gebhart/patrepeval huggingface dataset:
A New Structural Model of Apolipoprotein B100 Based on Computational Modeling and Cross Linking (2022)

ApoB-100 is a member of a large lipid transfer protein superfamily and is one of the main apolipoproteins found on low-density lipoprotein (LDL) and very low-density lipoprotein (VLDL) particles. Despite its clinical significance for the development of cardiovascular disease, there is limited information on apoB-100 structure. We have developed a novel method based on the "divide and conquer" algorithm, using PSIPRED software, by dividing apoB-100 into five subunits and 11 domains. Models of each domain were prepared using I-TASSER, DEMO, RoseTTAFold, Phyre2, and MODELLER. Subsequently, we used disuccinimidyl sulfoxide (DSSO), a new mass spectrometry cleavable cross-linker, and the known position of disulfide bonds to experimentally validate each model. We obtained 65 unique DSSO cross-links, of which 87.5% were within a 26 Å threshold in the final model. We also evaluated the positions of cysteine residues involved in the eight known disulfide bonds in apoB-100, and each pair was measured within the expected 5.6 Å constraint. Finally, multiple domains were combined by applying constraints based on detected long-range DSSO cross-links to generate five subunits, which were subsequently merged to achieve an uninterrupted architecture for apoB-100 around a lipoprotein particle. Moreover, the dynamics of apoB-100 during particle size transitions was examined by comparing VLDL and LDL computational models and using experimental cross-linking data. In addition, the proposed model of receptor ligand binding of apoB-100 provides new insights into some of its functions.
Discovery of a Novel and Selective Indoleamine 2,3-Dioxygenase (IDO-1) Inhibitor 3-(5-Fluoro-1H-indol-3-yl)pyrrolidine-2,5-dione (EOS200271/PF-06840003) and Its Characterization as a Potential Clinical Candidate (2017)

Tumors use tryptophan-catabolizing enzymes such as indoleamine 2,3-dioxygenase (IDO-1) to induce an immunosuppressive environment. IDO-1 is induced in response to inflammatory stimuli and promotes immune tolerance through effector T-cell anergy and enhanced Treg function. As such, IDO-1 is a nexus for the induction of a key immunosuppressive mechanism and represents an important immunotherapeutic target in oncology. Starting from HTS hit 5, IDO-1 inhibitor 6 (EOS200271/PF-06840003) has been developed. The structure-activity relationship around 6 is described and rationalized using the X-ray crystal structure of 6 bound to human IDO-1, which shows that 6, differently from most of the IDO-1 inhibitors described so far, does not bind to the heme iron atom and has a novel binding mode. Clinical candidate 6 shows good potency in an IDO-1 human whole blood assay and also shows a very favorable ADME profile leading to favorable predicted human pharmacokinetic properties, including a predicted half-life of 16-19 h.
Sender Reputation Construction method using Sender Authentication (2021)

Spam is not just annoying, it is a serious problem that causes security problems. Mail filters are effective and widely used as anti-spam measures. However, spam senders are also becoming more sophisticated in their content and transmission methods, and countermeasures are becoming more difficult. In addition, if the mail filter makes a false judgment, there is also the problem that the necessary mail will not be delivered. In this paper, we propose a method for constructing sender reputation using sender authentication technologies. The sender of the forwarded mail is used as a method to determine the legitimate mail server. To determine the sender of the forwarded mail, use the authentication result of SPF and DKIM authentication. In addition, we propose a method using DKIM’s block list as a countermeasure against forwarded spam. We used these methods to validate the sender reputation using the mails we actually received.
ABOUT THE AUTHORS (2003)

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Growth of Epitaxial 100-Oriented KNbO3–NaNbO3Solid Solution Films on (100)cSrRuO3∥(100)SrTiO3by Hydrothermal Method and Their Characterization (2011)

Films of solid solution in KNbO3–NaNbO3 (KNN) were deposited at 240 °C on (100)cSrRuO3∥(100)SrTiO3 substrates by the hydrothermal method. (KxNa1-x)NbO3 films with x = 0–1.0 were synthesized by changing the fraction of KOH in a solution of KOH and NaOH. The x in (KxNa1-x)NbO3 continuously changed with the volume fraction of KOH, while the deposition amount strongly depended on x. Epitaxial films with 100 orientation were obtained in the entire composition range and their out-of-plane lattice spacing changed with x. All the films showed ferroelectricity and their remanent polarization became larger than what above x = 0.58.
Oversampled ITOF Imaging Techniques using SPAD-based Quanta Image Sensors (2024)

A time-gated global shutter SPAD-based QVGA image sensor is employed as a quanta image sensor (QIS). QIS behaviour is experimentally demonstrated. Real-time temporal oversampling of time-gated images is implemented, facilitating two-bin indirect time of flight (ITOF) imaging with and without background rejection achieving worst case 38mm RMS precision in 600mm dynamic range.
MR Voiding Cystography for Evaluation of Vesicoureteral Reflux (2009)

MR voiding cystography with a real-time interactive MR fluoroscopic technique on an open MRI magnet is feasible for the evaluation of VUR in children.
Effects of Metal-Centered Reduction on the Structural, Electronic, and Coordination Properties of Nickel and Copper Octaethylisobacteriochlorins. [Erratum to document cited in CA121:157240] (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEffects of Metal-Centered Reduction on the Structural, Electronic, and Coordination Properties of Nickel and Copper Octaethylisobacteriochlorins. [Erratum to document cited in CA121:157240]Mark W. Renner, Lars R. Furenlid, and Alan M. StolzenbergCite this: J. Am. Chem. Soc. 1995, 117, 8, 2379Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://pubs.acs.org/doi/10.1021/ja00113a039https://doi.org/10.1021/ja00113a039research-articleACS PublicationsRequest reuse permissionsArticle Views49Altmetric-Citations1LEARN 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
Monocular vision-based vehicular speed estimation from compressed video streams (2013)

This paper introduces a monocular vision-based vehicular speed estimation algorithm that operates in the compressed domain. The algorithm relies on the use of motion vectors associated with video compression to achieve computationally efficient and accurate speed estimation. Building the speed estimation directly into the compression step adds only a small amount of computation which is conducive to real-time performance. We demonstrate the effectiveness of the algorithm on 30 fps video of one hundred and forty vehicles travelling at speeds ranging from 30 to 60 mph. The average speed estimation accuracy of our algorithm across the test set was better than 2.50% at a yield of 100%, with the accuracy increasing as the yield decreases and as the frame rate increases.
A Novel Optical Method for Real-Time Control of Bolt Tightening (2011)

A digital speckle pattern interferometry (DSPI) system is developed for the real-time measurement and monitoring of the out-of-plane surface deformation around a preloaded bolt head or nut. The proposed system is specifically developed for the dynamic control of the bolt tightening process by continuously monitoring the out-of-plane joint surface deformation that will have been independently correlated to the bolt preload. Spatial phase shifting is employed to quantitatively determine the distribution of phase data by introducing a spatial carrier fringe pattern to the speckle interferogram. This is achieved by leading the object and reference beams through two separate apertures. The configuration is also suitable for collecting the real-time surface deformation during bolt tightening. The experimental DSPI system is set-up with optical components on a vibration-isolation table. A MATLAB software is developed for image acquisition and phase data calculations that yield the out-of-plane surface deformation caused by the bolt preload. The test fixture uses an M12 steel fastener and aluminum joint. For miniature screw applications, however, a plastic joint is used.
Supplemental Methods and Results from First-in-Human Trial of a Novel Anti-Trop-2 Antibody-SN-38 Conjugate, Sacituzumab Govitecan, for the Treatment of Diverse Metastatic Solid Tumors (2023)

&lt;p&gt;This file contains additional methods, including eligibility criteria, study design, pharmacokinetics and immunogenicity, and immunohistology, as well as additional results related to several notable patient narratives.&lt;/p&gt;
Preparation of high surface area vanadium phosphate catalysts using water as solvent (2002)

The synthesis of vanadium phosphorus oxide catalysts using water as solvent is described and discussed. The use of H3PO3 as a reducing agent is contrasted with aqueous hydrochloric acid. Using H3PO3 as a reducing agent for V2O5 at 145 °C for 72 h, together with H3PO4 or H4P2O7 as the additional phosphorus source, is found to produce VOHPO4·0.5H2O. Following activation in n-butane–air for 72 h, the catalysts derived from this method have surface areas (17–23 m2 g−1) that are comparable to those prepared using a standard non-aqueous solvent method. The specific (mol maleic anhydride per g catalyst per h) and intrinsic (mol maleic anhydride m−2 h−1) activities of the catalysts derived from using H3PO3 with water as solvent are also comparable to those for catalysts prepared using non-aqueous solvents. The activated catalysts comprise (VO)2P2O7, together with αII- and δ-VOPO4. Refluxing the VOHPO4·0.5H2O catalyst precursors in water is found to decrease the crystallite size of the precursor, and this leads to higher area activated catalysts, but does not affect the specific or intrinsic activity significantly.
Observability Linear Hybrid Systems (2003)

We analyze the observability of the continuous and discrete states of a class of continuous-time linear hybrid systems. We derive necessary and sufficient conditions that the structural parameters of the model must satisfy in order for filtering and smoothing algorithms to operate correctly. Our conditions are simple rank tests that exploit the geometry of the observability subspaces generated by the output of a linear hybrid system. We also derive weaker rank conditions that guarantee the uniqueness of the reconstruction of the state trajectory from a specific output, even when the hybrid system is unobservable.
INTERLEUKIN-1β STIMULATES SOMATOSTATIN BIOSYNTHESIS IN PRIMARY CULTURES OF FETAL RAT BRAIN (1989)

Interleukin-1 (IL-1), a secretory product of activated macrophages and many other cell types, is an important mediator of the acute phase reaction to infection and to endotoxin administration. Previous reports that GH and TSH secretion are decreased following injection of endotoxin or IL-1 led us to test the hypothesis that IL-1 acts by releasing increased amounts of somatostatin (SS), a hypothalamic factor inhibitory of both GH and TSH release. Primary cultures of dispersed fetal rat diencephalic cells were found to contain increasing amounts of immunoreactive SS in both cells and media after addition of recombinant human IL-1 beta. This increase was detectable at 24 hours and continued for up to 6 days, the longest time interval tested. Increased content of SS peptide was accompanied by marked increases in SS mRNA. These changes were dose-related, the lowest effective dose being 10(-10) M. In contrast to the long term response, exposure of the cells to IL-1 beta for one hour had only minimal stimulating effects on somatostatin release. These data indicate that IL-1 beta is neurotrophic for the somatostatinergic neuron, an action that may be responsible at least in part, for the neuroendocrine response to infection.
Selenopeptide chemistry (2008)

This review focuses on the chemical aspects of the 21st proteinogenic amino acid, selenocysteine in peptides and proteins. It describes the physicochemical properties of selenium/sulfur and selenocysteine/cysteine based on comprehensive structural (X-ray, NMR, CD) and biological data, and illustrates why selenocysteine is considered the most conservative substitution of cysteine. The main focus lies on the synthetic methods on selenocysteine incorporation into peptides and proteins, including an overview of the selenocysteine building block syntheses for Boc- and Fmoc-SPPS. Selenocysteine-mediated reactions such as native chemical ligation and dehydroalanine formation are addressed towards peptide conjugation. Selenopeptides have very interesting and distinct properties which lead to a diverse range of applications such as structural, functional and mechanistic probes, robust scaffolds, enzymatic reaction design, peptide conjugations and folding tools.
Solvents for Processing Stable Tin Halide Perovskites (2021)

Tin is one of the most promising alternatives to lead to make lead-free halide perovskites for optoelectronics. However, the stability of tin-based perovskites is hindered by the oxidation of Sn(II) to Sn(IV). Recent works established that dimethyl sulfoxide, which is one of the best-performing solvents for processing perovskite, is the primary source of tin oxidation. The quest for a stable solvent could be a game-changer in the stability of tin-based perovskites. Starting from a database of over 2000 solvents, we identified a series of 12 new solvents suitable for the processing of formamidinium tin iodide perovskite (FASnI3) by investigating (1) the solubility of the precursor chemicals FAI and SnI2, (2) the thermal stability of the precursor solution, and (3) the possibility of forming perovskite. Finally, we demonstrate a new solvent system to produce solar cells outperforming those based on DMSO. Our work provides guidelines for further identification of new solvents or solvent mixtures for preparing stable tin-based perovskites.
Oxidation of diols with alkali hypochlorites catalyzed by oxammonium salts under two-phase conditions (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOxidation of diols with alkali hypochlorites catalyzed by oxammonium salts under two-phase conditionsPier Lucio Anelli, Stefano Banfi, Fernando Montanari, and Silvio QuiciCite this: J. Org. Chem. 1989, 54, 12, 2970–2972Publication Date (Print):June 1, 1989Publication History Published online1 May 2002Published inissue 1 June 1989https://pubs.acs.org/doi/10.1021/jo00273a038https://doi.org/10.1021/jo00273a038research-articleACS PublicationsRequest reuse permissionsArticle Views2670Altmetric-Citations204LEARN 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
Dissecting binding of a β-barrel membrane protein by phage display (2017)

Membrane proteins (MPs) constitute a third of all proteomes, and contribute to a myriad of cellular functions including intercellular communication, nutrient transport and energy generation. For example, TonB-dependent transporters (TBDTs) in the outer membrane of Gram-negative bacteria play an essential role transporting iron and other nutrients into the bacterial cell. The inherently hydrophobic surfaces of MPs complicates protein expression, purification, and characterization. Thus, dissecting the functional contributions of individual amino acids or structural features through mutagenesis can be a challenging ordeal. Here, we apply a new approach for the expedited protein characterization of the TBDT ShuA from Shigella dysenteriae, and elucidate the protein's initial steps during heme-uptake. ShuA variants were displayed on the surface of an M13 bacteriophage as fusions to the P8 coat protein. Each ShuA variant was analyzed for its ability to display on the bacteriophage surface, and functionally bind to hemoglobin. This technique streamlines isolation of stable MP variants for rapid characterization of binding to various ligands. Site-directed mutagenesis studies targeting each extracellular loop region of ShuA demonstrate no specific extracellular loop is required for hemoglobin binding. Instead two residues, His420 and His86 mediate this interaction. The results identify a loop susceptible to antibody binding, and also a small molecule motif capable of disrupting ShuA from S. dysenteriae. The approach is generalizable to the dissection of other phage-displayed TBDTs and MPs.
An Improved Synthesis of Hydroxyindoles (2004)

An improved synthetic procedure for the synthesis of 6- and 7-hydroxyindoles is described. In this method, the addition of two chlorine atoms in 1-benzyloxy-4,5-dichloro-2-nitrobenzene (3) and 1-benzyloxy-2,6-dichloro-3-nitrobenzene (9) facilitated the subsequent cyanomethylation step to give substituted cyanomethyl-dichloronitrobenzenes 4 and 10, leading to an overall increase in the yield of the hydroxyindoles 6 and 12.
Bounded Recursive Self-Improvement (2013)

We have designed a machine that becomes increasingly better at behaving in underspecified circumstances, in a goal-directed way, on the job, by modeling itself and its environment as experience accumulates. Based on principles of autocatalysis, endogeny, and reflectivity, the work provides an architectural blueprint for constructing systems with high levels of operational autonomy in underspecified circumstances, starting from a small seed. Through value-driven dynamic priority scheduling controlling the parallel execution of a vast number of reasoning threads, the system achieves recursive self-improvement after it leaves the lab, within the boundaries imposed by its designers. A prototype system has been implemented and demonstrated to learn a complex real-world task, real-time multimodal dialogue with humans, by on-line observation. Our work presents solutions to several challenges that must be solved for achieving artificial general intelligence.
Early somatic mosaicism is a rare cause of long-QT syndrome (2016)

Somatic mosaicism, the occurrence and propagation of genetic variation in cell lineages after fertilization, is increasingly recognized to play a causal role in a variety of human diseases. We investigated the case of life-threatening arrhythmia in a 10-day-old infant with long QT syndrome (LQTS). Rapid genome sequencing suggested a variant in the sodium channel Na<sub>V</sub>1.5 encoded by SCN5A, NM_000335:c.5284G > T predicting p.(V1762L), but read depth was insufficient to be diagnostic. Exome sequencing of the trio confirmed read ratios inconsistent with Mendelian inheritance only in the proband. Genotyping of single circulating leukocytes demonstrated the mutation in the genomes of 8% of patient cells, and RNA sequencing of cardiac tissue from the infant confirmed the expression of the mutant allele at mosaic ratios. Heterologous expression of the mutant channel revealed significantly delayed sodium current with a dominant negative effect. To investigate the mechanism by which mosaicism might cause arrhythmia, we built a finite element simulation model incorporating Purkinje fiber activation. This model confirmed the pathogenic consequences of cardiac cellular mosaicism and, under the presenting conditions of this case, recapitulated 2:1 AV block and arrhythmia. To investigate the extent to which mosaicism might explain undiagnosed arrhythmia, we studied 7,500 affected probands undergoing commercial gene-panel testing. Four individuals with pathogenic variants arising from early somatic mutation events were found. Here we establish cardiac mosaicism as a causal mechanism for LQTS and present methods by which the general phenomenon, likely to be relevant for all genetic diseases, can be detected through single-cell analysis and next-generation sequencing.
Supplementary Tables 1 - 4 from Identification of Campath-1 (CD52) as Novel Drug Target in Neoplastic Stem Cells in 5q-Patients with MDS and AML (2023)

&lt;p&gt;PDF file - 85K, Supplementary Table S1: Characteristics of patients with MDS Supplementary Table S2: Characteristics of patients with AML Supplementary Table S3: Characteristics of patients with CML, CMML, MPS, AUL, and ALL Supplementary Table S4: Characteristics of patients with ICUS, normal/reactive bone marrow and long-term complete remission.&lt;/p&gt;
Silica hollow-core anti-resonant fiber for harsh environment mid-infrared sensing applications (2022)

Mid-infrared absorption spectroscopy is nowadays considered as a routine analysis and sensing tool providing highly discriminatory information on organic and inorganic molecules. The specific needs of the transport, aerospace or energy industries may involve applications for which the spectroscopic sensor has to withstand high temperatures. This paper reports the design and fabrication of a silica hollow-core anti-resonant fiber with 8 non touching capillaries primarily designed for mid-infrared CO<sub>x</sub> sensing inside engines. Numerical and analytical simulations performed to ensure fiber transparency in the 4-5 µm region are reported. Optical transmission between 3.9 µm and 4.7 µm is observed and demonstrate attenuation below 1 dB/m for single capillary ring fibers in this range. A preliminary scheme for CO<sub>2</sub> sensing using a quantum cascade laser operating in one of the fiber’s transmission windows (λ=4.3 µm) is depicted.