gebhart/patrepeval huggingface dataset:
Simulation-based architectural design and implementation of a real-time collaborative editing system (2007)

Real-time collaborative editing systems allow multiple users to synchronously edit a shared document in a geographically-distributed environment. In order to maintain high responsiveness, a distributed copy model is used wherein each user maintains a local copy of the shared document; as a result, techniques such as Operation Transformation (OT) are employed to ensure consistency among the copies; but OT is costly with regard to computation and communication. We have previously developed a distributed architecture and associated algorithms that dynamically lock sections of a document such that users are able to retain a high level of responsiveness within the system while reducing the computation and communication costs. However, a key limitation has been locking out all contending users except one for the smallest indivisible subsection, resulting in scenarios with significant lock request failures. This study expands our work by examining how OT may be integrated into our dynamic locking algorithms such that all users are always able to edit their copy of the document while avoiding costly global messaging. We present an overview of our updated architecture and algorithms, show how they have been simulated using the DEVSJAVA package at the client and server, and then demonstrate the efficiencies achieved by our approach relative to existing OT algorithms. In scenarios featuring clustered editing, large document, and a large number of users, our system incurs up to 80% less communication cost than existing pure OT systems. Additionally, we discuss how our simulation design process has allowed us to first simulate both client and server and then begin progress to a functional implementation of both client and server technologies - better achieving an efficient implementation of our algorithms and ideas based upon our empirical simulation results.
3-D image guidance for minimally invasive robotic coronary artery bypass. (2000)

The VCSP image-guided surgical system allows a surgeon to visualize a patient's thorax in a 3-D interactive environment for planning surgical procedures, and to determine the optimum port placement based on preoperative 3-D images. However, during an operation, the positions and orientation of the heart and the coronary arteries are changed from their corresponding locations in the preoperative images due to carbon-dioxide insufflation, lung deflation, and dynamic motions of the beating heart. One of our future goals of this project is the use of mathematical models that correct for these changes so that our system could be applied to intra-operative image guidance.
TIGIT predominantly regulates the immune response via regulatory T cells (2015)

Coinhibitory receptors are critical for the maintenance of immune homeostasis. Upregulation of these receptors on effector T cells terminates T cell responses, while their expression on Tregs promotes their suppressor function. Understanding the function of coinhibitory receptors in effector T cells and Tregs is crucial, as therapies that target coinhibitory receptors are currently at the forefront of treatment strategies for cancer and other chronic diseases. T cell Ig and ITIM domain (TIGIT) is a recently identified coinhibitory receptor that is found on the surface of a variety of lymphoid cells, and its role in immune regulation is just beginning to be elucidated. We examined TIGIT-mediated immune regulation in different murine cancer models and determined that TIGIT marks the most dysfunctional subset of CD8+ T cells in tumor tissue as well as tumor-tissue Tregs with a highly active and suppressive phenotype. We demonstrated that TIGIT signaling in Tregs directs their phenotype and that TIGIT primarily suppresses antitumor immunity via Tregs and not CD8+ T cells. Moreover, TIGIT+ Tregs upregulated expression of the coinhibitory receptor TIM-3 in tumor tissue, and TIM-3 and TIGIT synergized to suppress antitumor immune responses. Our findings provide mechanistic insight into how TIGIT regulates immune responses in chronic disease settings.
A miniaturized microwave resonator for rubidium frequency standards (2003)

Summary form only given. A new type of miniaturized resonator based on the magnetron resonator theory has been developed. The resonator is of small size and high quality factor, and has been used in a rubidium frequency standard.
Epstein-Barr virus in hepatocellular carcinogenesis (2004)

The existence of EBV infection in HCC tissues suggests that EBV may be involved in the hepatocellular carcinogenesis in China. HBV infection may be a major cause of HCC. There is no correlation between EBV and HBV in the development of HCC. The prevalence of HCV infection is low in our area, and HDV appears not to play a direct role in hepatocellular carcinogenesis.
Role of Early Growth Response-1 (Egr-1) in Interleukin-13-induced Inflammation and Remodeling (2006)

IL-13 is an important stimulator of inflammation and tissue remodeling at sites of Th2 inflammation, which plays a key role in the pathogenesis of a variety of human disorders. We hypothesized that the ubiquitous transcription factor, early growth response-1 (Egr-1), plays a key role in IL-13-induced tissue responses. To test this hypothesis we compared the expression of Egr-1 and related moieties in lungs from wild type mice and transgenic mice in which IL-13 was overexpressed in a lung-specific fashion. We simultaneously characterized the effects of a null mutation of Egr-1 on the tissue effects of transgenic IL-13. These studies demonstrate that IL-13 stimulates Egr-1 via an Erk1/2-independent Stat6-dependent pathway(s). They also demonstrate that IL-13 is a potent stimulator of eosinophil- and mononuclear cell-rich inflammation, alveolar remodeling, and tissue fibrosis in mice with wild type Egr-1 loci and that these alterations are ameliorated in the absence of Egr-1. Lastly, they provide insights into the mechanisms of these processes by demonstrating that IL-13 stimulates select CC and CXC chemokines (MIP-1alpha/CCL-3, MIP-1beta/CCL-4, MIP-2/CXCL2/3, MCP-1/CCL-2, MCP-2/CCL-8, MCP-3/CCL-7, MCP-5/CCL-12, KC/CXCL-1, and Lix/CXCL-5), matrix metalloproteinase-9, tissue inhibitor of metalloproteinase-1, and apoptosis regulators (caspase-3, -6, -8, and -9 and Bax) and activates transforming growth factor-beta1 and pulmonary caspases via Egr-1-dependent pathways. These studies demonstrate that Egr-1 plays a key role in the pathogenesis of IL-13-induced inflammatory and remodeling responses.
Modification of DNA duplexes to smooth their thermal stability independently of their base content for DNA sequencing by hybridization (1997)

The possibility of equalizing DNA duplex stability is essential for the application of sequencing by hybridization. In this paper we describe a new strategy to obtain DNA duplexes with a thermal stability independent of their base content. Modified *C bases have been developed and incorporated into oligonucleotides. The influence of these modifications on duplex stability has been studied by absorption spectroscopy, thus allowing selection of N -4-ethyl-2'-deoxycytidine (d4EtC), which hybridizes specifically with natural dG to give a G4EtC base pair whose stability is very close to that of natural AT base pairs. Duplexes built with AT and/or G4EtC base pairs exhibit thermal stabilities independent of their base content in a classical buffer solution, thus enabling control of the stability of DNA hybrids as a function of their length only.
Dynamic capabilities-based strategy innovation: a theoretical framework and empirical studies in Chinese firms (2002)

Based on investigations of 112 Chinese firms and studies on foreign leading corporations, a theoretical framework of dynamic capabilities-based strategy innovation (SI) is put forward. Several large firms in China winning through SI were studied empirically. This paper complements previous publications on the theories of innovation and strategy. This work’ s findings will be useful for managers interested in our approach, which highlights the importance of SI and focuses on and points out the major pitfalls in the innovation processes. Implementing the dynamic capabilities-based strategy innovation can effectively cultivate and develop core competences of corporations. It is concluded that implementing SI is the only path for Chinese enterprise growth in the intensified competition in the knowledge economy.
Identification of a 68-kilodalton nuclear ATP-binding phosphoprotein encoded by bovine papillomavirus type 1 (1990)

E1 is the largest open reading frame (ORF) of bovine papillomavirus type 1 (BPV-1) and is highly conserved among all papillomaviruses, maintaining its size, amino acid composition, and location in the viral genome with respect to other early genes. Multiple viral replication functions have been mapped to the E1 ORF of BPV-1, and evidence suggested that more than one protein was encoded by this ORF. We previously identified a small protein (M) whose gene consists of two exons, one encoded by the 5' end of the E1 ORF. We show here that a 68-kilodalton (kDa) phosphoprotein made from the E1 ORF can be detected in BPV-1-transformed cells, and we present evidence that this protein is encoded by sequences colinear with the entire E1 ORF. The full-length E1 protein immunoprecipitated from virally transformed cells and identified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis comigrates with a protein expressed from a recombinant DNA construct capable of producing only the complete E1 protein. In addition, two different antisera directed against polypeptides encoded from either the 3' or the 5' end of the E1 ORF both recognize the full-length E1 product. A mutation converting the first methionine codon in the ORF to an isoleucine codon abolishes BPV-1 plasmid replication and E1 protein production. Consistent with the notion that this methionine codon is the start site for E1, a mutant with a termination codon placed after the splice donor at nucleotide 1235 in E1 produces a truncated protein with the molecular mass predicted from the primary sequence as well as the previously identified M protein. When visualized by immunostaining, the E1 protein expressed in COS cells is localized to the cell nucleus. A high degree of similarity exists between the BPV-1 E1 protein and polyomavirus and simian virus 40 large-T antigens in regions of the T antigens that bind ATP. We show by ATP affinity labeling that the E1 protein produced in COS cells binds ATP and that this activity is abolished by a point mutation which converts the codon for proline 434 to serine. Furthermore, this mutation renders the viral genome defective for DNA replication, suggesting that the ATP-binding activity of E1 is necessary for its putative role in viral DNA replication.(ABSTRACT TRUNCATED AT 400 WORDS)
Biodegradation of Methyl tert -Butyl Ether by a Bacterial Pure Culture (1999)

A bacterial strain, PM1, which is able to utilize methyl tert-butyl ether (MTBE) as its sole carbon and energy source, was isolated from a mixed microbial consortium in a compost biofilter capable of degrading MTBE. Initial linear rates of MTBE degradation by 2 x 10(6) cells ml(-1) were 0.07, 1.17, and 3.56 microg ml(-1) h(-1) for initial concentrations of 5, 50, and 500 microg MTBE ml(-1), respectively. When incubated with 20 microg of uniformly labeled [(14)C]MTBE ml(-1), strain PM1 converted 46% to (14)CO(2) and 19% to (14)C-labeled cells within 120 h. This yield is consistent with the measurement of protein accumulation at different MTBE concentrations from which was estimated a biomass yield of 0.18 mg of cells mg MTBE(-1). Strain PM1 was inoculated into sediment core material collected from a contaminated groundwater plume at Port Hueneme, California, in which there was no evidence of MTBE degradation. Strain PM1 readily degraded 20 microg of MTBE ml(-1) added to the core material. The rate of MTBE removal increased with additional inputs of 20 microg of MTBE ml(-1). These results suggest that PM1 has potential for use in the remediation of MTBE-contaminated environments.
Molecular Quantum Similarity Analysis of Estrogenic Activity (2003)

The main objective of this study was to evaluate the capability of 120 aromatic chemicals to bind to the human alpha estrogen receptor (hER alpha) by the use of quantum similarity methods. The experimental data were segregated into two categories, i.e., those compounds with and without estrogenicity activity (active and inactive). To identify potential ligands, semiquantitative structure-activity relationships were developed for the complete set correlating the presence or lack of binding affinity to the estrogen receptor with structural features of the molecules. The structure-activity relationships were based upon molecular similarity indices, which implicitly contain information related to changes in the electron distributions of the molecules, along with indicator variables, accounting for several structural features. In addition, the whole set was split into several chemical classes for modeling purposes. Models were validated by dividing the complete set into several training and test sets to allow for external predictions to be made.
Effects of site-directed removal of N-glycosylation sites in human erythropoietin on its production and biological properties. (1991)

Erythropoietin (Epo) has three N-linked sugar chains. Codons for asparagine at N-glycosylation sites in genomic human Epo DNA were replaced with those for glutamine. The wild-type Epo gene and seven mutants that lacked N-glycosylation sites in every possible combination were introduced into baby hamster-kidney cells. To study the role of the N-linked sugars in Epo biosynthesis, Epo protein expressed transiently was measured by an enzyme-linked immunoassay. The elimination of all three N-glycosylation sites decreased Epo production to 10% of that of the wild-type Epo. Wild-type and mutant Epos produced by stably transfected cells were partially purified to investigate their properties. Removal of N-glycosylation sites changed affinity of Epo to the receptor. The in vitro activity of Epo that lost all N-glycosylation sites was comparable with that of the wild-type Epo, while the in vivo activity severely decreased. These results indicate that N-linked sugars of Epo have two major functions; N-linked sugars are important for 1) proper biosynthesis and/or secretion and 2) expression of the in vivo activity probably by enhancing survival in the circulation. N-Linked sugars of Epo affect binding affinity of the ligand to the receptor but do not play a key role in expression of the in vitro activity.
Bidirectional control of the chicken beta- and epsilon-globin genes by a shared enhancer. (1988)

An enhancer specific to erythroid cells was identified previously in the 3' flanking sequence of the chicken adult beta-globin gene and shown to act on the beta-globin promoter. This enhancer lies between the adult beta-globin gene and the embryonic epsilon-globin gene, about equidistant from the two promoters. To determine whether this enhancer acts also on the epsilon-globin promoter, we constructed plasmids containing the enhancer and either the beta- or the epsilon-globin promoter fused to the bacterial chloramphenicol acetyltransferase gene. Primary chicken erythrocytes of both primitive and definitive lineages were transfected with these plasmids. We show that the enhancer is able to stimulate expression from the epsilon-globin promoter as well as the beta-globin promoter. Levels of expression change with the developmental stage of the cell in a way that is partially consistent with the observed developmental regulation of the beta- and epsilon-globin genes in vivo. There appear to be no other enhancer elements either 5' of the epsilon-globin gene or within 6 kilobase pairs of its 3' end. Thus, the enhancer between the beta- and epsilon-globin genes apparently serves to regulate both genes.
Expression of Vascular Endothelial Growth Factor From a Defective Herpes Simplex Virus Type 1 Amplicon Vector Induces Angiogenesis in Mice (1995)

Vascular endothelial growth factor (VEGF) is a secreted endothelial cell-specific angiogenic growth factor. VEGF gene transfer strategies to stimulate focal angiogenesis could be used to ameliorate myocardial ischemia. To induce angiogenesis in vivo, we have constructed a replication-defective herpes simplex virus type 1 (HSV-1) amplicon vector that places the human VEGF-165 cDNA under the transcriptional control of the HSV immediate-early 4/5 promoter (HSVhvegf). Transduction of NIH 3T3 fibroblasts with HSVhvegf resulted in the secretion of high levels of biologically active VEGF, as assayed by microvascular endothelial mitogenesis. By use of an ex vivo protocol, BLK-CL4 fibroblasts were transduced with HSVhvegf or control HSVlac virus (expressing Escherichia coli beta-galactosidase), resuspended in basement membrane extract (matrigel), and coinjected subcutaneously into syngeneic C57BL/6 mice. One week later, the matrigel plugs with HSVhvegf showed a strong angiogenic response, in contrast to the plugs with HSVlac-transduced fibroblasts. These data indicate that transduction with HSVhvegf virus can induce an angiogenic response in vivo and suggest that this is a viable gene therapy approach for tissue ischemia.
CD44 is a metastasis suppressor gene for prostatic cancer located on human chromosome 11p13. (1997)

We have used microcell fusion-mediated chromosomal transfer to introduce normal human chromosomes into highly metastatic rodent prostatic cancer cells to map the location of a metastasis suppressor gene(s). Using this approach, several chromosomal regions have been identified that harbor such metastatic suppressor genes, including human chromosome 11 between p11.2-13 (T. Ichikawa et al., Cancer Res., 52: 3486-3490, 1992, 54: 2299-2302, 1994; N. Nihei et al., Genes Chromosomes & Cancer, 14: 112-119, 1995; C. W. Rinker-Schaeffer et al., Cancer Res., 54: 6249-6256, 1994). Using positional cloning, a metastatic suppressor gene, termed KAI1, was identified, which is located at human chromosome 11p11.2 (5). Overexpression of KAI1 results in metastasis suppression in certain highly metastatic Dunning R-3327 rat prostatic cancer sublines, such as AT6.1, without metastasis suppression in other highly metastatic sublines, such as AT3.1. This suggests that an additional metastasis suppressor gene is located within the human chromosome 11p11.2-13 region. The CD44 gene is located on human chromosome 11p13 and encodes an integral membrane glycoprotein that participates in specific cell-cell and cell-extracellular matrix interactions. Down-regulation of CD44 expression both at the mRNA and protein levels correlates with metastatic potential within the Dunning system of rat prostatic cancer sublines. Transfection-induced enhanced expression of the Mr 85,000 standard form of CD44 in the highly metastatic AT3.1 rat prostatic cells greatly suppresses their metastatic ability to the lungs without suppression of their in vivo growth rate or tumorigenicity. These results suggest that CD44 is a metastasis suppressor for prostatic cancer and that decreased expression of the standard form of CD44 is involved in the progression of prostatic cancer to a metastatic state.
THE PREDICTIVE NATURE OF HIGH-THROUGHPUT TOXICITY SCREENING USING A HUMAN HEPATOCYTE CELL LINE (2002)

Drug discovery has become an industrialized process in which vast libraries of compounds are screened for activity against a chosen target. The wealth of active compounds that emerge from these primary screens has created a bottleneck in drug development. Firstround hits do not often meet the safety and efficacy criteria required for human therapeutics, so sequential rounds of optimization are required before a product can be administered to humans. Optimization requires assays that test Absorption, Distribution, Metabolism, Elimination, and Toxicity (ADME/Tox). In this paper we demonstrate the utility of high-throughput testing in a human liver cell line. If the technologies and reagents presented in this article had been available earlier, ADME/Tox screening could have prevented deaths and costly drug recalls by two major pharmaceutical companies.
Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis (2000)

The molecular mechanisms of pulmonary fibrosis are poorly understood. We have used oligonucleotide arrays to analyze the gene expression programs that underlie pulmonary fibrosis in response to bleomycin, a drug that causes lung inflammation and fibrosis, in two strains of susceptible mice (129 and C57BL/6). We then compared the gene expression patterns in these mice with 129 mice carrying a null mutation in the epithelial-restricted integrin beta6 subunit (beta6(-/-)), which develop inflammation but are protected from pulmonary fibrosis. Cluster analysis identified two distinct groups of genes involved in the inflammatory and fibrotic responses. Analysis of gene expression at multiple time points after bleomycin administration revealed sequential induction of subsets of genes that characterize each response. The availability of this comprehensive data set should accelerate the development of more effective strategies for intervention at the various stages in the development of fibrotic diseases of the lungs and other organs.
Ac-Trp-DPhe(p-I)-Arg-Trp-NH2, a 250-Fold Selective Melanocortin-4 Receptor (MC4R) Antagonist over the Melanocortin-3 Receptor (MC3R), Affects Energy Homeostasis in Male and Female Mice Differently (2016)

The melanocortin-4 receptor (MC4R) has been indicated as a therapeutic target for metabolic disorders such as anorexia, cachexia, and obesity. The current study investigates the in vivo effects on energy homeostasis of a 15 nM MC4R antagonist SKY2-23-7, Ac-Trp-DPhe(p-I)-Arg-Trp-NH2, that is a 3700 nM melanocortin-3 receptor (MC3R) antagonist with minimal MC3R and MC4R agonist activity. When monitoring both male and female mice in TSE metabolic cages, sex-specific responses were observed in food intake, respiratory exchange ratio (RER), and energy expenditure. A 7.5 nmol dose of SKY2-23-7 increased food intake, increased RER, and trended toward decreasing energy expenditure in male mice. However, this compound had minimal effect on female mice's food intake and RER at the 7.5 nmol dose. A 2.5 nmol dose of SKY2-23-7 significantly increased female food intake, RER, and energy expenditure while having a minimal effect on male mice at this dose. The observed sex differences of SKY2-23-7 administration result in the discovery of a novel chemical probe for elucidating the molecular mechanisms of the sexual dimorphism present within the melanocortin pathway. To further explore the melanocortin sexual dimorphism, hypothalamic gene expression was examined. The mRNA expression of the MC3R and proopiomelanocortin (POMC) were not significantly different between sexes. However, the expression of agouti-related peptide (AGRP) was significantly higher in female mice which may be a possible mechanism for the sex-specific effects observed with SKY2-23-7.
60 years since "kpb wcy xz" became more informative than "I love you" (2010)

We have attempted to give a gentle overview of the concept of information theory, proposed by Claude E Shannon in 1948. Though the idea of "informative message" as per Shannon's theory is counterintuitive, on closer inspection, it is found to be not so. We have demonstrated the application of information content and information entropy on a couple of types of symbol sequences. Primarily, such analysis provides us with limits of compression possible on the sequences. However, wider scope has also evolved in analyzing sequences, especially biosequences like DNA, RNA and amino acids, to derive informational signatures in the sequences to classify them or to detect hidden features.