gebhart/patrepeval huggingface dataset:
Fas antigen stimulation induces marked apoptosis of T lymphocytes in human immunodeficiency virus-infected individuals. (1995)

Apoptosis (programmed cell death) of T lymphocytes has been proposed as a mechanism which plays an important role in the pathogenesis of human immunodeficiency virus (HIV) disease. Activation of Fas (CD95) can either result in costimulation of proliferation and cytokine production or in the induction of apoptosis of T lymphocytes. This raises the possibility that Fas is involved in the observed T cell apoptosis during HIV disease. In this report we show that peripheral blood CD4+ and CD8+ T lymphocytes from HIV-infected individuals undergo apoptosis in vitro in response to antibody stimulation (cross-linking) of Fas at a much higher frequency than from uninfected controls. This anti-Fas-induced T cell apoptosis is markedly higher than spontaneous T cell apoptosis in HIV-infected individuals. Antibodies against other members of the tumor necrosis factor (TNF)/nerve growth factor receptor family such as CD27, CD30, CD40, 4-1BB, p55 TNF receptor, p75 TNF receptor, and TNF receptor-related protein did not result in any increase of T cell apoptosis above that spontaneously observed in HIV+ individuals. Anti-Fas-induced apoptosis was much higher in symptomatic HIV-infected individuals; and the magnitude of anti-Fas-induced CD4+ T cell apoptosis correlated inversely with peripheral blood CD4+ T cell absolute counts. Surface expression of Fas on T cells was also found to be higher in HIV-infected individuals. Resting and activated CD4+ and CD8+ T cells both underwent apoptosis in response to anti-Fas antibody. L-Selectin positive memory CD4+ T cells were especially susceptible to anti-Fas-induced apoptosis. These findings show that CD4+ and CD8+ T lymphocytes in HIV-infected individuals are primed in vivo to undergo apoptosis in response to Fas stimulation, suggesting that Fas signaling may be responsible for the T lymphocyte functional defects and depletion observed in HIV disease.
Treatment-Induced Oxidative Stress and Cellular Antioxidant Capacity Determine Response to Bortezomib in Mantle Cell Lymphoma (2011)

Bortezomib triggers an oxidative stress response in vitro and in vivo. High cellular antioxidant capacity contributes to bortezomib resistance.
Colorectal Cancer Screening (2011)

Although colorectal cancer is the third leading cause of cancer-related deaths in the U.S., the burden of this disease could be dramatically reduced by increased utilization of screening. Evidence-based recommendations and guidelines from national societies recommend screening all average risk adults starting at age fifty. However, the myriad of screening options and slight differences in screening recommendations between guidelines may lead to confusion among patients and their primary care providers. This goal of this review is to briefly summarize the colorectal cancer screening guidelines issued by three major organizations, compare their recommendations, and address emerging issues in colorectal cancer screening.
The Intrinsic Anodic Stability of Several Anions Comprising Solvent‐Free Ionic Liquids (1996)

Salts of the form 1,2‐dimethyl‐3‐propylimidazolium X [where , and were prepared and purified. Linear sweep voltammetry was conducted at 80°C, a temperature at which all four salts were molten, at Pt, W, and glassy carbon working electrodes. We found that the intrinsic anodic stability of these anions was in the order . These experimental solution‐phase oxidation potentials correlated well with gas‐phase highest occupied molecular orbital energies calculated by an ab initio technique.
Biosynthesis of Chondroitin Sulfate (1997)

A photoaffinity analogue, [beta-32P]5-azido-UDP-GlcA, was used to photolabel the enzymes that utilize UDP-GlcA in cartilage microsomes and rat liver microsomes. SDS-polyacrylamide gel electrophoresis analysis of photolabeled cartilage microsomes, which are specialized in chondroitin sulfate synthesis, showed a major radiolabeled band at 80 kDa and other minor radiolabeled bands near 40 and 60 kDa. Rat liver microsomes, which are enriched for enzymes of detoxification by glucuronidation, had a different pattern with multiple major labeled bands near 50-60 and 35 kDa. To determine that the photolabeled 80-kDa protein is the GlcA transferase II, we have purified the enzyme from cartilage microsomes. This membrane-bound enzyme, involved in the transfer of GlcA residues to non-reducing terminal GalNAc residues of the chondroitin polymer, has now been solubilized, stabilized, and then purified greater than 1350-fold by sequential chromatography on Q-Sepharose, heparin-Sepharose, and WGA-agarose. The purified enzyme exhibited a conspicuous silver-stained protein band on SDS-polyacrylamide gel electrophoresis that coincided with the major radiolabeled band of 80 kDa. SDS-polyacrylamide gel analysis of photoaffinity-labeled active fractions from the Q-Sepharose, heparin-Sepharose, and WGA-agarose also indicated only the single radiolabeled band at 80 kDa. Intensity of photolabeling in each of the fractions examined coincided with enzyme activity. The photolabeling of this 80-kDa protein was saturable with the photoprobe and could be inhibited by the addition of UDP-GlcA prior to the addition of the photoprobe. Thus, the photolabeling with [beta-32P]5-azido-UDP-GlcA has identified the GlcA transferase II as an 80-kDa protein. The purified enzyme was capable of transferring good amounts of GlcA residues to chondroitin-derived pentasaccharide with negligible transfer to pentasaccharides derived from hyaluronan or heparan.
Stretch-A-Sketch: a dynamic diagrammer (2002)

Stretch-A-Sketch is a pen-based drawing program that combines recognition of hand-drawn glyphs with constraint based maintenance of spatial relations. The recognition program identifies hand drawn glyphs, spatial relations between them, and higher-level configurations, such as graph and tree diagrams and floorplan bubble diagrams. Stretch-A-Sketch then maintains the essential relations in these configurations as the user edits the diagram.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Therapeutic effects of electromagnetic fields in the stimulation of connective tissue repair (1993)

The therapeutic effects of electric and magnetic fields have been studied largely for their promotion of connective tissue repair. The most widely studied application concerns bone repair and deals with acceleration of the healing of fresh fractures, delayed and non-unions, incorporation of bone grafts, osteoporosis, and osteonecrosis. More recently the effects of these fields upon the repair of cartilage and soft fibrous tissues have been described. In all these experimental systems and clinical applications an acceleration of extracellular matrix synthesis and tissue healing has been observed. A degree of specificity, in terms of the parameters of applied energy and biological response, is hypothesized.
In vivo imaging of human colorectal cancer using radiolabeled analogs of the uroguanylin peptide hormone. (2009)

Use of uroguanylin-targeting vectors for in vivo imaging of colorectal cancers expressing GC-C resulted in tumor uptake that paralleled that of higher affinity heat-stable enterotoxin peptides, but also resulted in increased kidney uptake in vivo.
Automatic retrieval and clustering of similar words (1998)

Bootstrapping semantics from text is one of the greatest challenges in natural language learning. We first define a word similarity measure based on the distributional pattern of words. The similarity measure allows us to construct a thesaurus using a parsed corpus. We then present a new evaluation methodology for the automatically constructed thesaurus. The evaluation results show that the thesaurus is significantly closer to WordNet than Roget Thesaurus is.
Stealthy malware detection and monitoring through VMM-based “out-of-the-box” semantic view reconstruction (2010)

An alarming trend in recent malware incidents is that they are armed with stealthy techniques to detect, evade, and subvert malware detection facilities of the victim. On the defensive side, a fundamental limitation of traditional host-based antimalware systems is that they run inside the very hosts they are protecting (“in-the-box”), making them vulnerable to counter detection and subversion by malware. To address this limitation, recent solutions based on virtual machine (VM) technologies advocate placing the malware detection facilities outside of the protected VM (“out-of-the-box”). However, they gain tamper resistance at the cost of losing the internal semantic view of the host, which is enjoyed by “in-the-box” approaches. This poses a technical challenge known as the semantic gap. In this article, we present the design, implementation, and evaluation of VMwatcher —an “out-of-the-box” approach that overcomes the semantic gap challenge. A new technique called guest view casting is developed to reconstruct internal semantic views (e.g., files, processes, and kernel modules) of a VM nonintrusively from the outside. More specifically, the new technique casts semantic definitions of guest OS data structures and functions on virtual machine monitor (VMM)-level VM states, so that the semantic view can be reconstructed. Furthermore, we extend guest view casting to reconstruct details of system call events (e.g., the process that makes the system call as well as the system call number, parameters, and return value) in the VM, enriching the semantic view. With the semantic gap effectively narrowed, we identify three unique malware detection and monitoring capabilities: (i) view comparison-based malware detection and its demonstration in rootkit detection; (ii) “out-of-the-box” deployment of off-the-shelf anti malware software with improved detection accuracy and tamper-resistance; and (iii) nonintrusive system call monitoring for malware and intrusion behavior observation. We have implemented a proof-of-concept VMwatcher prototype on a number of VMM platforms. Our evaluation experiments with real-world malware, including elusive kernel-level rootkits, demonstrate VMwatcher's practicality and effectiveness.
Geldanamycin Restores a Defective Heat Shock Responsein Vivo (2001)

Induced expression of heat shock proteins (Hsps) plays a central role in promoting cellular survival after environmental and physiological stress. We have previously shown that scrapie-infected mouse neuroblastoma (ScN2a) cells fail to induce the expression of Hsp72 and Hsp28 after various stress conditions. Here we present evidence that this impaired stress response is due to an altered regulation of HSF1 activity. Upon stress in ScN2a cells, HSF1 was converted into hyperphosphorylated trimers but failed to acquire transactivation competence. A kinetic analysis of HSF1 activation revealed that in ScN2a cells trimer formation after stress was efficient, but disassembly of trimers proceeded much faster than in the uninfected cell line. Geldanamycin, a Hsp90-binding drug, significantly delayed disassembly of HSF1 trimers after a heat shock and restored stress-induced expression of Hsp72 in ScN2a cells. Heat-induced Hsp72 expression required geldanamycin to be present; following removal of the drug ScN2a cells again lost their ability to mount a stress response. Thus, our studies show that a defective stress response can be pharmacologically restored and suggest that the HSF1 deactivation pathway may play an important role in the regulation of Hsp expression.
Abstract 16194: PCSK9 Inhibitor Alirocumab as Add-on to Atorvastatin versus Other Lipid Treatment Strategies in Patients at High CVD Risk: ODYSSEY OPTIONS I (2014)

Introduction: Not all patients at high cardiovascular (CV) risk achieve sufficient reduction in LDL-C levels by commonly used statin doses. Among patients treated with atorvastatin (ATV) 20 or 40 mg who did not achieve specified LDL-C treatment levels, ODYSSEY OPTIONS I compared: (1) adding the PCSK9 antibody, alirocumab; (2) adding ezetimibe (EZE); (3) doubling ATV dose, or (4) switching to rosuvastatin 40 mg.

Methods: A Phase 3, randomized, double-blind, active-comparator and parallel-group study ([NCT01730040][1]) in high CV risk patients with CVD and LDL-C ≥70 mg/dL or without CVD but with CVD risk factors and LDL-C ≥100 mg/dL. Patients had stable ATV 20 or 40 mg/day for ≥4 weeks prior to study entry. Within each baseline ATV dose regimen, randomization included (Figure): (1) add-on alirocumab 75 mg administered subcutaneously (SC) every 2 weeks (Q2W) using a 1-mL autoinjector; (2) add-on EZE orally (PO) 10 mg/day; (3) doubling of ATV dose; or (4) switch from ATV 40 mg to rosuvastatin 40 mg (for ATV cohort 40 mg). Alirocumab dose was up-titrated at Week 12 in a blinded manner to 150 mg Q2W (using a 1-mL autoinjector) in patients not achieving their predetermined LDL-C level. The primary endpoint was the % change in calculated LDL-C from baseline to 24 weeks in the intent-to-treat population, and with prespecified on-treatment analysis.

Results: In total, 355 patients were randomized: 231 (65.1%) were male, mean (SD) age was 62.9 (10.2) years, 211 (59.4%) had CHD, 178 (50.1%) had diabetes, and mean (SD) baseline LDL-C was 105.1 (34.1) mg/dL. Primary efficacy and safety analyses will be available for AHA.

Conclusions: OPTIONS I is the only clinical trial of a PCSK9 inhibitor to compare alirocumab as add-on therapy to ATV to commonly used lipid treatment strategies: (1) addition of EZE, (2) doubling statin dose, or (3) a switch to more potent statin, in high CV-risk patients.

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Intervention of Ticlopidine on Silica-induced Inflammatory Reaction and Apoptosis (2005)

Silica is a potent inducer of pulmonary inflammation that involves leucocyte apoptosis. It is hypothesised that regulation of the apoptotic reaction might occur in this condition through platelet activation arising from endothelial injury, by releasing products that modify the inflammatory cell function or life span, thereby influencing the reaction of inflammation. Because neutrophil apoptosis contributes to the resolution of acute inflammation induced by endotoxin, promotion of the apoptosis process might also inhibit the inflammatory reaction induced by silica. In order to test this hypothesis, rats were intratracheally instilled with 22.5 mg silica dust suspension, together with or without a four-week treatment of intraperitoneally injected daily (30mg/kg) doses of ticlopidine; a drug that can inhibit platelet aggregation in the process of activation. The results indicate that ticlopidine administration significantly enhanced the percentage of apoptotic neutrophils and reduced the number of lavagable cells and rate of lung weight increase. This evidence suggests that ticlopidine is an effective agent for producing an enhanced resolution of inflammation by the action of promoting neutrophil apoptosis.
Transcriptomic changes induced by mycophenolic acid in gastric cancer cells. (2013)

These results suggest that MPA has beneficial anticancer activity through diverse molecular pathways and biological processes.
Nickel‐Rich Layered Lithium Transition‐Metal Oxide for High‐Energy Lithium‐Ion Batteries (2015)

High energy-density lithium-ion batteries are in demand for portable electronic devices and electrical vehicles. Since the energy density of the batteries relies heavily on the cathode material used, major research efforts have been made to develop alternative cathode materials with a higher degree of lithium utilization and specific energy density. In particular, layered, Ni-rich, lithium transition-metal oxides can deliver higher capacity at lower cost than the conventional LiCoO2 . However, for these Ni-rich compounds there are still several problems associated with their cycle life, thermal stability, and safety. Herein the performance enhancement of Ni-rich cathode materials through structure tuning or interface engineering is summarized. The underlying mechanisms and remaining challenges will also be discussed.
Matrix genes of measles virus and canine distemper virus: cloning, nucleotide sequences, and deduced amino acid sequences (1986)

The nucleotide sequences encoding the matrix (M) proteins of measles virus (MV) and canine distemper virus (CDV) were determined from cDNA clones containing these genes in their entirety. In both cases, single open reading frames specifying basic proteins of 335 amino acid residues were predicted from the nucleotide sequences. Both viral messages were composed of approximately 1,450 nucleotides and contained 400 nucleotides of presumptive noncoding sequences at their respective 3' ends. MV and CDV M-protein-coding regions were 67% homologous at the nucleotide level and 76% homologous at the amino acid level. Only chance homology was observed in the 400-nucleotide trailer sequences. Comparisons of the M protein sequences of MV and CDV with the sequence reported for Sendai virus (B. M. Blumberg, K. Rose, M. G. Simona, L. Roux, C. Giorgi, and D. Kolakofsky, J. Virol. 52:656-663; Y. Hidaka, T. Kanda, K. Iwasaki, A. Nomoto, T. Shioda, and H. Shibuta, Nucleic Acids Res. 12:7965-7973) indicated the greatest homology among these M proteins in the carboxyterminal third of the molecule. Secondary-structure analyses of this shared region indicated a structurally conserved, hydrophobic sequence which possibly interacted with the lipid bilayer.
Bone graft materials. An overview of the basic science. (2000)

Autograft, allograft, and synthetic bone graft substitute materials play an important role in reconstructive orthopaedic surgery, and understanding the biologic effects of these materials is necessary for optimum use. Although vascularized and cancellous autograft show optimum skeletal incorporation, host morbidity limits autograft availability. Experimental studies have confirmed an immune response to allograft bone, but the clinical significance of this response in humans still is unclear. Small amounts of cancellous allograft in humans usually are remodeled completely; large allografts become incorporated by limited, surface intramembranous bone formation suggesting that these graft are primarily osteoconductive. Several synthetic skeletal substitute materials also are osteoconductive, and may show remodeling characteristics similar to allograft. Demineralized bone matrix and some isolated or synthetic proteins can induce endochondral bone formation, and therefore are osteoinductive. The extent and distribution of remodeling of bone graft materials are influenced by many factors, including the quality of the host site and the local mechanical environment (strain). Graft materials are likely to become more specialized for use in specific clinical applications, and composite preparations may soon provide bone graft materials with efficacy that equals or exceeds that of autogenous grafts.
Ca2+-dependent Binding of a Synthetic Arg-Gly-Asp (RGD) Peptide to a Single Site on the Purified Platelet Glycoprotein IIb-IIIa Complex (1989)

The platelet glycoprotein IIb-IIIa complex (GP IIb-IIIa) is a member of the integrin receptor family that recognizes adhesive proteins containing the Arg-Gly-Asp (RGD) sequence. In the present study the binding characteristics of the synthetic hexapeptide Tyr-Asn-Arg-Gly-Asp-Ser (YNRGDS, a sequence present in the fibrinogen alpha-chain at position 570-575) to purified GP IIb-IIIa were determined by equilibrium dialysis. The binding of 125I-YNRGDS to GP IIb-IIIa was specific, saturable, and reversible. The apparent dissociation constant was 1.0 +/- 0.2 microM, and the maximal binding capacity was 0.92 +/- 0.02 mol of 125I-YNRGDS/mol of GP IIb-IIIa, indicating that GP IIb-IIIa contains a single binding site for RGD peptides. The binding of 125I-YNRGDS to purified GP IIb-IIIa showed many of the characteristics of fibrinogen binding to activated platelets: the binding was inhibited by fibrinogen, by the monoclonal antibody A2A9, and by the dodecapeptide from the C terminus of the fibrinogen gamma-chain. In addition, the binding of 125I-YNRGDS to GP IIb-IIIa was divalent cation-dependent. Our data suggest that two divalent cation binding sites must be occupied for YNRGDS to bind: one site is specific for calcium and is saturated at 1 microM free Ca2+, whereas the other site is less specific and reaches saturation at millimolar concentrations of either Ca2+ or Mg2+. The results of the present study support the hypothesis that the RGD domains within the adhesive proteins are responsible for their binding to GP IIb-IIIa.
Optical coating design algorithm based on the equivalent layers theory (2006)

New optical coating design algorithm with the equivalent layers theory is presented. The algorithm is based on the merit-function-constrained optimization in the accessible domain of equivalent phase thicknesses and equivalent refractive indices. It allows for creation of design coatings with sophisticated narrowband spectral characteristics. (
Phosphorylation of phospholamban by calcium-activated, phospholipid-dependent protein kinase. Stimulation of cardiac sarcoplasmic reticulum calcium uptake. (1984)

Ca2+-activated, phospholipid-dependent protein kinase (protein kinase C) is able to catalyze the phosphorylation of phospholamban in a canine cardiac sarcoplasmic reticulum preparation. This phosphorylation is associated with a 2-fold stimulation of Ca2+ uptake by cardiac sarcoplasmic reticulum similar to that seen following phosphorylation of phospholamban by an endogenous calmodulin-dependent protein kinase or by the catalytic subunit of cAMP-dependent protein kinase. Two-dimensional peptide maps of the tryptic fragments of phospholamban indicate that the three protein kinases differ in their selectivity for sites of phosphorylation. However, one common peptide appears to be phosphorylated by all three protein kinases. These findings suggest that protein kinase C may play a role similar to those played by cAMP- and calmodulin-dependent protein kinases in the regulation of Ca2+ uptake by cardiac sarcoplasmic reticulum, and raise the possibility that the effects of all three protein kinases are mediated through phosphorylation of a common peptide in phospholamban.