gebhart/patrepeval huggingface dataset:
Visual models of plants interacting with their environment (1996)

Interaction with the environment is a key factor affecting the development of plants and plant ecosystems. In this paper we introduce a modeling framework that makes it possible to simulate and visualize a wide range of interactions at the level of plant architecture. This framework extends the formalism of Lindenmayer systems with constructs needed to model bi-directional information exchange between plants and their environment. We illustrate the proposed framework with models and simulations that capture the development of tree branches limited by collisions, the colonizing growth of clonal plants competing for space in favorable areas, the interaction between roots competing for water in the soil, and the competition within and between trees for access to light. Computer animation and visualization techniques make it possible to better understand the modeled processes and lead to realistic images of plants within their environmental context.
Fibronectin-binding protein of Streptococcus pyogenes: sequence of the binding domain involved in adherence of streptococci to epithelial cells (1992)

The sequence of the fibronectin-binding domain of the fibronectin-binding protein of Streptococcus pyogenes (Sfb protein) was determined, and its role in streptococcal adherence was investigated by use of an Sfb fusion protein in adherence studies. A 1-kb DNA fragment coding for the binding domain of Sfb protein was cloned into the expression vector pEX31 to produce an Sfb fusion protein consisting of the N-terminal part of MS2 polymerase and a C-terminal fragment of the streptococcal protein. Induction of the vector promoter resulted in hyperexpression of fibronectin-binding fusion protein in the cytoplasm of the recombinant Escherichia coli cells. Sequence determination of the cloned 1-kb fragment revealed an in-frame reading frame for a 268-amino-acid peptide composed of a 37-amino-acid sequence which is completely repeated three times and incompletely repeated a fourth time. Cloning of one repeat into pEX31 resulted in expression of small fusion peptides that show fibronectin-binding activity, indicating that one repeat contains at least one binding domain. Each repeat exhibits two charged domains and shows high homology with the 38-amino-acid D3 repeat of the fibronectin-binding protein of Staphylococcus aureus. Sequence comparison with other streptococcal ligand-binding surface proteins, including M protein, failed to reveal significant homology, which suggests that Sfb protein represents a novel type of functional protein in S. pyogenes. The Sfb fusion protein isolated from the cytoplasm of recombinant cells was purified by fast protein liquid chromatography. It showed a strong competitive inhibition of fibronectin binding to S. pyogenes and of the adherence of bacteria to cultured epithelial cells. In contrast, purified streptococcal lipoteichoic acid showed only a weak inhibition of fibronectin binding and streptococcal adherence. These results demonstrate that Sfb protein is directly involved in the fibronectin-mediated adherence of S. pyogenes to epithelial cells.
Learning Transferable Features with Deep Adaptation Networks (2015)

Recent studies reveal that a deep neural network can learn transferable features which generalize well to novel tasks for domain adaptation. However, as deep features eventually transition from general to specific along the network, the feature transferability drops significantly in higher layers with increasing domain discrepancy. Hence, it is important to formally reduce the dataset bias and enhance the transferability in task-specific layers. In this paper, we propose a new Deep Adaptation Network (DAN) architecture, which generalizes deep convolutional neural network to the domain adaptation scenario. In DAN, hidden representations of all task-specific layers are embedded in a reproducing kernel Hilbert space where the mean embeddings of different domain distributions can be explicitly matched. The domain discrepancy is further reduced using an optimal multi-kernel selection method for mean embedding matching. DAN can learn transferable features with statistical guarantees, and can scale linearly by unbiased estimate of kernel embedding. Extensive empirical evidence shows that the proposed architecture yields state-of-the-art image classification error rates on standard domain adaptation benchmarks.
Antitumor activity of Lactobacillus casei in mice. (1981)

The effect of Lactobacillus casei YIT 9018 (LC 9018) on the growth of transplantable allogeneic and syngeneic mouse tumors was studied. Intraperitoneal treatment of LC 9018 caused a significant prolongation of the life span of ICR mice inoculated with sarcoma-180 intraperitoneally and BDF1 mice inoculated with L1210 leukemia intraperitoneally. Intravenous injection of LC 9018 markedly inhibited the growth of subcutaneously inoculated sarcoma-180. This organism was also effective against methylcholanthrene-induced syngeneic MCA K-1 tumor in BALB/c mice. The antitumor activity of LC 9018 was reduced by treatment with carrageenan, an anti-macrophage agent, and was also observed in T-cell deficient athymic nude mice. These results suggested that the antitumor activity of LC 9018 may be macrophage-dependent.
Effective pure states for bulk quantum computation (1998)

In bulk quantum computation one can manipulate a large number of indistinguishable quantum computers by parallel unitary operations and measure expectation values of certain observables with limited sensitivity. The initial state of each computer in the ensemble is known but not pure. Methods for obtaining effective pure input states by a series of manipulations have been described by Gershenfeld and Chuang (logical labeling) [Science 275, 350 (1997)] and Cory et al. (spatial averaging) [Proc. Natl. Acad. Sci. USA 94, 1634 (1997)] for the case of quantum computation with nuclear magnetic resonance. We give a different technique called temporal averaging. This method is based on classical randomization, requires no ancilla quantum bits, and can be implemented in nuclear magnetic resonance without using gradient fields. We introduce several temporal averaging algorithms suitable for both high-temperature and low-temperature bulk quantum computing and analyze the signal-to-noise behavior of each. Most of these algorithms require only a constant multiple of the number of experiments needed by the other methods for creating effective pure states.
A monoclonal antibody to CD4 domain 2 blocks soluble CD4-induced conformational changes in the envelope glycoproteins of human immunodeficiency virus type 1 (HIV-1) and HIV-1 infection of CD4+ cells (1992)

The murine monoclonal antibody (MAb) 5A8, which is reactive with domain 2 of CD4, blocks human immunodeficiency virus type 1 (HIV-1) infection and syncytium formation of CD4+ cells (L. C. Burkly, D. Olson, R. Shapiro, G. Winkler, J. J. Rosa, D. W. Thomas, C. Williams, and P. Chisholm, J. Immunol., in press). Here we show that, in contrast to the CD4 domain 1 MAb 6H10, 5A8 and its Fab fragment do not block soluble CD4 (sCD4) binding to virions, whereas they do inhibit sCD4-induced exposure of cryptic epitopes on gp41 and dissociation of gp120 from virions. Two other MAbs, OKT4 and L120, which are reactive with domains 3 and 4 of CD4, have little or no effect on HIV-1 infection, syncytium formation, or sCD4-induced conformational changes in the envelope glycoproteins. The mechanisms of action of 5A8 and 6H10 can be further distinguished in syncytium inhibition assays: 6H10 blocks competitively, while 5A8 does not. We opine that 5A8 blocks HIV-1 infection and fusion by interfering with conformational changes in gp120/gp41 and/or CD4 that are necessary for virus-cell fusion.
Immunochemistry, genuine size and tissue localization of collagen VI (1984)

Collagen VI was solubilized with pepsin from human placenta and used for preparing rabbit antisera. Major antigenic determinants were located in the central region of the antigen including triple-helical and globular structures. Antisera prepared against a constituent-chain showed preferential reactions with unfolded structures. Antibodies were purified by affinity chromatography and failed to cross-react with other collagen types I-V and with fibronectin. These antibodies demonstrated intracellular and extracellular collagen VI in fibroblast and smooth muscle cell cultures. Immunoblotting identified a disulfide-bonded constituent chain about twice as large as those of the pepsin fragments in both cell cultures and tissue extracts. Rotary shadowing electron microscopy indicated that the increase in mass is due to larger globular domains present at both ends of collagen VI monomers. Indirect immunofluorescence demonstrated a wide occurrence of collagen VI in connective tissue particularly of large vessels, kidney, skin, liver and muscle. Collagen VI is apparently not a typical constituent of cartilage or of basement membranes. Ultrastructural studies using the immunoferritin technique showed collagen VI along thin filaments or in amorphous regions of aortic media or placenta but not in association with thick, cross-striated collagen fibrils or elastin. This supports previous suggestions that collagen VI is a constituent of microfibrillar structures of the body.
Estimating analogical similarity by dot-products of Holographic Reduced Representations (1993)

Models of analog retrieval require a computationally cheap method of estimating similarity between a probe and the candidates in a large pool of memory items. The vector dot-product operation would be ideal for this purpose if it were possible to encode complex structures as vector representations in such a way that the superficial similarity of vector representations reflected underlying structural similarity. This paper describes how such an encoding is provided by Holographic Reduced Representations (HRRs), which are a method for encoding nested relational structures as fixed-width distributed representations. The conditions under which structural similarity is reflected in the dot-product rankings of HRRs are discussed. 1 INTRODUCTION Gentner and Markman (1992) suggested that the ability to deal with analogy will be a &amp;quot;Watershed or Waterloo&amp;quot; for connectionist models. They identified &amp;quot;structural alignment&amp;quot; as the central aspect of analogy making. They noted the apparent ease with w...
Catalytic, Asymmetric Dimerization of Methylketene (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTCatalytic, Asymmetric Dimerization of MethylketeneMichael A. CalterView Author Information Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0212 Cite this: J. Org. Chem. 1996, 61, 23, 8006–8007Publication Date (Web):November 15, 1996Publication History Received9 September 1996Published online15 November 1996Published inissue 15 November 1996https://pubs.acs.org/doi/10.1021/jo961721chttps://doi.org/10.1021/jo961721crapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views1787Altmetric-Citations92LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Amines,Catalysts,Dimerization,Enolates,Transfer reactions Get e-Alerts
Induction of spermidine/spermine N1-acetyltransferase (SSAT) by aspirin in Caco-2 colon cancer cells (2006)

Epidemiological, experimental and clinical results suggest that aspirin and other NSAIDs (non-steroidal anti-inflammatory drugs) inhibit the development of colon cancer. It has been shown that the NSAID sulindac induces apoptosis and suppresses carcinogenesis, in part, by a mechanism leading to the transcriptional activation of the gene encoding SSAT (spermidine/spermine N1-acetyltransferase), a rate-limiting enzyme in polyamine catabolism. In the present study, we show that a variety of NSAIDs, including aspirin, sulindac, ibuprofen and indomethacin, can induce SSAT gene expression in Caco-2 cells. Aspirin, at physiological concentrations, can induce SSAT mRNA via transcriptional initiation mechanisms. This induction leads to increased SSAT protein levels and enzyme activity. Promoter deletion analysis of the 5' SSAT promoter-flanking region led to the identification of two NF-kappaB (nuclear factor kappaB) response elements. Electrophoretic mobility-shift assays showed binding of NF-kappaB complexes at these sequences after aspirin treatment. Aspirin treatment led to the activation of NF-kappaB signalling and increased binding at these NF-kappaB sites in the SSAT promoter, hence providing a potential mechanism for the induction of SSAT by aspirin in these cells. Aspirin-induced SSAT ultimately leads to a decrease in cellular polyamine content, which has been associated with decreased carcinogenesis. These results suggest that activation of SSAT by aspirin and different NSAIDs may be a common property of NSAIDs that plays an important role in their chemopreventive actions in colorectal cancer.
Stereoselective Synthesis of Both Enantiomers of Axially Chiral Biaryls Utilizing Planar Chiral Tricarbonyl(arene)chromium Complexes (1996)

Tricarbonyl(2,6-disubstituted 1-bromobenzene)chromium complexes were treated with ortho-substituted arylboronic acids in the presence of Pd(0) catalyst to give mono Cr(CO)3 complexes of biphenyl compounds with complementary axial chirality, with extremely high stereoselectively depending upon the steric bulkiness of the ortho substituents. Cross-coupling of o-alkyl- or hydroxymethyl-substituted phenylboronic acids with (arene)chromium complexes diastereoselectively gave Cr(CO)3-complexed biaryls in which the ortho substituents are in a syn-orientation to the tricarbonylchromium fragment. With o-formyl phenylboronic acids, diastereoisomeric anti-coupling products were stereoselectively obtained. The kinetically controlled coupling products were easily isomerized to thermodynamically more stable mono-Cr(CO)3-complexed biaryls by modification of the o-substituents to less hindered ones, or the thermal conditions assisted the axial isomerization. The overall process can be considered to be an enantioselective preparation of both axially chiral biaryls starting from a single planar chiral (arene)chromium complex.
Docosahexaenoic Acid Protects from Amyloid and Dendritic Pathology in an Alzheimer's Disease Mouse Model (2006)

Genetic data argues that Alzheimer's disease (AD) can be initiated by aggregates of a 42 amino acid beta amyloid peptide (Abeta42). The Abeta aggregates, notably small oligomer species, cause a cascade of events including oxidative damage, inflammation, synaptic toxicity and accumulation of intraneuronal inclusions; notably neurofibrillary tangles. Cognitive deficits are likely to begin with a failure of synaptogenesis and synaptic plasticity with dendritic spine loss and dying back of dendritic arbor. This is followed by neuron loss in key areas involved in learning and memory. Significant prevention or delay of clinical onset may be achievable by modifying environmental risk factors that impact the underlying pathogenic pathways. Because low fish intake and low blood levels of the marine lipid, docosahexaenoic acid (DHA) have been associated with increased AD risk we have tested the impact of depleting or supplementing with dietary DHA on AD pathogenesis in transgenic mice bearing a mutant human gene known to cause AD in people. We reported that even with intervention late in life dietary DHA depletion dramatically enhanced oxidative damage and the loss of dendritic markers, while DHA supplementation markedly reduced Abeta42 accumulation and oxidative damage, corrected many synaptic deficits and improved cognitive function. Loss of brain DHA was exacerbated in mice expressing the mutant human AD transgene, this is consistent with evidence for increased oxidative attack on DHA oxidation in AD. Treatment with the curry spice extract curcumin, a polyphenolic antioxidant that inhibits AP aggregation, has been strongly protective in the same mouse model. Many Western diets are typically deficient in DHA and low in polyphenolic antioxidant intake. These and other data argue that increasing dietary intake of both DHA and polyphenolic antioxidants may be useful for AD prevention.
Methylation of the T-DNA inAgrobacterium tumefaciensand In several crown gall tumors (1983)

Methylation of the T-DNA in Agrobacterium tumefaciens and in four octopine-type (A6S/2, E9, 15955/1, 15955/01) and one nopaline-type (HT37#15) crown gall tumors was investigated using the isoschizomeric restriction endonucleases Msp I and Hpa II. T-DNA in the octopine-type Ti-plasmid pTiB6(806) was not methylated at the sequence 5'CCGG3' in Agrobacterium. With two possible exceptions, neither was the T-DNA of the nopaline-type Ti-plasmid pTiT37 methylated in the bacterium. In all tumor lines investigated, at least one copy of the T-DNA was not methylated. DNA methylation was not detected in the lines A6S/2, 15955/1, HT37#15, and the TL region of E9. DNA methylation of some copies of TR in the E9 tumor line, and possibly in the 15955/01 line, was detected. The methylation of some copies of TR in the E9 line may indicate that not all copies of TR are transcribed in this tumor.
Short Related Sequences in the Cytoplasmic Domains of CD4 and CD8 Mediate Binding to the Amino-Terminal Domain of the p56 lck Tyrosine Protein Kinase (1990)

We report that the cytoplasmic domains of the T-lymphocyte glycoproteins CD4 and CD8 alpha contain short related amino acid sequences that are involved in binding the amino-terminal domain of the intracellular tyrosine protein kinase, p56lck. Transfer of as few as six amino acid residues from the cytoplasmic domain of the CD8 alpha protein to the cytoplasmic domain of an unrelated protein conferred p56lck binding to the hybrid protein in HeLa cells. The common sequence motif shared by CD4 and CD8 alpha contains two cysteines, and mutation of either cysteine in the CD4 sequence eliminated binding of p56lck.p56lck also contains two cysteine residues within its CD4-CD8 alpha-binding domain, and both are critical to the interaction with CD4 or CD8 alpha. Because the interaction does not involve disulfide bond formation, a metal ion could stabilize the complex.
Investigation of How IT Leadership Impacts IT-Business Alignment through Shared Domain Knowledge and Knowledge Integration (2015)

Using full range leadership model and the knowledge-based view of organizations, we develop and test a model linking Information Technology (IT) leadership to IT-business alignment. Specifically, we examine how transformational IT leadership behaviors influence IT-business alignment through mechanisms that develop shared domain knowledge between IT and business personnel and mechanisms that integrate specialized IT and business knowledge. We also examine how the former mechanisms influence the efficiency of the latter. This study contributes to the existing literature by suggesting transformational leadership and mechanisms related to knowledge integration as key factors in IT-business alignment.
Critical Role of cAMP-GEFII·Rim2 Complex in Incretin-potentiated Insulin Secretion (2001)

Incretins such as glucagon-like peptide-1 and gastric inhibitory polypeptide/glucose-dependent insulinotropic peptide are known to potentiate insulin secretion mainly through a cAMP/protein kinase A (PKA) signaling pathway in pancreatic beta-cells, but the mechanism is not clear. We recently found that the cAMP-binding protein cAMP-GEFII (or Epac 2), interacting with Rim2, a target of the small G protein Rab3, mediates cAMP-dependent, PKA-independent exocytosis in a reconstituted system. In the present study, we investigated the role of the cAMP-GEFII--Rim2 pathway in incretin-potentiated insulin secretion in native pancreatic beta-cells. Treatment of pancreatic islets with antisense oligodeoxynucleotides (ODNs) against cAMP-GEFII alone or with the PKA inhibitor H-89 alone inhibited incretin-potentiated insulin secretion approximately 50%, while a combination of antisense ODNs and H-89 inhibited the secretion approximately 80-90%. The effect of cAMP-GEFII on insulin secretion is mediated by Rim2 and depends on intracellular calcium as well as on cAMP. Treatment of the islets with antisense ODNs attenuated both the first and second phases of insulin secretion potentiated by the cAMP analog 8-bromo-cAMP. These results indicate that the PKA-independent mechanism involving the cAMP-GEFII--Rim2 pathway is critical in the potentiation of insulin secretion by incretins.
Modular Design of a Synthetic Payload Delivery Device (2013)

Predictable engineering of complex biological behaviors using characterized molecular functions remains a key challenge in synthetic biology. To explore the process of engineering biological behaviors, we applied a modular design strategy to the development of E. coli that deliver macromolecules to the cytoplasm of cancer cells in vitro. First, we specified five abstract, qualitative behaviors that would act in concert to achieve payload delivery. Drawing from disparate sources of previously described genetic components, we then designed, constructed, and tested individual genetic circuits to implement each module. Subsequent coupling of the modules and system optimization, aided by quantitative predictions, generated a system that delivers proteins to 80% of targeted cancer cells. Development of an effective delivery system provides strong evidence that advanced cellular behaviors, not just transcriptional circuits, can be rationally decomposed into a series of functional genetic modules and then constructed to achieve the target activity with the existing synthetic biology toolkit.
Gene expression profile of cultured adult compared to immortalized human RPE. (2006)

There are significant differences in the gene expression profile of ahRPE compared to ARPE19, and with some genes exclusively being expressed in one group and other genes being upregulated or downregulated by threefold. Caution should be exercised when generalizing results obtained from ARPE19 to the behavior of ahRPE.
Novel somatic frameshift mutations of genes related to cell cycle and DNA damage response in gastric and colorectal cancers with microsatellite instability. (2011)

Novel frameshift mutations occurred in seven genes in GC and CRC with MSI-H. The results of our study suggest that the mutations might contribute to the development of GC and CRC with MSI by deregulation of the cell cycle and DNA damage signaling/repair.