gebhart/patrepeval huggingface dataset:
Interactions of linear dicationic molecules with lipid A: structural requisites for optimal binding affinity (1995)

The structural determinants of the binding affinity of linear dicationic molecules toward lipid A have been examined with respect to the distance between the terminal cationic functions, the basicity, and the type of cationic moieties using a series of spermidine derivatives and pentamidine analogs by fluorescence spectroscopic methods. The presence of two terminal cationic groups corresponds to enhanced affinity. A distinct sigmoidal relationship between the intercationic distance and affinity was observed with a sharp increase at 11 Å, levelling off at about 13 Å. The basicity (pK) and nature of the cationic functions are poor correlates of binding potency, since molecules bearing primary amino, imidazolino, or guanido termini are equipotent. The interaction of pentamidine, a bisamidine drug, with lipid A, characterized in considerable detail employing the putative intermolecular excimerization of the drug, suggests a stoichiometry of 1:1 in the resultant complex. The binding is driven almost exclusively by electrostatic forces, and is dependent on the ionization states of both lipid A and the drug. Under conditions when lipid A is highly disaggregated, pentamidine binds specifically to bis-phosphoryl- but not to monophosphoryl-lipid A indicating that both phosphate groups of lipid A are necessary for electrostatic interactions by the terminal amidininium groups of the drug. Based on these data, a structural model is proposed for the pentamidine-lipid A complex, which may be of value in designing endotoxin antagonists from first principles.
Arene-metal complexes in organic synthesis: addition to styrene-type ligands (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTArene-metal complexes in organic synthesis: addition to styrene-type ligandsM. F. Semmelhack, Walter Seufert, and Leonard KellerCite this: J. Am. Chem. Soc. 1980, 102, 21, 6584–6586Publication Date (Print):October 8, 1980Publication History Published online1 May 2002Published inissue 8 October 1980https://pubs.acs.org/doi/10.1021/ja00541a048https://doi.org/10.1021/ja00541a048research-articleACS PublicationsRequest reuse permissionsArticle Views383Altmetric-Citations58LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Inter‐core crosstalk measurement in multi‐core fibre amplifier using multiple intensity tones (2014)

An inter‐core crosstalk measurement method in a multi‐core erbium‐doped fibre amplifier that uses a single‐wavelength signal with multiple intensity tones is investigated. Its feasibility is confirmed and the output signal power dependence of the crosstalk values for the same signal gains between cores is successfully characterised.
CD13/aminopeptidase N, a Novel Chemoattractant for T Lymphocytes in Pulmonary Sarcoidosis (2000)

CD13/aminopeptidase N (E.C.3.4.11.2) is an ectoenzyme located in the outer membrane of a variety of cells. Because aminopeptidase expression was shown to be upregulated by a Th1-related cytokine, IFN-gamma, we examined here the significance of CD13/aminopeptidase N in pulmonary sarcoidosis. The activity of aminopeptidase in bronchoalveolar lavage fluid (BALF) was significantly higher in patients with sarcoidosis than in normal volunteers (NV) and control patients (CP). The activity significantly correlated with lymphocyte percentages and the ratio of CD4+ to CD8+ T lymphocytes in the BALF, and was higher in patients with sarcoidosis with parenchymal involvement than in those without the involvement. CD13/aminopeptidase N protein, which has a molecular mass of approximately 150 kD, was detectable in alveolar macrophages (AM) from patients with sarcoidosis at higher levels than in those from NV. CD13/aminopeptidase N induced in vitro chemotactic migration of human lymphocytes in a concentration range of 10(-)(5) to 10(-)(1) U/ml. The chemotactic activity was greater for CD4+ T lymphocytes than for CD8+ T lymphocytes. The enzymatic activity of CD13/aminopeptidase N was responsible for the chemotactic activity because bestatin, an inhibitor of CD13/aminopeptidase N, abolished the chemotactic activity. Higher chemotactic activity for lymphocytes was detected in the BALF from patients with sarcoidosis than in that from NV, and the activity was significantly decreased by treatment with bestatin. This study indicates that CD13/ aminopeptidase N expressed in AM may have a role in T-lymphocyte involvement in the sarcoid lung and the pathogenesis of alveolitis in this disorder.
The contribution of the glenoid labrum to glenohumeral stability under physiological joint loading using finite element analysis (2017)

The labrum contributes to passive glenohumeral joint stability. Cadaveric studies have demonstrated that this has position and load dependency, which has not been quantified under physiological loads. This study aims to validate subject-specific finite element (FE) models against in vitro measurements of joint stability and to utilise the FE models to predict joint stability under physiological loads. The predicted stability values were within ± one standard deviation of experimental data and the FE models showed a reduction in stability of 10-15% with high, physiological, loads. The developed regression equations provide the first representation of passive glenohumeral stability and will aid surgical decision-making.
Systematic Identification of Culture Conditions for Induction and Maintenance of Naive Human Pluripotency (2014)

(Cell Stem Cell 15, 471–487; October 2, 2014) We have identified two errors in the data presentation in the version of this paper originally published online on July 24, 2014. Neither of them affects the results or conclusions presented in any significant way. The issues are as follows: Figure 3. The chemical structure shown in Figure 3C did not represent WH-4-023, but instead a closely related LCK/SRC inhibitor called WH-4-025. To correct the figure we have replaced the structure shown originally with the correct structure for WH-4-023 and, for completeness, added a citation to the figure legend of the original study describing identification of these compounds. [The reference has also been added to the manuscript and is as follows: Martin, M.W., Newcomb, J., Nunes, J.J., McGowan, D.C., Armistead, D.M., Boucher, C., Buchanan, J.L., Buckner, W., Chai, L., Elbaum, D., et al. (2006). Novel 2-aminopyrimidine carbamates as potent and orally active inhibitors of Lck: Synthesis, SAR, and in vivo antiinflammatory activity. J. Med. Chem. 49, 4981–4991.] All of the other panels in the corrected figure are the same as originally published. Figure 6. The expression data from Gafni et al. (2013) were incorrectly classified as naive versus primed in the original analysis in Figures 6B and 6C. Reanalysis of the data with the correct classifications shows that OTX2 and ZIC2 are, in fact, downregulated more than 2-fold in the naive conditions of Gafni et al. (2013). However, none of the pluripotency genes examined in these panels show a significant fold change (log2 fold change >1 or <−1, p value < 0.05) in the naive conditions of Gafni et al. (2013) compared to the primed state, so the overall conclusions drawn from this analysis remain the same as originally presented. We have corrected Figures 6B and 6C to reflect the revised analysis. All of the other panels in the corrected figure are the same as originally published. The corrected versions of Figure 3 and Figure 6 are shown below and in the print version of our article in this issue. The html and PDF versions of this paper have also been corrected to reflect the changes described above. We apologize to the scientific community for any confusion caused by these data presentation issues.Figure 6Transcriptional Profiling of Naive Human ESCs in 5i/L/AView Large Image Figure ViewerDownload Hi-res image Download (PPT) Systematic Identification of Culture Conditions for Induction and Maintenance of Naive Human PluripotencyTheunissen et al.Cell Stem CellJuly 24, 2014In BriefThrough sequential chemical screening, Theunissen et al. identify a combination of kinase inhibitors that induces and maintains defining features of naive pluripotency in human embryonic stem cells. Full-Text PDF Open Access
Detection of the L-Band Galactic Glint on the Sea Surface With the Airborne MIRAS (2009)

This paper presents the results of the processing of the data acquired with the Airborne Microwave Imaging Radiometer with Aperture Synthesis, the European Space Agency's airborne 2-D aperture synthesis radiometer, in a circular flight over the sea in the vicinity of Helsinki (Finland). The goal of the analysis of these data is the detection of the galactic glint on the sea surface. These results are the first measurements with an L-band 2-D aperture synthesis radiometer that show the signature of the galaxy signal reflected on the sea surface.
Programmable Sensors of 5-Hydroxymethylcytosine (2015)

5-Hydroxymethylcytosine (hmC), the sixth base of the mammalian genome, is increasingly recognized as an epigenetic mark with important biological functions. We report engineered, programmable transcription-activator-like effectors (TALEs) as the first DNA-binding receptor molecules that provide direct, individual selectivities for cytosine (C), 5-methylcytosine (mC), and hmC at user-defined DNA sequences. Given the wide applicability of TALEs for programmable targeting of DNA sequences in vitro and in vivo, this provides broad perspectives for epigenetic research.
Accelerating Generalized Linear Models with MLWeaving: A One-Size-Fits-All System for Any-precision Learning (Technical Report) (2019)

Learning from the data stored in a database is an important function increasingly available in relational engines. Methods using lower precision input data are of special interest given their overall higher efficiency but, in databases, these methods have a hidden cost: the quantization of the real value into a smaller number is an expensive step. To address the issue, in this paper we present MLWeaving, a data structure and hardware acceleration technique intended to speed up learning of generalized linear models in databases. ML-Weaving provides a compact, in-memory representation enabling the retrieval of data at any level of precision. MLWeaving also takes advantage of the increasing availability of FPGA-based accelerators to provide a highly efficient implementation of stochastic gradient descent. The solution adopted in MLWeaving is more efficient than existing designs in terms of space (since it can process any resolution on the same design) and resources (via the use of bit-serial multipliers). MLWeaving also enables the runtime tuning of precision, instead of a fixed precision level during the training. We illustrate this using a simple, dynamic precision schedule. Experimental results show MLWeaving achieves up to16 performance improvement over low-precision CPU implementations of first-order methods.
Notes on Hierarchical Splines, DCLNs and i-theory (2015)

We define an extension of classical additive splines for multivariate function approximation that we call hierarchical splines. We show that the case of hierarchical, additive, piece-wise linear splines includes present-day Deep Convolutional Learning Networks (DCLNs) with linear rectifiers and pooling (sum or max). We discuss how these observations together with i-theory may provide a framework for a general theory of deep networks.
Linkage Analysis of Classical and Finnish Variant Late Infantile Neuronal Ceroid Lipofuscinosis (1994)

Conference Abstract| December 01 1994 Linkage Analysis of Classical and Finnish Variant Late Infantile Neuronal Ceroid Lipofuscinosis R Williams; R Williams 1Department of Paediatrics, UCL Medical School, The Rayne Institute, University Street, London WC1E 6JJ, UK. Search for other works by this author on: This Site PubMed Google Scholar J Sharp; J Sharp 1Department of Paediatrics, UCL Medical School, The Rayne Institute, University Street, London WC1E 6JJ, UK. Search for other works by this author on: This Site PubMed Google Scholar I Jarvela; I Jarvela 1Department of Paediatrics, UCL Medical School, The Rayne Institute, University Street, London WC1E 6JJ, UK. Search for other works by this author on: This Site PubMed Google Scholar M Savukoski; M Savukoski 2National Public Health Institute, Mannerheimintie 166, Helsinki, Finland Search for other works by this author on: This Site PubMed Google Scholar L Peltonen; L Peltonen 2National Public Health Institute, Mannerheimintie 166, Helsinki, Finland Search for other works by this author on: This Site PubMed Google Scholar RM Gardiner RM Gardiner 1Department of Paediatrics, UCL Medical School, The Rayne Institute, University Street, London WC1E 6JJ, UK. Search for other works by this author on: This Site PubMed Google Scholar Clin Sci (Lond) (1994) 87 (s31): 43P. https://doi.org/10.1042/cs045043P_pt2 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation R Williams, J Sharp, I Jarvela, M Savukoski, L Peltonen, RM Gardiner; Linkage Analysis of Classical and Finnish Variant Late Infantile Neuronal Ceroid Lipofuscinosis. Clin Sci (Lond) 1 December 1994; 87 (s31): 43P. doi: https://doi.org/10.1042/cs045043P_pt2 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsClinical Science Search Advanced Search This content is only available as a PDF. © 1994 The Biochemical Society and the Medical Research Society1994 Article PDF first page preview Close Modal You do not currently have access to this content.
Juvenile nasopharyngeal angiofibroma: Management of intracranial extension (1979)

Juvenile nasopharyngeal angiofibroma (JNA) is a histologically benign, locally invasive tumor of the nasopharynx that is found primarily in the pubescent male. While most authors recommend surgical excision for smaller, localized extracranial tumors, opinion varies on the management of more aggressive tumors with intracranial extension. The authors present their experience over the past 15 years with 15 cases of JNA with intracranial extension, and formulate a plan of management. A combined otolaryngologic/neurosurgical approach is recommended in order to assess the extent of the tumor and to isolate feeding vessels. Lateral extension into the middle cranial fossae should be resected in continuity with the nasopharyngeal component, which is approached from below in a separate operative field. Medial extensions are transected, verified angiographically three months after surgery, and irradiated. The results of therapy are presented, and a case of dural penetration by JNA is described.
Design layout analysis and DFM optimization using topological patterns (2015)

During the yield ramp of semi-conductor manufacturing, data is gathered on specific design-related process window limiters, or yield detractors, through a combination of test structures, failure analysis, and model-based printability simulations. Case-by-case, this data is translated into design for manufacturability (DFM) checks to restrict design usage of problematic constructs. This case-by-case approach is inherently reactive: DFM solutions are created in response to known manufacturing marginalities as they are identified. In this paper, we propose an alternative, yet complementary approach. Using design-only topological pattern analysis, all possible layout constructs of a particular type appearing in a design are categorized. For example, all possible ways via forms a connection with the metal above it may be categorized. The frequency of occurrence of each category indicates the importance of that category for yield. Categories may be split into sub-categories to align to specific manufacturing defect mechanisms. Frequency of categories can be compared from product to product, and unexpectedly high frequencies can be highlighted for further monitoring. Each category can be weighted for yield impact, once manufacturing data is available. This methodology is demonstrated on representative layout designs from the 28 nm node. We fully analyze all possible categories and sub-categories of via enclosure such that 100% of all vias are covered. The frequency of specific categories is compared across multiple designs. The 10 most frequent via enclosure categories cover ≥90% of all the vias in all designs. KL divergence is used to compare the frequency distribution of categories between products. Outlier categories with unexpected high frequency are found in some designs, indicating the need to monitor such categories for potential impact on yield.
Compositional and chemical characteristics of dissolved organic matter in various types of cropped and natural Chinese soils (2019)

Abstract Background Exploration of composition and chemical characteristics of soil dissolved organic matter (DOM) is significant to understand its biogeochemical role in terrestrial ecosystems. A total of 43 cropped and 16 natural soils (0–20 cm) under four soil types (cinnamon, chernozem, red and paddy soils) across China were collected to investigate the spectral characteristics of DOM using UV–Vis and 3D-EEM spectroscopy. Results The chernozem soils exhibited the highest aromaticity and humification degree among the four soil types. Ranges of biological index (BIX, 0.53–1.17) and fluorescence index (FI, 1.55–2.10) were found in the investigated DOM, showing joint contribution from allochthonous and autochthonous sources. Higher BIX and FI in the DOM of the paddy and red soils indicated a greater reliance on autochthonous sources for these two soil types. The cropped soils showed no significant differences in chemical characteristics and sources from the natural soils for the cinnamon, chernozem and red soils. UVA (16.2–47.9%) and UVC fulvic-like substances (15.4–40.5%) were the prevailing DOM components, which were highest in the chernozem soils. Additionally, the cropped soils had a higher proportion of humic-like substances than the natural soils in the DOM. Conclusions Both soil type and land-use strongly affected the chemical characteristics of soil DOM, but only soil type had an impact on the DOM composition for the collected soils. These findings may contribute to the prediction of the biochemical behavior of soil DOM under different soil types and land-uses in terrestrial ecosystems.
Molecular Imprinting Catalyst Based Artificial Enzyme Sensor for Fructosylamines (2003)

Abstract The molecular imprinting technology is becoming a versatile tool in constructing tailor-made molecular recognition elements. However, no oxidoreductase mimics which can be utilized for the amperometric sensor has ever been developed using molecularly imprinting technology. Glycated hemoglobin, HbA1c, is an important indicator for diabetic control. In order to develop a novel diagnostic system for the measurement of HbA1c, we developed molecularly imprinting technology based artificial enzyme which can catalyze the oxidative cleavage of fructosyl valine, a model compound for HbA1c. Based on our previous report, that polyvinylimidazole functioned as the catalyst for this reaction, we developed the molecularly imprinted catalyst (MIC). Molecularly imprinted catalyst was synthesized by imprinting polyvinylimidazole based polymer using fructosyl valine (Fru-val) that is the model compound for HbA1c as template molecules, based on both typical principles for molecular imprinting, noncovalent and covalent approaches. Fructosyl valine bound to the imprinted polymer more than two times higher than the control polymer, which was prepared in the same way but without the template molecule. The MIC-employing sensor showed high current response to Fru-val compared with the sensor employing the control polymer, due to the increase in the affinity toward cis-diol harboring compound. The amperometric sensor employing MIC showed the selectivity toward Fru-val compared with the sensor signal toward fructosyl-ε-lysine (Fru-ε-lys), while the sensor employing the control polymer showed almost identical responses to Fru-val as that to Fru-ε-lys.
Agents that bind annexin A2 suppress ocular neovascularization (2010)

TM601 is a synthetic polypeptide with sequence derived from the venom of the scorpion Leiurus quinquestriatus that has anti-neoplastic activity. It has recently been demonstrated to bind annexin A2 on cultured tumor and vascular endothelial cells and to suppress blood vessel growth on chick chorioallantoic membrane. In this study, we investigated the effects of TM601 in models of ocular neovascularization (NV). When administered by intraocular injection, intravenous injections, or periocular injections, TM601 significantly suppressed the development of choroidal NV at rupture sites in Bruch's membrane. Treatment of established choroidal NV with TM601 caused apoptosis of endothelial cells and regression of the NV. TM601 suppressed ischemia-induced and vascular endothelial growth factor-induced retinal NV and reduced excess vascular permeability induced by vascular endothelial growth factor. Immunostaining with an antibody directed against TM601 showed that after intraocular or periocular injection, TM601 selectively bound to choroidal or retinal NV and co-localized with annexin A2, which is undetectable in normal retinal and choroidal vessels, but is upregulated in endothelial cells participating in choroidal or retinal NV. Intraocular injection of plasminogen or tissue plasminogen activator, which like TM601 bind to annexin A2, also suppressed retinal NV. This study supports the hypothesis that annexin A2 is an important target for treatment of neovascular diseases and suggests that TM601, through its interaction with annexin A2, causes suppression and regression of ocular NV and reduces vascular leakage and thus may provide a new treatment for blinding diseases such as neovascular age-related macular degeneration and diabetic retinopathy.
Using a variation of empirical mode decomposition to remove noise from signals (2011)

This paper will describe the application of τ-based decomposition, which is a variation of the empirical mode decomposition method based on modified peak selection, to de-noising and de-trending of signals. The τ-based decomposition method will be explained, and its application to synthetic and real-world signals in the context of de-noising and de-trending will be described. Comparison between the computational simplicity of the τ-based decomposition method to de-noising and de-trending of signals and approaches based on empirical mode decomposition will be highlighted.
Role of low-density lipoprotein receptor in the hepatitis C virus life cycle (2011)

The LDLR is not essential for infectious HCV particle entry, whereas the physiological function of this receptor is important for optimal replication of the HCV genome.