gebhart/patrepeval huggingface dataset:
Upregulation of Integrin 6/β1 and Chemokine Receptor CCR1 by Interleukin-12 Promotes the Migration of Human Type 1 Helper T Cells (1999)

CD4+ T helper 1 (Th1) cells and Th2 cells are distinguished based on the pattern of cytokines they are able to produce. Selectin ligands and chemokine receptors are differentially expressed in Th1 and Th2 cells, providing a basis for tissue-specific recruitment of helper T-cell subsets. However, the modes and mechanisms regulating tissue-specific localization of Th1 and Th2 cells are still largely unknown. Here, we show the preferential expression on Th1 cells of the integrin 6/β1, which is distinctly regulated by the Th1-inducing cytokines interleukin-12 (IL-12) and interferon-alfa (IFN-). The pattern of integrin 6/β1 regulation closely mirrors that of the chemokine receptor CCR1. Analysis of signal transducer and activator of transcription 4 (Stat4) activation by IL-12 and IFN- shows distinct signaling kinetics by these cytokines, correlating with the pattern of CCR1 and integrin 6/β1 expression. Unlike IFN-, the ability of IL-12 to generate prolonged intracellular signals appears to be critical for inducing integrin 6/β1 upregulation in Th1 cells. The expression and upregulation of CCR1 and 6/β1 integrin promotes the migration of Th1 cells. These findings suggest that the exquisite regulation of integrin 6/β1 and CCR1 may play an important role in tissue-specific localization of Th1 cells.
Herpesviral Deoxythymidine Kinases Contain a Site Analogous to the Phosphoryl-binding Arginine-rich Region of Porcine Adenylate Kinase; Comparison of Secondary Structure Predictions and Conservation (1990)

Twelve herpesviral deoxythymidine kinases were examined for regions of sequence similarity by multiple alignment. Six highly conserved sites were observed. Site 1 corresponded to a glycine-rich loop that forms part of the ATP-binding pocket in porcine adenylate kinase (PAK), and site 5 corresponded to a region in PAK, located on one lobe of the cleft, that contains arginine residues that bind substrate phosphoryl groups. Site 3, consisting of the motif -DRH-, is thought to be involved in thymine/deoxythymidine recognition; site 4, which is nearby, probably participates in this function as well. The functions of sites 2 and 6 have not been identified. Secondary structure predictions were made by the Garnier method and averaged for each position in the multiple alignment. The structure predicted for all six sites was typically a short flexible region (turn or coil) at or adjacent to the site, flanked by rigid structures (helix or sheet) on either side.
Evidence That Collapsin Response Mediator Protein-2 Is Involved in the Dynamics of Microtubules (2000)

Collapsin response mediator protein-2 (CRMP-2) is a member of the CRMP/TOAD/Ulip/DRP family of cytosolic phosphoproteins involved in neuronal differentiation and axonal guidance. CRMP-2 mediates the intracellular response to collapsin 1/semaphorin 3A, a repulsive extracellular guidance cue for axonal outgrowth. The mutation of UNC-33, a Caenorhabditis elegans homolog of CRMP-2, results in abnormality of microtubules in neurites, but the mechanism of CRMP-2 action remains to be clarified. Here, we report that overexpression of human CRMP-2 in Neuro2a cells, a mouse neuroblastoma cell line, results in blebbing of the cytoplasm. Furthermore, some cells exhibited intranuclear inclusions, which were labeled with antibodies to CRMP-2 and tubulin. CRMP-2 was found to be associated with microtubule bundles in the spindles at the metaphase and in the midbodies at the late telophase in mitotic cells. Thus, it is most likely that failure of complete disassembly of the spindle microtubules during mitosis is responsible for the formation of these intranuclear inclusions. We suggest that CRMP-2 functions by regulating the dynamics of microtubules.
The Catalytic Properties of Supported Sodium and Lithium Catalysts (1957)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Catalytic Properties of Supported Sodium and Lithium CatalystsSterling E. VoltzCite this: J. Phys. Chem. 1957, 61, 6, 756–758Publication Date (Print):June 1, 1957Publication History Published online1 May 2002Published inissue 1 June 1957https://pubs.acs.org/doi/10.1021/j150552a012https://doi.org/10.1021/j150552a012research-articleACS PublicationsRequest reuse permissionsArticle Views170Altmetric-Citations10LEARN 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 Get e-Alerts
Static and dynamic light-scattering solution behavior of pullulan and dextran in comparison (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStatic and dynamic light-scattering solution behavior of pullulan and dextran in comparisonEckhard NordmeierCite this: J. Phys. Chem. 1993, 97, 21, 5770–5785Publication Date (Print):May 1, 1993Publication History Published online1 May 2002Published inissue 1 May 1993https://pubs.acs.org/doi/10.1021/j100123a050https://doi.org/10.1021/j100123a050research-articleACS PublicationsRequest reuse permissionsArticle Views1142Altmetric-Citations133LEARN 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 Get e-Alerts
Detection and characterization of mammalian DNA polymerase beta mutants by functional complementation in Escherichia coli. (1993)

We have designed and utilized a bacterial complementation system to identify and characterize mammalian DNA polymerase beta mutants. In this complementation system, wild-type rat DNA polymerase beta replaces both the replicative and repair functions of DNA polymerase I in the Escherichia coli recA718 polA12 double mutant; our 263 DNA polymerase beta mutants replace E. coli polymerase I less efficiently or not at all. Of the 10 mutants that have been shown to contain DNA sequence alterations, 2 exhibit a split phenotype with respect to complementation of the growth defect and methylmethanesulfonate sensitivity of the double mutant; one is a null mutant. The mutants possessing a split phenotype contain amino acid residue alterations within a putative nucleotide binding site of DNA polymerase beta. This approach for the isolation and evaluation of mutants of a mammalian DNA polymerase in E. coli may ultimately lead to a better understanding of the mechanism of action of this enzyme and to precisely defining its role in vertebrate cells.
Peer Reviewed: Capillary Electrochromatography (1997)

ADVERTISEMENT RETURN TO ISSUEPREVFeaturesNEXTPeer Reviewed: Capillary Electrochromatography Electroosmosis drives this separation that can be performed on CE systems Luis A. Colón, Yong Guo, and Adam FermierCite this: Anal. Chemi. 1997, 69, 15, 461A–467APublication Date (Web):June 1, 2011Publication History Published online1 June 2011Published inissue 1 August 1997https://pubs.acs.org/doi/10.1021/ac9717245https://doi.org/10.1021/ac9717245research-articleACS PublicationsRequest reuse permissionsArticle Views540Altmetric-Citations146LEARN 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
Iterative Spectral Unmixing for Optimizing Per-Pixel Endmember Sets (2006)

Fractional abundances predicted for a given pixel using spectral mixture analysis (SMA) are most accurate when only the endmembers that comprise it are used, with larger errors occurring if inappropriate endmembers are included in the unmixing process. This paper presents an iterative implementation of SMA (ISMA) to determine optimal per-pixel endmember sets from the image endmember set using two steps: 1) an iterative unconstrained unmixing, which removes one endmember per iteration based on minimum abundance and 2) analysis of the root-mean-square error as a function of iteration to locate the critical iteration defining the optimal endmember set. The ISMA was tested using simulated data at various signal-to-noise ratios (SNRs), and the results were compared with those of published unmixing methods. The ISMA method correctly selected the optimal endmember set 96% of the time for SNR of 100 : 1. As a result, per-pixel errors in fractional abundances were lower than for unmixing each pixel using the full endmember set. ISMA was also applied to Airborne Visible/Infrared Imaging Spectrometer hyperspectral data of Cuprite, NV. Results show that the ISMA is effective in obtaining abundance fractions that are physically realistic (sum close to one and nonnegative) and is more effective at selecting endmembers that occur within a pixel as opposed to those that are simply used to improve the goodness of fit of the model but not part of the mixture
Maximizing the Value of Milk Through Separation Technologies (1999)

Milk is the source of a wide range of proteins that deliver nutrition to the most promising new food products today. Isolated milk proteins are natural, trusted food ingredients with excellent functionality. Separation technologies provide the basis for adding value to milk through the production of proteins that provide the food industry with ingredients to meet specific needs, not possible with milk itself or with other ingredients. The major milk proteins, casein and whey protein, can be isolated by manipulating their compositional and physical properties and then by using various separation technologies to recover the proteins. Additionally, they can be processed in various ways to create a wide range of ingredients with diverse functional characteristics. These ingredients include milk protein concentrate, milk protein isolate, casein, caseinate, whey protein concentrate, whey protein isolate, hydrolysates, and various milk fractions. Within each of these ingredient categories, there is further differentiation according to the functional and nutritional requirements of the finished food. Adding value to milk by expanding from consumer products to ingredients often requires different technologies, marketing structure and distribution channels. The worldwide market for both consumer products and ingredients from milk continues to grow. Technology often precedes market demand. Methods for the commercial production of individual milk components now exist, and in the future as clinical evidence develops, the opportunity for adding value to dairy products as functional foods with health benefits may be achieved. The research and development of today will be the basis of those value-added milk products for tomorrow.
A novel aspartyl protease allowing KEX2‐independent MFα propheromone processing in yeast (1990)

Mutants of Saccharomyces cerevisiae which lack the KEX2-encoded endopeptidase are unable to process proteolytically the mating factor alpha (MF alpha) propheromone produced from the chromosomal MF alpha 1 and MF alpha 2 genes (Julius et al., 1983). Overproduction of pheromone precursor from multiple, plasmid-borne MF alpha genes did, however, lead to the production of active MF alpha peptides in the absence of the KEX2 gene product. S. cerevisiae therefore must possess an alternative processing enzyme. The cleavage site of this enzyme appeared identical to that of the KEX2-encoded endopeptidase. To identify the gene responsible for the alternative processing, we have isolated clones which allowed production of mature MF alpha in a kex2-disrupted strain even from the chromosomal MF alpha genes. The gene isolated in this way was shown also to be essential for the KEX2-independent processing of propheromone overproduced from plasmid-borne MF alpha 1. The amino acid sequence deduced from the gene shows extensive homology to a number of aspartyl proteases including the PEP4 and BAR1 gene products from S. cerevisiae. In contrast to the BAR1 gene product, the novel aspartyl protease (YAP3 for Yeast Aspartyl Protease 3) contains a C-terminal serine/threonine-rich sequence and potential transmembrane domain similar to those found in the KEX2 gene product. The corresponding gene YAP3 was located to chromosome XII. The normal physiological role of the YAP3 gene product is not known. Strains disrupted in YAP3 are both viable and able to process the mating factor a precursor.
Characterization of a herpes simplex virus type 2 75,000-molecular-weight glycoprotein antigenically related to herpes simplex virus type 1 glycoprotein C (1983)

Evidence is presented that the herpes simplex virus type 2 glycoprotein previously designated gF is antigenically related to herpes simplex virus type 1 gC (gC-1). An antiserum prepared against type 1 virion envelope proteins immunoprecipitated gF of type 2 (gF-2), and competition experiments revealed that the anti-gC-1 component of the antiserum was responsible for the anti-gF-2 cross-reactivity. An antiserum prepared against fully denatured purified gF-2, however, and three anti-gF-2 monoclonal antibodies failed to precipitate any type 1 antigen, indicating that the extent of cross-reactivity between gC-1 and gF-2 may be limited. Several aspects of gF-2 synthesis and processing were investigated. Use of the enzymes endo-beta-N-acetylglucosaminidase H and alpha-D-N-acetylgalactosaminyl oligosaccharidase revealed that the fully processed form of gF-2 (about 75,000 [75K] apparent molecular weight) had both complex-type N-linked and O-linked oligosaccharides, whereas newly synthesized forms (67K and 69K) had only high-mannose N-linked oligosaccharides. These last two forms were both reduced in size to 54K by treatment with endo-beta-N-acetylglucosaminidase H and therefore appear to differ only in the number of N-linked chains. Neutralization tests and radioiodination experiments revealed that gF-2 is exposed on the surfaces of virions and that the 75K form of gF-2 is exposed on cell surfaces. The similarities and differences of gF-2 and gC-1 are discussed in light of recent mapping results which suggest collinearity of their respective genes.
DNA Library Preparation: Simultaneous DNA Fragmentation and Adaptor Tagging by In Vitro Transposition (2010)

RP-69 DNA library preparation is a common entry point and bottleneck for next-generation sequencing. Current methods generally consist of distinct DNA fragmentation, end-polishing, and adaptor-ligation steps; often with significant sample loss and hands-on time. EPICENTRE Biotechnologies has developed Nextera™ technology which combines these distinct steps into a single reaction; providing a streamlined, efficient, and high-throughput method for generating bar-coded sequencing libraries from nanogram amounts of DNA, in less than two hours. In vitro transposition with Nextera Transposomes simultaneously fragments and covalently tags the target DNA. Di-tagged sequencing libraries compatible with multiple sequencing platforms can be enriched and bar-coded using suppression PCR. Deep sequencing of Nextera libraries yields sequence depth, coverage, and accuracy that is comparable to control libraries produced using nebulization and standard protocols.
Low nonalloyed Ohmic contact resistance to nitride high electron mobility transistors using N-face growth (2007)

Nonalloyed Ohmic contacts on Ga-face n+-GaN∕AlGaN∕GaN high electron mobility transistor (HEMT) structures typically have significant contact resistance to the two-dimensional electron gas (2DEG) due to the AlGaN barrier. By growing the HEMT structure inverted on the N-face, electrons from the contacts were able to access the 2DEG without going through an AlGaN layer. A low contact resistance of 0.16Ωmm and specific contact resistivity of 5.5×10−7Ωcm2 were achieved without contact annealing on the inverted HEMT structure.
Human keratinocytes express a new CD44 core protein (CD44E) as a heparan-sulfate intrinsic membrane proteoglycan with additional exons. (1991)

We previously identified a 90-kD (GP90), collagen-binding, membrane glycoprotein, termed extracellular matrix receptor III (ECMR III), that is homologous to the lymphocyte homing receptor and CD44 antigen (Gallatin, W. M., E. A. Wayner, P. A. Hoffman, T. St. John, E. C. Butcher, and W. G. Carter. 1989. Proc. Natl. Acad. Sci. USA. 86:4654-4658). CD44 is abundantly expressed in many epithelial tissues, and is localized predominantly to filopodia in cultured keratinocytes. Here we establish CD44 as a polymorphic family of related membrane proteoglycans and glycoproteins possessing extensive diversity in both glycosylation and core protein sequence. Human neonatal foreskin keratinocytes (HFKs) and QG56 lung squamous carcinoma cells express an alternatively spliced form of the CD44 core protein (termed CD44E) that contains an additional 132 amino acids in the carbohydrate attachment region of the extracellular domain. HFKs, HT1080 fibrosarcoma and QG56 cells, as well as many other human cells, contain varying ratios of GP90 and structurally related, higher molecular mass forms of CD44 that express the following characteristics: (a) each form reacted with anti-CD44 (mAbs) P1G12, P3H9, and P3H5. Each of these mAbs recognized a distinct, nonoverlapping epitope present on each CD44 form. (b) Differences in mass were due primarily to variation in carbohydrate moieties, including sulfated aspargine-linked glycopeptides (GP), chondroitin sulfate (CS), and heparan sulfate (HS) glycosaminoglycans, as well as O-linked mucin and polylactosamine structure(s). The major polymorphic forms were designated HT1080 GP90 and CS180, QG56 GP230, and HFK HS/CS250, based on dominant carbohydrate moieties and relative mass. (c) The polymorphic forms use CD44 and CD44E core proteins, each containing a unique set of potential attachment sites for O- and N-glycosides and glycosaminoglycans. (d) Immunofluorescence microscopy, differential extraction with Triton-X-114 detergent, and incorporation into liposomes indicated that all the forms were membrane bound glycoconjugates. These results define CD44 as a structurally diverse, but immunologically related, set of intrinsic membrane macromolecules, and suggests that these structurally varied forms might be expected to manifest multiple functions.
[O2–17–02]: DISCOVERY AND EARLY CLINICAL DEVELOPMENT OF IONIS‐MAPTRX, THE FIRST TAU‐LOWERING ANTISENSE OLIGONUCLEOTIDE, IN PATIENTS WITH MILD AD (2017)

There is a critical role for tau in transducing Aβ-linked neurotoxicity and tau pathology is temporally and regionally-related to the expression of Alzheimer's disease (AD). Reducing the synthesis of tau should decrease all isoforms and conformational states of tau in all compartments. Therapeutic targeting is not limited to the non-exosomal transmission-dependent extracellular pool. In animals, homozygous and hemizygous knockout of endogenous tau expression is protective against many Aβ insults (Morris M, et al. Neuron 2011; 70; 410–26). In transgenic mouse models, antisense oligonucleotide (ASO) mediated binding and degradation of human MAPT gene pre-mRNA reversed pre-existing tau pathology and seeding activity, prevented neurodegeneration and functional deficits and extended survival (DeVos SL, et al. Science Translational Medicine 9, 2017). Based on these findings, an ASO that would bind and degrade the pre-mRNA transcribed from the MAPT gene and thereby reduce synthesis of tau protein was identified suitable for human clinical trials. ASOs were designed and tested in cell cultures and in transgenic mice to identify the optimal drug candidate. Toxicology studies were performed in rodents and non-human primates (NHPs) to determine the candidate's safety, pharmacokinetic and pharmacodynamic profiles. The results from the toxicology studies informed the design of the early clinical program. Ionis-MAPTRx, a second generation 2'-O-methoxyethyl chimeric ASO, was documented to reduce tau expression in transgenic mice and was tested in IND-enabling toxicology studies in rodents and NHPs. Intrathecal administration of the highest dose in NHPs resulted in a mean MAPT mRNA reduction of 77% in frontal cortex and 74% in hippocampus without dose-limiting side effects. The first clinical trial, Ionis-MAPTRx-CS1, is a multi-center, randomized, double-blind, placebo-controlled study assessing multiple ascending doses of intrathecally administered Ionis-MAPTRx in patients with mild AD. The study endpoints, which include CSF biomarker, neuroimaging, and clinical outcomes, serve both as safety measures and as exploratory measures of pharmacodynamic effect. Ionis-MAPTRx is a potent ASO with specificity for human MAPT pre-mRNA to suppress translation of tau protein. This promising therapeutic approach for primary and secondary tauopathies is about to enter clinical investigation in patients with mild AD.