gebhart/patrepeval huggingface dataset:
Detection of DNA Hybridization via Fluorescent Polymer Superquenching (2002)

An assay for a target single strand 20-base sequence of DNA coding for the anthrax lethal factor, based on conjugated polymer fluorescence superquenching, is reported. The assay employs a platform in which the receptor (a biotinylated complementary sequence "capture strand") and polymer (two components: an anionic poly(phenylene ethynylene) (PPE) and a biotinylated −PPE) are co-located on streptavidin-derivatized polystyrene microspheres. A conjugate of the target strand with the energy transfer quencher QSY-7 (DNA-QTL) is used to construct competition assays for the target. A direct competition assay between the target-DNA and DNA-QTL for the microsphere-bound capture is only marginally successful due evidently to greater kinetic affinity of the polymer-capture ensemble for the conjugate. However a sequential addition of target, followed by DNA-QTL affords a quantitative assay for the target by attenuation of PPE fluorescence quenching by the DNA-QTL. Likewise a direct competition in solution between the target and DNA-QTL for the biotinylated capture strand followed by addition of microspheres provides a sensitive and quantitative assay for the target single strand DNA.
High-Brightness White Organic Light-Emitting Diodes Featuring a Single Emission Layer (2008)

We have developed high-brightness, color-stable, broad-spectrum white organic light-emitting diodes featuring a single emission layer comprising a green light-emitting host material [1,3,5-tris(1-pyrenyl)benzene (TPB3)], which has a large bandgap, doped with red [4-(dicyanomethylene)-2-tert-butyl-6-(1,1,7,7-tetramethyljulolidyl-9-enyl)--pyran (DCJTB)], and blue [di(4-fluoro phenyl)amino-di(styryl)biphenyl (DSB)] dyes. A device having the simple configuration indium tin oxide/-bis(1- naphthyl)--diphenyl--biphenyl--diamine (NPB) /TPB3:0.6% DCJTB:6% DSB /tris(8-hydroxy- quinoline)aluminum exhibited a broad-spectrum white emission with a maximum luminance at of , a maximum current efficiency of at , a maximum power efficiency of at , and a maximum external quantum efficiency of 3.08% at . The Commission Internationale de l'Eclairage coordinates of (0.34, 0.39) changed only slightly over a large range of potentials . We attribute the high brightness and color-stability of this system to the strong electroluminescence of the host and the dopants, the relatively high energy-transfer efficiency from the host to the red dopant, effective carrier-direct-recombination on the blue dopant, and the confinement of the charge recombination zone within a single layer.
Functions of Cell Surface Heparan Sulfate Proteoglycans (1999)

The heparan sulfate on the surface of all adherent cells modulates the actions of a large number of extracellular ligands. Members of both cell surface heparan sulfate proteoglycan families, the transmembrane syndecans and the glycosylphosphoinositide-linked glypicans, bind these ligands and enhance formation of their receptor-signaling complexes. These heparan sulfate proteoglycans also immobilize and regulate the turnover of ligands that act at the cell surface. The extracellular domains of these proteoglycans can be shed from the cell surface, generating soluble heparan sulfate proteoglycans that can inhibit interactions at the cell surface. Recent analyses of genetic defects in Drosophila melanogaster, mice, and humans confirm most of these activities in vivo and identify additional processes that involve cell surface heparan sulfate proteoglycans. This chapter focuses on the mechanisms underlying these activities and on the cellular functions that they regulate.
Inactivation differences of microorganisms by low pressure UV and pulsed xenon lamps (2003)

UV disinfection has been applied to water treatment in recent years with low-pressure and medium-pressure UV lamps mainly used as the light source. In general, UV disinfection is considered to be inefficient with water of high turbidity because of inhibition of light penetration. Additionally, photoreactivation may be a problem that should be considered in case a disinfected water is discharged to the environment where sunlight causes reactivation. Recently, other types of lamps have been proposed including a flush-type lamp (such as a pulsed-xenon lamp) that emits high energy and wide wavelength intermittently. In this study, the difference between inactivation efficiencies by low-pressure UV (LPUV) and pulsed-xenon (PXe) lamps was investigated using two coliphage types and three strains of Escherichia coli. PXe had a suppressive effect on photoreactivation rate of the E. coli strains even though there was no significant effect on inactivation rate and maximum survival ratio after photoreactivation. PXe also had a benefit when applied to high turbidity waters as no tailing phenomena were observed in the low survival ratio area although it was observed in LPUV inactivation. This efficiency difference was considered to be due to the difference in irradiated wavelength of both lamps.
Subunit Association and DNA Binding Activity of the Heterotrimeric Transcription Factor NF-Y Is Regulated by Cellular Redox (1996)

NF-Y is a heterotrimeric transcription factor that specifically recognizes a CCAAT box motif found in a variety of eukaryotic promoter and enhancer elements. The subunit association and DNA binding properties of the NF-Y complex were examined as a function of redox state using recombinant NF-YA, NF-YB, and NF-YC subunits. Reduction of NF-YB by dithiothreitol (DTT) was essential for reconstitution of specific NF-Y CCAAT box DNA binding activity in vitro. Approximately 30% of the Escherichia coli-derived NF-YB subunit existed as intermolecular disulfide-linked dimers. NF-YB mutants in which the highly conserved cysteine residues at positions 85 and 89 had been converted to serines existed only as monomers and did not require DTT for functional NF-Y DNA binding activity. DTT was required, however, for the functional association of NF-YC with wild-type NF-YB but not with the NF-YB cysteine mutants. The cellular redox factors Ref-1 and adult T-cell leukemia-derived factor stimulated the DNA binding activity of recombinant NF-Y in the absence of DTT. Cells treated with 1-chloro-2,4-dinitrobenzene, an irreversible inhibitor of thioredoxin reductase, exhibited reduced endogenous NF-Y DNA binding activity. Together these results suggest that the cellular redox environment of mammalian cells is an important posttranscriptional regulator of NF-Y subunit association and DNA binding activities.
Epidermal Wnt/β-catenin signaling regulates adipocyte differentiation via secretion of adipogenic factors (2014)

It has long been recognized that the hair follicle growth cycle and oscillation in the thickness of the underlying adipocyte layer are synchronized. Although factors secreted by adipocytes are known to regulate the hair growth cycle, it is unclear whether the epidermis can regulate adipogenesis. We show that inhibition of epidermal Wnt/β-catenin signaling reduced adipocyte differentiation in developing and adult mouse dermis. Conversely, ectopic activation of epidermal Wnt signaling promoted adipocyte differentiation and hair growth. When the Wnt pathway was activated in the embryonic epidermis, there was a dramatic and premature increase in adipocytes in the absence of hair follicle formation, demonstrating that Wnt activation, rather than mature hair follicles, is required for adipocyte generation. Epidermal and dermal gene expression profiling identified keratinocyte-derived adipogenic factors that are induced by β-catenin activation. Wnt/β-catenin signaling-dependent secreted factors from keratinocytes promoted adipocyte differentiation in vitro, and we identified ligands for the bone morphogenetic protein and insulin pathways as proadipogenic factors. Our results indicate epidermal Wnt/β-catenin as a critical initiator of a signaling cascade that induces adipogenesis and highlight the role of epidermal Wnt signaling in synchronizing adipocyte differentiation with the hair growth cycle.
Multivalency as a Chemical Organization and Action Principle (2012)

Multivalent interactions can be applied universally for a targeted strengthening of an interaction between different interfaces or molecules. The binding partners form cooperative, multiple receptor-ligand interactions that are based on individually weak, noncovalent bonds and are thus generally reversible. Hence, multi- and polyvalent interactions play a decisive role in biological systems for recognition, adhesion, and signal processes. The scientific and practical realization of this principle will be demonstrated by the development of simple artificial and theoretical models, from natural systems to functional, application-oriented systems. In a systematic review of scaffold architectures, the underlying effects and control options will be demonstrated, and suggestions will be given for designing effective multivalent binding systems, as well as for polyvalent therapeutics.
Modic Vertebral Body Changes (2011)

Our findings reflect the dynamic nature of pathological changes in the spine and have demonstrated that Modic changes are reversible. They also raise further doubt that these MRI changes should be used as an indicator of clinical symptoms or of surgical outcome.
Cloning and molecular characterization of a soluble epoxide hydrolase from Aspergillus niger that is related to mammalian microsomal epoxide hydrolase (1999)

Aspergillus niger strain LCP521 harbours a highly processive epoxide hydrolase (EH) that is of particular interest for the enantioselective bio-organic synthesis of fine chemicals. In the present work, we report the isolation of the gene and cDNA for this EH by use of inverse PCR. The gene is composed of nine exons, the first of which is apparently non-coding. The deduced protein of the A. niger EH shares significant sequence similarity with the mammalian microsomal EHs (mEH). In contrast to these, however, the protein from A. niger lacks the common N-terminal membrane anchor, in line with the fact that this enzyme is, indeed, soluble in its native environment. Recombinant expression of the isolated cDNA in Escherichia coli yielded a fully active EH with similar characteristics to the fungal enzyme. Sequence comparison with mammalian EHs suggested that Asp192, Asp348 and His374 constituted the catalytic triad of the fungal EH. This was subsequently substantiated by the analysis of respective mutants constructed by site-directed mutagenesis. The presence of an aspartic acid residue in the charge-relay system of the A. niger enzyme, in contrast to a glutamic acid residue in the respective position of all mEHs analysed to date, may be one important contributor to the exceptionally high turnover number of the fungal enzyme when compared with its mammalian relatives. Recombinant expression of the enzyme in E. coli offers a versatile tool for the bio-organic chemist for the chiral synthesis of a variety of fine chemicals.
Therapy for macular degeneration: Insights from acne (2003)

Individuals with Stargardt's disease can navigate a crowd by using peripheral vision, but reading and recognizing faces can be onerous and shapes and contours may appear distorted. This progressive and devastating visual impairment reflects the loss of light-absorbing photoreceptor cells in the central area of the retina (macula), which is typical of this juvenile form of macular degeneration (1). Yet to understand the cause of photoreceptor cell degeneration in Stargardt's macular degeneration it is necessary to take into account the retinal pigment epithelium (RPE), a cell layer lying adjacent to the photoreceptor cells. Because the RPE is vital to the integrity of the photoreceptor cells, the demise of RPE cells brings about the loss of photoreceptors (2).
Peripheral nerve repair in humans using muscle autografts. A new technique (1988)

Coaxial autografts of skeletal muscle which had been frozen then thawed were used to repair injured digital nerves in eight patients. Assessment from three to 11 months after operation showed recovery to MRC sensory category S3+ in all but one patient, an excellent level of recovery. We conclude that bespoke muscle grafts treated and used in this way may offer significant advantages over conventional nerve grafts or cable grafts especially where large peripheral nerves are involved.
CD16+ and CD16− human blood monocyte subsets differentiate in vitro to dendritic cells with different abilities to stimulate CD4+ T cells (2001)

Experimental protocols for cancer immunotherapy include the utilization of autologous monocyte-derived dendritic cells (moDC) pulsed with tumor antigens. However, disease can alter the characteristics of monocyte precursors and some patients have increased numbers (up to 40%) of the minor CD16(+) monocyte subpopulation, which in healthy individuals represent 10% of blood monocytes. At the present, the capacity of CD16(+) monocytes to differentiate into DC has not been evaluated. Here, we investigated the ability of CD16(+) monocytes cultured with granulocyte- macrophage colony-stimulating factor, IL-4 and tumor necrosis factor-alpha to generate DC in vitro, and we compared them to DC derived from regular CD16(-) monocytes. Both monocyte subsets gave rise to cells with DC characteristics. They internalized soluble and particulate antigens similarly, and both were able to stimulate T cell proliferation in autologous and allogeneic cultures. Nevertheless, CD16(+) moDC expressed higher levels of CD86, CD11a and CD11c, and showed lower expression of CD1a and CD32 compared to CD16(-) moDC. Lipopolysaccharide-stimulated CD16(-) moDC expressed increased levels of IL-12 p40 mRNA and secreted greater amounts of IL-12 p70 than CD16(+) moDC, whereas levels of transforming growth factor-beta1 mRNA were higher on CD16(+) moDC. Moreover, CD4(+) T cells stimulated with CD16(+) moDC secreted increased amounts of IL-4 compared to those stimulated by CD16(-) moDC. These data demonstrate that both moDC are not equivalent, suggesting either that they reach different stages of maturation during the culture or that the starting monocytes belong to cell lineages with distinct differentiation capabilities.
Statistical modeling and analysis of the LAGLIDADG family of site- specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family (1997)

The LAGLIDADG and HNH families of site-specific DNA endonucleases encoded by viruses, bacteriophages as well as archaeal, eucaryotic nuclear and organellar genomes are characterized by the sequence motifs 'LAGLIDADG' and 'HNH', respectively. These endonucleases have been shown to occur in different environments: LAGLIDADG endonucleases are found in inteins, archaeal and group I introns and as free standing open reading frames (ORFs); HNH endonucleases occur in group I and group II introns and as ORFs. Here, statistical models (hidden Markov models, HMMs) that encompass both the conserved motifs and more variable regions of these families have been created and employed to characterize known and potential new family members. A number of new, putative LAGLIDADG and HNH endonucleases have been identified including an intein-encoded HNH sequence. Analysis of an HMM-generated multiple alignment of 130 LAGLIDADG family members and the three-dimensional structure of the I- Cre I endonuclease has enabled definition of the core elements of the repeated domain (approximately 90 residues) that is present in this family of proteins. A conserved negatively charged residue is proposed to be involved in catalysis. Phylogenetic analysis of the two families indicates a lack of exchange of endonucleases between different mobile elements (environments) and between hosts from different phylogenetic kingdoms. However, there does appear to have been considerable exchange of endonuclease domains amongst elements of the same type. Such events are suggested to be important for the formation of elements of new specficity.
Molecularly distilled monoglycerides (1950)

Summary Monoglyceride concentrates of high purity can be readily prepared by molecular distillation. Their properties are, in general, about what would be expected from the high content of monoglycerides and absence of catalyst. The interfacial tension lowering produced by monoglycerides is essentially proportional to the monoester content of the monoglyceride product. In a water absorption test the unsaturated fatty acid monoglycerides are considerably more active than the monoesters of saturated fatty acids.
Engraftment of peripheral blood mononuclear cells from systemic lupus erythematosus and antiphospholipid syndrome patient donors into BALB‐RAG‐2−/−IL‐2Rγ−/− mice: A promising model for studying human disease (2011)

We established a novel humanized SLE-DKO mouse exhibiting many of the immunologic and clinical features of human SLE.
NLA-QAM: A Method for Generating High-Power QAM Signals Through Nonlinear Amplification (1982)

A generalized technique for generating quadrature amplitude modulated (QAM) signals that permits nonlinear amplification is presented. With this technique a high-power <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2^{2n}</tex> -state QAM signal is generated by combining <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</tex> unfiltered, nonlinear amplified, QPSK signals, <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</tex> being a positive integer. The specific methods of generating 16- and 64-state signals using this technique are presented. An attractive feature of the technique is that despite significant difference with the conventional method of generating QAM signals, the same straightforward demodulation techniques apply to both, and the P <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</inf> versus <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S/N</tex> performances are essentially identical. In the 16-state version employing traveling wave tubes (TWT's) or GaAsFET amplifiers, the technique is shown to result in a transmitter output power advantage that is on the order of 5 dB compared to the conventional method. This advantage is achieved, however, at the expense of an additional output power amplifier.
Transmembrane Transport of Diphtheria Toxin, Related Toxins, and Colicins (1986)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Adsorption inhibition as a mechanism of freezing resistance in polar fishes. (1977)

Polar fishes are known to have serum proteins and glycoproteins that protect them from freezing, by a noncolligative process. Measurements of antifreeze concentrations in ice and scanning electron micrographs of freeze-dried antifreeze solutions indicate that the antifreezes are incorporated in ice during freezing. The antifreezes also have a pronounced effect on the crystal habit of ice grown in their presence. Each of four antifreezes investigated caused ice to grow in long needles whose axes were parallel to the ice c axis. Together these results indicate the antifreezes adsorb to ice surfaces and inhibit their growth. A model in which adsorbed antifreezes raise the curvature of growth steps on the ice surface is proposed to account for the observed depression of the temperature at which freezing occurs and agrees well with experimental observations. The model is similar to one previously proposed for other cases of crystal growth inhibition.
Trust network-based filtering of aggregated claims (2006)

On the semantic web, assertions may be aggregated from many sources, those aggregations filtered, reasoned over, aggregated with other aggregators, displayed, scraped, extracted, recombined, and otherwise processed without significant human oversight. To preserve the connection between assertions and their source, various provenance schemes for semantic web data have been explored. However, the primary focus has been on authenticating the author of a particular statement, e.g., using digital signatures, but there is no provision for relating the authenticity of the source of the assertion and the trustworthiness of the assertion itself. This paper presents a method for using semantic web based trust networks to infer the reputation of sources for a statement and compose the reputation of several sources. By calculating a trust rating for each statement based on the ratings of its sources, the set of statements can be filtered based on the rating.
Synthesis and Characterization of a Lithium-Doped Fullerane (Lix-C60-Hy) for Reversible Hydrogen Storage (2011)

Herein, we present a lithium-doped fullerane (Li(x)-C(60)-H(y)) that is capable of reversibly storing hydrogen through chemisorption at elevated temperatures and pressures. This system is unique in that hydrogen is closely associated with lithium and carbon upon rehydrogenation of the material and that the weight percent of H(2) stored in the material is intimately linked to the stoichiometric ratio of Li:C(60) in the material. Characterization of the material (IR, Raman, UV-vis, XRD, LDI-TOF-MS, and NMR) indicates that a lithium-doped fullerane is formed upon rehydrogenation in which the active hydrogen storage material is similar to a hydrogenated fullerene. Under optimized conditions, a lithium-doped fullerane with a Li:C(60) mole ratio of 6:1 can reversibly desorb up to 5 wt % H(2) with an onset temperature of ~270 °C, which is significantly less than the desorption temperature of hydrogenated fullerenes (C(60)H(x)) and pure lithium hydride (decomposition temperature 500-600 and 670 °C respectively). However, our Li(x)-C(60)-H(y) system does not suffer from the same drawbacks as typical hydrogenated fullerenes (high desorption T and release of hydrocarbons) because the fullerene cage remains mostly intact and is only slightly modified during multiple hydrogen desorption/absorption cycles. We also observed a reversible phase transition of C(60) in the material from face-centered cubic to body-centered cubic at high levels of hydrogenation.
Project snowflake: non-blocking safe manual memory management in .NET (2017)

Garbage collection greatly improves programmer productivity and ensures memory safety. Manual memory management on the other hand often delivers better performance but is typically unsafe and can lead to system crashes or security vulnerabilities. We propose integrating safe manual memory management with garbage collection in the .NET runtime to get the best of both worlds. In our design, programmers can choose between allocating objects in the garbage collected heap or the manual heap. All existing applications run unmodified, and without any performance degradation, using the garbage collected heap. Our programming model for manual memory management is flexible: although objects in the manual heap can have a single owning pointer, we allow deallocation at any program point and concurrent sharing of these objects amongst all the threads in the program. Experimental results from our .NET CoreCLR implementation on real-world applications show substantial performance gains especially in multithreaded scenarios: up to 3x savings in peak working sets and 2x improvements in runtime.