gebhart/patrepeval huggingface dataset:
Conservation of Meningococcal Antigens in the Genus Neisseria (2013)

Neisseria meningitidis, one of the major causes of bacterial meningitis and sepsis, is a member of the genus Neisseria, which includes species that colonize the mucosae of many animals. Three meningococcal proteins, factor H-binding protein (fHbp), neisserial heparin-binding antigen (NHBA), and N. meningitidis adhesin A (NadA), have been described as antigens protective against N. meningitidis of serogroup B, and they have been employed as vaccine components in preclinical and clinical studies. In the vaccine formulation, fHbp and NHBA were fused to the GNA2091 and GNA1030 proteins, respectively, to enhance protein stability and immunogenicity. To determine the possible impact of vaccination on commensal neisseriae, we determined the presence, distribution, and conservation of these antigens in the available genome sequences of the genus Neisseria, finding that fHbp, NHBA, and NadA were conserved only in species colonizing humans, while GNA1030 and GNA2091 were conserved in many human and nonhuman neisseriae. Sequence analysis showed that homologous recombination contributed to shape the evolution and distribution of both NHBA and fHbp, three major variants of which have been defined. fHbp variant 3 was probably the ancestral form of meningococcal fHbp, while fHbp variant 1 from N. cinerea was introduced into N. meningitidis by a recombination event. fHbp variant 2 was the result of a recombination event inserting a stretch of 483 bp from variant 1 into the variant 3 background. These data indicate that a high rate of exchange of genetic material between neisseriae that colonize the human upper respiratory tract exists. IMPORTANCE The upper respiratory tract of healthy individuals is a complex ecosystem colonized by many bacterial species. Among these, there are representatives of the genus Neisseria, including Neisseria meningitidis, a major cause of bacterial meningitis and sepsis. Given the close relationship between commensal and pathogenic species, a protein-based vaccine against N. meningitidis has the potential to impact the other commensal species of Neisseria. For this reason, we have studied the distribution and evolutionary history of the antigen components of a recombinant vaccine, 4CMenB, that recently received approval in Europe under the commercial name of Bexsero®. We found that fHbp, NHBA, and NadA can be found in some of the human commensal species and that the evolution of these antigens has been essentially shaped by the high rate of genetic exchange that occurs between strains of neisseriae that cocolonize the same environment.
Using Artificial Intelligence in Predicting Ischemic Stroke Events After Percutaneous Coronary Intervention (2023)

The RF model accurately predicts short- and long-term risk of IS and outperforms logistic regression analysis in patients undergoing PCI. Patients with periprocedural stroke may benefit from aggressive management to reduce the future risk of IS.
E-band fiber laser performance and power analysis with longitudinally averaged population modeling (2018)

To help facilitate the modeling of new fiber laser systems, such as those with complex functional microstructures, we report on a simplified modeling methodology that can accommodate the parasitic kinetic effects often present in such systems. The essence of our approach is to integrate kinetics over the length of the gain medium at the outset, thereby forfeiting longitudinally resolved information about the system but simplifying its energetics analysis. To illustrate the benefits of our new approach over more conventional coupled-rate-equation analyses, we apply our model to an Nd3+-doped fiber laser operating on the F3/24&#x2212;I413/2 transition at 1400&#x00A0;nm. The model produces closed-form solutions for the various output channels available to the pump power and enables projections of ultimate laser performance to be conveniently generated.
EUV resist chemical gradient enhancement by UV flood exposure for improvement in EUV resist resolution, process control, roughness, sensitivity and stochastic defectivity (2020)

Flood Exposure Assisted Chemical Gradient Enhancement Technology (FACET) is introduced for improvement in EUV resist resolution, process control, roughness, patterning failure and sensitivity. Experimental EUV exposure latitude was enhanced (~1.5 times) with FACET using the assist of UV flood exposure. The mechanism of the process window improvement by FACET is explained by non-linear resist coloring (enhancement of UV absorption) vs. EUV exposure dose to enhance acid image contrast during UV flood exposure. To balance chemical gradient enhancement and stochastic effects, Stochastic Aware Resist Formulation and Process optimizer (SARF-Pro) with a fast stochastic simulation model is created. SARF-Pro predicts stochastic patterning failure risks, and optimizes resist formulation and processes by putting emphasis on stochastic variation across patterns. Photosensitized Chemically Amplified ResistTM (PSCARTM) 2.0 with FACET and standard chemically amplified resist (CAR) optimized in SARF-Pro suggests that PSCAR 2.0 with FACET has the potential of better process window, roughness, sensitivity and, we hypothesize, reduced risk of stochastic defects compared with standard CAR.
Teleoperation Performance with a Kinematically Redundant Slave Robot (1998)

This paper studies the effects of three methods of kinematic redun dancy resolution on teleoperation performance with a redundant slave robot in telemanipulation. First, we derive three kinematic redundancy control modes expressing different trade-offs between kinetic energy, joint usage, and joint-limit avoiding. To validate our algorithms, we perform simulations, autonomous robot tests, and teleoperation experiments. The trade-off between kinetic en ergy and joint-limit index is clearly shown in the autonomous test. For teleoperation, four tasks and seven indices are defined. A three-degrees-of freedom (DOF), pen-based master and a 5-DOF, mini-direct-drive robot are used with position-to-position control in Cartesian space. Tasks are x-, y-, and z-positioning and contact- force control giving 2-DOFkinematic redundancy in the slave robot. Overall, the inertia-weighted pseudo-inverse, proposed by Whitney in 1969, shows best performance, while the least-square mode (us ing no inertial information) shows the worst performance.
Evolution maps and applications (2016)

Common tasks in document analysis, such as binarization, line extraction etc., are still considered difficult for highly degraded text documents. Having reliable fundamental information regarding the characters of the document, such as the distribution of character dimensions and stroke width, can significantly improve the performance of these tasks. We introduce a novel perspective of the image data which maps the evolution of connected components along the change in gray scale threshold. The maps reveal significant information about the sets of elements in the document, such as characters, noise, stains, and words. The information is further employed to improve state of the art binarization algorithm, and achieve automatically character size estimation, line extraction, stroke width estimation, and feature distribution analysis, all of which are hard tasks for highly degraded documents.
CO2 Conversion with Alcohols and Amines into Carbonates, Ureas, and Carbamates over CeO2 Catalyst in the Presence and Absence of 2‐Cyanopyridine (2018)

Recent progress on the CeO<sub>2</sub> catalyzed synthesis of organic carbonates, ureas, and carbamates from CO<sub>2</sub> +alcohols, CO<sub>2</sub> +amines, and CO<sub>2</sub> +alcohols+amines, respectively, is reviewed. The reactions of CO<sub>2</sub> with alcohols and amines are reversible ones and the degree of the equilibrium limitation of the synthesis reactions is strongly dependent on the properties of alcohols and amines as the substrates. When the equilibrium limitation of the reaction is serious, the equilibrium conversion of the substrate and the yield of the target product is very low, therefore, the shift of the equilibrium reaction to the product side by the removal of H<sub>2</sub> O is essential in order to get the target product in high yield. One of the effective method of the H<sub>2</sub> O removal from the related reaction systems is the combination with the hydration of 2-cyanopyridine to 2-picolinamide, which is also catalyzed by CeO<sub>2</sub> .
Effect of Low Temperature on Growth and Ultra-Structure of Staphylococcus spp (2012)

The effect of temperature fluctuation is an important factor in bacterial growth especially for pathogens such as the staphylococci that have to remain viable during potentially harsh and prolonged transfer conditions between hosts. The aim of this study was to investigate the response of S. aureus, S. epidermidis, and S. lugdunensis when exposed to low temperature (4°C) for prolonged periods, and how this factor affected their subsequent growth, colony morphology, cellular ultra-structure, and amino acid composition in the non-cytoplasmic hydrolysate fraction. Clinical isolates were grown under optimal conditions and then subjected to 4°C conditions for a period of 8 wks. Cold-stressed and reference control samples were assessed under transmission electron microscopy (TEM) to identify potential ultra-structural changes. To determine changes in amino acid composition, cells were fractured to remove the lipid and cytoplasmic components and the remaining structural components were hydrolysed. Amino acid profiles for the hydrolysis fraction were then analysed for changes by using principal component analysis (PCA). Exposure of the three staphylococci to prolonged low temperature stress resulted in the formation of increasing proportions of small colony variant (SCV) phenotypes. TEM revealed that SCV cells had significantly thicker and more diffuse cell-walls than their corresponding WT samples for both S. aureus and S. epidermidis, but the changes were not significant for S. lugdunensis. Substantial species-specific alterations in the amino acid composition of the structural hydrolysate fraction were also observed in the cold-treated cells. The data indicated that the staphylococci responded over prolonged periods of cold-stress treatment by transforming into SCV populations. The observed ultra-structural and amino acid changes were proposed to represent response mechanisms for staphylococcal survival amidst hostile conditions, thus maintaining the viability of the species until favourable conditions arise again.
Nanomaterials by severe plastic deformation: review of historical developments and recent advances (2022)

Severe plastic deformation (SPD) is effective in producing bulk ultrafine-grained and nanostructured materials with large densities of lattice defects. This field, also known as NanoSPD, experienced a significant progress within the past two decades. Beside classic SPD methods such as high-pressure torsion, equal-channel angular pressing, accumulative roll-bonding, twist extrusion, and multi-directional forging, various continuous techniques were introduced to produce upscaled samples. Moreover, numerous alloys, glasses, semiconductors, ceramics, polymers, and their composites were processed. The SPD methods were used to synthesize new materials or to stabilize metastable phases with advanced mechanical and functional properties. High strength combined with high ductility, low/room-temperature superplasticity, creep resistance, hydrogen storage, photocatalytic hydrogen production, photocatalytic CO2 conversion, superconductivity, thermoelectric performance, radiation resistance, corrosion resistance, and biocompatibility are some highlighted properties of SPD-processed materials. This article reviews recent advances in the NanoSPD field and provides a brief history regarding its progress from the ancient times to modernity. Abbreviations: ARB: Accumulative Roll-Bonding; BCC: Body-Centered Cubic; DAC: Diamond Anvil Cell; EBSD: Electron Backscatter Diffraction; ECAP: Equal-Channel Angular Pressing (Extrusion); FCC: Face-Centered Cubic; FEM: Finite Element Method; FSP: Friction Stir Processing; HCP: Hexagonal Close-Packed; HPT: High-Pressure Torsion; HPTT: High-Pressure Tube Twisting; MDF: Multi-Directional (-Axial) Forging; NanoSPD: Nanomaterials by Severe Plastic Deformation; SDAC: Shear (Rotational) Diamond Anvil Cell; SEM: Scanning Electron Microscopy; SMAT: Surface Mechanical Attrition Treatment; SPD: Severe Plastic Deformation; TE: Twist Extrusion; TEM: Transmission Electron Microscopy; UFG: Ultrafine Grained. Â© 2022 The Author(s). Published by Informa UK Limited, trading as Taylor &amp; Francis Group.
X-Ray Mask Fabrication Process Using Cr Mask and ITO Stopper in the Dry Etching of W Absorber (1992)

An X-ray mask fabrication technology using a tungsten (W) absorber with a chromium (Cr) mask and indium titanium oxide (ITO) stopper was developed. When SF 6 was used as the dry etching gas, substantial side etching occurred because the F radical reacts with W on the sidewall. In order to prevent side etching, a SF 6 and CHF 3 gas mixture was applied; however, the ratio of dry etching rate of W to that of resist is low. Furthermore, the underlying layer such as that of silicon dioxide (SiO 2 ), which was used as the etching stopper, was easily damaged. Instead of a resist mask and SiO 2 stopper, a Cr layer as the etching mask and ITO layer as the stopper layer were applied. By the use of these structures and etching procedures, high aspect ratio W patterns with vertical sidewalls have been successfully fabricated.
Novel Histone Deacetylase Inhibitors in the Treatment of Thyroid Cancer (2005)

Histone deacetylases (HDAC) and histone acetyltransferases exert opposing enzymatic activities that modulate the degree of acetylation of histones and other intracellular molecular targets, thereby regulating gene expression, cellular differentiation, and survival. HDAC inhibition results in accumulation of acetylated histones and induces differentiation and/or apoptosis in transformed cells. In this study, we characterized the effect of two HDAC inhibitors, suberoylanilide hydroxamic acid (SAHA) and m-carboxycinnamic acid bis-hydroxamide, on thyroid carcinoma cell lines, including lines originating from anaplastic and medullary carcinomas. In these models, both SAHA and m-carboxycinnamic acid bis-hydroxamide induced growth arrest and caspase-mediated apoptosis and increased p21 protein levels, retinoblastoma hypophosphorylation, BH3-interacting domain death agonist cleavage, Bax up-regulation, down-regulation of Bcl-2, A1, and Bcl-x(L) expression, and cleavage of poly(ADP-ribose) polymerase and caspase-8, -9, -3, -7, and -2. Transfection of Bcl-2 cDNA partially suppressed SAHA-induced cell death. SAHA down-regulated the expression of the apoptosis inhibitors FLIP and cIAP-2 and sensitized tumor cells to cytotoxic chemotherapy and death receptor activation. Our studies provide insight into the tumor type-specific mechanisms of antitumor effects of HDAC inhibitors and a framework for future clinical applications of HDAC inhibitors in patients with thyroid cancer, including histologic subtypes (e.g., anaplastic and medullary thyroid carcinomas) for which limited, if any, therapeutic options are available.
Transparent Peer Review: A Look Inside the Peer Review Process (2021)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTTransparent Peer Review: A Look Inside the Peer Review ProcessSofia GarakyaraghiSofia GarakyaraghiMore by Sofia Garakyaraghihttps://orcid.org/0000-0001-7835-1888, William AumillerWilliam AumillerMore by William Aumillerhttps://orcid.org/0000-0002-9260-3575, Carolyn R. Bertozzi​Carolyn R. BertozziE-mail: [email protected]More by Carolyn R. Bertozzihttps://orcid.org/0000-0003-4482-2754, and Gregory ScholesGregory ScholesMore by Gregory Scholeshttps://orcid.org/0000-0003-3336-7960Cite this: ACS Cent. Sci. 2021, 7, 11, 1771–1772Publication Date (Web):November 3, 2021Publication History Published online3 November 2021Published inissue 24 November 2021https://pubs.acs.org/doi/10.1021/acscentsci.1c01238https://doi.org/10.1021/acscentsci.1c01238editorialACS PublicationsCopyright © 2021 American Chemical Society. This publication is licensed under CC-BY-NC-ND 4.0. License Summary*You are free to share (copy and redistribute) this article in any medium or format within the parameters below:Creative Commons (CC): This is a Creative Commons license.Attribution (BY): Credit must be given to the creator.Non-Commercial (NC): Only non-commercial uses of the work are permitted. No Derivatives (ND): Derivative works may be created for non-commercial purposes, but sharing is prohibited. View full license*DisclaimerThis summary highlights only some of the key features and terms of the actual license. It is not a license and has no legal value. Carefully review the actual license before using these materials. This publication is Open Access under the license indicated. Learn MoreArticle Views4142Altmetric-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 PDF (534 KB) Get e-AlertscloseSUBJECTS:Physical chemistry Get e-Alerts
Pure squamous cell carcinoma of the pancreas: a rare and challenging diagnosis (case report) (2023)

Squamous cell carcinoma (SCC) of the pancreas is a rare exocrine ductal tumour with unknown pathophysiology and poor treatment options. We present a case of SCC in a 59-year-old male patient who presented with epigastric pain, vomiting, anorexia, asthenia, and weight loss. Abdomino-pelvic CT revealed a pancreatic mass with adenopathy satellites. Surgical biopsies were negative, and a trans-duodenal gastric endoscopy showed suspicious lymphadenopathies and a hypoechoic lesion invading the portal vein. An anapathological study confirmed SCC at the site of intense necrotic and inflammatory changes. The patient received radio-chemotherapy, but ultimately developed peritoneal carcinoma.
Interfacial Recognition by Bee Venom Phospholipase A2:  Insights into Nonelectrostatic Molecular Determinants by Charge Reversal Mutagenesis (1998)

The basis for tight binding of bee venom phospholipase A2 (bvPLA2) to anionic versus zwitterionic phospholipid interfaces is explored by charge reversal mutagenesis of basic residues (lysines/arginines to glutamates) on the putative membrane binding surface. Single-site mutants and, surprisingly, multisite mutants (2-5 of the 6 basic residues mutated) are fully functional on anionic vesicles. Mutants bind tightly to anionic vesicles, and active-site substrate and Ca2+ binding are not impaired. Multisite mutants undergo intervesicle exchange slightly faster than wild type, especially in the presence of salt. It is estimated that electrostatic contribution to interfacial binding is modest, perhaps 2-3 kcal/mol of the estimated 15 kcal/mol. Elution properties of bvPLA2 from HPLC columns containing solid phases of tightly packed monolayers of phosphocholine amphiphiles suggest that ionic effects provide a modest portion of the interfacial binding energy and that this contribution decreases as the number of cationic residues mutated is increased. These results are consistent with the observation that Gila monster venom PLA2 (Pa2), which is homologous to bvPLA2, has high activity on anionic vesicles despite the fact that it has only a single basic residue on its putative interfacial recognition face. Results with bvPLA2 mutants show that manoalogue and 12-epi-scalaradial inactivate bvPLA2 by modification of K94. Also, deletion of the large beta-loop (residues 99-118) is without consequence for interfacial binding and catalysis of bvPLA2. All together, the preferential binding of bvPLA2 to anionic vesicles versus phosphatidylcholine vesicles is mainly due to factors other than electrostatics. Therefore hydrogen-bonding and hydrophobic interactions must provide a major portion of the interfacial binding energy, and this is consistent with recent spectroscopic studies.
ChemInform Abstract: Ring‐Closing Metathesis Strategies to Amino Acid Derived P‐Heterocycles. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Native myocardial T1 mapping in pulmonary hypertension: correlations with cardiac function and hemodynamics (2016)

• Native T1 mapping detects left ventricular myocardial alterations in pulmonary hypertension • In pulmonary hypertension, native T1 times at ventricular insertion points are increased • These T1 times correlate strongly with left ventricular eccentricity • In pulmonary hypertension, global and segmental myocardial T1 times are increased • Global, segmental and ventricular insertion point T1 times are strongly correlated.