gebhart/patrepeval huggingface dataset:
Functions of hyaluronan in wound repair (1999)

Hyaluronan is a major carbohydrate component of the extracellular matrix and can be found in skin, joints, eyes and most other organs and tissues. It has a simple, repeated disaccharide linear copolymer structure that is completely conserved throughout a large span of the evolutionary tree, indicating a fundamental biological importance. Amongst extracellular matrix molecules, it has unique hygroscopic, rheological and viscoelastic properties. Hyaluronan binds to many other extracellular matrix molecules, binds specifically to cell bodies through cell surface receptors, and has a unique mode of synthesis in which the molecule is extruded immediately into the extracellular space upon formation. Through its complex interactions with matrix components and cells, hyaluronan has multifaceted roles in biology utilizing both its physicochemical and biological properties. These biological roles range from a purely structural function in the extracellular matrix to developmental regulation through effects of cellular behavior via control of the tissue macro- and microenvironments, as well as through direct receptor mediated effects on gene expression. Hyaluronan is also thought to have important biological roles in skin wound healing, by virtue of its presence in high amounts in skin. Hyaluronan content in skin is further elevated transiently in granulation tissue during the wound healing process. In this review, the general physicochemical and biological properties of hyaluronan, and how these properties may be utilized in the various processes of wound healing: inflammation, granulation and reepithelization, are presented.
People, Politics, and Plazas: A Comparative Analysis of Dallas (City Hall Plaza) and Copenhagen (Rådhuspladsen) (2019)

Public plazas are an integral part of urban life and they generally take familiar forms. Yet not all public spaces function as intended and, ultimately, not all are successful. The following comparative analysis of Dallas City Hall Plaza and Copenhagen’s Rådhuspladsen explores what makes public plazas “work.” More specifically, while, both plazas are architecturally similar, City Hall Plaza remains largely unused and desolate while Rådhuspladsen is bustling and lively. This multi-method project begins by exploring the historical development of public space in Dallas and Copenhagen and continues with an ethnographic study of each plaza. Findings suggest that the success of public plazas can be attributed to five recurrent themes: attraction and engagement, sustainability and nature, visibility, public transportation and pedestrian accessibility, and integration. By systematically comparing the two cases, we can identify modest design changes that can soften inhospitable public plazas and make them spaces that people will use and enjoy.
Novel Compliance Index derived from digital volume pulse associated with risk factors and exercise capacity in patients undergoing treadmill exercise tests (2007)

The Compliance Index was lower in patients with risk factors and was associated with poor exercise capacity. This index may be clinically useful for evaluating arterial stiffness.
Lysis of leukemic cells by human macrophages: inhibition by 4-(2-aminoethyl)-benzenesulfonyl fluoride (AEBSF), a serine protease inhibitor (1996)

Proteases are known to be involved in regulation of macrophage activation and killing. We examined the effect of a serine protease inhibitor, 4-(2-aminoethyl)-benzenesulfonyl fluoride (AEBSF), on lysis of leukemic cells by human macrophages. Monocytes, isolated by Histopaque gradients and centrifugal elutriation, were cultured for 5 days in RPMI-1640 medium with 5% AB serum, and then activated with interferon-gamma (IFN-gamma; 100 U/mL) and lipopolysaccharide (LPS) (5 ng/mL), with or without AEBSF, for 2 days. On day 7, macrophages were washed, fresh medium without AEBSF added, and target cells added for 2 days. Lytic activity against two leukemic cell lines (K562 and HL-60) was assessed by an 111indium-releasing assay. Macrophages treated with IFN-gamma + LPS lysed K562 and HL-60 cells. AEBSF (50-150 microM) blocked the killing of these leukemic cells in a concentration-dependent manner. Other protease inhibitors were not effective. AEBSF was nontoxic at the concentrations used, and did not inhibit tumor necrosis factor-alpha (TNF-alpha) and interleukin-1 beta (IL-1 beta) secretion from the macrophages. The lytic activity against leukemic cells was inhibited by anti-TNF-alpha antibody, but not by anti-IL-1 beta, nor by superoxide dismutase or catalase. However, the leukemic cells were resistant to being killed by recombinant TNF-alpha alone in the absence of macrophages, indicating that TNF-alpha was required for killing, but that other factors that were inhibited by AEBSF were also required. Serum-free culture supernatant of activated macrophages had significant cytotoxic activity against leukemic cells. This cytotoxic activity was not altered by addition of AEBSF to the culture supernatant, suggesting that AEBSF affected macrophage activation, rather than inhibiting cytotoxic proteases secreted by the macrophages, or affecting the target cells themselves. Thus, a protease, which is susceptible to AEBSF, might be involved in the activation of macrophages, and might regulate the secretion of antitumor effector molecules other than TNF-alpha.
Threshold conditions for the air plasma initiation near solid surfaces under the action of powerful pulsed CO2 laser radiation (1985)

New data are reported concerning the plasma initiation in front of metallic and dielectric surfaces under the action of pulsed CO2 laser radiation.
Analysis of Chromatin Attachment and Partitioning Functions of Bovine Papillomavirus Type 1 E2 Protein (2004)

Recent studies have suggested that the tethering of viral genomes to host cell chromosomes could provide one of the ways to achieve their nuclear retention and partitioning during extrachromosomal maintenance in dividing cells. The data we present here provide firm evidence that the partitioning of the bovine papillomavirus type 1 (BPV1) genome is dependent on the chromatin attachment process mediated by viral E2 protein and its multiple binding sites. On the other hand, the attachment of E2 and the E2-mediated tethering of reporter plasmids to host chromosomes are not necessarily sufficient for efficient partitioning, suggesting that additional E2-dependent activities might be involved in the latter process. The activity of E2 protein in chromatin attachment and partitioning is more sensitive to the point mutations in the N-terminal domain than its transactivation and replication initiation functions. Therefore, at least part of the interactions of the E2 N-terminal domain with its targets during the chromatin attachment and partitioning processes are likely to involve specific receptors not involved in transactivation and replication activities of the protein. The mutational analysis also indicates that the binding of E2 to chromatin is not achieved through interaction of linear N-terminal subsequences of the E2 protein with putative receptors. Instead, the composite surface elements of the N-terminal domain build up the receptor-binding surface of E2. In this regard, the interaction of BPV1 E2 with its chromosomal targets clearly differs from the interactions of LANA1 protein from Kaposi's sarcoma-associated human herpesvirus and EBNA1 from Epstein-Barr virus with their specific receptors.
Head Pose Estimation in Computer Vision: A Survey (2009)

The capacity to estimate the head pose of another person is a common human ability that presents a unique challenge for computer vision systems. Compared to face detection and recognition, which have been the primary foci of face-related vision research, identity-invariant head pose estimation has fewer rigorously evaluated systems or generic solutions. In this paper, we discuss the inherent difficulties in head pose estimation and present an organized survey describing the evolution of the field. Our discussion focuses on the advantages and disadvantages of each approach and spans 90 of the most innovative and characteristic papers that have been published on this topic. We compare these systems by focusing on their ability to estimate coarse and fine head pose, highlighting approaches that are well suited for unconstrained environments.
Characterization of antisense binding properties of peptide nucleic acids by capillary gel electrophoresis (1993)

The binding of peptide nucleic acids (PNAs), novel antisense agents, to their complementary oligonucleotide is characterized by capillary gel electrophoresis (CGE). The ability of CGE to resolve the free and bound species enables the measurement of relative binding kinetics and the stoichiometry of binding. The binding kinetics depend on the relative sequence orientation of the target oligonucleotides. The stoichiometry of binding is 1:1 for the PNA-oligodeoxynucleotide heteroduplex whereas the stoichiometry for the PNA-oligoribonucleotide is more complicated.
Dielectric cover effect on rectangular microstrip antenna array (1994)

A theoretical model to analyze a covered rectangular antenna with an arbitrary dielectric constant superstrate is developed. The antenna is simulated by the radiation of two magnetic dipoles located at the radiating edges of the patch. The Green's function of an elementary magnetic dipole in a superstrate-substrate structure, utilizing spectral-domain analysis, is formulated, and the surface-wave and radiation field are computed. An improved transmission line model, which considers the stored energy near the radiating edges and the external mutual coupling, is used to compute the input impedances and radiation efficiency. Design considerations on the superstrate thickness and its dielectric constant are discussed. Experimental data for a single element and a 4/spl times/4 microstrip array is presented to validate the theory.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cancer metastasis therapeutic targets and drug discovery: emerging small-molecule protein kinase inhibitors (2004)

Cancer metastasis is a significant problem and a tremendous challenge to drug discovery relative to identifying key therapeutic targets as well as developing breakthrough medicines. Recent progress in unravelling the complex molecular circuitry of cancer metastasis, including receptors, intracellular proteins and genes, is highlighted. Furthermore, recent advances in drug discovery to provide novel proof-of-concept ligands, in vivo effective lead compounds and promising clinical candidates, are summarised. Such drug discovery efforts illustrate the integration of functional genomics, cell biology, structural biology, drug design, molecular/cellular screening and chemical diversity (e.g., small molecules, peptides/peptidomimetics, natural products, antisense, vaccines and antibodies). Promising therapeutic targets for cancer metastasis have been identified, including Src, focal adhesion kinase, the integrin receptor, the vascular endothelial growth factor receptor, the epidermal growth factor receptor, Her-2/neu, c-Met, Ras/Rac GTPases, Raf kinase, farnesyl diphosphate synthase (i.e., amino-bisphosphonate therapeutic target) and matrix metalloproteases within the context of their implicated functional roles in cancer growth, invasion, angiogenesis and survival at secondary sites. Clinical and preclinical drug discovery is described and emerging small-molecule inhibitors of protein kinases are highlighted.
The Leucine-Rich Repeat Domain Can Determine Effective Interaction Between RPS2 and Other Host Factors in Arabidopsis RPS2-Mediated Disease Resistance (2001)

Abstract Like many other plant disease resistance genes, Arabidopsis thaliana RPS2 encodes a product with nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains. This study explored the hypothesized interaction of RPS2 with other host factors that may be required for perception of Pseudomonas syringae pathogens that express avrRpt2 and/or for the subsequent induction of plant defense responses. Crosses between Arabidopsis ecotypes Col-0 (resistant) and Po-1 (susceptible) revealed segregation of more than one gene that controls resistance to P. syringae that express avrRpt2. Many F2 and F3 progeny exhibited intermediate resistance phenotypes. In addition to RPS2, at least one additional genetic interval associated with this defense response was identified and mapped using quantitative genetic methods. Further genetic and molecular genetic complementation experiments with cloned RPS2 alleles revealed that the Po-1 allele of RPS2 can function in a Col-0 genetic background, but not in a Po-1 background. The other resistance-determining genes of Po-1 can function, however, as they successfully conferred resistance in combination with the Col-0 allele of RPS2. Domain-swap experiments revealed that in RPS2, a polymorphism at six amino acids in the LRR region is responsible for this allele-specific ability to function with other host factors.
The Krüppel-like factor 9 (KLF9) network in HEC-1-A endometrial carcinoma cells suggests the carcinogenic potential of dys-regulated KLF9 expression (2008)

KLF9 influences the expression of uterine epithelial genes through mechanisms likely involving its transcriptional activator and repressor functions and which may underlie altered tumor biology with aberrant KLF9 expression.
Elastin Structure, Biosynthesis, and Relation to Disease States (1981)

Elastin, a component of connective tissue, is present in virtually every organ of the body. Its role is unique and undoubtedly important, even though it may make up only a small percentage of a tissue. Its role is being appreciated increasingly in the pathogenesis of atherosclerosis, emphysema, and other diseases.Definitions and MorphologyElastin is the functional protein component of the elastic fiber, the component of connective tissue that has an amorphous, highly refractive, generally wavy appearance under the light microscope. When elastin is stretched, its waviness disappears and it takes on increased birefringence, which is usually attributed to a . . .
CD98 as a novel prognostic indicator for patients with stage III/IV hypopharyngeal squamous cell carcinoma (2014)

CD98 is a promising prognostic marker for predicting outcomes after surgical treatment in patients with advanced hypopharyngeal SCC.
A Novel Endothelial Cell Surface Receptor Tyrosine Kinase with Extracellular Epidermal Growth Factor Homology Domains (1992)

Endothelial cell surfaces play key roles in several important physiological and pathological processes such as blood clotting, angiogenic responses, and inflammation. Here we describe the cloning and characterization of tie, a novel type of human endothelial cell surface receptor tyrosine kinase. The extracellular domain of the predicted tie protein product has an exceptional multidomain structure consisting of a cluster of three epidermal growth factor homology motifs embedded between two immunoglobulinlike loops, which are followed by three fibronectin type III repeats next to the transmembrane region. Additionally, a cDNA form lacking the first of the three epidermal growth factor homology domains was isolated, suggesting that alternative splicing creates different tie-type receptors. Cells transfected with tie cDNA expression vector produce glycosylated polypeptides of 117 kDa which are reactive to antisera raised against the tie carboxy terminus. The tie gene was located in chromosomal region 1p33 to 1p34. Expression of the tie gene appeared to be restricted in some cell lines; large amounts of tie mRNA were detected in endothelial cell lines and in some myeloid leukemia cell lines with erythroid and megakaryoblastoid characteristics. In addition, mRNA in situ studies further indicated the endothelial expression of the tie gene. The tie receptor tyrosine kinase may have evolved for multiple protein-protein interactions, possibly including cell adhesion to the vascular endothelium.
Genome‐wide screening for gene function using RNAi in mammalian cells (2005)

Mammalian genome sequencing has identified numerous genes requiring functional annotation. The discovery that dsRNA can direct gene-specific silencing in both model organisms and mammalian cells through RNA interference (RNAi) has provided a platform for dissecting the function of independent genes. The generation of large-scale RNAi libraries targeting all predicted genes within mouse, rat and human cells, combined with the large number of cell-based assays, provides a unique opportunity to perform high-throughput genetics in these complex cell systems. Many different formats exist for the generation of genome-wide RNAi libraries for use in mammalian cells. Furthermore, the use of these libraries in either genetic screens or genetic selections allows for the identification of known and novel genes involved in complex cellular phenotypes and biological processes, some of which underpin human disease. In this review, we examine genome-wide RNAi libraries used in model organisms and mammalian cells and provide examples of how these information rich reagents can be used for determining gene function, discovering novel therapeutic targets and dissecting signalling pathways, cellular processes and complex phenotypes.
Immunohistochemical detection of NAD(P)H:quinone oxidoreductase in human lung and lung tumors. (1998)

NAD(P)H:quinone oxidoreductase (NQO1) is a flavoenzyme that catalyzes the two-electron reduction of quinones and related compounds. With the use of biochemical assays, NQO1 has been shown to be overexpressed in many types of cancer, including non-small cell lung cancer (NSCLC). NQO1 can bioactivate antitumor quinones such as mitomycin C, and new quinone-based drugs are currently being developed to target this enzyme in tumors such as NSCLC. Because there is no information on the cell-specific expression of NQO1 in lung, the purpose of this study was to examine the expression of NQO1 in human NSCLC, small cell lung cancer, carcinoid lung tumors, and normal lung using immunohistochemistry. A high level of NQO1 protein expression was detected by immunohistochemistry in NSCLC (adenocarcinoma, squamous cell carcinoma, and bronchoalveolar carcinoma), but no NQO1 protein could be detected in small cell lung cancer or carcinoid lung tumors. In addition, NQO1 protein expression was examined by immunohistochemistry in normal lung tissue. A high level of NQO1 protein expression was detected by immunohistochemistry in normal lung respiratory epithelium, with the highest levels of expression observed in ciliated columnar epithelial cells. Significant amounts of NQO1 protein were also detected in the vascular endothelium and adipocytes. These data demonstrate that NQO1 is overexpressed in NSCLC. Cells in normal lung also contain marked NQO1 protein and may be damaged by drugs activated by NQO1. These data validate NSCLC as a target for NQO1-directed agents and suggest that the potential for lung toxicity be considered in the preclinical development of quinone-based antitumor drugs.
Characterization of a cDNA encoding the heparin and collagen binding domains of human thrombospondin. (1986)

Thrombospondin (TSP) cDNA clones were isolated from a human fibroblast cDNA library by screening with degenerate synthetic oligodeoxynucleotides. The probes were designed based on the sequences of peptides isolated from tryptic digests of TSP. The largest clone identified contains an open reading frame that encodes the amino-terminal heparin binding domain of TSP and part of the immediately adjacent collagen binding domain, a region of TSP that includes the site of disulfide crosslinking responsible for trimer formation. In addition to the known amino-terminal sequence of mature TSP (which is identical to that of the heparin binding domain) and that of the collagen binding domain, the open reading frame predicts the amino acid sequences of four tryptic peptides including the one from which the probe sequences were derived. The sequence of the mature protein is preceded by an unusual signal peptide sequence of 18 residues. The heparin binding domain contains 240 amino acids including only one intradomain disulfide bond. In contrast, 80 residues beyond the start of the collagen binding domain, a cluster of 10 cysteine residues occurs within 40 amino acids corresponding to the point of interchain disulfide crosslinking in the TSP trimer. RNA blot analysis indicates a TSP mRNA size of approximately equal to 8 kilobases and Southern blots are consistent with a single gene encoding TSP.
Modified deoxyoligonucleotides stable to exonuclease degradation in serum (1991)

Unmodified deoxyoligonucleotides are rapidly degraded in serum-containing medium. Utilizing internally labelled deoxyoligonucleotides the deoxyribonuclease profile for fetal calf serum and human serum was determined. It was found that the predominate nuclease activity in both systems was 3' exonuclease. Deoxyoligonucleotides are protected from exonuclease degradation in sera and cell media by simple terminal modifications that maintain high binding activity for the complementary DNA sequence.
Mechanism of Silicon Exfoliation by Hydrogen Implantation and He, Li and Si CO-implantation (1997)

Different hydrogen implantation conditions as well as co-implantation of various elemental species are used to study the different exfoliation mechanisms. Substantial differences between the concentration/thermal evolution of the bound hydrogen of pure H-implantation and He/H co-implantation are shown. For co-implantation, the initial concentration of Si-H species decreased compared to pure H-implantation. The balance of implanted hydrogen must be in the form of molecular hydrogen that is invisible to infrared radiation.
ARR1, a Transcription Factor for Genes Immediately Responsive to Cytokinins (2001)

Cytokinins are a class of phytohormones involved in various physiological events of plants. The Arabidopsis sensor histidine kinase CRE1 was recently reported to be a cytokinin receptor. We used a steroid-inducible system to show that the transcription factor-type response regulator ARR1 directs transcriptional activation of the ARR6 gene, which responds to cytokinins without de novo protein synthesis. This fact, together with characteristics of ARR1-overexpressing plants and arr1 mutant plants, indicates that the phosphorelay to ARR1, probably from CRE1, constitutes an intracellular signal transduction occurring immediately after cytokinin perception.
Targeted DNA Mutagenesis for the Cure of Chronic Viral Infections (2012)

Human immunodeficiency virus type 1 (HIV-1), hepatitis B virus (HBV), and herpes simplex virus (HSV) have been incurable to date because effective antiviral therapies target only replicating viruses and do not eradicate latently integrated or nonreplicating episomal viral genomes. Endonucleases that can target and cleave critical regions within latent viral genomes are currently in development. These enzymes are being engineered with high specificity such that off-target binding of cellular DNA will be absent or minimal. Imprecise nonhomologous-end-joining (NHEJ) DNA repair following repeated cleavage at the same critical site may permanently disrupt translation of essential viral proteins. We discuss the benefits and drawbacks of three types of DNA cleavage enzymes (zinc finger endonucleases, transcription activator-like [TAL] effector nucleases [TALENs], and homing endonucleases [also called meganucleases]), the development of delivery vectors for these enzymes, and potential obstacles for successful treatment of chronic viral infections. We then review issues regarding persistence of HIV-1, HBV, and HSV that are relevant to eradication with genome-altering approaches.