gebhart/patrepeval huggingface dataset:
Secondary structure and hybridization accessibility of the hepatitis C virus negative strand RNA 5′‐terminus (2004)

The positive strand RNA genome of hepatitis C virus (HCV) is transcribed exclusively from a full-length cytoplasmic replication intermediate, the negative strand RNA. Despite this essential role in hepatocellular infection, the negative strand has not yet been subjected to extensive molecular characterization, and in comparison with the HCV genome and proteome, remains relatively unexplored as a target for antiviral therapy. The highly conserved negative strand terminal sequences, complementary to the positive strand 5'- and 3'-untranslated regions, are believed to contribute structural features essential for the initiation of positive strand synthesis and the maintenance of template integrity. We investigated the solution structure of the HCV negative strand 5'-terminal region by endoribonuclease mapping and thermodynamic modelling of RNA secondary structure. The enzymatic probing data are consistent with structural models featuring a large terminal stem loop (SL), which constitutes a mirror image of the complementary 3'-X region SL I structure. Nucleotide positions within the negative strand accessible to hybridization were mapped by RNase H digestion in the presence of combinatorial oligonucleotide libraries. The hybridization data further support the existence of a terminal SL, and reveal target sites within the negative strand 5'-terminus which may be susceptible to antisense-mediated inhibition.
DNA Polymorphism at the Cytosolic Phosphoglucose Isomerase (PgiC) Locus of the Wild Plant Arabidopsis thaliana (2000)

DNA variation in a 4.7-kb region of the cytosolic phosphoglucose isomerase (PgiC) locus was investigated for 21 ecotypes of Arabidopsis thaliana. The estimated nucleotide diversity was 0.0038, which was one-third of those in previously investigated loci. Since most of the nucleotide variations (93%) were singleton and doubleton, Tajima's test statistic was significantly negative. About 50% of nucleotide polymorphisms in exons were replacement, which caused significance in McDonald and Kreitman's test when compared with Arabis gemmifera and Cardaminopsis petraea. These results indicated that DNA polymorphism at the PgiC locus was not under neutrality. There were two divergent sequence types in the PgiC region, which were associated with allozyme variation. The Fast allozyme was shown to have originated from the Slow allozyme, since two outgroup species had the Slow form. A phylogenetic tree of ecotypes with the Fast allozyme had the shape of a star phylogeny. Mismatch distribution of the Fast allozyme ecotypes resembled that expected under an expanding population model. These results suggest positive selection for the Fast allozyme of the PGIC in A. thaliana.
Expression cloning of a novel alpha 1,3-fucosyltransferase that is involved in biosynthesis of the sialyl Lewis x carbohydrate determinants in leukocytes. (1994)

The sialyl Lewis x (NeuAc alpha 2-3Gal beta 1-4(Fuc alpha 1-3)Glc-NAc) determinants serve as ligands in the selectin-mediated adhesion of leukocytes to activated endothelium or platelets. In our efforts to identify glycosyltransferases involved in the biosynthesis of those ligands, we achieved expression cloning of a novel human alpha 1,3-fucosyltransferase termed Fuc-TVII from a THP-1 cDNA library by enrichment of the Namalwa cells highly expressing that determinant with a fluorescence-activated cell sorter. Expression of the COOH-terminal catalytic domain of Fuc-TVII showed an alpha 1,3-fucosyltransferase activity for a type II oligosaccharide with a terminal alpha 2,3-linked sialic acid among various acceptors, consistent with that in vivo acceptor specificity. Alignment of the primary sequences of five alpha 1,3-fucosyltransferases and assignment of the chromosomal location of Fuc-TVII gene, together with that acceptor specificity, indicate that Fuc-TVII consists of a unique class of the alpha 1,3-fucosyltransferase family. Determination of the expression levels of these alpha 1,3-fucosyltransferases in various cells revealed that both Fuc-TVII and a myeloid fucosyltransferase Fuc-TIV were significantly expressed in myeloid lineage cells. Fuc-TVII-transfected Namalwa cells exhibited significant binding to E-selectin in contrast to little binding of the Fuc-TIV-transfected cells. These results suggest that Fuc-TVII may participate in the biosynthesis of the selectin ligands.
Presentation of Ligands on Hydroxylapatite (1997)

Conjugates of biotin with the decamer of glutamic acid (glu10) and the trimer of D,L-2-amino-5-phosphonovaleric acid (I) have been synthesized, and it has been shown that they mediate the binding of avidin to hydroxylapatite. In a similar way a conjugate of methotrexate with glu10 mediates the binding of dihydrofolate reducatase to the mineral. The presentation of ligands on the hydroxylapatite component of bone may find applications in clinical medicine.
Nitrogen Trifluoride: A New Reactant Gas in Chemical Reaction Interface Mass Spectrometry for Detection of Phosphorus, Deuterium, Chlorine, and Sulfur (1995)

A new set of reactions that involve fluorine have been investigated in chemical reaction interface mass spectrometry (CRIMS). The primary goal of this study was to provide a means to selectively detect phosphorus-containing compounds, which fluorine does by generating PF 5 . P F 4 + , the main fragment ion of PF 5 , provides a sensitive (10 pg/s), selective, and linear (> 10 5 dynamic range) channel for phosphorus-containing analytes. This fluorine-rich environment also provides new ways to selectively and simultaneously detect hydrogen isotopes, chlorine, and sulfur. NF 3 as a reactant gas provides the most comprehensive array of elemental and isotopic detection yet available for CRIMS. An application of phosphorus-selective detection was attempted by examination of a plasma sample from a patient who had been treated with cyclophosphamide. The phosphorus-selective channel showed six peaks: one is derivatized phosphate, two are t -butyldimethylsilyl (TBDMS) derivatives of cyclophosphamide, another two are TBDMS derivatives of 4-hydroxy-yclophosphamide, and one is from underivatized cyclophosphamide. The simultaneous detection of chlorinecontaining compounds confirmed our results for those peaks related to cyclophosphamide and its metabolite.
Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes (2018)

The architecture of normal and diseased tissues strongly influences the development and progression of disease as well as responsiveness and resistance to therapy. We describe a tissue-based cyclic immunofluorescence (t-CyCIF) method for highly multiplexed immuno-fluorescence imaging of formalin-fixed, paraffin-embedded (FFPE) specimens mounted on glass slides, the most widely used specimens for histopathological diagnosis of cancer and other diseases. t-CyCIF generates up to 60-plex images using an iterative process (a cycle) in which conventional low-plex fluorescence images are repeatedly collected from the same sample and then assembled into a high-dimensional representation. t-CyCIF requires no specialized instruments or reagents and is compatible with super-resolution imaging; we demonstrate its application to quantifying signal transduction cascades, tumor antigens and immune markers in diverse tissues and tumors. The simplicity and adaptability of t-CyCIF makes it an effective method for pre-clinical and clinical research and a natural complement to single-cell genomics.
Somatic generation of hybrid antibody H chain genes in transgenic mice via interchromosomal gene conversion. (1994)

We have constructed lines of mice with transgenes containing an antibody heavy (H) chain variable region (VHDJH) gene and various amounts of natural immunoglobulin (Ig) and plasmid flanking DNA. In these lines, recombination of the transgene and the endogenous Igh locus takes place in B cells, leading to the expression of functional H chains partially encoded by the transgenic VHDJH gene. Here, we demonstrate that the transgenic VHDJH gene, and various amounts of flanking sequence are recombined with Igh locus DNA via interchromosomal gene conversion. The structures of the resulting "hybrid" transgene-Igh H chain loci are consistent with the 3' end of the conversion occurring in regions of sequence identity, and the 5' end taking place between regions of little or no homology. This mode of antibody transgene recombination with the Igh locus is fundamentally different from the previously reported "trans H chain class switching" that results in reciprocal translocations. In contrast, this recombination resembles events previously observed in mammalian tissue culture cells between adjacent homologous chromosomal sequences, or transfected DNA and a homologous chromosomal target. Our data indicate that this recombination takes place at a low frequency, and that the frequency is influenced by both the length and extent of homology between the transgene and the Igh locus, but is not greatly affected by transgene copy number. This recombination pathway provides a novel approach for the subtle alteration of the clonal composition of the mouse B cell compartment in vivo using VH genes with defined structures and functions.
[Recombinant human bone morphogenetic protein-2 transform NIH3T3 fibroblast to osteo-like cells]. (2004)

50 microg/L rhBMP-2 can transform NIH3T3 fibroblasts to osteo-like cells.
Current Status of Binary Vectors and Superbinary Vectors (2007)

A binary vector was invented soon after it had been elucidated that crown gall tumorigenesis was caused by genetic transformation of plant cells with a piece of DNA, T-DNA for transferred DNA, from a Ti plasmid (tumor-inducing plasmid) harbored by the soil bacterium Agrobacterium tumefaciens ([
C5A Anaphylatoxin and Its Seven Transmembrane-Segment Receptor (1994)

The molecular cloning of the C5a receptor places this molecule in the superfamily of G-protein coupled receptors. This superfamily is characterized by the presence of signature motifs including seven hydrophobic domains which span the cell membrane and impart a predicted serpentine topology to the receptor proteins. The identification of other members of this family, including receptors for the chemokines IL-8 and Mip-1/Rantes, thrombin, formyl peptide, and platelet activating factor, provide new tools for understanding structure-function relationships relevant to the inflammatory process. This review focuses on the recent biological studies concerning the ligand C5a and its cellular receptor, the structure/activity relationships so far discerned, signal transduction mechanisms, progress toward identification of receptor antagonists, and some likely directions for future studies. Where appropriate, relevant work on related seven transmembrane segment receptors is discussed.
Stationary nanoliter droplet array with a substrate of choice for single adherent/nonadherent cell incubation and analysis (2014)

Microfluidic water-in-oil droplets that serve as separate, chemically isolated compartments can be applied for single-cell analysis; however, to investigate encapsulated cells effectively over prolonged time periods, an array of droplets must remain stationary on a versatile substrate for optimal cell compatibility. We present here a platform of unique geometry and substrate versatility that generates a stationary nanodroplet array by using wells branching off a main microfluidic channel. These droplets are confined by multiple sides of a nanowell and are in direct contact with a biocompatible substrate of choice. The device is operated by a unique and reversed loading procedure that eliminates the need for fine pressure control or external tubing. Fluorocarbon oil isolates the droplets and provides soluble oxygen for the cells. By using this approach, the metabolic activity of single adherent cells was monitored continuously over time, and the concentration of viable pathogens in blood-derived samples was determined directly by measuring the number of colony-formed droplets. The method is simple to operate, requires a few microliters of reagent volume, is portable, is reusable, and allows for cell retrieval. This technology may be particularly useful for multiplexed assays for which prolonged and simultaneous visual inspection of many isolated single adherent or nonadherent cells is required.
Automated Detection of Clinically Significant Prostate Cancer in mp-MRI Images Based on an End-to-End Deep Neural Network (2018)

Automated methods for detecting clinically significant (CS) prostate cancer (PCa) in multi-parameter magnetic resonance images (mp-MRI) are of high demand. Existing methods typically employ several separate steps, each of which is optimized individually without considering the error tolerance of other steps. As a result, they could either involve unnecessary computational cost or suffer from errors accumulated over steps. In this paper, we present an automated CS PCa detection system, where all steps are optimized jointly in an end-to-end trainable deep neural network. The proposed neural network consists of concatenated subnets: 1) a novel tissue deformation network (TDN) for automated prostate detection and multimodal registration and 2) a dual-path convolutional neural network (CNN) for CS PCa detection. Three types of loss functions, i.e., classification loss, inconsistency loss, and overlap loss, are employed for optimizing all parameters of the proposed TDN and CNN. In the training phase, the two nets mutually affect each other and effectively guide registration and extraction of representative CS PCa-relevant features to achieve results with sufficient accuracy. The entire network is trained in a weakly supervised manner by providing only image-level annotations (i.e., presence/absence of PCa) without exact priors of lesions' locations. Compared with most existing systems which require supervised labels, e.g., manual delineation of PCa lesions, it is much more convenient for clinical usage. Comprehensive evaluation based on fivefold cross validation using 360 patient data demonstrates that our system achieves a high accuracy for CS PCa detection, i.e., a sensitivity of 0.6374 and 0.8978 at 0.1 and 1 false positives per normal/benign patient.
Micro‐coaxial Ka‐band Gysel power dividers (2009)

Abstract Monolithic, 450‐μm tall, rectangular coaxial Gysel divider is presented in this article. The divider is fabricated by a surface micromachining process with six sequentially deposited copper layers. Athree‐port, resistor‐less divider has overall loss of 0.6 dB at 30 GHz, input port reflection coefficient better than −10 dB, and output amplitude and phase misbalances of ±0.18 dB and ±1.8°, respectively, throughout Ka‐band. The device is designed in a way that permits straightforward realization of a Gysel divider with integrated resistors. Electromagnetic and electrothermal analyses and design of the divider are conducted, and good agreement with measurements is obtained. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 52: 474–478, 2010; Published online in Wiley InterScience (www.interscience. wiley.com). DOI 10.1002/mop.24956
Dimerization of a Specific DNA-Binding Protein on the DNA (1992)

Many specific DNA-binding proteins bind to sites with dyad symmetry, and the bound form of the protein is a dimer. For some proteins, dimers form in solution and bind to DNA. LexA repressor of Escherichia coli has been used to test an alternative binding model in which two monomers bind sequentially. This model predicts that a repressor monomer should bind with high specificity to an isolated operator half-site. Monomer binding to a half-site was observed. A second monomer bound to an intact operator far more tightly than the first monomer; this cooperativity arose from protein-protein contacts.
Composition and Configuration Patterns in Multiple-View Visualizations (2020)

Multiple-view visualization (MV) is a layout design technique often employed to help users see a large number of data attributes and values in a single cohesive representation. Because of its generalizability, the MV design has been widely adopted by the visualization community to help users examine and interact with large, complex, and high-dimensional data. However, although ubiquitous, there has been little work to categorize and analyze MVs in order to better understand its design space. As a result, there has been little to no guideline in how to use the MV design effectively. In this paper, we present an in-depth study of how MVs are designed in practice. We focus on two fundamental measures of multiple-view patterns: composition, which quantifies what view types and how many are there; and configuration, which characterizes spatial arrangement of view layouts in the display space. We build a new dataset containing 360 images of MVs collected from IEEE VIS, EuroVis, and PacificVis publications 2011 to 2019, and make fine-grained annotations of view types and layouts for these visualization images. From this data we conduct composition and configuration analyses using quantitative metrics of term frequency and layout topology. We identify common practices around MVs, including relationship of view types, popular view layouts, and correlation between view types and layouts. We combine the findings into a MV recommendation system, providing interactive tools to explore the design space, and support example-based design.
Cyclic polymers and catenanes by atom transfer radical polymerization (ATRP) (2014)

The topologically interesting structures of cyclic polymers, catenanes and other macrocycles are of much interest for their unique chemical and physical properties. However, it is a challenge to design synthetic routes that afford controlled ring structures and connectivity, which is why the practical applications of these materials have not been explored. This review describes the advantages and disadvantages of ring expansion and ring closure methods for preparing cyclic polymers. This review also aims to provide a concise overview of the recent techniques of cyclization specifically by ring closure reactions from polymers grown primarily by atom transfer radical polymerization ( ATRP ). The ring closure techniques covered here are atom transfer radical coupling ( ATRC ), copper‐catalyzed Huisgen azide–alkyne cycloaddition, Diels–Alder cycloaddition and alkylation of carboxylate salts to form esters. Ring expansion and ring closure methods have also been used in the preparation of polymer catenanes. A combination of ATRP and ATRC has been applied to the synthesis of homopolymer and block copolymer catenanes using a supramolecular template with ATRP initiators.
Decoupling Mechanisms of Platinum Deposition on Colloidal Gold Nanoparticle Substrates (2014)

Nanoscale platinum materials are essential components in many technologies, including catalytic converters and fuel cells. Combining Pt with other metals can enhance its performance and/or decrease the cost of the technology, and a wide range of strategies have been developed to capitalize on these advantages. However, wet chemical synthesis of Pt-containing nanoparticles (NPs) is challenging due to the diverse metal segregation and metal-metal redox processes possible under closely related experimental conditions. Here, we elucidate the relationship between Pt(IV) speciation and the formation of well-known NP motifs, including frame-like and core-shell morphologies, in Au-Pt systems. We leverage insights gained from these studies to induce a controlled transition from redox- to surface chemistry-mediated growth pathways, resulting in the formation of Pt NPs in epitaxial contact and linear alignment along a gold nanoprism substrate. Mechanistic investigations using a combination of electron microscopy and (195)Pt NMR spectroscopy identify Pt(IV) speciation as a crucial parameter for understanding and controlling the formation of Pt-containing NPs. Combined, these findings point toward fully bottom-up methods for deposition and organization of NPs on colloidal plasmonic substrates.
Multilength-Scale Chemical Patterning of Self-Assembled Monolayers by Spatially Controlled Plasma Exposure: Nanometer to Centimeter Range (2009)

We present a generic and efficient chemical patterning method based on local plasma-induced conversion of surface functional groups on self-assembled monolayers (SAMs). Here, spatially controlled plasma exposure is realized by elastomeric poly(dimethylsiloxane) (PDMS) contact masks or channel stamps with feature sizes ranging from nanometer, micrometer, to centimeter. This chemical conversion method has been comprehensively characterized by a set of techniques, including contact angle measurements, X-ray photoelectron spectroscopy (XPS), scanning photoelectron microscopy (SPEM), scanning electron microscopy (SEM), and scanning Kelvin probe microscopy (SKPM). In particular, XPS and SPEM can be used to distinguish regions of different surface functionalities and elucidate the mechanism of plasma-induced chemical conversion. In the case of an octadecyltrichlorosilane (OTS) monolayer, we show that exposure to low-power air plasma causes hydroxylation and oxidation of the methyl terminal group on an OTS-covered Si surface and generates polar functional groups such as hydroxyl, aldehylde, and carboxyl groups, which can allow subsequent grafting of dissimilar SAMs and adsorption of colloid nanoparticles onto the patterned areas with an achievable resolution down to the 50 nm range.
TARDBP in amyotrophic lateral sclerosis: identification of a novel variant but absence of copy number variation (2009)

The findings stress the importance of TDP-43 in the pathogenesis of sporadic ALS.
The multicopper oxidase of Pseudomonas aeruginosa is a ferroxidase with a central role in iron acquisition (2002)

Recently it has been observed that multicopper oxidases are present in a number of microbial genomes, raising the question of their function in prokaryotes. Here we describe the analysis of an mco mutant from the opportunistic pathogen Pseudomonas aeruginosa. Unlike wild-type Pseudomonas aeruginosa, the mco mutant was unable to grow aerobically on minimal media with Fe(II) as sole iron source. In contrast, both the wild-type and mutant strain were able to grow either anaerobically via denitrification with Fe(II) or aerobically with Fe(III). Analysis of iron uptake showed that the mco mutant was impaired in Fe(II) uptake but unaffected in Fe(III) uptake. Purification and analysis of the MCO protein confirmed ferroxidase activity. Taken together, these data show that the mco gene encodes a multicopper oxidase that is involved in the oxidation of Fe(II) to Fe(III) subsequent to its acquisition by the cell. In view of the widespread distribution of the mco gene in bacteria, it is suggested that an iron acquisition mechanism involving multicopper oxidases may be an important and hitherto unrecognized feature of bacterial pathogenicity.
The Effects of Cheese Snacks on Caries in Desalivated Rats (1987)

Rats that had had their submandibular/sublingual glands removed surgically, and their parotid ducts tied, developed fewer and less severe caries lesions on coronal and root surfaces when fed cheese snacks in addition to a cariogenic diet than when fed additional cariogenic snacks or no additional snacks. The effects of cheese snacks were particularly dramatic on root-surface caries. These observations may be relevant for elderly humans who are most likely to develop root surface caries. Populations of Streptococcus mutans did not differ among the groups. Actinomyces viscosus was not detected at the end of the experiment in any of the groups. The results of this study demonstrate that cheese exerts a protective effect against coronal and root-surface caries in rats with a severely limited salivary function.