gebhart/patrepeval huggingface dataset:
HLA-E expression by gynecological cancers restrains tumor-infiltrating CD8+T lymphocytes (2011)

HLA-E is a nonclassical HLA class I molecule, which differs from classical HLA molecules by its nonpolymorphic, conserved nature. Expression and function of HLA-E in normal tissues and solid tumors is not fully understood. We investigated HLA-E protein expression on tissue sections of 420 ovarian and cervical cancers and found equal or higher levels than normal counterpart epithelia in 80% of the tumors. Expression was strongly associated with components of the antigen presentation pathway, e.g., transporter associated with antigen processing (TAP), endoplasmic reticulum aminopeptide (ERAP), β2 microglobulin (β2m), HLA classes I and II, and for ovarian cancer with tumor infiltrating CD8(+) T lymphocytes (CTLs). This association argues against the idea that HLA-E would compensate for the loss of classical HLA in tumors. In situ detection of HLA-E interacting receptors revealed a very low infiltrate of natural killer (NK) cells, but up to 50% of intraepithelial CTLs expressed the inhibiting CD94/NKG2A receptor. In cervical cancer, HLA-E expression did not alter the prognostic effect of CTLs, most likely due to very high infiltrating CTL numbers in this virus-induced tumor. Overall survival of ovarian cancer patients, however, was strongly influenced by HLA-E, because the beneficial effect of high CTL infiltration was completely neutralized in the subpopulation with strong HLA-E expression. Interestingly, these results indicate that CTL infiltration in ovarian cancer is associated with better survival only when HLA-E expression is low and that intratumoral CTLs are inhibited by CD94/NKG2A receptors on CTLs in the tumor microenvironment.
Correlation of real time spectroellipsometry and atomic force microscopy measurements of surface roughness on amorphous semiconductor thin films (1996)

We have correlated the results of real time spectroellipsometry (SE) and ex situ atomic force microscopy (AFM) measurements of surface roughness on amorphous semiconductor thin films. Roughness layer thicknesses deduced from real time SE, using a conventional approach based on the Bruggeman effective medium theory, closely obey a relationship of the form: ds(SE)≊1.5 drms(AFM)+4 Å, for 10≤dS(SE)&amp;lt;100 Å, where drms(AFM) is the root-mean-square roughness from AFM. The slope and intercept of this relationship provide insights into the origin and interpretation of the optically deduced roughness layer thicknesses.
A multi-purpose VLSI chip for adaptive data compression of bilevel images (1988)

A VLSI chip for data compression has been implemented based on a general-purpose adaptive binary arithmetic coding (ABAC) architecture. This architecture permits the reuse of adapter and arithmetic coder logic in a universal way, which together with application-specific model logic can create a variety of powerful compression systems. The specific version of the adapter/coder used herein is the “Q-Coder,” described in various companion papers. The hardware implementation is in a single HCMOS chip, to maximize speed and minimize cost. The primary purpose of the chip is to provide superior data compression performance for bilevel image data by using conditional binary source models together with adaptive arithmetic coding. The coding scheme implemented is called the Adaptive Bilevel Image Compression (ABIC) algorithm. On business documents, it consistently outperforms such nonadaptive algorithms as the CCITT Group 4 (T.6) Standard and comes into its own when adapting to documents scanned at different resolutions or which include significantly different data such as digital halftones. The multi-purpose nature of the chip allows access to internal partition combinations such as the “Q” adapter/coder, which in combination with external logic can be used to realize hardware for other compression applications. On-chip memory limitations can also be overcome by the addition of external memory in special cases. Other options include the uploading and downloading of adaptive statistics and choices to encode or decode, with or without adaptation of these statistics.
Roles of NPM2 in Chromatin and Nucleolar Organization in Oocytes and Embryos (2003)

Upon fertilization, remodeling of condensed maternal and paternal gamete DNA occurs to form the diploid genome. In Xenopus laevis, nucleoplasmin 2 (NPM2) decondenses sperm DNA in vitro. To study chromatin remodeling in vivo, we isolated mammalian NPM2 orthologs. Mouse NPM2 accumulates in oocyte nuclei and persists in preimplantation embryos. Npm2 knockout females have fertility defects owing to failed preimplantation embryo development. Although sperm DNA decondensation proceeds without NPM2, abnormalities are evident in oocyte and early embryonic nuclei. These defects include an absence of coalesced nucleolar structures and loss of heterochromatin and deacetylated histone H3 that normally circumscribe nucleoli in oocytes and early embryos, respectively. Thus, Npm2 is a maternal effect gene critical for nuclear and nucleolar organization and embryonic development.
Genomic Cloning, Molecular Characterization, and Functional Analysis of Human CLCA1, the First Human Member of the Family of Ca2+-Activated Cl−Channel Proteins (1998)

We have cloned and molecularly and functionally characterized the first human member of the family of Ca2+-activated Cl- channels, human (h) CLCA1. The 31,902-bp gene is located on chromosome 1p22-31 and is preceded by a canonic promoter region that contains an L1 transposable element. In contrast to all previously known homologs in other species, hCLCA1 is exclusively expressed in intestinal basal crypt epithelia and goblet cells, suggesting that it does not represent the human counterpart of any of them. Expression of the 914-amino-acid hCLCA1 protein in HEK 293 cells yielded a 125-kDa precursor that was processed to yield two cell-surface-associated subunits, a 90-kDa protein and a group of 37- to 41-kDa proteins. Four transmembrane domains were established within the 90-kDa subunit. HEK 293 cells transfected with CLCA1 exhibited an increase in whole-cell Ca2+-sensitive Cl- currents that were outwardly rectified and inhibited by 4,4'-diisothiocyanatostilbene-2, 2'-disulfonic acid, dithiothreitol, and niflumic acid. Cell-attached patch recordings of transfected cells revealed single channels with a slope conductance of 13.4 pS. These findings suggest that human CLCA1 mediates a Ca2+-activated Cl- conductance in the human intestine and make it an interesting candidate as a modulating factor in the pathogenesis of cystic fibrosis.
Analysis of human Y-chromosome-specific reiterated DNA in chromosome variants. (1977)

A number of individuals with aberrant Y chromosomes have been tested for the presence of Y-chromosome-specific reiterated DNA. These studies locate Y-chromosome-specific reiterated sequences on the long arm of the Y chromosome. Correlation with phenotype and other known Y chromosome markers establish that the Y-chromosome-specific reiterated DNA discussed here has no evident role in male determination.
Amplification and overexpression of the egf receptor gene in primary human glioblastomas (1985)

The expression of epidermal growth factor (EGF) receptor in brain tumours of glial origin was studied at the protein, mRNA and genomic levels. Four out of 10 glioblastomas that overexpress EGF receptor also have gene amplification. The amplified genes appear to be rearranged, generating an aberrant mRNA in at least one of these tumours. Such receptor defects may be relevant to tumorigenesis of human glioblastomas.
Application of Four Anti-Human Interferon-α Monoclonal Antibodies for Immunoassay and Comparative Analysis of Natural Interferon-α Mixtures (1991)

Four different mouse monoclonal antibodies to human interferon-alpha (IFN-alpha) were evaluated for application in quantitative and comparative analysis of natural IFN-alpha mixtures. Binding to IFN-alpha subtypes in solution revealed individual reactivity patterns. These patterns changed if the IFN-alpha molecules were immobilized either passively to a surface or bound by another antibody. Also, substitution of a single amino acid in IFN-alpha 2 affected the binding, apparently by altering the conformation. Isoelectric focusing of three natural IFN-alpha preparations from different sources, followed by immunoblotting, resulted in individual patterns with each of the four mAbs and also demonstrated variation in the composition of the IFN-alpha preparations. None of the mAbs was subtype specific, but by combining the different mAbs, and also applying polyclonal anti-human IFN-alpha antibodies, it was possible to design sensitive sandwich ELISAs with broad or more limited IFN-alpha subtype specificity.
BAY 41-4109 has multiple effects on Hepatitis B virus capsid assembly (2006)

Here we report the effect of a heteroaryldihydropyrimidine (HAP) antiviral compound, BAY 41-4109, on Hepatitis B virus (HBV) capsid assembly and on preformed HBV capsids. The HBV capsid is an icosahedral complex of 120 capsid protein dimers. BAY41-4109 inhibits virus production in vivo by a mechanism that targets the viral capsid. We found that BAY 41-4109 was able to both accelerate and misdirect capsid assembly in vitro. As little as one HAP molecule for every five HBV dimers was sufficient to induce formation of non-capsid polymers. Unlike the related molecule HAP-1 (Stray et al., Proc. Natl. Acad. Sci. USA 102:8138-43, 2005), no stable assembly intermediates were observed in assembly reactions with BAY 41-4109, indicating that accelerated assembly by BAY 41-4109 was still kinetically regulated by the nucleation rate. Preformed capsids were stabilized by BAY 41-4109, up to a ratio of one inhibitor molecule per two dimers. However, at BAY 41-4109:dimer ratios of 1:1 and greater, capsids were destabilized to yield very large non-capsid polymers. These data suggest the existence of two functionally distinguishable classes of drug-binding sites on HBV capsids. Occupation of the first class of site stabilizes capsid, while binding at the second class requires or induces structural changes that cannot be tolerated without destabilizing the capsid. Our data suggest that HAP compounds may inhibit virus replication by inducing assembly inappropriately and, when in excess, by misdirecting assembly decreasing the stability of normal capsids.
Modulation of cerebral GABA by topiramate, lamotrigine, and gabapentin in healthy adults (2002)

This study demonstrates that single doses of topiramate and gabapentin increase cerebral GABA concentrations acutely (hours) in healthy individuals, but all drugs at clinically utilized doses increase cerebral GABA at 4 weeks. These results suggest that the mechanisms of action of anticonvulsant drugs are more complex and are likely to be multiple in nature.
Nonparametric estimates of standard error: The jackknife, the bootstrap and other methods (1981)

We discuss several nonparametric methods for attaching a standard error to a point estimate: the jackknife, the bootstrap, half-sampling, subsampling, balanced repeated replications, the infinitesimal jackknife, influence function techniques and the delta method. The last three methods are shown to be identical. All the methods derive from the same basic idea, which is also the idea underlying the common parametric methods. Extended numerical comparisons are made for the special case of the correlation coefficient.
Material Properties and Cytocompatibility of Injectable MMP Degradable Poly(lactide ethylene oxide fumarate) Hydrogel as a Carrier for Marrow Stromal Cells (2007)

Injectable in situ crosslinkable biomaterials seeded with multipotent progenitor cells and coupled with minimally invasive arthroscopic techniques are an attractive alternative for treating irregularly shaped osteochondral defects. An in situ crosslinkable poly(lactide-co-ethylene oxide-co-fumarate) (PLEOF) macromer has been developed with ultralow molecular weight poly(L-lactide) and poly(ethylene glycol) (PEG) units linked by fumaryl unit. The PLEOF macromer was crosslinked with the MMP-13 degradable peptide sequence QPQGLAK with acrylate end-groups or the methylene bisacrylamide (BISAM) crosslinker to form enzymatically or hydrolytically degradable hydrogels, respectively. Cell viability of the peptide crosslinker was significantly higher than that of BISAM. The relatively higher molecular weight peptide crosslinker significantly affected the water content and the rate of crosslinking (e.g., sol vs gel fraction). The addition of a small fraction of a highly reactive BISAM crosslinker to the PLEOF/peptide mixture reduced the gelation time and increased the elastic modulus while retaining enzymatic degradability of the hydrogel. Bone marrow stromal (BMS) cells were encapsulated in the peptide crosslinked PLEOF hydrogel; 84% of the encapsulated cells was viable after 1 week of incubation in osteogenic media. The encapsulated BMS cells differentiated to osteoblasts and produced a mineralized matrix, as measured by ALPase activity and calcium content. The degradation rate of the hydrogel depended on the ratio of the peptide to the BISAM crosslinker, MMP-13 concentration, and incubation time. The results demonstrate that the peptide crosslinked PLEOF hydrogel with tunable degradation characteristics is potentially useful as an injectable in situ crosslinkable carrier for bone marrow stromal cells.
Characterization of Lung γδ T Cells Following Intranasal Infection with Mycobacterium bovis Bacillus Calmette-Guerin (2003)

The lungs are considered to have an impaired capacity to contain infection by pathogenic mycobacteria, even in the presence of effective systemic immunity. In an attempt to understand the underlying cellular mechanisms, we characterized the gammadelta T cell population following intranasal infection with Mycobacterium bovis bacillus Calmette-Guérin (BCG). The peak of gammadelta T cell expansion at 7 days postinfection preceded the 30 day peak of alphabeta T cell expansion and bacterial count. The expanded population of gammadelta T cells in the lungs of BCG-infected mice represents an expansion of the resident Vgamma2 T cell subset as well as an influx of Vgamma1 and of four different Vdelta gene-bearing T cell subsets. The gammadelta T cells in the lungs of BCG-infected mice secreted IFN-gamma following in vitro stimulation with ionomycin and PMA and were cytotoxic against BCG-infected peritoneal macrophages as well as against the uninfected J774 macrophage cell line. The cytotoxicity was selectively blocked by anti-gammadelta TCR mAb and strontium ions, suggesting a granule-exocytosis killing pathway. Depletion of gammadelta T cells by injection of specific mAb had no effect on the subsequent developing CD4 T cell response in the lungs of BCG-infected mice, but significantly reduced cytotoxic activity and IFN-gamma production by lung CD8 T cells. Thus, gammadelta T cells in the lungs might help to control mycobacterial infection in the period between innate and classical adaptive immunity and may also play an important regulatory role in the subsequent onset of alphabeta T lymphocytes.
Thermochemical Aspects of Arene C-H Activation by Tantalum Silyl Complexes: Relative Ta-Si and Ta-C Bond Enthalpies (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThermochemical Aspects of Arene C-H Activation by Tantalum Silyl Complexes: Relative Ta-Si and Ta-C Bond EnthalpiesQian Jiang, Doris C. Pestana, Patrick J. Carroll, and Donald H. BerryCite this: Organometallics 1994, 13, 9, 3679–3691Publication Date (Print):September 1, 1994Publication History Published online1 May 2002Published inissue 1 September 1994https://pubs.acs.org/doi/10.1021/om00021a048https://doi.org/10.1021/om00021a048research-articleACS PublicationsRequest reuse permissionsArticle Views204Altmetric-Citations24LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Prussian Blue Dispersed Sphere Catalytic Labels for Amplified Electronic Detection of DNA (2007)

A highly sensitive electrochemical DNA hybridization assay using Prussian blue (PB)-modified polymeric spheres as the oligonculeotide labeling tag is described. The sandwich assay relies on a secondary nucleic-acid probe functionalized with polystyrene beads loaded with numerous Prussian blue nanoparticles. The very strong catalytic activity of the captured PB 'artificial peroxidase' tag towards the reduction of hydrogen peroxide, along with the encapsulation of numerous catalytic particles onto polymeric beads, allows amperometric detection of the DNA target down to the 50 fM level (2.5 amol). Imaging and spectroscopic measurements are used to characterize the PB-tagged polystyrene beads. Such coupling of PB catalytic labels with polymeric carrier beads offers great promise for amplified transduction of different biomolecular interactions.
Strain Stiffening in Synthetic and Biopolymer Networks (2010)

Strain-stiffening behavior common to biopolymer networks is difficult to reproduce in synthetic networks. Physically associating synthetic polymer networks can be an exception to this rule and can demonstrate strain-stiffening behavior at relatively low values of strain. Here, the stiffening behavior of model elastic networks of physically associating triblock copolymers is characterized by shear rheometry. Experiments demonstrate a clear correlation between network structure and strain-stiffening behavior. Stiffening is accurately captured by a constitutive model with a single fitting parameter related to the midblock length. The same model is also effective for describing the stiffening of actin, collagen, and other biopolymer networks. Our synthetic polymer networks could be useful model systems for biological materials due to (1) the observed similarity in strain-stiffening behavior, which can be quantified and related to network structure, and (2) the tunable structure of the physically associating network, which can be manipulated to yield a desired response.
Runtime Defense against Code Injection Attacks Using Replicated Execution (2011)

The number and complexity of attacks on computer systems are increasing. This growth necessitates proper defense mechanisms. Intrusion detection systems play an important role in detecting and disrupting attacks before they can compromise software. Multivariant execution is an intrusion detection mechanism that executes several slightly different versions, called variants, of the same program in lockstep. The variants are built to have identical behavior under normal execution conditions. However, when the variants are under attack, there are detectable differences in their execution behavior. At runtime, a monitor compares the behavior of the variants at certain synchronization points and raises an alarm when a discrepancy is detected. We present a monitoring mechanism that does not need any kernel privileges to supervise the variants. Many sources of inconsistencies, including asynchronous signals and scheduling of multithreaded or multiprocess applications, can cause divergence in behavior of variants. These divergences cause false alarms. We provide solutions to remove these false alarms. Our experiments show that the multivariant execution technique is effective in detecting and preventing code injection attacks. The empirical results demonstrate that dual-variant execution has on average 17 percent performance overhead when deployed on multicore processors.
Purification, Biochemical Characterization and Protein-DNA Interactions of the I-CreI Endonuclease Produced in Escherichia Coli (1997)

I- CreI is a member of the LAGLI-DADG family of homing nucleases; however, unlike most members of this family it contains only a single copy of this signature motif. I- CreI was over-expressed in Escherichia coli, and a simple purification protocol developed that gave reasonably pure protein in high yield. Size-exclusion chromatography and chemical cross-linking indicated that the protein is a dimer in solution. DNA cleavage by I- CreI was absolutely dependent on Mg2+(or Mn2+), and was inhibited by monovalent cations. I- CreI displayed a surprisingly high temperature optimum (>50 degrees C), with full activity occurring even at 70 degrees C. Interestingly, SDS was needed for efficient release of the cleavage products from the protein, indicating formation of very stable DNA-protein complexes. In contrast to these robust characteristics, purified I- CreI was unstable; however, it could be stabilized by the addition of either target or non-target DNA. Mobility shift assays revealed that I- CreI binds to DNA in the absence of Mg2+. Hydroxyl radical footprinting showed that I- CreI strongly protected the backbone of a continuous stretch of at least 12 nt on each strand that were shifted, relative to each other, by 2 bp in the 3'direction. Methylation protection and interference analyses were also performed, and together with the hydroxyl radical footprinting, indicate that I- CreI binds in both the major and minor grooves of its target DNA.
Human Myocardial Pericytes: Multipotent Mesodermal Precursors Exhibiting Cardiac Specificity (2014)

Perivascular mesenchymal precursor cells (i.e., pericytes) reside in skeletal muscle where they contribute to myofiber regeneration; however, the existence of similar microvessel-associated regenerative precursor cells in cardiac muscle has not yet been documented. We tested whether microvascular pericytes within human myocardium exhibit phenotypes and multipotency similar to their anatomically and developmentally distinct counterparts. Fetal and adult human heart pericytes (hHPs) express canonical pericyte markers in situ, including CD146, NG2, platelet-derived growth factor receptor (PDGFR) β, PDGFRα, alpha-smooth muscle actin, and smooth muscle myosin heavy chain, but not CD117, CD133, and desmin, nor endothelial cell (EC) markers. hHPs were prospectively purified to homogeneity from ventricular myocardium by flow cytometry, based on a combination of positive- (CD146) and negative-selection (CD34, CD45, CD56, and CD117) cell lineage markers. Purified hHPs expanded in vitro were phenotypically similar to human skeletal muscle-derived pericytes (hSkMPs). hHPs express mesenchymal stem/stromal cell markers in situ and exhibited osteo-, chondro-, and adipogenic potentials but, importantly, no ability for skeletal myogenesis, diverging from pericytes of all other origins. hHPs supported network formation with/without ECs in Matrigel cultures; hHPs further stimulated angiogenic responses under hypoxia, markedly different from hSkMPs. The cardiomyogenic potential of hHPs was examined following 5-azacytidine treatment and neonatal cardiomyocyte coculture in vitro, and intramyocardial transplantation in vivo. Results indicated cardiomyocytic differentiation in a small fraction of hHPs. In conclusion, human myocardial pericytes share certain phenotypic and developmental similarities with their skeletal muscle homologs, yet exhibit different antigenic, myogenic, and angiogenic properties. This is the first example of an anatomical restriction in the developmental potential of pericytes as native mesenchymal stem cells.