gebhart/patrepeval huggingface dataset:
Biomimetic Total Synthesis and Investigation of the Non‐Enzymatic Chemistry of Oxazinin A (2022)

We report the first total synthesis of an antimycobacterial natural product oxazinin A that takes advantage of a multi-component cascade reaction of anthranilic acid and a precursor polyketide containing an aldehyde. The route utilized for the synthesis of the pseudodimeric oxazinin A validates a previously proposed biosynthetic mechanism, invoking a non-enzymatic pathway to the complex molecule. We found a 76 : 10 : 9 : 5 ratio of oxazinin diastereomers from the synthetic cascade, which is an identical match to that found in the fermentation media from the fungus Eurotiomycetes 110162. Further investigation of the non-enzymatic formation of oxazinin A using <sup>1</sup> H-<sup>15</sup> N HMBC NMR spectroscopy allowed for a plausible determination of the stepwise mechanism. The developed route is highly amenable for the synthesis of diverse sets of analogs around the oxazinin scaffold to study structure-activity relationships (SAR).
1A1-L07 Thermal Observation Robot System using 3-Dimensional Mapping (2015)

Thermal camera have been used to monitor thermal anomaly. But It is difficult to monitor a wide range because camera angle is narrow. In this study, we propose a robotic thermal observation system in consideration of 3D mapping for the geometry of the real environment. It is possible to combine thermal and RGBD camera information by having a calibration process with a thermal pattern. By integrating the camera system with a mobile robot, we are able to obtain a wide-area thermal map with 3D geometry. And the system performs visualization of the temperature change by comparing the 3D thermal model and current temperature.
Vorschlag zur Berechnung individueller thermodynamischer Aktivitätskoeffizienten einzelner Ionensorten in Elektrolytlösungen bis zu hohen Konzentrationen (1977)

Article Vorschlag zur Berechnung individueller thermodynamischer Aktivitätskoeffizienten einzelner Ionensorten in Elektrolytlösungen bis zu hohen Konzentrationen was published on February 1, 1977 in the journal Zeitschrift für Physikalische Chemie (volume 258O, issue 1).
Hydrophobic Interactions Control Zymogen Activation in the Trypsin Family of Serine Proteases (1996)

Trypsinogen is converted to trypsin by the removal of a peptide from the N terminus, which permits formation of a salt bridge between the new N-terminal Ile (residue 16) and Asp194. Formation of this salt bridge triggers a conformational change in the "activation domain" of trypsin, creating the S1 binding site and oxyanion hole. Thus, the activation of trypsinogen appears to represent an example of protein folding driven by electrostatic interactions. The following trypsin mutants have been constructed to explore this problem: Asp194Asn, Ile16Val, Ile16Ala, and Ile16Gly. The bovine pancreatic trypsin inhibitor (BPTI), benzamidine, and leupeptin affinities and activity and pH-rate profiles of these mutants have been measured. The changes in BPTI and benzamidine affinity measure destabilization of the activation domain. These experiments indicate that hydrophobic interactions of the Ile16 side chain provide 5 kcal/mol of stabilization energy to the activation domain while the salt bridge accounts for 3 kcal/mol. Thus, hydrophobic interactions provide the majority of stabilization energy for the trypsinogen to trypsin conversion. The pH-rate profiles of I16A and I16G are significantly different than the pH-rate profile of trypsin, further confirming that the activation domain has been destabilized. Moreover, these mutations decrease kcat/Km and leupeptin affinity in parallel with the decrease in stability of the activation domain. Acylation is selectively decreased, while substrate binding and deacylation are not affected. Together these observations indicate that the stability of protein structure is an important component of transition state stabilization in enzyme catalysis. These results also suggest that active zymogens can be created without providing a counterion for Asp194, and thus have important implications for the elucidation of the structural features which account for the zymogen activity of tissue plasminogen activator and urokinase.
Anterior Communicating Artery Aneurysms (2002)

Abstract ANTERIOR COMMUNICATING ARTERY aneurysms are complex lesions for which surgical success requires extensive preoperative and intraoperative planning. Adherence to the tenets of aneurysm surgery, including vascular control and preservation of perforating arteries, is essential for their exclusion from the circulation.
Control of tissue size and development by a regulatory element in the yorkie 3'UTR. (2017)

Regulation of the Hippo pathway via phosphorylation of Yorkie (Yki), the <i>Drosophila</i> homolog of human Yes-associated protein 1, is conserved from <i>Drosophila</i> to humans. Overexpression of a non-phosphorylatable form of Yki induces severe overgrowth in adult fly eyes. Here, we show that <i>yki</i> mRNA associates with microsomal fractions and forms foci that partially colocalize to processing bodies in the vicinity of endoplasmic reticulum. This localization is dependent on a stem-loop (SL) structure in the 3' untranslated region of <i>yki</i>. Surprisingly, expression of SL deleted <i>yki</i> in eye imaginal discs also results in severe overgrowth phenotypes. When the structure of the SL is disrupted, Yki protein levels increase without a significant effect on RNA levels. When the SL is completely removed, protein levels drastically increase, but in this case, due to increased RNA stability. In the latter case, we show that the increased RNA accumulation is due to removal of a putative <i>miR-8</i> seed sequence in the SL. These data demonstrate the function of two novel regulatory mechanisms, both controlled by the <i>yki</i> SL element, that are essential for proper Hippo pathway mediated growth regulation.
The interplay of intermolecular interactions, packing motifs and electron transport properties in perylene diimide related materials: a theoretical perspective (2012)

Perylene diimide (PDI) and its derivatives hold great promise, since they are undeniably considered as an important family of organic n-type semiconductors with both high carrier mobilities and air stabilities comparable to p-type ones, although they traditionally stand out as a class of high-performance dyes and pigments. In this feature article, we summarize the influences of substituents on different positions (imide, ortho, bay) of PDI on their electronic and morphological (packing) properties, which are in close connection with the ability for carrier transport. Then representative molecular packing motifs for PDIs are also classified, with an emphasis on the intricate interplay of intermolecular interactions, packing motifs and electron transport properties of perylene imide related carrier transport materials from a theoretical point of view, towards paving the way for boosting and improving the electron transport mobilities and air stabilities of PDIs-based materials.
Ultrastructural heterogeneity of epithelioid cells in cutaneous organized granulomas of diverse etiology (1991)

• In organized granulomatous inflammation, activated macrophages terminally differentiate into epithelioid cells (ECs). By light microscopy, individual ECs appear similar, irrespective of the inciting agent. Ultrastructural analysis of a number of clinical and experimental granulomas in man and mice reveals, however, three distinct varieties of these cells. They are classified as follows: (1) EC-I cells containing a mixture of lysosomal-dense bodies and phagolysosomes and arrays of rough endoplasmic reticulum in the cytoplasm; (2) EC-II cells showing primarily a secretory mode with prominent Golgi bodies and rich arrangement of dilated rough endoplasmic reticulum with no phagocytic vacuoles; and (3) EC-III cells containing large multisized vesicles crowded throughout the cytoplasm and presently of unknown function. Although the unique appearance of these cells offers little diagnostic help, the cells do distribute differentially in different granulomas. The EC-I cells tend to predominate in infectious granulomas and where an excess of foreign material and debris is present. The EC-II cells are most characteristic of active sarcoidal granulomas, and the EC-III cells appear in chronic, long-standing granulomas. The heterogeneic nature of these cells seems to suggest their functions in granulomatous inflammation are not always the same. (<i>Arch Dermatol.</i>1991;127:821-826)
Peptide Vaccination in Clinical Oncology (2000)

Tumor-associated antigens recognized by cellular or humoral effectors of the immune system represent attractive targets for antigen-specific cancer therapy. Different groups of cancer-associated antigens have been identified inducing cytotoxic T-lymphocyte (CTL) responses in vitro and in vivo: 1) 'Cancer-Testis' (CT) antigens, which are expressed in different tumors and normal testis, 2) melanocyte differentiation antigens, 3) point mutations of normal genes, 4) antigens that are overexpressed in malignant tissues, and 5) viral antigens. Clinical studies with peptides derived from these antigens have been initiated to study the induction of specific CTL responses in vivo. Immunological and clinical parameters for the assessment of peptide-specific reactions have been defined, i. e., delayed-type hypersensitivity (DTH), CTL, autoimmune, and tumor regression responses. Early results show that tumor-associated peptides alone induce specific DTH and CTL responses and tumor regression after intradermal administration. GM-CSF was used as an adjuvant to enhance peptide-specific immune reactions by amplification of dermal peptide-presenting dendritic cells. Complete tumor regressions have been observed in the context of measurable peptide-specific CTL. However, in single cases with disease progression after an initial tumor response, either a loss of the respective tumor antigen targeted by CTL or of the presenting MHC class I allele was detected, suggesting immunization-induced immune escape. Based on these observations, cytokines to modify antigen and MHC class I expression in vivo are being tested to prevent immunoselection. Recently, a new CT antigen, NY-ESO-1, has been identified with a strategy utilizing spontaneous antibody responses to tumor-associated antigens (SEREX). NY-ESO-1 is regarded as one of the most immunogenic antigens known today, inducing spontaneous immune responses in 50% of patients with NY-ESO-1-expressing cancers. Clinical studies with antigenic constructs to induce both humoral and cellular immune responses will show whether these are more effective for immunotherapy of cancer. Copyright 2000 S. Karger GmbH, Freiburg
Stille Couplings Catalytic in Tin:  Beyond Proof-of-Principle (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTStille Couplings Catalytic in Tin: Beyond Proof-of-PrincipleRobert E. Maleczka,, William P. Gallagher, and Ina TerstiegeView Author Information Department of Chemistry, Michigan State University East Lansing, Michigan 48824 Cite this: J. Am. Chem. Soc. 2000, 122, 2, 384–385Publication Date (Web):December 31, 1999Publication History Received23 September 1999Published online31 December 1999Published inissue 1 January 2000https://doi.org/10.1021/ja993446sCopyright © 2000 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1338Altmetric-Citations66LEARN 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 (72 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Byproducts,Chemical reactions,Coupling reactions,Cross coupling reaction,Hydrocarbons Get e-Alerts
Development of a Muon Linac for the G-2/EDM Experiment at J-PARC (2017)

Precision measurements of the muon's anomalous magnetic moment (g-2) and electric dipole moment (EDM) are one of the effective ways to test the standard model. An ultra-cold muon beam is generated from a surface muon beam by a thermal muonium production and accelerated to 300 MeV/c by a linac. The muon linac consists of an RFQ, an inter-digital IH, a Disk And Washer structure, and a disk loaded structure. The ultra-cold muons will have an extremely small momentum spread of 0.3 % with a normalized transverse emittance of around 1.5 pi mm-mrad. The design and status of the muon linac at J-PARC will be presented.
Transcoding Internet content for heterogeneous client devices (2002)

There is a growing diversity of client devices that have access to the Internet. However, much of the content on the Internet cannot be handled by the devices that have limited communication, processing, storage and display capabilities. In order to improve the utility of a wide range of client devices, we propose a network-based solution for transcoding Internet content. The system uses an InfoPyramid for representing and transcoding video, images, audio and text. The InfoPyramid manipulates the content along the dimensions of fidelity and modality, and aggregates the methods for content analysis, translation, filtering and selection. The InfoPyramid utilizes a policy engine, which incorporates user and publisher preferences, various transcoding policies, device descriptions, and real-time network constraints in order to adapt the Internet content to the client devices.
Transmission of Power-Efficient CO-OFDM Signals over 9360 km of Ultra-Large-Area Fiber (2012)

In this paper we introduced two power-efficient CO-OFDM systems and showed that both systems can have~1-dB gain in receiving sensitivity (BER = 1e-3) and exhibit~1.1-dB benefit in Q factor after 9360-km transmission when compared with the regular PDM-CO-OFDM.
From Cytosol to Organelles: 14‐3‐3 Proteins as Multifunctional Regulators of Plant Cell (2002)

14-3-3 proteins are a class of highly conserved proteins wide-spread in eukaryotes. They regulate several cellular processes through phosphorylation-dependent interaction with their targets. Since their discovery in plants, a number of peculiar functions have been ascertained, such as regulation of primary metabolism, ion transport, cellular trafficking, chloroplast and mitochondrial enzyme activities and gene transcription. The still increasing body of evidence suggests that 14-3-3s may function as versatile proteins able to move from cytosol to different cellular organelles. This review will focus on the broad range of regulatory tasks carried out by 14-3-3s in the different compartments.
Electronic structures and physical properties of Na2O doped silicate glass (2017)

Ab initio molecular dynamics has been applied to construct seven sodium silicate glass models with Na2O concentration ranging from 0 to 50 mol. %. The structures of the simulated (Na2O)x(SiO2)1-x glasses are critically analyzed and validated by comparing with available experimental data. Because the initial seed model is based on a near-perfect continuous random network model for amorphous SiO2 with periodic boundaries, the structures of these silicate glasses are highly reliable. The electronic structure, interatomic bonding, and the mechanical and optical properties of seven models are calculated using the first-principles density functional method. In particular, a single quantum mechanical metric, the total bond order density (TBOD), is used to characterize the internal cohesion of sodium silicate glass. This is a significant step beyond the traditional analysis of glasses based purely on the geometric parameters. The TBOD value is found to decrease with increasing Na content, indicating the destruction of silica network connectivity. The calculated mass density and refractive index increase with x are in good agreement with experiment. The elastic coefficients and bulk mechanical properties exhibit a nonlinear variation in the series and depend greatly on the internal bonding and cohesion of the glass. The calculated Poisson's ratio indicates that the glass becomes more ductile with the addition of Na2O. Our results indicate that sodium silicate glass tends to be unstable for x greater than 0.4 due to the total destruction of the SiO2 network.
An investigation of MoP catalysts for alcohol synthesis (2010)

Molecular simulation and experimental methods have been used to assess the catalytic behavior of MoP in the conversion of synthesis gas (CO, CO₂, H₂) to oxygenated hydrocarbons. The potential energy surface of synthesis gas conversion to methane and methanol was investigated on a Mo₆P₃ cluster model of the MoP catalyst. The potential energy surface (PES) for CH₄ formation was determined to be: COad → CHOad → CH₂Oad → CH₂OHad → CH₂.ad+H₂Oad → CH₃.ad+H₂Oad → CH₄+H₂O and for CH₃OH : COad → CHOad → CH₂Oad → CH₂OHad → CH₃OHad. The hydroxymethyl (CH₂OH) species was a common reaction intermediate for both CH₄ and CH₃OH formation and the simulation predicted selective formation of CH₄ rather than CH₃OH from syngas over MoP. The cluster model was modified to investigate the effect of a SiO₂ support and a K promoter. Both SiO₂ and K decreased the activation energy for methanol formation. However, the activation energy for methanol formation remained higher than the activation energy for C-O bond cleavage. The high adsorption energy of methanol and the formation of geminal dicarbonyl species on the K-Mo₆P₃-Si₃O₉ cluster suggested the possibility of the formation of higher oxygenates. The conversion of syngas to alcohols was also investigated on 5, 10, and 15 wt% MoP supported on silica, with 0, 1, and 5 wt% K added as a promoter The major products were acetaldehyde, acetone and ethanol. Low selectivities to methanol (&lt;5 C atom %) and methane (&lt; 10 C atom%) were observed on the 5%K-10%MoP-SiO₂ catalyst. The product distribution obtained over the K-MoP/SiO₂ catalyst was distinct from that reported in the literature over other Mo-based catalysts. Addition of Rh to the K-MoP/SiO₂ catalyst improved the stability of the catalyst. However, the Rh increased the selectivity to hydrocarbon products, especially CH4, while only increasing the selectivity to ethanol marginally. The reaction kinetics of the major products were described by a simple empirical power law. The activation energies of ethanol and acetaldehyde were very similar, suggesting that both originated from the same surface intermediate.
CRISPR-interference-based modulation of mobile genetic elements in bacteria (2019)

Spontaneous mutagenesis of synthetic genetic constructs by mobile genetic elements frequently results in the rapid loss of engineered functions. Previous efforts to minimize such mutations required the exceedingly time-consuming manipulation of bacterial chromosomes and the complete removal of insertional sequences (ISes). To this aim, we developed a single plasmid-based system (pCRIS) that applies CRISPR-interference to inhibit the transposition of bacterial ISes. pCRIS expresses multiple guide RNAs to direct inactivated Cas9 (dCas9) to simultaneously silence IS<i>1</i>, IS<i>3</i>, IS<i>5</i> and IS<i>150</i> at up to 38 chromosomal loci in <i>Escherichia coli</i>, <i>in vivo</i>. As a result, the transposition rate of all four targeted ISes dropped to negligible levels at both chromosomal and episomal targets. Most notably, pCRIS, while requiring only a single plasmid delivery performed within a single day, provided a reduction of IS-mobility comparable to that seen in genome-scale chromosome engineering projects. The fitness cost of multiple IS-knockdown, detectable in flask-and-shaker systems was readily outweighed by the less frequent inactivation of the transgene, as observed in green fluorescent protein (GFP)-overexpression experiments. In addition, global transcriptomics analysis revealed only minute alterations in the expression of untargeted genes. Finally, the transposition-silencing effect of pCRIS was easily transferable across multiple <i>E. coli</i> strains. The plasticity and robustness of our IS-silencing system make it a promising tool to stabilize bacterial genomes for synthetic biology and industrial biotechnology applications.
Synthesis of 2′,3′-Dideoxypurinenucleosides via the Palladium Catalyzed Reduction of 9-(2,5-Di-O-acetyl-3-bromo-3-deoxy-β-d-xylofuranosyl)purine Derivatives (1996)

Abstract Practical method to produce 2′,3′-dideoxypurinenucleosides from 9-(2,5-di-O-acetyl-3-bromo-3-deoxy-β-D-xylofuranosyl)purines (1) was developed. High ratio of 2′,3′-dideoxynucleoside to 3′-deoxyribonucleoside was obtained by selecting the reaction conditions (solvent, pH and/or base), or changing 2′-acyloxy leaving group. The reaction mechanism was studied by deuteration experiments of 1a and 1-(3,5-di-O-acety1-2-bromo-2-deoxy-β-D-ribofuranosyl)thymine (12).
Microstructure and Materials Properties of Understoichiometric TiBx Thin Films Grown by HiPIMS (2020)

&lt;p&gt;In the present research article we report synthesis of TiB&lt;sub&gt;x&lt;/sub&gt;, 1.43&lt;i&gt;n-situ&lt;/i&gt; mass- and energy-spectroscopy is used to explain the obtained compositional range. Excess B in overstoichiometric TiB&lt;i&gt;&lt;sub&gt;x&lt;/sub&gt;&lt;/i&gt;&lt;sub&gt; &lt;/sub&gt;thin films from DCMS results in a hardness up to 37.7±0.8 GPa, attributed to the formation of an amorphous B-rich tissue phase separating stoichiometric TiB&lt;sub&gt;2&lt;/sub&gt; columnar structures. With a particular focus on characterization of the understoichiometric samples, we show that understoichiometric TiB&lt;sub&gt;1.43&lt;/sub&gt; thin films synthesized by HiPIMS exhibit a superior hardness of 43.9±0.9 GPa, where the deficiency of B is found to be accommodated by Ti planar defects. The apparent fracture toughness, electrical resistivity and thermal conductivity of the same sample is 4.2±0.1 MPa√m, 367±7 μΩ·cm and 5.1 W/(m.K), respectively, as compared to corresponding values for overstoichiometric TiB&lt;sub&gt;2.20&lt;/sub&gt; DCMS thin film samples of 3.2±0.1 MPa√m, 309±4 μΩ·cm and 3.0 W/(m.K). &lt;/p&gt;
Computer-assisted medical direction of respiratory care. (1989)

As medical technology and the increased demand for respiratory care make concurrent monitoring of all respiratory care services more difficult, computers are coming to the aid of medical directors and quality assurance committees. The respiratory care staff at LDS Hospital, Salt Lake City, has used computers to enhance patient care and quality assurance.