gebhart/patrepeval huggingface dataset:
Design and Construction of 2A Peptide-Linked Multicistronic Vectors (2012)

The need for reliable, multicistronic vectors for multigene delivery is at the forefront of biomedical technology. This article describes the design and construction of 2A peptide-linked multicistronic vectors, which can be used to express multiple proteins from a single open reading frame (ORF). The small 2A peptide sequences, when cloned between genes, allow for efficient, stoichiometric production of discrete protein products within a single vector through a novel "cleavage" event within the 2A peptide sequence. Expression of more than two genes using conventional approaches has several limitations, most notably imbalanced protein expression and large size. The use of 2A peptide sequences alleviates these concerns. They are small (18-22 amino acids) and have divergent amino-terminal sequences, which minimizes the chance for homologous recombination and allows for multiple, different 2A peptide sequences to be used within a single vector. Importantly, separation of genes placed between 2A peptide sequences is nearly 100%, which allows for stoichiometric and concordant expression of the genes, regardless of the order of placement within the vector.
Improving Multimedia Streaming with Content-Aware Video Scaling. (2002)

Streaming video applications on the Internet generally have very high bandwidth requirements and yet are often unresponsive to network congestion. In order to avoid congestion collapse and improve video quality, these applications need to respond to congestion in the network by deploying mechanisms to reduce their bandwidth requirements under conditions of heavy load. In reducing bandwidth, video frames have low quality, while video with low motion will look better if some frames are dropped by the remaining frames have high quality. Unfortunately current video applications scale to fit the available bandwidth without regard to the video content. In this paper, we present a content-aware scaling mechanism that reduces the bandwidth occupied by an application by either dropping frames (temporal scaling) or by reducing the quality of the frames transmitted (quality scaling). We have designed a streaming video client and server with the server capable of quantifying the amount of motion in an MPEG stream and scaling each scene either temporally or by quality as appropriate, maximizing the appearance of each video stream. We have evaluated our setup by conducting a user study wherein the subjects rated the quality of video clips that were first scaled temporally and then by quality in order to establish the optimal mechanism for scaling a particular stream. We find that our content-aware scaling can improve video quality by as much as 50%.
A SOLUTION, FOR CESIUM REMOVAL FROM HIGH-SALINITY ACIDIC OR ALKALINE LIQUID WASTE: THE CROWN CALIX[4]ARENES (1999)

ABSTRACT The scientific literature abounds with articles on the extraction of cesium from liquid waste. From the 1940s, several classes of inorganic exchangers were used for cesium removal, such as zeolites, hexacyanoferrates, zirconium phosphate, ammonium phosphomolybdate, and, more recently, crystalline silicotitanate. Later, organic compounds like formophenolic resins, tetraphenylboron, or extractants such as dicarbollides or crown ethers were proposed. Generally, these compounds were only able to efficiently remove cesium under restrictive conditions (alkaline medium, low salinity, etc.) The performances of most of these compounds strongly decreased as the acidity (or salinity) of the liquid waste increased. Artifices had to be implemented to improve the performances of extractants. A restricted number of inorganic exchangers allowed the cesium removal, but often they could not be eluted or needed prohibitive volumes of saline eluent, leading to large volumes of secondary waste. Calix[4]arenes monocrown or biscrown, blocked in 1,3 alternative cone conformation, display an exceptional efficiency for cesium extraction, even from very acid or alkaline media. Moreover, they possess an important selectivity for cesium over sodium that makes possible the extraction of cesium from media containing high sodium nitrate loadings. Another advantage, since the extraction of cesium is reversible, is that the stripping of cesium can be carried out in deionized water, a property which leads to very high concentration factors.
Fibronectin is an immunosuppressive substance associated with epithelial ovarian cancer (1992)

Fibronectin is produced by some ovarian cancer cell lines and acts to inhibit proliferation of mitogen-stimulated lymphocytes. Additional studies are needed to clarify the role of fibronectin in ovarian cancer.
Interleukin (IL)‐31 activates signal transducer and activator of transcription (STAT)‐1, STAT‐5 and extracellular signal‐regulated kinase 1/2 and down‐regulates IL‐12p40 production in activated human macrophages (2013)

The T helper (Th) 2 cytokine IL-31 induces pro-inflammatory effects in activated human macrophages via STAT-1 and 5 phosphorylation. Interleukin-31-induced ERK 1/2 activation contributes to the underlying mechanism of Th1 cytokine IL-12 suppression in macrophages. This mechanism may be relevant in Th2 inflammatory responses and may help to develop therapeutic strategies in IL-31-associated diseases such as AD.
CAP37, a human neutrophil-derived chemotactic factor with monocyte specific activity. (1990)

CAP37, an antimicrobial protein of human neutrophil granules, is a specific chemoattractant for monocytes. Purified to homogeneity by sequential chromatography over carboxymethyl Sephadex, G-75 Sephadex, and hydrophobic interaction HPLC, demonstratively endotoxin-free CAP37 was maximally chemotactic over a range of 1.3 X 10(-9)-10(-8) M. Thus it was active in the same molar concentrations as formyl-methionyl-leucyl-phenylalanine. CAP37 lacked chemotactic activity for neutrophils and lymphocytes. In checkerboard assays CAP37 had some chemokinetic activity as well. It was also chemotactic for rabbit mononuclear cells. Higher concentrations (2.7 X 10(-8) M) were required for activity with rabbit cells than with human. Sequence analysis of the first 42 NH2-terminal amino acid residues of CAP37 showed strong homologies with known serine proteases that mediate various functions in inflammation. However, a critical substitution of a serine for a histidine at position 41 suggested that CAP37 lacked serine protease action. This impression was supported by the failure of CAP37 to bind tritiated diisopropyl fluorophosphate. 89% of total CAP37 was released extracellularly from human neutrophils while they phagocytized Staphylococcus aureus. We propose that CAP37 released from neutrophils during phagocytosis and degranulation may mediate recruitment of monocytes in the second wave of inflammation.
Rapid identification of yeast species using three primers in a polymerase chain reaction. (1993)

Classic methods for identification of yeasts rely on a variety of morphological and physiological tests that often take days to weeks to complete. We have been able to reduce the time to less than one day through the use of multiple segment-specific oligonucleotide priming of a region of the large subunit rDNA in a polymerase chain reaction. The "hot start" reaction was used with two universal external delimiting primers and one internal species-specific primer. Five specific primers were tested: a primer for a biologically similar group of Rhodotorula species, a generic (Cystofilobasidium) primer, and 3 species-specific primers (Leucosporidium scottii, Cryptococcus muscorum, and Rhodotorula mucilaginosa). In the absence of specific target DNA, the universal rDNA segment is amplified; in the presence of target DNA, the specific primer region is amplified. The technique is accurate within two base position differences when a 24 nucleotide-specific primer is used. The technique should be applicable to other marine eukaryotes.
Key Factors in the Hydrolysis of Cellulose (1981)

If a successful cellulose hydrolysis process were available, the food problems of the world would diminish and wood sugar could form the basis of new enterprises providing an important source of chemicals and fuels. This has been known for more than a century. Some hundred to perhaps hundreds of millions of dollars have been spent on research dealing with cellulose hydrolysis. Billions have been invested in commercial plants for the hydrolysis of wood. Success, however, has been limited and future prospects are uncertain. A review of early wood hydrolysis processes was published by Sherrard and Kressman (1). A more recent review was published by Wenzl (2). The coverage here is selective rather than comprehensive. It identifies some key issues that determine the future usefulness of wood hydrolysis processes. Cellulose is a polymeric carbohydrate (C6 H10 O5)x having the same elemental composition as starch and also yielding only glucose on complete
Endocytosis (1977)

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
Spatial and cellular localization of calcium-dependent protease (CDP II)inAllomyces arbuscula (2003)

Immunogold labeling of calcium-dependent neutral protease II (CDPII) with specific antibodies in near median longitudinal ultrathin sections of Allomyces arbuscula showed that the enzyme is predominantly localized in the growing hyphal and rhizoidal apices. The tips in both cell type had more enzyme than the distal regions and showed a gradient distribution. Labeling of the ultrathin sections and western blot analysis of purified subcellular fractions showed that CDPII is mainly cytosolic. Catalytic activity of the enzyme measured with synthetic substrate (Bz-Arg-pNA) showed that 90% of its activity is present in the soluble fraction, although a small amount is associated with the nuclei (0.2%), plasma membranes (0.7%) and microsomes (3.9%). This association is discussed in the context of the functional role of the enzyme and its possible localized activation. Western blot analysis of the crude extract and indirect immunofluorescence of the fixed permeabilized hypahe after treatment with CDPII showed that the alpha-tubulin is a specific target of the enzyme.
FluBreaks: Early Epidemic Detection from Google Flu Trends (2012)

We present the first detailed comparative analysis of popular early epidemic detection algorithms on Google Flu Trends data. We note that realizing this opportunity requires moving beyond the cumulative sum and historical limits method-based normal distribution approaches, traditionally employed by the CDC, to negative binomial- and Poisson-based algorithms to deal with potentially noisy search query data from regions with varying population and Internet penetrations. Based on our work, we have developed FluBreaks, an early warning system for flu epidemics using Google Flu Trends.
The Senescence-Associated Secretory Phenotype: The Dark Side of Tumor Suppression (2010)

Cellular senescence is a tumor-suppressive mechanism that permanently arrests cells at risk for malignant transformation. However, accumulating evidence shows that senescent cells can have deleterious effects on the tissue microenvironment. The most significant of these effects is the acquisition of a senescence-associated secretory phenotype (SASP) that turns senescent fibroblasts into proinflammatory cells that have the ability to promote tumor progression.
Dendritic Cells Infiltrating Tumors Cotransduced with Granulocyte/Macrophage Colony-Stimulating Factor (Gm-Csf) and Cd40 Ligand Genes Take up and Present Endogenous Tumor-Associated Antigens, and Prime Naive Mice for a Cytotoxic T Lymphocyte Response (1999)

We transduced BALB/c-derived C-26 colon carcinoma cells with granulocyte/macrophage colony-stimulating factor (GM-CSF) and CD40 ligand (CD40L) genes to favor interaction of these cells with host dendritic cells (DCs) and, therefore, cross-priming. Cotransduced cells showed reduced tumorigenicity, and tumor take was followed by regression in some mice. In vivo tumors were heavily infiltrated with DCs that were isolated, phenotyped, and tested in vitro for stimulation of tumor-specific cytotoxic T lymphocytes (CTLs). BALB/c C-26 carcinoma cells express the endogenous murine leukemia virus (MuLV) env gene as a tumor-associated antigen. This antigen is shared among solid tumors of BALB/c and C57BL/6 mice and contains two epitopes, AH-1 and KSP, recognized in the context of major histocompatibility complex class I molecules H-2Ld and H-2K(b), respectively. DCs isolated from C-26/GM/CD40L tumors grown in (BALB/c x C57BL/6)F1 mice (H-2d x b) stimulated interferon gamma production by both anti-AH-1 and KSP CTLs, whereas tumor-infiltrating DCs (TIDCs) of BALB/c mice stimulated only anti-AH-1 CTLs. Furthermore, TIDCs primed naive mice for CTL activity as early as 2 d after injection into the footpad, whereas double-transduced tumor cells required at least 5 d for priming; this difference may reflect direct DC priming versus indirect tumor cell priming. Immunohistochemical staining indicated colocalization of DCs and apoptotic bodies in the tumors. These data indicate that DCs infiltrating tumors that produce GM-CSF and CD40L can capture cellular antigens, likely through uptake of apoptotic bodies, and mature in situ to a stage suitable for antigen presentation. Thus, tumor cell-based vaccines engineered to favor the interaction with host DCs can be considered.
Dopability, Intrinsic Conductivity, and Nonstoichiometry of Transparent Conducting Oxides (2007)

Existing defect models for In(2)O(3) and ZnO are inconclusive about the origin of conductivity, nonstoichiometry, and coloration. We apply systematic corrections to first-principles calculated formation energies Delta H, and validate our theoretical defect model against measured defect and carrier densities. We find that (i) intrinsic acceptors ("electron killers") have a high Delta H explaining high n-dopability, (ii) intrinsic donors ("electron producers") have either a high Delta H or deep levels, and do not cause equilibrium-stable conductivity, (iii) the O vacancy V(O) has a low Delta H leading to O deficiency, and (iv) V(O) has a metastable shallow state, explaining the paradoxical coexistence of coloration and conductivity.
Insulin-like growth factor binding protein-related protein 1 inhibits proliferation of MCF-7 breast cancer cells via a senescence-like mechanism. (2002)

Elevated insulin-like growth factor binding protein-related protein 1 (IGFBP-rP1) mRNA in senescent human mammary epithelial cells suggested that the IGFBP-3 gene product may inhibit cell proliferation. To test this hypothesis, we used a retroviral vector to express IGFBP-rP1 cDNA in the IGFBP-rP1-deficient MCF-7 breast cancer cell line. Compared with control vector-transduced cells, cumulative cell numbers for IGFBP-rP1-transduced polyclonal or clonal cell cultures were reduced by 39 and 74%, respectively, after 1 week. Medium conditioned by IGFBP-rP1-producing cultures reduced cumulative cell numbers in parental MCF-7 cultures by 20% compared with medium from cultures of a control vector-transduced cell line. Nuclear fragmentation analysis and cell proliferation assays completed in the presence of the pan-caspase inhibitor benzyloxycarbonyl-Val-Ala-Asp(OMe)-fluoromethylketone excluded apoptosis as the responsible mechanism. The percentage of cells containing senescence-associated beta-galactosidase activity was doubled compared with control cell cultures. Flow cytometry analysis indicated that twice as many noncycling cells were present in the IGFBP-rP1-transduced MCF-7 cell cultures compared with controls. These findings indicate that IGFBP-rP1 is an inhibitor of MCF-7 breast cancer cell proliferation and may act via a cellular senescence-like mechanism.
A comparison of the responses of cultured myoblasts and chondrocytes to fibroblast and epidermal growth factors (1977)

The effects of fibroblast and epidermal growth factors on proliferation and differentiation of cultured myoblasts and chondrocytes have been compared. FGF stimulated myoblast proliferation, as determined by monitoring levels of DNA synthesis during seven days growth in vitro and by the morphology of the cultures after myotube formation. EGF has relatively little effect on myoblast proliferation. With chondrocytes, both FGF and EGF are mitogenic and FGF's, but not EGF's effect is potentiated by dexamethasone. One implication of these results is that in the course of differentiation cell types which develop from the same embryonic origin as fibroblasts are controlled by different sets of mitogenic factors. Myoblasts become primarily dependent on mitogenic agents such as FGF while chondrocytes can respond to both FGF and EGF.
Genomic repertoires of DNA-binding transcription factors across the tree of life (2010)

Sequence-specific transcription factors (TFs) are important to genetic regulation in all organisms because they recognize and directly bind to regulatory regions on DNA. Here, we survey and summarize the TF resources available. We outline the organisms for which TF annotation is provided, and discuss the criteria and methods used to annotate TFs by different databases. By using genomic TF repertoires from ∼700 genomes across the tree of life, covering Bacteria, Archaea and Eukaryota, we review TF abundance with respect to the number of genes, as well as their structural complexity in diverse lineages. While typical eukaryotic TFs are longer than the average eukaryotic proteins, the inverse is true for prokaryotes. Only in eukaryotes does the same family of DNA-binding domain (DBD) occur multiple times within one polypeptide chain. This potentially increases the length and diversity of DNA-recognition sequence by reusing DBDs from the same family. We examined the increase in TF abundance with the number of genes in genomes, using the largest set of prokaryotic and eukaryotic genomes to date. As pointed out before, prokaryotic TFs increase faster than linearly. We further observe a similar relationship in eukaryotic genomes with a slower increase in TFs.
Transfer of human serum IgG to nonobese diabetic Igμ null mice reveals a role for autoantibodies in the loss of secretory function of exocrine tissues in Sjögren’s syndrome (1998)

The NOD (nonobese diabetic) mouse has been studied as an animal model for autoimmune insulin-dependent diabetes and Sjögren's syndrome. NOD.Igmu null mice, which lack functional B lymphocytes, develop progressive histopathologic lesions of the submandibular and lachrymal glands similar to NOD mice, but in the absence of autoimmune insulitis and diabetes. Despite the focal appearance of T cells in salivary and lachrymal tissues, NOD.Igmu null mice fail to lose secretory function as determined by stimulation of the muscarinic/cholinergic receptor by the agonist pilocarpine, suggesting a role for B cell autoantibodies in mediating exocrine dryness. Infusion of purified serum IgG or F(ab')2 fragments from parental NOD mice or human primary Sjögren's syndrome patients, but not serum IgG from healthy controls, alters stimulated saliva production, an observation consistent with antibody binding to neural receptors. Furthermore, human patient IgG fractions competitively inhibited the binding of the muscarinic receptor agonist, [3H]quinuclidinyl benzilate, to salivary gland membranes. This autoantibody activity is lost after preadsorption with intact salivary cells. These findings indicate that autoantibodies play an important part in the functional impairment of secretory processes seen in connection with the autoimmune exocrinopathy of Sjögren's syndrome.
K562—A human erythroleukemic cell line (1979)

We have studied the surface membrane properties of the human leukemic cell line K562 which previously has been reported to represent an early stage of granulocyte maturation. The surface glycoprotein pattern of the K562 cells obtained after galactose oxidase-NaB[3H]4 labelling and slab gel electrophoresis shows striking similarities with that of normal erythrocytes but is completely different from the patterns of normal and malignant cells of various stages of the myeloblast to granulocyte differentiation. Moreover, the K562 cell expressed the major red cell sialoglycoprotein, glycophorin, on its surface as shown by immunofluorescence and by immunoprecipitation from labelled membrane preparations. As glycophorin is exclusively found on erythroid cells in human bone marrow we conclude that the K562 is a human erythroleukemic line.
Prostaglandin E2 modulates dendritic cell function via EP2 and EP4 receptor subtypes (2003)

We have reported previously that PGE(2) inhibits dendritic cells (DC) functions. Because E prostanoid receptor (EPR) subtypes involved in this action are unknown, expression and functions of these receptors were examined in DC. Western blot and flow cytometry analyses showed that all EPRs were coexpressed in DC. In a dose-dependent manner, lipopolysaccharide (LPS) enhanced EP(2)R/EP(4)R but not EP(1)R/EP(3)R expressions. NS-398, a cyclooxygenase (COX)-2-selective inhibitor, suppressed LPS-enhanced EP(2)R/EP(4)R expression, suggesting that COX-2-issued prostaglandin E(2) (PGE(2)) modulates DC function through stimulation of specific EPR subtypes. Using selective agonists, we found that butaprost, an EP(2)R agonist, and PGE(1) alcohol, an EP(2)R and EP(2)R/EP(4)R agonist, inhibited major histocompatibility complex class II expression and enhanced interleukin-10 production from DC. However, no effect was observed with sulprostone and 17-phenyl-omega-trinor-PGE(2), selective agonists for EP(1)R and EP(1)R/EP(3)R, respectively. Treatment of DC with dibutyryl cyclic adenosine monophosphate (cAMP), an analog of cAMP, mimics PGE(2)-induced, inhibitory effects. Taken together, our data demonstrate that EP(2)R/EP(4)R are efficient for mediating PGE(2)-induced modulation of DC functions.
A monoclonal antibody detects heterogeneity in vascular endothelium of tumours and normal tissues (1993)

A new murine monoclonal antibody (MAb), E-9, has been raised using tissue-cultured human umbilical vein endothelial cells. The antigen recognized by this MAb is a peptide of 170 kDa under non-reducing conditions and 96 kDa under reducing conditions. MAb E-9 showed marked heterogeneity in its distribution in various tissues. The antigen recognized by it was present in vascular endothelial cells of all tumours, foetal organs and in regenerating and inflamed tissues. It stained a few normal tissues. However, with the exception of tonsils, staining tended to be weak and limited to a few blood vessels, as revealed by double staining using pan-endothelial antibody (CD31) and antibody to von Willebrand factor, another marker of vascular endothelium. Surprisingly, blood vessels within the placental villi were completely negative. The function of the antigen recognized by MAb E-9 is not known, but its evaluation and use should increase our understanding of angiogenesis.