gebhart/patrepeval huggingface dataset:
Unsupervised Embedding Learning via Invariant and Spreading Instance Feature (2019)

This paper studies the unsupervised embedding learning problem, which requires an effective similarity measurement between samples in low-dimensional embedding space. Motivated by the positive concentrated and negative separated properties observed from category-wise supervised learning, we propose to utilize the instance-wise supervision to approximate these properties, which aims at learning data augmentation invariant and instance spread-out features. To achieve this goal, we propose a novel instance based softmax embedding method, which directly optimizes the `real' instance features on top of the softmax function. It achieves significantly faster learning speed and higher accuracy than all existing methods. The proposed method performs well for both seen and unseen testing categories with cosine similarity. It also achieves competitive performance even without pre-trained network over samples from fine-grained categories.
Antigen Receptor Proximal Signaling in Splenic B-2 Cell Subsets (2001)

Splenic marginal zone (MZ) and follicular mantle (FO) B cells differ in their responses to stimuli in vitro and in vivo. We have previously shown that MZ cells exhibit greater calcium responses after ligation of membrane IgM (mIgM). We have now investigated the molecular mechanism underlying the difference in calcium responses following ligation of mIgM and studied the response to total B cell receptor ligation in these two subsets. We compared key cellular proteins involved in calcium signaling in MZ and FO cells. Tyrosine phosphorylation and activity of phospholipase C-gamma 2 and Syk protein tyrosine kinase were significantly higher in MZ cells than in FO cells after mIgM engagement, providing a likely explanation for our previous findings. Tyrosine phosphorylation of CD22 and expression of Src homology 2-containing inositol phosphatase and Src homology 2-containing protein tyrosine phosphatase-1 were also higher in the MZ cells. Expression and tyrosine phosphorylation of Btk, BLNK, Vav, or phosphatidylinositol 3-kinase were equivalent. In contrast, stimulation with anti-kappa induced equivalent increases in calcium and activation of Syk in the two subsets. These signals were also equivalent in cells from IgM transgenic, J(H) knockout mice, which have equivalent levels of IgM in both subsets. With total spleen B cells, Btk was maximally phosphorylated at a lower concentration of anti-kappa than Syk. Thus, calcium signaling in the subsets of mature B cells reflects the amount of Ig ligated more than the isotype or the subset and this correlates with the relative tyrosine phosphorylation of Syk.
Identification of SRPK1 and SRPK2 as the Major Cellular Protein Kinases Phosphorylating Hepatitis B Virus Core Protein (2002)

Phosphorylation of hepatitis B virus (HBV) core protein has recently been shown to be a prerequisite for pregenomic RNA encapsidation into viral capsids, but the host cell kinases mediating this essential step of the HBV replication cycle have not been identified. We detected two kinases of 95 and 115 kDa in HuH-7 total cell lysates which interacted specifically with the HBV core protein and phosphorylated its arginine-rich C-terminal domain. The 95-kDa kinase was purified and characterized as SR protein-specific kinase 1 (SRPK1) by mass spectrometry. Based on this finding, the 115-kDa kinase could be identified as the related kinase SRPK2 by immunoblot analysis. In vitro, both SRPKs phosphorylated HBV core protein on the same serine residues which are found to be phosphorylated in vivo. Moreover, the major cellular HBV core kinase activity detected in the total cell lysate showed biochemical properties identical to those of SRPK1 and SRPK2, as examined by measuring binding to a panel of chromatography media. We also clearly demonstrate that neither the cyclin-dependent kinases Cdc2 and Cdk2 nor protein kinase C, previously implicated in HBV core protein phosphorylation, can account for the HBV core protein kinase activity. We conclude that both SRPK1 and SRPK2 are most likely the cellular protein kinases mediating HBV core protein phosphorylation during viral infection and therefore represent important host cell targets for therapeutic intervention in HBV infection.
Crystal structure of human selenocysteine tRNA (2009)

Selenocysteine (Sec) is the 21st amino acid in translation. Sec tRNA (tRNA(Sec)) has an anticodon complementary to the UGA codon. We solved the crystal structure of human tRNA(Sec). tRNA(Sec) has a 9-bp acceptor stem and a 4-bp T stem, in contrast with the 7-bp acceptor stem and the 5-bp T stem in the canonical tRNAs. The acceptor stem is kinked between the U6:U67 and G7:C66 base pairs, leading to a bent acceptor-T stem helix. tRNA(Sec) has a 6-bp D stem and a 4-nt D loop. The long D stem includes unique A14:U21 and G15:C20a pairs. The D-loop:T-loop interactions include the base pairs G18:U55 and U16:U59, and a unique base triple, U20:G19:C56. The extra arm comprises of a 6-bp stem and a 4-nt loop. Remarkably, the D stem and the extra arm do not form tertiary interactions in tRNA(Sec). Instead, tRNA(Sec) has an open cavity, in place of the tertiary core of a canonical tRNA. The linker residues, A8 and U9, connecting the acceptor and D stems, are not involved in tertiary base pairing. Instead, U9 is stacked on the first base pair of the extra arm. These features might allow tRNA(Sec) to be the target of the Sec synthesis/incorporation machineries.
Potential Anticancer Agents. LXXVIII.1 Nonclassical Antimetabolites. IV.2 Synthesis of Compounds Related to 4-(Iodoacetamido)salicylic Acid, an Exo-Alkylating Irreversible Inhibitor (1962)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPotential Anticancer Agents. LXXVIII.1 Nonclassical Antimetabolites. IV.2 Synthesis of Compounds Related to 4-(Iodoacetamido)salicylic Acid, an Exo-Alkylating Irreversible InhibitorB. R. Baker, William W. Lee, Abelardo P. Martinez, Leonard O. Ross, and Leon GoodmanCite this: J. Org. Chem. 1962, 27, 9, 3283–3295Publication Date (Print):September 1, 1962Publication History Published online1 May 2002Published inissue 1 September 1962https://doi.org/10.1021/jo01056a073RIGHTS & PERMISSIONSArticle Views214Altmetric-Citations8LEARN 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 InReddit PDF (2 MB) Get e-Alerts Get e-Alerts
Acid Phosphatases from <italic>Fusarium moniliforme</italic><subtitle>III. Mode of Action of Acid Phosphatase II on bis-<italic>p</italic>-Nitrophenyl Phosphate</subtitle> (1973)

1. Inorganic phosphate was liberated from bis-p-nitrophenyl phosphate by Fusarium acid phosphatase II at half the rate observed for the liberation of p-nitrophenol. No time lag was observed for the liberation of inorganic phosphate. These results indicate that bis-p-nitrophenyl phosphate is hydrolyzed to two moles of p-nitrophenol and one mole of inorganic phosphate without release of p-nitrophenyl phosphate as an intermediary product. 2. The kinetic parameters, Km and Vmax, for the hydrolysis of bis-p-nitrophenyl phosphate by Fusarium acid phosphatase II were determined at pH 5.3 to be 1.1 mM and 0.83 μmole/min/unit, respectively. 3. The kinetic parameters, Km and Vmax, for both p-nitrophenyl phosphate and bis-p-nitrophenyl phosphate showed the same pH dependence. In both cases, logVmax was independent of pH in the range pH 3.3–6.0. In the pKm-pH plot, the experimental points were on a line with a slope of -1.0 in the range pH 4.5–6.0. 4. Both activities of Fusarium acid phosphatase II for p-nitrophenyl phosphate and bis-p-nitrophenyl phosphate had the same pH optimum at 5.3 when assayed at a substrate concentration of 5 mM. 5. In any mixture containing given concentrations of p-nitrophenyl phosphate and bis-p-nitrophenyl phosphate, the total velocity of the liberation of p-nitrophenol by the enzyme lay between the two velocities which were obtained with these concentrations of the substrates separately. 6. Effects of various inhibitors on both activities of the enzyme were quite similar. 7. The activity of the enzyme for bis-p-nitrophenyl phosphate was destroyed by heat faster than that for p-nitrophenyl phosphate. 8. All these results are consistent with the hypothesis that a common or at least partly common catalytic site of a single protein is responsible for hydrolyzing both p-nitrophenyl phosphate and bis-p-nitrophenyl phosphate. A new name “phospho-diesterase-phosphomonoesterase ” is proposed on the basis of enzymatic properties.
Insulin-like growth factor II acts as an autocrine growth and motility factor in human rhabdomyosarcoma tumors. (1990)

Rhabdomyosarcoma is the most common soft tissue sarcoma of childhood and appears to arise from developing striated muscle-forming cells. Since insulin-like growth factor II (IGF-II) is involved in normal muscle growth and maturation and elevated IGF-II mRNA levels have previously been reported in rhabdomyosarcomas, we have been studying the possible role of IGF-II in the unregulated growth and invasive potential of these embryonal tumors. In this study, we demonstrate that 13 of 14 rhabdomyosarcoma tumors express high levels of IGF-II mRNA relative to normal adult muscle and also express mRNA for the type I IGF receptors on their cell surface, the receptor thought to mediate the effects of IGF-II on muscle cells. We have established several rhabdomyosarcoma cell lines in mitogen-free media and demonstrate that these cells express type I IGF receptors on their cell surface and secrete IGF-II into the media. Exogenous IGF-II is able to stimulate cellular motility in these cell lines as assayed in a modified Boyden chamber. Finally, alpha IR-3, a type I receptor antagonist, inhibits the growth of these cell lines in serum-free media but does not inhibit IGF-II-induced motility of these cells. These data suggest that endogenously produced IGF-II functions as an autocrine growth and motility factor in many rhabdomyosarcoma tumors. The mitogenic actions of IGF-II are mediated through a domain of the type I IGF receptor that is blocked by alpha IR-3. IGF-II-induced motility may be mediated through an alternative signaling pathway.
The effect of addition of calcipotriol ointment (50 mug/g) to acitretin therapy in psoriasis (1998)

Our purpose was to find out whether the addition of calcipotriol ointment (50 micrograms/g) to systemic treatment with acitretin produces additional therapeutic effects and thereby an acitretin-sparing effect, and further to investigate the safety and tolerability of this combination. A multicentre, randomized, double-blind placebo-controlled study was designed. Patients were randomized to receive calcipotriol or placebo. All patients were treated with a starting dose of 20 mg acitretin per day and doses were adjusted at 2-weekly intervals with increments of 10 mg per day up to a maximum of 70 mg per day. The dose requirement for acitretin, clinical signs and adverse events were recorded. Seventy-six patients were randomized to treatment with calcipotriol 50 micrograms/g ointment twice daily and 59 patients to treatment with the vehicle only twice daily. Clearance or marked improvement was achieved by 67% of the patients in the calcipotriol group and by 41% of the patients in the placebo group (P = 0.006). Calcipotriol treatment proved to have a statistically significant additional effect to acitretin on the Psoriasis Area and Severity Index, redness, thickness and scaliness as compared with placebo. Clearance or marked improvement was achieved with a statistically significantly lower cumulative dose of acitretin by the patients in the calcipotriol group as compared with the placebo group. The number of patients reporting adverse events was pronounced and largely related to acitretin. No significant differences were observed between the two treatment groups with respect to adverse events. Laboratory assessments were essentially normal. The addition of calcipotriol ointment to acitretin treatment contributes to the efficacy, reduces the cumulative dose of acitretin to reach marked improvement or clearance, and is well-tolerated and safe.
Identification of the Neogenin-Binding Site on the Repulsive Guidance Molecule A (2012)

Repulsive guidance molecule (RGM) is a membrane-bound protein that was originally identified as an axon guidance molecule in the chick retinotectal system. RGMa, one of the 3 isoforms found in mammals, is involved in laminar patterning, cephalic neural tube closure, axon guidance, and inhibition of axonal regeneration. In addition to its roles in the nervous system, RGMa plays a role in enhancing helper T-cell activation. Binding of RGM to its receptor, neogenin, is considered necessary to transduce these signals; however, information on the binding of RGM to neogenin is limited. Using co-immunoprecipitation studies, we have identified that the RGMa region required for binding to neogenin contains amino acids (aa) 259-295. Synthesized peptide consisting of aa 284-293 directly binds to the extracellular domain (ECD) of recombinant neogenin, and addition of this peptide inhibits RGMa-induced growth cone collapse in mouse cortical neurons. Thus, we propose that this peptide is a promising lead in finding reagents capable of inhibiting RGMa signaling.
Thrombin inactivates acidic fibroblast growth factor but not basic fibroblast growth factor (1988)

Incubation of bovine brain derived acidic fibroblast growth factor (aFGF) with bovine or human thrombin, 0.5 NIH unit/mL, for 24 h at 37 degrees C results in cleavage of the mitogen, generating a 14-kilodalton fragment which has significantly reduced affinity for immobilized heparin as compared to aFGF, and is at least 50-fold less potent at stimulating mitogenesis. In addition, an 18 amino acid peptide, aFGF(123-140), is generated, identifying one of the thrombin cleavage sites as the Arg-122/Thr-123 bond. The peptide, aFGF(123-140), is neither mitogenic itself nor an inhibitor of the mitogenic activity of aFGF. The cleavage of aFGF by thrombin is inhibited by heparin (50 micrograms/mL) and is completely blocked by the irreversible thrombin inhibitors D-Phe-Pro-Arg chloromethyl ketone and hirudin. Incubation of aFGF with 50 units/mL thrombin at 37 degrees C results in rapid cleavage of the mitogen into several fragments. In contrast, incubation of bovine brain derived basic fibroblast growth factor with 1 unit/mL thrombin for 24 h, or 50 units/mL thrombin for 6 h, does not result in significant cleavage of mitogen. The results show that the C-terminal region of aFGF is of functional importance in both mitogenesis and heparin binding. Most importantly, a novel role for anionic heparin-binding growth factors and their fragments is indicated in physiologic and pathologic situations associated with thrombin generation.
Look-ahead intelligent energy management of a parallel hybrid electric vehicle (2011)

Improving fuel efficiency in vehicles can reduce the energy consumption concerns associated with operating the vehicles. This paper presents a model for a parallel hybrid electric vehicle. In the model, the flow of energy starts from wheels and spreads toward engine and electric motor. A fuzzy logic based control strategy is implemented for the vehicle. The controller manages the energy flow from the engine and the electric motor, controlling transmission ratio, adjusting speed, and sustaining battery's state of charge. The controller examines the vehicle speed, demand torque, slope difference, state of charge of battery, and engine and electric motor rotation speeds. It then determines the best values for continuous variable transmission ratio, speed, and torque. A slope window method is formed that takes into account the look-ahead slope information, and determines the best vehicle speed. The developed model and control strategy are simulated using real highway data relating to Nowra-Bateman Bay in Australia, and SAE Highway Fuel Economy Driving Schedule. The simulation results are presented and discussed. It is shown that the use of the proposed fuzzy controller reduces the fuel consumption of the vehicle.
Therapeutic electromagnetic field effects on angiogenesis and tumor growth. (2002)

TEMF may prove a useful adjuvant to increase the therapeutic index of conventional cancer therapy.
Fragment-Based Drug Discovery (2004)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTFragment-Based Drug DiscoveryDaniel A. Erlanson, Robert S. McDowell, and Tom O'BrienView Author Information Sunesis Pharmaceuticals, Inc., 341 Oyster Point Boulevard, South San Francisco, California 94080 Cite this: J. Med. Chem. 2004, 47, 14, 3463–3482Publication Date (Web):June 4, 2004Publication History Received11 February 2004Published online4 June 2004Published inissue 1 July 2004https://doi.org/10.1021/jm040031vCopyright © 2004 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views12065Altmetric-Citations497LEARN 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 InReddit Read OnlinePDF (324 KB) Get e-AlertscloseSUBJECTS:Drug discovery,Inhibitors,Molecules,Peptides and proteins,Screening assays Get e-Alerts
Smart Technology Applications In Offshore Structural Systems: Status And Needs (1999)

Structural systems that can sense and adapt to the environment automatically offer new vistas for designers and lead to novel efficient developments. An offshore structure is defined as smart when sensor, actuator and even controller become integral part of the structure or structural material. The challenging part of the offshore structural control is that the structure is subjected to highly uncertain environmental forces. The deepwater structures for the future developments are expected to be floating structures. The developments in adaptive control of the floating systems have been reviewed. System for Offshore Structures Health Monitoring (SOSHM) based on smart technology and continuous online monitoring has been proposed. The key aspects of the available and required technology have been presented.
Local Anesthetics. Aminoalkoxyisoquinoline Derivatives (1949)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLocal Anesthetics. Aminoalkoxyisoquinoline DerivativesJames W. Wilson, Norman D. Dawson, Walter. Brooks, and Glenn E. UllyotCite this: J. Am. Chem. Soc. 1949, 71, 3, 937–938Publication Date (Print):March 1, 1949Publication History Published online1 May 2002Published inissue 1 March 1949https://pubs.acs.org/doi/10.1021/ja01171a047https://doi.org/10.1021/ja01171a047research-articleACS PublicationsRequest reuse permissionsArticle Views80Altmetric-Citations12LEARN 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
Ionic Conductivity of the Aqueous Layer Separating a Lipid Bilayer Membrane and a Glass Support (2006)

The in-plane ionic conductivity of the approximately 1-nm-thick aqueous layer separating a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer membrane and a glass support was investigated. The aqueous layer conductivity was measured by tip-dip deposition of a POPC bilayer onto the surface of a 20- to 75-microm-thick glass membrane containing a single conical-shaped nanopore and recording the current-voltage (i-V) behavior of the glass membrane nanopore/POPC bilayer structure. The steady-state current across the glass membrane passes through the nanopore (45-480 nm radius) and spreads radially outward within the aqueous layer between the glass support and bilayer. This aqueous layer corresponds to the dominant resistance of the glass membrane nanopore/POPC bilayer structure. Fluorescence recovery after photobleaching measurements using dye-labeled lipids verified that the POPC bilayer maintains a significant degree of fluidity on the glass membrane. The slopes of ohmic i-V curves yield an aqueous layer conductivity of (3 +/- 1) x 10(-3) Omega(-1) cm(-1) assuming a layer thickness of 1.0 nm. This conductivity is essentially independent of the concentration of KCl in the bulk solution (10-4 to 1 M) in contact with the membrane. The results indicate that the concentration and mobility of charge carriers in the aqueous layer between the glass support and bilayer are largely determined by the local structure of the glass/water/bilayer interface.
Comparative Virulence and Immunogenicity of the Towne Strain and a Nonattenuated Strain of Cytomegalovirus (1984)

The Towne strain cytomegalovirus and a low-passage strain, Toledo-1, were compared for virulence and immunogenicity in healthy adult male subjects to determine the suitability of the Towne strain for vaccination. Five seropositive subjects who received the Toledo-1 strain developed infections ranging in severity from laboratory abnormalities to mild mononucleosis syndromes (mean incubation, 4.7 weeks). None of the four seronegative subjects receiving the Towne strain developed systemic infection, but all developed delayed local reactions at the injection sites. All subjects developed cytotoxic lymphocyte responses specific to cytomegalovirus, usually HLA-restricted, but these were of greater magnitude and duration in the Toledo-1 recipients. The latter also developed natural killer cell and interferon responses, atypical lymphocytosis, inversion of helper/suppressor cell ratios, and depressed responses to T-cell mitogens, none of which occurred in Towne strain recipients. The results further substantiate the avirulence and immunogenicity of the Towne strain cytomegalovirus.