light Stage used in this work is a two-meter sphere of inward-pointing RGB light emitting diodes focused on the actor, where each light can be set to an arbitrary color and intensity to replicate a real-world or virtual lighting environment. We implement a digital two-camera infrared matting system to composite the actor into the background plate of the environment without affecting the visible-spectrum illumination on the actor. The color reponse of the system is calibrated to produce correct color renditions of the actor as illuminated by the environment. We demonstrate moving-camera composites of actors into real-world environments and virtual sets such that the actor is properly illuminated by the environment into which they are composited.
Normal left renal vein mimicking left renal artery aneurysm (1981)

On transverse ultrasound scans a small number of patients with a paucity of retroperitoneal fat show an initial false impression of a left renal artery aneurysm due to the confluence of two normal findings. The left renal vein is unusually prominent from the hilum of the left kidney to the area between the superior mesenteric artery and the aorta; and part of the normal aortic wall, adjacent to the left renal vein, is incompletely imaged. Explanations for the prominence in the left renal vein and the partial visualization of the aortic wall are discussed, and various maneuvers that allow for accurate identification of both are described. The use of this analysis should prevent the incorrect diagnosis of a left renal artery aneurysm, which might lead to more invasive diagnostic procedures.
OCNet: Object Context Network for Scene Parsing (2018)

In this paper, we address the semantic segmentation task with a new context aggregation scheme named \emph{object context}, which focuses on enhancing the role of object information. Motivated by the fact that the category of each pixel is inherited from the object it belongs to, we define the object context for each pixel as the set of pixels that belong to the same category as the given pixel in the image. We use a binary relation matrix to represent the relationship between all pixels, where the value one indicates the two selected pixels belong to the same category and zero otherwise. We propose to use a dense relation matrix to serve as a surrogate for the binary relation matrix. The dense relation matrix is capable to emphasize the contribution of object information as the relation scores tend to be larger on the object pixels than the other pixels. Considering that the dense relation matrix estimation requires quadratic computation overhead and memory consumption w.r.t. the input size, we propose an efficient interlaced sparse self-attention scheme to model the dense relations between any two of all pixels via the combination of two sparse relation matrices. To capture richer context information, we further combine our interlaced sparse self-attention scheme with the conventional multi-scale context schemes including pyramid pooling~\citep{zhao2017pyramid} and atrous spatial pyramid pooling~\citep{chen2018deeplab}. We empirically show the advantages of our approach with competitive performances on five challenging benchmarks including: Cityscapes, ADE20K, LIP, PASCAL-Context and COCO-Stuff
Effect of exposure duration, contrast and base blur on coding and discrimination of edges (2002)

We extend a neural network model, developed to examine neural correlates for the dynamic synthesis of edges from luminance gradients (Oğmen, 1993), to account for the effects of exposure duration, base blur and contrast on the perceived sharpness of edges. This model of REtino-COrtical Dynamics (RECOD) predicts that (i) a decrease in exposure duration causes an increase in the perceived blur and the blur discrimination threshold for edges, (ii) this increase in perceived blur is more pronounced for sharper edges than for blurred edges, (iii) perceived blur is independent of contrast while the blur discrimination threshold decreases with contrast, (iv) perceived blur increases with increasing base blur while the blur discrimination threshold has a nonmonotonic U-shaped dependence on base blur, (v) the perceived location of an edge shifts progressively towards the low-luminance side of the edge with increasing contrast, and (vi) perceived contrast of suprathreshold stimuli is essentially independent of spatial frequency over a wide range of contrast values. These predictions are shown to be in quantitative agreement with existing psychophysical data from the literature and with data collected on three observers to quantify the effect of exposure duration on perceived blur.
Biosynthesis and secretion of the third component of complement by human endothelial cells in vitro. (1987)

The third component of complement (C3) is synthesized and released by cultured human capillary endothelial cells. After the incubation of cells in a methionine-free medium containing 35S-methionine for 48 hr, culture supernatants were immunoprecipitated with anti-human C3 serum. SDS solubilization and 2-ME reduction of the immunoprecipitates, followed by separation with SDS-polyacrylamide gel electrophoresis and autoradiography, revealed two major bands comparable to those of the alpha and beta chains of human C3. The content of C3 in the culture medium harvested at different time-intervals was determined by ELISA. The C3 secretion rate was about 250 ng/10(6) cells/5 days in the primary culture medium and 75 ng/10(6) cells/5 days after seven passages. The capillary endothelial cells described here have factor VIIIRAg specific for endothelial cells, and exhibit ring formation resembling capillary lumina, but they lack Weibel-Palade bodies.
Genetic Polymorphisms and Weight Loss in Obesity: A Randomised Trial of Hypo-Energetic High- versus Low-Fat Diets (2006)

Polymorphisms in a panel of obesity-related candidate genes play a minor role, if any, in modulating weight changes induced by a moderate hypo-energetic low-fat or high-fat diet.
TCR V alpha 24 and V beta 11 coexpression defines a human NK1 T cell analog containing a unique Th0 subpopulation (1997)

Murine NK1 natural T (NT) cells are a population of alphabeta T cells that express NK cell receptors and an invariant TCR rearrangement. These cells rapidly produce large amounts of IL-4 upon activation and have been suggested to promote Th2 differentiation. We sought to determine whether a human NK1 T cell analogue could be detected in PBMC, and if so, characterize the TCR usage, cytokine expression, and surface phenotype of this subset. Using flow cytometry, we have demonstrated a distinct population of V alpha24+, V beta11+, CD56+ T cells consistent with NT cells. Upon sequencing, these cells expressed an invariant V alpha24-J alphaQ TCR rearrangement, verifying their identity as a human NK1 T cell analogue. NT cells demonstrated increased frequencies of both IFN-gamma and IL-4 production. Strikingly, 30 to 45% of CD4+ NT cells expressed IL-4, a sixfold greater frequency than that seen in mainstream CD4+ alphabeta T cells. Contrary to the pattern seen with mainstream T cells, virtually all IL-4-producing NT cells coexpressed IFN-gamma, indicating that this subset of NT cells has a unique Th0 phenotype. These data establish that V alpha24+ NT cells are a potent source of IL-4 and as such, may play a role in Th2 priming in human immune responses. This work demonstrates that human NT cells can be phenotypically identified and functionally studied in the blood of healthy or diseased subjects.
Elimination of HIV-1 infection by treatment with a doxorubicin-conjugated anti-envelope antibody (2006)

This indicates that doxorubicin is concentrated to HIV-infected cells by the P4/D10 antibody, significantly (P = 0.0001) contributing to HIV elimination. This concept could also be adapted to eradicate remaining antigen-expressing T cells in patients treated with antiretroviral therapy.
Receptor residence time trumps drug-likeness and oral bioavailability in determining efficacy of complement C5a antagonists (2016)

Drug discovery and translation are normally based on optimizing efficacy by increasing receptor affinity, functional potency, drug-likeness (rule-of-five compliance) and oral bioavailability. Here we demonstrate that residence time of a compound on its receptor has an overriding influence on efficacy, exemplified for antagonists of inflammatory protein complement C5a that activates immune cells and promotes disease. Three equipotent antagonists (3D53, W54011, JJ47) of inflammatory responses to C5a (3 nM) were compared for drug-likeness, receptor affinity and antagonist potency in human macrophages, and anti-inflammatory efficacy in rats. Only the least drug-like antagonist (3D53) maintained potency in cells against higher C5a concentrations and had a much longer duration of action (t1/2 ~ 20 h) than W54011 or JJ47 (t1/2 ~ 1 -3 h) in inhibiting macrophage responses. The unusually long residence time of 3D53 on its receptor was mechanistically probed by molecular dynamics simulations, which revealed long-lasting interactions that trap the antagonist within the receptor. Despite negligible oral bioavailability, 3D53 was much more orally efficacious than W54011 or JJ47 in preventing repeated agonist insults to induce rat paw oedema over 24 h. Thus, residence time on a receptor can trump drug-likeness in determining efficacy, even oral efficacy, of pharmacological agents.
A new tool for the observation of embryos and other large specimens: confocal theta fluorescence microscopy (1995)

SUMMARY A theta microscope for three objective lenses was designed and built at the European Molecular Biology Laboratory (EMBL). It was used to evaluate the principles of confocal theta fluorescence microscopy and to prove its ability to handle biological specimens. A resolution improvement over confocal fluorescence microscopy has been predicted due to a detection at an angle to the illumination axis. This is verified using fluorescent beads and a fluorophore‐coated capillary. The suitability of theta microscopy for the observation of biological specimens is verified by observing a FITC‐labelled mouse embryo. In addition, the design of a theta microscope and the handling of biological material are explained in detail.
Rapid RFLP screening using DNA from complete hydatidiform moles (1989)

Journal Article Rapid RFLP screening using DNA from complete hydatidiform moles Get access M. Litt, M. Litt Search for other works by this author on: Oxford Academic PubMed Google Scholar A. Buder, A. Buder Search for other works by this author on: Oxford Academic PubMed Google Scholar U. Surti U. Surti 1Department of Pathology, Magee Women's Hospital, University of PittsburghPittsburgh, PA 15213, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 1, 11 January 1989, Page 464, https://doi.org/10.1093/nar/17.1.464 Published: 11 January 1989 Article history Received: 16 November 1988 Published: 11 January 1989