gebhart/patrepeval huggingface dataset:
Conservation of folding and association within a family of spidroin N-terminal domains (2017)

Web spiders synthesize silk fibres, nature's toughest biomaterial, through the controlled assembly of fibroin proteins, so-called spidroins. The highly conserved spidroin N-terminal domain (NTD) is a pH-driven self-assembly device that connects spidroins to super-molecules in fibres. The degree to which forces of self-assembly is conserved across spider glands and species is currently unknown because quantitative measures are missing. Here, we report the comparative investigation of spidroin NTDs originating from the major ampullate glands of the spider species Euprosthenops australis, Nephila clavipes, Latrodectus hesperus, and Latrodectus geometricus. We characterized equilibrium thermodynamics and kinetics of folding and self-association using dynamic light scattering, stopped-flow fluorescence and circular dichroism spectroscopy in combination with thermal and chemical denaturation experiments. We found cooperative two-state folding on a sub-millisecond time scale through a late transition state of all four domains. Stability was compromised by repulsive electrostatic forces originating from clustering of point charges on the NTD surface required for function. pH-driven dimerization proceeded with characteristic fast kinetics yielding high affinities. Results showed that energetics and kinetics of NTD self-assembly are highly conserved across spider species despite the different silk mechanical properties and web geometries they produce.
Parkin Ubiquitinates Drp1 for Proteasome-dependent Degradation (2011)

Mutations in Parkin, an E3 ubiquitin ligase that regulates protein turnover, represent one of the major causes of familial Parkinson disease, a neurodegenerative disorder characterized by the loss of dopaminergic neurons and impaired mitochondrial functions. The underlying mechanism by which pathogenic Parkin mutations induce mitochondrial abnormality is not fully understood. Here, we demonstrate that Parkin interacts with and subsequently ubiquitinates dynamin-related protein 1 (Drp1), for promoting its proteasome-dependent degradation. Pathogenic mutation or knockdown of Parkin inhibits the ubiquitination and degradation of Drp1, leading to an increased level of Drp1 for mitochondrial fragmentation. These results identify Drp1 as a novel substrate of Parkin and suggest a potential mechanism linking abnormal Parkin expression to mitochondrial dysfunction in the pathogenesis of Parkinson disease.
Engineering Trust in Complex Automated Systems (2016)

We studied the transparency of automated tools used during emergency operations in commercial aviation. Transparency (operationalized as increasing levels of explanation associated with an automated tool recommendation) was manipulated to evaluate how transparent interfaces influence pilot trust of an emergency landing planning aid. We conducted a low-fidelity study in which commercial pilots interacted with simulated recommendations from NASA’s Emergency Landing Planner (ELP) that varied in their associated levels of transparency. Results indicated that trust in the ELP was influenced by the level of transparency within the human–machine interface of the ELP. Design recommendations for automated systems are discussed.
Continuous emission monitoring total mercury analysis (1997)

Mercury and its compounds is emitted from various sources, coal fired power plants and waste incinerators being the prime sources. Various methods for continuous automatic monitoring of Hg{sup 0} or [Hg{sup 0} & its compounds] are being used (optical in-situ, extractive with and without sample preparation). The methods are discussed and compared. The paper also describes an automatic, continuous Total Mercury Analyzer (HM-1400), which has received Equivalency in Germany. Applications industrial hospital, urban, hazardous waste incinerators, waste water sludge incineration are discussed, as well as field experience front over 7 years.
Asymmetric Synthesis of 2-Aryl-2,3-dihydro-4-quinolones via Bifunctional Thiourea-Mediated Intramolecular Cyclization (2010)

A novel asymmetric preparation of optically enriched 2-aryl-2,3-dihydroquinolin-4(1H)-ones has been developed. By installing a sulfonyl group on the nitrogen of the anilines and an ester function on the unsaturated ketones, an intramolecular organocatalytic cyclization took place readily in a stereoselective manner, resulting in the formation of dihydroquinolones with high enantioselectivity.
Synthesis and Polymerization of a Nonionic Surfactant: Poly(Ethylene Oxide) Macromonomer (1996)

Abstract A polymerizable nonionic surfactant macromonomer, ω-methoxy poly(ethylene oxide)nundecyl-α-methacrylate (n = 40) has been synthesized from poly(ethylene glycol) methyl ether, 11-bromoundecanol, and methacryloyl chloride. The critical micelle concentration of the macro-monomer is 6.6 × 10−5 mol/L at 25°C. The kinetics of its polymerization in aqueous medium follows conventional solution polymerization, i.e., first and half order with respect to the concentrations of the macro-monomer and K2S2O8, respectively. The rate of its polymerization in water was extremely rapid (within 30 minutes) as compared to its solution polymerization in benzene (days). The activation energies for the macromonomer polymerization were 57 kJ/mol in water but 179 kJ/mol in benzene. The aqueous system produced polymers with a number-average degree of polymerization (DPn) ranging from about 130 to 160, but it was much lower (DPn ≐ 7) for the benzene system. The possible micellar polymerization mechanism for the macromonomer...
Progress in Nanocomposite of Biodegradable Polymer (2007)

This paper reviews recent developments related to biodegradable polymer nanocomposites. The prepa- ration, characterization, properties, and applications of nanocomposites based on biodegradable polymers are in- troduced systemically. The related biodegradable polymers include aliphatic polyesters such as polylactide (PLA), poly(e -caprolactone) (PCL), poly(p-dioxanone) (PPDO), poly(butylenes succinate) (PBS), poly (hydroxyalkanoate)s such as poly(β -hydroxybutyrate) (PHB), poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), and natural renewable polymers such as starch, cellulose, chitin, chitosan, lignin, and proteins. The nanoparticles that have been also utilized to fabricate the nanocomposites include inorganic, organic, and metal particles such as clays, nanotubes, magnetites, Au and Ag, hydroxyapatite, cellulose, chitin whiskers and lignin.
Differences in Metabolism and Isomerization of All‐<i>trans</i>‐Retinoic Acid and 9‐<i>cis</i>‐Retinoic Acid between Human Endothelial Cells and Hepatocytes (1997)

Retinoic acid stimulates the expression of tissue-type plasminogen activator (t-PA) in vascular endothelial cells in vitro and enhances t-PA levels in plasma and tissues in vivo. Compared with the in vivo situation, high retinoic acid concentrations are required to induce optimally t-PA expression in vitro. These findings led us to study retinoic acid metabolism in cultured human endothelial cells. For comparison, these studies were also performed in the human hepatoma cell line, HepG2, and key experiments were repeated with human primary hepatocytes. Both hepatocyte cultures gave very similar results. Human endothelial cells were shown to possess an active retinoic acid metabolizing capacity, which is quantitatively comparable to that of hepatocytes, but different from that of hepatocytes in several qualitative aspects. Our results demonstrate that all-trans-retinoic acid is quickly metabolized by both endothelial cells and hepatocytes. All-trans-retinoic acid induces its own metabolism in endothelial cells but not in hepatocytes. 9-cis-Retinoic acid is degraded slowly by endothelial cells, whereas hepatocytes metabolize 9-cis-retinoic acid very quickly. Furthermore, our data show that hepatocytes, but not endothelial cells, detectably isomerise all-trans-retinoic acid to 9-cis-retinoic acid and vice versa. In both endothelial cells and hepatocytes all-trans-retinoic acid metabolism was inhibitable by the cytochrome P-450 inhibitors liarozole (10 microM) and ketoconazole (10 microM), albeit to different extents and with different specificities. In the presence of the most potent retinoic acid metabolism inhibitor in endothelial cells, liarozole, at least 10-fold lower all-trans-retinoic acid concentrations were required than in the absence of the inhibitor to obtain the same induction of t-PA. In conclusion, our results clearly demonstrate that all-trans-retinoic acid and 9-cis retinoic acid are actively but differently metabolized and isomerised by human endothelial cells and hepatocytes. The rapid metabolism of retinoic acid explains the relatively high concentrations of retinoic acid required to induce t-PA in cultured endothelial cells.
Recruitment of β-catenin to cadherin-mediated intercellular adhesions is involved in myogenic induction (2001)

Cadherin-mediated cell adhesion is involved in muscle differentiation from early stages of myogenic induction to late stages of myoblast interaction and fusion. beta-Catenin is a major constituent of cadherin-based adherens junctions and also serves as a signal transduction molecule that regulates gene expression during development. In this study, we explored the involvement of beta-catenin in myogenic differentiation. We show here that shortly after a switch from growth to differentiation medium, beta-catenin translocates to cell-cell junctions and its levels increase. We further show that elevation of beta-catenin levels, induced either by inhibition of its breakdown, using LiCl, or by its overexpression, suppresses the formation of adherens junctions, resulting in a sharp decline in myogenin expression and an arrest of myogenic progression. Recruitment of beta-catenin to adherens junctions after transfection with N-cadherin restores myogenin expression in the transfected cells. These results suggest that increased cadherin-mediated adhesion and translocation of beta-catenin to adherens junctions are involved in activating the early steps of myogenic differentiation.
The Need for Effective Communication (2014)

The paper presents part of a PhD research on the management of European communication on rural development. Improving communication and facilitating the access to information do not guarantee the comprehension of the European message. The paper emphasizes the need to adapt the informational phenomenon to the expectation horizon of the rural population, to its need for appropriate information. The European communication, besides the informative and propagandistic character, has a powerful social character too, being part of the public space. The relationship between the ordinary European citizens and the European Union consists of a mixture of rights and obligations, entailed by the European citizenship. In order to benefit from their European citizenship European citizens should be properly informed.
By-example synthesis of structurally sound patterns (2015)

Several techniques exist to automatically synthesize a 2D image resembling an input exemplar texture. Most of the approaches optimize a new image so that the color neighborhoods in the output closely match those in the input, across all scales. In this paper we revisit by-example texture synthesis in the context of additive manufacturing. Our goal is to generate not only colors, but also structure along output surfaces: given an exemplar indicating 'solid' and 'empty' pixels, we generate a similar pattern along the output surface. The core challenge is to guarantee that the pattern is not only fully connected, but also structurally sound. To achieve this goal we propose a novel formulation for on-surface by-example texture synthesis that directly works in a voxel shell around the surface. It enables efficient local updates to the pattern, letting our structural optimizer perform changes that improve the overall rigidity of the pattern. We use this technique in an iterative scheme that jointly optimizes for appearance and structural soundness. We consider fabricability constraints and a user-provided description of a force profile that the object has to resist. Our results fully exploit the capabilities of additive manufacturing by letting users design intricate structures along surfaces. The structures are complex, yet they resemble input exemplars, resulting in a modeling tool accessible to casual users.
Chemistry of Succinimido Esters. XIII. (1989)

Lys residues in porcine pancreatic α-amylase (PPA) were N-acylated by N-acyloxysuccinimides (1) and the amylase activity [hydrolytic activity of the α-D- (1, 4) glucoside bond in oligosaccharide] of PPA decreased by about 3515%, while the maltosidase activity (hydrolytic activity of p-nitrophenyl α-D-maltoside) of PPA increased more than 200%. The value of Km for amylase activity showed no change but that of maltosidase activity increased as a result of this chemical modification. The proteinaceous α-amylase inhibitor (phaseolamin) purified from white kidney bean (Phaseolus vulgaris) inhibited both the amylase and maltosidase activity of PPA. With modified PPA, however, amylase activity was inhibited completely but not maltosidase activity. These results indicate the Lys residue in PPA not to be directly related to the amylase activity but involved in some way with maltosidase activity. Furthermore, the incomplete inhibition of modified PPA maltosidase activity indicated the inhibitor not to influence the active site of p-nitrophenyl α-D-maltoside but that of oligosaccharide in modified PPA. The present study demonstrates improved enzyme activity by chemical modification using (1) as a modifier.
On–Engine Evaluation of Emissions Characteristics of a Variable Geometry Lean–Premixed Combustor (1995)

The design and on–engine testing of a lean–premixed, low–NOx combustor for a simple cycle, single shaft, 250–kW gas turbine engine of a pressure ratio of eight are described. A variable geometry system composed of butterfly air valves was used to control the combustor air split between combustion and dilution. Fuel was staged to a direct–injection pilot burner and a lean–premixed main burner fitted to the combustor liner. The NOx emissions with natural gas fueling were found to be less than 20 ppm (at 15% O2) at and near full load conditions with combustion efficiencies greater than 99.8%. Emissions data from early high–pressure rig tests of the combustor hardware are also presented.
Expression of an active form of recombinant Ty1 reverse transcriptase in Escherichia coli: a fusion protein containing the C-terminal region of the Ty1 integrase linked to the reverse transcriptase–RNase H domain exhibits polymerase and RNase H activities (2000)

Replication of the Saccharomyces cerevisiae Ty1 retrotransposon requires a reverse transcriptase capable of synthesizing Ty1 DNA. The first description of an active form of a recombinant Ty1 enzyme with polymerase and RNase H activities is reported here. The Ty1 enzyme was expressed as a hexahistidine-tagged fusion protein in Escherichia coli to facilitate purification of the recombinant protein by metal-chelate chromatography. Catalytic activity of the recombinant protein was detected only when amino acid residues encoded by the integrase gene were added to the N-terminus of the reverse transcriptase-RNase H domain. This suggests that the integrase domain could play a role in proper folding of reverse transcriptase. Several biochemical properties of the Ty1 enzyme were analysed, including the effect of MgCl(2), NaCl, temperature and of the chain terminator dideoxy GTP on its polymerase activity. RNase H activity was examined by monitoring the cleavage of a RNA-DNA template-primer. Our results suggest that the distance between the RNase H and polymerase active sites corresponds to the length of a 14-nucleotide RNA-DNA heteroduplex. The recombinant protein produced in E. coli should be useful for further biochemical and structural analyses and for a better understanding of the role of integrase in the activation of reverse transcriptase.
Security Analysis of Pseudo-Random Number Generators with Input: /dev/random is not Robust. (2013)

Abstract. A pseudo-random number generator (PRNG) is a deterministic algorithm that produces numbers whose distribution is indistinguishable from uniform. A formal security model for PRNGs with input was proposed in 2005 by Barak and Halevi (BH). This model involves an internal state that is refreshed with a (potentially biased) external random source, and a cryptographic function that outputs random numbers from the continually internal state. In this work we extend the BH model to also include a new security property capturing how it should accumulate the entropy of the input data into the internal state after state compromise. This property states that a good PRNG should be able to eventually recover from compromise even if the entropy is injected into the system at a very slow pace, and expresses the real-life expected behavior of existing PRNG designs. Unfortunately, we show that neither the model nor the specific PRNG construction proposed by Barak and Halevi meet this new property, despite meeting a weaker robustness notion introduced by BH. From a practical side, we also give a precise assessment of the security of the two Linux PRNGs, /dev/random and /dev/urandom. In particular, we show several attacks proving that these PRNGs are not robust according to our definition, and do not accumulate entropy properly. These attacks are due to the vulnerabilities of the entropy estimator and the internal mixing function of the Linux PRNGs. These attacks against the Linux PRNG show that it does not satisfy the &quot;robustness &quot; notion of security, but it remains unclear if these attacks lead to actual exploitable vulnerabilities in practice. Finally, we propose a simple and very efficient PRNG construction that is provably robust in our new and stronger adversarial model. We therefore recommend to use this construction whenever a PRNG with input is used for cryptography.
Spontaneous Expulsion of Giant Lipid Vesicles Induced by Laser Tweezers (1997)

Irradiation of a giant unilamellar lipid bilayer vesicle with a focused laser spot leads to a tense pressurized state which persists indefinitely after laser shutoff. If the vesicle contains another object it can then be gently and continuously expelled from the tense outer vesicle. Remarkably, the inner object can be almost as large as the parent vesicle; its volume is replaced during the exit process. We offer a qualitative theoretical model to explain these and related phenomena. The main hypothesis is that the laser trap pulls in lipid and ejects it in the form of submicron objects, whose osmotic activity then drives the expulsion.
AtHAP3b Plays a Crucial Role in the Regulation of Flowering Time in Arabidopsis during Osmotic Stress (2007)

The HAP complex has been found in many eukaryotic organisms. HAP recognizes the CCAAT box present in the promoters of 30% of all eukaryotic genes. The HAP complex consists of three subunits - HAP2, HAP3 and HAP5. In this paper, we report the biological function of the AtHAP3b gene that encodes one of the HAP3 subunits in Arabidopsis. Compared with wild-type plants, hap3b-1 and hap3b-2 mutants exhibited a delayed flowering time under long-day photoperiod conditions. Moreover, the transcription levels of FT were substantially lower in the mutants than in the wild-type plants. These results imply that AtHAP3b may function in the control of flowering time by regulating the expression of FT in Arabidopsis. In a subsequent study, AtHAP3b was found to be induced by osmotic stress. Under osmotic stress conditions, the hap3b- 1 and hap3b-2 mutants flowered considerably later than the wild-type plants. These results suggest that the AtHAP3b gene plays more important roles in the control of flowering under osmotic stress in Arabidopsis.
Modern Organocopper Chemistry (2002)

Foreword. Preface. List of Authors. Structures and Reactivities of Organocopper Compounds (Johann T.B.H. Jastrzebski and Gerard van Koten). Transmetalation Reactions Producing Organocopper Reagents (Paul Knochel and Bodo Betzemeier). Heteroatomcuprates and a--Heteroatomalkylcuprates in Organic Synthesis (R. Karl Dieter). Copper--mediated Addition and Substitution Reactions of Extended Multiple Bond Systems (Norbert Krause and Anja Hoffman--Roder). Copper(I)--mediated 1,2-- and 1,4--Reductions (Bruce H. Lipshutz). Copper--mediated Diastereoselective Conjugate Addition and Allylic Substitution Reactions (Bernhard Breit and Peter Demel). Copper--catalyzed Enantioselective Conjugate Addition Reactions of Organozinc Reagents (Ben L. Feringa, Robert Naasz, Rosalinde Imbos and Leggy A. Arnold). Copper--Mediated Enantioselective Substitution Reactions (A. Sofia E. Karlstroom and Jan--Erling Backvall). Copper--Mediated Synthesis of Natural and Unnatural Products (Yukiyasu Chounan and Yoshinori Yamamoto). Mechanisms of Copper--mediated Addition and Substitution Reactions (Seiji Mori and Eiichi Nakamura). Author Index. Subject Index.
Mevalonate-regulated mechanisms in cell growth control: role of dolichyl phosphate in expression of the insulin-like growth factor-1 receptor (IGF-1R) in comparison to Ras prenylation and expression of c-myc (1997)

One or more mevalonate derivatives of non-sterol type have been proposed to be of indispensable importance for cell growth. Conceivable mevalonate-dependent mechanisms involved in growth control are farnesylation of Ras proteins, regulation of c-myc expression, and N-linked glycosylation of the IGF-1 receptor. The latter mechanism might be rate-limited by dolichyl phosphate, which acts as a donor of oligosaccharides in glycoprotein synthesis in the endoplasmic reticulum. In order to study the significance for cell proliferation of the three aforementioned mevalonate-dependent processings, their inhibitory response due to mevalonate deprivation was explored and compared with the effect on DNA synthesis in the malignant melanoma cell line SK-MEL-2. We found that mevalonate depletion due to treatment with 3 microM lovastatin for 24 h, which efficiently growth-arrested the cells, hardly at all affected the expression of c-myc, and although Ras prenylation was inhibited by 50%, the most pronounced effect of lovastatin was seen on N-linked glycosylation of IGF-1 receptors, which was inhibited by more than 95%. The order and magnitude of the decreased IGF-1 receptor glycosylation, which was followed by a decreased expression of IGF-1 receptors at the cell membrane, correlated well with the inhibition of DNA synthesis. We investigated whether dolichol, and in particular dolichyl phosphate, through its participation in N-linked glycosylation, act as regulators of IGF-1 receptor expression. First, we could confirm that exogenous dolichol became phosphorylated and in this form took part in the glycosylation processing. Secondly, we showed that dolichyl phosphate, in a dose-dependent manner, could increase the number of IGF-1 receptors at the cell membrane, simultaneously as DNA synthesis was stimulated. Taken together, our results provide direct evidence for an important role of dolichyl phosphate as a regulator of cell growth through limiting N-linked glycosylation of the IGF-1 receptor.
CA‐PK: conditional access for broadcast networks (2003)

Abstract This paper presents a conditional access solution suitable for broadcast networks (e.g. Eureka‐147 DAB, XM Radio's SDARS, etc.). This solution, called CA‐PK (Conditional Access through Public Keys), can only be implemented in software, although it can utilize external crypto processors and allows a content provider to operate a conditional access system independently of third parties (i.e. DAB or GSM network operators). Furthermore, it integrates the consumer into the protection chain, creating a social environment that discourages illegal redistribution of access keys. Copyright © 2003 John Wiley & Sons, Ltd.