gebhart/patrepeval huggingface dataset:
Saccharomyces cerevisiae Spheroplasts Are Sensitive to the Action of Diphtheria Toxin (1982)

Diphtheria toxin kills spheroplasts of Saccharomyces cerevisiae but not the intact yeast cells. After 2 h of exposure to ca. 10(-7) M toxin, less than 1% of spheroplasts were able to regenerate into intact cells. The same high levels of toxin inhibited the rate of protein synthesis by more than 90% within 1 h, whereas RNA and DNA synthesis were not inhibited until 4 h or exposure. Both killing and protein synthesis inhibition were dependent on toxin concentration. The nature of the toxin-cell interaction was also studied by using fragments of intact toxin and mutant toxin proteins. Neither toxin fragment A nor CRM45 nor CRM197 affected spheroplasts, but CRM197 and ATP prevented the inhibitory action of intact toxin. These results suggest that toxin acts on S. cerevisiae spheroplasts in much the same manner as it acts on sensitive mammalian cells.
Photopolymerization kinetics and phase behaviour of acrylate based polymer dispersed liquid crystals (1998)

Polymer dispersed liquid crystal (PDLC) materials were prepared by a polymerization induced phase separation (PIPS) process using UV radiation. The samples were obtained from the liquid crystalline component E7 and a blend of monofunctional (2-ethylhexyl acrylate) and difunctional (1,6-hexane diol diacrylate) monomers as precursors of the matrix. Polymerization energetics and thermodynamic properties of PDLC materials were studied by differential scanning calorimetry. Photopolymerization kinetics and phase behaviour of the PDLC are presented and discussed as a function of UV polymerization conditions (UV light intensity, UV time exposure and isothermal curing temperature).
TNF-α increases human melanoma cell invasion and migration in vitro: the role of proteolytic enzymes (2003)

Inflammatory mediators have been reported to promote malignant cell growth, invasion and metastatic potential. More specifically, we have recently reported that tumour necrosis factor alpha (TNF-alpha) increases melanoma cell attachment to extracellular matrix (ECM) substrates and invasion through fibronectin. In this study, we extend these investigations asking specifically whether the TNF-alpha effect on cell invasion and migration involves activation of proteolytic enzymes. We examined the effect of TNF-alpha on melanoma expression/activation of type IV gelatinases matrix metalloproteinases 2 and 9 (MMPs -2 and -9) and general proteolytic enzymes. Stimulation with TNF-alpha significantly increased both melanoma cell migration at 24 h (+21%) and invasion through fibronectin (+35%) but did not upregulate/activate the expression of latent MMP-2 constitutively produced by these cells and did not upregulate their general protease activity. However, the increased cell migration and invasion through fibronectin observed following stimulation with TNF-alpha were inhibited by the general protease inhibitor alpha(2) macroglobulin. These findings suggest that the promigratory and proinvasive effect of TNF-alpha on this melanoma cell line may be mediated to some extent by induction of localised cell membrane-bound degradative enzyme activity, which is not readily detected in biochemical assays.
A phosphatidylinositol-linked peanut agglutinin-binding glycoprotein in central nervous system myelin and on oligodendrocytes. (1988)

Here we report the isolation and initial biochemical characterization of a 120-kD peanut agglutinin-binding glycoprotein from the adult human central nervous system (CNS), which is anchored to membranes through a phosphatidylinositol linkage. Myelin incubated with phosphatidylinositol-specific phospholipase C released the protein as a soluble polypeptide of 105 kD, which was isolated with peanut agglutinin-agarose affinity chromatography. The protein was found to be highly glycosylated. The protein appears to be confined to the CNS, where its developmental expression is region specific and parallels myelination. It is in greater quantity in white matter than in gray matter and it is in isolated human CNS myelin. Furthermore, ovine oligodendrocytes in culture contain the protein on their surfaces and release it into the supernatant as a soluble 105-kD form. We call this protein the oligodendrocyte-myelin protein.
The Biogenesis and Functions of Exosomes (2002)

Exosomes are membrane vesicles with a diameter of 40-100 nm that are secreted by many cell types into the extracellular milieu. They correspond to the internal vesicles of an endosomal compartment, the multivesicular body and are released upon exocytic fusion of this organelle with the plasma membrane. Intracellularly, they are formed by inward budding of the endosomal membrane in a process that sequesters particular proteins and lipids. The unique composition of exosomes may confer specific functions on them upon secretion. Although their physiological role in vivo is far from being unraveled, it is apparent that they function in a multitude of processes, including intercellular communication during the immune response. Exosomes may have evolved early in the evolution of multicellular organisms and also seem to be important for tissue developmental processes.
Experimental Determination of the Temperature Dependency of the Elastic Constants of Degenerately Doped Silicon (2013)

We study experimentally the temperature dependence of the elastic constants of degenerately doped silicon as a function of the doping level. First and second order thermal coefficients of the elastic constants are extracted from the temperature dependent resonance frequencies of a set of MEMS resonators fabricated on phosphorus, arsenic and boron doped wafers having maximum doping levels of 7.5 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">19</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> , 2.5 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">19</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> and 3 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">19</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> , respectively. Trends in the behavior of the thermal coefficients as a function of doping are identified and discussed.
Monobodies and other synthetic binding proteins for expanding protein science (2017)

Synthetic binding proteins are constructed using nonantibody molecular scaffolds. Over the last two decades, in-depth structural and functional analyses of synthetic binding proteins have improved combinatorial library designs and selection strategies, which have resulted in potent platforms that consistently generate binding proteins to diverse targets with affinity and specificity that rival those of antibodies. Favorable attributes of synthetic binding proteins, such as small size, freedom from disulfide bond formation and ease of making fusion proteins, have enabled their unique applications in protein science, cell biology and beyond. Here, we review recent studies that illustrate how synthetic binding proteins are powerful probes that can directly link structure and function, often leading to new mechanistic insights. We propose that synthetic proteins will become powerful standard tools in diverse areas of protein science, biotechnology and medicine.
An Efficient Method for the Synthesis of [4–15N]Cytidine, 2′-Deoxy[4–15N]Cytidine, [6–15N]adenosine, and 2′-Deoxy [6–15N]adenosine Derivatives (1996)

Abstract Nucleophilic substitution reactions of 4-azolyl-1 β-P-D-ribofuranosylpyrimidin-2(1H)-one and 6-azolyl-9-β-D-ribofuranosyl-9H-purine derivatives, which were converted from uridine and inosine, with [15N]phthalimide in the presence of triethylamine or DBU gave N 4-phthaloyl[4-15N]cytidine and N 6-phthaloyl[6-15N]- adenosine derivatives, respectively, in high yields. Similar reactions of those azolyl derivatives with succinimide afforded N 4-succinylcytidine and N 6-succinyladenosine derivatives in high yields. The corresponding 2′-deoxyribonucleosides were also synthesized efficiently through the same procedure. 1. Partial Protection of Carbohydrate Derivatives. Part 31. For Part 30, see Aoyama, Y.; Sekine, T.; Iwamoto, Y.; Kawashima, E.; Ishido, Y. Nucleosides Nucleotides, submitted. The present work has partly been communicated (cf. Kamaike, K.; Takahashi, M.; Utsugi, K.; Tomizuka, K.;Ishido, Y. Tetrahedron Lett. 1995, 36, 91–94.). #This paper is dedicated to Dr. Yoshihisa Mizuno on the occasion ...
Adenovirus Vector-Mediated In Vivo Gene Transfer of Brain-Derived Neurotrophic Factor (BDNF) Promotes Rubrospinal Axonal Regeneration and Functional Recovery after Complete Transection of the Adult Rat Spinal Cord (2004)

Neurotrophins have been shown to promote axonal regeneration, but the techniques available for delivering neurotrophins have limited effectiveness. The aim of this study was to evaluate the effect of adenovirus vector mediated gene transfer of brain-derived neurotrophic factor (BDNF) on axonal regeneration after spinal cord injury. We prepared adenovirus vectors encoding either beta-galactosidase (AxCALacZ) or BDNF (AxCABDNF). AxCALacZ was used to assess infection levels of the adenovirus BDNF produced by AxCABDNF was detected by Western blotting and its bioactivity was confirmed by bioassay. As a model of spinal cord injury, the rat spinal cord was completely transected at the T8 level. Immediately after transection, the vectors were injected into both stumps of the spinal cord. Axonal regeneration after transection was assessed by retrograde and anterograde tracing. In AxCALacZ-injected rats, adenovirus-infected cells were observed not only at the injected site but also in brainstem nuclei, as shown by LacZ expression. After the injection of the retrograde tracer fluorogold (FG) distal portion to the transection, AxCABDNF-injected rats showed FG-labeled neurons in the red nucleus. The anterograde tracer biotinylated dextran amine (BDA) injected into the red nucleus was also found in regenerating rubrospinal fibers distal to the transection. These tracing experiments demonstrated the regeneration of descending axons. In addition, rats of the AxCABDNF group showed significant locomotor recovery of hindlimb function, which was completely abolished by re-transection. These results indicate that the recovery was caused by regeneration of rubrospinal axons, not by simple enhancement of the central pattern generator.
Metabolic products of Aspergillus terreus. V. Demethylation of asterriquinones. (1981)

Demethylation of asterriquinones (AQ, bisindolyl-dimethoxyl benzoquinones) was investigated in connection with the determination of their structures and studies of their antitumor activity. Usually, the demethylation proceeded smoothly with KOH, but several types of side reactions were observed with acidic reagents.
Evaluation of trajectories and contact pressures for the straight nucleus cochlear implant electrode array — a two-dimensional application of finite element analysis (2002)

A two-dimensional (2D) finite element analysis has been used in this study to model the insertion of the Nucleus electrode array with different stiffness properties in order to evaluate the propensity of damage by visualizing the predicted trajectories and by comparing the buckling stresses and the contact pressures at the tip (and its distribution along the length) of the electrode array. Previous temporal bone studies have shown that damage during insertion of an electrode array around the basal turn of the cochlear spiral could be related to the design and the stiffness properties of the electrode array. However, it is difficult to evaluate different designs of electrode arrays purely by experimental methods as the experimental conditions and their results are difficult to reproduce. Three electrode arrays with different mechanical properties, i.e. uniform stiffness, graded stiffness, and a soft tip have been modelled. Buckling stress and contact pressure at the tip of the electrode array were found to be highest for the arrays with uniform stiffness. The contact pressures at the tip of the electrode array appeared strongly influenced by the stiffness profile and were optimal for graded stiffness. The results indicate the importance of the electrode array design and stiffness properties in minimizing trauma. However, there are a number of limitations in the present 2D evaluation which will require further analysis using a three-dimensional model to obtain definitive results.
Frequent, moderate-dose cyclophosphamide administration improves the efficacy of cytochrome P-450/cytochrome P-450 reductase-based cancer gene therapy. (2001)

Transduction of tumor cells with a cyclophosphamide (CPA)-activating cytochrome P-450 (P450) gene provides the capacity for localized prodrug activation and greatly sensitizes solid tumors to CPA treatment in vivo. The therapeutic impact of this P450-based cancer gene therapy strategy can be substantially enhanced by cotransduction of P450 reductase, a rate-limiting component of P450-dependent intratumoral CPA activation. The present study examined the possibility of further improving P450/P450 reductase-based gene therapy by using a novel schedule of CPA administration, involving repeated CPA injection every 6 days and previously shown to have an antiangiogenic component. 9L gliosarcoma cells transduced with the CPA-activating enzyme couple P450 2B6/P450 reductase and grown s.c. in immunodeficient severe combined immunodeficient (scid) mice were repeatedly challenged with 140 mg/kg CPA every 6 days. Full tumor regression leading to eradication of six of eight tumors was observed when the tumor size at the time of initial drug treatment was approximately 400 mm(3) (approximately 1.5% of body weight). Little or no overt toxicity of the repeated CPA treatment regimen was observed. The same CPA schedule was much less effective in inducing regression of 9L tumors that were not transduced with P450/P450 reductase. Repeated CPA treatment of mice bearing large, late-stage P450/P450 reductase-transduced tumors (approximately 9-16% of body weight) resulted in major (> or =95%) regression in 15 of 16 tumors, with tumor eradication observed in 2 cases. Although CPA resistance was found to emerge in the population of P450/P450 reductase-transduced tumors, this resistance primarily involved a loss of expression of the transduced P450 and/or P450 reductase gene, rather than development of intrinsic cellular resistance to the activated form of CPA. These findings demonstrate that repeated CPA treatment on a 6 day schedule can be highly effective when combined with P450/P450 reductase gene therapy and suggest that repeated transduction of tumors with prodrug-activation genes may be necessary to achieve tumor eradication and a sustained therapeutic response.
Voltage-VAr optimization (VVO) future trends, challenges and opportunities (2017)

Owing to the unprecedented challenges Distribution Network Operators (DNOs) are facing and driven by advances in information and communications technologies, Integrated Distribution Management Systems (IDMS) have been proposed and developed for more improved operation of distribution systems. Voltage and VAr control and Optimization becomes more and more critical in systems with increased operational uncertainty and complexity, hence Voltage-VAr Optimization (VVO) is one of the key applications offered by IDMS. This paper is focused on the application of Voltage-VAr Optimization (VVO) as part of an IDMS system. It aims to present industry best practices and future trends with regards to modelling and implementation and also to discuss barriers to wider VVO deployment. This paper could eventually inform strategies towards facilitating the advanced functionality of VVO which effectively advances grid capabilities.
Morphological study of the mammalian stress response: characterization of changes in cytoplasmic organelles, cytoskeleton, and nucleoli, and appearance of intranuclear actin filaments in rat fibroblasts after heat-shock treatment. (1985)

Using both electron microscopy and immunological methods, we have characterized a number of changes occurring in rat fibroblasts after heat-shock treatment. Incubation of the cells for 3 h at 42 degrees-43 degrees C resulted in a number of changes within the cytoplasm including: a disruption and fragmentation of the Golgi complex; a modest swelling of the mitochondria and subtle alterations in the packing of the cristae; and alterations in cytoskeletal elements, specifically a collapse and aggregation of the vimentin-containing intermediate filaments around the nucleus. A number of striking changes were also found within the nuclei of the heat-treated cells: (a) We observed the appearance of rod-shaped bodies consisting of densely packed filaments. Using biochemical and immunological methods, these nuclear inclusion bodies were shown to be comprised of actin filaments. (b) Considerable alterations in the integrity of the nucleoli were observed after the heat-shock treatment. Specifically, there appeared to be a general relaxation in the condensation state of the nucleoli, changes in both the number and size of the granular ribonucleoprotein components, and finally a reorganization of the nucleolar fibrillar reticulum. These morphological changes in the integrity of the nucleoli are of significant interest since previous work as well as studies presented here show that two of the mammalian stress proteins, the major stress-induced 72-kD protein and the 110-kD protein, localize within the nucleoli of the cells after heat-shock treatment. We discuss these morphological changes with regards to the known biological and biochemical events that occur in cells after induction of the stress response.
Systematic identification of microRNA functions by combining target prediction and expression profiling (2006)

Target predictions and validations are major obstacles facing microRNA (miRNA) researchers. Animal miRNA target prediction is challenging because of limited miRNA sequence complementarity to the targets. In addition, only a small number of predicted targets have been experimentally validated and the miRNA mechanism is poorly understood. Here we present a novel algorithm for animal miRNA target prediction. The algorithm combines relevant parameters for miRNA target recognition and heuristically assigns different weights to these parameters according to their relative importance. A score calculation scheme is introduced to reflect the strength of each parameter. We also performed microarray time course experiments to identify downregulated genes due to miRNA overexpression. The computational target prediction is combined with the miRNA transfection experiment to systematically identify the gene targets of human miR-124. miR-124 overexpression led to a significant downregulation of many cell cycle related genes. This may be the result of direct suppression of a few cell growth inhibitors at the early stage of miRNA overexpression, and these targeted genes were continuously suppressed over a long period of time. Our high-throughput approach can be generalized to globally identify the targets and functions of other miRNAs.
Lipoprotein Lipase Mutations, Plasma Lipids and Lipoproteins, and Risk of Ischemic Heart Disease (1999)

These meta-analyses suggest that compared with noncarriers, carriers of the Gly188Glu, Asp9Asn, and Asn291Ser substitutions have an atherogenic lipoprotein profile, whereas carriers of the Ser447Ter substitution have a protective lipoprotein profile. Accordingly, risk of ischemic heart disease in heterozygous carriers is increased for Gly188Glu carriers; at most, the increase is borderline for Asp9Asn and Asn291Ser carriers; and risk is possibly decreased for Ser447Ter carriers.
Functional Activation of Cerebral Blood Flow and Metabolism before and after Global Ischemia of Rat Brain (1988)

The effect of somatosensory stimulation on the local CBF (LCBF), CMRglu (LCMRglu), tissue pH, and tissue content of ATP, glucose, and lactate was studied in chloralose-anesthetized rats before and after 30 min of near-complete forebrain ischemia. In nonischemic rats LCBF in primary somatosensory cortex increased by 33%, LCMRglu increased by 55%, tissue glucose content decreased by 21%, and lactate increased by 30%. Local ATP and tissue pH did not change. Functional activation of the intact chloralose-anesthetized rat, in consequence, is associated with the stimulation of "aerobic" glycolysis but does not result in disturbances of energy or acid-base homeostasis. After 30-min ischemia and 3-h recirculation, somatosensory stimulation did not evoke any metabolic or hemodynamic alterations, although EEG and primary somatosensory evoked potentials recovered. The maintenance of normal energy state despite constant metabolic rate suggests that the postischemic generation of evoked potentials does not require measurable amounts of energy. Stimulation of glycolysis in the intact animal, therefore, may serve other purposes than fueling the energy requirements of evoked cortical activity.
Recent U.S. Patents on Protein Drug Formulation: 2000-2007 (2008)

This review summarizes U.S. patents on protein drug formulation issued during the period 2000-2007. The patents fall into four major areas: (i) protein stabilization in solution and solid formulations, (ii) polymer-conjugated and chemically modified proteins, (iii) controlled release protein formulations, and (iv) protein formulation for novel routes of administration. Patents issued in each of the four areas are described and possible areas for additional research are noted.
Fast Modeling Of Acoustic Reflections And Diffraction In Complex Environments Using Visibility Diagrams (2004)

Publication in the conference proceedings of EUSIPCO, Viena, Austria, 2004
Mechanisms by which common variants in the TCF7L2 gene increase risk of type 2 diabetes (2007)

Genetic variants in the gene encoding for transcription factor-7-like 2 (TCF7L2) have been associated with type 2 diabetes (T2D) and impaired beta cell function, but the mechanisms have remained unknown. We therefore studied prospectively the ability of common variants in TCF7L2 to predict future T2D and explored the mechanisms by which they would do this. Scandinavian subjects followed for up to 22 years were genotyped for 3 SNPs (rs7903146, rs12255372, and rs10885406) in TCF7L2, and a subset of them underwent extensive metabolic studies. Expression of TCF7L2 was related to genotype and metabolic parameters in human islets. The CT/TT genotypes of SNP rs7903146 strongly predicted future T2D in 2 independent cohorts (Swedish and Finnish). The risk T allele was associated with impaired insulin secretion, incretin effects, and enhanced rate of hepatic glucose production. TCF7L2 expression in human islets was increased 5-fold in T2D, particularly in carriers of the TT genotype. Overexpression of TCF7L2 in human islets reduced glucose-stimulated insulin secretion. In conclusion, the increased risk of T2D conferred by variants in TCF7L2 involves the enteroinsular axis, enhanced expression of the gene in islets, and impaired insulin secretion.