gebhart/patrepeval huggingface dataset:
Deoxygedunin, a Natural Product with Potent Neurotrophic Activity in Mice (2010)

Gedunin, a family of natural products from the Indian neem tree, possess a variety of biological activities. Here we report the discovery of deoxygedunin, which activates the mouse TrkB receptor and its downstream signaling cascades. Deoxygedunin is orally available and activates TrkB in mouse brain in a BDNF-independent way. Strikingly, it prevents the degeneration of vestibular ganglion in BDNF 2/2 pups. Moreover, deoxygedunin robustly protects rat neurons from cell death in a TrkBdependent manner. Further, administration of deoxygedunin into mice displays potent neuroprotective, anti-depressant and learning enhancement effects, all of which are mediated by the TrkB receptor. Hence, deoxygedunin imitates BDNF's biological activities through activating TrkB, providing a powerful therapeutic tool for treatment of various neurological diseases.
Comparative Study of Copper Oxidation Schemes and Their Effects on Surface Wettability (2008)

We present a comparative study of different oxidation methods for Cu, focusing on their effects on surface wettability for potential heat transfer applications. Various Cu2O/CuO nanostructures are formed on copper substrates using thermal and chemical oxidation methods. The morphology and chemical composition of the oxide layers are investigated using atomic force microscopy, scanning electron microscopy, and X-ray diffraction measurements. To evaluate the surface wettability, static contact angles are measured before and after each oxidation process. In thermal oxidation, the contact angle can be tailored from ∼15° to ∼90° by varying heating time (10 min ∼ 4 hrs) and temperature (150–250 °C). Chemical oxidation processes using hot alkali solutions yield stable CuO nanostructures with high roughness factors and unique morphologies, which cause significant changes in wettability. Both superhydrophilic and superhydrophobic surfaces are demonstrated using the chemical oxidation methods.
Reagent-Controlled Transition-Metal-Catalyzed Radical Reactions (2000)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReagent-Controlled Transition-Metal-Catalyzed Radical ReactionsAndreas Gansäuer and Harald BluhmView Author Information Institut für Organische Chemie und Biochemie der Albert-Ludwigs-Universität, Albertstr. 21, 79104 Freiburg, Germany Cite this: Chem. Rev. 2000, 100, 8, 2771–2788Publication Date (Web):July 14, 2000Publication History Received26 November 1999Published online14 July 2000Published inissue 1 August 2000https://pubs.acs.org/doi/10.1021/cr9902648https://doi.org/10.1021/cr9902648research-articleACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views6102Altmetric-Citations380LEARN 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 SUBJECTS:Cyclization,Ethers,Ligands,Reagents,Stereoselectivity Get e-Alerts
Multilevel genomics of colorectal cancers with microsatellite instability—clinical impact of JAK1 mutations and consensus molecular subtype 1 (2017)

Multilevel genomic analyses of MSI+ colorectal cancer revealed molecular heterogeneity with clinical relevance, including tumor immunogenicity and a favorable patient outcome associated with JAK1 mutations and the transcriptomic subgroup CMS1, emphasizing the potential for prognostic stratification of this clinically important subtype. See related research highlight by Samstein and Chan 10.1186/s13073-017-0438-9.
Extent, Characterization, and Sources of Soil Lead Contamination in Small-Urban Residential Neighborhoods (2013)

We present high spatial-resolution mapping of soil lead (Pb) concentrations in a small-urban residential setting. X-ray fluorescence was used to measure soil Pb at170 properties in the City Park neighborhood of Appleton, Wisconsin. Greater than two-thirds of soil samples collected from drip lines contained more than 400 μg g of Pb, and one third exceeded 1200 μg g. Soils adjacent to homes built before 1960 contained significantly higher Pb levels than those near younger homes. Three front yard locations (drip line, mid-yard, and terrace) were sampled at 71 properties. A general decline in soil Pb with increasing distance from the house was observed. Detailed sampling of individual homes within a single residential block revealed Pb-contaminated soil radiating outward from homes in all directions, creating a "bulls-eye" pattern. Approximately 40% of yard space exceeded concentrations of 400 μg g. These patterns of contamination are consistent with Pb paint as the main contributor of Pb to soil. This has important implications because spatial distribution of Pb contamination is fundamentally different if paint, rather than automobile exhaust, is the primary source. Selective sequential extraction analyses suggest that roughly half of the soil Pb resides in chemically reactive and bioavailable phases. The extent and persistence of soil Pb, the resurgence of home gardening, and the serious health consequences of Pb ingestion argue for attention to this problem, not just in dense urban centers but also in smaller urban settings across the country.
Expansion of Human and Murine Hematopoietic Stem and Progenitor Cells Ex Vivo without Genetic Modification Using MYC and Bcl-2 Fusion Proteins (2014)

The long-term repopulating hematopoietic stem cell (HSC) population can self-renew in vivo, support hematopoiesis for the lifetime of the individual, and is of critical importance in the context of bone marrow stem cell transplantation. The mechanisms that regulate the expansion of HSCs in vivo and in vitro remain unclear to date. Since the current set of surface markers only allow for the identification of a population of cells that is highly enriched for HSC activity, we will refer to the population of cells we expand as Hematopoietic Stem and Progenitor cells (HSPCs). We describe here a novel approach to expand a cytokine-dependent Hematopoietic Stem and Progenitor Cell (HSPC) population ex vivo by culturing primary adult human or murine HSPCs with fusion proteins including the protein transduction domain of the HIV-1 transactivation protein (Tat) and either MYC or Bcl-2. HSPCs obtained from either mouse bone marrow, human cord blood, human G-CSF mobilized peripheral blood, or human bone marrow were expanded an average of 87 fold, 16.6 fold, 13.6 fold, or 10 fold, respectively. The expanded cell populations were able to give rise to different types of colonies in methylcellulose assays in vitro, as well as mature hematopoietic populations in vivo upon transplantation into irradiated mice. Importantly, for both the human and murine case, the ex vivo expanded cells also gave rise to a self-renewing cell population in vivo, following initial transplantation, that was able to support hematopoiesis upon serial transplantation. Our results show that a self-renewing cell population, capable of reconstituting the hematopoietic compartment, expanded ex vivo in the presence of Tat-MYC and Tat-Bcl-2 suggesting that this may be an attractive approach to expand human HSPCs ex vivo for clinical use.
Aspen SP1, an exceptional thermal, protease and detergent‐resistant self‐assembled nano‐particle (2006)

Stable protein 1 (SP1) is a homo-oligomeric protein isolated from aspen (Populus tremula aspen) plants which forms a ring-shape dodecameric particle with a central cavity. The oligomeric form of SP1 is an exceptionally stable structure that is resistant to proteases (e.g., trypsin, V8, and proteinase K), high temperatures, organic solvents, and high levels of ionic detergent. Analytical ultra-centrifugation, chemical cross-linking, matrix-assisted laser-desorption time-of-flight mass spectrometry (MALDI-TOF-MS), and transmission electron microscopy were used to further characterize the SP1 dodecamer. Introduction of a single cysteine at the N-terminus of SP1 enabled the formation of disulfide bridges within the SP1 dodecamer, concurrent with increased melting point. A six-histidine tag was introduced at the N-terminus of SP1 to generate 6HSP1, and the DeltaNSP1 mutant was generated by a deletion of amino acids 2-6 at the N-terminus. Both 6HSP1 and DeltaNSP1 maintained their ability to assemble a stable dodecamer. Remarkably, these SP1 homo-dodecamers were able to re-assemble into stable hetero-dodecamers following co-electro-elution from SDS-PAGE. The exceptional stability of the SP1-nano ring and its ability to self-assemble hetero-complexes paves the way to further research in utilizing this unique protein in nano-biotechnology.
IDH1andIDH2Mutations Are Frequent Genetic Alterations in Acute Myeloid Leukemia and Confer Adverse Prognosis in Cytogenetically Normal Acute Myeloid Leukemia WithNPM1Mutation WithoutFLT3Internal Tandem Duplication (2010)

IDH1 and IDH2 mutations are recurring genetic changes in AML. They constitute a poor prognostic factor in CN-AML with mutated NPM1 without FLT3-ITD, which allows refined risk stratification of this AML subset.
Initiated and Oxidative Chemical Vapor Deposition of Polymeric Thin Films: iCVD and oCVD (2008)

Abstract The techniques of initiated chemical vapor deposition (iCVD) and oxidative chemical vapor deposition (oCVD) enable the fabrication of chemically well‐defined thin polymeric films on complex objects with micro‐ and nano‐scale features. By depositing polymers from the vapor phase, many wetting and solution effects are avoided, and conformal films can be created. In iCVD, a variant of hot filament CVD, the deposition rate is enhanced and chemical functionalities of the polymers' constituents are maintained by including a thermally labile initiator in the feed stream. Due to the low energy required when using an initiator, delicate substrates can be coated. In oCVD, infusible, electrically conductive films are formed directly on the substrate of interest as the oxidant and monomer are introduced into the reactor simultaneously. This Feature Article provides an overview of the work that has been done to develop iCVD and oCVD into platform technologies. Relevant background, fundamentals, and applications will be discussed.
DMP1-targeted Cre Expression in Odontoblasts and Osteocytes (2007)

Odontoblasts in dentin and osteocytes in bone contain dendritic processes. To test if their dendrites share a common feature, we compared their cellular morphology as visualized using scanning electron microscopy. Analysis of our data showed that both cells share an identical dendritic canalicular system and express extensive processes forming a complex network within the mineralized matrix. Because dentin matrix protein 1 (DMP1), an extracellular matrix protein, is highly expressed in both types of cells, we next tested, using a transgenic approach, whether a 9.6-kb Dmp1 promoter-4-kb 1st intron would be able to target Cre cDNA in these cells for expression/deletion of other genes in odontoblasts and osteocytes. We determined the specificity and efficiency of Cre activity by crossing Dmp1-Cre mice with ROSA26 reporter mice. Results showed that odontoblasts and osteocytes were specifically targeted, suggesting that this animal model will be useful for the preferential study of gene functions in both types of cells.
A Cyclopentane Conformational Restraint for a Peptide Nucleic Acid:  Design, Asymmetric Synthesis, and Improved Binding Affinity to DNA and RNA (2003)

[structure: see text] A strategy to restrict the highly flexible backbone conformation of a peptide nucleic acid (PNA) by incorporation of a cyclopentane ring is proposed. An asymmetric synthesis of cyclopentane-modified PNA is reported, and its binding properties were determined. The cyclopentane ring leads to a significant improvement in the binding properties of the resulting PNA to DNA and RNA.
Proposed Standardization of Neisseria meningitidis PorA Variable-Region Typing Nomenclature (1998)

Neisseria meningitidis isolates are conventionally classified by serosubtyping, which characterizes the reactivities of the PorA outer membrane protein variable-region (VR) epitopes with monoclonal antibodies (MAbs). A newer method (PorA VR typing) uses predicted amino acid sequences derived from DNA sequence analysis. The resulting classification schemes are not standardized, offering conflicting and sometimes irreconcilable data from the two methods. In this paper, we propose a standardization of the PorA VR typing nomenclature that incorporates serologic information from traditional PorA serosubtyping with molecular data from predicted VR sequences. We performed a comprehensive literature and database search, generating a collection of strains and DNA sequences that reflects the diversity within PorA that exists to date. We have arranged this information in a comprehensive logical model that includes both serosubtype and PorA VR type assignments. Our data demonstrate that the current panel of serosubtype-defining MAbs underestimates PorA VR variability by at least 50%. Our proposal for VR typing is informative because amino acid sequence and serologic information, when serosubtype-defining MAbs are available, can be deduced simultaneously from the PorA VR designation. This scheme will be useful in future classification and applied epidemiologic studies of N. meningitidis, being a systematic way of selecting PorA vaccine candidates and analyzing vaccine coverage and failure.
Virus-cell fusion targeted for drug development (1996)

RETURN TO ISSUEPREVNewsNEXTVirus-cell fusion targeted for drug developmentRUDYCite this: Chem. Eng. News 1996, 74, 20, 45Publication Date (Print):May 13, 1996Publication History Published online12 November 2010Published inissue 13 May 1996https://pubs.acs.org/doi/10.1021/cen-v074n020.p045https://doi.org/10.1021/cen-v074n020.p045newsACS PublicationsCopyright © 1996 American Chemical SocietyArticle Views4Altmetric-Citations-LEARN 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 options SUBJECTS:Infectious diseases Get e-Alerts
Purification and characterization of Clostridium perfringens 120-kilodalton collagenase and nucleotide sequence of the corresponding gene (1994)

Clostridium perfringens type C NCIB 10662 produced various gelatinolytic enzymes with molecular masses ranging from approximately 120 to approximately 80 kDa. A 120-kDa gelatinolytic enzyme was present in the largest quantity in the culture supernatant, and this enzyme was purified to homogeneity on the basis of sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The purified enzyme was identified as the major collagenase of the organism, and it cleaved typical collagenase substrates such as azocoll, a synthetic substrate (4-phenylazobenzyloxy-carbonyl-Pro-Leu-Gly-Pro-D-Arg [Pz peptide]), and a type I collagen fibril. In addition, a gene (colA) encoding a 120-kDa collagenase was cloned in Escherichia coli. Nested deletions were used to define the coding region of colA, and this region was sequenced; from the nucleotide sequence, this gene encodes a protein of 1,104 amino acids (M(r), 125,966). Furthermore, from the N-terminal amino acid sequence of the purified enzyme which was found in this reading frame, the molecular mass of the mature enzyme was calculated to be 116,339 Da. Analysis of the primary structure of the gene product showed that the enzyme was produced with a stretch of 86 amino acids containing a putative signal sequence. Within this stretch was found PLGP, the amino acid sequence constituting the Pz peptide. This sequence may be implicated in self-processing of the collagenase. A consensus zinc-binding sequence (HEXXH) suggested for vertebrate Zn collagenases is present in this bacterial collagenase. Vibrio alginolyticus collagenase and Achromobacter lyticus protease I showed significant homology with the 120-kDa collagenase of C. perfringens, suggesting that these three enzymes are evolutionarily related.
Proanthocyanidin Biosynthesis in Plants (2003)

Leucoanthocyanidin reductase (LAR) catalyzes the synthesis of catechin, an initiating monomer of condensed tannin or proanthocyanidin (PA) synthesis, from 3,4-cis-leucocyanidin and thus is the first committed step in PA biosynthesis. The enzyme was purified to near homogeneity from PA-rich leaves of the legume Desmodium uncinatum (Jacq.) DC, partially sequenced and the corresponding cDNA cloned. The identity of the enzyme was confirmed by expressing active recombinant LAR in Escherichia coli and in tobacco and white clover. The enzyme is a monomer of 43 kDa (382 amino acids) and is most active synthesizing catechin (specific activity of approximately 10 micromol min+1 mg of protein+1) but also synthesizes afzelechin and gallocatechin. LAR is most closely related to the isoflavone reductase group of plant enzymes that are part of the Reductase-Epimerase-Dehydrogenase (RED) family of proteins. Unlike all other plant isoflavone reductase homologues that are about 320 amino acids long, LAR has an additional 65-amino acid C-terminal extension whose function is not known. Curiously, although Arabidopsis makes PA, there is no obvious LAR orthologue in the Arabidopsis genome. This may be because Arabidopsis seems to produce only an epicatechin, rather than a dual catechin/epicatechin-based PA similar to many other plants.
Safety and Short-Term Toxicity of a Novel Cationic Lipid Formulation for Human Gene Therapy (1993)

Among the potential nonviral vectors for human gene therapy are DNA-liposome complexes. In a recent clinical study, this delivery system has been utilized. In this report, a novel cationic lipid, dimyristyloxypropyl-3-dimethyl-hydroxyethyl ammonium (DMRIE), has been substituted into the DNA-liposome complex with dioleoyl phosphatidylethanolamine (DOPE), which both improves transfection efficiencies and allows increased doses of DNA to be delivered in vivo. The safety and toxicity of this DNA-liposome complex has been evaluated in two species, mice and pigs. The efficacy of DMRIE/DOPE in inducing an antitumor response in mice after transfer of a foreign MHC has been confirmed. No abnormalities were detected after administration of up to 1,000-fold higher concentrations of DNA and lipid than could be tolerated in vivo previously. Examination of serum biochemical enzymes, pathologic examination of tissue, and analysis of cardiac function in mice and pigs revealed no toxicities related to this treatment. This improved cationic lipid formulation is well-tolerated in vivo and could therefore allow higher dose administration and potentially greater efficiency of gene transfer for gene therapy.
The distribution of synapsin I and synaptophysin in hippocampal neurons developing in culture (1991)

As a first step toward elucidating mechanisms involved in the sorting of synaptic vesicle proteins in neurons, we have used immunofluorescence microscopy to determine the distribution of two synaptic vesicle proteins, synapsin I and synaptophysin, in hippocampal neurons developing in culture. In mature cultures, synapsin I and synaptophysin immunoreactivity was concentrated in puncta that were restricted to sites where axons contacted neuronal cell bodies or dendrites. Electron-microscopic immunocytochemistry demonstrated that these puncta corresponded to vesicle-filled axonal varicosities that were exclusively presynaptic. At early stages of development, before cell-cell contact, both synapsin I and synaptophysin were preferentially localized in axons, where they were particularly concentrated in the distal axon and growth cone. In axons that did not contact other cells, immunostaining for these two proteins had a granular appearance, which persisted for at least 7 d, but focal accumulations of vesicles comparable to those seen at sites of synaptic contact were not observed. When neurons contacted one another, numerous puncta of synapsin I and synaptophysin formed within the first week in culture. Double-label immunofluorescence demonstrated that the two vesicle antigens were closely codistributed throughout these stages of development. These observations demonstrate that synaptic vesicle proteins assume a polarized distribution within nerve cells beginning early in development, as soon as the axon can be identified. In contrast, differences in microtubule polarity orientation that distinguish mature axons and dendrites, and that have been proposed to account for the selective sorting of some materials in nerve cells, first appear at a subsequent stage of development. The selective distribution of synaptic vesicle proteins to the axon occurs in isolated cells, independent of interactions with other cells. In contrast, the formation of large clusters of vesicles typical of presynaptic specializations requires contact with an appropriate postsynaptic target. Thus, in cultured hippocampal neurons, the localization of synaptic vesicles in presynaptic specializations is the result of sorting mechanisms intrinsic to individual neurons as well as to mechanisms mediated by cell-cell contact.
Performance of fractionally spaced linear and decision-feedback equalizers for multitone systems (2002)

When OFDM or multitone modulation is used, the channel dispersion is usually circumvented by means of the technique of guard time. As an alternative it is possible not to use a guard time but design receivers able to equalize the intersymbol interference (ISI) and inter-carrier interference (ICI). In the present paper we show how to design fractionally spaced linear or decision-feedback MIMO equalizers for multitone systems without guard time. Full complexity and reduced complexity solutions are investigated. The design is made for an MMSE criterion and the steady-state performance is analyzed. The performance of these detectors is investigated for BPSK modulation of the tones. In addition the robustness of the fractionally spaced detectors against timing errors is demonstrated.