gebhart/patrepeval huggingface dataset:
β1-6 Branching of Asn-Linked Oligosaccharides Is Directly Associated with Metastasis (1987)

Neoplastic transformation has been associated with a variety of structural changes in cell surface carbohydrates, most notably increased sialylation and beta 1-6-linked branching of complex-type asparagine (Asn)-linked oligosaccharides (that is, -GlcNAc beta 1-6Man alpha 1-6Man beta 1-). However, little is known about the relevant glycoproteins or how these transformation-related changes in oligosaccharide biosynthesis may affect the malignant phenotype. Here it is reported that a cell surface glycoprotein, gp 130, is a major target of increased beta 1-6-linked branching and that the expression of these oligosaccharide structures is directly related to the metastatic potential of the cells. Glycosylation mutants of a metastatic tumor cell line were selected that are deficient in both beta 1-6 GlcNAc transferase V activity and metastatic potential in situ. Moreover, induction of increased beta 1-6 branching in clones of a nonmetastatic murine mammary carcinoma correlated strongly with acquisition of metastatic potential. The results indicate that increased beta 1-6-linked branching of complex-type oligosaccharides on gp 130 may be an important feature of tumor progression related to increased metastatic potential.
Repression of the Insulin-Like Growth Factor II Gene by the Wilms Tumor Suppressor WT1 (1992)

The Wilms tumor suppressor gene wt1 encodes a zinc finger DNA binding protein, WT1, that functions as a transcriptional repressor. The fetal mitogen insulin-like growth factor II (IGF-II) is overexpressed in Wilms tumors and may have autocrine effects in tumor progression. The major fetal IGF-II promoter was defined in transient transfection assays as a region spanning from nucleotides -295 to +135, relative to the transcription start site. WT1 bound to multiple sites in this region and functioned as a potent repressor of IGF-II transcription in vivo. Maximal repression was dependent on the presence of WT1 binding sites on each side of the transcriptional initiation site. These findings provide a molecular basis for overexpression of IGF-II in Wilms tumors and suggest that WT1 negatively regulates blastemal cell proliferation by limiting the production of a fetal growth factor in the developing vertebrate kidney.
CsSnI3: Semiconductor or Metal? High Electrical Conductivity and Strong Near-Infrared Photoluminescence from a Single Material. High Hole Mobility and Phase-Transitions (2012)

CsSnI(3) is an unusual perovskite that undergoes complex displacive and reconstructive phase transitions and exhibits near-infrared emission at room temperature. Experimental and theoretical studies of CsSnI(3) have been limited by the lack of detailed crystal structure characterization and chemical instability. Here we describe the synthesis of pure polymorphic crystals, the preparation of large crack-/bubble-free ingots, the refined single-crystal structures, and temperature-dependent charge transport and optical properties of CsSnI(3), coupled with ab initio first-principles density functional theory (DFT) calculations. In situ temperature-dependent single-crystal and synchrotron powder X-ray diffraction studies reveal the origin of polymorphous phase transitions of CsSnI(3). The black orthorhombic form of CsSnI(3) demonstrates one of the largest volumetric thermal expansion coefficients for inorganic solids. Electrical conductivity, Hall effect, and thermopower measurements on it show p-type metallic behavior with low carrier density, despite the optical band gap of 1.3 eV. Hall effect measurements of the black orthorhombic perovskite phase of CsSnI(3) indicate that it is a p-type direct band gap semiconductor with carrier concentration at room temperature of ∼ 10(17) cm(-3) and a hole mobility of ∼585 cm(2) V(-1) s(-1). The hole mobility is one of the highest observed among p-type semiconductors with comparable band gaps. Its powders exhibit a strong room-temperature near-IR emission spectrum at 950 nm. Remarkably, the values of the electrical conductivity and photoluminescence intensity increase with heat treatment. The DFT calculations show that the screened-exchange local density approximation-derived band gap agrees well with the experimentally measured band gap. Calculations of the formation energy of defects strongly suggest that the electrical and light emission properties possibly result from Sn defects in the crystal structure, which arise intrinsically. Thus, although stoichiometric CsSnI(3) is a semiconductor, the material is prone to intrinsic defects associated with Sn vacancies. This creates highly mobile holes which cause the materials to appear metallic.
Supramolecular Assembly of 2,7‐Dimethyldiazapyrenium and Cucurbit[8]uril: A New Fluorescent Host for Detection of Catechol and Dopamine (2005)

The formation of a highly stable inclusion complex between 2,7-dimethyldiazapyrenium (Me(2)DAP(2+)) and the cucurbit[8]uril host (CB8) was demonstrated by X-ray crystallography; MALDI-TOF mass spectrometry; and (1)H NMR, electronic absorption, and emission spectroscopy. The equilibrium association constant was determined to be 8.9(+/-0.2)x10(5) L mol(-1) from UV-visible data and 8.4(+/-1.5) x 10(5) L mol(-1) from fluorescence data. The Me(2)DAP(2+).CB8 inclusion complex acted as a host to bind compounds containing aromatic pi-donor moieties (D), such as catechol and dopamine. This point was demonstrated by (1)H NMR spectroscopy, and electrochemical and emission measurements. Fluorescence detection of the Me(2)DAP(2+).D.CB8 ternary complexes was evident in aqueous solution and on the surface of silica particles, to which fluorescent diazapyrenium units had been covalently immobilized.
Temperature-sensitive HVJ (Sendai Virus) with Altered P Polypeptide Derived from Persistently Infected Cell Lines (1981)

HVJ isolated from culture fluids of G2, THEL and GM2 cells persistently infected with HVJ (G2-HVJ, THEL-HVJ and GM2-HVJ) were characterized in comparison with wild-type HVJ (HVJo). Viral structural proteins were analysed by 10% SDS-polyacrylamide gel electrophoresis and its was found that only the P polypeptides of all the HVJ clones isolated from G2-HVJ cells had a smaller size mol. wt. of 77 000 (77K), than that of HVJo with a mol. wt. of 79 000 (79K). One of six clones from THEL-HVJ cells and one of ten clones from GM2-HVJ cells exhibited the same migration pattern of P polypeptide as that of the clones from G2-HVJ cells. However, the other structural proteins were not different from those of the wild-type virions. All the clones from these carrier cultures were temperature-sensitive and were blocked in early step(s) required for RNA synthesis. These results indicate that some mutations(s) associated with P polypeptides could occur during the course of HVJ persistent infection in cell cultures.
Immunoassay for human serum hepcidin (2008)

We developed and validated the first serum enzyme-linked immunosorbent assay for hepcidin, the principal iron-regulatory hormone that has been very difficult to measure. In healthy volunteers, the 5% to 95% range of hepcidin concentrations was 29 to 254 ng/mL in men (n = 65) and 17 to 286 ng/mL in women (n = 49), with median concentrations 112 versus 65 (P < .001). The lower limit of detection was 5 ng/mL. Serum hepcidin concentrations in 24 healthy subjects correlated well with their urinary hepcidin (r = 0.82). Serum hepcidin appropriately correlated with serum ferritin (r = 0.63), reflecting the regulation of both proteins by iron stores. Healthy volunteers showed a diurnal increase of serum hepcidin at noon and 8 pm compared with 8 am, and a transient rise of serum hepcidin in response to iron ingestion. Expected alterations in hepcidin levels were observed in a variety of clinical conditions associated with iron disturbances. Serum hepcidin concentrations were undetectable or low in patients with iron deficiency anemia (ferritin < 10 ng/mL), iron-depleted HFE hemochromatosis, and juvenile hemochromatosis. Serum hepcidin concentrations were high in patients with inflammation (C-reactive protein > 10 mg/dL), multiple myeloma, or chronic kidney disease. The new serum hepcidin enzyme-linked immunosorbent assay yields accurate and reproducible measurements that appropriately reflect physiologic, pathologic, and genetic influences, and is informative about the etiology of iron disorders.
Apoptosis Overview Emphasizing the Role of Oxidative Stress, DNA Damage and Signal- Transduction Pathways (1995)

Apoptosis (programmed cell death) is a central protective response to excess oxidative damage (especially DNA damage), and is also essential to embryogenesis, morphogenesis and normal immune function. An understanding of the cellular events leading to apoptosis is important for the design of new chemotherapeutic agents directed against the types of leukemias and lymphomas that are resistant to currently used chemotherapeutic protocols. We present here a review of the characteristic features of apoptosis, the cell types and situations in which it occurs, the types of oxidative stress that induce apoptosis, the signal-transduction pathways that either induce or prevent apoptosis, the biologic significance of apoptosis, the role of apoptosis in cancer, and an evaluation of the methodologies used to identify apoptotic cells. Two accompanying articles, demonstrating classic apoptosis and non-classic apoptosis in the same Epstein-Barr virus-transformed lymphoid cell line, are used to illustrate the value of employing multiple criteria to determine the type of cell death occurring in a given experimental system. Aspects of apoptosis and programmed cell death that are not covered in this review include histochemistry, details of cell deletion processes in the sculpting of tissues and organs in embryogenesis and morphogenesis, and the specific pathways leading to apoptosis in specific cell types. The readers should refer to the excellent books and reviews on the morphology, biochemistry and molecular biology of apoptosis already published on these topics. Emphasis is placed, in this review, on a proposed common pathway of apoptosis that may be relevant to all cell types.
Contextual Anomaly Detection in Text Data (2012)

We propose using side information to further inform anomaly detection algorithms of the semantic context of the text data they are analyzing, thereby considering both divergence from the statistical pattern seen in particular datasets and divergence seen from more general semantic expectations. Computational experiments show that our algorithm performs as expected on data that reflect real-world events with contextual ambiguity, while replicating conventional clustering on data that are either too specialized or generic to result in contextual information being actionable. These results suggest that our algorithm could potentially reduce false positive rates in existing anomaly detection systems.
Dose‐Dependent Effects of Docosahexaenoic Acid Supplementation on Blood Lipids in Statin‐Treated Hyperlipidaemic Subjects (2007)

Abstract The objective of the study was to evaluate potential benefits of docosahexaenoic acid (DHA) rich fish oil supplementation as an adjunct to statin therapy for hyperlipidaemia. A total of 45 hyperlipidaemic patients on stable statin therapy with persistent elevation of plasma triglycerides (averaging 2.2 mmol/L) were randomised to take 4 g/day ( n = 15) or 8 g/day ( n = 15) of tuna oil or olive oil (placebo, n = 15) for 6 months. Plasma lipids, blood pressure and arterial compliance were assessed initially and after 3 and 6 months in 40 subjects who completed the trial. Plasma triglycerides were reduced 27% by 8 g/day DHA‐rich fish oil ( P &lt; 0.05) but not by 4 g/day when compared with the placebo and this reduction was achieved by 3 months and was sustained at 6 months. Even though total cholesterol was already well controlled by the statin treatment (mean initial level 4.5 mmol/L), there was a further dose‐dependent reduction with fish oil supplementation ( r = −0.344, P &lt; 0.05). The extent of total cholesterol reduction correlated ( r = −0.44) with the initial total cholesterol levels ( P &lt; 0.005). In the subset with initial plasma cholesterol above 3.8 mmol/L, plasma very low density lipoprotein (VLDL), intermediate‐density lipoprotein (IDL) and low‐density lipoprotein (LDL) were isolated and assayed for cholesterol and apolipoprotein B (apoB) at the commencement of the trial and at 3 months of intervention. Fish oil tended to lower cholesterol and apoB in VLDL and raise both in LDL. There were no changes in IDL cholesterol, IDL apoB and high‐density lipoprotein cholesterol. The results demonstrate that DHA‐rich fish oil supplementation (2.16 g DHA/day) can improve plasma lipids in a dose‐dependent manner in patients taking statins and these changes were achieved by 3 months. Fish oil in addition to statin therapy may be preferable to drug combinations for the treatment of combined hyperlipidaemia.
Knowledge-Based Protein Modeling (1994)

Knowledge, both from the three-dimensional structures of homologous proteins and from the general analysis of protein structure, is of value in modeling a protein of known sequence but unknown structure. While many models are still constructed at least in part by manual methods on graphics devices, automated procedures have come into greater use. These procedures include those that assemble fragments of structure from other known structures and those that derive coordinates for the model from the satisfaction of restraints placed on atomic positions.
Multiple imputation was a valid approach to estimate absolute risk from a prediction model based on case–cohort data (2017)

MI seems to be a valid method for deriving or extending a risk prediction model from case-cohort data and might be superior for absolute risk calculation when compared to weighted approaches.
A recombinant bispecific single‐chain antibody induces targeted, supra‐agonistic CD28‐stimulation and tumor cell killing (2003)

Abstract Endowing tumor cells with costimulatory signals for T cell activation has emerged as a promising strategy for tumor immunotherapy. Costimulatory molecules were either transfected into tumor cells to generate vaccines or were fused, e.g. to antibodies against tumor‐associated antigens, to achieve targeted T cell costimulation in vivo . Here we report the production and purification of rM28, a recombinant bispecific single‐chain antibody directed to a melanoma‐associated proteoglycan and to the costimulatory CD28 molecule on human T cells. We found that a dimer of the recombinant molecule, bound to tumor target cells, induced pronounced T cell activation in peripheral blood mononuclear cell preparations without additional TCR/CD3 stimulation being required. Thelytic activity generated after 3 days of stimulation effectively prevented tumor cell growth. However, it was unspecific and predominantly mediated by non T cells. Our findings demonstrate that presentation of a CD28 antibody within a suitable recombinant, bispecific format may result in a "targeted supra‐agonistic stimulation" of the CD28 molecule, which leads to effective tumor cell killing after induction of unspecifically lytic cells.
Pharmacogenetics and cardiovascular disease: Impact on drug response and applications to disease management (2002)

The genetic polymorphisms that may affect individual responses to cardiovascular agents are reviewed, and the application of pharmacogenetics to cardiovascular disease management is discussed. Pharmacogenetics is the search for genetic polymorphisms that affect responses to drug therapy. Investigators have found many associations between genetic polymorphisms and responses to cardiovascular drugs. Some of these relationships have been demonstrated in large patient populations, such as patients with ischemic heart disease receiving statins. Study data consistently show a greater response to statins in ischemic heart disease patients with genotypes associated with worse prognoses. Studies of other polymorphisms, such as those in the genes encoding anglotensin-converting enzyme and beta 1-adrenergic receptors, have less consistently found relationships between these variations and cardiovascular drug responses. For gene-drug response associations for which the data are inconsistent, the interaction of multiple polymorphisms in multiple genes coding for proteins affected by drug therapy or influencing drug metabolism may prove to have a greater influence on drug responses than any one polymorphism. Once the polymorphisms that best determine the response to a particular drug are known and tests to rapidly identify these variations are available, individual patients may be screened for genetic polymorphisms before drug therapy is begun and the information used to choose agents with the greatest potential for efficacy and least potential for toxicity. Pharmacogenetics has many possible applications in the drug therapy of cardiovascular diseases. Much more must be learned, however, before pharmacogenetic factors can be routinely incorporated into therapeutic decisions.
Evidence for regulation of the human ABL tyrosine kinase by a cellular inhibitor. (1991)

Phosphotyrosine cannot be detected on normal human ABL protein-tyrosine kinases, but activated oncogenic forms of the human ABL protein are phosphorylated on tyrosine in vivo. Activation of ABL can occur by substitution of the ABL first exon with breakpoint cluster region (BCR) sequences or by deletion of the noncatalytic SH3 (src homology region 3) domain. An alternative mode for the activation of the ABL kinases is hyperexpression at greater than 500-fold over endogenous levels. This is not a consequence of transphosphorylation of the hyperexpressed ABL molecules. ABL proteins translated in vitro lack phosphotyrosine, but tyrosine kinase activity is uncovered after immunoprecipitation and removal of lysate components. The rates of dephosphorylation of ABL and BCR-ABL fusion protein by phosphotyrosine-specific phosphatases are approximately the same. These combined results indicate that inhibition of ABL activity is reversible and suggest that a cellular component interacts noncovalently with ABL to inhibit its autophosphorylation.
Rapid Methods for Testing the Efficacy of Sterilization-Grade Filter Membranes (2000)

The validation of sterilization-grade membranes is integral to ensuring the efficient and safe use of microfiltration systems. Here validation refers to the production of sterile filtrate for sterilizing-grade membranes under challenge test conditions. Current validation methods require 48 h of culture for results to become available, which creates time delays within the manufacturing process and quality control (QC) backlogs. This work compares four methods for the production of filter challenge test data, to the desired test sensitivity, within 24 h using bioluminescent and fluorescent recombinant strains of the test organism Brevundimonas diminuta. These methods should provide a way to implement more rapid QC test regimens for filters.
[Oral administration of insulin by means of liposomes in animal experiments (author's transl)]. (1979)

Liposomes are an effective vehicle for the oral administration of insulin. They are prepared from lipid emulsions by sonication and particles of homogeneous size are generated by elution through sepharose columns. Liposomes are taken up into the gastric mucosa by endocytosis and then transported to the liver via the portal circulation. Oral administration of 10 U insulin/kg body weight to rats is followed by a reduction in blood glucose to 67% of the initial value. When liposome-trapped insulin was injected intravenously a decrease in blood glucose to 40% of the initial value was obtained by the administration of 5 IU insulin/kg body weight. While the effect of orally-administered liposome-trapped insulin is obvious, the problems of standardization of the insulin content of the liposomes and the great variability of liposome uptake into the gastric mucosa by endocytosis remain unsolved.
A defect-free mordenite membrane synthesized by vapour-phase transport method (1995)

A defect-free MOR membrane is synthesized on a porous alumina plate by a vapour phase transport method: shape selectivity is apparent in the pervaporation of a benzene–p-xylene mixture (the separation factor exceeded 160).
The Identification of Germinal Centres and Follicular Dendritic Cell Networks in Rheumatoid Synovial Tissue (1995)

We document here the identification of germinal centres with dark and light zones, a follicular dendritic cell network and clonal expansion in the synovium of rheumatoid arthritis patients. Synovial tissue from 24 patients suffering from rheumatoid arthritis or the polyarticular form of juvenile rheumatoid arthritis were screened for the presence of lymphoid follicles. The synovial tissues of 14 patients contained follicles and four of these had germinal centres and a follicular dendritic cell network. There was a statistically significant association between follicles in the synovium and the presence of rheumatoid factor autoantibodies in the patients' serum indicating a link between local germinal centre formation and the presence of pathological rheumatoid factors. Nucleotide sequencing of monoclonal rheumatoid factors from one of the patients' synovial tissue which contained germinal centres clearly supports the possibility that these rheumatoid factors have gone through a germinal centre reaction. While rheumatoid factors from healthy immunized donors are regulated through a tolerization mechanism which selects against replacement mutations and does not allow affinity maturation, synovial rheumatoid factors seem to lack this tolerization mechanism. The formation of germinal centres where B cells affinity mature and expand at the central site of disease in rheumatoid arthritis may explain why rheumatoid factors in rheumatoid arthritis develop into auto-aggressive antibodies.
Magnetic Nanoparticle−Peptide Conjugates for in Vitro and in Vivo Targeting and Extraction of Cancer Cells (2008)

Magnetic cobalt spinel ferrite nanoparticles coated with biocompatible polygalacturonic acid were functionalized with ligands specific for targeting expressed EphA2 receptors on ovarian cancer cells. By using such magnetic nanoparticle-peptide conjugates, targeting and extraction of malignant cells were achieved with a magnetic field. Targeting ovarian cancer cells with receptor specific peptide-modified magnetic nanoparticles resulted in cell capture from a flow stream in vitro and from the peritoneal cavity of mice in vivo. Successful removal of metastatic cancer cells from the abdominal cavity and circulation using magnetic nanoparticle conjugates indicate the feasibility of a dialysis-like treatment and may improve long-term survival rates of ovarian cancer patients. This approach can be applied for fighting other cancers, such as leukemia, once the receptors on malignant cells are identified and the efficacy of targeting ligands is established.