gebhart/patrepeval huggingface dataset:
Low-sidelobe limited diffraction optical coherence tomography (2002)

Optical Coherence Tomography (OCT) is a relatively new type of imaging system for medical diagnosis. Because most current OCT systems use a sharply focused beam in tissues, they have a short depth of field (high image resolution is near the focus only). In this paper, limited diffraction beams of different orders are used to increase depth of field and to reduce sidelobes in OCT. Results show that the proposed OCT system has a lateral resolution of about 4.4 wavelengths (the central wavelength of the source is about 940 nm with a bandwidth of about 70 nm) and lower than -60 dB sidelobes over an entire depth of field of 4.5 mm with the diameter of the objective lens of 1 mm.
Genetically encoded reporters of protein kinase A activity reveal impact of substrate tethering (2001)

The complexity and specificity of many forms of signal transduction are widely suspected to require spatial microcompartmentation of protein kinase and phosphatase activities, yet current relevant imaging methods such as phosphorylation-specific antibodies or fluorescent peptide substrates require fixation or microinjection and lack temporal or spatial resolution. We present a genetically encoded fluorescent reporter for protein kinase A (PKA) consisting of fusions of cyan fluorescent protein, a phosphoamino acid binding domain (14-3-3tau), a consensus substrate for PKA, and yellow fluorescent protein. cAMP elevations cause 25-50% changes in the ratios of yellow to cyan emissions in live cells caused by phosphorylation-induced changes in fluorescence resonance energy transfer. The reporter response was accelerated by tethering to PKA holoenzyme and slowed by localization to the nucleus. We demonstrate that deliberate redistribution of a substrate or colocalizing a substrate and PKA can modulate its susceptibility to phosphorylation by the kinase. The successful design of a fluorescent reporter of PKA activity and its application for studying compartmentalized and dynamic modulation of kinases lays a foundation for studying targeting and compartmentation of PKA and other kinases and phosphatases.
Isolation and Gene Expression Analysis of Arabidopsis thaliana Mutants With Constitutive Expression of ATL2, an Early Elicitor-Response RING-H2 Zinc-Finger GeneThis article is dedicated to the memory of the late Gilberto Mosqueda Cano. (2004)

Genes with unstable transcripts often encode proteins that play important regulatory roles. ATL2 is a member of a multigene family coding highly related RING-H2 zinc-finger proteins that may function as E3 ubiquitin ligases. ATL2 mRNA accumulation occurs rapidly and transiently after incubation with elicitors of pathogen response. We screened 50,000 M(2) families from a line that carries a fusion of pATL2 to the GUS reporter gene and isolated five mutants, which we named eca (expresión constitutiva de ATL2), that showed constitutive expression of the reporter gene. One mutant exhibits a drastic stunted phenotype while the other four grow similarly to wild type. Two early chitin-induced genes and known pathogenesis-related genes such as NPR1, PAL, and CHS are activated in all the mutants whereas members of the ATL family and PR-1 and PDF2.1, which are markers of the salicylic acid (SA) jasmonate (JA) defense-response pathways, display differential expression between the mutants. These observations indicate that the ECA gene products may function in the early steps of an elicitor-response pathway, although some of them may function at other stages on the SA or JA defense-response pathways. Likewise, the fact that ATL2 and other members of the ATL family are activated in eca mutants links the induction of this putative class of ubiquitin ligases to plant defense signaling pathways.
Hel-N1/Hel-N2 proteins are bound to poly(A)+ mRNA in granular RNP structures and are implicated in neuronal differentiation (1996)

Human proteins Hel-N1 and Hel-N2 contain three RNA recognition motifs (RRMs), and are members of a family of proteins highly homologous to Drosophila ELAV, which is essential for neuronal differentiation. Both proteins bind to A+U-rich 3' untranslated regions of a variety of growth-related mRNAs in vitro. Here we demonstrate that in medulloblastoma cells derived from childhood brain tumors, Hel-N1 and Hel-N2 are mainly expressed in the cytoplasm, but are detectable in the nucleus. Both proteins are associated with polysomes and can be UV-crosslinked to poly(A)+ mRNA in cell extracts. In the cytoplasm the Hel-N1 protein family resides in granular structures that may contain multiple protein molecules bound to each mRNA. Evidence supporting this multimeric ribonucleoprotein (RNP) model includes in vitro reconstitution and competition experiments in which addition of a single RRM (RRM3) can alter complex formation. As in medulloblastoma cells, the Hel-N1 protein family is present in granular particles in the soma and the proximal regions of dendrites of cultured neurons, and colocalizes with ribosomes. In addition, we demonstrate that expression of the Hel-N1 protein family is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Our data suggest that the Hel-N1 protein family is associated with the translational apparatus and implicated in both mRNA metabolism and neuronal differentiation. Furthermore, our findings open the possibility that these proteins participate in mRNA homeostasis in the dendrites and soma of mature neurons.
Highly activated cyclopropane for homoconjugate reactions (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHighly activated cyclopropane for homoconjugate reactionsS. Danishefsky and R. K. SinghCite this: J. Am. Chem. Soc. 1975, 97, 11, 3239–3241Publication Date (Print):May 1, 1975Publication History Published online1 May 2002Published inissue 1 May 1975https://pubs.acs.org/doi/10.1021/ja00844a065https://doi.org/10.1021/ja00844a065research-articleACS PublicationsRequest reuse permissionsArticle Views1397Altmetric-Citations84LEARN 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
Detection of Borrelia burgdorferi DNA by Polymerase Chain Reaction in Cerebrospinal Fluid in Lyme Neuroborreliosis (1996)

A polymerase chain reaction (PCR) assay that detects Borrelia burgdorferi DNA in cerebrospinal fluid (CSF) was evaluated as a diagnostic test for acute or chronic Lyme neuroborreliosis. In one laboratory, 102 samples were tested blindly, and 40 samples were retested in a second laboratory. In the first laboratory, B. burgdorferi DNA was detected in CSF samples in 6 (38%) of 16 patients with acute neuroborreliosis, 11 (25%) of 44 with chronic neuroborreliosis, and none of 42 samples from patients with other illnesses. There was a significant correlation between PCR results and the duration of previous intravenous antibiotic therapy. The overall frequency of positive results was similar in the second laboratory, but concordance between the laboratories and among primer-probe sets was limited because many samples were positive with only one primer-probe set. Thus, PCR testing can sometimes detect B. burgdorferi DNA in CSF in patients with acute or chronic neuroborreliosis, but with current methods, the sensitivity of the test is limited.
Apodised in-fibre Bragg grating reflectorsphotoimprinted using a phase mask (1995)

An apodised in-fibre Bragg grating reflector is fabricated using the phase mask photoimprinting technique. The reflector has a centre wavelength of 1550 nm, a bandwidth of 0.22 nm and a peak reflectivity of 90%. At 0.4 nm (50 GHz) from the centre wavelength the reflectivity is 40 dB lower than the peak reflectivity; this is an improvement of more than 20 dB over an unapodised Bragg grating reflector with similar bandwidth and peak reflectivity.
Probing the Structure of the Diphtheria Toxin Channel (1997)

Previous work has established that the 61 amino acid stretch from residue 322 to 382 in the T-domain of diphtheria toxin forms channels indistinguishable in ion-conducting properties from those formed by the entire T-domain. In the crystal structure of the toxin's water-soluble form, the bulk of this stretch is an alpha-helical hairpin, designated TH8-9. The present study was directed at determining which residues in TH8-9 line the ion-conducting pathway of the channel; i.e., its lumen or entrances. To this end, we singly mutated 49 of TH8-9's 51 residues (328-376) to cysteines, formed channels with the mutant T-domain proteins in planar lipid bilayers, and then determined whether they reacted with small, charged, lipid-insoluble, sulfhydryl-specific methanethiosulfonate (MTS) derivatives added to the bathing solutions. The indication of a reaction, and that the residue lined the ion-conducting pathway, was a sudden change in single-channel conductance and/or flickering behavior. The results of this study were surprising in two respects. First, of the 49 cysteine-substituted residues in TH8-9 tested, 23 reacted with MTS derivatives in a most unusual pattern consisting of two segments: one extending from 329 to 341 (11 of 13 reacted), and the other from 347 to 359 (12 of 13 reacted); none of the residues outside of these two segments appeared to react. Second, in every cysteine mutant channel manifesting an MTS effect, only one transition in single-channel conductance (or flickering behavior) occurred, not the several expected for a multimeric channel. Our results are not consistent with an alpha-helical or beta-strand model for the channel, but instead suggest an open, flexible structure. Moreover, contrary to common sense, they indicate that the channel is not multimeric but is formed from only one TH8-9 unit of the T-domain.
Natriuretic Peptide Regulation of Endochondral Ossification (1998)

The natriuretic peptide family consists of three structurally related endogenous ligands: atrial natriuretic peptide (ANP), brain natriuretic peptide (BNP), and C-type natriuretic peptide (CNP). The biological actions of natriuretic peptides are thought to be mediated through the activation of two guanylyl cyclase (GC)-coupled receptor subtypes (GC-A and GC-B). In this study, we examined the effects of ANP and CNP, which are endogenous ligands for GC-A and GC-B, respectively, on bone growth using an organ culture of fetal mouse tibias, an in vitro model of endochondral ossification. CNP increased the cGMP production much more potently than ANP, thereby resulting in an increase in the total longitudinal bone length. Histological examination revealed an increase in the height of the proliferative and hypertrophic chondrocyte zones in fetal mouse tibias treated with CNP. The natriuretic peptide stimulation of bone growth, which was mimicked by 8-bromo-cGMP, was inhibited by HS-142-1, a non-peptide GC-coupled natriuretic peptide receptor antagonist. The spontaneous increase in the total longitudinal bone growth and cGMP production was also inhibited significantly by HS-142-1. CNP mRNA was expressed abundantly in fetal mouse tibias, where no significant amounts of ANP and BNP mRNAs were detected. A considerable amount of GC-B mRNA was present in fetal mouse tibias. This study suggests the physiologic significance of the CNP/GC-B pathway in the process of endochondral ossification.
Identification of Promoter Elements Involved in the Cytosolic Ca2+-Mediated Photoregulation of Maize cab-m1 Expression (1997)

Changes in cytoplasmic Ca2+ levels are involved in the regulation of several plant genes. However, to our knowledge, no regions of genes or specific cis elements have been shown to be involved in the regulation of plant gene expression by cytosolic Ca2+ signaling. The maize (Zea mays) gene cab-m1, which encodes a light-harvesting chlorophyll a/b-binding apoprotein, is positively photoregulated in mesophyll cells (MC) but not in bundle-sheath cells (BSC). This gene is highly preferentially expressed in maize MC versus BSC. In situ transient expression assays have revealed that exposure of tissues to ethyleneglycol-bis(beta-aminoethyl ether)-N,N'-tetraacetic acid (EGTA), which chelates Ca2+, blocks the photostimulation of cab-m1 full promoter (-1026 to + 14) activity in MC of leaf segments of dark-grown maize seedlings. EGTA has no effect on expression in BSC. These results suggest that light-induced elevation of the cytosolic Ca2+ concentration in MC is required for the enhancement of cab-m1 expression in MC. Deletion of the sequence from -1026 to -360 completely abolished Ca2+ responsiveness of cab-m1 expression in MC. On the other hand, a 54-bp fragment in the 5' flanking region (-953 to -899 relative to the translation start site) conferred Ca2+ responsiveness on a -359 core promoter: reporter gene, suggesting that Ca2+ signaling is mediated via specific sequences in this short fragment. Furthermore, possible involvement of Ca(2+)-calmodulin in the signal transduction chain for regulating cab-m1 expression was suggested by the results of inhibitor experiments.
Enhanced IL-1 beta and tumor necrosis factor-alpha release and messenger RNA expression in macrophages from idiopathic pulmonary fibrosis or after asbestos exposure (1993)

Idiopathic pulmonary fibrosis (IPF) and asbestosis are fibrotic interstitial lung diseases characterized by alveolar wall fibrosis with accumulation of extracellular matrix, interstitial remodeling, and increased numbers of activated alveolar macrophages. Animal models and in vitro studies have shown that macrophage cytokines, namely IL-1 beta and TNF-alpha, play significant roles in the development of fibrosis. We found significant increases for TNF-alpha release in both diseases (p < 0.01) and a significant increase for IL-1 beta release in asbestosis compared to normal controls (p < 0.01). Also, the mRNA expression of these cytokines was increased in alveolar macrophages from patients with IPF or asbestosis compared with normals. The level of TNF-alpha release in macrophage supernatants correlated with the number of neutrophils per milliliter bronchoalveolar lavage fluid returned. Chrysotile, crocidolite, amosite asbestos, and silica stimulated IL-1 beta and TNF-alpha release and up-regulated their respective mRNA in macrophages or monocytes. To evaluate the role of IL-1 beta and TNF-alpha in the accumulation of extracellular matrix, we studied collagen types I and III and fibronectin gene expression in human diploid lung fibroblasts after short term (2 h) serum-free exposure to recombinant cytokines. Both cytokines up-regulated these genes 1.5- to 3.6-fold. These cytokines have the potential to influence the remodeling and fibrosis observed in the lower respiratory tract in IPF and asbestosis.
Reduction of halosilanes by organotin hydrides (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReduction of halosilanes by organotin hydridesJames W. Wilt, Frank G. Belmonte, and Paul A. ZieskeCite this: J. Am. Chem. Soc. 1983, 105, 17, 5665–5675Publication Date (Print):August 1, 1983Publication History Published online1 May 2002Published inissue 1 August 1983https://pubs.acs.org/doi/10.1021/ja00355a025https://doi.org/10.1021/ja00355a025research-articleACS PublicationsRequest reuse permissionsArticle Views678Altmetric-Citations28LEARN 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
Excitability changes that complement Hebbian learning (2006)

Experiments have shown that the intrinsic excitability of neurons is not constant, but varies with physiological stimulation and during various learning paradigms. We study a model of Hebbian synaptic plasticity which is supplemented with intrinsic excitability changes. The excitability changes transcend time delays and provide a memory trace. Periods of selective enhanced excitability can thus assist in forming associations between temporally separated events, such as occur in trace conditioning. We demonstrate that simple bidirectional networks with excitability changes can learn trace conditioning paradigms.
Single‐Screw devolatilizer for polymer melts (1983)

Abstract Changes in air quality standards and new polymer manufacturing technologies have renewed interest in polymer melt devolatilizing. Unfortunately, little data is available to aid in the design and scale up of melt devolatilizing single‐screw extruders. As part of the ongoing development activities of Farrel Company, melt devolatilizing in various devices has been under study for a number of years. In order to be able to develop analytical methods of predicting performance and scaling up from small scale test stands, some elementary devolatilizing studies were carried out. Theoretical predictions based on classical diffusion theory were compared with actual results, leading to a revised model of the actual melt devolatilizing process. Based on this revised model, several novel single screw devolatilizing concepts were proposed, built and tested. In this paper, we are presenting some of the theoretical work underlying these studies as well as test results on conventional single‐screw devolatilizing sections. We hope to be in a position to divulge additional information on some of the novel devolatilizing devices at the time of the presentation of the paper.
RPD3 encodes a second factor required to achieve maximum positive and negative transcriptional states in Saccharomyces cerevisiae. (1991)

In Saccharomyces cerevisiae, TRK1 and TRK2 encode the high- and low-affinity K+ transporters, respectively. In cells containing a deletion of TRK1, transcription levels of TRK2 are extremely low and are limiting for growth in media containing low levels of K+ (Trk- phenotype). Recessive mutations in RPD1 and RPD3 suppress the TRK2, conferring an approximately fourfold increase in transcription. rpd3 mutations confer pleiotropic phenotypes, including (i) mating defects, (ii) hypersensitivity to cycloheximide, (iii) inability to sporulate as homozygous diploids, and (iv) constitutive derepression of acid phosphatase. RPD3 was cloned and is predicted to encode a 48-kDa protein with no extensive similarity to proteins contained in current data bases. Deletion of RPD3 is not lethal but confers phenotypes identical to those caused by spontaneous mutations. RPD3 is required for both full repression and full activation of transcription of target genes including PHO5, STE6, and TY2. RPD3 is the second gene required for this function, since RPD1 is also required. The effects of mutations in RPD1 and RPD3 are not additive, suggesting that these genes are involved in the same transcriptional regulatory function or pathway.
Validation in a component-based design flow for multicore SoCs (2002)

Currently, since many SoCs include heterogeneous components such as CPUs, DSPs, ASICs, memories, buses, etc., system integration becomes a major step in the design flow. To enable this integration, we use a design approach called component based-design approach. In this approach, the validation of system integration takes most of design efforts. This paper presents an automatic method of SoCs design validation. Based on a generic simulation wrapper architecture, the presented method provides automatic generation of executable models throughout different stages of SoC design flow. A case study of validating a VDSL application shows the effectiveness of the method.
HemaMax™, a Recombinant Human Interleukin-12, Is a Potent Mitigator of Acute Radiation Injury in Mice and Non-Human Primates (2012)

HemaMax, a recombinant human interleukin-12 (IL-12), is under development to address an unmet medical need for effective treatments against acute radiation syndrome due to radiological terrorism or accident when administered at least 24 hours after radiation exposure. This study investigated pharmacokinetics, pharmacodynamics, and efficacy of m-HemaMax (recombinant murine IL-12), and HemaMax to increase survival after total body irradiation (TBI) in mice and rhesus monkeys, respectively, with no supportive care. In mice, m-HemaMax at an optimal 20 ng/mouse dose significantly increased percent survival and survival time when administered 24 hours after TBI between 8-9 Gy (p<0.05 Pearson's chi-square test). This survival benefit was accompanied by increases in plasma interferon-γ (IFN-γ) and erythropoietin levels, recovery of femoral bone hematopoiesis characterized with the presence of IL-12 receptor β2 subunit-expressing myeloid progenitors, megakaryocytes, and osteoblasts. Mitigation of jejunal radiation damage was also examined. At allometrically equivalent doses, HemaMax showed similar pharmacokinetics in rhesus monkeys compared to m-HemaMax in mice, but more robustly increased plasma IFN-γ levels. HemaMax also increased plasma erythropoietin, IL-15, IL-18, and neopterin levels. At non-human primate doses pharmacologically equivalent to murine doses, HemaMax (100 ng/Kg and 250 ng/Kg) administered at 24 hours after TBI (6.7 Gy/LD(50/30)) significantly increased percent survival of HemaMax groups compared to vehicle (p<0.05 Pearson's chi-square test). This survival benefit was accompanied by a significantly higher leukocyte (neutrophils and lymphocytes), thrombocyte, and reticulocyte counts during nadir (days 12-14) and significantly less weight loss at day 12 compared to vehicle. These findings indicate successful interspecies dose conversion and provide proof of concept that HemaMax increases survival in irradiated rhesus monkeys by promoting hematopoiesis and recovery of immune functions and possibly gastrointestinal functions, likely through a network of interactions involving dendritic cells, osteoblasts, and soluble factors such as IL-12, IFN-γ, and cytoprotectant erythropoietin.
Broadband Light Bending with Plasmonic Nanoantennas (2011)

The precise manipulation of a propagating wave using phase control is a fundamental building block of optical systems. The wavefront of a light beam propagating across an interface can be modified arbitrarily by introducing abrupt phase changes. We experimentally demonstrated unparalleled wavefront control in a broadband optical wavelength range from 1.0 to 1.9 micrometers. This is accomplished by using an extremely thin plasmonic layer (~λ/50) consisting of an optical nanoantenna array that provides subwavelength phase manipulation on light propagating across the interface. Anomalous light-bending phenomena, including negative angles of refraction and reflection, are observed in the operational wavelength range.