gebhart/patrepeval huggingface dataset:
Synergistic Color Variants of Aureobasidium Pullulans (1975)

SUMMARYColor variants of Aureobasidium pullulans were isolated from materials collected in tropical and subtropical regions of the world. Three different types of variants produce colonies that are either yellow, red, or purple. When the variants are either mixed with or grown near many different species of yeasts and other microfungi, the rapidity and intensity with which pigment is produced are markedly enhanced. Yellow variants are moderately unstable and change to red. The red variaants are highly unstable, changing to yellow. Reversion to the normal wild type is seldom observed. Addition of acid or base causes the pigments to function as pH indicators. Pigment formation is temperature sensitive and mixtures of variants and elicitor strains are colorless at 35 C, but show typical enhancement of pigmentation when removed to 25 C. Variants incubated alone at 35 C show temporary intense pigmentation upon removal to 25 C.
Deformation of DNA molecules by hydrodynamic focusing (2003)

The motion of a DNA molecule in a solvent flow reflects the deformation of a nano/microscale flexible mass–spring structure by the forces exerted by the fluid molecules. The dynamics of individual molecules can reveal both fundamental properties of the DNA and basic understanding of the complex rheological properties of long-chain molecules. In this study, we report the dynamics of isolated DNA molecules under homogeneous extensional flow. Hydrodynamic focusing generates homogeneous extensional flow with uniform velocity in the transverse direction. The deformation of individual DNA molecules in the flow was visualized with video fluorescence microscopy. A coil–stretch transition was observed when the Deborah number ( De ) is larger than 0.8. With a sudden stopping of the flow, the DNA molecule relaxes and recoils. The longest relaxation time of T2 DNA was determined to be 0.63 s when scaling viscosity to 0.9 cP.
Giftedness and evidence for reproducibly superior performance: an account based on the expert performance framework (2007)

Giftedness researchers have long debated whether there is empirical evidence to support a distinction between giftedness and attained level of achievement. In this paper we propose a general theoretical framework that establishes scientific criteria for acceptable evidence of superior reproducible performance, which any theory of exceptional performance must explain. We review evidence for superior reproducible performance, generally emerging only after extended periods of deliberate practice that result in subsequent physiological adaptations and complex cognitive mechanisms. We also apply this framework to examine proposed evidence for innate talents. With the exception of fixed genetic factors determining body size and height, we were unable to find evidence for innate constraints to the attainment of elite achievement for healthy individuals.
Effect of NKG2D ligand expression on host immune responses (2010)

Natural killer group 2, member D (NKG2D) is an activating receptor present on the surface of natural killer (NK) cells, some NKT cells, CD8(+) cytotoxic T cells, gammadelta T cells, and under certain conditions CD4(+) T cells. Present in both humans and mice, this highly conserved receptor binds to a surprisingly diverse family of ligands that are distant relatives of major histocompatibility complex class I molecules. There is increasing evidence that ligand expression can result in both immune activation (tumor clearance, viral immunity, autoimmunity, and transplantation) and immune silencing (tumor evasion). In this review, we describe this family of NKG2D ligands and the various mechanisms that control their expression in stressed and normal cells. We also discuss the host response to both membrane-bound and secreted NKG2D ligands and summarize the models proposed to explain the consequences of this differential expression.
Immortalized N/TERT keratinocytes as an alternative cell source in 3D human epidermal models (2017)

The strong societal urge to reduce the use of experimental animals, and the biological differences between rodent and human skin, have led to the development of alternative models for healthy and diseased human skin. However, the limited availability of primary keratinocytes to generate such models hampers large-scale implementation of skin models in biomedical, toxicological, and pharmaceutical research. Immortalized cell lines may overcome these issues, however, few immortalized human keratinocyte cell lines are available and most do not form a fully stratified epithelium. In this study we compared two immortalized keratinocyte cell lines (N/TERT1, N/TERT2G) to human primary keratinocytes based on epidermal differentiation, response to inflammatory mediators, and the development of normal and inflammatory human epidermal equivalents (HEEs). Stratum corneum permeability, epidermal morphology, and expression of epidermal differentiation and host defence genes and proteins in N/TERT-HEE cultures was similar to that of primary human keratinocytes. We successfully generated N/TERT-HEEs with psoriasis or atopic dermatitis features and validated these models for drug-screening purposes. We conclude that the N/TERT keratinocyte cell lines are useful substitutes for primary human keratinocytes thereby providing a biologically relevant, unlimited cell source for in vitro studies on epidermal biology, inflammatory skin disease pathogenesis and therapeutics.
Adhesion of copper films on ABS polymers deposited in an internal magnet magnetron sputtering system (1979)

In order to metallize ABS polymer surfaces without electroless plating, thin copper films were deposited by an internal magnet, coaxial cylindrical magnetron sputtering system. The adhesion of the metallized layers was evaluated by measuring peel strength. Average strength higher than 1 kg/cm was obtained with an appropriate process of metallizing. Several factors, which might influence the adhesion, such as conditions of sputtering, pretreatment of the polymer before sputtering, and the constitution of the polymer were studied. Oxygen plasma treatment before the metallization was found to improve the adhesion. Topographical change of the polymer surface was observed with SEM for the oxygen-plasma-treated substrate. Also, surface change in atomic constitution and chemical bonding energies were detected by ESCA and ir spectroscopy. It was found that the peel strength was higher for substrates of smaller butadiene content, which implied that tensile strength of polymer affected the peel strength of the metallized layer.
Antibody Discovery Ex Vivo Accelerated by the LacO/LacI Regulatory Network (2012)

Monoclonal antibodies (mAbs) can be potent and highly specific therapeutics, diagnostics and research reagents. Nonetheless, mAb discovery using current in vivo or in vitro approaches can be costly and time-consuming, with no guarantee of success. We have established a platform for rapid discovery and optimization of mAbs ex vivo. This DTLacO platform derives from a chicken B cell line that has been engineered to enable rapid selection and seamless maturation of high affinity mAbs. We have validated the DTLacO platform by generation of high affinity and specific mAbs to five cell surface targets, the receptor tyrosine kinases VEGFR2 and TIE2, the glycoprotein TROP2, the small TNF receptor family member FN14, and the G protein-coupled receptor FZD10. mAb discovery is rapid and humanization is straightforward, establishing the utility of the DTLacO platform for identification of mAbs for therapeutic and other applications.
Development of Protein-based Inhibitors of the Proprotein of Convertase SKI-1/S1P (2004)

Processing of membrane-bound transcription factors such as sterol regulatory element-binding proteins (SREBPs) and the ER-stress response factor ATF6, and glycoproteins of some hemorrhagic fever viruses are initiated by the proprotein convertase SKI-1/S1P. So far, no cellular protein-based inhibitor of the hydrophobic-amino acid specific SKI-1 is known. The prosegment of the basic-amino acid specific convertases (e.g. furin and PC5) or alpha(1)-PDX, a variant of alpha(1)-antitrypsin (alpha(1)-AT) exhibiting an RIPR(358) sequence at the reactive site loop, were shown to potently inhibit these secretory proteinases. Accordingly, we tested the SKI-1-inhibitory potential of various point mutants of either the 198 amino acid preprosegment of SKI-1-(1-198) or alpha(1)-AT. Transient transfections data showed that, out of numerous mutants studied, the R134E prosegment mutant or the alpha(1)-AT reactive site loop variants RRVL(358), RRYL(358) and RRIL(358) are the best specific cellular inhibitors of SKI-1. The observed inhibition of the processing of endogenous SREBP-2, exogenous ATF6 and a PDGF-A (RRLL(86)) variant were >55% and reach approximately 80% in stable transfectants. We also show that SKI-1 forms SDS-stable complexes with these alpha(1)-AT variants, but not with wild-type alpha(1)-AT or alpha(1)-PDX. Finally, these inhibitors were also shown to affect the processing and stability of the Crimean-Congo hemorrhagic fever virus glycoprotein.
Striving towards the Deployment of Bio-Energy with Carbon Capture and Storage (BECCS): A Review of Research Priorities and Assessment Needs (2018)

Assessing the performance or the implications of climate change mitigation options (CCMOs) is instrumental in achieving research and innovation efficiency in the field of climate change and becomes more imperative considering the Paris Agreement (‘the Agreement’). Many climate scientists already believe that meeting the Agreement’s goals and stabilizing “well-below 2 °C above pre-industrial levels” signals the deployment of currently undetermined and contentious mitigation technologies, such as bio-energy with carbon capture and storage (BECCS). BECCS is considered one of the most promising negative emissions technologies (NETs) with many scenarios already exhibiting its mitigation potential. However, stakeholders and policymakers remain skeptical about widespread reliance on BECCS questioning its unproven credibility. In this article, we aim at identifying research priorities and assessment needs to intensify the further deployment of BECCS, considering relevant technology associations’ and platforms’ perspectives and insights raised by scientific literature. The main outcome of our study is a list of 10 research priorities along with more specific assessment needs for each priority area. We also focus attention on several implications for potential end-users involved in the field of policy and practice. Overall, our work seeks to bridge the gap between market/industry and academia and to assist policymakers to make better-informed decisions.
Morphologic Analysis of Bipolar Radiofrequency Lesions: Implications for Treatment of the Sacroiliac Joint (2005)

Bipolar radiofrequency treatment creates continuous "strip" lesions proportional in size to the distance between the probes when the distance between cannulae is 6 mm or less. Spacing the cannulae 4 to 6 mm apart and treating at 90 degrees C for 120 to 150 seconds maximizes the surface area of the lesion.
Nonmechanical microscanning using optical space-fed phased arrays (1994)

A method for microscanning in imaging sensors is developed that allows liquid-crystal beam steerers to be used as nonmechanical microscan devices. This submicroscanning method involves using the beam steerers to shift images on a focal-plane array by a fraction of the amount used in typical microscan methods. Interpolation techniques based on interlaced sampling are used to produce images free of aliasing out to twice the Nyquist frequency determined by the focal-plane array. Since a continuous phase ramp is produced by the liquid-crystal beam steerer, dispersion effects due to the gratinglike nature of the devices are avoided. Simulations for both one- and two-dimensional cases are presented, as well as experimental results using a 3- to 5-μm imaging sensor and a liquid-crystal beam steerer designed for operation at 1.064 μm.
Association between Hepatocyte Nuclear Factor 6 (HNF-6) and FoxA2 DNA Binding Domains Stimulates FoxA2 Transcriptional Activity but Inhibits HNF-6 DNA Binding (2002)

In previous studies we used transgenic mice or recombinant adenovirus infection to increase hepatic expression of forkhead box A2 (FoxA2, previously called hepatocyte nuclear factor 3beta [HNF-3beta]), which caused diminished hepatocyte glycogen levels and reduced expression of glucose homeostasis genes. Because this diminished expression of FoxA2 target genes was associated with reduced levels of the Cut-Homeodomain HNF-6 transcription factor, we conducted the present study to determine whether there is a functional interaction between HNF-6 and FoxA2. Human hepatoma (HepG2) cotransfection assays demonstrated that HNF-6 synergistically stimulated FoxA2 but not FoxA1 or FoxA3 transcriptional activity, and protein-binding assays showed that this protein interaction required the HNF-6 Cut-Homeodomain and FoxA2 winged-helix DNA binding domains. Furthermore, we show that the HNF-6 Cut-Homeodomain sequences were sufficient to synergistically stimulate FoxA2 transcriptional activation by recruiting the p300/CBP coactivator proteins. This was supported by the fact that FoxA2 transcriptional synergy with HNF-6 was dependent on retention of the HNF-6 Cut domain LXXLL sequence, which mediated recruitment of the p300/CBP proteins. Moreover, cotransfection and DNA binding assays demonstrated that increased FoxA2 levels caused a decrease in HNF-6 transcriptional activation of the glucose transporter 2 (Glut-2) promoter by interfering with the binding of HNF-6 to its target DNA sequence. These data suggest that at a FoxA-specific site, HNF-6 serves as a coactivator protein to enhance FoxA2 transcription, whereas at an HNF-6-specific site, FoxA2 represses HNF-6 transcription by inhibiting HNF-6 DNA binding activity. This is the first reported example of a liver-enriched transcription factor (HNF-6) functioning as a coactivator protein to potentiate the transcriptional activity of another liver factor, FoxA2.
SERS as a bioassay platform: fundamentals, design, and applications (2008)

Bioanalytical science is experiencing a period of unprecedented growth. Drivers behind this growth include the need to detect markers central to human and veterinary diagnostics at ever-lower levels and greater speeds. A set of parallel arguments applies to pathogens with respect to bioterrorism prevention and food and water safety. This tutorial review outlines our recent explorations on the use of surface enhanced Raman scattering (SERS) for detection of proteins, viruses, and microorganisms in heterogeneous immunoassays. It will detail the design and fabrication of the assay platform, including the capture substrate and nanoparticle-based labels. The latter, which is the cornerstone of our strategy, relies on the construction of gold nanoparticles modified with both an intrinsically strong Raman scatterer and an antibody. This labelling motif, referred to as extrinsic Raman labels (ERLs), takes advantage of the well-established signal enhancement of scatterers when coated on nanometre-sized gold particles, whereas the antibody imparts antigenic specificity. We will also examine the role of plasmon coupling between the ERLs and capture substrate, and challenges related to particle stability, nonspecific adsorption, and assay speed.
Early delayed‐type hypersensitivity eosinophil infiltrates depend on T helper 2 cytokines and interferon‐γ via CXCR3 chemokines (2004)

We investigated the role of T helper (Th)1- and Th2-type cytokines in delayed-type hypersensitivity to soluble protein antigens elicited early postimmunization. Mice were sensitized by intradermal injection without adjuvants, or subcutaneously with complete Freund's adjuvant, and subsequently ear challenged intradermally. As soon as day 3, antigen-specific eosinophil-rich responses were elicited in wild-type mice, but not in T-cell receptor-alpha-/- mice without adjuvant. Draining lymph node T cells stimulated with antigen secreted interleukin (IL)-4, IL-5 and interferon-gamma (IFN-gamma). IFN-gamma-dependent specific immunoglobulin G (IgG)2a and IL-4-dependent IgG1 were also generated. Delayed-type hypersensitivity ear swelling and local eosinophil recruitment were decreased in IL-5-/-, IL-4-/- and signal transducer and activator of transcription-6 (STAT-6)-/- mice, and with anti-IL-4 treatment of wild-type mice, suggesting Th2 mechanisms. Interestingly, responses were also decreased in IFN-gamma-/- mice, and IFN-gamma protein and the IFN-gamma-inducible CXC chemokine, IP-10, were present in 24-hr ear tissue extracts, suggesting Th1 effects. Finally, ear swelling, total histology and eosinophils were decreased in mice deficient in CXCR3, the chemokine receptor for IP-10. These results suggest that both a Th2-like (IL-5, IL-4 and STAT-6) and a Th1-like (IFN-gamma, IP-10, CXCR3) pathway contribute to eosinophil recruitment in early delayed-type hypersensitivity.
Constitutive mitogen-activated protein kinase activation in melanoma is mediated by both BRAF mutations and autocrine growth factor stimulation. (2003)

Dysregulated activation of Ras or its downstream effectors such as mitogen-activated protein kinase kinase and ERK has been shown to play a critical role in tumorigenesis of many cancer types. However, in melanoma, activating mutations in Ras are rarely observed and are limited to N-Ras in UV-exposed cells. In this study, we identify constitutively activated ERK in almost all melanoma cell lines and in tumor tissues tested, which is in contrast to normal melanocytes and several early stage radial growth phase melanoma lines where ERK can be activated by serum or growth factors. Constitutive activation of ERK is preceded by phosphorylation of mitogen-activated protein kinase kinase and c-RAF. In all of the melanoma cell lines tested, Ras is constitutively activated without underlying mutations. On the contrary, activating mutations in the kinase domain of BRAF are present in the majority of the cell lines tested. Furthermore, ERK activation can be partially inhibited from the cell surface using inhibitors of fibroblast growth factor and hepatocyte growth factor but not interleukin 8 signaling pathways. These data suggest that melanoma growth, invasion, and metastasis are attributable to constitutively activated ERK apparently mediated by excessive growth factors through autocrine mechanisms and BRAF kinase activation.
CD8 T‐cell priming upon mRNA vaccination is restricted to bone‐marrow‐derived antigen‐presenting cells and may involve antigen transfer from myocytes (2015)

Self-amplifying mRNAs (SAM(®) ) are a novel class of nucleic acid vaccines, delivered by a non-viral delivery system. They are effective at eliciting potent and protective immune responses and are being developed as a platform technology with potential to be used for a broad range of targets. However, their mechanism of action has not been fully elucidated. To date, no evidence of in vivo transduction of professional antigen-presenting cells (APCs) by SAM vector has been reported, while the antigen expression has been shown to occur mostly in the muscle fibres. Here we show that bone-marrow-derived APCs rather than muscle cells are responsible for induction of MHC class-I restricted CD8 T cells in vivo, but direct transfection of APCs by SAM vectors is not required. Based on all our in vivo and in vitro data we propose that upon SAM vaccination the antigen is expressed within muscle cells and then transferred to APCs, suggesting cross-priming as the prevalent mechanism for priming the CD8 T-cell response by SAM vaccines.
Synthesis of a Novel Enantiomerically Pure Chlorin as a Potential Subunit for an Artificial Photosynthetic Reaction Center (1997)

The total synthesis of an enantiomerically pure chlorin with two different functional groups as a potential subunit for the construction of artificial photosynthetic reaction centers was achieved.
Synthesis and Characterization of Nitroaromatic Peptoids: Fine Tuning Peptoid Secondary Structure through Monomer Position and Functionality (2009)

N-substituted glycine oligomers, or peptoids, have emerged as an important class of foldamers for the study of biomolecular interactions and for potential use as therapeutic agents. However, the design of peptoids with well-defined conformations a priori remains a formidable challenge. New approaches are required to address this problem, and the systematic study of the role of individual monomer units in the global peptoid folding process represents one strategy. Here, we report our efforts toward this approach through the design, synthesis, and characterization of peptoids containing nitroaromatic monomer units. This work required the synthesis of a new chiral amine building block, (S)-1-(2-nitrophenyl)ethanamine (s2ne), which could be readily installed into peptoids using standard solid-phase peptoid synthesis techniques. We designed a series of peptoid nonamers that allowed us to probe the effects of this relatively electron-deficient and sterically encumbered alpha-chiral side chain on peptoid structure, namely, the peptoid threaded loop and helix. Circular dichroism spectroscopy of the peptoids revealed that the nitroaromatic monomer has a significant effect on peptoid secondary structure. Specifically, the threaded loop structure was disrupted in a nonamer containing alternating N-(S)-1-phenylethylglycine (Nspe) and Ns2ne monomers, and the major conformation was helical instead. Indeed, placement of a single Ns2ne at the N-terminal position of (Nspe)(9) resulted in a destabilized form of the threaded loop structure relative to the homononamer (Nspe)(9). Conversely, we observed that incorporation of N-(S)-1-(4-nitrophenyl)ethylglycine (Nsnp, a p-nitro monomer) at the N-terminal position stabilized the threaded loop structure relative to (Nspe)(9). Additional experiments revealed that nitroaromatic side chains can influence peptoid nonamer folding by modulating the strength of key intramolecular hydrogen bonds in the peptoid threaded loop structure. Steric interactions were also implicated for the Ns2ne monomer. Overall, this study provides further evidence that aromatic side-chain structure, even if perturbed in a single monomer unit, can strongly influence local peptoid backbone conformation.