gebhart/patrepeval huggingface dataset:
Partial primary structure of bovine plasma fibronectin: Three types of internal homology (1983)

Approximately one-half of the amino acid sequence (911 amino acid residues out of 1,880 expected) for bovine plasma fibronectin (cold-insoluble globulin) has been determined. Three types of internal homology were identified, showing that a number of partial gene duplications (multiplications) have occurred during the evolution of this protein. Digestion of fibronectin with plasmin results in major fragments with molecular masses of 29, 170, 23, and 6 kilodaltons (kDal). The NH(2)-terminal 29-kDal fragment consists of 259 residues ordered as five mutually homologous domains (type I homology) with two disulfide bonds in each domain. The 170-kDal fragment shows two to three bands after NaDodSO(4) gel electrophoresis, indicating heterogeneity. This fragment contains the gelatin binding site and the strong heparin binding site present in fibronectin. Digestion of the 170-kDal fragment with chymotrypsin liberates a 45-kDal fragment that also binds to gelatin. This fragment contains at least one domain of type I homology and two domains of type II homology. Further digestion of the 170-kDal fragment with chymotrypsin results in the formation of a 30-kDal fragment that retains the heparin binding activity. This fragment contains sequences constituting type III homology. The 23-kDal fragment consists of 178 residues having three domains of type I homology. The 6-kDal fragment consists of two identical peptides of 26 residues, and these two peptides are linked to each other by two disulfide bonds that form the interchain bridges. Another one of the peptides for which the sequence was determined links the COOH-terminus of the 29-kDal fragment to the NH(2)-terminus of the 170-kDal fragment. This and the fact that the COOH-terminal residue of the 6-kDal fragment is a glutamic acid residue order the four plasmin-digestion fragments as 29-, 170-, 23-, and 6-kDal in the intact fibronectin molecule.
Comparison of 3H- and 125I-Radioimmunoassay and Gas Chromatography/Mass Spectrometry for the Determination of 9-Tetrahydrocannabinol and Cannabinoids in Blood and Serum (1983)

Blood and serum specimens from 100 subjects in a driving study were tested for the presence of delta 9-tetrahydrocannabinol (THC) by 3H- and 125I-labeled RIA and GC/MS. The specimens were also analyzed for 11-nor-9-carboxy-delta 9-tetrahydrocannabinol by the two RIA methods. Blind quality control specimens containing THC were included with each batch of subject specimens and sent coded to three participating laboratories. The methods were assessed for accuracy, reproducibility, detectability, specificity, and the results correlated. It was found that serum was a better matrix than blood for determination of cannabinoids. The three methods gave parallel but significantly different quantitative results, apparently due to calibration problems. However, each technique was capable of measuring THC concentrations up to three hours after usage.
Growth, geometry, and mechanics of a blooming lily (2011)

Despite the common use of the blooming metaphor, its floral inspiration remains poorly understood. Here we study the physical process of blooming in the asiatic lily Lilium casablanca. Our observations show that the edges of the petals wrinkle as the flower opens, suggesting that differential growth drives the deployment of these laminar shell-like structures. We use a combination of surgical manipulations and quantitative measurements to confirm this hypothesis and provide a simple theory for this change in the shape of a doubly curved thin elastic shell subject to differential growth across its planform. Our experiments and theory overturn previous hypotheses that suggest that blooming is driven by differential growth of the inner layer of the petals and in the midrib by providing a qualitatively different paradigm that highlights the role of edge growth. This functional morphology suggests new biomimetic designs for deployable structures using boundary or edge actuation rather than the usual bulk or surface actuation.
Dublin Core-Based Metadata Extracting Algorithm from RDF-Based Information Elements (2008)

The semantic Web and semantic Web technologies offer us a new approach to managing information and processes, the fundamental principle of which is the creation and use of semantic metadata. A Dublin core-based metadata extracting algorithm from RDF-based information elements is proposed in this paper. The rule library is designed in the paper after introducing the semantic rules. The system named IDPMS (integration design platform management system) based on the above-mentioned algorithm is developed, which can perform automatic Dublin core-based metadata extracting algorithm from information elements which is described by RDF documents. The Dublin core-based metadata extracting algorithm from RDF-based information elements is described in this paper. The experiment is analyzed in the end.
ERG induces a mesenchymal-like state associated with chemoresistance in leukemia cells (2013)

Overexpression of the oncogene ERG (ETS-related gene) is an adverse prognostic factor in acute myeloid and T-cell lymphoblastic leukemia (AML and T-ALL). We hypothesize that ERG overexpression is associated with primary drug resistance thereby influencing the outcome in leukemia. We previously reported a cell-line based model of ERG overexpression which induced a potentially chemo-resistant spindle shape cell type. Herein, we report a specific transcriptional gene signature for the observed spindle shaped morphology. Genes significantly over-expressed after ERG induction strongly resembled adhesive mesenchymal-like genes that included integrins (ITGA10, ITGB5, ITGB3, ITGA2B), CD44, and CD24. Interestingly, the mesenchymal-like signature was accompanied by the repression of DNA chromatin remodeling and DNA repair genes, such as CHEK1, EZH2, SUZ12, and DNMT3a. The ERG-induced mesenchymal-like signature positively correlated with TMPRSS2-ERG prostate tissues and invasive breast cancer mRNA expression datasets reflecting a general ERG-driven pattern of malignancy. Furthermore, inhibitors modulating ERG druggable pathways WNT, PKC, and AKT, and chemotherapeutic agent cytarabine revealed ERG-induced drug resistance. In particular, PKC412 treatment enhanced proliferative rates and promoted spindle shape formation in ERG-induced cells. Nilotinib and dasatinib were effective at abolishing ERG-induced cells. Moreover, ERG overexpression also led to an increase in double strand breaks. This report provides mechanistic clues into ERG-driven drug resistance in the poor prognostic group of high ERG expressers, provides insight to improved drug targeted therapies, and provides novel markers for a mesenchymal-like state in acute leukemia.
Augmentation of CD134 (OX40)-dependent NK anti-tumour activity is dependent on antibody cross-linking (2018)

CD134 (OX40) is a member of the tumour necrosis factor receptor superfamily (TNFRSF). It acts as a costimulatory receptor on T cells, but its role on NK cells is poorly understood. CD137, another TNFRSF member has been shown to enhance the anti-tumour activity of NK cells in various malignancies. Here, we examine the expression and function of CD134 on human and mouse NK cells in B-cell lymphoma. CD134 was transiently upregulated upon activation of NK cells in both species. In contrast to CD137, induction of CD134 on human NK cells was dependent on close proximity to, or cell-to-cell contact with, monocytes or T cells. Stimulation with an agonistic anti-CD134 mAb but not CD134 ligand, increased IFNγ production and cytotoxicity of human NK cells, but this was dependent on simultaneous antibody:Fcγ receptor binding. In complementary murine studies, intravenous inoculation with BCL<sub>1</sub> lymphoma into immunocompetent syngeneic mice resulted in transient upregulation of CD134 on NK cells. Combination treatment with anti-CD20 and anti-CD134 mAb produced a synergistic effect with durable remissions. This therapeutic benefit was abrogated by NK cell depletion and in Fcγ chain -/- mice. Hence, anti-CD134 agonists may enhance NK-mediated anti-tumour activity in an Fcγ receptor dependent fashion.
Wafer scale integration (2003)

A description is given of the Westinghouse RF Wafer-Scale Integration (RFWSI) program, a novel approach to controlling the cost of fighter aircraft radar modules. The technologies required for the program include three implants of silicon into 3-inch-diameter semi-insulating GaAs wafers and proton implants providing isolation between the closely spaced elements. Wafers will be cut so that a 'tile' containing several modules may be mounted on a carrier and form part of a tiled array of several hundred modules. Each tile will have electric feeds that pass through the gallium arsenide to the underlying layers. Integral to this structure are the cooling channels, the RF and DC manifolds for the distribution of signals, and the wideband flared notch antenna. Construction of an active array using this configuration will result in reduced assembly costs because the parts count is reduced. The implementation of this approach in the design of advanced fighter aircraft is considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Putative polyadenylation signals in nuclear genes of higher plants: a compilation and analysis (1987)

In animal and viral pre-mRNAS, the process of polyadenylation is mediated through several cis-acting poly (A) signals present upstream and downstream from poly (A) sites. The situation regarding polyadenylation of higher plant pre-mRNAS, however, has remained obscure so far. In this paper, a search for putative poly (A) signals is made by considering the published data from 46 plant genomic DNA sequences. Certain domains in the 3' untranslated regions from nuclear genes of higher plants were compiled and occurrence of sequence motifs such as AATAAA, CAYTG, YGTGTTYY and YAYTG was scored in relation to poly (A) sites. Moreover, consensus sequences for important regions in the 3' untranslated sequences and poly (A) signals were also deduced from the data. It was inferred that sequence motifs similar to poly (A) signals exist around poly (A) sites but some of them are in entirely different spatial relationship than observed in other eukaryotes. This indicates their probable non-involvement in the process of polyadenylation in higher plants necessitating a functional analysis approach to define the plant specific poly (A) signals.
Systematic Analysis of the Intramolecular Competition Associated with the Ring Closing Metathesis of Ene-Diene Systems of Differing Chain Length with a Pair of Ruthenium Catalysts (2002)

The (alkylidene) ruthenium complexes 1 and 2b were examined as catalysts for the ring-closing metathesis of the homologous series of ene-dienes 16 to ascertain the extent to which a divergence in product distribution would be observed. In each case, the levels of cyclic alkene and conjugated diene were determined (see Table 1). Double bond geometric assignments were made on the basis of vinyl proton 1H-NMR chemical shifts and coupling constants. MM3 Calculations were undertaken to gauge the levels of steric strain in end products of varying ring size. The global ensemble of facts, including key control experiments, demonstrate the striking differences between 1 and 2b. Finally, the steric energies are seen not to correlate with the product distributions, most probably due to the distinctive reactivity patterns of the metathesis reagents.
Cloning Genes Encoding MHC Class II-Restricted Antigens: Mutated CDC27 as a Tumor Antigen (1999)

In an effort to identify tumor-specific antigens recognized by CD4(+) T cells, an approach was developed that allows the screening of an invariant chain-complementary DNA fusion library in a genetically engineered cell line expressing the essential components of the major histocompatibility complex (MHC) class II processing and presentation pathway. This led to the identification of a mutated form of human CDC27, which gave rise to an HLA-DR4-restricted melanoma antigen. A mutated form of triosephosphate isomerase, isolated by a biochemical method, was also identified as an HLA-DR1-restricted antigen. Thus, this approach may be generally applicable to the identification of antigens recognized by CD4(+) T cells, which could aid the development of strategies for the treatment of patients with cancer, autoimmune diseases, or infectious diseases.
Epidemiology and etiology of bladder cancer (1997)

The incidence of bladder cancer continues to increase, with an estimated 53,000 new cases diagnosed in the United States in 1996-90% of which are transitional cell carcinomas. The male-to-female ratio is 3:1. A number of etiological factors are associated with the development of bladder cancer, but in industrialized countries, cigarette smoking is the most important. Specific chemicals have also been identified as causing bladder cancer, as have a number of occupational exposures to less well-defined specific agents. Treatment with cytostatic drugs, especially cyclophosphamide, is associated with increased risk of bladder cancer, as is treatment with radiotherapy for uterine cancer. In developing countries, especially in the Middle East and parts of Africa, infections with members of the genus Schistosoma are responsible for a high incidence of bladder cancer-75% of which are squamous cell carcinomas. Arsenic has been indicated as a bladder carcinogen in Argentina, Chile, and Taiwan. The reason for the high incidence of urinary tract cancer in individuals suffering from Balkan nephropathy has yet to be determined. A careful history of patients with bladder cancer is an important and useful process in helping to identify causal factor and, in more than one-half the cases, a known relationship is found. Bladder cancer is a potentially preventable disease, with a significant morbidity and mortality in many parts of the world.
Autoantibodies to cyclic citrullinated peptides predict progression to rheumatoid arthritis in patients with undifferentiated arthritis: A prospective cohort study (2004)

Testing for anti-CCP antibodies in UA allows accurate prediction of a substantial number of patients who will fulfill the ACR criteria for RA.
Transcription of the Herpes Simplex Virus Latency-Associated Transcript Promotes the Formation of Facultative Heterochromatin on Lytic Promoters (2009)

An important question in virology is the mechanism(s) by which persistent viruses such as the herpesviruses and human immunodeficiency virus (HIV) establish a latent infection in specific types of cells. In the case of herpesviruses, herpes simplex virus (HSV) infection of epithelial cells results in a lytic infection, whereas latent infection is established in sensory neurons. Recent studies have shown the importance of chromatin structure in the regulation of latent infection for both HSV and HIV. For HSV, we have shown previously that the viral latency-associated transcript (LAT) promotes lytic gene silencing and the association of one heterochromatin marker, dimethylation of lysine 9 on histone H3 (H3K9me2), with viral lytic genes. In this study, we further defined the structure of latent viral chromatin by examining the heterochromatin markers on histones associated with the HSV latent genome. We detected the H3K9me2, H3K9me3, and H3K27me3 modifications, with H3K27me3, which is indicative of facultative heterochromatin, exhibiting the highest enrichment on all viral promoters tested. A modification associated with cellular centromeric heterochromatin, H4K20me3, was not detected. A mutant virus containing a 1.8-kbp deletion within the LAT region showed reduced levels of the facultative heterochromatin marker (H3K27me3) along with H3K9me3 during latency, whereas a viral mutant defective for the LAT promoter showed a specific reduction in H3K27me3. Cellular long, noncoding RNAs induce facultative heterochromatin, and this study shows that transcription of a viral noncoding RNA can also induce facultative heterochromatin to promote lytic gene silencing during latency.
Deduced Amino Acid Sequence of the Fusion Glycoprotein of Turkey Rhinotracheitis Virus has Greater Identity with that of Human Respiratory Syncytial Virus, a Pneumovirus, than that of Paramyxoviruses and Morbilliviruses (1991)

The sequence of the fusion (F) glycoprotein of turkey rhinotracheitis virus (TRTV) has been deduced from cDNA clones derived from oligo(dT)-selected infected cell RNA. The protein consists of 538 amino acids, the F2 and F1 subunits containing 102 (including the F2-F1 connecting peptide RRRR) and 436 residues, respectively. Each subunit has one potential N-linked glycosylation site. The protein has 38 to 39% amino acid identity with the F protein of respiratory syncytial virus (Pneumovirus genus) but only about half that with members of the other two genera (Paramyxovirus and Morbillivirus) in the Paramyxoviridae family. This is the first sequence evidence to support the view that TRTV is a pneumovirus, the first avian member of the genus to be described.
Folic acid—an innocuous means to reduce plasma homocysteine (1988)

With an improved highly reproducible method, we measured total plasma homocysteine (free plus protein-bound) and related amino acids in the fasting state in healthy subjects, before and after treatment with co-factors for homocysteine metabolism: 1 mg cyanocobalamin (n = 14), 5 mg folic acid (n = 13) or 40 mg pyridoxine hydrochloride (n = 15) daily for 14 days. Cyanocobalamin and pyridoxine hydrochloride had no effects on plasma levels of amino acids, but folic acid had a considerable homocysteine-lowering effect. Total plasma homocysteine was reduced in all but two subjects, from 19.9 +/- 4.4 (mean +/- SEM) to 9.5 +/- 1.0 mumol/l (-52%, p less than 0.01). We propose that folic acid in excess acts by enhancing the remethylation of homocysteine to methionine. The finding confirms a previous report by us. Since homocysteine is considered to be an atherogenic amino acid and recent reports suggest that mild to moderate homocysteinaemia is also associated with premature vascular disease, treatment with folic acid might be of use as prophylaxis.
The Role of the Thioredoxin and Glutaredoxin Pathways in Reducing Protein Disulfide Bonds in the Escherichia coliCytoplasm (1997)

In Escherichia coli, two pathways use NADPH to reduce disulfide bonds that form in some cytoplasmic enzymes during catalysis: the thioredoxin system, which consists of thioredoxin reductase and thioredoxin, and the glutaredoxin system, composed of glutathione reductase, glutathione, and three glutaredoxins. These systems may also reduce disulfide bonds which form spontaneously in cytoplasmic proteins when E. coli is grown aerobically. We have investigated the role of both systems in determining the thiol-disulfide balance in the cytoplasm by determining the ability of protein disulfide bonds to form in mutants missing components of these systems. We find that both the thioredoxin and glutaredoxin systems contribute to reducing disulfide bonds in cytoplasmic proteins. In addition, these systems can partially substitute for each other in vivo since double mutants missing parts of both systems generally allow substantially more disulfide bond formation than mutants missing components of just one system. Some of these double mutants were found to require the addition of a disulfide reductant to the medium to grow well aerobically. Thus, E. coli requires either a functional thioredoxin or glutaredoxin system to reduce disulfide bonds which appear after each catalytic cycle in the essential enzyme ribonucleotide reductase and perhaps to reduce non-native disulfide bonds in cytoplasmic proteins. Our results suggest the existence of a novel thioredoxin in E. coli.
A novel class of materials for ferroelectric liquid crystals containing siloxy chain end groups (1993)

Abstract Novel liquid crystals containing a siloxy chain as an end tail group instead of an alkyl chain were synthesized. The substitution effects were studied for ferroelectric liquid crystal materials. It was found that the temperature range for the chiral smectic C phase was reduced and shifted to lower temperature in comparison with the analogous alkyl chain derivatives. The crystallinity of the siloxy chain derivatives decreased and cholesteric phases were not observed. The influence of siloxy chains on ferroelectric liquid crystal properties, especially spontaneous polarizations and tilt angles, also greatly depended upon the mesogenic group structure. The X-ray diffraction results showed that the end tail group occupied a larger thickness in the chiral smectic C layer for the siloxy chain derivative than that for the alkyl chain derivative.
DNA Methylation in Cancer: A Gene Silencing Mechanism and the Clinical Potential of Its Biomarkers (2013)

Initiation and progression of human cancer not only depends on genetic alterations but also on epigenetic changes such as DNA methylation and histone modifications. Aberrant DNA hypermethylation in the promoter regions of genes is the most well-defined epigenetic change in tumors and is associated with inappropriate gene silencing. This feature can be utilized to search for tumor-specific DNA methylation biomarkers and to examine candidate DNA biomarkers for clinical use. DNA methylation biomarker is defined as a molecular target that undergoes DNA methylation changes in carcinogenesis. Such a biomarker is useful for early detection of cancer, predicting and/or monitoring the therapeutic response, and detection of recurrent cancer. In this review, we describe the mechanism that establishes and maintains DNA methylation patterns as well as the mechanism of aberrant gene silencing in cancer, and then we introduce methods to isolate the DNA methylation biomarkers. We also summarize the current status of clinical implementation for some of the most widely studied and well-validated DNA methylation biomarkers, including tissue factor pathway inhibitor 2 (TFPI2), septin 9 (SEPT9), glutathione S-transferase pi 1 (GSTP1), and O(6)-methylguanine-DNA methyltransferase (MGMT), and assess the clinical potential of these biomarkers for risk assessment, early diagnosis, prognosis, treatment, and the prevention of cancer. Finally we describe the possible involvement of 5-hydroxymethylcytosine in cancer; this is a recently discovered 5-methylcytosine oxidation derivative and might have a diagnostic potential in certain cancers. Abnormal DNA methylations are leading candidates for the development of specific markers for cancer diagnosis and therapy.