gebhart/patrepeval huggingface dataset:
A trusted ecosystem for Android applications based on context-aware access control (2012)

Private data stored on smartphones is a precious target for malware attacks. A constantly changing environment, e.g. switching network connections, can cause unpredictable threats, and require an adaptive approach to access control. Context-based access control is using dynamic environmental information, including it into access decisions. We propose an “ecosystem-in-an-ecosystem” which acts as a secure container for trusted software aiming at enterprise scenarios where users are allowed to use private devices. We have implemented a proof-of-concept prototype for an access control framework that processes changes to low-level sensors and semantically enriches them, adapting access control policies to the current context. This allows the user or the administrator to maintain fine-grained control over resource usage by compliant applications. Hence, resources local to the trusted container remain under control of the enterprise policy. Our results show that context-based access control can be done on smartphones without major performance impact.
OFDM with trailing zeros versus OFDM with cyclic prefix: links, comparisons and application to the HiperLAN/2 system (2002)

This paper proposes a simple equalizer for a multicarrier block transmission scheme which pads zeros (as opposed to a cyclic prefix) in each transmitted block. In the absence of high-power amplifier induced nonlinear effects, it is shown that the resulting scheme is simply the dual of the classical cyclic prefix OFDM transceiver. Comparison between the two systems that takes into account nonlinear distortions introduced by the clipper is also performed in the practical context of the wireless broadband 5 GHz HiperLAN/2 system. Both the classical pilot-based as well as novel (semi-) blind subspace algorithms are applied for channel estimation. The advantage of subspace methods in lowering the variation of channel tracking is corroborated with simulations which verify practically accurate channel estimates along the bursts.
Trans−Cis Isomerization of Proline 22 in Bovine Prothrombin Fragment 1:  A Surprising Result of Structural Characterization (1998)

The calcium ion-mediated interaction of bovine prothrombin (BF1) with negatively charged phospholipid membranes is assumed to be largely via the Gla domain of BF1 with the fold of the Gla domain essential for binding. It has been reported that Pro22 undergoes classical trans to cis isomerization in the presence of calcium ions with the cis conformation of Pro22 of BF1 responsible for membrane binding [Evans, T. C., Jr., and Nelsestuen, G. L. (1996) Biochemistry 35, 8210-8215]. However, Pro22 was found to be in the trans conformation in the crystal structure of BF1. In the present work, we have used molecular dynamics simulations to investigate the relative importance of the two conformations of Pro22 to the structural and dynamical properties of BF1. The initial trans conformation of Pro22 in BF1 was slowly converted to cis-Pro22 using constrained dynamics. The second-generation AMBER force field in conjunction with the particle mesh Ewald method to accommodate long-range interaction was employed in the trajectory calculations. Comparison of the BF1(trans-Pro22) and BF1(cis-Pro22) equilibrated structures reveals surprisingly that the overall structural changes associated with the trans-cis isomerization is minimal and only minor modifications to the hydrogen bond network and the network of N-terminus Ala1 take place. The calculated electrostatic potential energy surfaces of the two protein structures also appear to be very similar, indicating the near equality of the local interaction site environments in the protein prior to lipid binding.
Regional distribution and developmental expression of epidermal growth factor and transforming growth factor-alpha mRNA in mouse brain by a quantitative nuclease protection assay (1992)

A solution-hybridization ribonuclease-protection assay was used to identify epidermal growth factor (EGF) mRNA in mouse brain and to compare the regional and developmental levels of EGF gene expression in the CNS with those of its structural homolog, transforming growth factor-alpha (TGF-alpha). Adult brain regions examined included brainstem, cerebellum, cerebral cortex, hippocampus, basal hypothalamus, olfactory bulb, olfactory tubercle, striatum, and thalamus. While both EGF and TGF-alpha mRNAs were detected in all regions, TGF-alpha mRNA levels were 15-170 times higher, ranging from 0.39 (cerebellum and cerebral cortex) to 2.93 (striatum) pg TGF-alpha mRNA/micrograms total cytoplasmic RNA. In contrast, EGF mRNA levels ranged from 11 to 36 fg EGF mRNA/micrograms, with the highest regional concentrations observed in olfactory bulb, basal hypothalamus, and cerebellum. In our comparison between sexes, no significant male-female differences in EGF or TGF-alpha mRNA levels were observed for any region of adult brain. However, in the pituitary gland, consisting of both endocrine and neural elements, EGF and TGF-alpha mRNA levels were significantly higher in males (234 and 215 fg/micrograms, respectively) than in females (172 and 118 fg/micrograms, respectively). An examination of growth factor gene expression in the developing CNS revealed EGF and TGF-alpha mRNAs detectable as early as embryonic day 14 (earliest time point studied). While gene expression for both peptides continued into the postnatal period, EGF and TGF-alpha mRNA levels were nearly equal to adult concentrations by postnatal day 10. Taken together, our findings provide evidence for the synthesis of EGF in brain and suggest a role for both EGF and TGF-alpha in the development and support of the mammalian CNS.
High-level expression of hepatitis B virus HBx gene and hepatocarcinogenesis in transgenic mice (1994)

We studied the development of liver tumors in male HBx gene transgenic mice. Of two lineages studied, in the lineage with the lowest HBx gene expression liver tumors developed only in an incidence comparable with that in normal CD-1 strain, whereas 84% of male mice with a high level of the HBx gene product succumbed to liver neoplasia, indicating that continued HBx gene expression higher than a certain threshold level may be necessary for the development of hepatic neoplasia. Sixty-five mice from a lineage with a high level of HBx expression were then followed throughout their 24-mo lifespan. The livers of transgenic mice showed foci of cellular alteration with cytoplasmic vacuolations around the central veins from the age of 2 mo, but these foci did not expand progressively by the age of 12 mo. Immunostaining demonstrated such hepatocytes had higher expression of HBx protein than surrounding cells. Neoplastic lesions including liver cell adenomas and hepatocellular carcinomas developed from the age of 13 mo. By bromodeoxyuridine labeling analysis, hepatocytes in altered foci were found to have increased DNA synthesis, whereas no labeling was observed in age- and sex-matched nontransgenic littermate controls. Furthermore, DNA content analysis revealed the existence of several small aneuploid peaks in the transgenic liver before the age of tumor development. These results suggest that the continued expression of HBx gene may initiate a complex process to hepatocellular carcinoma by inducing DNA synthesis and placing large numbers of hepatocytes subjective to secondary events for transformation.
Development of ferroelectric materials for explosively driven pulsed-power systems (2009)

First demonstrated in the 1950's, ferroelectric generators (FEG) have been shown to be versatile compact pulsed-power sources. An FEG works by subjecting a ferroelectric ceramic to a high-pressure shock-wave typically produced by a high-explosive charge. The resulting compression causes the ferroelectric to release the electric charge stored within its crystal structure. Most explosively-driven FEG research has used commercial-off-the-shelf piezoelectric compositions such as lead zirconate-titanate ( Pb(Zr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.52</sub> Ti <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.48</sub> )O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , i.e. PZT ). Although these materials can be used to demonstrate pulsed-power and RF weapons concepts, they do not deliver enough energy to field compact devices. To solve this problem a manufacturing process was developed to produce a higher energy-density composition known as PZT 95/5 ( Pb(Zr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.95</sub> Ti <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.05</sub> )O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> ). This material, originally developed by Sandia National Laboratories in the 1960's, is capable of storing much more energy than commercially available PZT materials and is also capable of releasing all of its stored energy very rapidly (~1 ¿s) by virtue of a pressure-induced phase transition. This paper discusses the development, testing, and scale-up of TRS' 'Shock-HV' FEG material. This modified PZT 95/5 has been demonstrated to provide 2 to 3 times more power output than state-of-the-art materials. This new material will allow the development of a new generation of powerful, yet compact, FEG-based devices thus enabling a broad range of man-portable pulsed-power devices and RF weapons.
Histone Deacetylase Inhibitor Valproic Acid Enhances the Cytokine-Induced Expansion of Human Hematopoietic Stem Cells (2005)

Ex vivo amplification of human hematopoietic stem cells (HSC) without loss of their self-renewing potential represents an important target for transplantation, gene and cellular therapies. Valproic acid is a safe and widely used neurologic agent that acts as a potent inhibitor of histone deacetylase activities. Here, we show that valproic acid addition to liquid cultures of human CD34+ cells isolated from cord blood, mobilized peripheral blood, and bone marrow strongly enhances the ex vivo expansion potential of different cytokine cocktails as shown by morphologic, cytochemical, immunophenotypical, clonogenic, and gene expression analyses. Notably, valproic acid highly preserves the CD34 positivity after 1 week (range, 40-89%) or 3 weeks (range, 21-52%) amplification cultures with two (Flt3L + thrombopoietin) or four cytokines (Flt3L + thrombopoietin + stem cell factor + interleukin 3). Moreover, valproic acid treatment increases histone H4 acetylation levels at specific regulatory sites on HOXB4, a transcription factor gene with a key role in the regulation of HSC self-renewal and AC133, a recognized marker gene for stem cell populations. Overall, our results relate the changes induced by valproic acid on chromatin accessibility with the enhancement of the cytokine effect on the maintenance and expansion of a primitive hematopoietic stem cell population. These findings underscore the potentiality of novel epigenetic approaches to modify HSC fate in vitro.
Expression of human pancreatic polypeptide in heterologous cell lines. (1991)

Pancreatic polypeptide (PP) is initially synthesized as a larger precursor that requires post-translational processing to produce the biologically active hexatriacontapeptide. These steps include tryptic cleavage at paired basic residues, their subsequent removal by a carboxypeptidase B-like enzyme, and formation of a carboxyl-terminal amide moiety via the action of peptidyl-glycyl alpha-amidating monooxygenase. To examine these reactions further, we utilized the pZIPneo(SVX) retroviral vector to express a cDNA clone encoding human PP in several cell lines including a fibroblast line (psi-2), two endocrine cell lines known to produce amidated peptides (AtT-20 and PC12), and two lines that do not ordinarily produce amidated peptides (RIN5-f and GH3). Transfected psi-2 cells produced an unprocessed precursor of PP that appeared to be secreted constitutively with little remaining in intracellular stores. No post-translational processing of the PP precursor was evident in these cells. By contrast, all 4 endocrine-derived cell lines, regardless of the nature of their endogenous products, were capable of expressing fully processed and carboxyl-terminally amidated PP. Moreover, these lines had the ability to store the processed products. Our results support the notion that post-translational processing of peptide hormone precursors requires storage in secretory granules that contain the appropriate processing enzymes. Furthermore, enzymes such as peptidyl-glycyl alpha-amidating monooxygenase that are required for processing peptides may be a common feature of endocrine-derived cells regardless of the requirement for their activity to process endogenous products.
The herpes simplex virus type 1 latency-associated transcript gene regulates the establishment of latency (1997)

Herpes simplex virus type 1 establishes latent infections in sensory neurons. During latency only one locus, the latency-associated transcript (LAT), is abundantly transcribed. Several lines of evidence suggest that this locus is required for the efficient reactivation from latency in experimental models. However, it is not yet clear whether this is a direct effect on the reactivation process per se or, as we have suggested, an indirect effect resulting from a decreased efficiency of establishment of latent infections. In this report wild-type and genetically engineered viral mutants were analyzed in a mouse model using a recently developed approach to precisely quantify latently infected neurons. It was found that strain KOS/M established latent infections, as defined by the presence of the viral genome, in about 30% of the neurons. Thirty-three percent of the mice with this latent viral burden reactivated in vivo following hyperthermic stress. In contrast, mutants in which either the basal LAT promoter or the 5' end of the LAT gene was deleted established latency in only 10% of trigeminal neurons (P < 0.00001), and these mice were impaired for reactivation. Repair of the locus resulted in wild-type levels of establishment and reactivation, mapping this function to the LAT region. Finer mapping demonstrated that a 2.3-kb fragment that contains the major LAT transcripts was sufficient to promote efficient establishment and subsequent reactivation when expressed in the context of a foreign gene. Hyperthermic stress applied during the first 3 days postinfection resulted in greatly increased numbers of neurons harboring the latent viral genome. This approach was found to increase the level of establishment of LAT-null mutants to that normally achieved by wild-type KOS/M. These establishment-repaired mice reactivated with wild-type efficiency. Thus, the LAT gene serves to increase the number of neurons in which latency is established, and no direct role for the LAT locus in reactivation could be demonstrated.
A Study of a Gasoline-fueled Compression Ignition Engine ∼ Expansion of HCCI Operation Range Using SI Combustion as a Trigger of Compression Ignition ∼ (2005)

&lt;div class="htmlview paragraph"&gt;A new combustion concept, called spark-ignited compression ignition (SI-CI) combustion, is proposed for expanding the operation range of homogeneous charge compression ignition (HCCI) combustion. The authors previously showed that raising the mixture temperature before compression so as to induce auto-ignition near top dead center reduces the quantity of trapped gas, resulting in a lower maximum indicated mean effective pressure (IMEP). With the newly proposed combustion concept, auto-ignition of a homogeneous lean mixture is accomplished by the additional compression resulting from SI combustion of a small quantity of stratified mixture instead of raising the intake air temperature.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This SI-CI combustion process reduced the necessary increase in intake air temperature compared with conventional HCCI combustion. A higher maximum IMEP was achieved with SI-CI combustion than with conventional HCCI combustion, as was planned. However, nitrogen oxide (NOx) emissions increased due to the SI portion of the combustion process. Reducing NOx emissions through the application of exhaust gas recirculation is an issue of SI-CI combustion for future research.&lt;/div&gt;
A comprehensive study of the friction and dynamic motion of the piston assembly (1998)

A mixed lubrication model based on a two-dimensional average Reynolds equation is presented in this paper. It is developed for use in conjunction with a piston secondary motion analysis. The motion has been studied and the effects of structure parameters and different profiles of piston skirts on the motion are also investigated. The friction force and power loss consisting of piston skirt friction and the friction of the piston ring pack are also given.
Real-time facial feature detection using conditional regression forests (2012)

Although facial feature detection from 2D images is a well-studied field, there is a lack of real-time methods that estimate feature points even on low quality images. Here we propose conditional regression forest for this task. While regression forest learn the relations between facial image patches and the location of feature points from the entire set of faces, conditional regression forest learn the relations conditional to global face properties. In our experiments, we use the head pose as a global property and demonstrate that conditional regression forests outperform regression forests for facial feature detection. We have evaluated the method on the challenging Labeled Faces in the Wild [20] database where close-to-human accuracy is achieved while processing images in real-time.
Designing Miktoarm Polymers Using a Combination of “Click” Reactions in Sequence with Ring-Opening Polymerization (2010)

The design and synthesis of a well-defined molecular building block with three orthogonal functionalities which facilitate the construction of ABC-type miktoarm star polymers via a combination of sequential CuI-catalyzed cycloaddition of an azide to an alkyne (“click”) followed by ring-opening polymerization are reported. Using this simple and highly versatile methodology, a variety of miktoarm star polymers were prepared which consisted of hydrophilic poly(ethylene glycol) and hydrophobic polystyrene and poly(ε-caprolactone) arms. Their self-assembly in an aqueous medium was examined using dynamic light scattering and transmission electron microscopy. These ABC miktoarm polymers were found to self-assemble into spherical micelles whose core size and hydrodynamic diameter were found to be inversely proportional to the size of the PEG arm. The potential of encapsulating small molecules into these micelles was explored using Disperse Red 1 dye. An enhancement in the loading capacity of the micelles was observed with an increase in the length of the hydrophobic arm.
Gene therapy using self-complementary Y733F capsid mutant AAV2/8 restores vision in a model of early onset Leber congenital amaurosis (2011)

Defects in the photoreceptor-specific gene aryl hydrocarbon receptor interacting protein-like 1 (Aipl1) are associated with Leber congenital amaurosis (LCA), a childhood blinding disease with early-onset retinal degeneration and vision loss. Furthermore, Aipl1 defects are characterized at the most severe end of the LCA spectrum. The rapid photoreceptor degeneration and vision loss observed in the LCA patient population are mimicked in a mouse model lacking AIPL1. Using this model, we evaluated if gene replacement therapy using recent advancements in adeno-associated viral vectors (AAV) provides advantages in preventing rapid retinal degeneration. Specifically, we demonstrated that the novel self-complementary Y733F capsid mutant AAV2/8 (sc-Y733F-AAV) provided greater preservation of photoreceptors and functional vision in Aipl1 null mice compared with single-stranded AAV2/8. The benefits of sc-Y733F-AAV were evident following viral administration during the active phase of retinal degeneration, where only sc-Y733F-AAV treatment achieved functional vision rescue. This result was likely due to higher and earlier onset of Aipl1 expression. Based on our studies, we conclude that the sc-Y733F-AAV2/8 viral vector, to date, achieves the best rescue for rapid retinal degeneration in Aipl1 null mice. Our results provide important considerations for viral vectors to be used in future gene therapy clinical trials targeting a wider severity spectrum of inherited retinal dystrophies.
Pancreatic trypsin inhibitor. 2. Reaction with trypsin (1953)

The reactions of trypsin with
Etoposide Induces ATM-Dependent Mitochondrial Biogenesis through AMPK Activation (2008)

These results suggest that activation of ATM by etoposide can lead to mitochondrial biogenesis through AMPK activation. We propose that ATM-dependent mitochondrial biogenesis may play a role in DNA damage response and ROS regulation, and that defect in ATM-dependent mitochondrial biogenesis could contribute to the manifestations of A-T disease.
Delivery of Small Interfering RNA by Peptide-Targeted Mesoporous Silica Nanoparticle-Supported Lipid Bilayers (2012)

The therapeutic potential of small interfering RNAs (siRNAs) is severely limited by the availability of delivery platforms that protect siRNA from degradation, deliver it to the target cell with high specificity and efficiency, and promote its endosomal escape and cytosolic dispersion. Here we report that mesoporous silica nanoparticle-supported lipid bilayers (or "protocells") exhibit multiple properties that overcome many of the limitations of existing delivery platforms. Protocells have a 10- to 100-fold greater capacity for siRNA than corresponding lipid nanoparticles and are markedly more stable when incubated under physiological conditions. Protocells loaded with a cocktail of siRNAs bind to cells in a manner dependent on the presence of an appropriate targeting peptide and, through an endocytic pathway followed by endosomal disruption, promote delivery of the silencing nucleotides to the cytoplasm. The expression of each of the genes targeted by the siRNAs was shown to be repressed at the protein level, resulting in a potent induction of growth arrest and apoptosis. Incubation of control cells that lack expression of the antigen recognized by the targeting peptide with siRNA-loaded protocells induced neither repression of protein expression nor apoptosis, indicating the precise specificity of cytotoxic activity. In terms of loading capacity, targeting capabilities, and potency of action, protocells provide unique attributes as a delivery platform for therapeutic oligonucleotides.
Photometric stereo with non-parametric and spatially-varying reflectance (2008)

We present a method for simultaneously recovering shape and spatially varying reflectance of a surface from photometric stereo images. The distinguishing feature of our approach is its generality; it does not rely on a specific parametric reflectance model and is therefore purely ldquodata-drivenrdquo. This is achieved by employing novel bi-variate approximations of isotropic reflectance functions. By combining this new approximation with recent developments in photometric stereo, we are able to simultaneously estimate an independent surface normal at each point, a global set of non-parametric ldquobasis materialrdquo BRDFs, and per-point material weights. Our experimental results validate the approach and demonstrate the utility of bi-variate reflectance functions for general non-parametric appearance capture.