gebhart/patrepeval huggingface dataset:
Follow My Recommendations: A Personalized Privacy Assistant for Mobile App Permissions (2020)

Modern smartphone platforms have millions of apps, many of which request permissions to access private data and resources, like user accounts or location. While these smartphone platforms provide varying degrees of control over these permissions, the sheer number of decisions that users are expected to manage has been shown to be unrealistically high. Prior research has shown that users are often unaware of, if not uncomfortable with, many of their permission settings. Prior work also suggests that it is theoretically possible to predict many of the privacy settings a user would want by asking the user a small number of questions. However, this approach has neither been operationalized nor evaluated with actual users before. We report on a field study (n=72) in which we implemented and evaluated a Personalized Privacy Assistant (PPA) with participants using their own Android devices. The results of our study are encouraging. We find that 78.7% of the recommendations made by the PPA were adopted by users. Following initial recommendations on permission settings, participants were motivated to further review and modify their settings with daily “privacy nudges.” Despite showing substantial engagement with these nudges, participants only changed 5.1% of the settings previously adopted based on the PPA's recommendations. The PPA and its recommendations were perceived as useful and usable. We discuss the implications of our results for mobile permission management and the design of personalized privacy assistant solutions<br>Presented at the 12th Symposium on Usable Privacy and Security (SOUPS) 2016, June 22–24, 2016, Denver, Colorado.
Adenoviruses of Chickens: Serologic Groups (1975)

By literature review and experimental studies, 57 adenovirus isolants from chickens were grouped into 10 distinct serotypes. In plaque-reduction tests, 20 antibody units were reacted with 32-320 plaque-forming units of virus. Viruses that were neutralized (80% or greater reduction in titer) by a given serum were considered to belong to that serotype. Used to distinguish among serotypes were their antisera. One-way neutralization occurred in only two instances; in both cases it was traced to contamination of the virus inocula used to induce specific antiserum. Recloning corrected the problem. Of the 10 serotypes described, all are known to exist in the United States, 7 were found in Northern Ireland, and at least 6 have been shown to occur in Japan.
Prevalence of albuminuria and renal insufficiency and associated clinical factors in type 2 diabetes: the Japan Diabetes Clinical Data Management study (JDDM15) (2008)

A significant proportion of type 2 diabetic patients have normoalbuminuric RI. Renal disease in type 2 diabetes could be heterogeneous, implying the possibility of involvement of renal atherosclerosis and lipid toxicity.
Heat-shock Treatment-mediated Increase in Transduction by Recombinant Adeno-associated Virus 2 Vectors Is Independent of the Cellular Heat-shock Protein 90 (2004)

Recombinant adeno-associated virus 2 (AAV) vectors transduction efficiency varies greatly in different cell types. We have described that a cellular protein, FKBP52, in its phosphorylated form interacts with the D-sequence in the viral inverted terminal repeat, inhibits viral second strand DNA synthesis, and limits transgene expression. Here we investigated the role of cellular heat-shock protein 90 (HSP90) in AAV transduction because FKBP52 forms a complex with HSP90, and because heat-shock treatment augments AAV transduction efficiency. Heat-shock treatment of HeLa cells resulted in tyrosine dephosphorylation of FKBP52, led to stabilization of the FKBP52-HSP90 complex, and resulted in approximately 6-fold increase in AAV transduction. However, when HeLa cells were pre-treated with tyrphostin 23, a specific inhibitor of cellular epidermal growth factor receptor tyrosine kinase, which phosphorylates FKBP52 at tyrosine residues, heat-shock treatment resulted in a further 18-fold increase in AAV transduction. HSP90 was shown to be a part of the FKBP52-AAV D-sequence complex, but HSP90 by itself did not bind to the D-sequence. Geldanamycin treatment, which disrupts the HSP90-FKBP52 complex, resulted in >22-fold increase in AAV transduction in heat-shock-treated cells compared with heat shock alone. Deliberate overexpression of the human HSP90 gene resulted in a significant decrease in AAV-mediated transduction in tyrphostin 23-treated cells, whereas down-modulation of HSP90 levels led to a decrease in HSP90-FKBP52-AAV D-sequence complex formation, resulting in a significant increase in AAV transduction following pre-treatment with tyrphostin 23. These studies suggest that the observed increase in AAV transduction efficiency following heat-shock treatment is unlikely to be mediated by HSP90 alone and that increased levels of HSP90, in the absence of heat shock, facilitate binding of FKBP52 to the AAV D-sequence, thereby leading to inhibition of AAV-mediated transgene expression. These studies have implications in the optimal use of recombinant AAV vectors in human gene therapy.
High quality coding of wideband audio signals using transform coded excitation (TCX) (2002)

This paper describes the application of transform coded excitation (TCX) coding to encoding wideband speech and audio signals in the bit rate range of 16 kbits/s to 32 kbits/s. The approach uses a combination of time domain (linear prediction; pitch prediction) and frequency domain (transform coding; dynamic bit allocation) techniques, and utilizes a synthesis model similar to that of linear prediction coders such as CELP. However, at the encoder, the high complexity analysis-by-synthesis technique is bypassed by directly quantizing the so-called target signal in the frequency domain. The innovative excitation is derived at the decoder by inverse filtering the quantized target signal. The algorithm is intended for applications whereby a large number of bits is available for the innovative excitation. The TCX algorithm is utilized to encode wideband speech and audio signals with a 50-7000 Hz bandwidth. Novel quantization procedures including inter-frame prediction in the frequency domain are proposed to encode the target signal. The proposed algorithm achieves very high quality for speech at 16 kbits/s, and for music at 24 kbits/s.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Addition of Escherichia coli K-12 Growth Observation and Gene Essentiality Data to the EcoCyc Database (2013)

The sets of compounds that can support growth of an organism are defined by the presence of transporters and metabolic pathways that convert nutrient sources into cellular components and energy for growth. A collection of known nutrient sources can therefore serve both as an impetus for investigating new metabolic pathways and transporters and as a reference for computational modeling of known metabolic pathways. To establish such a collection for Escherichia coli K-12, we have integrated data on the growth or nongrowth of E. coli K-12 obtained from published observations using a variety of individual media and from high-throughput phenotype microarrays into the EcoCyc database. The assembled collection revealed a substantial number of discrepancies between the high-throughput data sets, which we investigated where possible using low-throughput growth assays on soft agar and in liquid culture. We also integrated six data sets describing 16,119 observations of the growth of single-gene knockout mutants of E. coli K-12 into EcoCyc, which are relevant to antimicrobial drug design, provide clues regarding the roles of genes of unknown function, and are useful for validating metabolic models. To make this information easily accessible to EcoCyc users, we developed software for capturing, querying, and visualizing cellular growth assays and gene essentiality data.
Identification of a DNA segment that is necessary and sufficient for alpha-specific gene control in Saccharomyces cerevisiae: implications for regulation of alpha-specific and a-specific genes. (1988)

STE3 mRNA is present only in Saccharomyces cerevisiae alpha cells, not in a or a/alpha cells, and the transcript level increases about fivefold when cells are treated with a-factor mating pheromone. Deletions in the 5' noncoding region of STE3 defined a 43-base-pair (bp) upstream activation sequence (UAS) that can impart both modes of regulation to a CYC1-lacZ fusion when substituted for the native CYC1 UAS. UAS activity required the alpha 1 product of MAT alpha, which is known to be required for transcription of alpha-specific genes. A chromosomal deletion that removed only 14 bp of the STE3 UAS reduced STE3 transcript levels 50- to 100-fold, indicating that the UAS is essential for expression. The STE3 UAS shares a 26-bp homology with the 5' noncoding sequences of the only other known alpha-specific genes, MF alpha 1 and MF alpha 2. We view the homology as having two components--a nearly palindromic 16-bp "P box" and an adjacent 10-bp "Q box." A synthetic STE3 P box was inactive as a UAS; a perfect palindrome P box was active in all three cell types. We propose that the P box is the binding site for a transcription activator, but that alpha 1 acting via the Q box is required for this activator to bind to the imperfect P boxes of alpha-specific genes. Versions of the P box are also found upstream of a-specific genes, within the binding sites of the repressor alpha 2 encoded by MAT alpha. Thus, the products of MAT alpha may render gene expression alpha or a-specific by controlling access of the same transcription activator to its binding site, the P box.
Retinoids in cosmeceuticals (2006)

Retinoids are natural and synthetic vitamin A derivatives. They are lipophilic molecules and easily penetrate the epidermis. Their biologically active forms can modulate the expression of genes involved in cellular differentiation and proliferation. Retinoic acid (tretinoin), its 13-cis isomer isotretinoin, as well as various synthetic retinoids are used for therapeutic purposes, whereas retinaldehyde, retinol, and retinyl esters, because of their controlled conversion to retinoic acid or their direct receptor-independent biologic action, can be used as cosmeceuticals. These natural retinoic acid precursors are thus expected to be helpful in (i) renewing epidermal cells, (ii) acting as UV filters, (iii) preventing oxidative stress, (iv) controlling cutaneous bacterial flora, and (v) improving skin aging and photoaging. Retinol and retinyl esters are not irritant, whereas demonstrating only a modest clinical efficiency. On the other hand, retinaldehyde, which is fairly well tolerated, seems to be the most efficient cosmeceutical retinoid; it has significant efficiency toward oxidative stress, cutaneous bacterial flora, epidermis renewing, and photoaging.
A Proteolytic Pathway That Recognizes Ubiquitin as a Degradation Signal (1995)

Previous work has shown that a fusion protein bearing a "nonremovable" N-terminal ubiquitin (Ub) moiety is short-lived in vivo, the fusion's Ub functioning as a degradation signal. The proteolytic system involved, termed the UFD pathway (Ub fusion degradation), was dissected in the yeast Saccharomyces cerevisiae by analyzing mutations that perturb the pathway. Two of the five genes thus identified, UFD1 and UFD5, function at post-ubiquitination steps in the UFD pathway. UFD3 plays a role in controlling the concentration of Ub in a cell: ufd3 mutants have greatly reduced levels of free Ub, and the degradation of Ub fusions in these mutants can be restored by overexpressing Ub. UFD2 and UFD4 appear to influence the formation and topology of a multi-Ub chain linked to the fusion's Ub moiety. UFD1, UFD2, and UFD4 encode previously undescribed proteins of 40, 110, and 170 kDa, respectively. The sequence of the last approximately 280 residues of Ufd4p is similar to that of E6AP, a human protein that binds to both the E6 protein of oncogenic papilloma viruses and the tumor suppressor protein p53, whose Ub-dependent degradation involves E6AP. UFD5 is identical to the previously identified SON1, isolated as an extragenic suppressor of sec63 alleles that impair the transport of proteins into the nucleus. UFD5 is essential for activity of both the UFD and N-end rule pathways (the latter system degrades proteins that bear certain N-terminal residues). We also show that a Lys --> Arg conversion at either position 29 or position 48 in the fusion's Ub moiety greatly reduces ubiquitination and degradation of Ub fusions to beta-galactosidase. By contrast, the ubiquitination and degradation of Ub fusions to dihydrofolate reductase are inhibited by the UbR29 but not by the UbR48 moiety. ufd4 mutants are unable to ubiquitinate the fusion's Ub moiety at Lys29, whereas ufd2 mutants are impaired in the ubiquitination at Lys48. These and related findings suggest that Ub-Ub isopeptide bonds in substrate-linked multi-Ub chains involve not only the previously identified Lys48 but also Lys29 of Ub, and that structurally different multi-Ub chains have distinct functions in Ub-dependent protein degradation.
Mechanism and Application of a Microcapsule Enabled Multicatalyst Reaction (2007)

In this paper, we describe the development and application of a multistep one-pot reaction that is made possible by the site isolation of two otherwise incompatible catalysts. We prepared a microencapsulated amine catalyst by interfacial polymerization and used it in conjunction with a nickel-based catalyst for the transformation of an aldehyde to a Michael adduct via a nitroalkene intermediate. The amine-catalyzed conversion of an aldehyde to a nitroalkene was found to proceed through an imine rather than a nitroalcohol. Kinetic studies indicated that the reaction is first order in both the nickel catalyst and the shell of the encapsulated amine catalyst. Furthermore, we provide evidence against interaction between amine and nickel catalysts and present kinetic data that demonstrates that there is a rate enhancement of the Michael addition due to the urea groups on the surface of the microencapsulated catalyst. We applied our one-pot reaction to the development of a new synthetic route for pregabalin that proceeds with an overall yield of 74%.
Conductivity and permittivity of midel 7131: effect of temperature, moisture content, hydrostatic pressure and electric field (2016)

Knowledge of the conductivity and permittivity of materials used in subsea connectors is needed to predict the electric field distribution in the connectors. The synthetic ester Midel 7131, being one of several dielectric liquids used in subsea connectors, has been chosen as a relevant candidate material. The conductivity and permittivity of Midel was measured by an IRLAB conductivity meter and an IDA insulation diagnostic analyzer. The temperatures were 30, 60 and 90 °C, the hydrostatic pressures were 0.1, 1 and 10 MPa (1, 10 and 100 bar), the water content varied between 20 and 5600 ppmw, and the applied electric fields varied between 2.5 V/mm and 9.4 kV/mm. The results show that the conductivity increases linearly with increasing levels of water content, whereas the temperature dependency follows an Arrhenius relation. The conductivity was found to increase slightly with increased pressure, the differences between samples were higher, rendering this increase insignificant. Measurements of the permittivity showed a linear increase in permittivity with increasing water content. The measured permittivity was found to follow the Clausius-Mossotti relation when varying the temperature and hydrostatic pressure. Based on the dependence of the conductivity and permittivity on water content, it seems that water molecules in Midel have a reduced degree of mutual interaction compared to liquid water.
Site-directed mutants, at position 166, of RTEM-1 beta-lactamase that form a stable acyl-enzyme intermediate with penicillin. (1991)

Class A beta-lactamases are known to hydrolyze substrates through a Ser70-linked acyl-enzyme intermediate, although the detailed mechanism remains unknown. On the basis of the tertiary structure of the active site, the role of Glu166 of class A enzymes was investigated by replacing the residue in RTEM-1 beta-lactamase with Ala, Asp, Gln, or Asn. All the mutants, in contrast to the wild-type, accumulated a covalent complex with benzylpenicillin which corresponds to an acyl-enzyme intermediate. For the Asp mutant, the complex decayed slowly and the hydrolytic activity was slightly retained both in vivo and in vitro. In contrast, the other mutants lost the hydrolytic activity completely and their complexes were stable. These results indicate that the side-chain carboxylate of Glu166 acts as a special catalyst for deacylation. Residues for deacylation have not been identified in other acyl enzymes, such as serine proteases and class C beta-lactamases. Furthermore, the acyl-enzyme intermediates obtained are so stable that they are considered to be ideal materials for crystallographic studies for elucidating the catalytic mechanism in more detail. In addition, the mutants can more easily form inclusion bodies than the wild-type, when they are produced in a large amount, suggesting that the residue also plays an important role in proper folding of the enzyme.
High Density Orthogonal Surface Immobilization via Photoactivated Copper-Free Click Chemistry (2010)

Surfaces containing reactive ester polymer brushes were functionalized with cyclopropenone-masked dibenzocyclooctynes for the light activated immobilization of azides using catalyst-free click chemistry. The photodecarbonylation reaction in the amorphous brush layer is first order for the first 45 s with a rate constant of 0.022 s(-1). The catalyst-free cycloaddition of surface bound dibeznocyclooctynes proceeds rapidly in the presence of azides under ambient conditions. Photolithography using a shadow mask was used to demonstrate patterning with multiple azide containing molecules. This surface immobilization strategy provides a general and facile platform for the generation of multicomponent surfaces with spatially resolved chemical functionality.
Hydrogenated Ring-Opened Poly(endo-dicyclopentadiene)s Made via Stereoselective ROMP Catalyzed by Tungsten Complexes:  Crystalline Tactic Polymers and Amorphous Atactic Polymer (2006)

Properties of the tactic and atactic hydrogenated ring-opened poly(endo-dicyclopentadiene)s and features of the tungsten imido/phenolate-catalyzed stereoselective ring-opening metathesis polymerizations (ROMP) were studied. Several tungsten(VI) imido phenolate complexes were synthesized and exhibited moderate ROMP activity in the presence of n-BuLi. W(NPh)((R)-(+)-5,5‘,6,6‘-Me4-3,3‘-t-Bu2-biphenolate)2 was found to be effective for cis-, isoselective ROMP of endo-dicyclopentadiene (DCPD), while W(NPh)Cl4·Et2O promoted cis-, syndioselective ROMP. On the other hand, W(NPh)(2,6-Me2-phenolate)4 provided atactic poly(DCPD). Isotactic, atactic, and syndiotactic hydrogenated ring-opened poly(DCPD)s were characterized well by various methods for the first time. Both tactic polymers were shown to be crystalline polymers by means of DSC, WAXD, and TEM measurements. In contrast, atactic poly(DCPD) was an amorphous polymer. The crystallization rate of the syndiotactic hydrogenated poly(DCPD) was significantly higher than that of the isotactic polymer.
Freedom From Atrial Tachyarrhythmias After Catheter Ablation of Atrial Fibrillation (2005)

This study demonstrates no superiority of the circumferential pulmonary vein ablation over segmental pulmonary vein ablation for treatment of atrial fibrillation in terms of efficacy and safety.
Overlapping Repressor Binding Sites Result in Additive Regulation ofEscherichia coliFadH by FadR and ArcA (2010)

Escherichia coli fadH encodes a 2,4-dienoyl reductase that plays an auxiliary role in beta-oxidation of certain unsaturated fatty acids. In the 2 decades since its discovery, FadH biochemistry has been studied extensively. However, the genetic regulation of FadH has been explored only partially. Here we report mapping of the fadH promoter and document its complex regulation by three independent regulators, the fatty acid degradation FadR repressor, the oxygen-responsive ArcA-ArcB two-component system, and the cyclic AMP receptor protein-cyclic AMP (CRP-cAMP) complex. Electrophoretic mobility shift assays demonstrated that FadR binds to the fadH promoter region and that this binding can be specifically reversed by long-chain acyl-coenzyme A (CoA) thioesters. In vivo data combining transcriptional lacZ fusion and real-time quantitative PCR (qPCR) analyses indicated that fadH is strongly repressed by FadR, in agreement with induction of fadH by long-chain fatty acids. Inactivation of arcA increased fadH transcription by >3-fold under anaerobic conditions. Moreover, fadH expression was increased 8- to 10-fold under anaerobic conditions upon deletion of both the fadR and the arcA gene, indicating that anaerobic expression is additively repressed by FadR and ArcA-ArcB. Unlike fadM, a newly reported member of the E. coli fad regulon that encodes another auxiliary beta-oxidation enzyme, fadH was activated by the CRP-cAMP complex in a manner similar to those of the prototypical fad genes. In the absence of the CRP-cAMP complex, repression of fadH expression by both FadR and ArcA-ArcB was very weak, suggesting a possible interplay with other DNA binding proteins.
Functional Role of Lipoprotein Receptors in Alzheimers Disease (2008)

The LDL receptor gene family constitutes a class of structurally closely related cell surface receptors fulfilling diverse functions in different organs, tissues, and cell types. The LDL receptor is the prototype of this family, which also includes the VLDLR, ApoER2/LRP8, LRP1 and LRP1B, as well as Megalin/GP330, SorLA/LR11, LRP5, LRP6 and MEGF7. Recently several lines of evidence have positioned the LDL receptor gene family as one of the key players in Alzheimer's disease (AD) research. Initially this receptor family was of high interest due to its key function in cholesterol/apolipoprotein E (ApoE) uptake, with the epsilon4 allele of ApoE as the strongest genetic risk factor for late-onset AD. It has been established that the cholesterol metabolism of the cell has a strong impact on the production of Abeta, the major component of the plaques found in the brain of AD-patients. The original report that soluble amyloid precursor protein (APP) containing the kunitz proteinase inhibitor (KPI) domain might act as a ligand for LRP1 led to a complex investigation of the interaction of both proteins and their potential function in AD development. Meanwhile, it has been demonstrated that LRP1 might bind to APP independent of the KPI domain in APP. This APP - LRP1 interaction is facilitated through a trimeric complex of APP-FE65-LRP1, which has a functional role in APP processing. Along with LRP1, APP is transported from the early secretory compartments to the cell surface and subsequently internalised into the endosomal / lysosomal compartments. Recent investigations indicate that ApoER2 and SorLA fulfil a similar role in shifting APP localisation in the cell, which affects APP processing and the production of the APP derived amyloid beta-peptide (Abeta). In addition to the effect of lipoprotein receptors on APP processing and Abeta production, LRP1 has been shown to bind Abeta directly or indirectly through Abeta-lactoferrin, Abeta-alpha2M and Abeta-ApoE complexes in vitro and in vivo. Based on these observations two LRP1 mediated clearance mechanisms of Abeta are proposed to play a crucial role in the prevention of AD: either Abeta-uptake into a cell with its subsequent degradation or its transport out of the brain over the blood brain barrier into the periphery. Following this export Abeta is degraded in the liver, where LRP1 potentially conducts the removal of Abeta from the blood stream. Although the involvement of LDLR family members in AD is not yet fully understood it becomes clear that they can directly affect APP production, Abeta-clearance and Abeta-transport over the blood brain barrier.