gebhart/patrepeval huggingface dataset:
Barrett's esophagus. Correlation between mucin histochemistry, flow cytometry, and histologic diagnosis for predicting increased cancer risk. (1988)

A predominance of sulfated mucin in the nongoblet columnar cells of Barrett's specialized metaplastic epithelium has been postulated to be a form of mild dysplasia and to indicate an increased risk of adenocarcinoma. Flow cytometry for the analysis of nuclear DNA content and cell cycle parameters has also been postulated to be an objective aid in the diagnosis of dysplasia and carcinoma in Barrett's esophagus. The authors investigated the relationship among sulfated mucin, flow cytometric data, and histologic diagnosis in each of 152 biopsies from 42 patients who had Barrett's specialized metaplastic epithelium. Sulfated mucin, as detected by the high iron diamine-Alcian blue stain, was present in biopsies from 8 of 11 (73%) patients with the histologic diagnosis of dysplasia or carcinoma, in 7 of 9 (78%) patients whose biopsies were indefinite for dysplasia, and in 12 of 22 (55%) patients whose biopsies were negative for dysplasia (P = 0.37). Sulfated mucins predominated in 9%, 22%, and 9% of the patients, respectively (P = 0.56). Abnormal flow cytometry (aneuploidy or increased G2/tetraploid fraction) was found in all patients with the histologic diagnosis of dysplasia or carcinoma, in 3 of 9 (33%) indefinite for dysplasia, and in 1 of 22 (5%) negative for dysplasia (P = less than 0.0001). Neither the presence nor the predominance of sulfated mucin in the specialized metaplastic epithelium of Barrett's esophagus has sufficiently high sensitivity or specificity for dysplasia or carcinoma to be of value in managing patients. Abnormal flow cytometry shows excellent correlation with the histologic diagnosis of dysplasia and carcinoma; it detects a subset of patients whose biopsies are histologically indefinite or negative for dysplasia, but who have flow cytometric abnormalities similar to those otherwise seen only in dysplasia and carcinoma.
Molecular characterization of the rat Kupffer cell glycoprotein receptor (2003)

The Kupffer cell receptor for glycoproteins has been reported to have a role in clearance of galactose- and fucose-terminated glycoproteins from circulation. Although the gene and a cDNA encoding the receptor have been described, there has been little study of the receptor protein. To address some questions about possible ligands and functions for this receptor, fragments representing portions of the extracellular domain have been expressed and characterized. The extracellular domain consists of a trimer stabilized by an extended coiled-coil of alpha-helices. The receptor displays monosaccharide-binding characteristics similar to the hepatic asialoglycoprotein receptor, but with somewhat less selectivity. The two best monosaccharide ligands are GalNAc and galactose. alpha-Methyl fucoside is a particularly poor ligand. Analysis of Kupffer cell receptor binding to glycoproteins and oligosaccharides released from them reveals highest affinity for desialylated, complex N-linked glycans. The best glycoprotein ligands contain multiple highly branched oligosaccharides. A human ortholog of the rat receptor gene does not encode a full-length protein and is not expressed in liver. These characteristics suggest that the receptor may have functions parallel to those of the hepatocyte asialoglycoprotein receptor in some (but not all) mammalian species.
Glycoprotein Hormones: Structure and Function (1981)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
T Cell Receptor Gene Therapy for Cancer (2009)

T cell-based adoptive immunotherapy has been shown to be a promising treatment for various types of cancer. However, adoptive T cell therapy currently requires the custom isolation and characterization of tumor-specific T cells from each patient—a process that can be not only difficult and time-consuming but also often fails to yield high-avidity T cells, which together have limited the broad application of this approach as a clinical treatment. Employing T cell receptor (TCR) gene therapy as a component of adoptive T cell therapy strategies can overcome many of these obstacles, allowing autologous T cells with a defined specificity to be generated in a much shorter time period. Initial studies using this approach have been hampered by a number of technical difficulties resulting in low TCR expression and acquisition of potentially problematic specificities due to mispairing of introduced TCR chains with endogenous TCR chains. The last several years have seen substantial progress in our understanding of the multiple facets of TCR gene therapy that will have to be properly orchestrated for this strategy to succeed. Here we outline the challenges of TCR gene therapy and the advances that have been made toward realizing the promise of this approach.
Sensitive and Specific Serodiagnosis of Lyme Disease by Enzyme-Linked Immunosorbent Assay with a Peptide Based on an Immunodominant Conserved Region ofBorrelia burgdorferiVlsE (1999)

VlsE, the variable surface antigen of Borrelia burgdorferi, contains an immunodominant conserved region named IR(6). In the present study, the diagnostic performance of a peptide enzyme-linked immunosorbent assay (ELISA) based on a 26-mer synthetic peptide (C(6)) with the IR(6) sequence was explored. Sensitivity was assessed with serum samples (n = 210) collected from patients with clinically defined Lyme disease at the acute (early localized or early disseminated disease), convalescent, or late disease phase. The sensitivities for acute-, convalescent-, and late-phase specimens were 74% (29 of 39), 85 to 90% (34 of 40 to 35 of 39), and 100% (59 of 59), respectively. Serum specimens from early neuroborreliosis patients were 95% positive (19 of 20), and those from an additional group of patients with posttreatment Lyme disease syndrome yielded a sensitivity of 62% (8 of 13). To assess the specificity of the peptide ELISA, 77 serum samples from patients with other spirochetal or chronic infections, autoimmune diseases, or neurologic diseases and 99 serum specimens from hospitalized patients in an area where Lyme disease is not endemic were examined. Only two potential false positives from the hospitalized patients were found, and the overall specificity was 99% (174 of 176). Precision, which was assessed with a panel of positive and negative serum specimens arranged in blinded duplicates, was 100%. Four serum samples with very high anti-OspA antibody titers obtained from four monkeys given the OspA vaccine did not react with the C(6) peptide. This simple, sensitive, specific, and precise ELISA may contribute to alleviate some of the remaining problems in Lyme disease serodiagnosis. Because of its synthetic peptide base, it will be inexpensive to manufacture. It also will be applicable to serum specimens from OspA-vaccinated subjects.
The I domain is a major recognition site on the leukocyte integrin Mac-1 (CD11b/CD18) for four distinct adhesion ligands. (1993)

Despite the identification and characterization of several distinct ligands for the leukocyte integrin (CD11/CD18) family of adhesion receptors, little is known about the structural regions on these molecules that mediate ligand recognition. In this report, we use alpha subunit chimeras of Mac-1 (CD11b/CD18) and p150,95 (CD11c/CD18), and an extended panel of newly generated and previously characterized mAbs specific to the alpha chain of Mac-1 to map the binding sites for four distinct ligands for Mac-1: iC3b, fibrinogen, ICAM-1, and the as-yet uncharacterized counter-receptor responsible for neutrophil homotypic adhesion. Epitopes of mAbs that blocked ligand binding were mapped with the chimeras and used to localize the ligand recognition sites because the data obtained from functional assays with the Mac-1/p150,95 chimeras were not easily interpreted. Results show that the I domain on the alpha chain of Mac-1 is an important recognition site for all four ligands, and that the NH2-terminal and perhaps divalent cation binding regions but not the COOH-terminal segment may contribute. The recognition sites in the I domain appear overlapping but not identical as individual Mac-1-ligand interactions are distinguished by the discrete patterns of inhibitory mAbs. Additionally, we find that the alpha subunit NH2-terminal region and divalent cation binding region, despite being separated by over 200 amino acids of the I domain, appear structurally apposed because three mAbs require the presence of both of these regions for antigenic reactivity, and chimeras that contain the NH2 terminus of p150,95 require the divalent cation binding region of p150,95 to associate firmly with the beta subunit.
A glycomic approach to the identification and characterization of glycoprotein function in cells transfected with glycosyltransferase genes (2001)

The transfection of glycoprotein glycosyltransferase genes into cells leads to modification of both the structure and function of the glycoproteins and as a result, changes in glycome patterns. N-glycan branching enzymes hold some promise as a model system for the identification of glycome patterns. Both N-acetylglucosaminyltransferase III and α1–6 fucosyltransferase are typical glycosyltransferases, which are involved in the branching of N-glycans. The resulting enzymatic products, bisecting N-GlcNAc and α1–6 fucose residues, are no longer modified by other glycosyltransferases and it is a relatively simple task to identify their modification by means of lectins. In this review, the glycome patterns of glycosyltransferase gene transfectants and the nontransfectants were compared by two-dimensional gel electrophoresis and lectin staining, and the biological significance of the two genes are described. Analyses of glycome patterns by transfecting glycosyltransferase genes will lead to new fields of study in the area of postgenome research.
Complement activation upon binding of mannan-binding protein to HIV envelope glycoproteins (1993)

Activation of the classical complement pathway by retrovirus envelope proteins can be initiated by the binding of MBP to carbohydrate side chains of envelope glycoproteins.
Example-centric programming (2010)

The ready availability of online source-code examples has fundamentally changed programming practices. However, current search tools are not designed to assist with programming tasks and are wholly separate from editing tools. This paper proposes that embedding a task-specific search engine in the development environment can significantly reduce the cost of finding information and thus enable programmers to write better code more easily. This paper describes the design, implementation, and evaluation of Blueprint, a Web search interface integrated into the Adobe Flex Builder development environment that helps users locate example code. Blueprint automatically augments queries with code context, presents a code-centric view of search results, embeds the search experience into the editor, and retains a link between copied code and its source. A comparative laboratory study found that Blueprint enables participants to write significantly better code and find example code significantly faster than with a standard Web browser. Analysis of three months of usage logs with 2,024 users suggests that task-specific search interfaces can significantly change how and when people search the Web.
Physiology of the Control of Food Intake (1982)

INTRODUCTION AND SCOPE 371 DEFINITIONS 373 PHENOMENA TO BE EXPLAINED 375 THEORIES 386 TESTS OF THE THEORIES BY NUTRIENT ADMINISTRATION 392 MECHANISMS 402 CONCLUSIONS 405
Dried plasma: state of the science and recent developments (2016)

The early transfusion of plasma is important to ensure optimal survival of patients with traumatic hemorrhage. In military and remote or austere civilian settings, it may be impossible to move patients to hospital facilities within the first few hours of injury. A dried plasma product with reduced logistical requirements is needed to enable plasma transfusion where medically needed, instead of only where freezers and other equipment are available. First developed in the 1930s, pooled lyophilized plasma was widely used by British and American forces in WWII and the Korean War. Historical dried plasma products solved the logistical problem but were abandoned because of disease transmission. Modern methods to improve blood safety have made it possible to produce safe and effective dried plasma. Dried plasma products are available in France, Germany, South Africa, and a limited number of other countries. However, no product is available in the US. Promising products are in development that employ different methods of drying, pathogen reduction, pooling, packaging, and other approaches. Although challenges exist, the in vitro and in vivo data suggest that these products have great potential to be safe and effective. The history, state of the science, and recent developments in dried plasma are reviewed.
Nucleoside Phosphotransferase from Malt Sprouts. I. Isolation, Characterization and Specificity of the Enzyme (1986)

The nucleoside phosphotransferase of barley was isolated in four steps from dried malt sprouts and was obtained homogeneous according to several criteria. The enzyme transfers the phospho group from the 3'- or 5'-position of a nucleotide to the 5'-OH group of another nucleoside. Activated phosphomonoesters (e.g. 4-nitrophenyl phosphate) can be used as donors as well. In the absence of nucleosides the enzyme shows pronounced phosphatase activity towards 3'- and 5'-nucleotides as well as towards activated phosphomonoesters. 2'-Nucleotides are not hydrolysed. Studies of the phosphatase activity with a number of modified nucleotides demonstrate that the nucleotide substrates are bound by the phosphate group and by the base. The base can be extensively modified compared to naturally occurring nucleobases. Obviously, only a hydrophobic interaction with the enzyme is required; base-specific hydrogen bonds are of no importance. In the transferase reaction the acceptor nucleoside interacts only with the base which has a much more restricted specificity. Nucleotides which are donors do not need to be acceptors when they are nucleosides, while all acceptor nucleosides are efficient donors. Due to the pre-orientation of the base, the phosphate groups of the 3'- and 5'-nucleotides are in different positions relative to the groups of the enzyme that are involved in the catalysis. This is reflected in the kinetic parameters which are interpreted on the basis of a mechanism with a phospho-intermediate as postulated for the enzyme of Ives et al. [(1979) J. Biol. Chem. 254, 4339; (1982) J. Biol. Chem. 257, 4931]. Evidence is obtained that Km represents the ratio of the rate constants for the decay and the formation of the intermediate and that the kcat/Km-value can be used as indicator for the formation step.
Reversal of the antiinflammatory effects of methotrexate by the nonselective adenosine receptor antagonists theophylline and caffeine: Evidence that the antiinflammatory effects of methotrexate are mediated via multiple adenosine receptors in rat adjuvant arthritis (2000)

These results provide strong evidence that adenosine mediates the antiinflammatory effects of MTX in this model of RA. Moreover, the findings suggest that abstinence from caffeine, a ubiquitous food additive and medication, may enhance the therapeutic effects of MTX in RA.
Overexpression of HOXB4 in hematopoietic cells causes the selective expansion of more primitive populations in vitro and in vivo. (1995)

Hox genes were first recognized for their role in embryonic development and may also play important lineage-specific functions in a variety of somatic tissues including the hematopoietic system. We have recently shown that certain members of the Hox A and B clusters, such as HOXB3 and HOXB4, are preferentially expressed in subpopulations of human bone marrow that are highly enriched for the most primitive hematopoietic cell types. To assess the role these genes may play in regulating the proliferation and/or differentiation of such cells, we engineered the overexpression of HOXB4 in murine bone marrow cells by retroviral gene transfer and analyzed subsequent effects on the behavior of various hematopoietic stem and progenitor cell populations both in vitro and in vivo. Serial transplantation studies revealed a greatly enhanced ability of HOXB4-transduced bone marrow cells to regenerate the most primitive hematopoietic stem cell compartment resulting in 50-fold higher numbers of transplantable totipotent hematopoietic stem cells in primary and secondary recipients, compared with serially passaged neo-infected control cells. This heightened expansion in vivo of HOXB4-transduced hematopoietic stem cells was not accompanied by identifiable anomalies in the peripheral blood of these mice. Enhanced proliferation in vitro of day-12 CFU-S and clonogenic progenitors was also documented. These results indicate HOXB4 to be an important regulator of very early but not late hematopoietic cell proliferation and suggest a new approach to the controlled amplification of genetically modified hematopoietic stem cell populations.
Multi-scale surface texture to improve blue response of nanoporous black silicon solar cells (2011)

We characterize the optical and carrier-collection physics of multi-scale textured p-type black Si solar cells with conversion efficiency of 17.1%. The multi-scale texture is achieved by combining density-graded nanoporous layer made by metal-assisted etching with micron-scale pyramid texture. We found that (1) reducing the thickness of nanostructured Si layer improves the short-wavelength spectral response and (2) multi-scale texture permits thinning of the nanostructured layer while maintaining low surface reflection. We have reduced the nanostructured layer thickness by 60% while retaining a solar-spectrum-averaged black Si reflectance of less than 2%. Spectral response at 450 nm has improved from 57% to 71%.
Cognitive deficits in asymptomatic first-degree relatives of Alzheimer's disease patients (1994)

The present study was designed to determine whether neuropsychological deficits exist in asymptomatic first-degree relatives of Alzheimer's disease (AD) patients. The neuropsychological performances of 20 first-degree asymptomatic relatives of NINCDS-ADRDA diagnosed AD patients were compared to 20 normal controls without family history of AD. Cognitive functions assessed included intelligence, memory, overall brain function, verbal learning, and language and constructional abilities. Significant statistical differences were found between the groups across several cognitive areas indicating lower functioning in the first-degree relatives of AD patients. Fifty percent of the first-degree subjects but only 20% of controls showed a pattern of significant neuropsychological deficit. The results demonstrate neuropsychological deficits in asymptomatic first-degree relatives of AD patients, suggesting that preclinical markers for AD may be present long before the clinical manifestation of the disease.
The effects of thermal equilibrium and contrast in LWIR polarimetric images (2007)

Long-wave infrared (LWIR) polarimetric signatures provide the potential for day-night detection and identification of objects in remotely sensed imagery. The source of optical energy in the LWIR is usually due to thermal emission from the object in question, which makes the signature dependent primarily on the target and not on the external environment. In this paper we explore the impact of thermal equilibrium and the temperature of (unseen) background objects on LWIR polarimetric signatures. We demonstrate that an object can completely lose its polarization signature when it is in thermal equilibrium with its optical background, even if it has thermal contrast with the objects that appear behind it in the image.
Site-specific attachment to recombinant antibodies via introduced surface cysteine residues (1990)

Many diagnostic and therapeutic applications of monoclonal antibodies require the covalent linking of effector or reporter molecules to the immunoglobulin polypeptides. Existing methods generally involve the non-selective modification of amino acid side chains, producing one or more randomly distributed attachment sites. This results in heterogeneous labelling of the antibody molecules and often to a decrease in antigen-binding due to the modification of residues close to the antigen-binding site. We report a novel strategy for site-specifically labelling antibodies through surface cysteine residues. Examination of molecular structures was used to identify amino acids of the CH1 domain of the IgG heavy chain that were accessible to solvent but not to larger molecules. Site-directed mutagenesis was used to substitute cysteine residues at these positions in the heavy chain of a mouse/human chimaeric version of the tumour-binding monoclonal antibody, B72.3. Expression of the modified antibody genes in mammalian cells yielded correctly assembled proteins that had thiol groups in pre-determined positions and showed no loss of antigen-binding activity. One of the mutants was used to demonstrate the site-specific attachment of a radio-iodinated ligand to the chimaeric B72.3 antibody.
Oral tolerance. (1994)

Autoimmune conditions caused by injurious immune responses against self-antigens can be ameliorated if the inappropriate responses to self-components that cause tissue injury can be modulated by regulatory cells or shut off via the induction of anergy or via deletion of pathogenic immune responses. Antigen encounter at the gut mucosa can lead to suppression of injurious immune responses to self-antigen via these mechanisms. This type of immunological vent is termed oral tolerance. In this review, we examine the mechanisms behind the induction of oral tolerance and provide findings from its use as a form of treatment for autoimmune diseases.
Microfluidic systems for chemical kinetics that rely on chaotic mixing in droplets (2004)

This paper reviews work on a microfluidic system that relies on chaotic advection to rapidly mix multiple reagents isolated in droplets (plugs). Using a combination of turns and straight sections, winding microfluidic channels create unsteady fluid flows that rapidly mix the multiple reagents contained within plugs. The scaling of mixing for a range of channel widths, flow velocities and diffusion coefficients has been investigated. Due to rapid mixing, low sample consumption and transport of reagents with no dispersion, the system is particularly appropriate for chemical kinetics and biochemical assays. The mixing occurs by chaotic advection and is rapid (sub-millisecond), allowing for an accurate description of fast reaction kinetics. In addition, mixing has been characterized and explicitly incorporated into the kinetic model.
Mathematical Analysis of Random Noise (1944)

THIS paper deals with the mathematical analysis of noise obtained by passing random noise through physical devices. The random noise considered is that which arises from shot effect in vacuum tubes or from thermal agitation of electrons in resistors. Our main interest is in the statistical properties of such noise and we leave to one side many physical results of which Nyquist's law may be given as an example. <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup>