gebhart/patrepeval huggingface dataset:
CLMP, a Novel Member of the CTX Family and a New Component of Epithelial Tight Junctions (2003)

The CTX family is a growing group of type I transmembrane proteins within the immunoglobulin superfamily (IgSF). They localize to junctional complexes between endothelial and epithelial cells and seem to participate in cell-cell adhesion and transmigration of leukocytes. Here, we report the identification of a new member of the CTX family. This protein, which was designated CLMP (coxsackie- and adenovirus receptor-like membrane protein), is composed of 373 amino acids including an extracellular part containing a V- and a C2-type domain, a transmembrane region and a cytoplasmic tail. CLMP mRNA was detected in a variety of both human and mouse tissues and cell lines. The protein migrated with an Mr of around 48 on SDS-PAGE and was predominantly expressed in epithelial cells within different tissues. In cultured epithelial cells, CLMP was detected in areas of cell-cell contacts. When exogenously expressed in polarized MDCK cells, CLMP was restricted to the subapical area of the lateral cell surface, where it co-localized with the tight junction markers ZO-1 and occludin. Also endogenous CLMP showed association with tight junctions, as analyzed in polarized human CACO-2 cells. This suggested a role for CLMP in cell-cell adhesion and indeed, overexpressed CLMP induced aggregation of non-polarized CHO cells. Furthermore, CLMP-expressing MDCK cells showed significantly increased transepithelial resistance, indicating a role for CLMP in junctional barrier function. Thus, we conclude that CLMP is a novel cell-cell adhesion molecule and a new component of epithelial tight junctions. We also suggest, based on phylogenetic studies, that CLMP, CAR, ESAM, and BT-IgSF form a new group of proteins within the CTX family.
Mechanically robust nanoparticle stabilized transparent liquid marbles (2008)

Optically transparent liquid marbles were made from water and glycerol drops embedded in surface-treated fumed silica nanoparticles. The mechanical robustness of such liquid marbles is shown to be greater than similar marbles made from microparticulate poly(tetrafluoroethylene), both under compressive and tensile loading conditions. Using liquid evaporation data and environmental scanning electron microscope images, we demonstrate that their robustness may be attributed to a nanoparticulate elastic thin film that self-assembles on the liquid-vapor interface.
Discovery of a Novel Inhibitor of Histone Lysine-Specific Demethylase 1A (KDM1A/LSD1) as Orally Active Antitumor Agent (2015)

We report the stereoselective synthesis and biological activity of a novel series of tranylcypromine (TCPA) derivatives (14a-k, 15, 16), potent inhibitors of KDM1A. The new compounds strongly inhibit the clonogenic potential of acute leukemia cell lines. In particular three molecules (14d, 14e, and 14g) showing selectivity versus MAO A and remarkably inhibiting colony formation in THP-1 human leukemia cells, were assessed in mouse for their preliminary pharmacokinetic. 14d and 14e were further tested in vivo in a murine acute promyelocytic leukemia model, resulting 14d the most effective. Its two enantiomers were synthesized: the (1S,2R) enantiomer 15 showed higher activity than its (1R,2S) analogue 16, in both biochemical and cellular assays. Compound 15 exhibited in vivo efficacy after oral administration, determining a 62% increased survival in mouse leukemia model with evidence of KDM1A inhibition. The biological profile of compound 15 supports its further investigation as a cancer therapeutic.
Nanoporosity-Driven Superhydrophilicity:  A Means to Create Multifunctional Antifogging Coatings (2006)

Multifunctional nanoporous thin films have been fabricated from layer-by-layer assembled silica nanoparticles and a polycation. The resultant multilayer films were found to exhibit both antifogging and antireflection properties. The antifogging properties are a direct result of the development of superhydrophilic wetting characteristics (water droplet contact angle <5 degrees within 0.5 s or less). The nearly instantaneous sheetlike wetting promoted by the superhydrophilic multilayer prevents light scattering water droplets from forming on a surface. The low refractive index of the multilayer film (as low as 1.22) resulting from the presence of nanopores was found to impart excellent antireflection properties. Glass slides coated on both sides with a nanoporous multilayer film exhibited transmission levels as high as 99.8%. Stable superhydrophilic wetting characteristics were obtained only after a critical number of bilayers were deposited onto a surface. The assembly conditions (solution pH and nanoparticle concentration), as well as the choice of nanoparticle size, were found to strongly influence film properties. It is suggested that the superhydrophilic behavior is driven by the rapid infiltration of water into a 3D nanoporous network created under specific assembly conditions.
Fast profiling of chemical constituents in Yiqing Capsule by ultra‐performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry (2011)

An ultra-performance liquid chromatography/electrospray ionization tandem mass spectrometry (UPLC-ESI-MS(n)) has been developed for structural characterization and identification of multi-constituents in Yiqing Capsule, a well-known combined herbal remedy prepared from the extract mixtures of Rhizoma Coptidis, Radix et Rhizoma Rhei and Radix Scutellariae. The UPLC analysis was performed on an Agilent ZorBax SB-C(18) column (4.6 mm×50 mm, 1.8 μm) and gradient elution of 0.1% formic acid solution and acetonitrile in 16 min. Based on their retention times and mass spectra in comparison with the data from standards or references, a total of 29 compounds including 3 phenolic acids and 4 anthraquinones from Radix et Rhizoma Rhei, 8 alkaloids from Rhizoma Coptidis and 14 flavonoids from Radix Scutellariae were unambiguously identified or tentatively characterized in the complex system. The MS data and fragmentation information of two isomers of feruloylquinic acid were first reported in Radix et Rhizoma Rhei and in Yiqing Capsules. This study is expected to be accepted as an effective and reliable pattern for comprehensive and systematic characterization of this commonly used Chinese herbal preparation.
An Artificial Primosome: Design, Function, and Applications (2001)

Double-stranded (ds) DNA is capable of the sequence-specific accommodation of an additional oligodeoxyribonucleotide strand by the peptide nucleic acid(PNA)-assisted formation of a so-called PD-loop. We demonstrate here that the PD-loop may function as an artificial primosome within linear, nonsupercoiled DNA duplexes. DNA polymerase with its strand displacement activity uses this construct to initiate the primer extension reaction at a designated dsDNA site. The primer is extended by several hundred nucleotides. The efficiency of dsDNA priming by the artificial primosome assembly is comparable to the single-stranded DNA priming used in various assays. The ability of the PD-loop structure to perform like an artificial primosome on linear dsDNA may find applications in biochemistry, molecular biology, and molecular biotechnology, as well as for DNA diagnostics. In particular, multiple labels can be incorporated into a chosen dsDNA site resulting in ultrasensitive direct quantification of specific sequences. Furthermore, nondenaturing dsDNA sequencing proceeds from the PD-loop. This approach opens the way to direct isothermal reading of the DNA sequence against a background of unrelated DNA, thereby eliminating the need for purification of the target DNA.
In vitro culture of leukemic cells in t(4;11) acute leukemia (1985)

Abstract In the present study we utilized a semisolid culture system with feeder cells and enriched media to evaluate the growth of acute leukemia associated with the 4;11 chromosomal translocation. We compared growth of t(4;11) leukemia to typical acute nonlymphocytic leukemia (ANL) and acute lymphocytic leukemia (ALL). The two cases of t(4;11) leukemia tested exhibited the highest cloning efficiency of cells tested. The growth characteristics of t(4;11) leukemia were more similar to ANL than ALL.
Gene Discovery Using Computational and Microarray Analysis of Transcription in the Drosophila melanogaster Testis (2000)

Identification and annotation of all the genes in the sequenced Drosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcription units. We therefore undertook a survey of the repertoire of genes expressed in the Drosophila testis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). Testis ESTs computationally collapsed into 1560 cDNA set used for further analysis. Of those, 11% correspond to named genes, and 33% provide biological evidence for a predicted gene. A surprising 47% fail to align with existing ESTs and 16% with predicted genes in the current genome release. EST frequency and microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furthermore, &gt;80% of the genes expressed in the testis showed onefold overexpression relative to ovaries, or gonadectomized flies. Additionally, &gt;3% showed more than threefold overexpression at p &lt;0.05. Surprisingly, 22% of the genes most highly overexpressed in testis match Drosophila genomic sequence, but not predicted genes. These data strongly support the idea that sequencing additional cDNA libraries from defined tissues, such as testis, will be important tools for refined annotation of the Drosophila genome. Additionally, these data suggest that the number of genes in Drosophila will significantly exceed the conservative estimate of 13,601. [The sequence data described in this paper have been submitted to the dbEST data library under accession nos. AI944400 – AI947263 and BE661985 – BE662262 .] [The microarray data described in this paper have been submitted to the GEO data library under accession nos. GPLS, GSM3–GSM10.]
Dynamics of concentrated polymer systems. Part 1.—Brownian motion in the equilibrium state (1978)

In this series of papers, the dynamics of polymers in melts and concentrated solutions are discussed with the eventual aim of constructing the rheological constitutive equation. The basic ideas are introduced in this paper. A mathematical model chain which describes the motion of the polymer in the fully entangled state is presented and its Brownian motion in equilibrium is studied. The model chain, called the primitive chain, shows much qualitatively different behaviour from that of the Rouse chain used in dilute solution theory.
Identification of a vaccinia virus gene encoding a type I DNA topoisomerase. (1987)

Vaccinia virus encapsidates a type I DNA topoisomerase (EC 5.99.1.2). The enzyme was purified from virus cores to apparent homogeneity, yielding a protein of Mr 32,000. The amino-terminal sequence of the isolated Mr 32,000 polypeptide was determined and used to map the putative structural gene for the vaccinia topoisomerase to the H7r open reading frame of the vaccinia genome. This gene encodes a 314-amino acid polypeptide containing a region homologous to a region of the type I topoisomerase from the yeast Saccharomyces cerevisiae.
Analysis of the brain mural cell transcriptome (2016)

Pericytes, the mural cells of blood microvessels, regulate microvascular development and function and have been implicated in many brain diseases. However, due to a paucity of defining markers, pericyte identification and functional characterization remain ambiguous and data interpretation problematic. In mice carrying two transgenic reporters, Pdgfrb-eGFP and NG2-DsRed, we found that double-positive cells were vascular mural cells, while the single reporters marked additional, but non-overlapping, neuroglial cells. Double-positive cells were isolated by fluorescence-activated cell sorting (FACS) and analyzed by RNA sequencing. To reveal defining patterns of mural cell transcripts, we compared the RNA sequencing data with data from four previously published studies. The meta-analysis provided a conservative catalogue of 260 brain mural cell-enriched gene transcripts. We validated pericyte-specific expression of two novel markers, vitronectin (Vtn) and interferon-induced transmembrane protein 1 (Ifitm1), using fluorescent in situ hybridization and immunohistochemistry. We further analyzed signaling pathways and interaction networks of the pericyte-enriched genes in silico. This work provides novel insight into the molecular composition of brain mural cells. The reported gene catalogue facilitates identification of brain pericytes by providing numerous new candidate marker genes and is a rich source for new hypotheses for future studies of brain mural cell physiology and pathophysiology.
In silico study of amyloid β-protein folding and oligomerization (2004)

Experimental findings suggest that oligomeric forms of the amyloid beta protein (Abeta) play a critical role in Alzheimer's disease. Thus, elucidating their structure and the mechanisms of their formation is critical for developing therapeutic agents. We use discrete molecular dynamics simulations and a four-bead protein model to study oligomerization of two predominant alloforms, Abeta40 and Abeta42, at the atomic level. The four-bead model incorporates backbone hydrogen-bond interactions and amino acid-specific interactions mediated through hydrophobic and hydrophilic elements of the side chains. During the simulations we observe monomer folding and aggregation of monomers into oligomers of variable sizes. Abeta40 forms significantly more dimers than Abeta42, whereas pentamers are significantly more abundant in Abeta42 relative to Abeta40. Structure analysis reveals a turn centered at Gly-37-Gly-38 that is present in a folded Abeta42 monomer but not in a folded Abeta40 monomer and is associated with the first contacts that form during monomer folding. Our results suggest that this turn plays an important role in Abeta42 pentamer formation. Abeta pentamers have a globular structure comprising hydrophobic residues within the pentamer's core and hydrophilic N-terminal residues at the surface of the pentamer. The N termini of Abeta40 pentamers are more spatially restricted than Abeta42 pentamers. Abeta40 pentamers form a beta-strand structure involving Ala-2-Phe-4, which is absent in Abeta42 pentamers. These structural differences imply a different degree of hydrophobic core exposure between pentamers of the two alloforms, with the hydrophobic core of the Abeta42 pentamer being more exposed and thus more prone to form larger oligomers.
Mechanisms regulating the recruitment of macrophages into hypoxic areas of tumors and other ischemic tissues (2004)

The mechanisms responsible for recruiting monocytes from the bloodstream into solid tumors are now well characterized. However, recent evidence has shown that these cells then differentiate into macrophages and accumulate in large numbers in avascular and necrotic areas where they are exposed to hypoxia. This parallels their tendency to congregate in ischemic areas of other diseased tissues such as atherosclerotic plaques and arthritic joints. In tumors, macrophages appear to undergo marked phenotypic changes when exposed to hypoxia and to switch on their expression of a number of mitogenic and proangiogenic cytokines and enzymes. This then promotes tumor growth, angiogenesis, and metastasis. Here, we compare the various mechanisms responsible for monocyte recruitment into tumors with those regulating the accumulation of macrophages in hypoxic/necrotic areas. Because the latter are best characterized in human tumors, we focus mainly on these but also discuss their relevance to macrophage migration in ischemic areas of other diseased tissues. Finally, we discuss the relevance of these mechanisms to the development of novel cancer therapies, both in providing targets to reduce the proangiogenic contribution made by hypoxic macrophages in tumors and in developing the use of macrophages to deliver therapeutic gene constructs to hypoxic areas of diseased tissues.
UHF SATCOM downlink interference for the mobile platform (2002)

UHF satellite communications (SATCOM) aboard mobile platforms are difficult to achieve compared to stable platforms. Mobile platforms use hemispherical-coverage or quad diversity antennas. Hemispherical antenna coverage is required because of continuous changes in path geometry. Mobile antennas are limited both in size and gain. Selectivity requirements for narrowband (5 kHz) and wideband (25 kHz) SATCOM channel operation are about 10 dB more difficult for the mobile platform. SATCOM receiver selectivity is needed to limit AGC, control intermod products and allow quad diversity reception. The design of a UHF SATCOM terminal should consider worse-case narrowband and wideband channel downlink interference for the mobile platform, assuming the advent of the UHF Follow-On (UFO) satellite. Presently many of FLTSAT and LEASAT satellite narrowband channels are spaced on 5 kHz centers, which impose very tight selectivity requirements on SATCOM terminals. UFO narrowband channel spacing has been increased to 10 kHz easing selectivity requirements. Even though the wideband channel spacing for UFO remains at 100 kHz, half of the channels appear to the hemispherical-coverage antenna user to be spaced 50 kHz apart. Wideband selectivity requirements for the SATCOM terminal are dictated by the high dynamic range for adjacent channel interference with 50 kHz spacing for line-of-sight operation, whereas narrowband selectivity requirements result from consideration of noise interference from adjacent idle SATCOM channels. Narrowband selectivity can be upgraded in firmware as FLTSAT/LEASAT satellites are transitioned to UFO.
Vertical-cavity surface-emitting lasers: the next generation (1993)

This paper reviews our recent progress in the design, fabrication, and performance of Vertical Cavity Surface Emitting Laser (VCSEL) devices and arrays. High power (&gt; 11 mW cw), high speed (10 GHz), high temperature (&gt; 130 degree(s)C) and low voltage (&lt; 2 V) and low threshold current operation are demonstrated. A monolithic spatial filtering technique is implemented for transverse mode control resulting in exceptional optical characteristics. Novel high power 2D coherently-coupled VCSEL arrays emitting over 1 W are discussed. One and two-dimensional individually- and matrix-addressable arrays are demonstrated.
Extending Pummerer Reaction Chemistry. Development of a Strategy for the Regio- and Stereoselective Oxidative Cyclization of 3-(ω-Nucleophile)-Tethered Indoles (2005)

The brominative cyclization of diastereomeric beta-silyloxy tryptophan derivatives proceeded with divergent regiochemistry (C(2) or C(3) addition), depending on the relative stereochemistry of the silyloxy substituent. This lack of C(2) vs C(3) regiochemical predictability led to the development of a new approach, which featured Pummerer-type chemistry on an indole C(2) sulfoxide or sulfide substrate, for steering nucleophilic addition to C(3) of the indole. Extension of this transformation from carboxylate nucleophiles to carbon analogues such as allylsilane, silyl enol ether, and silyl ketene iminal bearing substrates led to the formation of spirocyclic oxindole derivatives in good yields with complete regioselectivity for C(3) cyclization and with good diastereoselectivity where relevant.
Discrimination between related DNA sites by a single amino acid residue of Myc-related basic-helix-loop-helix proteins. (1992)

A yeast genetic system was developed to study how the basic regions of basic-helix-loop-helix (bHLH) proteins distinguish between related consensus bHLH binding sites, with nucleotide sequence CANNTG. The yeast bHLH protein CBF1 binds to the sequence CAC(A/G)TG found in the yeast centromere element CDE1 and in promoter regions of several yeast genes involved in methionine biosynthesis. Using a functional assay to rescue a mutant cbf1 yeast strain from methionine auxotrophy, we determined that the basic region of CBF1 could be replaced by the homologous region of either the vertebrate USF transcription factor or c-Myc, both of which bind CACGTG. The homologous region of the AP4 transcription factor, which recognizes the sequence CAGCTG, could not functionally replace the CBF1 basic region. However, only a single substitution, Met----Arg, in the AP4 basic region of the inactive chimera CBF-AP4 was sufficient to restore CBF1 function. In randomization experiments, only arginine or lysine provided functional substitutions at the AP4 methionine position. The results suggest that this conserved arginine residue in the basic regions of Myc-related bHLH proteins discriminates between CAC(A/G)TG and related sites.
AMP Deaminase as a Novel Practical Catalyst in the Synthesis of 6-Oxopurine Ribosides and their Analogs (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAMP Deaminase as a Novel Practical Catalyst in the Synthesis of 6-Oxopurine Ribosides and their AnalogsAlexey L. Margolin, David R. Borcherding, Dominique Wolf-Kugel, and Nara MargolinCite this: J. Org. Chem. 1994, 59, 24, 7214–7218Publication Date (Print):December 1, 1994Publication History Published online1 May 2002Published inissue 1 December 1994https://pubs.acs.org/doi/10.1021/jo00103a010https://doi.org/10.1021/jo00103a010research-articleACS PublicationsRequest reuse permissionsArticle Views343Altmetric-Citations27LEARN 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-Alertsclose Get e-Alerts
Polyethylenimine, a cost‐effective transfection reagent (2006)

Abstract In search for a cheap and effective transfection reagent we used the positively charged polyplex‐forming compound polyethylenimine (PEI). This compound is commercially available from different companies either as a non‐modified chemical reagent or with additives as a more cost intensive transfection reagent. Here we used the non‐modified PEI reagent to optimize transfection protocols for different cell‐lines. With these optimized conditions we were able to transiently transfect a number of cell‐lines up to 40–90%.
Laser-induced optical breakdown on hard and soft tissues and its dependence on the pulse duration: experiment and model (1996)

Threshold values of laser-induced optical breakdown (LIOB) on the surface of human corneal tissues, human enamel, and bovine brain tissues are presented. The data are obtained by using a regeneratively amplified Nd:YLF laser and a multistage dye laser system, respectively. The measured decrease in threshold fluence at shorter pulse durations is in good agreement with the authors' theoretical model.
Convenient Synthetic Sequence for the Preparation of Indanones (1990)

Abstract A convenient and general method is reported for the synthesis of indanones from aryl ketones or aldehydes.