gebhart/patrepeval huggingface dataset:
Graphene-based optical phase modulation of waveguide transverse electric modes (2014)

In this paper we report TE-mode phase modulation obtained by inducing a capacitive charge on graphene layers embedded in the core of a waveguide. There is a biasing regime in which graphene absorption is negligible but large index variations can be achieved with a voltage–length product as small as VπLπ≃0.07  V  cm for straight waveguides and VπLπ≃0.0024  V  cm for 12 μm radius microring resonators. This phase modulation device uniquely enables a small signal amplitude <1  V with a micrometer-sized footprint for compatibility with CMOS circuit integration. Examples of phase-induced changes are computed for straight waveguides and for microring resonators, showing the possibility of implementing several optoelectronic functionalities as modulators, tunable filters, and switches.
Induction of Cardiomyopathy in Severe Combined Immunodeficiency Mice by Transfer of Lymphocytes from Patients with Idiopathic Dilated Cardiomyopathy (2000)

Growing evidence suggests that autoimmune mechanisms play an important role in the pathogenesis of idiopathic dilated cardiomyopathy (DCM). The aim of the study was to evaluate the effects of transfer of lymphocytes from patients with DCM into severe combined immunodeficiency (SCID) mice on the heart structure and function. Thirty CB-17 SCID (6-8 weeks old) mice were used and divided into 3 groups (n = 10). Mice were injected intraperitoneally with up to 25 x 10(6) peripheral blood lymphocytes (PBL) from either patients with DCM which contain human autoantibodies against cardiac beta1-adrenergic receptors and M2-muscarinic receptors (DCM group) or PBL from healthy controls (control-H group). Ten mice did not receive any injections and were used as baseline controls (control-N group). Echocardiography and morphological studies were performed seventy five days after the transfer. Results showed that in DCM group, left ventricle dimensions (LVD) in diastole were increased (4.2 +/- 0.1mm) as compared to both control-H group (3.8 +/- 0.1mm) and control-N group (3.6 +/- 0.1 mm) (p < 0.01). Further, there was a trend for increased LVD in systole. Fractional shortening was not different between groups. Histological evaluation revealed accumulation of human lymphocytes in the capillaries and scarce infiltration of the lymphocytes in the hearts from DCM group. Diffuse fibrosis was significant increased in DCM mice as compared to mice receiving PBL from normal subjects (2.2 +/- 0.3% vs. 0.8 +/- 0.1%, p < 0.01). In conclusion, transfer of the PBL from the patients with DCM was able to induce early stage of heart dilatation in SCID mice. These data provide for the first time the direct evidence supporting that the autoimmune mechanism is important in the pathogenesis of human DCM.
B- and C-RAF Display Essential Differences in Their Binding to Ras (2007)

Recruitment of RAF kinases to the plasma membrane was initially proposed to be mediated by Ras proteins via interaction with the RAF Ras binding domain (RBD). Data reporting that RAF kinases possess high affinities for particular membrane lipids support a new model in which Ras-RAF interactions may be spatially restricted to the plane of the membrane. Although the coupling features of Ras binding to the isolated RAF RBD were investigated in great detail, little is known about the interactions of the processed Ras with the functional and full-length RAF kinases. Here we present a quantitative analysis of the binding properties of farnesylated and nonfarnesylated H-Ras to both full-length B- and C-RAF in the presence and absence of lipid environment. Although isolated RBD fragments associate with high affinity to both farnesylated and nonfarnesylated H-Ras, the full-length RAF kinases revealed fundamental differences with respect to Ras binding. In contrast to C-RAF that requires farnesylated H-Ras, cytosolic B-RAF associates effectively and with significantly higher affinity with both farnesylated and nonfarnesylated H-Ras. To investigate the potential farnesyl binding site(s) we prepared several N-terminal fragments of C-RAF and found that in the presence of cysteine-rich domain only the farnesylated form of H-Ras binds with high association rates. The extreme N terminus of B-RAF turned out to be responsible for the facilitation of lipid independent Ras binding to B-RAF, since truncation of this region resulted in a protein that changed its kinase properties and resembles C-RAF. In vivo studies using PC12 and COS7 cells support in vitro results. Co-localization measurements using labeled Ras and RAF documented essential differences between B- and C-RAF with respect to association with Ras. Taken together, these data suggest that the activation of B-RAF, in contrast to C-RAF, may take place both at the plasma membrane and in the cytosolic environment.
Integration of geometric and conceptual reasoning for interacting with virtual environments (1998)

This paper describes the knowledge processing in the CODY Virtual Constructor, an operational system enabling the interactive assembly of complex aggregates in a virtual environment. Two forms of reasoners are used: a geometric reasoner that infers spatial properties of scene objects and a conceptual reasoner that keeps track of the evolving aggregate&amp;apos;s assembly structure. The combination of the two reasoners enables the system both to simulate assembly processes in the virtual environment and to understand natural language instructions. By maximizing the mutual exchange of information between the reasoners, additional knowledge can be inferred that not only improves understanding of language instructions but also increases efficiency of inferencing. Virtual Assembly by Natural Language Instruction The CODY Virtual Constructor is a knowledge-based system for the interactive assembly of complex aggregates on a virtual assembly bench (Cao, Jung, &amp;amp; Wachsmuth 1995). In our testbed scenari...
Benchmarking short sequence mapping tools (2013)

The mapping process is still a hard problem that is affected by many factors. In this work, we provided a benchmarking suite that reveals and evaluates the different factors affecting the mapping process. Still, there is no tool that outperforms all of the others in all the tests. Therefore, the end user should clearly specify his needs in order to choose the tool that provides the best results.
Sequence‐based identification of T‐DNA insertion mutations in Arabidopsis: actin mutants act2‐1 and act4‐1 (1995)

A method is presented to facilitate the isolation of mutations in plant genes, which requires knowledge of the target gene or protein sequence, and is independent of mutant phenotype. The polymerase chain reaction was used to amplify the junctions between a T-DNA insert and the gene of interest from pools of mutant plant lines. The approach was used to identify mutations in Arabidopsis thaliana actin genes. The Arabidopsis genome encodes 10 actins in six ancient subclasses each with distinct expression patterns. Primers in the T-DNA border and highly degenerate actin primers, designed from conserved amino acid motifs, were used to prime the amplification. The PCR products were transferred to filters and probed for actin at low stringency. Thus, mutations in all 10 actin genes were screened for simultaneously. Mutations in the vegetative constitutive actin gene, ACT2, and the pollen-specific actin gene, ACT4, were identified in a population of 5300 lines containing approximately 1.5 T-DNA insertions per line. The screen was sensitive enough that actin insertion alleles were easily distinguished among pools of 100 plant lines. PCR techniques were used which accelerated the purification of mutant lines, and segregation, physical mapping, and sequencing of the act2-1 and act4-1 mutations. This strategy should be generally useful in screening mutant libraries made with a variety of plant insertion elements for mutations in any known sequence.
ITAM-mediated Signaling by the T-Cell Antigen Receptor (2010)

Signal transduction by the T-cell antigen receptor (TCR) is initiated by phosphorylation of conserved motifs (ITAMs) contained within the cytoplasmic domains of the invariant subunits. TCR complexes contain a total of 10 ITAMs and this unusual configuration has prompted studies of the role of specific ITAMs, or of ITAM multiplicity, in regulating TCR-directed developmental and effector responses. Here, we summarize data generated during the past two decades and discuss how these findings have in some cases resolved, and in others complicated, outstanding questions relating to the function of TCR ITAMs.
Identification of a Chlamydial Protease–Like Activity Factor Responsible for the Degradation of Host Transcription Factors (2001)

Microbial pathogens have been selected for the capacity to evade or manipulate host responses in order to survive after infection. Chlamydia, an obligate intracellular pathogen and the causative agent for many human diseases, can escape T lymphocyte immune recognition by degrading host transcription factors required for major histocompatibility complex (MHC) antigen expression. We have now identified a chlamydial protease- or proteasome-like activity factor (CPAF) that is secreted into the host cell cytosol and that is both necessary and sufficient for the degradation of host transcription factors RFX5 and upstream stimulation factor 1 (USF-1). The CPAF gene is highly conserved among chlamydial strains, but has no significant overall homology with other known genes. Thus, CPAF represents a unique secreted protein produced by an obligate intracellular bacterial pathogen to interfere with effective host adaptive immunity.
Plant nuclear factor Y (NF-Y) B subunits confer drought tolerance and lead to improved corn yields on water-limited acres (2007)

Commercially improved crop performance under drought conditions has been challenging because of the complexity of the trait and the multitude of factors that influence yield. Here we report the results of a functional genomics approach that identified a transcription factor from the nuclear factor Y (NF-Y) family, AtNF-YB1, which acts through a previously undescribed mechanism to confer improved performance in Arabidopsis under drought conditions. An orthologous maize transcription factor, ZmNF-YB2, is shown to have an equivalent activity. Under water-limited conditions, transgenic maize plants with increased ZmNF-YB2 expression show tolerance to drought based on the responses of a number of stress-related parameters, including chlorophyll content, stomatal conductance, leaf temperature, reduced wilting, and maintenance of photosynthesis. These stress adaptations contribute to a grain yield advantage to maize under water-limited environments. The application of this technology has the potential to significantly impact maize production systems that experience drought.
RNA isolation using immobilized PNA (2005)

A novel method to isolate a single kind of RNA from RNA mixture was developed by using a biotinylated-PNA (peptide nucleic acid) that is complementary to the RNA. Efficient bindings of Escherichia coli tRNA(Leu)CUC were observed to the 9-mer and 12-mer PNAs that are complementary to the 3'-end region of the tRNA. Purified E. coli tRNA(Leu)CUC was obtained from E. coli tRNA mixture.
Melanoma-Associated Adhesion Molecule MUC18/MCAM (CD146) and Transcriptional Regulator Mader in Normal Human CNS (1998)

The proteins MUC18 and Mader have been identified as markers of tumor progression in melanoma cells. MUC18, also known as MCAM (melanoma cell adhesion molecule) and as CD146 (endothelial antigen), is a cell adhesion molecule belonging to the immunoglobulin superfamily. Mader is a transcriptional regulator shown to negatively regulate EGR-1. As it is known that neoplastic cells of neuroectodermal origin frequently express neuron-specific molecules, we studied whether these melanoma-associated antigens are found in normal CNS tissue. We investigated the expression of MUC18/MCAM and Mader in adult human post mortem CNS tissue by immunohistochemistry, immunoblot and two-dimensional gel electrophoresis. Our results show that Mader is preferentially expressed on neurons and glial cells and that the adhesion protein MUC18/MCAM is mainly expressed on vasculature within the CNS. These observations may have important implications for further studies investigating their possible roles in cell adhesion and proliferation control within the CNS.
HLA class II alleles are not a general susceptibility factor in Guillain–Barre syndrome (2005)

Human leukocyte antigen (HLA) class II antigens are not a general susceptibility factor in Guillain-Barre syndrome (GBS). However, HLA class II alleles may be a determinant in distinct subgroups of GBS, indicating the need for further exploration in large-scale studies.
Broad spectrum chemokine antagonistic activity of a human poxvirus chemokine homolog (1998)

A secreted CC chemokine homolog, encoded by the MC148 gene of molluscum contagiosum virus, potently interfered with the chemotaxis of human monocytes, lymphocytes, and neutrophils in response to a large number of CC and CXC chemokines with diverse receptor specificities. Evidence that the viral protein binds to human chemokine receptors was obtained by competition binding and calcium mobilization experiments. The broad spectrum chemokine antagonistic activity of MC148 can explain the prolonged absence of an inflammatory response in skin tumors that harbor replicating molluscum contagiosum virus.
Characterization of acid catalytic domains for cellulose hydrolysis and glucose degradation (2002)

Cellulolytic enzymes consist of a catalytic domain, a linking peptide, and a binding domain. The paper describes research on carboxylic acids that have potential as catalytic domains for constructing organic macromolecules for use in cellulose hydrolysis that mimic the action of enzymes. The tested domains consist of the series of mono-, di-, and tricarboxylic acids with a range of pK(a)'s. This paper systematically characterizes the acids with respect to hydrolysis of cellobiose, cellulose in biomass, and degradation of glucose and compares these kinetics data to dilute sulfuric acid. Results show that acid catalyzed hydrolysis is proportional to H+ concentration. The tested carboxylic acids did not catalyze the degradation of glucose while sulfuric acid catalyzed the degradation of glucose above that of water alone. Consequently, overall yields of glucose obtained from cellobiose and cellulose are higher for the best carboxylic acid tested, maleic acid, when compared to sulfuric acid at equivalent solution pH.
Synthesis and Formulation of Neoglycolipids for the Functionalization of Liposomes and Lipoplexes (2003)

Novel carbohydrate-based agents for the stabilization of ternary liposome:mu:DNA (LMD) nonviral vector systems are described. LMD vector systems comprise plasmid DNA (pDNA; D,7.5 kb) expressing a reporter gene (in this instance beta-galactosidase expressing gene) that is precondensed with the adenoviral core peptide mu (mu, M; MRRAHHRRRRASHRRMRGG) and then further packaged by means of DC-Chol:DOPE (3:2; m/m) cationic liposomes. Final optimized lipid:mu:pDNA ratio is typically 12:0.6:1 (w/w/w). We report the synthesis of a series of nine neoglycolipids prepared by coupling completely unprotected sugar monomers or oligomers (mannose, glucose, galactose, glucuronic acid, maltose, lactose, maltotriose, maltotetraose, and maltoheptaose) through their reducing-residue termini to an aminoxy-functionalized cholesterol-based lipid. Characterization of these novel neoglycolipids by (1)H NMR reveals that the coupling reaction has a major configurational preference for the beta-anomer. Unusually, even mannose coupling results in a neoglycolipid product with a predominantly beta-anomeric conformation (>85%). Formulation of neoglycolipids into LMD vector systems by incubation of LMD particles with neoglycolipid micelles results in the formation of a range of potential stabilized-LMD (sLMD) vector systems. Those potential sLMD systems prepared with longer chain neoglycolipids are found to have enhanced stabilities, with respect to aggregation in high ionic strength buffers, and enhanced transfection efficacies in comparison to the transfection properties of the naked first generation LMD vector system (i.e., gene delivery and expression). By contrast, when LMD vector systems are incubated with poly(ethylene glycol) DSPE-PEG micelles, resulting PEG-LMD vector systems are very stable with respect to colloidal instablility and aggregation in high ionic strength buffers and in serum, but are completely refractory to transfection. These data suggest that oligosaccharides could represent an alternative to PEG as a stealth polymer able to stabilize synthetic nonviral vector systems in some fluids but without impairing transfection efficiency. Furthermore, sLMD systems prepared with longer chain neoglycolipids appear to have sufficient useful characteristics to form the basis of viable second-generation LMD vector systems after further development.
Cytotoxicity of .ALPHA.-Tocopheryl Succinate, Malonate and Oxalate in Normal and Cancer Cells In Vitro and Their Anti-Cancer Effects on Mouse Melanoma In Vivo (2005)

alpha-Tocopheryl succinate (TS), which is known to induce apoptosis selectively in cancer cells, has attracted attention as a chemotherapeutic agent. Recently, we found that alpha-tocopheryl malonate (TM) and alpha-tocopheryl oxalate (TO), among the alpha-tocopheryl esters tested, have high apoptogenic activity as well as TS. In this study, we investigated the characteristics of their cytotoxicity on normal cells and cancer cells in vitro, and their anti-cancer effects on mice inoculated with melanoma B16-F1 cells in vivo. The order of in vitro cytotoxicity was TO > or = TM >> TS in all cell lines examined. Addition of exogenous superoxide dismutase (SOD) and the antioxidant N-acetyl cysteine (NAC) inhibited TS- and TM- but not TO-induced cell deaths. A selective cytotoxic effect on cancer cells was observed with TS but not with TM or TO. c-Jun N-terminal kinase (JNK) inhibitor II prevented cell death induced by TS but did not prevent cell deaths induced either by TM or TO. Intravenous administration of vesiculated TS and TM to mice inoculated with melanoma B16-F1 cells prevented tumor growth and enhanced the mean survival time, but TO administration killed the mice due to its acute high toxicity. From these results, we discussed the characteristics of their selective cytotoxicity toward tumor cells in vitro and anti-cancer effects in vivo.
The Diels--Alder Reaction of 1-Vinylnaphthalene with α,β- and α,β,γ,δ-Unsaturated Acids and Derivatives (1949)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Diels--Alder Reaction of 1-Vinylnaphthalene with α,β- and α,β,γ,δ-Unsaturated Acids and DerivativesW. E. Bachmann and N. C. DenoCite this: J. Am. Chem. Soc. 1949, 71, 9, 3062–3072Publication Date (Print):September 1, 1949Publication History Published online1 May 2002Published inissue 1 September 1949https://pubs.acs.org/doi/10.1021/ja01177a035https://doi.org/10.1021/ja01177a035research-articleACS PublicationsRequest reuse permissionsArticle Views480Altmetric-Citations75LEARN 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 peptidoglycan hydrolase motif within the mycobacteriophage TM4 tape measure protein promotes efficient infection of stationary phase cells (2006)

The predominant morphotype of mycobacteriophage virions has a DNA-containing capsid attached to a long flexible non-contractile tail, features characteristic of the Siphoviridae. Within these phage genomes the tape measure protein (tmp) gene can be readily identified due to the well-established relationship between the length of the gene and the length of the phage tail--because these phages typically have long tails, the tmp gene is usually the largest gene in the genome. Many of these mycobacteriophage Tmp's contain small motifs with sequence similarity to host proteins. One of these motifs (motif 1) corresponds to the Rpf proteins that have lysozyme activity and function to stimulate growth of dormant bacteria, while the others (motifs 2 and 3) are related to proteins of unknown function, although some of the related proteins of the host are predicted to be involved in cell wall catabolism. We show here that motif 3-containing proteins have peptidoglycan-hydrolysing activity and that while this activity is not required for phage viability, it facilitates efficient infection and DNA injection into stationary phase cells. Tmp's of mycobacteriophages may thus have acquired these motifs in order to avoid a selective disadvantage that results from changes in peptidoglycan in non-growing cells.
Pathways to Macroscale Order in Nanostructured Block Copolymers (1997)

Polymeric materials undergo dramatic changes in orientational order in response to dynamic processes, such as flow. Their rich cascade of dynamics presents opportunities to create and combine distinct alignments of polymeric nanostructures through processing. In situ rheo-optical measurements complemented by ex situ x-ray scattering reveal the physics of three different trajectories to macroscopic alignment of lamellar diblock copolymers during oscillatory shearing. At the highest frequencies, symmetry arguments explain the transient development of a bimodal texture en route to the alignment of layers parallel to the planes of shear. At lower frequencies, larger-scale relaxations introduce rearrangements out of the deformation plane that permit the formation of lamellae perpendicular to the shear plane. These explain the change in the character of the pathway to parallel alignment and the emergence of perpendicular alignment as the frequency decreases.