gebhart/patrepeval huggingface dataset:
Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition (2016)

Resistance to the Bruton's tyrosine kinase (BTK) inhibitor ibrutinib has been attributed solely to mutations in BTK and related pathway molecules. Using whole-exome and deep-targeted sequencing, we dissect evolution of ibrutinib resistance in serial samples from five chronic lymphocytic leukaemia patients. In two patients, we detect BTK-C481S mutation or multiple PLCG2 mutations. The other three patients exhibit an expansion of clones harbouring del(8p) with additional driver mutations (EP300, MLL2 and EIF2A), with one patient developing trans-differentiation into CD19-negative histiocytic sarcoma. Using droplet-microfluidic technology and growth kinetic analyses, we demonstrate the presence of ibrutinib-resistant subclones and estimate subclone size before treatment initiation. Haploinsufficiency of TRAIL-R, a consequence of del(8p), results in TRAIL insensitivity, which may contribute to ibrutinib resistance. These findings demonstrate that the ibrutinib therapy favours selection and expansion of rare subclones already present before ibrutinib treatment, and provide insight into the heterogeneity of genetic changes associated with ibrutinib resistance.
Role of Fibrin(ogen) in Progression of Liver Disease: Guilt by Association? (2016)

Strong experimental evidence indicates that components of the hemostatic system, including thrombin, exacerbate diverse features of experimental liver disease. Clinical studies have also begun to address this connection and some studies have suggested that anticoagulants can improve outcome in patients with liver disease. Among the evidence of coagulation cascade activation in models of liver injury and disease is the frequent observation of thrombin-driven hepatic fibrin(ogen) deposition. Indeed, hepatic fibrin(ogen) deposition has long been recognized as a consequence of hepatic injury. Although commonly inferred as pathologic due to protective effects of anticoagulants in mouse models, the role of fibrin(ogen) in acute liver injury and chronic liver disease may not be universally detrimental. The localization of hepatic fibrin(ogen) deposits within the liver is connected to the disease stimulus and in animal models of liver toxicity and chronic disease, fibrin(ogen) deposition may not always be synonymous with large vessel thrombosis. Here, we provide a balanced review of the experimental evidence supporting a direct connection between fibrin(ogen) and liver injury/disease pathogenesis, and suggest a path forward bridging experimental and clinical research to improve our knowledge on the nature and function of fibrin(ogen) in liver disease.
Newcastle disease virus contains a linkage-specific glycoprotein sialidase. Application to the localization of sialic acid residues in N-linked oligosaccharides of alpha 1-acid glycoprotein. (1982)

Newcastle disease virus sialidase was found to exhibit strict specificity for hydrolysis of the NeuAc alpha 2 leads to 3Gal linkage contained in glycoprotein oligosaccharides both N-linked to asparagine and O-linked to threonine or serine under conditions that left oligosaccharides containing the NeuAc alpha 2 leads to 2 leads to 6Gal and NeuAc alpha 2 leads to 6GallNAc linkages intact. This was determined, in part, by examining the viral sialidase for its ability to hydrolyze glycoprotein oligosaccharides derivatized with purified sialyltransferases to contain the [14C]NeuAc alpha 2 leads to 3Gal, [14C]NeuAc alpha 2 leads to 6GalNAc, and [14C]NeuAc alpha 2 leads to 6Gal linkages. The viral sialidase was also tested for hydrolysis of the NeuAc alpha 2 leads to 3Gal and NeuAc alpha 2 leads to 6Gal linkages on the N-linked oligosaccharides of alpha 1-acid glycoprotein. Selective hydrolysis of the NeuAc alpha 2 leads to 3Gal linkage was shown by periodate oxidation and by 500-MHz 1H-NMR spectroscopy of native and sialidase-treated glycopeptides. The NMR spectra, together with composition data, further indicated that the NeuAc alpha 2 leads to 3Gal and NeuAc alpha 2 leads to 6Gal linkages were localized to specific branches of the major tri- and tetraantennary oligosaccharides of alpha 1-acid glycoprotein. The results indicate that the Newcastle disease virus sialidase can initiate the selective degradation of N-linked oligosaccharide branches containing the NeuAc alpha 2 leads to 3Gal linkage.
Cationic Bis- and Tris(η2-(pyrazol-1-yl)methane) Acetyl Complexes of Iron(II) and Ruthenium(II):  Synthesis, Characterization, Reactivity, and Interionic Solution Structure by NOESY NMR Spectroscopy (1997)

The complexes trans,cis-M(PMe3)2(CO)2(Me)I (M = Fe and Ru, 1a,b) react with bis- and tris(pyrazol-1-yl)methane, in the presence of NaBPh4, affording trans-[M(PMe3)2(CO)(COMe)(pz2-CH2)]BPh4 (2a,b) and trans-[M(PMe3)2(CO)(COMe)(η2-pz3-CH)]BPh4 (3a,b), respectively (pz = pyrazolyl ring). The reactions of 1b with 5,5‘-Me2-pz2-CH2 and 3,5‘-Me2-pz2-CH2 produce trans-[Ru(PMe3)2(CO)(COMe)(5,5‘-Me2-pz2-CH2)]BPh4 (4) and trans-[Ru(PMe3)2(CO)(COMe)(3,5‘-Me2-pz2-CH2)]BPh4 (5), respectively. A mixture of trans,cis-[Ru(PMe3)2(CO)2(η1-3,3‘-Me2-pz2-CH2)(Me)]BPh4 (6) and trans-[Ru(PMe3)2(CO)(COMe)(3,3‘-Me2-pz2-CH2)]BPh4 (7) is obtained from reaction of 1b and 3,3‘-Me2-pz2-CH2. The reactions of 2−7 with nucleophiles either give back the starting complex (Nu = I-) or analogous complexes (Nu = Br- and Cl-) or produce decomposition products of the complexes (Nu = I2, Br2, Cl2, and OMe-). The solid state structures of 2b and 3b were obtained using single-crystal X-ray diffraction. For all complexes, 2−7 as well as complex 8 (analogue to 2a, having a BF4- counterion instead of BPh4-), the ion-pair structures and the localization of the counterion in solution with respect to the organometallic moiety were investigated by the detection of interionic contacts in the 1H-NOESY and 19F{1H}-HOESY NMR spectra.
Intranodal immunization with tumor lysate-pulsed dendritic cells enhances protective antitumor immunity. (2001)

We developed a technique for direct inguinal lymph node injection in mice to compare various routes of immunization with tumor lysate-pulsed dendritic cell (DC) vaccines. Syngeneic, bone marrow-derived, tumor lysate-pulsed DCs administered intranodally generated more potent protective antitumor immunity than s.c. or i.v. DC immunizations. Intranodal immunization with ovalbumin peptide-pulsed DCs induced significantly greater antigen-specific T-lymphocyte expansion in the spleen than either s.c. or i.v. immunization. Furthermore, a significantly more potent, antigen-specific TH1-type response to the ovalbumin peptide was induced by intranodal, compared with s.c. or i.v., immunization. Intranodal immunization, designed to enhance DC-T cell interaction in a lymphoid environment, optimizes induction of T lymphocyte-mediated protective antitumor immunity. These results support the use of intranodal immunization as a feasible and effective route of DC vaccine administration.
Modulation and coding for information storage (1991)

Many of the types of modulation codes designed for use in storage devices using magnetic recording are discussed. The codes are intended to minimize the negative effects of intersymbol interference. The channel model is first presented. The peak detection systems used in most commercial disk drives are described, as are the run length-limited (d,k) codes they use. Recently introduced recording channel technology based on sampling detection-partial-response (or PRML) is then considered. Several examples are given to illustrate that the introduction of partial response equalization, sampling detection, and digital signal processing has set the stage for the invention and application of advanced modulation and coding techniques in future storage products.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Skin Homing (Cutaneous Lymphocyte-Associated Antigen-Positive) CD8+ T Cells Respond to Superantigen and Contribute to Eosinophilia and IgE Production in Atopic Dermatitis (1999)

In allergic inflammations of the skin, activation of CD4+ T cells was demonstrated to play an important role; however, a minor role for CD8+ T cells is implied. In the present study, we compared cutaneous lymphocyte-associated Ag (CLA)-expressing CD4+ and CD8+ subsets, which were isolated from peripheral blood and lesional skin biopsies in atopic dermatitis (AD) patients. We demonstrated that CD8+CLA+ T cells proliferate in response to superantigen and are as potent as CD4+CLA+ T cells in IgE induction and support of eosinophil survival. In atopic skin inflammation, the existence of high numbers of CD4+ and CD8+ T cells was demonstrated by immunohistochemistry and by culturing T cells from skin biopsies. In peripheral blood, both CD4+ and CD8+ subsets of CLA+CD45RO+ T cells were in an activated state in AD. The in vivo-activated CLA+ T cells of both subsets spontaneously released an IL-5- and IL-13-dominated Th2 type cytokine pattern. This was confirmed by intracytoplasmic cytokine staining immediately after isolation of the cells from peripheral blood. In consequence, both CD4+ and CD8+, CLA+ memory/effector T cells induced IgE production by B cells mainly by IL-13, and enhanced eosinophil survival in vitro by delaying eosinophil apoptosis, mainly by IL-5. These results indicate that in addition to the CD4+ subset, the CD8+CLA+ memory/effector T cells are capable of responding to superantigenic stimulation and play an important role in the pathogenesis of AD.
Tissue engineered perivascular endothelial cell implants regulate vascular injury. (1995)

Molecular biomaterial engineering permits in vivo transplantation of cells and tissues, offering the promise of restoration of physiologic control rather than pharmacologic dosing with isolated compounds. We engrafted endothelial cells on Gelfoam biopolymeric matrices with retention of viability, normal growth kinetics, immunoreactivity, and biochemical activity. The production of heparan sulfate proteoglycan and inhibition of basic fibroblast growth factor binding and activity by engrafted cells were indistinguishable from endothelial cells grown in culture. Perivascular implantation of Gelfoam-endothelial cell scaffolds around balloon-denuded rat carotid arteries reduced intimal hyperplasia 88.1%, far better than the isolated administration of heparin, the most effective endothelial mimic compound. In concert with a reduction in intimal area, cell proliferation was reduced by > 90%. To our knowledge, there have been no previous reports of extravascular cell implants controlling vasculoproliferative disease. Tissue engineered cells offer the potential for potent methods of vascular growth regulation and insight into the complex autocrine-paracrine control mechanisms within the blood vessel wall.
Increased rates of CD4+and CD8+T lymphocyte turnover in simian immunodeficiency virus-infected macaques (1998)

Defining the rate at which T cells turn over has important implications for our understanding of T lymphocyte homeostasis and AIDS pathogenesis, yet little information on T cell turnover is available. We used the nucleoside analogue bromodeoxyuridine (BrdUrd) in combination with five-color flow cytometric analysis to evaluate T lymphocyte turnover rates in normal and simian immunodeficiency virus (SIV)-infected rhesus macaques. T cells in normal animals turned over at relatively rapid rates, with memory cells turning over more quickly than naive cells. In SIV-infected animals, the labeling and elimination rates of both CD4(+) and CD8(+) BrdUrd-labeled cells were increased by 2- to 3-fold as compared with normal controls. In normal and SIV-infected animals, the rates of CD4(+) T cell BrdUrd-labeling and decay were closely correlated with those of CD8(+) T cells. The elimination rate of BrdUrd-labeled cells was accelerated in both naive and memory T lymphocytes in SIV-infected animals. Our results provide direct evidence for increased rates of both CD4(+) and CD8(+) T cell turnover in AIDS virus infection and have important implications for our understanding of T cell homeostasis and the mechanisms responsible for CD4(+) T cell depletion in AIDS.
Interleukin-3 is significantly more effective than other colony- stimulating factors in long-term maintenance of human bone marrow- derived colony-forming cells in vitro (1989)

Human bone marrow cells cultured for 21 days in the presence of recombinant human interleukin-3 (IL-3) produced up to 28 times more colony-forming cells (CFC) than could be obtained from cultures stimulated with granulocyte colony stimulating factor (G-CSF) or granulocyte-macrophage CSF (GM-CSF). IL-3-cultured cells retained a multipotent response to IL-3 in colony assays but were restricted to formation of granulocyte colonies in G-CSF and granulocyte or macrophage colonies in GM-CSF. Culture of bone marrow cells in IL-3 also led to accumulation of large numbers of eosinophils and basophils. These data contrast with the effects of G-CSF, GM-CSF, and IL-3 in seven-day cultures. Here both GM-CSF and IL-3 amplified total CFC that had similar multipotential colony-forming capability in either factor. G-CSF, on the other hand, depleted IL-3-responsive colony-forming cells dramatically, apparently by causing these cells to mature into granulocytes. The data suggest that a large proportion of IL-3- responsive cells in human bone marrow express receptors for G-CSF and can respond to this factor, the majority becoming neutrophils. Furthermore, the CFC maintained for 21 days in IL-3 may be a functionally distinct population from that produced after seven days culture of bone marrow cells in either IL-3 or GM-CSF.
IDENTIFICATION OF A2B5+CD133− TUMOR-INITIATING CELLS IN ADULT HUMAN GLIOMAS (2008)

Together, these results demonstrate that human gliomas contain multiple populations of cells with the capacity to form tumors and specifically identify a population of tumorigenic A2B5+ cells that are phenotypically distinct from CD133+ cells.
Cutaneous T-cell lymphoma in a patient infected with human immunodeficiency virus type 1: Use of radiation therapy (1990)

A patient with cutaneous T-cell lymphoma (CTCL) and acquired immune deficiency syndrome (AIDS) is presented. The patient had a localized lesion on his scalp. Evaluation for systemic lymphoma was negative. A biopsy specimen showed superficial and deep dermal infiltrates of pleomorphic lymphocytes. Immunohistochemistry was consistent with T-cell lymphoma. The patient was treated successfully with local irradiation. He remained free of further systemic and cutaneous recurrences of the lymphoma until he died 8 months after treatment of pneumonia. This case is the first to our knowledge to describe a localized CTCL in a patient infected with human immunodeficiency virus type 1 (HIV-1).
FIELD TESTING AND EVALUATION OF INNOVATIVE TECHNOLOGIES FOR MAINTENANCE DATA COLLECTION (1995)

Automated electronic procedures for data capture and transmission appear to be superior compared with manual paper-based methods. Many highway agencies are now either using or exploring some of these innovative technologies for many of their data collection activities. For maintenance management, a variety of recording and data entry procedures involving pen and paper could be considerably improved using electronic equipment such as portable and pen-based computers, identification technologies including barcoding and voice recognition, and location systems such as global positioning system and geographic information system. In addition, data transmission can be accomplished much faster and in real time between distant locations using telecommunications systems such as mobile phones. The application of advanced data acquisition technologies for maintenance management in state highway departments is summarized.
Association between Plasma Angiopoietin-Like Protein 3 and Arterial Wall Thickness in Healthy Subjects (2006)

These results demonstrate for the first time that ANGPTL3 is closely associated with arterial wall thickness in human subjects.
"Living" Radical Polymerization of Styrene Initiated by Arenesulfonyl Chlorides and CuI(bpy)nCl (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticle"Living" Radical Polymerization of Styrene Initiated by Arenesulfonyl Chlorides and CuI(bpy)nClVirgil Percec and Bogdan BarboiuCite this: Macromolecules 1995, 28, 23, 7970–7972Publication Date (Print):November 1, 1995Publication History Published online1 May 2002Published inissue 1 November 1995https://pubs.acs.org/doi/10.1021/ma00127a057https://doi.org/10.1021/ma00127a057research-articleACS PublicationsRequest reuse permissionsArticle Views2797Altmetric-Citations781LEARN 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
Compilation and analysis ofEscherichia colipromoter DNA sequences (1983)

The DNA sequence of 168 promoter regions (-50 to +10) for Escherichia coli RNA polymerase were compiled. The complete listing was divided into two groups depending upon whether or not the promoter had been defined by genetic (promoter mutations) or biochemical (5' end determination) criteria. A consensus promoter sequence based on homologies among 112 well-defined promoters was determined that was in substantial agreement with previous compilations. In addition, we have tabulated 98 promoter mutations. Nearly all of the altered base pairs in the mutants conform to the following general rule: down-mutations decrease homology and up-mutations increase homology to the consensus sequence.
Structure and Substance: Developing a Practical and Effective Prohibition on Discrimination under the European Convention on Human Rights (2003)

Article 14 of the European Convention on Human Rights has not had any real measure of success. This may be explained in part by its lack of free-standing status and in part by the unwillingness of Convention bodies to give it full effect. All too common to European human rights jurisprudence is the Court's exercise of discretion to refrain from ruling on the discrimination claim when another substantive article has been breached. Common too is the failure to apply rigorously standards of interpretation which have rendered the article weak in terms of a substantive equality guarantee. Protocol 12 seeks to overcome these difficulties, by creating an equality guarantee with equal weight as other Convention rights. The Protocol is not likely to enter into force in the near future. In the meantime, the European Court of Human Rights appears to be making efforts to strengthen the Article 14 jurisprudence. First, the Court seems to be showing some increased willingness to deal with the discrimination claim. Second, the prohibited grounds have been extended, in terms that invite comment on the rationale for prohibited grounds. Third, a claim based on indirect discrimination has finally succeeded. Each of these disparate developments, taken together, signal attempts on the part of the Court to take Article 14 seriously. It is suggested that these attempts, while important, lack principled reasoning, and that domestic courts should take seriously the task of supplying principles on which the Court can rely for guidance.
Multicopy integration and expression of heterologous genes in the oleaginous yeast, Lipomyces starkeyi (2014)

The oleaginous yeast, Lipomyces starkeyi, is an excellent lipid producer with great industrial potential. However, methods for molecular breeding have not been established for L. starkeyi. We describe the development of a system for targeted rDNA integration of multiple copies of a gene into L. starkeyi genome by spheroplast-polyethylene glycol transformation.
Modal reflection of quarter-wave mirrors in vertical-cavity lasers (1993)

Very high plane-wave reflection coefficients can be obtained with practical semiconductor quarter-wave mirrors, but for beams of finite width, the reflection coefficient of a mirror with no lateral guiding and hence the finesse of cavities that use such structures will be limited by diffraction loss. The authors analytically and numerically study the modal reflection of practical semiconductor quarter-wave mirrors. They introduce a quantity called the diffraction range of a quarter-wave mirror as a means of exact analytical comparison between infinite lossless mirrors (and approximate comparison for finite mirrors) in the Fresnel diffraction limit. The exact modal reflection coefficient for an arbitrary incident mode pattern is determined by vector plane-wave decomposition. The modal reflection coefficients of two representative semiconductor quarter-wave mirrors used in vertical cavity laser technology, AlAs/GaAs and InGaAsP/InP, are studied.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Covariance Estimation for High Dimensional Data Vectors Using the Sparse Matrix Transform (2008)

Covariance estimation for high dimensional vectors is a classically difficult problem in statistical analysis and machine learning. In this paper, we propose a maximum likelihood (ML) approach to covariance estimation, which employs a novel sparsity constraint. More specifically, the covariance is constrained to have an eigen decomposition which can be represented as a sparse matrix transform (SMT). The SMT is formed by a product of pairwise coordinate rotations known as Givens rotations. Using this framework, the covariance can be efficiently estimated using greedy minimization of the log likelihood function, and the number of Givens rotations can be efficiently computed using a cross-validation procedure. The resulting estimator is positive definite and well-conditioned even when the sample size is limited. Experiments on standard hyperspectral data sets show that the SMT covariance estimate is consistently more accurate than both traditional shrinkage estimates and recently proposed graphical lasso estimates for a variety of different classes and sample sizes. 1