gebhart/patrepeval huggingface dataset:
Soybean Bowman–Birk Protease Inhibitor Is a Highly Effective Inhibitor of Human Mast Cell Chymase (1997)

Soybean Bowman-Birk protease inhibitor (BBI) is an inhibitor of serine proteases with two functional inhibitory domains of different specificities: one is specific for chymotrypsin-like proteases, the other for trypsin-like proteases. Chymase and tryptase are serine proteases which are stored in mast cell granules and released upon degranulation. This work investigated the inhibition of human chymase and tryptase by BBI. Active-site titration of human skin chymase by BBI demonstrated that BBI was a highly effective inhibitor of human chymase. Virtually stoichiometric inhibition of chymase by BBI was observed at 10 nM chymase. Kinetic studies of the inhibition reaction yielded an association rate constant of 4.0 x 10(5) M(-1) s(-1) and a dissociation rate constant of 1.7 x 10(-5) s(-1). From these two constants we estimate a K(i) of 50 pM. Chymase/BBI complexes did not dissociate in SDS-PAGE analyses under nonreducing conditions, consistent with the formation of a very tight complex with little tendency to dissociate. In contrast to chymase, human tryptase was not inhibited by BBI. These studies demonstrate that BBI is a good inhibitor of human chymase, exhibiting reaction properties better than physiological inhibitors described to date.
Peptide‐loaded dendritic‐cell vaccination followed by treatment interruption for chronic HIV‐1 infection: A phase 1 trial (2006)

Immune response enhanced by therapeutic HIV-1 vaccine may control viral proliferation after discontinuation of highly active antiretroviral therapy (HAART). Although which strategies for therapeutic vaccination are feasible remains controversial, application of dendritic cells (DCs) as a vaccine adjuvant represents a promising approach to improving deteriorated immune function in HIV-1-infected individuals. The safety and efficacy of DC-based vaccine loaded with HIV-1-derived cytotoxic T lymphocytes (CTL) peptides were thus investigated in this study. Autologous DCs loaded with seven CTL peptides with HLA-A*2402 restriction were immunized to four HIV-1-infected individuals under HAART. In terms of safety, peptide-loaded DCs were well tolerated, and only mild local and general symptoms were observed during vaccine administration. ELISPOT assays to detect IFN-gamma production in CD8(+) lymphocytes revealed a limited breadth of responses to immunized peptides in two of four participants, but no response in the remaining two participants. Differences in immunological response might be attributable to the fact that responders displayed higher nadir CD4 counts before starting HAART and were immunized with a larger number of DCs per reactive peptide than non-responders. Discontinuation of HAART after vaccination failed to lower viral set points compared to those before starting HAART. This early outcome warrants further exploration to elucidate the therapeutic value of vaccination with DCs in HIV-1 infection.
DNA bifunctional intercalators. 2. Fluorescence properties and DNA binding interaction of an ethidium homodimer and an acridine ethidium heterodimer. Appendix: Numerical solution of McGhee and von Hippel equations for competing ligands (1978)

An ethidium homodimer and acridine ethidium heterodimer have been synthesized (Gaugain, B., Barbet, J., Oberlin, R., Roques, B. P., & Le Pecq, J. B. (1978) Biochemistry 17 (preceding paper in this issue)). The binding of these molecules to DNA has been studied. We show that these dimers intercalate only one of their chromophores in DNA. At high salt concentration (Na+ greater than 1 M) only a single type of DNA-binding site exists. Binding affinity constants can then be measured directly using the Mc Ghee & Von Hippel treatment (Mc Ghee, J. D., & Von Hippel, P. H. (1974) J. Mol. Biol. 86, 469). In these conditions the dimers cover four base pairs when bound to DNA. Binding affinities have been deduced from competition experiments in 0.2 M Na+ and are in agreement with the extrapolated values determined from direct DNA-binding measurements at high ionic strength. As expected, the intrinsic binding constant of these dimers is considerably larger than the affinity of the monomer (ethidium dimer K = 2 X 10(8) M-1; ethidium bromide K = 1.5 X 10(5) M-1 in 0.2 M Na+). The fluorescence properties of these molecules have also been studied. The efficiency of the energy transfer from the acridine to the phenanthridinium chromophore, in the acridine ethidium heterodimer when bound to DNA, depends on the square of the AT base pair content. The large increase of fluorescence on binding to DNA combined with a high affinity constant for nucleic acid fluorescent probes. In particular, such molecules can be used in competition experiments to determine the DNA binding constant of ligands of high binding affinity such as bifunctional intercalators.
The analysis of the surface chemical structure of biomedical aliphatic polyanhydrides using XPS and ToF‐SIMS (1991)

Abstract The surface chemical structure of a range of aliphatic polyanhydride films has been examined using XPS and ToF‐SIMS. The XPS data confirms the purity of the surface, and the experimental surface elemental ratios are in good general agreement with the known stoichiometry of the polyanhydrides. The ToF‐SIMS spectra of the polyanhydrides are shown to be significantly different. The SIMS data conforms to a systematic fragmentation, in both negative‐ and positive‐ion SSIMS spectra, occurring throughout the entire series of polyanhydrides examined. Radical cations are observed in the positive‐ion spectra. These results are discussed in terms of the general fragmentation patterns observed in the SIMS analysis of polymers. The combined use of ToF‐SIMS and XPS is shown, to provide a detailed insight into the interfacial chemical structure of these polyanhydrides.
The role of CD40/CD154 interactions in the priming, differentiation, and effector function of helper and cytotoxic T cells (1998)

This review focuses on the emerging body of literature suggesting a critical role for CD40/CD154 interactions in antigen-presenting cell (APC) activation, CD4+ and CD8+ T cell priming, and effector T cell maturation. In this context effective antigen presentation involves not only T cell expansion and long-term survival but also the ability of the APC to guide the T cell response toward the Th1 (interferon-gamma producing) or the Th2 (interleukin-4 producing) phenotype. We suggest a model to explain why CD40/CD154 interactions are critical for some helper and cytotoxic T cell responses, whereas others occur independently of this receptor/ligand pair. In addition, we will discuss the potential role for CD40/CD154 interactions in effector T cell maturation and cytokine production.
A KIND OF FIBER FORMATING MATERIAL WITH ABUNDANT SOURCE-CHITN-THE STRUCTURE OF CHITIN (1996)

This paper is discussed the molecular structure, crystalline structure, orientational structure and the microfibrils of chitin. Chitin is a kind of natural polymer with high linear degree. There are three crystallines in nature,such as α-,β-,and γ-crystalline. α-crystalline is orthorhombic form, β-crystalline is monoclinic form and γ-crystalline is bidimensional crystalline. In certain conditions,α-β and γ-crystalline can be transformed into each other. The molecular and the crystalline units can get a high degree of orientation with suituble conditions,so chitin is a good material for making fiber with excellent physico-mechanical properties.
Planarization coating for polyimide substrates used in roll-to-roll fabrication of active matrix backplanes for flexible displays (2012)

Good surface quality of plastic substrates is essential to reduce pixel defects during roll-to-roll fabrication of flexible display active matrix backplanes. Standard polyimide substrates have a high density of "bumps" from fillers and belt marks and other defects from dust and surface scratching. Some of these defects could be the source of shunts in dielectrics. The gate dielectric must prevent shorts between the source/drain and the gate in the transistors, resist shorts in the hold capacitor and stop shorts in the data/gate line crossovers in active matrix backplanes fabricated by self-aligned imprint lithography (SAIL) roll-to-roll processes. Otherwise data and gate lines will become shorted creating line or pixel defects. In this paper, we discuss the development of a proprietary UV curable planarization material that can be coated by roll-to-roll processes. This material was engineered to have low shrinkage, excellent adhesion to polyimide, high dry etch resistance, and great chemical and thermal stability. Results from PECVD deposition of an amorphous silicon stack on the planarized polyimide and compatibility with roll-to-roll processes to fabricate active matrix backplanes are also discussed. The effect of the planarization on defects in the stack, shunts in the dielectric and curvature of finished arrays will also be described.
Studies on the Pharmaceutical Potentiation of Drugs. I. p-Aminosalicylic Acid Derivatives. (1967)

Three series of PAS derivatives, alkyl, ω-hydroxyalkyl, and ω-phenylalkyl esters, were synthesized systematically and their evaluations were made with testing their tuberculostatic activities and with measuring their physico-chemical characteristics, such as partition coefficients and protein binding ratio that might considerably influence biological effects in animal body. It is recognized that these derivatives may extensively improve the defects of the parent compound. It is also demonstrated that the substituents on the end of the alkyl chain and the length of the alkyl chain of these compounds considerably influence on their antitubercular activities and physico-chemical properties.
A "flight data recorder" for enabling full-system multiprocessor deterministic replay (2003)

Debuggers have been proven indispensable in improving software reliability. Unfortunately, on most real-life software, debuggers fail to deliver their most essential feature --- a faithful replay of the execution. The reason is non-determinism caused by multithreading and non-repeatable inputs. A common solution to faithful replay has been to record the non-deterministic execution. Existing recorders, however, either work only for datarace-free programs or have prohibitive overhead.As a step towards powerful debugging, we develop a practical low-overhead hardware recorder for cachecoherent multiprocessors, called Flight Data Recorder (FDR). Like an aircraft flight data recorder, FDR continuously records the execution, even on deployed systems, logging the execution for post-mortem analysis.FDR is practical because it piggybacks on the cache coherence hardware and logs nearly the minimal threadordering information necessary to faithfully replay the multiprocessor execution. Our studies, based on simulating a four-processor server with commercial workloads, show that when allocated less than 7% of system's physical memory, our FDR design can capture the last one second of the execution at modest (less than 2%) slowdown.
Protein Expression Profiling in Esophageal Adenocarcinoma Patients Indicates Association of Heat-Shock Protein 27 Expression and Chemotherapy Response (2008)

Albeit preliminary, our encouraging data suggest that protein expression profiling may distinguish cancers with a different response to chemotherapy. Our results suggest that response to chemotherapy may be related to a different activation of stress response and inflammatory biology in general. Moreover, the potential of HSPs and GRPs as biomarkers of chemotherapy response warrants further validation.
A Focused Ultrasound System for Tissue Volume Ablation in Deep Seated Brain Sites (1986)

A new intense focused ultrasound system operating in the transcutaneous mode has been constructed for study of its utility in the treatment of deep seated brain tumors in the human. In preparation for treatment the human will have surgical removal of an appropriate skull section and the o verlying t issues will be left to heal before starting the irradiation process. treatment will be done with CT scanning involving a rigid l ight weight skull fixation fixture which remains rigidly attached to the patient's skull for the CT scan as well as for the irradiation procedure. Once the lesion volume coordinates are determined and the patient is attached to the irradiation system the 1 MHz focused beam is automatically brought to an array of positions within the tissue volume. Each position is individually lesioned and the tissue volume ablated is constructed f rom a multiplicity of individual site lesions. Localization of a tumor site for
A Tumour Necrosis Factor Beta Gene Polymorphism in Relation to Monokine Secretion and Insulin‐Dependent Diabetes Mellitus (1991)

HLA-class III region genes may be associated with susceptibility to insulin-dependent diabetes mellitus (IDDM). In this study an NcoI polymorphism of the tumour necrosis factor beta (TNF-beta) gene, which is positioned next to the tumour necrosis factor alpha (TNF-alpha) gene in the HLA class III region, was detected by restriction fragment length polymorphism (RFLP). This polymorphism has previously been reported to be located in the TNF-alpha gene. Caucasian HLA-DR3,4 heterozygous IDDM patients (n = 26) and DR-matched healthy controls (n = 19), as well as randomly selected IDDM patients (n = 27) and controls (n = 25) were studied. In addition four multiplex families (49 individuals) and eight HLA-non-identical sibpairs concordant for IDDM were analysed. The TNF-beta gene RFLP analysis showed fragments of 5.5 kb and 10.5 kb, which behaved as alleles. In all groups there was a haplotype assignment of the TNF-beta 5.5-kb allele to B8,DR3 haplotypes, and of the TNF-beta 10.5-kb allele to B15,DR4-positive haplotypes. The allelic and genotypic frequencies differed between DR3,4 IDDM patients and DR3,4 controls, and the DR3,4 control group differed significantly from the randomly selected control group (P less than 0.0079). In HLA-DR3,4- and DQw8-positive persons, the DR3 haplotypes carried the 10.5-kb allele three times more frequently in IDDM patients than in controls, suggesting that the 10.5-kb allele when present on DR3 haplotypes may contribute to susceptibility to IDDM in DR3,4 heterozygous individuals. A contributory role of the 10.5-kb allele in genetic IDDM susceptibility was supported by the sibpair analysis, in which all were TNF-beta identical. Five were 10.5 kb homozygous, and the remaining three pairs were 5.5/10.5 kb heterozygous. Twenty-five healthy and eight newly diagnosed IDDM patients were randomly selected to study the Escherichia coli lipopolysaccharides (LPS)-purified protein derivate (tuberculin) (PPD)-, and phytohaemagglutinin (PHA)-stimulated monocyte (Mo) secretions of interleukin 1 beta (IL-1 beta) and TNF-alpha in relation to the NcoI TNF-beta gene polymorphism. The LPS- and PHA-stimulated Mo IL-1 beta and TNF-alpha secretions were significantly lower for the TNF-beta 5.5/10.5 kb heterozygous individuals than for TNF-beta 10.5 kb homozygous individuals. Furthermore, the Mo IL-1 beta and TNF-alpha secretions of IDDM patients were significantly higher than the Mo secretions of TNF-beta genotype-matched healthy controls. This study suggests an association between the 10.5 kb TNF-beta allele and IDDM, and demonstrates an association between monokine responses and TNF-beta genotypes.(ABSTRACT TRUNCATED AT 400 WORDS)
Coil combination for receive array spectroscopy: Are data‐driven methods superior to methods using computed field maps? (2015)

In the human torso, at frequencies ≥49 MHz, data-driven combination is preferable to using computed coil sensitivities. Magn Reson, 2015. © 2015 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Magn Reson Med 75:473-487, 2016. © 2015 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.
PCR and DNA Fingerprinting Used as Quality Control in the Production of Wine Yeast Strains (1994)

Unambiguous identification of wine yeast strains has always been a prime concern for the yeast producer. Because of the increasing number of commercialized strains, novel methodologies had to be developed to identify and to certify the origin of the different strains. We present here our work on DNA fingerprinting and polymerase chain reaction (PCR) as identification tools. Both methods were tested for their reproducibility and their use to study the genetic stability of more than a hundred wine yeast strains during standard industrial propagation conditions. The techniques used herein demonstrated that a wide diversity exists in the strains analyzed, as more than 95% of the profiles could be used to uniquely identify the corresponding strain.
A cyanobacterial LPS antagonist prevents endotoxin shock and blocks sustained TLR4 stimulation required for cytokine expression (2006)

Toll-like receptors (TLRs) function as primary sensors that elicit coordinated innate immune defenses through recognition of microbial products and induction of immune and proinflammatory genes. Here we report the identification and biological characterization of a lipopolysaccharide (LPS)-like molecule extracted from the cyanobacterium Oscillatoria Planktothrix FP1 (cyanobacterial product [CyP]) that is not stimulatory per se but acts as a potent and selective antagonist of bacterial LPS. CyP binds to MD-2 and efficiently competes with LPS for binding to the TLR4-MD-2 receptor complex. The addition of CyP together with LPS completely inhibited both MyD88- and TRIF-dependent pathways and suppressed the whole LPS-induced gene transcription program in human dendritic cells (DCs). CyP protected mice from endotoxin shock in spite of a lower capacity to inhibit LPS stimulation of mouse DCs. Interestingly, the delayed addition of CyP to DCs responding to LPS strongly inhibited signaling and cytokine production by immediate down-regulation of inflammatory cytokine mRNAs while not affecting other aspects of DC maturation, such as expression of major histocompatibility complex molecules, costimulatory molecules, and CCR7. Collectively, these results indicate that CyP is a potent competitive inhibitor of LPS in vitro and in vivo and reveal the requirement of sustained TLR4 stimulation for induction of cytokine genes in human DCs.
Understanding and controlling heteroepitaxy with the kinetic Wulff plot: A case study with GaN (2011)

This work represents a comprehensive attempt to correlate the heteroepitaxial dynamics in experiments with fundamental principles in crystal growth using the kinetic Wulff plot (or v-plot). Selective area growth is employed to monitor the advances of convex and concave facets toward the construction of a comprehensive v-plot as a guidepost for GaN heteroepitaxy. A procedure is developed to apply the experimentally determined kinetic Wulff plots to the interpretation and the design of evolution dynamics in nucleation and island coalescence. This procedure offers a cohesive and rational model for GaN heteroepitaxy on polar, nonpolar, and semipolar orientations and is broadly extensible to other heteroepitaxial material systems. We demonstrate furthermore that the control of morphological evolution, based on invoking a detailed knowledge of the v-plots, holds a key to the reduction of microstructural defects through effective bending of dislocations and geometrical blocking of stacking faults, paving a way to device-quality heteroepitaxial nonpolar and semipolar GaN materials.
Compartment-specific accumulation of recombinant immunoglobulins in plant cells: an essential tool for antibody production and immunomodulation of physiological functions and pathogen activity. (1998)

Expression and stability of immunoglobulins in transgenic plants have been investigated and optimized by accumulation in different cellular compartments as cytosol, apoplastic space and endoplasmic reticulum (ER) as will be discussed in this review. In several cases described the highest accumulation of complete active antibodies was achieved by targeting into the apoplastic space. High-level expression of active recombinant single-chain Fv antibodies (scFv's) was obtained by retention of these proteins in the lumen of the endoplasmic reticulum. This has been shown for leaves and seeds of transgenic tobacco as well as for potato tubers. Transgenic tobacco seeds, potato tubers and tobacco leaves can facilitate stable storage of scFv's accumulated in the ER over an extended (seeds, tubers) or a short (leaves) period of time. The expression of specific scFv's in different plant species, plant organs and cellular compartments offers the possibility of blocking regulatory factors or pathogens specifically. Examples are scFv's expressed in the cytosol and the apoplastic space of transgenic plant cells modulating the infection process of plant viruses and a cytosolically expressed scFv that influenced the activity of phytochrome A protein. The immunomodulation approach has been shown to be also applicable for investigating the action of the phyto-hormone abscisic acid (ABA). High-level accumulation of specific anti-ABA scFv's in the ER of all leaf cells has been used to block the influence of ABA on the stomatal functions. Seed-specific expression of high amounts of anti-ABA-scFv's at a defined time of seed-development induced a developmental switch from seed ripening to vegetative growth. It has been demonstrated that ER retention is essential for the accumulation of sufficient scFv to bind high concentrations of ABA in the transgenic seeds.
What stay‐green mutants tell us about nitrogen remobilization in leaf senescence (2002)

Leaf senescence has an important role in the plant's nitrogen economy. Chlorophyll catabolism is a visible symptom of protein mobilization. Genetic and environmental factors that interfere with yellowing tend to modify protein degradation as well. The chlorophyll-protein relationship is much closer for membrane proteins than it is for soluble or total leaf proteins. In stay-greens, genotypes with a specific defect in the chlorophyll catabolism pathway, soluble protein degradation during senescence may be close to normal, but light-harvesting and reaction centre thylakoid membrane proteins are much more stable. Genes for the chlorophyll catabolism pathway and its control are important in the regulation of protein mobilization. Genes for three steps in the pathway are reported to have been isolated. The gene responsible for the stay-green phenotype in grasses and legumes has not yet been cloned but a fair amount is known about it. Pigment metabolism in senescing leaves of the Festuca-Lolium stay-green mutant is clearly disturbed and is consistent with a blockage at the ring-opening (PaO) step in chlorophyll breakdown. PaO is de novo synthesized in senescence and thought to be the key enzyme in the chlorophyll a catabolic pathway. The stay-green mutation is likely to be located in the PaO gene, or a specific regulator of it. These genes may well be in the various senescence-enhanced cDNA collections that have been generated, but functional handles on them are currently lacking. When the stay-green locus from Festuca pratensis was introgressed into Lolium temulentum, a gene encoding F. pratensis UDPG-pyrophosphorylase was shown to have been transferred on the same chromosome segment. A strategy is described for cloning the stay-green gene, based on subtractive PCR-based analyses of intergeneric introgressions and map-based cloning.