gebhart/patrepeval huggingface dataset:
γPNA FRET Pair Miniprobes for Quantitative Fluorescent In Situ Hybridization to Telomeric DNA in Cells and Tissue (2017)

Measurement of telomere length by fluorescent in situ hybridization is widely used for biomedical and epidemiological research, but there has been relatively little development of the technology in the 20 years since it was first reported. This report describes the use of dual gammaPNA (γPNA) probes that hybridize at alternating sites along a telomere and give rise to Förster resonance energy transfer (FRET) signals. Bright staining of telomeres is observed in nuclei, chromosome spreads and tissue samples. The use of FRET detection also allows for elimination of wash steps, normally required to remove unhybridized probes that would contribute to background signals. We found that these wash steps can diminish the signal intensity through the removal of bound, as well as unbound probes, so eliminating these steps not only accelerates the process but also enhances the quality of staining. Thus, γPNA FRET pairs allow for brighter and faster staining of telomeres in a wide range of research and clinical formats.
Adsorption of polyamides and polyamide–silane mixtures at glass surfaces (2003)

Abstract The individual and combined adsorption behavior of polyamides and two different silanes to multicomponent glass surfaces was probed with a combination of x‐ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM) and static contact angle measurements. Samples were analyzed with and without solvent rinsing to separate the weakly bound (physisorbed) and more strongly bound (chemisorbed) species. High‐resolution XPS on N 1s revealed that the polyamides adsorb to the glass surfaces via protonated amine species at the acidic (OH) sites on the glass surface. Angle‐resolved XPS confirmed this by showing that the alkyl portion of the polymer is oriented away from the glass interface. In competitive coadsorption studies it was found that amino‐terminated silanes preferentially adsorb to the glass surface, relegating the polyamide to a physisorbed outer layer. When mercaptoterminated silanes were competitively coadsorbed the polyamide was preferentially adsorbed even when present at a concentration twenty times less than that of the silane. Altogether, this work reveals the strong interaction between surface silanols and amino‐functionalized organics. Copyright © 2003 John Wiley &amp; Sons, Ltd.
Monokine production by human T cells; IL-1 alpha production restricted to memory T cells (1991)

The production of cytokines is a key event of inflammation. In this report we demonstrate that normal human T cells are capable to produce IL-1 alpha, IL-6, and TNF-alpha, cytokines formerly considered to be monokines. This production was optimal after stimulation with a combination of anti-CD2, PMA, and anti-CD28. All three cytokines were produced in a bioactive form. Both naive (CD4+CD45RA+) and memory (CD4+CD45RO+) subsets of T cells were shown to produce similar amounts of IL-6 and TNF-alpha. In contrast the production of IL-1 alpha was found to be completely restricted to the CD4+CD45RO+ subset. The finding that T cells are such potent producers of these important mediators of the inflammatory response might be a key observation in the appreciation of the role of T cells in chronic inflammation.
Epidemiology of haemoglobin disorders in Europe: an overview (2007)

There is a strong case for pan-European collaboration on haemoglobin disorders to share policies, standards and the instruments required to support them. These include methods for needs assessment, service standards, education and information strategies and materials, and methods for evaluating service delivery.
Perspectives on mammalian cell death. (1987)

C.S. Potten: Introduction C. Sato: Membrane changes R.T. Dean: Some critical membrane events during mammalian cell death T.D. Allen: Ultrastructural aspects of cell death W.J. Hume: A pathologist's view of cell death J.F.R. Kerr, B.V. Harmon & C.J. Bishop: Apoptosis K.-H. von Wangenheim: Cell death through differentiation. Potential immortality of somatic cells: a failure in control of differentiation J.H. Hendry & D. Scott: Loss of reproductive integrity of irradiated cells, and its importance in tissues S. Shall: Mortalization or reproductive sterility of animal cells in culture M.H.L. Snow: Cell death in embryonic development D.J. Allan, B.V. Harmon & J.F.R. Kerr: Cell death in spermatogenesis S.E. Christmas & M. Moore: Immunologically-mediated cell death J.V. Moore: Death of cells and necrosis of tumours K. Ijiri & C.S. Potten: Cell death in cell hierarchies in adult mammalian tissue.
Solid-phase methods for sequencing of nucleic acids I. Simultaneous sequencing of different oligodeoxyribonucleotides using a new, mechanically stable anion-exchange paper (1985)

A solid-phase method for simultaneous sequencing of large numbers of oligodeoxyribonucleotides has been developed using a new, mechanically stable anion-exchange paper. The excellent mechanical properties of the polymer allow the processing of several paper segments in one reaction vessel or to carry out all necessary operations on a larger area of the paper. In addition, DNA material can be chemically eluted from the new carrier during the piperidine reaction, thus avoiding salt elution of DNA and subsequent ethanol precipitation steps - a prerequisite for sequencing oligonucleotides. The approach involves 7 operations including: i) immobilization; ii) washing; iii) modification; iv) washing; v) sorting of the papers; vi) piperidine reaction and chemical elution and vii) lyophilization. All steps can be carried out in 4 to 5 hours independently of the number of oligonucleotides to be sequenced. It is also possible to sequence small oligonucleotides with 3 to 4 base pairs. The method can be fully automated.
Configuration Tracking for Continuum Manipulators With Coupled Tendon Drive (2009)

Robotic control of flexible devices can enhance and simplify many medical procedures. We present a method for controlling a tendon-driven continuum manipulator by means of specifying the shape configuration. The basis for control is a linear beam configuration model that transforms beam configuration to tendon displacement by modeling internal loads of the compliant system. An essential aspect of this model is the inclusion of both the mechanical and geometrical coupling among serial articulating sections. Important capabilities of this model are the general forward kinematics and the decoupled inverse kinematics that allow for independent control of multiple sections. Tracking results are presented for a cardiac catheter with two articulating sections.
40.1: A New MVA‐LCD by Polymer Sustained Alignment Technology (2004)

Abstract A new MVA‐LCD using Polymer Sustained Alignment technology (PSA‐LCD) has been developed. This technology can realize a stable alignment with protrusion free structure by polymer sustainment. PSA‐LCD has established high brightness, high contrast ratio and fast response speed.
SPARC/osteonectin induces matrix metalloproteinase 2 activation in human breast cancer cell lines. (1998)

Activation of the matrix metalloproteinase 2 (MMP-2) has been shown to play a major role in the proteolysis of extracellular matrix (ECM) associated with tumor invasion. Although the precise mechanism of this activation remains elusive, levels of the membrane type 1-MMP (MT1-MMP) at the cell surface and of the tissue inhibitor of MMP-2 (TIMP-2) appear to be two important determinants. Induction of MMP-2 activation in cells cultivated on collagen type I gels indicated that the ECM is important in the regulation of this process. In this study, we show that SPARC/osteonectin, a small ECM-associated matricellular glycoprotein, can induce MMP-2 activation in two invasive breast cancer cell lines (MDA-MB-231 and BT549) but not in a noninvasive counterpart (MCF-7), which lacks MT1-MMP. Using a set of peptides from different regions of SPARC, we found that peptide 1.1 (corresponding to the NH2-terminal region of the protein) contained the activity that induced MMP-2 activation. Despite the requirement for MT1-MMP, seen in MCF-7 cells transfected with MT1-MMP, the activation of MMP-2 by SPARC peptide 1.1 was not associated with increased steady-state levels of MT1-MMP mRNA or protein in either MT1-MMP-transfected MCF-7 cells or constitutively expressing MDA-MB-231 and BT549 cells. We did, however, detect decreased levels of TIMP-2 protein in the media of cells incubated with peptide 1.1 or recombinant SPARC; thus, the induction of MMP-2 activation by SPARC might be due in part to a diminution of TIMP-2 protein. We conclude that SPARC, and specifically its NH2-terminal domain, regulates the activation of MMP-2 at the cell surface and is therefore likely to contribute to the proteolytic pathways associated with tumor invasion.
Dual‐Scale Roughness Produces Unusually Water‐Repellent Surfaces (2004)

Super-hydrophobicity can be achieved on relatively smooth surfaces. Short, wide pillars on slightly rough surfaces are shown to produce super-hydrophobic surfaces (see Figure) where neither the pillars nor the slight roughness suffice alone. This use of two length scales to create super-hydrophobic surfaces directly mimics the mechanism used by some plants including the lotus.
ThraustochytridAurantiochytriumsp. 18W-13a Accummulates High Amounts of Squalene (2011)

Here we report on the 18W-13a strain of Aurantiochytrium sp., which accumulates very high amounts of squalene. The squalene contents and production at 4 d of culture were 198 mg/g and 1.29 ± 0.13 g/L, respectively, exceptionally high values compared to previous reports.
Liposome-Based Chemical Barcodes for Single Molecule DNA Detection Using Imaging Mass Spectrometry (2010)

We report on a mass-spectrometry (time-of-flight secondary ion mass spectrometry, TOF-SIMS) based method for multiplexed DNA detection utilizing a random array, where the lipid composition of small unilamellar liposomes act as chemical barcodes to identify unique DNA target sequences down to the single molecule level. In a sandwich format, suspended target-DNA to be detected mediates the binding of capture-DNA modified liposomes to surface-immobilized probe-DNA. With the lipid composition of each liposome encoding a unique target-DNA sequence, TOF-SIMS analysis was used to determine the chemical fingerprint of the bound liposomes. Using high-resolution TOF-SIMS imaging, providing sub-200 nm spatial resolution, single DNA targets could be detected and identified via the chemical fingerprint of individual liposomes. The results also demonstrate the capability of TOF-SIMS to provide multiplexed detection of DNA targets on substrate areas in the micrometer range. Together with a high multiplexing capacity, this makes the concept an interesting alternative to existing barcode concepts based on fluorescence, Raman, or graphical codes for small-scale bioanalysis.
The Role of Targeted Agents in the Treatment of Metastatic Breast Cancer (2010)

To date, blockade of growth factor receptors is the mainstay of targeted therapy in metastatic breast cancer (mBC). Monoclonal antibodies such as trastuzumab and bevacizumab represent the first generation of molecular-based therapies. Both the HER2 inhibitors and the vascular endothelial growth factor (VEGF) antagonists have shown synergism with a broad spectrum of established cytotoxins, thus being approved for first-line treatment of mBC in combination with taxanes. As a next step, tyrosine kinase inhibitors (TKIs) have been integrated into daily routine as an alternative approach for targeting HER2: The dual HER1/2 inhibitor lapatinib demonstrated activity in trastuzumab-pretreated mBC patients in combination with capecitabine. Furthermore, chemotherapy-free regimens (trastuzumab or lapatinib plus aromatase inhibitors) have been identified as additional options for hormone receptor (HR)- and HER2-positive patients. Recently published data indicate that a combination of two biologicals such as lapatinib and trastuzumab can be effective as a treatment beyond trastuzumab related progression. Multitarget TKIs have the potential to inhibit several signaling pathways involved in breast cancer-related angiogenesis. Until now, they have failed to show a clear benefit in mBC. On the other hand, poly(ADP-ribose) polymerase (PARP) inhibition, mediated by a new class of small molecules, is an interesting area of investigation. Future directions of research in HER2-positive breast cancer focus on the evaluation of novel antibodies (pertuzumab, T-DM1), and irreversible TKIs (neratinib, BIBW 2992) and inhibitors of HER2-related downstream signaling (mTOR, TORC 1/2, PI3K/Akt) and of receptor cross-talk (IGFR).
Thymic epithelial cells provide Wnt signals to developing thymocytes (2003)

Interactions with thymic stromal cells are known to be critical for the development of T cells from progenitors entering the thymus, yet the molecular mechanisms of stromal cell function remain poorly understood. Accumulating evidence has highlighted the importance of beta-catenin-mediated activation of T cell factor (TCF)/lymphoid enhancer factor (LEF) transcription during thymocyte development. As regulation of this signaling pathway is controlled by binding of soluble Wnt proteins to cell surface Frizzled (Fz) receptors, we studied components of Wnt/Fz-mediated signaling in thecontext of stromal cell regulation of thymocyte development. We show that mRNA for a variety of Wnt family members, notably Wnt-4, Wnt-7a and 7b, and Wnt-10a and 10b, are expressed by thymic epithelium rather then by thymocytes, while thymocytes demonstrate a developmentally regulated pattern of Fz receptor expression. Collectively these findings suggest (1) a functional role for Wnt-producing thymic epithelium in determining TCF/LEF-mediated transcriptional regulation in Fz-bearing thymocytes, and (2) a role for defined Wnt-Fz interactions at successive stages of thymocyte maturation. In support of this we show that separation of thymocytes from Wnt-producing epithelial cells and the thymic microenvironment, triggers beta-catenin phosphorylation and degradation in thymocytes. Thus, sustained exposure to Wnt in the context of an intact stromal microenvironment is necessary for stabilization of beta-catenin-mediated signaling in thymocytes.
High-frequency intrachromosomal gene conversion induced by triplex-forming oligonucleotides microinjected into mouse cells (2000)

To test the ability of triple helix-forming oligonucleotides (TFOs) to promote recombination within chromosomal sites in mammalian cells, a mouse LTK(-) cell line was established carrying two mutant copies of the herpes simplex virus thymidine kinase (TK) gene as direct repeats in a single chromosomal locus. Recombination between these repeats can produce a functional TK gene and occurs at a spontaneous frequency of 4 x 10(-6) under standard culture conditions. When cells were microinjected with TFOs designed to bind to a 30-bp polypurine site situated between the two TK genes, recombination was observed at frequencies in the range of 1%, 2,500-fold above the background. Recombination was induced efficiently by injection of both psoralen-conjugated TFOs (followed by long-wave UVA light; 1. 2%) and unconjugated TFOs alone (1.0%). Control oligomers of scrambled sequence but identical base composition were ineffective, and no TFO-induced recombination was seen in a control LTK(-) cell line carrying an otherwise identical dual TK gene construct lacking the 30-bp polypurine target site. TFOs transfected with cationic lipids also induced recombinants in a highly sequence-specific manner but were less effective, with induced recombination frequencies of 6- to 7-fold over background. Examination of the TFO-induced recombinants by genomic Southern blotting revealed gene conversion events in which both TK genes were retained, but either the upstream (57%) or the downstream gene (43%) was corrected to wild type. These results suggest that, with efficient intracellular delivery, TFOs may be effective tools to promote site-specific recombination and targeted modification of chromosomal loci.
Infectious adult rhinosinusitis: etiology, diagnosis, and management principles. (2005)

Rhinosinusitis represents a complicated and multifaceted group of diseases that is generally classified into the categories of acute and chronic. Although many instances of acute rhinosinusitis lasting longer than 7 days are thought to be of bacterial origin, most are thought to be inflammatory rather than infectious. The contribution of infectious organisms to the pathogenesis of chronic rhinosinusitis is an area of controversy and active investigation. Examples of these areas of investigation include biofilms, osteitis, and bacterial superantigens. This review discusses the role of infectious organisms in both acute and chronic sinusitis, with special focus on the etiology and diagnosis of these conditions, and includes a discussion of principles of their management.
Cc Chemokine Receptor (Ccr)2 Is Required for Langerhans Cell Migration and Localization of T Helper Cell Type 1 (Th1)-Inducing Dendritic Cells (2000)

There is growing evidence that chemokines and their receptors regulate the movement and interaction of antigen-presenting cells such as dendritic cells (DCs) and T cells. We tested the hypothesis that the CC chemokine receptor (CCR)2 and CCR5 and the chemokine macrophage inflammatory protein (MIP)-1alpha, a ligand for CCR5, influence DC migration and localization. We found that deficiency of CCR2 but not CCR5 or MIP-1alpha led to distinct defects in DC biology. Langerhans cell (skin DC) density in CCR2-null mice was normal, and their ability to migrate into the dermis was intact; however, their migration to the draining lymph nodes was markedly impaired. CCR2-null mice had lower numbers of DCs in the spleen, and this was primarily due to a reduction in the CD8alpha(1) T helper cell type 1 (Th1)-inducing subset of DCs. Additionally, there was a block in the Leishmania major infection-induced relocalization of splenic DCs from the marginal zone to the T cell areas. We propose that these DC defects, in conjunction with increased expression of B lymphocyte chemoattractant, a B cell-specific chemokine, may collectively contribute to the striking B cell outgrowth and Th2 cytokine-biased nonhealing phenotype that we observed in CCR2-deficient mice infected with L. major. This disease phenotype in mice with an L. major-resistant genetic background but lacking CCR2 is strikingly reminiscent of that observed typically in mice with an L. major-susceptible genetic background. Thus, CCR2 is an important determinant of not only DC migration and localization but also the development of protective cell-mediated immune responses to L. major.
[IFN combined cyclosporin A therapy]. (2001)

Current therapy of chronic hepatitis C with a 6 months course of alpha interferon shows limited effectiveness for patients with chronic hepatitis C. In particular more effective therapy is needed to treat patients who have high serum level of group 1-HCV RNA. We previously reported that a combination of interferon and cyclosporin A was more effective than interferon monotherapy. We also examined whether CsA has an antiviral effect on HCV using cultured human hepatocyte cell line. Propagation of HCV seems to be inhibited by CsA in a dose dependent manner. Further study is needed to clarify the action of cyclosporin A.
PHYSIOLOGICAL TESTING OF CARBON NANOTUBES: ARE THEY ASBESTOS-LIKE? (2001)

Abstract To determine whether carbon nanotubes can induce any significant health hazards we applied methods routinely used in the pathophysiological testing of asbestos-induced disease to show that the soot with a high content of CNTs does not induce any abnormalities of pulmonary function or measurable inflammation in guinea pigs treated with carbon nanotubes. ACKNOWLEDGMENTS The work was supported by the Committee for Scientific Research (KBN) through the Department of Chemistry, Warsaw University, under grant No. 3 T09A 05816. The homogeneous catalyst-doped graphite material was kindly provided by Dr. T. Sogabe from Toyo Tanso Co. Ltd., Japan.
Preclinical studies of the pan-Bcl inhibitor obatoclax (GX015-070) in multiple myeloma (2007)

Bcl family members Bcl-2, Bcl-x(L), and Mcl-1, are frequently expressed and implicated in the survival of myeloma cells. Obatoclax (GX015-070) is a novel, small-molecule antagonist of the BH3-binding groove of the Bcl family of proteins. We show that GX015-070 inhibits the binding of Bak to Mcl-1, up-regulates Bim, induces cytochrome c release, and activates capase-3 in human myeloma cell lines (HMCLs), confirming the predicted mechanism of action. Consequently, GX015-070 potently inhibited the viability of 15 of 16 HMCLs (mean IC(50) of 246 nM), including those resistant to melphalan and dexamethasone. In combination studies, GX015-070 enhanced the antimyeloma activity induced by melphalan, dexamethasone, or bortezomib. Sensitivity to GX015-070 correlated with the absence or near absence of Bcl-x(L). Coculture with interleukin-6 or adherence to bone marrow stroma conferred modest resistance; however, it did not overcome GX015-070-induced cytotoxicity. Of importance, GX015-070 as a single agent induced potent cytotoxic responses against patient-derived tumor cells. GX015-070 inhibited normal bone marrow-derived colony formation; however, cytotoxicity to human blood lymphocytes was not observed. Taken together, these studies describe a novel BH3 mimic with selectivity for Mcl-1, and support the therapeutic application of GX015-070 for diverse neoplasias including multiple myeloma.
Beyond online aggregation (2010)

There are only few data mining algorithms that work in a massively parallel and yet online (i.e. incremental) fashion. A combination of both features is essential for mining of large data streams and adds scalability to the concept of Online Aggregation introduced by J. M. Hellerstein et al. in 1997. We show how an online version of the Map-Reduce programming model can be used to implement such algorithms, and propose a solution for the hardest class of these algorithms - those requiring multiple Map-Reduce phases. An experimental evaluation confirms that the proposed methods can substantially accelerate interactive analysis of large data sets and facilitate scalable stream mining.
Insulin-like growth factors I and II stimulate endocytosis but do not affect sorting of lysosomal enzymes in human fibroblasts. (1990)

The mannose 6-phosphate (Man-6-P)/insulin-like growth factor (IGF) II receptor has separate binding sites for Man-6-P and IGF II. It targets newly synthesized lysosomal enzymes from the Golgi to acidic pre-lysosomal organelles and mediates endocytosis of Man-6-P-containing ligands and IGF II. The two classes of ligands, Man-6-P and IGF II, as well as IGF I and the epidermal growth factor, induce in fibroblasts a transient redistribution of the receptor from internal membranes to the cell surface (Braulke, T., Tippmer, S., Neher, E., and von Figura, K. (1989) EMBO J. 8, 681-686). Here we show that the redistribution induced by IGF I and IGF II is accomplished without affecting the internalization rate of cell surface receptors. The redistribution results in an increased binding of ligands to the Man-6-P- and IGF II-binding sites of the receptor. Furthermore, the uptake of the lysosomal enzyme arylsulfatase A and of a Man-6-P neoglycoprotein is stimulated 2-3-fold by IGF I and IGF II, and this effect persists for at least 6 h. The IGF I- and IGF II-induced receptor redistribution does not affect the targeting of newly synthesized lysosomal enzymes. These results show that important functions of the Man-6-P/IGF II receptor such as binding and internalization of ligands can be up-regulated by the ligands of this receptor and other growth factors such as IGF I through redistribution of the receptor.