gebhart/patrepeval huggingface dataset:
Transfer of T-DNA from Agrobacterium to the Plant Cell (1995)

Agrobacterium tumefaciens is the causative agent of crown gall, a disease of dicotyledonous plants characterized by a tumorous phenotype. Earlier in this century, scientific interest in A. tumefaciens was based on the possibility that the study of plant tumors might reveal mechanisms that were also operating in animal neoplasia. In the recent past, the tumorous growth was shown to result from the expression of genes coded for by a DNA segment of bacterial origin that was transferred and became stably integrated into the plant genome. This initial molecular characterization of the infection process suggested that Agrobacterium might be used to deliver genetic material into plants. The potential to genetically engineer plants generated renewed interest in the study of A. tumefaciens. In this review, we concentrate on the most recent advances in the study of Agrobacterium-mediated gene transfer, its relationship to conjugation, DNA processing and transport, and nuclear targeting. In the following discussion, references for earlier work can be found in more comprehensive reviews (Hooykaas and Schilperoort, 1992; Zambryski, 1992; Hooykaas and Beijersbergen, 1994).
Biochemical characterization of Arabidopsis wild-type and mutant phytochrome B holoproteins. (1997)

Although phytochrome B (phyB) plays a particularly important role throughout the life cycle of a plant, it has not been studied in detail at the molecular level due to its low abundance. Here, we report on the expression, assembly with chromophore, and purification of epitope-tagged Arabidopsis phyB. In addition, we have reconstructed two missense mutations, phyB-4 and phyB-101, isolated in long hypocotyl screens. We show that mutant proteins phyB-4 and phyB-101 exhibit altered spectrophotometric and biochemical properties relative to the wild-type protein. In particular, we demonstrate that phyB-101 Pfr exhibits rapid nonphotochemical (dark) reversion to Pr that results in a lower photoequilibrium level of the active Pfr form. We conclude that this occurs in vivo as well because phyB-101 mutants are shown to lack an end-of-day-far-red hypocotyl elongation response that requires a stable Pfr species. We propose that this Pfr instability may be the primary molecular mechanism underlying the phyB-101 mutant phenotype.
Empirical Analysis of an Evolving Social Network (2006)

Social networks evolve over time, driven by the shared activities and affiliations of their members, by similarity of individuals' attributes, and by the closure of short network cycles. We analyzed a dynamic social network comprising 43,553 students, faculty, and staff at a large university, in which interactions between individuals are inferred from time-stamped e-mail headers recorded over one academic year and are matched with affiliations and attributes. We found that network evolution is dominated by a combination of effects arising from network topology itself and the organizational structure in which the network is embedded. In the absence of global perturbations, average network properties appear to approach an equilibrium state, whereas individual properties are unstable.
Polymer-on-Polymer Stamping:  Universal Approaches to Chemically Patterned Surfaces (2002)

A new approach to create chemically patterned surfaces utilizing polymers and copolymers is introduced. In this approach, chemical patterns are achieved by the direct stamping of functional polymers onto a surface containing complementary functional groups. The resulting pattern is then used as a template for the further deposition of materials on the surface. This concept can be applied to various functional polymer and substrate systems as well as different thin film deposition techniques. This approach is demonstrated with the direct stamping of polystyrene−poly(acrylic acid) block copolymers (PS−PAA) to create alternating hydrophobic/hydrophilic regions and polyelectrolytes to create alternating positively and negatively charged regions. This approach has been used for patterning surfaces and templating materials deposition. When a patterned polyelectrolyte film is used as the base layer or substrate in this process, functionality can be incorporated in the underlying layer, making this approach particularly relevant to device and sensor applications. This approach is universal to a number of substrates, many of which can be used to adsorb a polyelectrolyte layer to provide a functional surface. Various substrates such as Si, glass, and plastic can be patterned with this method with relative ease, and without the need for traditional alkanethiol or silane monolayers. Factors such as stamping temperature, contact time, and substrate pretreatment on the nature of the transferred pattern have been investigated and will be discussed.
Reduction by tributyltin hydride of carbonyl compounds adsorbed on silica gel: selective reduction of aldehydes (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReduction by tributyltin hydride of carbonyl compounds adsorbed on silica gel: selective reduction of aldehydesNorman Y. M. Fung, Paul De Mayo, J. Herman Schauble, and Alan C. WeedonCite this: J. Org. Chem. 1978, 43, 20, 3977–3979Publication Date (Print):September 1, 1978Publication History Published online1 May 2002Published inissue 1 September 1978https://pubs.acs.org/doi/10.1021/jo00414a043https://doi.org/10.1021/jo00414a043research-articleACS PublicationsRequest reuse permissionsArticle Views658Altmetric-Citations61LEARN 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-Alertsclose Get e-Alerts
A Synthetic Method for Palladium-Catalyzed Stannylation at the 5- and 6-Benzo Positions of Indoles (2012)

The stannylation of indole derivatives proceeds in good yields under palladium catalysis (5 mol %) without protection of the indolic nitrogen. The general utility of both PdCl(2)(PhCN)(2)/PCy(3) and Pd(2)dba(3)/PCy(3) as catalytic systems for the stannylation of three indole derivatives, with varying degrees of electron density, is presented.
Transient perturbation of endothelial integrity induced by natural antibodies and complement. (1995)

The barrier function of blood vessels is though to be regulated at least in part by endothelium. This concept is supported by the dramatic loss of barrier function occurring in the hyperacute rejection of vascularized grafts mediated by anti-endothelial cell (EC) antibodies and complement. In this process, the endothelium is not destroyed but instead loses the ability to retain blood cells and plasma proteins within capillaries. The noncytotoxic mechanism that allows this change in EC function has been unknown. Here we report that within 10 to 20 min of exposure to human xenoreactive natural antibodies and complement, porcine EC undergo alterations in cell shape and in the cytoskeleton that disrupt monolayer integrity and lead to formation of intercellular gaps. Gap formation is not associated with cell death but requires the complement complex C5b67. The gaps induced by anti-EC antibodies and complement are transient; gap closure requires formation of C5b-9 complexes on the cells and the rate of recovery depends on the release of cellular products into the medium. Preincubation of EC with dibutyryl cAMP (0.5 mM) prevents gap formation and disruption of the cytoskeleton caused by antibodies and complement. These results provide evidence that the integrity of endothelium is regulated by components of the complement system and suggest a mechanism that may explain the prominent loss of endothelial integrity seen in humoral immune responses.
A Screen for Dominant Negative Mutants ofSEC18Reveals a Role for the AAA Protein Consensus Sequence in ATP Hydrolysis (2000)

An evolutionarily ancient mechanism is used for intracellular membrane fusion events ranging from endoplasmic reticulum-Golgi traffic in yeast to synaptic vesicle exocytosis in the human brain. At the heart of this mechanism is the core complex of N-ethylmaleimide-sensitive fusion protein (NSF), soluble NSF attachment proteins (SNAPs), and SNAP receptors (SNAREs). Although these proteins are accepted as key players in vesicular traffic, their molecular mechanisms of action remain unclear. To illuminate important structure-function relationships in NSF, a screen for dominant negative mutants of yeast NSF (Sec18p) was undertaken. This involved random mutagenesis of a GAL1-regulated SEC18 yeast expression plasmid. Several dominant negative alleles were identified on the basis of galactose-inducible growth arrest, of which one, sec18-109, was characterized in detail. The sec18-109 phenotype (abnormal membrane trafficking through the biosynthetic pathway, accumulation of a membranous tubular network, growth suppression, increased cell density) is due to a single A-G substitution in SEC18 resulting in a missense mutation in Sec18p (Thr(394)-->Pro). Thr(394) is conserved in most AAA proteins and indeed forms part of the minimal AAA consensus sequence that serves as a signature of this large protein family. Analysis of recombinant Sec18-109p indicates that the mutation does not prevent hexamerization or interaction with yeast alpha-SNAP (Sec17p), but instead results in undetectable ATPase activity that cannot be stimulated by Sec17p. This suggests a role for the AAA protein consensus sequence in regulating ATP hydrolysis. Furthermore, this approach of screening for dominant negative mutants in yeast can be applied to other conserved proteins so as to highlight important functional domains in their mammalian counterparts.
Unsupervised Spoken Language Understanding for a Multi-Domain Dialog System (2013)

This paper proposes an unsupervised spoken language understanding (SLU) framework for a multi-domain dialog system. Our unsupervised SLU framework applies a non-parametric Bayesian approach to dialog acts, intents and slot entities, which are the components of a semantic frame. The proposed approach reduces the human effort necessary to obtain a semantically annotated corpus for dialog system development. In this study, we analyze clustering results using various evaluation metrics for four dialog corpora. We also introduce a multi-domain dialog system that uses the unsupervised SLU framework. We argue that our unsupervised approach can help overcome the annotation acquisition bottleneck in developing dialog systems. To verify this claim, we report a dialog system evaluation, in which our method achieves competitive results in comparison with a system that uses a manually annotated corpus. In addition, we conducted several experiments to explore the effect of our approach on reducing development costs. The results show that our approach be helpful for the rapid development of a prototype system and reducing the overall development costs.
Akt Protein Kinase Inhibits Rac1-GTP Binding through Phosphorylation at Serine 71 of Rac1 (2000)

A putative Akt kinase phosphorylation site ((64)ydRIRplSYp(73)) was found in Rac1/CDC42 and Rho family proteins (RhoA, RhoB, RhoC, and RhoG). Phosphorylation of Rac1 by Akt kinase was assayed with recombinant Rac1 protein and the fluorescein-labeled Rac1 peptide. It was shown that the Rac1 peptide and the recombinant protein were phosphorylated by the activated recombinant Akt kinase and the lysate of SK-MEL28 cells, a human melanoma cell line. The phosphorylation of Rac1 inhibited its GTP-binding activity without any significant change in GTPase activity. Both the GTP-binding and GTPase activities of Rac1 S71A protein (with the serine residue to be phosphorylated replaced with alanine) were abolished regardless of the treatment of Akt kinase. Akt kinase activity and Rac1 peptide phosphorylation were down-regulated by the treatment of SK-MEL28 cells with wortmannin or LY294002 (a phosphoinositide 3-kinase inhibitor), but JNK/SAPK kinase activity was up-regulated. Thus, the results suggest that Akt kinase of the phosphoinositide 3-kinase signal transduction pathway phosphorylates serine 71 of Rac1 as one of its authentic substrates and modulates the Rac1 signal transduction pathway through phosphorylation.
NY-ESO-1 Expression and Immunogenicity in Malignant and Benign Breast Tumors (2004)

NY-ESO-1 is a cancer/testis antigen expressed in normal adult tissues solely in the testicular germ cells of normal adults and in various cancers. It induces specific humoral and cellular immunity in patients with NY-ESO-1-expressing cancer. The aim of this study was to determine the frequency of NY-ESO-1 mRNA and protein expression in malignant and benign breast tumors. NY-ESO-1 mRNA expression was detected by conventional reverse transcription-PCR and real-time PCR, and that of the protein expression by immunohistochemistry and Western blot analysis. Expression of NY-ESO-1 mRNA was detected in 37 of 88 (42%) cancer specimens, whereas that of the NY-ESO-1 protein was detected only in 1 mRNA-positive specimen. In the latter case, expression level of NY-ESO-1 mRNA relative to that in the testis was relatively high (75% of testicular expression) and to the other among breast cancer specimens. In benign breast lesions, 21 of 31 (68%) specimens expressed low levels of NY-ESO-1 mRNA. In 1 case of fibroadenoma, NY-ESO-1 mRNA was 8% of the testicular level, and protein was detected by Western blot analysis. Only 1 breast cancer patient had detectable antibody at time of surgery, which disappeared within 2 years. Tumor specimen from this patient was both NY-ESO-1 mRNA and protein positive, and NY-ESO-1-specific CD8 T cells were detected in this patient by IFN-gamma enzyme-linked immunospot assay using NY-ESO-1 recombinant adeno and vaccinia virus. A higher rate of NY-ESO-1 expression was noted in breast cancer with high histological grade and negative hormone receptor status, suggesting NY-ESO-1 as a potential tumor antigen for immunotherapy in patients with breast cancer and poor prognosis.
Expression of c-myc and bcl-2 oncogene products in Reed-Sternberg cells independent of presence of Epstein-Barr virus. (1993)

Reed-Sternberg cells in Hodgkin's disease frequently express both bcl-2 and c-myc oncogene products, suggesting that these oncogenes may act in concert in the pathogenesis of the disease. Moreover, the expression of c-myc and bcl-2 proteins in Reed-Sternberg cells is independent of EBV and LMP status.
114 NK cells contribute to the constitution of HIV reservoirs in dendritic cells (2009)

Early stages of viral infections are associated with local recruitment and activation of effectors of innate immunity, i.e. NK cells and DCs. DCs are essential for both antigen-presentation and activation of naïve CD4+ T cells, and further Th1 polarization. DCs also constitute early targets for HIV. NK-DC crosstalk is important for DC homeostasis and maturation, but its contribution to susceptibility of DCs to infection, and to DC-dependent Th1 polarisation is unknown. We addressed this question in the present study. We report that HIV-infection of immature DC did not induce their maturation, as evaluated by the coexpression of CD86 and HLA-DR, while their coculture with activated NK cells did. NK-induced maturation of DC was inhibited by polyclonal antibodies specific for HMGB1 molecule or by glycyrrhizin, suggesting an important role of the pro-inflammatory cytokine HMGB1 in this process. Interestingly, activated NK were also able to polarize the production of IL-12 by DC that in turn induced a T helper 1-like immune response when cocultured with naive CD4+ T cells. In contrast, infected DCs were no more susceptible to NK-dependent IL-12 polarization, and thus no more able to induce a Th1 response. In addition, NK-dependent DC maturation was associated with an increased production of HIV-1 p24 and an increased expression of proviral DNA by DC. Altogether, our results show that activated NK cells 1- induce the maturation of DC through an HMGB-1-dependent mechanism; 2- trigger IL-12 production by DC and further Th1 polarization; 3- increase HIV production and the constitution of viral reservoirs in infected DC; 4- facilitate HIV-1 transmission from DC to T cells.
Towards Combining Probabilistic and Interval Uncertainty in Engineering Calculations (2004)

Abstract. In many engineering applications, we have to combine probabilistic and interval errors. For example, in environmental analysis, we observe a pollution level x(t) in a lake at different moments of time t, and we would like to estimate standard statistical characteristics such as mean, variance, autocorrelation, correlation with other measurements. In environmental measurements, we often only know the values with interval uncertainty. We must therefore modify the existing statistical algorithms to process such interval data. Such modification are described in this paper.
Magnetic Hollow Spheres of Periodic Mesoporous Organosilica and Fe3O4 Nanocrystals: Fabrication and Structure Control (2008)

Periodic mesoporous organosilica magnetic hollow spheres (PMO–MHS) are synthesized. The particle size, shell wall thickness and saturation magnetization value of PMO–MHS are tunable by varying the ratio of templating agent to magnetic nanoparticles. The high saturation magnetization ensures that these functional mesoporous hollow spheres can be efficient materials for targeted drug delivery assisted by magnetic fields.
Update on the development of enterovirus 71 vaccines (2014)

Although inactivated EV71 vaccines are safe, efficient and elicit strong immune responses to protect adults, children and infants against infection, the quality control of production is critical.
Ectopic Expression of Interferon Regulatory Factor-1 Promotes Human Breast Cancer Cell Death and Results in Reduced Expression of Survivin (2004)

The overexpression of the inhibitor of apoptosis protein, survivin, may provide tumor cells with a distinct survival advantage in situ; hence, therapeutic strategies have been designed to inhibit its expression. In this study, we ectopically expressed the interferon regulatory factor (IRF)-1 protein in the breast carcinoma cell lines MDA-MB-468 and SK-BR-3 using a recombinant adenovirus (Ad-IRF-1). By screening microarray analysis of cDNA from the human breast cancer cell line MDA-MB-468 infected with Ad-IRF-1, we observed a 15-fold down-regulation of the survivin gene when compared with uninfected cells. Consequently, we tested survivin expression in Ad-IRF-1-infected MDA-MB-468 and SK-BR-3 breast cancer cell lines. Immunoblotting analyses supported the contention that ectopic expression of the IRF-1 protein results in down-regulation of survivin protein expression that is independent of p53. In addition, Ad-IRF-1 infection of these human breast cancer cell lines induces the expression of p21. We also report that increased apoptosis is observed in tumor cells infected with Ad-IRF-1 compared with Ad-Psi5 mock-infected cells and that cell death is further augmented when the IRF-1-infected cells are cultured with Adriamycin. Moreover, in a xenogeneic mouse model of breast carcinoma, in vivo treatment of tumor-bearing mice with intratumoral Ad-IRF-1 injections results in tumor growth inhibition. In resected tumors from mice that had been treated with Ad-IRF-1, tumor cells that express the IRF-1 transgene have a predominant IRF-1-positive, survivin-negative phenotype. Collectively, these observations suggest that therapies designed to enhance IRF-1 expression within tumor cells may represent novel treatment strategies for breast cancer.
Both E6 and E7 Oncoproteins of Human Papillomavirus 16 Inhibit IL-18-Induced IFN-γ Production in Human Peripheral Blood Mononuclear and NK Cells (2001)

Cervical carcinoma is the predominant cancer among malignancies in women throughout the world, and human papillomavirus (HPV) 16 is the most common agent linked to human cervical carcinoma. The present study was performed to investigate the mechanisms of immune escape in HPV-induced cervical cancer cells. The presence of HPV oncoproteins E6 and E7 in the extracellular fluids of HPV-containing cervical cancer cell lines SiHa and CaSki was demonstrated by ELISA. The effect of HPV 16 oncoproteins E6 and E7 on the production of IFN-gamma by IL-18 was assessed. E6 and E7 proteins reduced IL-18-induced IFN-gamma production in both primary PBMCs and the NK0 cell line. FACS analysis revealed that the viral oncoproteins reduced the binding of IL-18 to its cellular surface receptors on NK0 cells, whereas there was no effect of oncoproteins on IL-1 binding to its surface IL-1 receptors on D10S, a subclone of the murine Th cell D10.G4.1. In vitro pull-down assays also revealed that the viral oncoproteins and IL-18 bound to IL-18R alpha-chain competitively. These results suggest that the extracellular HPV 16 E6 and E7 proteins may inhibit IL-18-induced IFN-gamma production locally in HPV lesions through inhibition of IL-18 binding to its alpha-chain receptor. Down-modulation of IL-18-induced immune responses by HPV oncoproteins may contribute to viral pathogenesis or carcinogenesis.
Employment Privacy Law for the 1990's (1988)

the employee and the employer, 3
A chameleon-inspired stretchable electronic skin with interactive colour changing controlled by tactile sensing (2015)

Some animals, such as the chameleon and cephalopod, have the remarkable capability to change their skin colour. This unique characteristic has long inspired scientists to develop materials and devices to mimic such a function. However, it requires the complex integration of stretchability, colour-changing and tactile sensing. Here we show an all-solution processed chameleon-inspired stretchable electronic skin (e-skin), in which the e-skin colour can easily be controlled through varying the applied pressure along with the applied pressure duration. As such, the e-skin's colour change can also be in turn utilized to distinguish the pressure applied. The integration of the stretchable, highly tunable resistive pressure sensor and the fully stretchable organic electrochromic device enables the demonstration of a stretchable electrochromically active e-skin with tactile-sensing control. This system will have wide range applications such as interactive wearable devices, artificial prosthetics and smart robots.
Optimizations and oracle parallelism with dynamic translation (1999)

We describe several optimizations which can be employed in a dynamic binary translation (DBT) system, where low compilation/translation overhead is essential. These optimizations achieve a high degree of ILP, sometimes even surpassing a static compiler employing more sophisticated, and more time-consuming algorithms [9]. We present results in which we employ these optimizations in a dynamic binary translation system capable of computing oracle parallelism.
Gene Therapy for Ocular Disease (2000)

The tremendous progress in the past decade in delineating the molecular bases of ocular diseases has been accompanied by the realization that it may be possible to harness this information to generate rational treatment strategies. The concept that treatments might be performed at the genetic level has been a driving force in research involving several blinding ocular diseases. Although there has not, as yet, been a demonstration of cure using gene therapy approaches, proof-of-principle has been established in a number of animal models for a diverse set of ocular diseases.