gebhart/patrepeval huggingface dataset:
Reaction of argon plasma‐treated teflon PFA with aminopropyltriethoxysilane in its n‐hexane solution (1999)

Aspects of argon plasma treatment of tetrafluoroethylene–perfluoropropylvinylether copolymer (PFA) films, followed by air exposure and its subsequent reaction with 3-aminopropyltriethoxy silane (3-APS) have been investigated using XPS and electron spin resonance (ESR) to gain a better understanding about the surface bonding between the modified PFA and 3-APS. The plasma treatment was performed under varying parameters such as radiofrequency power, gas pressure and treatment time. A good correlation was found between the atomic ratios of O/F and Si/F for PFA before and after the reaction with 3-APS. The amount of peroxy radicals before the reaction with 3-APS was also closely related with the atomic ratio of Si/F. By the derivatization reaction of plasma-treated PFA with NaOH it was confirmed that C(O)OH groups exist on the treated PFA surfaces. These observations revealed that the oxygen incorporated at the surface leading to C(O)OH groups plays a substantial role as the reaction site for 3-APS. A similar trend was found between the atomic ratios of Na/F and Si/F after the reactions with NaOH and 3-APS. Based on this observation it is proposed that the surface bonding of 3-APS to the C(O)OH group at the surface occurs through its NH2 group. The analysis of the atomic ratios of O/F, N/F and Si/F after the reaction with 3-APS revealed that a polyaminosiloxane oligomer with a stoichiometry different from that expected for the original 3-APS is formed. The wettability of 3-APS-bound PFA was found to become much greater than that of PFA plasma treated alone. The ageing effect of the wettability of 3-APS-bound PFA was observed, whereas the Si atomic concentration at the surface remained nearly unchanged during ageing. Copyright © 1999 John Wiley & Sons, Ltd.
Dose-dependent response of FGF-2 for lymphangiogenesis (2004)

Spatio-temporal studies on the growth of capillary blood vessels and capillary lymphatic vessels in tissue remodeling have suggested that lymphangiogenesis is angiogenesis-dependent. We revisited this concept by using fibroblast growth factor 2 (FGF-2) (80 ng) to stimulate the growth of both vessel types in the mouse cornea. When we lowered the dose of FGF-2 in the cornea 6.4-fold (12.5 ng), the primary response was lymphangiogenic. Further investigation revealed that vascular endothelial growth factor-C and -D are required for this apparent lymphangiogenic property of FGF-2, and when the small amount of accompanying angiogenesis was completely suppressed, lymphangiogenesis remained unaffected. Our findings demonstrate that there is a dose-dependent response of FGF-2 for lymphangiogenesis, and lymphangiogenesis can occur in the absence of a preexisting or developing vascular bed, i.e., in the absence of angiogenesis, in the mouse cornea.
Identification of a highly specific chymase as the major angiotensin II-forming enzyme in the human heart. (1990)

Although angiotensin II (Ang II)-forming enzymatic activity in the human left cardiac ventricle is minimally inhibited by angiotensin I (Ang I) converting enzyme inhibitors, over 75% of this activity is inhibited by serine proteinase inhibitors (Urata, H., Healy, B., Stewart, R. W., Bumpus, F. M., and Husain, A. (1990) Circ. Res. 66, 883-890). We now report the identification and characterization of the major Ang II-forming, neutral serine proteinase, from left ventricular tissues of the human heart. A 115,150-fold purification from human cardiac membranes yielded a purified protein with an Mr of 30,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Based upon its amino-terminal sequence, the major human cardiac Ang II-forming proteinase appears to be a novel member of the chymase subfamily of chymotrypsin-like serine proteinases. Human heart chymase was completely inhibited by the serine proteinase inhibitors, soybean trypsin inhibitor, phenylmethylsulfonyl fluoride, and chymostatin. It was partially inhibited by p-tosyl-L-phenylalanine chloromethyl ketone, but was not inhibited by p-tosyl-L-lysine chloromethyl ketone, and aprotinin. Also, human heart chymase was not inhibited by inhibitors of the other three classes of proteinases. Human heart chymase has a high specificity for the conversion of Ang I to Ang II and the Ang I-carboxyl-terminal dipeptide His-Leu (Km = 60 microM; Kcat = 11,900 min-1; Kcat/Km = 198 min-1 microM-1). Human heart chymase did not degrade several peptide hormones, including Ang II, bradykinin, and vasoactive intestinal peptide, nor did it form Ang II from angiotensinogen. The high substrate specificity of human heart chymase for Ang I distinguishes it from other Ang II-forming enzymes including Ang I converting enzyme, tonin, kallikrein, cathepsin G, and other known chymases.
Two alternatively spliced Meig1 messenger RNA species are differentially expressed in the somatic and in the germ-cell compartments of the testis. (1999)

Previous studies regarding the transcriptional pattern of the murine Meig1 gene (formally designated meg1) suggested that its transcription is restricted to germ cells at the first meiotic prophase, in both primary spermatocytes and primary oocytes. However, protein analysis revealed that certain forms of the MEIG1 protein exist in testes of early postnatal pups at stages that have no germ cells in the testis, excluding very few primitive type A spermatogonia cells. This suggested that MEIG1 expression is not confined to germ cells. In this study, we show that testicular somatic cells do, indeed, express MEIG1. This is especially evident in Leydig cells, where this protein is highly abundant. We also demonstrate that alternatively spliced mRNAs of Meig1 are differentially transcribed in the germ cell and the somatic compartments of the testis. There is a very low level of somatic transcript, whether labile or transcriptionally regulated, in contrast to the abundant MEIG1 protein in the somatic cells. This implies that the somatic transcript is very efficiently translated and reconfirms that protein levels do not necessarily reflect transcript abundancy. Structural features of the Meig1 transcript that would be expected to inhibit translation are discussed in light of the efficient translation of this RNA species.
Properties of recA441 protein-catalyzed DNA strand exchange can be attributed to an enhanced ability to compete with SSB protein. (1990)

We have investigated the recombinase activity of recA441 protein by comparing its in vitro DNA strand exchange activity to that of wild-type recA protein. Consistent with its proficiency in recombination in vivo, recA441 protein is able to catalyze the in vitro exchange of a circular single-stranded DNA molecule for a homologous strand in a linear double-stranded DNA molecule. Under conditions optimal for wild-type recA protein, the rates of joint molecule formation are the same for the two recA proteins, but the wild-type protein converts these intermediate species to gapped circular heteroduplex DNA product molecules more rapidly than recA441 protein. In the recA441 protein reaction, joint molecules are instead converted to extensive homology-dependent DNA networks via presumed reinitiation reactions. Under some conditions, the DNA strand exchange activity of recA441 protein is enhanced relative to the wild-type. These conditions include when single-stranded DNA.SSB protein (where SSB is Escherichia coli single-stranded DNA-binding protein) complexes are formed prior to the addition of recA protein, at low magnesium ion concentration in the presence of spermidine, and at low ATP concentrations. Under the conditions examined, recA441 protein competes more effectively with SSB protein for DNA-binding sites; thus, the differences between the strand exchange activities of the wild-type and recA441 proteins can be attributed to this enhanced ability in SSB protein competition.
A novel 4T SRAM cell using 'self-body-biased" SOI MOSFET structure operating at 0.5 volt (2002)

A novel 4T SRAM cell utilizing the 'self-body-biased' ('SBB') SOI MOSFET structure (Terauchi and Terada, Proc. IEEE Int. SOI Conf., p. 36, 1999) is proposed. The body region of an SOI MOSFET with an 'H-shaped' gate electrode is used as a resistor in the inverter pair of the SRAM cell. The resistance of the body region is controlled by the low impurity concentration region beneath the auxiliary gate electrode and its geometry, independently from the threshold voltage of the MOSFET. Device simulation reveals the stable operation of the proposed SRAM cell under supply voltage of as low as 0.5 V.
Inference of the Human Polyadenylation Code (2017)

Abstract Processing of transcripts at the 3’-end involves cleavage at a polyadenylation site followed by the addition of a poly(A)-tail. By selecting which polyadenylation site is cleaved, alternative polyadenylation enables genes to produce transcript isoforms with different 3’-ends. To facilitate the identification and treatment of disease-causing mutations that affect polyadenylation and to understand the underlying regulatory processes, a computational model that can accurately predict polyadenylation patterns based on genomic features is desirable. Previous works have focused on identifying candidate polyadenylation sites and classifying sites which may be tissue-specific. What is lacking is a predictive model of the underlying mechanism of site selection, competition, and processing efficiency in a tissue-specific manner. We develop a deep learning model that trains on 3’-end sequencing data and predicts tissue-specific site selection among competing polyadenylation sites in the 3’ untranslated region of the human genome. Two neural network architectures are evaluated: one built on hand-engineered features, and another that directly learns from the genomic sequence. The hand-engineered features include polyadenylation signals, cis-regulatory elements, n-mer counts, nucleosome occupancy, and RNA-binding protein motifs. The direct-from-sequence model is inferred without prior knowledge on polyadenylation, based on a convolutional neural network trained with genomic sequences surrounding each polyadenylation site as input. Both models are trained using the TensorFlow library. The proposed polyadenylation code can predict site selection among competing polyadenylation sites in different tissues. Importantly, it does so without relying on evolutionary conservation. The model can distinguish pathogenic from benign variants that appear near annotated polyadenylation sites in ClinVar and inspect the genome to find candidate polyadenylation sites. We also provide an analysis on how different features affect the model’s performance.
Memory-centric accelerator design for Convolutional Neural Networks (2013)

In the near future, cameras will be used everywhere as flexible sensors for numerous applications. For mobility and privacy reasons, the required image processing should be local on embedded computer platforms with performance requirements and energy constraints. Dedicated acceleration of Convolutional Neural Networks (CNN) can achieve these targets with enough flexibility to perform multiple vision tasks. A challenging problem for the design of efficient accelerators is the limited amount of external memory bandwidth. We show that the effects of the memory bottleneck can be reduced by a flexible memory hierarchy that supports the complex data access patterns in CNN workload. The efficiency of the on-chip memories is maximized by our scheduler that uses tiling to optimize for data locality. Our design flow ensures that on-chip memory size is minimized, which reduces area and energy usage. The design flow is evaluated by a High Level Synthesis implementation on a Virtex 6 FPGA board. Compared to accelerators with standard scratchpad memories the FPGA resources can be reduced up to 13× while maintaining the same performance. Alternatively, when the same amount of FPGA resources is used our accelerators are up to 11× faster
An orally bioavailable small-molecule inhibitor of Hedgehog signaling inhibits tumor initiation and metastasis in pancreatic cancer (2008)

Recent evidence suggests that blockade of aberrant Hedgehog signaling can be exploited as a therapeutic strategy for pancreatic cancer. Our previous studies using the prototype Hedgehog small-molecule antagonist cyclopamine had shown the striking inhibition of systemic metastases on Hedgehog blockade in spontaneously metastatic orthotopic xenograft models. Cyclopamine is a natural compound with suboptimal pharmacokinetics, which impedes clinical translation. In the present study, a novel, orally bioavailable small-molecule Hedgehog inhibitor, IPI-269609, was tested using in vitro and in vivo model systems. In vitro treatment of pancreatic cancer cell lines with IPI-269609 resembled effects observed using cyclopamine (i.e., Gli-responsive reporter knockdown, down-regulation of the Hedgehog target genes Gli1 and Ptch, as well as abrogation of cell migration and colony formation in soft agar). Single-agent IPI-269609 profoundly inhibited systemic metastases in orthotopic xenografts established from human pancreatic cancer cell lines, although Hedgehog blockade had minimal effect on primary tumor volume. The only discernible phenotype observed within the treated primary tumor was a significant reduction in the population of aldehyde dehydrogenase-bright cells, which we have previously identified as a clonogenic tumor-initiating population in pancreatic cancer. Selective ex vivo depletion of aldehyde dehydrogenase-bright cells with IPI-269609 was accompanied by significant reduction in tumor engraftment rates in athymic mice. Pharmacologic blockade of aberrant Hedgehog signaling might prove to be an effective therapeutic strategy for inhibition of systemic metastases in pancreatic cancer, likely through targeting subsets of cancer cells with tumor-initiating ("cancer stem cell") properties.
α‐Melanocyte‐Stimulating Hormone and Oxytocin: A Peptide Signalling Cascade in the Hypothalamus (2006)

alpha-Melanocyte-stimulating hormone (alpha-MSH) and oxytocin share remarkable similarities of effects on behaviour in rats; in particular, they both inhibit feeding behaviour and stimulate sexual behaviour. Recently, we showed that alpha-MSH interacts with the magnocellular oxytocin system in the supraoptic nucleus; alpha-MSH induces the release of oxytocin from the dendrites of magnocellular neurones but it inhibits the secretion of oxytocin from their nerve terminals in the posterior pituitary. This effect of alpha-MSH on supraoptic nucleus oxytocin neurones is remarkable for two reasons. First, it illustrates the capacity of magnocellular neurones to differentially regulate peptide release from dendrites and axons and, second, it emphasises the putative role of magnocellular neurones as a major source of central oxytocin release, and as a likely substrate of some oxytocin-mediated behaviours. The ability of peptides to differentially control secretion from different compartments of their targets indicates one way by which peptide signals might have a particularly significant effect on neuronal circuitry. This suggests a possible explanation for the striking way in which some peptides can influence specific, complex behaviours.
Recent Advances in the Liquid-Phase Syntheses of Inorganic Nanoparticles (2004)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRecent Advances in the Liquid-Phase Syntheses of Inorganic NanoparticlesBrian L. Cushing, Vladimir L. Kolesnichenko, and Charles J. O'ConnorView Author Information Advanced Materials Research Institute, University of New Orleans, New Orleans, Louisiana 70148-2820 Cite this: Chem. Rev. 2004, 104, 9, 3893–3946Publication Date (Web):August 20, 2004Publication History Received28 October 2003Published online20 August 2004Published inissue 1 September 2004https://pubs.acs.org/doi/10.1021/cr030027bhttps://doi.org/10.1021/cr030027bresearch-articleACS PublicationsCopyright © 2004 American Chemical SocietyRequest reuse permissionsArticle Views35286Altmetric-Citations2536LEARN 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 SUBJECTS:Gold,Metal nanoparticles,Metals,Nanoparticles,Oxides Get e-Alerts
A Seven-transmembrane, G Protein–coupled Receptor, FPRL1, Mediates the Chemotactic Activity of Serum Amyloid A for Human Phagocytic Cells (1999)

We have previously reported (Badolato, R., J.M. Wang, W.J. Murphy, A. R. Lloyd, D.F. Michiel, L.L. Bausserman, D.J. Kelvin, and J.J. Oppenheim. 1994. J. Exp. Med. 180:203; Xu, L., R. Badolato, W.J. Murphy, D.L. Longo, M. Anver, S. Hale, J.J. Oppenheim, and J.M. Wang. 1995. J. Immunol. 155:1184.) that the acute phase protein serum amyloid A (SAA) is a potent chemoattractant for human leukocytes in vitro and mouse phagocytes in vivo. To identify the signaling mechanisms, we evaluated patterns of cross-desensitization between SAA and other leukocyte chemoattractants. We found that the chemotactic bacterial peptide, N-formyl- methionyl-leucyl-phenylalanine (fMLP), was able to specifically attenuate Ca2+ mobilization in human phagocytes induced by SAA, but only at very high concentrations, suggesting that SAA uses a low affinity fMLP receptor. Here we demonstrate that SAA selectively induced Ca2+ mobilization and migration of HEK cells expressing FPRL1, a human seven-transmembrane domain phagocyte receptor with low affinity for fMLP, and high affinity for lipoxin A4. Furthermore, radiolabeled SAA specifically bound to human phagocytes and FPRL1-transfected 293 cells. In contrast, SAA was not a ligand or agonist for FPR, the high affinity fMLP receptor. Thus, SAA is the first chemotactic ligand identified for FPRL1. Our results suggest that FPRL1 mediates phagocyte migration in response to SAA.
Human embryonic and neuronal stem cell markers in retinoblastoma. (2007)

Small subpopulation(s) of RB cells express human embryonic and neuronal stem cell markers. There are also subpopulations that demonstrate functional behavior (label retention and self-renewal) consistent with cancer stem cells. These findings support the hypothesis that RB is a heterogeneous tumor comprised of subpopulation(s) with stem cell-like properties.
Fabrication of conducting GeSi/Si micro- and nanotubes and helical microcoils (2001)

Conducting micro-and nanotubes and free-standing flexible helical microcoils have been fabricated from strained Ge x Si 1-x /Si heterolayers.The fabrication technique was based on self-rolling of a thin highly strained epitaxial Ge x Si 1-x /Si bifilm detached from the substrate by selective etching of a sacrificial layer in a roll-shaped tube.The obtained tube diameters varied from 10 nm to 13 m, depending on the thickness and lattice mismatch of the GeSi/Si bilayer.GeSi/Si tubes and helical coils, up to 70 nm in diameter, exhibit good conducting properties and high mechanical strength.
Acute inflammation regulates neuroregeneration through the NF-κB pathway in olfactory epithelium (2017)

Adult neural stem cells/progenitor cells residing in the basal layer of the olfactory epithelium are capable of reconstituting the neuroepithelium even after severe damage. The molecular events underlying this regenerative capacity remain elusive. Here we show that the repair of neuroepithelium after lesioning is accompanied by an acute, but self-limited, inflammatory process. Attenuation of inflammatory cell recruitment and cytokine production by dexamethasone impairs proliferation of progenitor horizontal basal cells (HBCs) and subsequent neuronal differentiation. Using TNF-α receptor-deficient mice, we identify TNF-α signaling as an important contributor to this inflammatory and reparative process, mainly through TNF-α receptor 1. HBC-selective genetic ablation of RelA (p65), the transcriptional activator of the NF-κB pathway, retards inflammation and impedes proliferation at the early stages of regeneration and suggests HBCs directly participate in cross-talk between immune response and neurogenesis. Loss of RelA in the regenerating neuroepithelium perturbs the homeostasis between proliferation and apoptosis while enhancing JNK signaling. Together, our results support a model in which acute inflammation after injury initiates important regenerative signals in part through NF-κB-mediated signaling that activates neural stem cells to reconstitute the olfactory epithelium.
Differentiation of Candida albicans and Candida dubliniensis by Fluorescent In Situ Hybridization with Peptide Nucleic Acid Probes (2001)

The recent discovery of Candida dubliniensis as a separate species that traditionally has been identified as Candida albicans has led to the development of a variety of biochemical and molecular methods for the differentiation of these two pathogenic yeasts. rRNA sequences are well-established phylogenetic markers, and probes targeting species-specific rRNA sequences have been used in diagnostic assays for the detection and identification of microorganisms. Peptide nucleic acid (PNA) is a DNA mimic with improved hybridization characteristics, and the neutral backbone of PNA probes offers significant advantages in whole-cell in situ hybridization assays. In this study, we developed PNA probes targeting the rRNAs of C. albicans and C. dubliniensis and applied them to a fluorescence in situ hybridization method (PNA FISH) for differentiation between C. albicans and C. dubliniensis. Liquid cultures were smeared onto microscope slides, heat fixed, and then hybridized for 30 min. Unhybridized PNA probe was removed by washing, and smears were examined by fluorescence microscopy. Evaluation of the PNA FISH method using smears of 79 C. dubliniensis and 70 C. albicans strains showed 100% sensitivity and 100% specificity for both PNA probes. We concluded that PNA FISH is a powerful tool for the differentiation of C. albicans and C. dubliniensis.
Video-rate three-dimensional optical coherence tomography (2002)

Most current optical coherence tomography systems provide two-dimensional cross-sectional or en face images. Successive adjacent images have to be acquired to reconstruct three-dimensional objects, which can be time consuming. Here we demonstrate three-dimensional optical coherence tomography (3D OCT) at video rate. A 58 by 58 smart-pixel detector array was employed. A sample volume of 210x210x80 m3 (corresponding to 58x58x58 voxels) was imaged at 25 Hz. The longitudinal and transverse resolutions are 3 m and 9 m respectively. The sensitivity of the system was 76 dB. Video rate 3D OCT is illustrated by movies of a strand of hair undergoing fast thermal damage.