gebhart/patrepeval huggingface dataset:
A broadly protective vaccine against cutaneous human papillomaviruses (2022)

Skin colonization by human papillomavirus (HPV) is typically related to inconspicuous cutaneous infections without major disease or complications in immunocompetent individuals. However, in immunosuppressed patients, especially organ transplanted recipients, cutaneous HPV infections may cause massive, highly spreading and recurrent skin lesions upon synergism with UV-exposure. Current HPV prophylactic vaccines are not effective against cutaneous HPV types (cHPV). By applying a modular polytope-based approach, in this work, we explored different vaccine candidates based on selected, tandemly arranged cHPV-L2 epitopes fused to thioredoxin (Trx) as a scaffold protein. Upon conversion to heptameric nanoparticles with the use of a genetically fused oligomerization domain, our candidate Trx-L2 vaccines induce broadly neutralizing immune responses against 19 cHPV in guinea pigs. Similar findings were obtained in mice, where protection against virus challenge was also achieved via passive transfer of immune sera. Remarkably, immunization with the candidate cHPV vaccines also induced immune responses against several mucosal low- and high-risk HPV types, including HPV16 and 18. Based on cumulative immunogenicity data but also on ease and yield of production, we identified a lead vaccine candidate bearing 12 different cHPV-L2 epitopes that holds great promise as a scalable and GMP production-compatible lead molecule for the prevention of post-transplantation skin lesions caused by cHPV infection.
Environmentally responsible fabrication of efficient perovskite solar cells from recycled car batteries (2014)

This report presents a process to fabricate perovskite hybrid solar cells in an environmentally responsible fashion by recycling lead materials from spent car batteries.
An Automatic Testbench Generator for Test Patterns Validation (2018)

The growing size and complexity of digital ICs, along with the requirement for better test quality (high test coverage of diversified fault type models) had resulted in an explosion of test data volume and complicated test protocols. What used to be a recommended optional step in the past, is becoming a mandatory and even a crucial step for the overall test process efficiency. Test patterns validation allows for early detection of issues introduced by successive and cumulative modeling and processing steps (from DFT insertion to ATPG generation). The earlier issues are detected, the better in term of debug and fix time point of view, thus in term of test cost. The expensive ATE time should be made profitable by reserving it to only screening real defect issues on the test chip. In this paper, we address the problematic of efficient test pattern validation. Almost no literature exists concerning this area, and giving its current and future growing criticality, we start addressing this domain with a set of innovative ideas that have been implemented in an industrial tool. Unlike some existing solutions that use a PLI (Programming Language Interface) based approach, the proposed tool is a standalone tool, that translates a cycle based test pattern file to an equivalent event based HDL (Hardware Description Language) testbench for sake of validation under logic simulator. Industrial experiments demonstrated that this novel tool is surpassing our previous PLI based tool in terms of performance (> 2X runtime improvement and > 3X memory consumption saving), while achieving better results in terms of robustness and validation confidence. As a matter of fact, it has gained a major success where it is now adopted by our customers worldwide.
Septum-less, hexagonal waveguide based circularly polarized horn antenna for mm-wave and terahertz band (2017)

T Traditional circularly polarized (CP) horn antennas use a septum (or a partition) based feed, which is difficult to fabricate beyond 60 GHz. As an alternative, here we propose hexagonal waveguide based CP antenna design that is fabrication friendly and low-cost. Design, fabrication and characterization is shown for an F-band prototype. The prototype exhibits 18 dBi mid-band gain with three dB axial-ratio (AR) bandwidth beyond thirty percent.
Syntheses, Photophysics, and Application of Iridium(III) Phosphorescent Emitters for Highly Efficient, Long‐Life Organic Light‐Emitting Diodes (2009)

Rational design and synthesis of Ir(III) complexes (1-3) bearing two cyclometalated ligands (C--N) and one 2-(diphenylphosphino)phenolate chelate (P--O) as well as the corresponding Ir(III) derivatives (4-6) with only one (C--N) ligand and two P--O chelates are reported, where (C--NH)=phenylpyridine (ppyH), 1-phenylisoquinoline (piqH), and 4-phenylquinazoline (nazoH). Single crystal X-ray diffraction studies of 3 reveal a distorted octahedral coordination geometry, in which two nazo ligands adopt an eclipsed configuration, with the third P--O ligand located trans to the phenyl group of both nazo ligands, confirming the general skeletal pattern for 1-3. In sharp contrast, complex 4 reveals a trans-disposition for the PPh2 groups, along with the phenolate groups residing opposite the unique cyclometalated ppy ligand, which is the representative structure for 4-6. These Ir(III) complexes exhibit green-to-red photoluminescence with moderate to high quantum efficiencies in the degassed fluid state and bright emission in the solid state. For 1-6, the resolved emission spectroscopy and relaxation dynamics are well rationalized by the computational approach. OLEDs fabricated using 12 wt. % of 3 doped in CBP and with BCP as hole blocking material, give bright electroluminescence with lambda(max)=628 nm and CIE(xy) coordinates (0.65, 0.34). The turn-on voltage is 3.2 V, while the current efficiency and the power efficiency reach 11.2 cd A(-1) and 4.5 lm W(-1) at 20 mA cm(-2). The maximum efficiency reaches 14.7 cd A(-1)and 6.8 lm W(-1) upon switching to TPBI as hole blocking material. For evaluating device lifespan, the tested device incorporating CuPc as a passivation layer, 3 doped in CTP as an emitting layer, and BAlq as hole blocking material, shows a remarkably long lifetime up to 36,000 h at an initial luminance of 500 cd m(-2).
Analysis of a conserved cellulase transcriptional regulator reveals inducer‐independent production of cellulolytic enzymes in <i>Neurospora crassa</i> (2013)

Cellulose is recalcitrant to deconstruction to glucose for use in fermentation strategies for biofuels and chemicals derived from lignocellulose. In Neurospora crassa, the transcriptional regulator, CLR-2, is required for cellulolytic gene expression and cellulose deconstruction. To assess conservation and divergence of cellulase gene regulation between fungi from different ecological niches, we compared clr-2 function with its ortholog (clrB) in the distantly related species, Aspergillus nidulans. Transcriptional profiles induced by exposure to crystalline cellulose were similar in both species. Approximately 50% of the cellulose-responsive genes showed strict dependence on functional clr-2/clrB, with a subset of 28 genes encoding plant biomass degrading enzymes that were conserved between N. crassa and A. nidulans. Importantly, misexpression of clr-2 under noninducing conditions was sufficient to drive cellulase gene expression, secretion, and activity in N. crassa, to a level comparable to wild type exposed to Avicel. However, misexpression of clrB in A. nidulans was not sufficient to drive cellulase gene expression under noninducing conditions, although an increase in cellulase activity was observed under crystalline cellulose conditions. Manipulation of clr-2 orthologs among filamentous fungi may enable regulated cellulosic enzyme production in a wide array of culture conditions and host strains, potentially reducing costs associated with enzyme production for plant cell wall deconstruction. However, this functionality may require additional engineering in some species.
Demonstration of rare protein in the outer membrane of Treponema pallidum subsp. pallidum by freeze-fracture analysis (1989)

The surface of Treponema pallidum subsp. pallidum (T. pallidum), the etiologic agent of syphilis, appears antigenically inert and lacks detectable protein, as judged by immunocytochemical and biochemical techniques commonly used to identify the outer membrane (OM) constituents of gram-negative bacteria. We examined T. pallidum by freeze-fracture electron microscopy to visualize the architecture of its OM. Treponema phagedenis biotype Reiter (T. phagedenis Reiter), a nonpathogenic host-associated treponeme, and Spirochaeta aurantia, a free-living spirochete, were studied similarly. Few intramembranous particles interrupted the smooth convex and concave fracture faces of the OM of T. pallidum, demonstrating that the OM of this organism is an unusual, nearly naked lipid bilayer. In contrast, the concave fracture face of the OM of S. aurantia was densely covered with particles, indicating the presence of abundant integral membrane proteins, a feature shared by typical gram-negative organisms. The concentration of particles in the OM concave fracture face of T. phagedenis Reiter was intermediate between those of T. pallidum and S. aurantia. Similar to typical gram-negative bacteria, the OM convex fracture faces of the three spirochetes contained relatively few particles. The unique molecular architecture of the OM of T. pallidum can explain the puzzling in vitro properties of the surface of the organism and may reflect a specific adaptation by which treponemes evade the host immune response.
Electrical impedance scanning as a new breast cancer risk stratification tool for young women (2007)

EIS can identify a subset of young women with a relative probability of breast cancer almost five times greater than in the population of young women at-large. T-Scan+ women have a sufficiently high risk of Br-Ca to warrant further surveillance or imaging.
Anti-AIDS (Acquired Immune Deficiency Syndrome) Agents. 17. New Brominated Hexahydroxybiphenyl Derivatives as Potent Anti-HIV Agents (1995)

Sixteen biphenyl derivatives were synthesized and evaluated for their inhibitory activity against HIV-1 replication in acutely infected H9 cells. 3-Bromo- (4) and 3,3'-dibromo-4,4'-dimethoxy-5,6,5',6'-bis(methylenedioxy)-2,2'- bis(methoxycarbonyl)biphenyl (5) demonstrated potent anti-HIV activity with EC50 values of 0.52 and 0.23 micrograms/mL and therapeutic index values of > 190 and > 480, respectively. A comparison of the anti-HIV activity of these biphenyl derivatives suggested that the types of substituents on the phenolic hydroxy groups rather than the number of bromine(s) on the aromatic rings are important to the enhanced anti-HIV activity. Compounds 4 and 5 also showed potent inhibitory activity against HIV-1 reverse transcriptase in a template-primer dependent manner. The site of inhibition of HIV could be related to inhibition of this enzyme. Compounds 4 and 5 did not induce virus expression from the chronic HIV-1-infected cell lines ACH-2 and U1. Furthermore, these two agents did not inhibit an increase in virus production from the chronic HIV-1-infected cell lines when the phorbol ester PMA was present.
Use of Functionalized Filter Medium for Nutrient Removal in Stormwater Ponds (2010)

Many best-management practices (BMPs) currently used in urban regions have been developed to minimize flood risk, sustain downstream ecosystems, and secure the quality of groundwater sources either directly or indirectly. One such BMP is the reuse of Stormwater by removing nutrients from the nutrient-laden “first flush” water collected in wet or dry ponds; this practice has led to the development of multifunctional sorption materials. In the interests of sustainable infrastructure, this chapter describes a design philosophy for proper use of functionalized green sorption or filter media placed in Stormwater ponds for nutrient removal. The chapter includes a thorough literature review of past uses of green sorption media and also describes the results of a laboratory column test conducted to mimic a field environment and evaluate the feasibility of the design philosophy. This approach to Stormwater treatment has “green” implications because it includes recycled material in the sorption media to promote treatment efficiency and effectiveness. Such design strategies may be extended to enhance the sustainability of low-impact developments such as rain gardens, bioswales, and green roofs where plants, sorption media, and soils naturally filter nutrients and other pollutants from Stormwater.
Hydrogen Peroxide– and Peroxynitrite-Induced Mitochondrial DNA Damage and Dysfunction in Vascular Endothelial and Smooth Muscle Cells (2000)

The mechanisms by which reactive species (RS) participate in the development of atherosclerosis remain incompletely understood. The present study was designed to test the hypothesis that RS produced in the vascular environment cause mitochondrial damage and dysfunction in vitro and, thus, may contribute to the initiating events of atherogenesis. DNA damage was assessed in vascular cells exposed to superoxide, hydrogen peroxide, nitric oxide, and peroxynitrite. In both vascular endothelial and smooth muscle cells, the mitochondrial DNA (mtDNA) was preferentially damaged relative to the transcriptionally inactive nuclear beta-globin gene. Similarly, a dose-dependent decrease in mtDNA-encoded mRNA transcripts was associated with RS treatment. Mitochondrial protein synthesis was also inhibited in a dose-dependent manner by ONOO(-), resulting in decreased cellular ATP levels and mitochondrial redox function. Overall, endothelial cells were more sensitive to RS-mediated damage than were smooth muscle cells. Together, these data link RS-mediated mtDNA damage, altered gene expression, and mitochondrial dysfunction in cell culture and reveal how RS may mediate vascular cell dysfunction in the setting of atherogenesis.
Nanophase Magnetic Materials: Synthesis and Properties (1999)

Abstract Self-assembly preparative techniques in confined media that lead to magnetic materials with nanometer dimensions are described. Synthesis of nanoparticles using the restricted environments offered by surfactant systems such as water-in-oil microemulsions (reverse micelles) provide excellent control over particle size, inter-particle spacing, and particle shape. These environments have been used in the synthesis of γ-Fe2O3, Fe3O4, MnFe2O4, CoFe2O4, Fe and Fe/Au with particle sizes ranging from 10–20 nm. The controlled environment of the reverse micelle also allows sequential synthesis, which can produce a core-shell type structure (e.g., iron nanoparticles with gold coatings). Lyotropic liquid crystal media also offer template effects for the synthesis of non-spherical magnetic nanostructures. The structures, theory and modeling concepts and novel physical properties of these materials are discussed with emphasis given to the differences between course and fine grained magnetic materials.
(Vinyloxy)chlorocyclotriphosphazenes (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT(Vinyloxy)chlorocyclotriphosphazenesKolikkara Ramachandran and Christopher W. AllenCite this: Inorg. Chem. 1983, 22, 10, 1445–1448Publication Date (Print):May 1, 1983Publication History Published online1 May 2002Published inissue 1 May 1983https://doi.org/10.1021/ic00152a006Request reuse permissionsArticle Views142Altmetric-Citations36LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (563 KB) Get e-Alertsclose Get e-Alerts
Synthetic Glycolipid Adjuvants (1976)

Abstract In the course of the organic synthesis of model compounds similar in some features to the lipid moiety of endotoxic lipopolysaccharide (LPS), N-acylated-D-glucosamine derivatives were prepared. One of these, N-palmitoyl-D-glucosamine, has been previously found to be mitogenic for athymic nude mouse B cells. This and other N-acylated homologs were tested for adjuvant activity in the immune response to human γ-globulin (HGG) and sheep red blood cells (SRBC) in mice. Comparable or superior enhancement of the immune response was obtained for these glycolipids when compared to LPS in assays measuring anti-SRBC or HGG hemagglutinin titers. In the determination of hemolytic plaque formation, considerable adjuvant effect was shown by the lauroyl derivative, and less but still significant enhancement was achieved by the N-palmitoyl-d-glucosamine. In the rosette formation assay, in addition to the above two glycolipids, N-oleyl-D-glucosamine showed good adjuvant effect. In the latter two assays, the LPS was a superior adjuvant as compared to the synthetic glycolipids. The radiation protective effect of some of the better synthetic adjuvants was also investigated in mice. It was found that although LPS was more effective in this assay, the N-myristoyl-D-glucosamine and N-decanoyl-d-glucosamine compounds gave a definite protection, since up to 40% of the lethally irradiated (700 R) mice survived.
Engineering enhanced protein disaggregases for neurodegenerative disease (2015)

Protein misfolding and aggregation underpin several fatal neurodegenerative diseases, including Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). There are no treatments that directly antagonize the protein-misfolding events that cause these disorders. Agents that reverse protein misfolding and restore proteins to native form and function could simultaneously eliminate any deleterious loss-of-function or toxic gain-of-function caused by misfolded conformers. Moreover, a disruptive technology of this nature would eliminate self-templating conformers that spread pathology and catalyze formation of toxic, soluble oligomers. Here, we highlight our efforts to engineer Hsp104, a protein disaggregase from yeast, to more effectively disaggregate misfolded proteins connected with PD, ALS, and FTD. Remarkably subtle modifications of Hsp104 primary sequence yielded large gains in protective activity against deleterious α-synuclein, TDP-43, FUS, and TAF15 misfolding. Unusually, in many cases loss of amino acid identity at select positions in Hsp104 rather than specific mutation conferred a robust therapeutic gain-of-function. Nevertheless, the misfolding and toxicity of EWSR1, an RNA-binding protein with a prion-like domain linked to ALS and FTD, could not be buffered by potentiated Hsp104 variants, indicating that further amelioration of disaggregase activity or sharpening of substrate specificity is warranted. We suggest that neuroprotection is achievable for diverse neurodegenerative conditions via surprisingly subtle structural modifications of existing chaperones.
Alkylidenediquinocyclopropanes. Synthesis and properties (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAlkylidenediquinocyclopropanes. Synthesis and propertiesKoichi Komatsu, Robert West, and Douglas BeyerCite this: J. Am. Chem. Soc. 1977, 99, 19, 6290–6296Publication Date (Print):September 1, 1977Publication History Published online1 May 2002Published inissue 1 September 1977https://pubs.acs.org/doi/10.1021/ja00461a018https://doi.org/10.1021/ja00461a018research-articleACS PublicationsRequest reuse permissionsArticle Views131Altmetric-Citations15LEARN 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
Mitochondrial Nitroreductase Activity Enables Selective Imaging and Therapeutic Targeting (2016)

Nitroreductase (NTR) activities have been known for decades, studied extensively in bacteria and also in systems as diverse as yeast, trypanosomes, and hypoxic tumors. The putative bacterial origin of mitochondria prompted us to explore the possible existence of NTR activity within this organelle and to probe its behavior in a cellular context. Presently, by using a profluorescent near-infrared (NIR) dye, we characterize the nature of NTR activity localized in mammalian cell mitochondria. Further, we demonstrate that this mitochondrially localized enzymatic activity can be exploited both for selective NIR imaging of mitochondria and for mitochondrial targeting by activating a mitochondrial poison specifically within that organelle. This constitutes a new mechanism for mitochondrial imaging and targeting. These findings represent the first use of mitochondrial enzyme activity to unmask agents for mitochondrial fluorescent imaging and therapy, which may prove to be more broadly applicable.
Preclinical assessment of clinically streamlined, <scp>3D‐printed</scp>, biocompatible single‐ and two‐stage tissue scaffolds for ear reconstruction (2020)

Auricular reconstruction is a technically demanding procedure requiring significant surgical expertise, as the current gold standard involves hand carving of the costal cartilage into an auricular framework and re-implantation of the tissue. 3D-printing presents a powerful tool that can reduce technical demands associated with the procedure. Our group compared clinical, radiological, histological, and biomechanical outcomes in single- and two-stage 3D-printed auricular tissue scaffolds in an athymic rodent model. Briefly, an external anatomic envelope of a human auricle was created using DICOM computed tomography (CT) images and modified in design to create a two-stage, lock-in-key base and elevating platform. Single- and two-stage scaffolds were 3D-printed by laser sintering poly-L-caprolactone (PCL) then implanted subcutaneously in five athymic rats each. Rats were monitored for ulcer formation, site infection, and scaffold distortion weekly, and scaffolds were explanted at 8 weeks with analysis using microCT and histologic staining. Nonlinear finite element analysis was performed to determine areas of high strain in relation to ulcer formation. Scaffolds demonstrated precise anatomic appearance and maintenance of integrity of both anterior and posterior auricular surfaces and scaffold projection, with no statistically significant differences in complications noted between the single- and two-staged implantation. While minor superficial ulcers occurred most commonly at the lateral and superior helix coincident with finite element predictions of high skin strains, evidence of robust tissue ingrowth and angiogenesis was visible grossly and histologically. This promising preclinical small animal model supports future initiatives for making clinically viable options for an ear tissue scaffold.