gebhart/patrepeval huggingface dataset:
Patterns of antigen distribution in human carcinomas. (1990)

Ten epithelial-specific monoclonal antibodies, including monoclonal antibodies to antigens that have been used extensively in immunodiagnosis and immunotherapy experiments, were tested for reactivity with 20 human carcinomas each of the colon, lung, and breast. The antibodies tested included B72.3, OC125, and antibodies to carcinoembryonic antigen, the 17-1A antigen, and the milk fat globule mucin antigen (epithelial membrane antigen). Striking differences in the pattern of antigen distribution were seen, with each antibody having a fairly consistent staining pattern, which was dependent on the tumor type. Two antibodies reacted with most or all tumor specimens and, when positive, reacted homogeneously with apparently every cell in the specimen. Other antibodies consistently produced a variegated staining pattern, typically with areas of positive cells surrounded by areas of negative tumor cells. A third pattern was strong localization to the luminal edge and/or secretions of glandular tumors; this pattern was seen primarily in colon carcinomas which have more well-developed glandular structures than breast or lung carcinomas. A correlation with biochemical properties of the antigens was evident, in that mucins or mucin-related antigens generally produced variegated staining of lung and breast carcinomas and luminal edge/secretion staining of colon carcinomas. Such differences in antigen distribution are likely to be a major factor in developing methods for immunodiagnosis and immunotherapy.
High resolution imaging through integrated nanoholes image sensor (2008)

A new imaging sensor with high resolution independent of the image sensorpsilas pixel size is presented. This sensor combines an integrated nanohole patterned in the first metal layer within each pixel and it can be fabricated in any standard submicron CMOS process. The final high resolution image requires a relative scanning motion between the sensor and the object under test; this relative motion can be achieved in an optofluidic microscopy system whereas the sample flows in a microfluidic channel while the image sensor acquires the high resolution image. Here, we describe the concept of the presented high resolution imaging sensor and elaborate on the optofludic microscopy system as one example of its implementation for a real biomedical imaging application.
Pressure Gradient Effects on Low-Wavenumber Wall-Pressure Fluctuations in Turbulent Boundary Layer Flows (2022)

Vehicle flow surfaces subject to turbulent boundary layer pressure fluctuations experience flow-induced sound and structural vibrations. Low-wavenumber surface pressure fluctuations are the source of such excitations. This paper utilizes a novel method to quantify low wavenumber pressure fluctuations on a flat plate subjected to turbulent boundary layer flow in the presence of a range of pressure gradients. An array based on Kevlar-covered resonating cavity sensors is employed to take non-intrusive measurements at high Reynolds numbers. Measurements reveal the form of the subconvective wavenumber-frequency spectrum and its dependence on Mach number and pressure gradients.
Inhibition of Aeromonas sobria serine protease (ASP) by α2-macroglobulin (2012)

ASP is a serine protease secreted by Aeromonas sobria. ASP cleaves various plasma proteins, which is associated with onset of sepsis complications, such as shock and blood coagulation disorder. To investigate a host defense mechanism against this virulence factor, we examined the plasma for ASP inhibitor(s). Human plasma inhibited ASP activity for azocasein, which was almost completely abolished by treating plasma with methylamine, which inactivates α2-macroglobulin (α2-MG). The ASP-inhibitor complex in ASP-added plasma was not detected by immunoblotting using anti-ASP antibody; however, using gel filtration of the plasma ASP activity for an oligopeptide, the ASP substrate was eluted in the void fraction (Mw>200 000), suggesting ASP trapping by α2-MG. Indeed, human α2-MG inhibited ASP azocaseinolytic activity in a dose-dependent manner, rapidly forming a complex with the ASP. Fibrinogen degradation by ASP was completely inhibited in the presence of α2-MG. α1-Protease inhibitor, antithrombin, and α2-plasmin inhibitor neither inhibited ASP activity nor formed a complex with ASP. Surprisingly, ASP degraded these plasma serine protease inhibitors. Thus, α2-MG is the major ASP inhibitor in the human plasma and can limit ASP virulence activities in A. sobria infection sites. However, as shown by fluorescence correlation spectroscopy, slow ASP inhibition by α2-MG in plasma may indicate insufficient ASP control in vivo.
Role of efficacy as a determinant of locomotor activation by mu‐opioid receptor (MOR) ligands in female and male mice. II. Effects of novel MOR‐selective phenylmorphans with high‐to‐low MOR efficacy (2023)

Low-efficacy mu-opioid receptor (MOR) agonists represent promising therapeutics, but existing compounds (e.g., buprenorphine, nalbuphine) span a limited range of low MOR efficacies and have poor MOR selectivity. Accordingly, new and selective low-efficacy MOR agonists are of interest. A novel set of chiral C9-substituted phenylmorphans has been reported to display improved MOR selectivity and a range of high-to-low MOR efficacies under other conditions; however, a full opioid receptor binding profile for these drugs has not been described. Additionally, studies in mice will be useful for preclinical characterization of these novel compounds, but the pharmacology of these drugs in mice has also not been examined. Accordingly, the present study characterized the binding selectivity and in vitro efficacy of these compounds using assays of opioid receptor binding and ligand-stimulated [<sup>35</sup> S]GTPɣS binding. Additionally, locomotor effects were evaluated as a first step for in vivo behavioral assessment in mice. The high-efficacy MOR agonist and clinically effective antidepressant tianeptine was included as a comparator. In binding studies, all phenylmorphans showed improved MOR selectivity relative to existing lower-efficacy MOR agonists. In the ligand-stimulated [<sup>35</sup> S]GTPɣS binding assay, seven phenylmorphans had graded levels of sub-buprenorphine MOR efficacy. In locomotor studies, the compounds again showed graded efficacy with a rapid onset and ≥1 h duration of effects, evidence for MOR mediation, and minor sex differences. Tianeptine functioned as a high-efficacy MOR agonist. Overall, these in vitro and in vivo studies support the characterization of these compounds as MOR-selective ligands with graded MOR efficacy and utility for further behavioral studies in mice.
Three-dimensional sensing of the magnetic-field vector by a compact planar-type Hall device (2021)

Abstract Smart society is forthcoming with a rapid development in the automation of electric appliances requiring abundant sensors. One of the key sensors is a three-dimensional magnetometer for detecting the motion of objects, which is usually driven by cooperative multiple sensors on three orthogonal planes. Here, we demonstrate the fundamental operation of a three-dimensional magnetometer based on a simple Fe-Sn heterostructure Hall device in a planar geometry. Polar coordinates of the magnetic-field vector are uniquely determined by the combination of the sizable anomalous Hall effect, the anisotropic magnetoresistance, and the unidirectional magnetoresistance. Thanks to the ferromagnetic topological features in the Fe-Sn heterostructure, the above-mentioned device overcomes the limitation of conventional semiconductor devices and is highly sensitive even at room temperature. The compact planar geometry will be particularly useful in versatile electrical applications requiring a low-cost three-dimensional magnetometer with space- and energy-saving features.
Self‐complementary monopole‐notch array antennas (1982)

Abstract The constant impedance characteristics of self‐complementary antennas are theoretically established; however, the wideband nature of their radiation patterns is not in general assured. A number of works have been published in which widebanding of radiation patterns is attempted by creating axially symmetric self‐complementary monopole‐notch array antennas on the edge of a conductor. However, for the most part these studies are based on experimental procedures. In this paper the radiation characteristics of the self‐complementary monopole‐notch antenna are analyzed theoretically and the array structure with wideband constant gain characteristics is discussed. A monopole‐notch antenna created on the edge of an ideal semiinfinite conducting plane is first analyzed and found to possess wideband radiation characteristics. A more practical monopolenotch antenna created on a finite conducting plate is then analyzed by the induced e.m.f. method. The results show that the gain is higher for the structure with a longer edge in the main beam direction. It is also found that an antenna with constant impedance and constant gain characteristic can be obtained by setting up a monopole‐notch array on a triangular conducting plate. The validity of the theoretical analysis is experimentally confirmed and the limitation of the induced e.m.f. method is evaluated.
Supplementary Data from Rebalancing Protein Homeostasis Enhances Tumor Antigen Presentation (2023)

&lt;p&gt;Summary of MC38 MHC-I Peptides&lt;/p&gt;
PURIFICATION AND CHARACTERIZATION OF TWO XYLANASES FROM TRICHODERMA LIGNORUM (1981)

Conference Abstract| April 01 1981 PURIFICATION AND CHARACTERIZATION OF TWO XYLANASES FROM TRICHODERMA LIGNORUM M. John; M. John 1Institut für Biotechnologie der Kernforschungsanlage Jülich GmbH, Postfach 1913, D-5170 Jülich (GFR Search for other works by this author on: This Site PubMed Google Scholar J. Schmidt; J. Schmidt 1Institut für Biotechnologie der Kernforschungsanlage Jülich GmbH, Postfach 1913, D-5170 Jülich (GFR Search for other works by this author on: This Site PubMed Google Scholar H. Sahm; H. Sahm 1Institut für Biotechnologie der Kernforschungsanlage Jülich GmbH, Postfach 1913, D-5170 Jülich (GFR Search for other works by this author on: This Site PubMed Google Scholar C. Wandrey C. Wandrey 1Institut für Biotechnologie der Kernforschungsanlage Jülich GmbH, Postfach 1913, D-5170 Jülich (GFR Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1981) 9 (2): 166P. https://doi.org/10.1042/bst009166pd Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation M. John, J. Schmidt, H. Sahm, C. Wandrey; PURIFICATION AND CHARACTERIZATION OF TWO XYLANASES FROM TRICHODERMA LIGNORUM. Biochem Soc Trans 1 April 1981; 9 (2): 166P. doi: https://doi.org/10.1042/bst009166pd Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1981 Biochemical Society1981 Article PDF first page preview Close Modal You do not currently have access to this content.
Stability of extended structures stabilized by light as governed by the competition of two length scales (2008)

Light-induced forces can bind dielectric spheres into extended structures through two mechanisms, each with its own length scale which can be adjusted by the configuration of the external light source. By manipulating the commensurability of the two length scales, these two mechanisms can cooperate to bind a large number of spheres. When the two length scales become incommensurate for some particular incident angle, the competition between the two mechanisms can lead to modulated structures and other complex phenomena such as reentrant stability.
Incorporating differential constraints in a 3D reconstruction process application to stereo (2002)

We propose to incorporate a priori geometric constraints in a 3-D stereo reconstruction scheme to cope with the many cases where image information alone is not sufficient to accurately recover 3-D shape. Our approach is based on the iterative deformation of a 3-D surface mesh to minimize an objective function. We show that combining anisotropic meshing with a nonquadratic approach to regularization enables us to obtain satisfactory reconstruction results using triangulations with few vertices. Structural or numerical constraints can then be added locally to the reconstruction process through a constrained optimization scheme. They improve the reconstruction results and enforce their consistency with a priori knowledge about object shape. The strong description and modeling properties of differential features make them useful tools that can be efficiently used as constraints for 3-D reconstruction.
Protective effect of Ocimum sanctum on ethanol-induced oxidative stress in swiss albino mice brain (2008)

Chronic ethanol consumption is a medical problem with important socio-economic repercussions worldwide. Its chronic consumption enhances the oxidative damage to neurons and resulting in cell death. In this study we evaluated the protective effect of Ocimum sanctum on ethanol-induced oxidative stress in Swiss albino mice brain. Mice were divided into groups comprising of vehicle control, ethanol control, Ocimum sanctum water extract (OSWE) treatment at three doses, quercetin as a reference drug control and the treatment was given orally for 30 days. Oxidative stress and anti-oxidant related enzymes were estimated from brain homogenate. OSWE was found to inhibit the lipid peroxidation and nitric oxide and enhance the superoxide dismutase in dose dependent manner.
ChemInform Abstract: Unexpected Formation of Novel Butenolides by Thermolysis of o‐Carboranyl Substituted Cyclobutenones. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A Transgenic Tri-Modality Reporter Mouse (2013)

Transgenic mouse with a stably integrated reporter gene(s) can be a valuable resource for obtaining uniformly labeled stem cells, tissues, and organs for various applications. We have generated a transgenic mouse model that ubiquitously expresses a tri-fusion reporter gene (fluc2-tdTomato-ttk) driven by a constitutive chicken β-actin promoter. This "Tri-Modality Reporter Mouse" system allows one to isolate most cells from this donor mouse and image them for bioluminescent (fluc2), fluorescent (tdTomato), and positron emission tomography (PET) (ttk) modalities. Transgenic colonies with different levels of tri-fusion reporter gene expression showed a linear correlation between all three-reporter proteins (R(2)=0.89 for TdTomato vs Fluc, R(2)=0.94 for Fluc vs TTK, R(2)=0.89 for TdTomato vs TTK) in vitro from tissue lysates and in vivo by optical and PET imaging. Mesenchymal stem cells (MSCs) isolated from this transgenics showed high level of reporter gene expression, which linearly correlated with the cell numbers (R(2)=0.99 for bioluminescence imaging (BLI)). Both BLI (R(2)=0.93) and micro-PET (R(2)=0.94) imaging of the subcutaneous implants of Tri-Modality Reporter Mouse derived MSCs in nude mice showed linear correlation with the cell numbers and across different imaging modalities (R(2)=0.97). Serial imaging of MSCs transplanted to mice with acute myocardial infarction (MI) by intramyocardial injection exhibited significantly higher signals in MI heart at days 2, 3, 4, and 7 (p<0.01). MSCs transplanted to the ischemic hindlimb of nude mice showed significantly higher BLI and PET signals in the first 2 weeks that dropped by 4(th) week due to poor cell survival. However, laser Doppler perfusion imaging revealed that blood circulation in the ischemic limb was significantly improved in the MSCs transplantation group compared with the control group. In summary, this mouse can be used as a source of donor cells and organs in various research areas such as stem cell research, tissue engineering research, and organ transplantation.
Numerical computation of acoustic radiation force in two and three dimensional resonators (2013)

Large scale acoustophoretic separation of particles in a flow field can be accomplished by trapping the particles, i.e., remain in a stationary position, in ultrasonic standing waves. The particles are collected in a column pattern, separated by half a wavelength. Within each nodal plane, the particles are trapped in the minima of the acoustic radiation potential. The axial component of the acoustic radiation force drives the particles to their stable axial position. The radial or lateral component of the acoustic radiation force is the force that traps the particle. It must be larger than the combined effect of fluid drag force, i.e., Stokes drag, and gravitational force. There is a need for a better understanding of the lateral acoustic radiation force in realistic acoustophoretic separation devices. COMSOL Multiphysics® software was used to predict the acoustic field in two and three dimensional models of acoustophoretic separation devices driven by piezoelectric transducers. The resulting acoustic field was then used to calculate the acoustic radiation force acting on a suspended particle in two and three dimensions by applying Gor’kov’s equation. Measurements of trapped particles in standing waves indicate accurate calculations of acoustic field and radiation force. [Work supported by NSF PFI:BIC 1237723.]
Fluorescence Studies of Pyrene Maleimide-Labeled Translin:  Excimer Fluorescence Indicates Subunits Associate in a Tail-to-Tail Configuration to Form Octamer (2002)

Translin is an octameric single-stranded DNA binding protein consisting of 228 amino acid residues per monomer. This protein contains two cysteine residues per monomer. Studies of reactions with DTNB show that both cysteines are reactive and exhibit biphasic reaction kinetics. Further studies with two site-directed mutants, C58S and C225S, confirm that Cys-58 reacts slowly while Cys-225 reacts quickly. Pyrene excimer emission was observed for pyrene maleimide-labeled C58S mutant. This was not observed, however, with the pyrene maleimide-labeled C225S mutant. DAS (decay associated spectra) revealed that all excited pyrene labels on C225 residues can form excimers with pyrenes of adjacent subunits within a few nanoseconds. Time-resolved emission anisotropy detects a rotational correlation time appropriate for octameric but not dimeric species. These results indicate proximity for the Cys-225 residues on adjacent monomers and that the subunits must interact in a tail-to-tail orientation. Moreover, disulfide bonds are not required for the formation of an octamer.
Multicenter evaluation of the novel ABN Western blot (immunoblot) system in comparison with an enzyme-linked immunosorbent assay and a different Western blot (1992)

A new, modular Western blot (immunoblot) system for human immunodeficiency virus (HIV) antibodies (ABN WesPage; Wellcome) was compared with enzyme immunoassays (Wellcome, Behringwerke, and Abbott) and with a U.S. Food and Drug Administration (FDA)-licensed Western blot (DuPont) in a multicenter study. A total of 649 serum samples from HIV patients at different stages of the disease, as well as from high-risk patients, from patients with conditions unrelated to AIDS, and from healthy blood donors, were used in the evaluation along with nine seroconversion panels. For evaluation of Western blot reactivity, both Centers for Disease Control (CDC) and FDA criteria were used. With the DuPont Western blot as the reference assay, the overall sensitivity and specificity of the ABN WesPage were 100 and 99.1%, respectively, when indeterminate results were not taken into account and when both tests were interpreted in accordance with CDC criteria. The DuPont Western blot detected significantly more antibodies to pol and gag gene products than the ABN WesPage. The ABN WesPage showed a higher positive rate of detection of viral envelope band gp160. When both Western blots were interpreted in accordance with CDC criteria, the ABN WesPage and the DuPont Western blot yielded 9.3 and 10.4% indeterminate results, respectively. When the DuPont Western blot was interpreted in accordance with the manufacturer's instructions (FDA criteria), 25.7% of the samples tested were regarded as indeterminate. The choice of interpretation criteria is of paramount importance for the evaluation of HIV Western blot patterns.
A framework for quad/triangle subdivision surface fitting: Application to mechanical objects (2007)

Abstract In this paper we present a new framework for subdivision surface approximation of three‐dimensional models represented by polygonal meshes. Our approach, particularly suited for mechanical or Computer Aided Design (CAD) parts, produces a mixed quadrangle‐triangle control mesh, optimized in terms of face and vertex numbers while remaining independent of the connectivity of the input mesh. Our algorithm begins with a decomposition of the object into surface patches. The main idea is to approximate the region boundaries first and then the interior data. Thus, for each patch, a first step approximates the boundaries with subdivision curves (associated with control polygons) and creates an initial subdivision surface by linking the boundary control points with respect to the lines of curvature of the target surface. Then, a second step optimizes the initial subdivision surface by iteratively moving control points and enriching regions according to the error distribution. The final control mesh defining the whole model is then created assembling every local subdivision control meshes. This control polyhedron is much more compact than the original mesh and visually represents the same shape after several subdivision steps, hence it is particularly suitable for compression and visualization tasks. Experiments conducted on several mechanical models have proven the coherency and the efficiency of our algorithm, compared with existing methods.
The propagation of spark-produced N waves through turbulence (1994)

A model experiment was designed and built to simulate the propagation of sonic booms through atmospheric turbulence. The setup of the model experiment is described briefly. Measurements of the N waves after they propagated across the turbulent velocity field reveal the same waveform distortion and change in rise time as for sonic booms. The data from the model experiment is used to test sonic boom models. Some models yield predictions for the waveform distortion, while others give estimates of the rise time of the sonic booms. A new theoretical model for the propagation of plane N waves through a turbulent medium is described.
A Framework for Multi-Platform SOA Security Analyses (2007)

The myriad of SOA platforms and the complexity of the Web services standards has meant that it is difficult for users to ensure that their deployments are appropriately secure. Despite the compilation of various SOA security "best practices''', detecting violations of such practices has proven difficult. To address this need, we developed a tool that can analyze the deployment configurations of multiple SOA platforms and report potential SOA best practice violations. In this paper, we compare, contrast and categorize SOA platforms, and describe the analysis challenges posed by each category. We describe our framework architecture for our multi-platform analyses, and further describe our prototype implementation of this architecture.