gebhart/patrepeval huggingface dataset:
Epigenetic-Genetic Chromosome Dosage Approach for Fetal Trisomy 21 Detection Using an Autosomal Genetic Reference Marker (2010)

As a proof-of-concept study, we have demonstrated that the epigenetic-genetic chromosome dosage approach can be applied to the prenatal diagnosis of trisomy 21 for both male and female fetuses.
Magnetic separation techniques in diagnostic microbiology (1994)

The principles of magnetic separation aided by antibodies or other specific binding molecules have been used for isolation of specific viable whole organisms, antigens, or nucleic acids. Whereas growth on selective media may be helpful in isolation of a certain bacterial species, immunomagnetic separation (IMS) technology can isolate strains possessing specific and characteristic surface antigens. Further separation, cultivation, and identification of the isolate can be performed by traditional biochemical, immunologic, or molecular methods. PCR can be used for amplification and identification of genes of diagnostic importance for a target organism. The combination of IMS and PCR reduces the assay time to several hours while increasing both specificity and sensitivity. Use of streptavidin-coated magnetic beads for separation of amplified DNA fragments, containing both biotin and a signal molecule, has allowed for the conversion of the traditional PCR into an easy-to-read microtiter plate format. The bead-bound PCR amplicons can also easily be sequenced in an automated DNA sequencer. The latter technique makes it possible to obtain sequence data of 300 to 600 bases from 20 to 30 strains, starting with clinical samples, within 12 to 24 h. Sequence data can be used for both diagnostic and epidemiologic purposes. IMS has been demonstrated to be a useful method in diagnostic microbiology. Most recent publications describe IMS as a method for enhancing the specificity and sensitivity of other detection systems, such as PCR, and providing considerable savings in time compared with traditional diagnostic systems. The relevance to clinical diagnosis has, however, not yet been fully established for all of these new test principles. In the case of PCR, for example, the presence of specific DNA in a food sample does not demonstrate the presence of a live organism capable of inducing a disease. However, all tests offering increased sensitivity and specificity of detection, combined with reduced time of analysis, have to be seriously evaluated.
Stabilities of 3H- and 2H-labelled camptothecins (1996)

Commercially available [3H]-camptothecin, labeled mainly at the C-5 position, had partially lost the tritium label after recovery from the plasma of a patient injected with this drug or after incubation in plasma at 38°C for 72 h. Camptothecin dissolved in CH3O2H/2H2O, incorporated deuterium at the C-5 position with a 50% uptake after one day at pH 11.0 or after 10–11 days at pH 7.4. At pH 2.0, the deuterium uptake was negligible. Camptothecin, dissolved in deuterated sulfuric acid, incorporated 37 or 80% deuterium at C-14 when heated to 65 or 80°C, respectively. Commercially available [3H]-camptothecin, labeled mainly at the C-5 position, is thus not useful for in vivo metabolism or pharmacokinetic studies due to rapid loss of tritium in plasma. In contrast, [3H]-camptothecin prepared as described in this paper for [2H]-camptothecin is expected to be useful.
Distinct human leukemia-associated cell surface glycoprotein GP160 defined by monoclonal antibody SN6. (1986)

In this study, a monoclonal antibody (mAb) termed SN6 was generated by immunizing a mouse with a non-T-cell leukemia antigen preparation isolated from cell membranes of leukemia cells derived from a patient (FJ) with non-T/non-B-cell-type acute lymphoblastic leukemia (ALL). SN6 was tested against a variety of cultured and uncultured human cell specimens by using a sensitive cellular radioimmunoassay. Among the 26 cultured malignant and nonmalignant cell lines tested, SN6 reacted with all of the 6 leukemic non-T/non-B (including pre-B)-cell lines tested--i.e., KM-3, NALM-16, REH, NALL-1, NALM-1, and NALM-6. Of these cell lines, 5 were derived from individual patients with ALL; the remaining 1 was from a patient with chronic myelocytic leukemia in blast crisis. In addition, SN6 reacted with 3 of 3 leukemic myelo-monocytic cell lines tested--i.e., ML-2, HL-60, and U937. SN6 did not react with any other cell lines. A consistent result was obtained with 42 fresh (uncultured) cell specimens derived from individual patients with several different types of leukemias. SN6 reacted with 11 of 16 non-T/non-B (including pre-B)-cell ALL specimens. In addition, it reacted with various myelo-monocytic leukemia cell specimens to various degrees. SN6 did not show a significant reaction with normal peripheral blood cells tested, which included B cells, T cells, granulocytes, monocytes, and erythrocytes. However, it reacted with a small population (approximately 1% as determined by immunofluorescence staining) of normal bone marrow cells. The approximate molecular mass of the glycoprotein antigen defined by SN6 was determined to be 160,000 by radioimmunoprecipitation followed by sodium dodecyl sulfate/polyacrylamide gel electrophoresis. Only one component of 80,000 daltons was formed upon reduction of the 160,000 molecular mass antigen. Therefore, this antigen is apparently a homodimer of a 80,000-dalton subunit. This conclusion was further corroborated by two-dimensional gel analysis, which showed a single well-defined spot for the reduced antigen. We designate this distinct human leukemia-associated cell surface antigen "GP160."
COX-2 inhibition improves immunotherapy and is associated with decreased numbers of myeloid-derived suppressor cells in mesothelioma. Celecoxib influences MDSC function (2010)

Abstract Background Myeloid-derived suppressor cells (MDSC) are a heterogeneous population of immature cells that accumulates in tumour-bearing hosts. These cells are induced by tumour-derived factors (e.g. prostaglandins) and have a critical role in immune suppression. MDSC suppress T and NK cell function via increased expression of arginase I and production of reactive oxygen species (ROS) and nitric oxide (NO). Immune suppression by MDSC was found to be one of the main factors for immunotherapy insufficiency. Here we investigate if the in vivo immunoregulatory function of MDSC can be reversed by inhibiting prostaglandin synthesis by specific COX-2 inhibition focussing on ROS production by MDSC subtypes. In addition, we determined if dietary celecoxib treatment leads to refinement of immunotherapeutic strategies. Methods MDSC numbers and function were analysed during tumour progression in a murine model for mesothelioma. Mice were inoculated with mesothelioma tumour cells and treated with cyclooxygenase-2 (COX-2) inhibitor celecoxib, either as single agent or in combination with dendritic cell-based immunotherapy. Results We found that large numbers of infiltrating MDSC co-localise with COX-2 expression in those areas where tumour growth takes place. Celecoxib reduced prostaglandin E2 levels in vitro and in vivo . Treatment of tumour-bearing mice with dietary celecoxib prevented the local and systemic expansion of all MDSC subtypes. The function of MDSC was impaired as was noticed by reduced levels of ROS and NO and reversal of T cell tolerance; resulting in refinement of immunotherapy. Conclusions We conclude that celecoxib is a powerful tool to improve dendritic cell-based immunotherapy and is associated with a reduction in the numbers and suppressive function of MDSC. These data suggest that immunotherapy approaches benefit from simultaneously blocking cyclooxygenase-2 activity.
Enantioselective Desymmetrization of meso‐Aziridines with TMSN3 or TMSCN Catalyzed by Discrete Yttrium Complexes (2008)

Y is it so? Dimeric yttrium–salen complexes (see structure; N blue, O red, Y magenta) catalyze the highly enantioselective ring-opening of meso-aziridines by TMSCN and TMSN3. To explain the dramatic differences in the selectivity between mono- and dimeric catalysts, a dimetallic mechanism based on the solid-state structure of the dimer is proposed. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Respiratory Syncytial Virus Induces Pneumonia, Cytokine Response, Airway Obstruction, and Chronic Inflammatory Infiltrates Associated with Long‐Term Airway Hyperresponsiveness in Mice (2004)

This model provides a means to investigate the immunopathogenesis of RSV infection and its association with reactive airway disease.
A set of benchmarks for modular testing of SOCs (2003)

This paper presents the ITC'02 SOC test benchmarks. The purpose of this new benchmark set is to stimulate research into new methods and tools for modular testing of SOCs and to enable the objective comparison of such methods and tools with respect to effectiveness and efficiency. The paper defines the benchmark format and naming scheme, and presents the benchmark SOCs. In addition, it provides an overview of the research problems that can be addressed and evaluated by means of this benchmark set. These research problems include the design of optimized test access infrastructures and test schedules.
Synthesis and Evaluation of Heat-treated, Cyanamide-derived Non-precious Catalysts for Oxygen Reduction (2009)

Metal-nitrogen-carbon type (M-N-C type) non-precious catalysts have been prepared using cyanamide as the nitrogen precursor and pyrolysis to improve the activity and stability. Good activity has been observed for the best catalyst prepared with 1050{degree sign}C pyrolysis: E1/2 = 0.77 V by RDE, and current density = 80 mA at 0.80 V in H2/O2 fuel cell testing. M-N-C catalysts prepared using cyanamide as a nitrogen source show a complex dependence of activity on pyrolysis temperature: first increasing (up to 900{degree sign}C), then decreasing (1000{degree sign}C), before increasing again (1050{degree sign}C). The reappearance of activity may relate to an increase in defects induced at higher temperature, such as a greater exposure of the edges of graphene planes. The increased hydrophilicity of the sample after pyrolysis at 1050{degree sign}C suggests this outcome. Further study will be required to confirm the hypothesis.
Genetic ablation of zyxin causes Mena/VASP mislocalization, increased motility, and deficits in actin remodeling (2006)

Focal adhesions are specialized regions of the cell surface where integrin receptors and associated proteins link the extracellular matrix to the actin cytoskeleton. To define the cellular role of the focal adhesion protein zyxin, we characterized the phenotype of fibroblasts in which the zyxin gene was deleted by homologous recombination. Zyxin-null fibroblasts display enhanced integrin-dependent adhesion and are more migratory than wild-type fibroblasts, displaying reduced dependence on extracellular matrix cues. We identified differences in the profiles of 75- and 80-kD tyrosine-phosphorylated proteins in the zyxin-null cells. Tandem array mass spectrometry identified both modified proteins as isoforms of the actomyosin regulator caldesmon, a protein known to influence contractility, stress fiber formation, and motility. Zyxin-null fibroblasts also show deficits in actin stress fiber remodeling and exhibit changes in the molecular composition of focal adhesions, most notably by severely reduced accumulation of Ena/VASP proteins. We postulate that zyxin cooperates with Ena/VASP proteins and caldesmon to influence integrin-dependent cell motility and actin stress fiber remodeling.
Outreach and Early Warning Systems (EWS) for the prevention of Intensive Care admission and death of critically ill adult patients on general hospital wards (2007)

The evidence from this review highlights the diversity and poor methodological quality of most studies investigating outreach. The results of the two included studies showed either no evidence of the effectiveness of outreach or a reduction in overall mortality in patients receiving outreach. The lack of evidence on outreach requires further multi-site RCT's to determine potential effectiveness.
A Cell Proliferation Signature Is a Marker of Extremely Poor Outcome in a Subpopulation of Breast Cancer Patients (2005)

Breast cancer comprises a group of distinct subtypes that despite having similar histologic appearances, have very different metastatic potentials. Being able to identify the biological driving force, even for a subset of patients, is crucially important given the large population of women diagnosed with breast cancer. Here, we show that within a subset of patients characterized by relatively high estrogen receptor expression for their age, the occurrence of metastases is strongly predicted by a homogeneous gene expression pattern almost entirely consisting of cell cycle genes (5-year odds ratio of metastasis, 24.0; 95% confidence interval, 6.0-95.5). Overexpression of this set of genes is clearly associated with an extremely poor outcome, with the 10-year metastasis-free probability being only 24% for the poor group, compared with 85% for the good group. In contrast, this gene expression pattern is much less correlated with the outcome in other patient subpopulations. The methods described here also illustrate the value of combining clinical variables, biological insight, and machine-learning to dissect biological complexity. Our work presented here may contribute a crucial step towards rational design of personalized treatment.
Interleukin 4 potently enhances murine macrophage mannose receptor activity: a marker of alternative immunologic macrophage activation. (1992)

Expression of the macrophage mannose receptor is inhibited by interferon gamma (IFN-gamma), a T helper type 1 (Th-1)-derived lymphokine. Interleukin 4 (IL-4), a Th-2 lymphocyte product, upregulates major histocompatibility class II antigen expression but inhibits inflammatory cytokine production by macrophages. We have studied the effect of IL-4 on expression of the macrophage mannose receptor (MMR) by elicited peritoneal macrophages. We found that recombinant murine IL-4 enhances MMR surface expression (10-fold) and activity (15-fold), as measured by the respective binding and degradation of 125I-mannose-bovine serum albumin. Polymerase chain reaction analysis of cDNAs from purified primary macrophage populations revealed that MMR, but not lysozyme or tumor necrosis factor alpha, mRNA levels were markedly increased by IL-4. The above effects were associated with morphologic changes. These data establish IL-4 as a potent and selective enhancer of murine MMR activity in vitro. IL-4 induces inflammatory macrophages to adopt an alternative activation phenotype, distinct from that induced by IFN-gamma, characterized by a high capacity for endocytic clearance of mannosylated ligands, enhanced (albeit restricted) MHC class II antigen expression, and reduced proinflammatory cytokine secretion.
Towards global in vitro diagnostic standards, Part I. (2000)

The first global harmonized standards for in vitro diagnostic products (IVD) are nearing completion. The ISO Technical Committee overseeing this work will meet in June 2000 to prepare for the final vote. Six of these standards are mandated for the IVD Directive. This two-part report on the current status of these standards provides an insight into the international standardization process and suggests ways that industry can make it work more effectively.
Deep sequencing of B cell receptor repertoire (2019)

Immune repertoire is a collection of enormously diverse adaptive immune cells within an individual. As the repertoire shapes and represents immunological conditions, identification of clones and characterization of diversity are critical for understanding how to protect ourselves against various illness such as infectious diseases and cancers. Over the past several years, fast growing technologies for high throughput sequencing have facilitated rapid advancement of repertoire research, enabling us to observe the diversity of repertoire at an unprecedented level. Here, we focus on B cell receptor (BCR) repertoire and review approaches to B cell isolation and sequencing library construction. These experiments should be carefully designed according to BCR regions to be interrogated, such as heavy chain full length, complementarity determining regions, and isotypes. We also highlight preprocessing steps to remove sequencing and PCR errors with unique molecular index and bioinformatics techniques. Due to the nature of massive sequence variation in BCR, caution is warranted when interpreting repertoire diversity from error-prone sequencing data. Furthermore, we provide a summary of statistical frameworks and bioinformatics tools for clonal evolution and diversity. Finally, we discuss limitations of current BCR-seq technologies and future perspectives on advances in repertoire sequencing. [BMB Reports 2019; 52(9): 540-547].
Protocol for 3‐D visualization of molecules on mica via the quick‐freeze, deep‐etch technique (1989)

Molecular imaging by freeze-drying of molecules adsorbed to a mica substrate often provides better images of molecules than those attainable with other methods; the images are easier to interpret than those obtained with frozen thin film or negative staining, and the 3-dimensional information content is greater. The complete procedure for the production and examination of platinum-carbon replicas of molecules is described. Topics include production of a mica flake suspension, chemical pretreatment of the flakes to enhance adsorption, quick-freezing of the samples on mica, optimal operation of the freeze-fracture equipment, and orientation of replica topography. The production of stereo micrographs is analyzed in detail, with emphasis on the photographic procedures necessary for interpretation and on the identification of correct micrograph orientation. Guidelines are provided for the extrapolation from observed molecular size in platinum replicas to expected molecular weight.
Growth factor activity of IL-6 in the synovial fluid of patients with rheumatoid arthritis. (1995)

These results strongly suggest that IL-6 is responsible for the observed correlation between the growth factor activity of SF and inflammatory indexes such as ESR and CRP. However, neither IL-6 nor PDGF were responsible for the observed positive effect of SF on synovial fibroblastic cell lines.
Importance of Environment in Determining Secondary Structure in Proteins (1994)

We report here the effect of bulk solvent environment on the secondary structure of several peptides. In previous work, equivocal peptide sequences that are predicted to be alpha-helical from amino acid preference but are found to be beta-strand in their proteins were shown to be alpha-helical in alcohol solvents and beta-strand in nonmicellar sodium dodecyl sulfate (SDS) by circular dichroism (CD) spectroscopy [Zhong, L., & Johnson, W. C., Jr. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 4462-4465]. Here we show that equivocal sequences that are predicted to be beta-strand but are found to be alpha-helical follow the same pattern; they are alpha-helical in alcohol solvents and beta-strand in nonmicellar SDS. Furthermore, we investigated a control sequence with only a strong alpha-helical propensity and a control sequence with only a strong beta-strand propensity. Both of these well-behaved sequences followed the same pattern as the equivocal sequences. The exceptionally stable Y(EAAAK)3A is an alpha-helix in all solvents, but analyses of the CD spectra indicate the loss of helix with an increase in beta-strand and other structures on changing solvent from trifluoroethanol (TFE) to SDS, similar to the other peptides. We find that solvent is a very important factor in determining the secondary structure of an amino acid sequence in vitro and can override the propensity for a secondary structure due to sequence.(ABSTRACT TRUNCATED AT 250 WORDS)
Identifying differentially expressed genes usingfalse discovery rate controlling procedures (2003)

An R program that adjusts p-values using FDR controlling procedures is freely available over the Internet at www.math.tau.ac.il/~ybenja.
Discovery of a Potent, Selective, Orally Bioavailable, and Efficacious Novel 2-(Pyrazol-4-ylamino)-pyrimidine Inhibitor of the Insulin-like Growth Factor-1 Receptor (IGF-1R) (2016)

Optimization of cellular lipophilic ligand efficiency (LLE) in a series of 2-anilino-pyrimidine IGF-1R kinase inhibitors led to the identification of novel 2-(pyrazol-4-ylamino)-pyrimidines with improved physicochemical properties. Replacement of the imidazo[1,2-a]pyridine group of the previously reported inhibitor 3 with the related pyrazolo[1,5-a]pyridine improved IGF-1R cellular potency. Substitution of the amino-pyrazole group was key to obtaining excellent kinase selectivity and pharmacokinetic parameters suitable for oral dosing, which led to the discovery of (2R)-1-[4-(4-{[5-chloro-4-(pyrazolo[1,5-a]pyridin-3-yl)-2-pyrimidinyl]amino}-3,5-dimethyl-1H-pyrazol-1-yl)-1-piperidinyl]-2-hydroxy-1-propanone (AZD9362, 28), a novel, efficacious inhibitor of IGF-1R.
Preparation of Core-Shell Microspheres by Changing Reaction Solvent (2013)

We have successfully prepared monodispersed core-shell microspheres with polystyrene cores and poly(N-isopropylacrylamide) shells by changing solvent from nonpolar to polar for the first time. Effects of stirring time and reaction temperature on the particle size, monodispersity of the microspheres were investigated. With increasing stirring time at 800 rpm, the size of the spheres and the monodispersity are the best when stirring time is 60 min. And with increasing reaction temperature (above phase transition), the size of the microspheres decreases and the monodispersity becomes better.
ChemInform Abstract: Synthesis of Oligonucleotides Labeled with a Novel Type of Chemically Stable Acridine Dye (I). (1996)

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.
Rosette spectroscopic imaging: Optimal parameters for alias‐free, high sensitivity spectroscopic imaging (2009)

This work demonstrates the use of Rosette trajectories and how to achieve improved efficiency for these trajectories in a two-dimensional spectroscopic imaging experiment.