gebhart/patrepeval huggingface dataset:
Ultraviolet light-induced keratinocyte apoptosis: A potential mechanism for the induction of skin lesions and autoantibody production in LE (1997)

Systemic lupus erythematosus (SLE) is a prototype systemic autoimmune disease which is characterized clinically by pleiotropy and periodicity. The immune features which accompany the characteristic flares of the disease have strongly suggested that the autoimmune response is driven by self antigen, and is T cell-dependent. These features have prompted the search for potential initiating process(es) which induce the release of self-antigens in a form which causes T cell tolerance to those self molecules to be broken. We review here several recent observations which implicate apoptotic cells as an important potential source of clustered and concentrated autoantigens in SLE, and present our current model whereby the novel autoantigen fragments generated in apoptotic surface blebs initiate and drive the autoimmune response in this disease.
Branch regulation: Low-overhead protection from code reuse attacks (2012)

Code reuse attacks (CRAs) are recent security exploits that allow attackers to execute arbitrary code on a compromised machine. CRAs, exemplified by return-oriented and jump-oriented programming approaches, reuse fragments of the library code, thus avoiding the need for explicit injection of attack code on the stack. Since the executed code is reused existing code, CRAs bypass current hardware and software security measures that prevent execution from data or stack regions of memory. While software-based full control flow integrity (CFI) checking can protect against CRAs, it includes significant overhead, involves non-trivial effort of constructing a control flow graph, relies on proprietary tools and has potential vulnerabilities due to the presence of unintended branch instructions in architectures such as ×86 - those branches are not checked by the software CFI. We propose branch regulation (BR), a lightweight hardware-supported protection mechanism against the CRAs that addresses all limitations of software CFI. BR enforces simple control flow rules in hardware at the function granularity to disallow arbitrary control flow transfers from one function into the middle of another function. This prevents common classes of CRAs without the complexity and run-time overhead of full CFI enforcement. BR incurs a slowdown of about 2% and increases the code footprint by less than 1% on the average for the SPEC 2006 benchmarks.
Apoptosis in bone marrow biopsy samples involving stromal and hematopoietic cells in 50 patients with myelodysplastic syndromes [see comments] (1995)

Cell-cycle kinetics were measured in situ after infusions of iododeoxyuridine and/or bormodeoxyuridine in 50 patients with myelodysplastic syndromes (MDS) and the median labeling index in bone marrow (BM) biopsy samples was 28.6%. Unfortunately, 26 of 50 patients showed that > or = 75% of hematopoietic cells of all three lineages were undergoing programmed cell death (PCD) in their biopsy samples as shown by the in situ end labeling (ISEL) technique. Ten patients had 1/3 and eight had 2/3 ISEL+ cells. Stromal cells were frequently ISEL+ and often S-phase cells were also found to be simultaneously ISEL+. Nucleosomal DNA fragments as a ladder in agarose gel were present in BM aspirates of four patients who showed high ISEL and were absent in two who had no ISEL staining in biopsy samples, but only when DNA was extracted after a 4-hour in vitro incubation in complete medium. Therefore, laddering data confirmed the ISEL findings that the majority of hematopoietic cells in MDS are in early stages of PCD. We conclude that extensive intramedullary cell death may explain the paradox of pancytopenia despite hypercellular marrows in MDS patients. Investigating approaches that protect against PCD in some MDS subsets would be of interest.
Torsades de Pointes Occurring in Association With Terfenadine Use (1991)

<h3>To the Editor.</h3> —Monahan et al<sup>1</sup>reported a case of torsades de pointes after concomitant administration of terfenadine (Seldane) and ketoconazole (Nizoral). We would like to comment on this report and share results from subsequent studies at Marion Merrell Dow Inc, Kansas City, Mo. Terfenadine normally undergoes extensive (99%) first-pass metabolism to two metabolites: an active acid metabolite and an inactive dealkylated metabolite. Therefore, unchanged terfenadine is normally undetectable (ie, &lt;10 ng/mL) in plasma. However, in cases of hepatic impairment or when certain concurrent medications (eg, ketoconazole) inhibit the metabolism of terfenadine, unchanged terfenadine can become detectable in plasma while metabolite formation is decreased. In cases of terfenadine overdose, unchanged terfenadine can become detectable and acid metabolite levels increase.<sup>2</sup> In a study of 24 subjects given a single 60-mg dose of terfenadine, the mean peak plasma acid metabolite level was 263 ng/mL and occurred 2.5 hours after dosing.
Immune responses in vitro. iii. enhancement of the mouse mixed lymphocyte interaction by isologous and homologous sera (1973)

Abstract This report describes the enhancement of the mouse mixed lymphocyte interaction which results from supplementing a protein‐free medium with either isologous or homologous sera. The degree of stimulation is affected by several variables which include serum preparation and concentration, the genetic relationship of the responder and stimulator cells to the source of sera, and the composition of the medium.
Nanoscale patterning using self-assembled polymers for semiconductor applications (2001)

Thin films of self-organizing diblock copolymers may be suitable for semiconductor applications since they enable patterning of ordered domains with dimensions below photolithographic resolution over wafer-scale areas. We investigate the process window for forming ordered arrays of nanoscale polymer domains in thin films across 8-in.-diam silicon wafers, including the effect of substrate material and surface treatment, annealing conditions, copolymer molecular weight, and film thickness. We also demonstrate pattern transfer of the nanoporous polymer template using both reactive ion etching and metal lift off.
VLA-6 (CDw49f) is an important adhesion molecule in NK cell-mediated cytotoxicity following autologous or allogeneic bone marrow transplantation. (1995)

Graft-vs.-leukemia (GVL) is postulated to be the principal mechanism responsible for continued remission after allogeneic bone marrow transplantation (BMT). The specific cytotoxic effectors mediating this effect are as yet undefined, but the major histocompatibility complex (MHC)-nonrestricted lysis of tumor cell lines by natural killer (NK) and lymphokine-activated killer (LAK) cells from recipients of allogeneic BMTs has been proposed as an in vitro correlate of GVL. In vitro culture or treatment in vivo with interleukin-2 (IL-2) is associated with enhanced NK cytotoxicity and lysis of NK-resistant targets (LAK cytotoxicity). NK, LAK, and cytotoxic T lymphocytes (CTL) have cytotoxic properties against autologous and allogeneic leukemic targets. These immune effector cells require receptor-ligand interaction for target recognition and adhesion via specific molecules such as integrins, a group of heterodimeric transmembrane glycoproteins. The integrins include the very late activation (VLA) subfamily, which all share the same beta 1 subunit but have distinct chains. VLA-6 (CDw49f) has been identified on NK cells and binds to laminin, a basement membrane protein found on malignant tumor cells but not normal cells. Monoclonal antibodies (mAbs) to laminin have been found to inhibit in vitro cytotoxicity of the tumor cell line K562, suggesting an important role for VLA-6 in this interaction. The specific aim of this study was to investigate the role of VLA-6 in the interactions of the tumor cell lines K562 and Daudi with peripheral blood lymphocytes (PBL) acting as effectors in cell-mediated cytotoxicity from normal volunteers, patients recovering from chemotherapy, and patients recovering from autologous or allogeneic BMT. In over 96% of assays, incubation of effector cells with anti-CDw49f mAbs led to detectable inhibition of NK and LAK cell-mediated cytotoxicity. More notably, the degree of anti-VLA6-induced suppression of LAK activity was significantly greater in the normal donors than in any of the patient groups, despite a significantly lower incidence of expression of VLA-6 on NK cells from controls than from patients. This implies a reduced role for this adhesion molecule in LAK activity following some form of in vivo stimulation. This hypothesis is supported by the observation that addition of exogenous IL-2 to the cultures ameliorated the effect of VLA-6 blockade, although the incidence and level of VLA-6 expression was unchanged by IL-2. In contrast, VLA-6 blocking led to a greater reduction in NK activity of BMT recipients than of normal donors, demonstrating that the VLA-6 adhesion pathway is important in this group of patients. These results indicate that the VLA-6-laminin interaction is important in normal NK-target interaction but may play a less significant role in the innate cytotoxic response post-BMT, perhaps reflecting subtle differences in the subsets of NK cells present in BMT recipients compared with normal donors.
Effects of electroplating on the mechanical properties of stereolithography and laser sintered parts (2004)

This paper provides a quantitative and qualitative assessment of the effects of electroplating on polymer parts made by stereolithography (SL) and laser sintering. A series of test samples were coated with copper and nickel with varying thickness. Thicker coatings (120 μ m) were reproduced with a repeatability that should not adversely affect the tolerances with which such parts may be produced given the tolerances of the initial rapid prototyping processes themselves. Thinner coatings (20 μ m) resulted in a smother surface finish than thicker coatings for SL parts, however the converse was true for laser‐sintered parts. Composite theory was used to predict that thicker coating would lead to higher Young's modulus in parts and this was shown to be true in physical tests although the practical values were lower than the predicted values especially for thicker coatings. Physical tests also confirmed that thicker coatings increased UTS and impact energy but had a minimal effect on the ductility of parts.
Induction of antitumor cytotoxic T lymphocytes with a MAGE-3-encoded synthetic peptide presented by human leukocytes antigen-A24. (1997)

For the development of immunotherapy using MAGE peptides, the identification of additional tumor antigens is required. Because HLA-A24 is the most common allele in Japanese and is also frequently present in Caucasians, MAGE-3-encoded synthetic peptides with binding affinity for HLA-A24 were thus tested for the induction of specific CTLs from the peripheral blood mononuclear cells (PBMCs) of HLA-A24 healthy donors using a simplified method. By using a peptide with a sequence of IMPKAGLLI (amino acid position in MAGE-3 195-203), the CTL responses could thus be induced from unseparated PBMCs by stimulation with freshly isolated, peptide-pulsed PBMCs as antigen-presenting cells (APCs) and by also using interleukin 7 and keyhole limpet hemocyanin for a primary culture. The induced CTLs could lyse HLA-A24 carcinoma cells expressing MAGE-3, as well as the peptide-pulsed target cells, in an HLA class-I restricted manner. The identification of the MAGE-3/HLA-A24 peptide, IMPKAGLLI, may thus potentially offer the opportunities to design peptide-based immunotherapeutic approaches that might prove to be effective in treating patients with MAGE-3-positive malignant tumors.
New tight frames of curvelets and optimal representations of objects with C² singularities (2002)

This paper introduces new tight frames of curvelets to address the problem of finding optimally sparse representations of objects with discontinuities along C edges. Conceptually, the curvelet transform is a multiscale pyramid with many directions and positions at each length scale, and needle-shaped elements at fine scales. These elements have many useful geometric multiscale features that set them apart from classical multiscale representations such as wavelets. For instance, curvelets obey a parabolic scaling relation which says that at scale 2−j , each element has an envelope which is aligned along a ‘ridge’ of length 2−j/2 and width 2−j . We prove that curvelets provide an essentially optimal representation of typical objects f which are C except for discontinuities along C curves. Such representations are nearly as sparse as if f were not singular and turn out to be far more sparse than the wavelet decomposition of the object. For instance, the n-term partial reconstruction f n obtained by selecting the n largest terms in the curvelet series obeys ‖f − f n ‖2L2 ≤ C · n −2 · (log n), n→∞. This rate of convergence holds uniformly over a class of functions which are C except for discontinuities along C curves and is essentially optimal. In comparison, the squared error of n-term wavelet approximations only converges as n−1 as n → ∞, which is considerably worst than the optimal behavior.
CGRP and VIP Levels as Predictors of Efficacy of Onabotulinumtoxin Type A in Chronic Migraine (2014)

Interictal CGRP and, to a lesser degree, VIP levels measured in peripheral blood are of great help in predicting response to onabotA.
Best practice in the treatment of advanced squamous cell lung cancer (2015)

The management of advanced stage nonsmall cell lung cancer (NSCLC) has been altered by the recognition of histology-based treatment and the use of targeted therapy. Whilst outcomes have improved with adenocarcinoma, treatment options are still limited in advanced stage squamous cell lung cancer. With advances in the molecular characterization of squamous cell cancers (SCCs), new potential targets have been identified. In this review, we discuss the role of histology in the treatment of NSCLC, cytotoxic chemotherapy, existing targeted therapies, the new molecular subsets and novel inhibitors in squamous cell lung carcinoma, and the emerging role of immune checkpoint inhibitors. Based on the results of two recent studies, nivolumab, a programmed death 1 (PD-1) immune checkpoint inhibitor, has been approved by the US Food and Drug Administration (FDA) in the treatment of squamous cell NSCLC in the second-line setting. Well-designed biomarker driven studies are needed to accelerate the development and approval of novel therapies for patients with lung SCC.
The impacts of pretreatment on the fermentability of pretreated lignocellulosic biomass: a comparative evaluation between ammonia fiber expansion and dilute acid pretreatment (2009)

The selection of pretreatment will determine the biomass-processing configuration, requirements for hydrolysate conditioning (if any) and fermentation strategy. Through dilute acid pretreatment, the need for hemicellulase in biomass processing is negligible. AFEX-centered cellulosic technology can alleviate fermentation costs through reducing inoculum size and practically eliminating nutrient costs during bioconversion. However, AFEX requires supplemental xylanases as well as cellulase activity. As for long-term sustainability, AFEX has greater potential to diversify products from a cellulosic biorefinery due to lower levels of inhibitor generation and lignin loss.
Racemization in Suzuki Couplings: A Quantitative Study Using 4-Hydroxyphenylglycine and Tyrosine Derivatives as Probe Molecules (2007)

Reaction conditions considered to be typical in Suzuki couplings can cause significant (up to 34% of the unwanted enantiomer) loss of optical purity in sensitive substrates such as hydroxyphenylglycine 1. This may be remedied using sodium succinate instead of sodium carbonate as base, but chemical yields are somewhat lower. Optically pure biaryl amino acids related to those found in the chloropeptins and vancomycin were synthesized by Suzuki coupling of 1 with indolylboronic acids 6−8 and with cyclic boronic acid 9.
Gene expression analysis of purified hematopoietic stem cells and committed progenitors (2003)

Lifelong self-renewal is a unique property of somatic stem cells. Recently, several primitive multipotent yet committed (non-self-renewing) hematopoietic progenitor populations were identified in mouse bone marrow. We have characterized the expression of 1200 selected mouse genes using the Atlas cDNA array in highly purified hematopoietic stem cells (HSCs) and 6 closely related progenitor populations: common myeloid progenitors (CMPs), granulocyte-macrophage progenitors (GMPs), megakaryocyte-erythrocyte progenitors (MEPs), common lymphoid progenitors (CLPs), and pro-T and pro-B cells. Cluster analysis revealed that nearly half of all differentially expressed transcripts are associated with HSCs, supporting the notion of an active transcriptional status of HSCs. Genes found enriched in the HSC cluster encompass many developmentally regulated genes, some previously associated with HSC self-renewal. In contrast, genes that are enriched in committed progenitors are mostly associated with hematopoietic differentiation, immune regulation, and metabolism. Thus, the transition from HSCs toward committed progenitors correlates with the down-regulation of a large number of HSC-associated genes and progressive up-regulation of a limited number of lineage-specific genes. These genetic analyses revealed both quantitative and qualitative differences between the transcripts associated with HSCs versus downstream progenitors and produced a list of the candidate genes, potentially involved in HSC self-renewal.
Molecular Cloning of a Neurospora crassa Carotenoid Biosynthetic Gene (Albino-3) Regulated by Blue Light and the Products of the White Collar Genes (1989)

The albino-3 (al-3) gene of Neurospora crassa, which probably encodes the carotenoid biosynthetic enzyme geranylgeranyl pyrophosphate synthetase, was cloned. The N. crassa triple mutant al-3 qa-2 aro-9 was transformed to qa-2+ with mixtures of plasmids bearing N. crassa DNA inserts, and the transformants were screened for the al-3+ phenotype. One al-3+ qa-2+ transformant (AL3-1) was examined in detail and shown to contain intact vector sequences integrated into the N. crassa genome. The vector and some flanking sequences were recovered from AL3-1 after restriction, ligation, and selection of chloramphenicol-resistant transformants of Escherichia coli. The flanking sequences were subsequently used to detect the al-3-containing plasmid in the mixture of about 1,800 plasmids. Restriction fragment length polymorphism mapping was carried out to confirm the identity of the cloned fragment. The level of the al-3 mRNA was shown to be increased 15-fold in light-induced (compared with that in dark-grown) wild-type mycelia. The light-dependent increase in al-3 mRNA levels was not observed in presumed regulatory mutant (white collar) strains.
DEVELOPMENT OF LAYERED FUNCTIONAL FIBER BASED MICRO-TUBES (2003)

Microtubes and microtubules are very small diameter tubes (in the micron range) with high aspect ratio that can be made of almost any material. Microtubes have almost universal application in areas as diverse as electronics, medical technology, and optics. Specific use of microtubes may include encapsulation, sensing, actuation, etc. The objective of the research is to explore the fundamental technological potential of fabrication of microtubes substantially in the form of textile fibers. The long-term objective is to develop various functional characteristics in fibers by incorporating functional micro-devices in fiber based systems at various scales. ABSTARCT Evaluation of various polymer-graphite systems and polypyrolle for the fabrication of electrodes in microtubes has been completed. Conducting layered electrospun webs have been prepared using the electro-spinning process. Polyurethane has been used as the fiber forming polymer and carbon black (CB) and carbon nanotubes (CNT) as conductive fillers. Effect of particle loading on the electrospun web resistivity has been studied. Microtube actuators have been fabricated using commercially available dielectric elastomer tubes and the polymer-particle systems. Axial and radial actuation strains produced in a microtube actuator upon application of an external electric field, and effect of pre-strain on actuation behavior of microtubes have been studied.
Natural Killer Cells: Their Roles in Defenses Against Disease (1981)

Natural killer cells are a recently discovered subpopulation of lymphoid cells that are present in most normal individuals of a range of mammalian and avian species. Natural killer cells have spontaneous cytolytic activity against a variety of tumor cells and some normal cells, and their reactivity can be rapidly augmented by interferon. They have characteristics distinct from other types of lymphoid cells and are closely associated with large granular lymphocytes, which comprise about 5 percent of blood or splenic leukocytes. There is increasing evidence that natural killer cells, with the ability to mediate natural resistance against tumors in vivo, certain virus and other microbial diseases, and bone marrow transplants, may play an important role in immune surveillance.
Development and Characterization of a CP4 EPSPS‐Based, Glyphosate‐Tolerant Corn Event (2005)

5‐Enol‐pyruvylshikimate‐3‐phosphate synthase from Agrobacterium sp. CP4 (CP4 EPSPS) confers tolerance to the nonselective herbicide glyphosate (marketed under the trade name Roundup) when sufficiently expressed in transgenic plants. Dual CP4 EPSPS transgene cassettes were transformed into corn ( Zea mays L.) under the transcriptional regulatory control of the rice ( Oryza sativa L.) actin 1 (P‐Ract1) and the enhanced Cauliflower mosaic virus 35S (P‐e35S) promoters, respectively, to impart fully constitutive expression in corn. Resulting events were tested for lack of chlorosis and malformation injury after two sequential applications of 1.68 kg acid equivalents (a.e.) ha −1 glyphosate. Agronomic parameters, male fertility, appropriate Mendelian segregation of the trait, plus characteristics of the transgenic integration site were also evaluated. From this selection process, the NK603 event was chosen for commercialization as the event that embodied the most optimal profile of tolerance, agronomics, and molecular characteristics. The NK603 event exhibited high glyphosate tolerance from one transgenic locus bearing a single copy of the dual cassettes integrated into the corn genome with a minimum of target sequence disruption. Trait expression in the NK603 event has remained stable over more than eight generations as shown through tolerance testing, western blots of CP4 EPSPS accumulation, and Southern blot analysis of the transgene.
Analyses of Plant Leaf Cell Size, Density and Number, as Well as Trichome Number Using Cell Counter Plugin (2014)

An Arabidopsis leaf blade is composed of many layers that are sandwiched between two layers of tough skin cells (called the epidermis). Four layers (adaxial epidermis, palisade layer, spongy mesophyll and abaxial epidermis) contain specialized cells. Here we describe a quick and simple method for analyzing the size, number and density of different types of cells in an Arabidopsis leaf blade. This method would be of interest to people who would like to investigate cell size and number changs in different cell layers in leaves or leaf-like organs without having to dissect the samples.
Regulation of Immune Responses by T Cells (2006)

This review summarizes recent advances in the understanding of how the immune system averts autoimmunity while maintaining protective immunity.