gebhart/patrepeval huggingface dataset:
All-Star Polymer Multilayers as pH-Responsive Nanofilms (2008)

Star polymers with globular architecture and multiple arms are among the simplest forms of polymers with branched topologies. The combination of their unique architecture and high local densities of active functional groups makes star polymers unique candidates for a diverse range of applications. In this article, we describe the synthesis of star polymers with precisely controlled structures via atom transfer radical polymerization (ATRP) using the one-pot arm-first method. Specifically, two types of highly defined, high charge density star polymers with oppositely charged arm structures were prepared: poly[2-(dimethylamino)ethyl methacrylate] (PDMAEMA) star and poly(acrylic acid) (PAA) star polymers with cross-linked cores. By exploiting the electrostatic interactions between the polyelectrolyte arms, we have integrated the PDMAEMA star and PAA star polymers within alternating multilayer thin films using layer-by-layer (LbL) assembly to generate all-star polyelectrolyte LbL films. The prepared star/star multilayer films illustrate nonuniform and nanoporous structures, which result from the characteristic architecture of star polymers. The thickness, porosity, and refractive index of star/star multilayer films are precisely tunable by assembly pH conditions. Furthermore, as-assembled star/star multilayer films exhibit distinct morphological changes by undergoing extensive structural reorganization upon post-treatment under different pH conditions that do not lead to any changes with their linear compositional counterparts; it is hypothesized that these differences are due to the star polyelectrolyte’s compact structure and decreased extent of entanglement and interpenetration, which lead to a low degree of ionic cross-linking compared to their linear counterparts. The pH-responsive structural changes of the films are characterized by AFM, SEM, and FTIR. Finally, we have observed an enhanced ionic (proton) conductivity of star/star multilayers following the pH-induced structural reorganization.
Stance Classification of Context-Dependent Claims (2017)

Roy Bar-Haim, Indrajit Bhattacharya, Francesco Dinuzzo, Amrita Saha, Noam Slonim. Proceedings of the 15th Conference of the European Chapter of the Association for Computational Linguistics: Volume 1, Long Papers. 2017.
Effect of DNase and Antibiotics on Biofilm Characteristics (2008)

The role of extracellular DNA in the maintenance of biofilms formed by gram-positive and gram-negative bacteria was studied. This study evaluated all the bacterial strains that were tested for the presence of extracellular DNA with an average size of 30 kb in the matrix. Our results indicate changes in community biomass, architecture, morphology, and the numbers of CFU in the presence of DNase. This effect seems to be common to biofilms established by various unrelated gram-positive and gram-negative bacteria. The cleavage of extracellular DNA leads to the formation of an altered biofilm that permits the increased penetration of antibiotics. Thus, the addition of DNase enhances the effect of antibiotics, resulting in decreased biofilm biomass and numbers of CFU.
Effect of Ammonium Sulfate, Imazapyr, and Environment on the Phytotoxicity of Imazethapyr (1991)

The effects of 1.24 kg ha -1 ammonium sulfate, 5 g ae ha -1 of the isopropylamine salt of imazapyr, and air temperature of 18, 27, and 35 C at 40 and 100% relative humidity on the phytotoxicity of 35 g ae ha -1 of the ammonium salt of imazethapyr applied postemergence to pitted morningglory were evaluated. Both ammonium sulfate and imazapyr increased imazethapyr phytotoxicity to pitted morningglory. Ammonium sulfate enhanced imazethapyr phytotoxicity the most at 40% whereas imazapyr was most effective at 100% relative humidity. Imazethapyr phytotoxicity was enhanced more by the combination of ammonium sulfate and imazapyr than with either alone regardless of relative humidity. Variations in temperature had little effect on phytotoxicity.
Paclitaxel Induced Acute ST Elevation Myocardial Infarction: A Rare Case Report (2016)

Paclitaxel, is a frequently used anti-neoplastic agent and is included in various chemotherapy regimens. The life threatening cardio toxicity associated with its use and the still unclear pathophysiology, has limited the use of this drug. Acute myocardial infarction is a rare adverse event associated with this drug. We report a case of acute ST-elevation myocardial infarction induced by paclitaxel infusion in a patient of oesophageal carcinoma who was saved by percutaneous primary intervention. The authors emphasize the awareness of this side effect of Paclitaxel among the clinicians.
The Interleukin 13 (IL-13) Pathway in Human Macrophages Is Modulated by MicroRNA-155 via Direct Targeting of Interleukin 13 Receptor α1 (IL13Rα1) (2010)

Macrophages play a central role in the balance and efficiency of the immune response and are at the interface between innate and adaptive immunity. Their phenotype is a delicate equilibrium between the M1 (classical, pro-Th(1)) and M2 (alternative, pro-Th(2)) profiles. This balance is regulated by cytokines such as interleukin 13 (IL-13), a typical pro-M2-Th(2) cytokine that has been related to allergic disease and asthma. IL-13 binds to IL-13 receptor α1 (IL13Rα1), a component of the Type II IL-4 receptor, and exerts its effects by activating the transcription factor signal transducer and activator of transcription 6 (STAT6) through phosphorylation. MicroRNAs are short (∼22 nucleotide) inhibitory non-coding RNAs that block the translation or promote the degradation of their specific mRNA targets. By bioinformatics analysis, we found that microRNA-155 (miR-155) is predicted to target IL13Rα1. This suggested that miR-155 might be involved in the regulation of the M1/M2 balance in macrophages by modulating IL-13 effects. miR-155 has been implicated in the development of a healthy immune system and function as well as in the inflammatory pro-Th(1)/M1 immune profile. Here we have shown that in human macrophages, miR-155 directly targets IL13Rα1 and reduces the levels of IL13Rα1 protein, leading to diminished activation of STAT6. Finally we also demonstrate that miR-155 affects the IL-13-dependent regulation of several genes (SOCS1, DC-SIGN, CCL18, CD23, and SERPINE) involved in the establishment of an M2/pro-Th(2) phenotype in macrophages. Our work shows a central role for miR-155 in determining the M2 phenotype in human macrophages.
Isolation and characterization of a novel gene expressed in multiple cancers. (1996)

Using differential display method, we have isolated and characterized a novel gene, N8, encoding an approximately 24 kDa protein. It is located on human chromosome 8q13 region. N8 gene is expressed at high levels in tumor derived cell lines from multiple cancers. It is also expressed at higher levels in lung tumors than normal lung tissue. N8 is also differentially expressed in fetal and adult tissues. In adult, N8 is expressed at high levels in brain, kidney, prostate, pancreas and intestine and at very low levels in lung, liver, hematopoietic cells and gonads. During murine embryonic development N8 is expressed in the epithelium of the intestine, stomach, olfactory epithelium, neuronal layers of retina, kidney and salivary gland. Taken together, these results suggest that N8 may play different roles during embryogenesis and in the adult animals.
Pyruvate kinase M2 promotes de novo serine synthesis to sustain mTORC1 activity and cell proliferation (2012)

Despite the fact that most cancer cells display high glycolytic activity, cancer cells selectively express the less active M2 isoform of pyruvate kinase (PKM2). Here we demonstrate that PKM2 expression makes a critical regulatory contribution to the serine synthetic pathway. In the absence of serine, an allosteric activator of PKM2, glycolytic efflux to lactate is significantly reduced in PKM2-expressing cells. This inhibition of PKM2 results in the accumulation of glycolytic intermediates that feed into serine synthesis. As a consequence, PKM2-expressing cells can maintain mammalian target of rapamycin complex 1 activity and proliferate in serine-depleted medium, but PKM1-expressing cells cannot. Cellular detection of serine depletion depends on general control nonderepressible 2 kinase-activating transcription factor 4 (GCN2-ATF4) pathway activation and results in increased expression of enzymes required for serine synthesis from the accumulating glycolytic precursors. These findings suggest that tumor cells use serine-dependent regulation of PKM2 and GCN2 to modulate the flux of glycolytic intermediates in support of cell proliferation.
Modeling evolution of hydrogen bonding and stabilization of transition states in the process of cocaine hydrolysis catalyzed by human butyrylcholinesterase (2005)

Molecular dynamics (MD) simulations and quantum mechanical/molecular mechanical (QM/MM) calculations were performed on the prereactive enzyme-substrate complex, transition states, intermediates, and product involved in the process of human butyrylcholinesterase (BChE)-catalyzed hydrolysis of (-)-cocaine. The computational results consistently reveal a unique role of the oxyanion hole (consisting of G116, G117, and A199) in BChE-catalyzed hydrolysis of cocaine, compared to acetylcholinesterase (AChE)-catalyzed hydrolysis of acetylcholine. During BChE-catalyzed hydrolysis of cocaine, only G117 has a hydrogen bond with the carbonyl oxygen (O31) of the cocaine benzoyl ester in the prereactive BChE-cocaine complex, and the NH groups of G117 and A199 are hydrogen-bonded with O31 of cocaine in all of the transition states and intermediates. Surprisingly, the NH hydrogen of G116 forms an unexpected hydrogen bond with the carboxyl group of E197 side chain and, therefore, is not available to form a hydrogen bond with O31 of cocaine in the acylation. The NH hydrogen of G116 is only partially available to form a weak hydrogen bond with O31 of cocaine in some structures involved in the deacylation. The change of the estimated hydrogen-bonding energy between the oxyanion hole and O31 of cocaine during the reaction process demonstrates how the protein environment can affect the energy barrier for each step of the BChE-catalyzed hydrolysis of cocaine. These insights concerning the effects of the oxyanion hole on the energy barriers provide valuable clues on how to rationally design BChE mutants with a higher catalytic activity for the hydrolysis of (-)-cocaine.
Immune Responses and Viral Replication in Long-Term Inapparent Carrier Ponies Inoculated with Equine Infectious Anemia Virus (2000)

Persistent infection of equids by equine infectious anemia virus (EIAV) is typically characterized by a progression during the first year postinfection from chronic disease with recurring disease cycles to a long-term asymptomatic infection that is maintained indefinitely. The goal of the current study was to perform a comprehensive longitudinal analysis of the course of virus infection and development of host immunity in experimentally infected horses as they progressed from chronic disease to long-term inapparent carriage. We previously described the evolution of EIAV genomic quasispecies (C. Leroux, C. J. Issel, and R. C. Montelaro, J. Virol. 71:9627-9639, 1997) and host immune responses (S. A. Hammond, S. J. Cook, D. L. Lichtenstein, C. J. Issel, and R. C. Montelaro, J. Virol. 71:3840-3852, 1997) in four experimentally infected ponies during sequential disease episodes associated with chronic disease during the first 10 months postinfection. In the current study, we extended the studies of these experimentally infected ponies to 3 years postinfection to characterize the levels of virus replication and development of host immune responses associated with the progression from chronic disease to long-term inapparent infection. The results of these studies revealed over a 10(3)-fold difference in the steady-state levels of plasma viral RNA detected during long-term inapparent infection that correlated with the severity of chronic disease, indicating different levels of control of virus replication during long-term inapparent infections. Detailed analyses of antibody and cellular immune responses in all four ponies over the 3-year course of infection revealed a similar evolution during the first year postinfection of robust humoral and cellular immunity that then remained relatively constant during long-term inapparent infection. These observations indicate that immune parameters that have previously been correlated with EIAV vaccine protection fail to provide reliable immune correlates of control of virus replication or clinical outcome in experimental infections. Thus, these data emphasize the differences between immunity to virus exposure and immune control of an established viral infection and further emphasize the need to develop and evaluate novel immunoassays to define reliable immune correlates to vaccine and infection immunity, respectively.
Use of recombinant antigens expressed in Escherichia coli K-12 to map B-cell and T-cell epitopes on the immunodominant 65-kilodalton protein of Mycobacterium bovis BCG (1988)

In gene libraries of Mycobacterium bovis BCG, Mycobacterium tuberculosis, and Mycobacterium leprae, recombinants were frequently encountered that expressed an immunodominant 65-kilodalton (kDa) protein antigen that was shown to react with a high proportion of mycobacterium-reactive human and murine T cells and murine monoclonal antibodies. In this study, recombinant antigens were used to map T-cell and B-cell epitopes on the M. bovis BCG 65-kDa protein that was previously designated MbaA. Four different T-cell-epitope-containing regions (amino acid residues 1 through 16, 17 through 61, 85 through 108, and 235 through 279) were defined that were recognized by seven T-cell clones from patients with tuberculoid leprosy. These regions are distinct from two previously described T-cell epitopes recognized by T cells from a tuberculosis patient. As T-cell clones restricted by different class II determinants were shown to be specific for different regions on the 65-kDa protein, the presented data suggested that the products of different human leukocyte antigen class II loci and alleles present different parts of MbaA to the immune system. B-cell epitopes recognized by 20 monoclonal antibodies were assigned to eight different regions of MbaA. Using 15 of these antibodies, we previously showed that MbaA was antigenically related to a common antigen present in many bacterial species. The dispersed localization of the involved epitopes defined here shows that various different parts of MbaA are indeed conserved. These results show that well-defined recombinant antigens are useful tools for the localization of both B- and T-cell-epitope-containing regions of a protein. Peptides synthesized from the sequences of such regions may then exactly define the epitopes relevant for the development of specific diagnostic tests or of vaccines against mycobacteria.
Real-time Clock Estimation for Precise Orbit Determination of LEO-Satellites (2008)

In this paper, a real-time system for clock offset estimation of GPS satellites is presented. The algorithm is based on a Kalman-filter and processes undifferenced code and carrier-phase measurements of a global NTRIP tracking network. The clock offset and drift of the satellite clocks are estimated along with tracking station clock offsets, tropospheric zenith path delay and carrier-phase ambiguities. The filter algorithm and data processing scheme is presented. The accuracy of the orbit and clock product is assessed with a precise orbit determination of the TerraSar-X satellite and compared to results gained with the IGU predicted&#13;\nproducts.
High molecular weight RNAs and small interfering RNAs induce systemic posttranscriptional gene silencing in plants (2002)

Posttranscriptional gene silencing (PTGS) in transgenic plants is an epigenetic form of RNA degradation related to PTGS and RNA interference (RNAi) in fungi and animals. Evidence suggests that transgene loci and RNA viruses can generate double-stranded RNAs similar in sequence to the transcribed region of target genes, which then undergo endonucleolytic cleavage to generate small interfering RNAs (siRNA) that promote degradation of cognate RNAs. The silent state in transgenic plants and in Caenorhabditis elegans can spread systemically, implying that mobile silencing signals exist. Neither the chemical nature of these signals nor their exact source in the PTGS pathway is known. Here, we use a positive marker system and real-time monitoring of green fluorescent protein expression to show that large sense, antisense, and double-stranded RNAs as well as double-stranded siRNAs delivered biolistically into plant cells trigger silencing capable of spreading locally and systemically. Systemically silenced leaves show greatly reduced levels of target RNA and accumulate siRNAs, confirming that RNA can induce systemic PTGS. The induced siRNAs represent parts of the target RNA that are outside of the region of homology with the triggering siRNA. Our results imply that siRNAs themselves or intermediates induced by siRNAs could comprise silencing signals and that these signals induce self-amplifying production of siRNAs.
On-Line Liquid Chromatography Mass Spectrometry: A Useful Tool for the Detection of DNA Sequence Variation (2001)

Indications of the occurrence of mutations can be gained from accurate mass measurements by electrospray ionization mass spectrometry. On-line coupling to liquid chromatography is essential for the application to real samples. By utilizing the coupled method, insertions, deletions, and point mutations are rapidly discovered in DNA restriction fragments and PCR products.
Commercial Fibrinogen, Autogenous Plasma, Whole Blood and Cryoprecipitate for Coagulum Pyelolithotomy: A Comparative Study (1978)

Coagulation pyelolithotomy provides an effective means to remove multiple calculi from the renal collecting system. The strength of the coagulum is directly proportional to the concentration of fibrinogen and inversely proportional to the concentration of thrombin. Because of the fear of hepatitis fibrinogen may soon be unavailable commercially. It will then become necessary to use plasma from the patient as the source of fibrinogen. By the process of cryoprecipitation fibrinogen levels can be increased about 10-fold, yielding clots of greater tensile strength than would be obtained from non-concentrated plasma.
On the development of the Anuloid, a disk-shaped VTOL aircraft for urban areas (2014)

This paper deals with the early development of the Anuloid, an innovative disk-shaped VTOL aircraft. The Anuloid concept is based on the following three main features: the use of a ducted fan powered by a turboshaft for the lift production to take-off and fly; the Coanda effect that is developed through the circular internal duct and the bottom portion of the aircraft to provide further lift and control capabilities; the adoption of a system of ducted fixed and swiveling radial and circumferential vanes for the anti-torque mechanism and the flight control. The early studies have been focused on the CFD analysis of the Coanda effect and of the control vanes; the flyability analysis of the aircraft in terms of static performances and static and dynamic stability; the preliminary structural design of the aircraft. The results show that the Coanda effect is stable in most of the flight phases, vertical flight has satisfactory flyability qualities, whereas horizontal flight shows dynamic instability, requiring the development of an automatic control system.
Frontiers in Gastroenterology (2002)

There have been a number of exciting advancements and changes in the gastroenterology field over the last few years. A new mesalamine formulation, balsalazide disodium, is now available for the treatment of ulcerative colitis (UC). Balsalazide may be utilized as first line therapy for patients with UC, or patients who are intolerant to other mesalamine preparations. In the area of irritable bowel syndrome, alosetron was removed from the market after reports that it was associated with severe constipation and death, although a causal relationship could not be established. Published data examines the risk of certain medications and the development of reflux disease and esophageal adenocarcinoma. Also, new proton pump inhibitors (PPIs) are available, esomeprazole, as well as alternate methods of administration for others. The first intravenous PPI, pantoprazole, is available in the United States, although currently there is a paucity of data regarding its efficacy. Peptic ulcer disease is also discussed, including Helicobacter pylori resistance, nonsteroidal anti-inflammatory drugs, and the treatment of bleeding ulcers. With pegylated interferon, progress in the treatment of hepatitis C offers promise for many patients. This review will highlight many recent changes in gastroenterology an offer a perspective on how disease management has changed.
Evanescent Wave Long-Period Fiber Bragg Grating as an Immobilized Antibody Biosensor (2000)

An immunosensor using a long-period grating (LPG) was used for sensitive detection of antibody-antigen reactions. Goat anti-human IgG (antibody) was immobilized on the surface of the LPG, and detection of specific antibody-antigen binding was investigated. This sensor operates using total internal reflection where an evanescent field interacts with bound antibody immobilized over the grating region. The reaction between antibody and antigen altered the LPG transmission spectrum and was monitored in real time as a change in refractive index, thereby eliminating the need for labeling antigen molecules. Human IgG binding was observed to be concentration dependent over a range of 2-100 microg mL-1, and equilibrium bound antigen levels could be attained in approximately 5 min using an initial rate determination. Binding specificity was confirmed using human interleukin-2 and bovine serum albumin as controls, and nonspecific adsorption of proteins did not significantly interfere with detection of binding. Antigen detection in a heterogeneous protein mixture and in crude cell lysate from Escherichia coli was also confirmed. Moreover, regeneration of the LPG surface via diethylamine treatment resulted in approximately 80% removal of bound antigen. Subsequently, fibers reexposed to antigen retained greater than 85% of the initial signal after five consecutive regeneration cycles.
Endoplasmic reticulum stress and the unfolded protein response regulate genomic cystic fibrosis transmembrane conductance regulator expression (2006)

The unfolded protein response (UPR) is a cellular recovery mechanism activated by endoplasmic reticulum (ER) stress. The UPR is coordinated with the ER-associated degradation (ERAD) to regulate the protein load at the ER. In the present study, we tested how membrane protein biogenesis is regulated through the UPR in epithelia, using the cystic fibrosis transmembrane conductance regulator (CFTR) as a model. Pharmacological methods such as proteasome inhibition and treatment with brefeldin A and tunicamycin were used to induce ER stress and activate the UPR as monitored by increased levels of spliced XBP1 and BiP mRNA. The results indicate that activation of the UPR is followed by a significant decrease in genomic CFTR mRNA levels without significant changes in the mRNA levels of another membrane protein, the transferrin receptor. We also tested whether overexpression of a wild-type CFTR transgene in epithelia expressing endogenous wild-type CFTR activated the UPR. Although CFTR maturation is inefficient in this setting, the UPR was not activated. However, pharmacological induction of ER stress in these cells also led to decreased endogenous CFTR mRNA levels without affecting recombinant CFTR message levels. These results demonstrate that under ER stress conditions, endogenous CFTR biogenesis is regulated by the UPR through alterations in mRNA levels and posttranslationally by ERAD, whereas recombinant CFTR expression is regulated only by ERAD.