gebhart/patrepeval huggingface dataset:
Antibodies against the mono-methylated arginine-glycine repeat (MMA-RG) of the Epstein–Barr virus nuclear antigen 2 (EBNA2) identify potential cellular proteins targeted in viral transformation (2017)

The Epstein-Barr virus is a human herpes virus with oncogenic potential. The virus-encoded nuclear antigen 2 (EBNA2) is a key mediator of viral tumorigenesis. EBNA2 features an arginine-glycine (RG) repeat at amino acids (aa)339-354 that is essential for the transformation of lymphocytes and contains symmetrically (SDMA) and asymmetrically (ADMA) di-methylated arginine residues. The SDMA-modified EBNA2 binds the survival motor neuron protein (SMN), thus mimicking SMD3, a cellular SDMA-containing protein that interacts with SMN. Accordingly, a monoclonal antibody (mAb) specific for the SDMA-modified RG repeat of EBNA2 also binds to SMD3. With the novel mAb 19D4 we now show that EBNA2 contains mono-methylated arginine (MMA) residues within the RG repeat. Using 19D4, we immune-precipitated and analysed by mass spectrometry cellular proteins in EBV-transformed B-cells that feature MMA motifs that are similar to the one in EBNA2. Among the cellular proteins identified, we confirmed by immunoprecipitation and/or Western blot analyses Aly/REF, Coilin, DDX5, FXR1, HNRNPK, LSM4, MRE11, NRIP, nucleolin, PRPF8, RBM26, SMD1 (SNRDP1) and THRAP3 proteins that are either known to contain MMA residues or feature RG repeat sequences that probably serve as methylation substrates. The identified proteins are involved in splicing, tumorigenesis, transcriptional activation, DNA stability and RNA processing or export. Furthermore, we found that several proteins involved in energy metabolism are associated with MMA-modified proteins. Interestingly, the viral EBNA1 protein that features methylated RG repeat motifs also reacted with the antibodies. Our results indicate that the region between aa 34-52 of EBNA1 contains ADMA or SDMA residues, while the region between aa 328-377 mainly contains MMA residues.
Soft Breakdown of Ultra-Thin Gate Oxide Layers (1995)

The dielectric breakdown of ultra-thin 3 to 4 nm SiO 2 layers used as a gate dielectric in poly-Si gate capacitors is investigated with tunnel current stressing. A soft breakdown phenomenon is demonstrated for these ultra-thin gate oxide layers that corresponds with an anomalous increase of the stress induced leakage current and the occurrence of fluctuations in the current. The occurrence of soft breakdown in these ultra-thin gate oxide layers however is difficult to detect during a standard high-field time dependent dielectric breakdown (TDDB) test.
Impaired leucocyte rolling, adhesion and transendothelial migration following cuprophane haemodialysis (1997)

In this study, we investigated how different steps in the extravasation process of leucocytes, i.e. rolling, adhesion and transendothelial migration, are affected by haemodialysis with cuprophane membranes. Human leucocytes obtained from whole blood prior to clinical haemodialysis and from the afferent blood line (post-dialyser) 15 min after the initiation of dialysis were injected into the mesenteric microcirculation of urethane anaesthetized rabbits and analysed for their ability to roll in the microvessels by use of intravital fluorescence microscopy. Moreover, neutrophils from the two leucocyte populations were compared with respect to chemoattractant-induced adhesion and transmigration across confluent monolayers of bovine aortic endothelial cells. Our results show that, as compared with pre-dialysis leucocytes, 15 min of cuprophane haemodialysis impaired leucocyte rolling by 78 +/- 7%, reduced N-formyl-methionyl-leucyl-phenylalanin (fMLP)-induced adhesion by 34 +/- 9%, and abolished transendothelial migration. These findings demonstrate that intradialytical activation of leucocytes during cuprophane haemodialysis severely affects leucocyte functions that are critical in the extravasation process of these cells at inflammatory tissue sites, and thus may help explain the increased susceptibility to infections observed in patients on chronic haemodialysis.
A Comparative Ab Initio Study of the Primary Hydration and Proton Dissociation of Various Imide and Sulfonic Acid Ionomers (2012)

We compare the role of neighboring group substitutions on proton dissociation of hydrated acidic moieties suitable for proton exchange membranes through electronic structure calculations. Three pairs of ionomers containing similar electron withdrawing groups within the pair were chosen for the study: two fully fluorinated sulfonyl imides (CF(3)SO(2)NHSO(2)CF(3) and CF(3)CF(2)SO(2)NHSO(2)CF(3)), two partially fluorinated sulfonyl imides (CH(3)SO(2)NHSO(2)CF(3) and C(6)H(5)SO(2)NHSO(2)CF(2)CF(3)), and two aromatic sulfonic acid based materials (CH(3)C(6)H(4)SO(3)H and CH(3)OC(6)H(3)OCH(3)C(6)H(4)SO(3)H). Fully optimized counterpoise (CP) corrected geometries were obtained for each ionomer fragment with the inclusion of water molecules at the B3LYP/6-311G** level of density functional theory. Spontaneous proton dissociation was observed upon addition of three water molecules in each system, and the transition to a solvent-separated ion pair occurred when four water molecules were introduced. No considerable quantitative or qualitative differences in proton dissociation, hydrogen bond networks formed, or water binding energies were found between systems containing similar electron withdrawing groups. Each of the sulfonyl imide ionomers exhibited qualitatively similar results regarding proton dissociation and separation. The fully fluorinated sulfonyl imides, however, showed a greater propensity to exist in dissociated and ion-pair separated states at low degrees of hydration than the partially fluorinated sulfonyl imides. This effect is due to the additional electron withdrawing groups providing charge stabilization as the dissociated proton migrates away from the imide anion.
Duality of MIMO multiple access channel and broadcast channel with amplify-and-forward relays (2010)

In this work, we consider a two-hop multiuser amplify-and-forward relay network with multi-antenna nodes. The results are three-fold. First, for any relay amplification matrix D in the multiple-access channel (MAC), we show that duality holds when ¿D <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">¿</sup> is employed in the broadcast channel (BC), and vice versa, where re is obtained from switching the total source and relay power constraints. Second, under a total network power constraint, we show that MAC-BC duality holds when D and D <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">¿</sup> are the relaying matrices in the MAC and BC respectively. Third, for any D in the MAC and cD <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">¿</sup> in the BC where c is any positive real scalar, MAC-BC duality under total network power constraint holds only for the above two cases.
Tearing instability in an anisotropic neutral sheet. Memorandum report (1983)

A study is made of the collisionless tearing-mode stability properties of a field-reversed plasma layer whose temperature distribution is anisotropic. The plasma is confined by its self magnetic field with no external field. A kinetic description is used for both ions and electrons. The effects of the axis-crossing and nonaxis-crossing orbits are discussed. It is found that the conventional technique of matching the inner and outer asymptotic solutions at the electron inner-region is inadequate for the anisotropic case. An intermediate region in which the axis-crossing ion orbits are important is identified. The eigenvalue equation is solved using both analytic approximations and numerical methods to obtain the eigenmode structure and the linear dispersion relation.
Improved Synthesis of gem-Diiodoalkanes (2008)

gem-Diiodoalkanes are useful precursors in several organic transformations like Simmons-Smith cyclopropanation and Takai olefination. This method allows a convenient preparation of gem-diiodides by the alkylation of diiodo­methyl anion with alkyl iodides or benzylic and allylic bromides. A broad functional group tolerance is demonstrated for this reaction.
A Survey of Signed Network Mining in Social Media (2015)

Many real-world relations can be represented by signed networks with positive and negative links, as a result of which signed network analysis has attracted increasing attention from multiple disciplines. With the increasing prevalence of social media networks, signed network analysis has evolved from developing and measuring theories to mining tasks. In this article, we present a review of mining signed networks in the context of social media and discuss some promising research directions and new frontiers. We begin by giving basic concepts and unique properties and principles of signed networks. Then we classify and review tasks of signed network mining with representative algorithms. We also delineate some tasks that have not been extensively studied with formal definitions and also propose research directions to expand the field of signed network mining.
A Reduced Organic Carbon Component in Martian Basalts (2012)

Abiotic Martian Organics Understanding the sources and the formation mechanisms of organic carbon compounds on Mars has implications for our understanding of the martian carbon cycle. Steele et al. (p. 212 , published online 24 May) present measurements of organic material in 11 martian meteorites, including the Tissint meteorite, which fell in the Moroccan desert in July 2011. Ten of the meteorites contain complex hydrocarbons encased within igneous minerals. The results imply that the organics formed as the magma melt crystallized and are thus of abiotic origin.
Micro to Nano Conversion: A One-Step, Environmentally Friendly, Solid State, Bulk Fabrication of WS2 and MoS2 Nanoplates (2008)

A top down (micro to nano conversion) approach is presented for the fabrication of WS2 and MoS2 nanoplates employing a single-step, scalable, and environmentally friendly reaction under autogenic pressure at elevated temperature (RAPET). The thermal (750 °C) solid-state reaction between micrometer-sized W or Mo with microsized S in an inert atmosphere yielded a high yield of WS2 or MoS2 nanoplates via carving phenomena. The as-prepared carved microstructures are comprised of two-dimensional WS2/MoS2 nanoplates. The systematic compositional, structural, morphological, and BET surface area analysis is presented, and a mechanistic elucidation for the fabrication of WS2/MoS2 nanoplates is provided.
Templated self-assembly of iron oxide nanoparticles (2010)

We report on self-assembled iron oxide nanoparticle films on silicon substrates. In addition to homogeneously assembled layers, we fabricated patterned trenches of 40-1000 nm width using electron beam lithography for the investigation of assisted self-assembly. The nanoparticles with a diameter of 20 nm +/- 7% were synthesized by thermal decomposition of iron oleate complexes in trioctylamine in presence of oleic acid. Samples with different track widths and nanoparticle concentration were characterized by scanning electron microscopy and by superconducting quantum interference device magnetometry.
Inhibition of pestivirus infection in cell culture by envelope proteins E(rns) and E2 of classical swine fever virus: E(rns) and E2 interact with different receptors. (1997)

Pure preparations of envelope glycoproteins E(rns) and E2 of classical swine fever virus (CSFV) synthesized in insect cells were used to study infection of porcine and bovine cells with the pestiviruses CSFV and bovine viral diarrhoea virus (BVDV). Almost 100% inhibition of infection of porcine kidney cells with CSFV was produced by 100 microg/ml E(rns). After removal of the virus no E(rns) was needed in the overlay medium (growth medium) to maintain this level of inhibition. In contrast, 100% inhibition of infection of porcine kidney cells with CSFV by 10 microg/ml E2 was only achieved when E2 was added to the overlay medium. When E2 was omitted, a maximum of 50% inhibition was achieved. This indicated that after the virus and E2 were removed from the cells, infection still occurred, by virus particles which were still bound to the cell surface. Treatment with 100 microg/ml E(rns) released these particles from the cell surface. Furthermore, E(rns) bound irreversibly to the surface of cells susceptible or unsusceptible to pestivirus infection and cell-to-cell spread of CSFV was completely inhibited by E2 but not by E(rns). These results demonstrated that E(rns) and E2 interacted with different cell surface receptors. Inhibition of BVDV infection of porcine and bovine cells by CSFV E2 suggested that CSFV E2 and BVDV E2 share an identical receptor. BVDV strain 5250 isolated from pigs was efficiently inhibited by CSFV E(rns), whereas several BVDV strains isolated from cattle were not, suggesting that the conformation of E(rns) plays a role in host tropism.
[Effect of allopurinol on adrenergically induced changes in serum lipid levels, heart rate and blood pressure in normal and ischemic rabbits (author's transl)]. (1982)

In accordance with previous results obtained in healthy volunteers 1H-pyrazolo[3,4-d]pyrimidin-4-ol (allopurinol) showed an inhibiting effect on the adrenergically induced mobilization of free fatty acids in normal rabbits. The effect of allopurinol was nearly equal to that of prostaglandin E1 but less than that of pyridyl carbinol. Similarly like in patients with coronary heart disease, this effect was not found in rabbits with cardiac damage following isoprenaline pretreatment. Allopurinol at higher dosage diminished the noradrenaline-induced decrease of heart rate and increase of blood pressure.
Abstract 16930: Asymmetric Chromatid Segregation Identifies Human Cardiac Stem Cells that Regenerate Extensively the Infarcted Myocardium (2012)

According to the immortal DNA strand hypothesis, dividing stem cells selectively segregate chromosomes carrying the old DNA template, opposing accumulation of replication errors and attenuating tel...
Voxel-wise displacement as independent features in classification of multiple sclerosis (2013)

We present a method that utilizes registration displacement fields to perform accurate classification of magnetic resonance images (MRI) of the brain acquired from healthy individuals and patients diagnosed with multiple sclerosis (MS). Contrary to standard approaches, each voxel in the displacement field is treated as an independent feature that is classified individually. Results show that when used with a simple linear discriminant and majority voting, the approach is superior to using the displacement field with a single classifier, even when compared against more sophisticated classification methods such as adaptive boosting, random forests, and support vector machines. Leave-one-out cross-validation was used to evaluate this method for classifying images by disease, MS subtype (Acc: 77%-88%), and age (Acc: 96%-100%).
A Soluble Fluorous Palladium Complex that Promotes Heck Reactions and Can Be Recovered and Reused. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Skeletal muscle myocytes undergo protein loss and reactive oxygen-mediated NF-κB activation in response to tumor necrosis factor α (1998)

Skeletal muscle atrophy and weakness are thought to be stimulated by tumor necrosis factor alpha (TNF-alpha) in a variety of chronic diseases. However, little is known about the direct effects of TNF-alpha on differentiated skeletal muscle cells or the signaling mechanisms involved. We have tested the effects of TNF-alpha on the mouse-derived C2C12 muscle cell line and on primary cultures from rat skeletal muscle. TNF-alpha treatment of differentiated myotubes stimulated time- and concentration-dependent reductions in total protein content and loss of adult myosin heavy chain (MHCf) content; these changes were evident at low TNF-alpha concentrations (1-3 ng/ml) that did not alter muscle DNA content and were not associated with a decrease in MHCf synthesis. TNF-alpha activated binding of nuclear factor kappaB (NF-kappaB) to its targeted DNA sequence and stimulated degradation of I-kappaBalpha, an NF-kappaB inhibitory protein. TNF-alpha stimulated total ubiquitin conjugation whereas a 26S proteasome inhibitor (MG132 10-40 microM) blocked TNF-alpha activation of NF-kappaB. Catalase 1 kU/ml inhibited NF-kappaB activation by TNF-alpha; exogenous hydrogen peroxide 200 microM activated NF-kappaB and stimulated I-kappaBalpha degradation. These data demonstrate that TNF-alpha directly induces skeletal muscle protein loss, that NF-kappaB is rapidly activated by TNF-alpha in differentiated skeletal muscle cells, and that TNF-alpha/NF-kappaB signaling in skeletal muscle is regulated by endogenous reactive oxygen species.
Physical simulation of dynamic resistive switching in metal oxides using a Schottky contact barrier model (2015)

We present a numerical drift-diffusion model of electronic-ionic transport combined with a Schottky contact barrier model to study resistive switching phenomena in ReRAM devices. Capturing the transition between Schottky and ohmic contact resistances upon temperature-accelerated ion migration, our model correctly describes the quasi-static I-V switching characteristics as well as dynamic set and reset events. It is shown to account for a transition between bipolar resistive switching and complementary switching when reducing the asymmetry between the contact barriers. Further, it is used to characterize the abrupt and gradual behavior of the set and the reset process, respectively.
Inference of Poisson count processes using low-rank tensor data (2013)

A novel regularizer capturing the tensor rank is introduced in this paper as the key enabler for completion of three-way data arrays with missing entries. The novel regularized imputation approach induces sparsity in the factors of the tensor's PARAFAC decomposition, thus reducing its rank. The focus is on count processes which emerge in diverse applications ranging from genomics to computer and social networking. Based on Poisson count data, a maximum aposteriori (MAP) estimator is developed using the Kullback-Leibler divergence criterion. This probabilistic approach also facilitates incorporation of correlated priors regularizing the rank, while endowing the tensor imputation method with extra smoothing and prediction capabilities. Tests on simulated and real datasets corroborate the sparsifying regularization effect, and demonstrate recovery of 15% missing RNA-sequencing data with an inference error of -12dB.
Determining viability of using APNG status as a prognostic marker in patients with glioblastoma multiforme. (2015)

2028 Background: Expression of the enzyme alkylpurine-DNA-N-glycosylase (APNG) has been associated with poor outcome in patients with glioblastoma multiforme (GBM). APNG is part of the base excision repair system, and expression of APNG is related to resistance towards temozolomide (TMZ). This study evaluates the prognostic value of APNG in a population-based cohort of 185 Danish GBM patients diagnosed between 2005 and 2009. Due to GBM’s cellular heterogeneity, APNG contribution from non-tumor cells was excluded. Methods: APNG expression was evaluated using image analysis and a novel quantitative immunohistochemical (IHC) assay (qIHC, Dako), where APNG protein levels were represented through dots. Non-tumor cells, which were found to express APNG, were excluded using an IHC/qIHC double-staining. To verify the qIHC results, APNG was measured in 177 of the patients using a quantitative in-house developed APNG immunofluorescence (IF) assay. MGMT methylation status was obtained in 152 patients by pyrosequencing. Results: Using qIHC, median expression of APNG was 0.31 dots/cell (range 0.099-0.96). An optimal cut-point was identified dichotomizing the patients at an APNG value of 0.24 (25% vs. 75% of the patients). In Cox regression high expression of APNG was associated with better overall survival (OS) (HR 0.53, p = 0.001) adjusting for the effect of age, performance status, tumor crossing midline, treatment and gender. APNG was associated with better OS (HR 0.57, p = 0.012) when adjusting for MGMT status. Retesting the cohort using IF, demonstrated similar results (HR 0.81, p = 0.2). Patients with methylated MGMT promoters and high APNG expression demonstrated a better OS, than with non-methylated MGMT promoters and low APNG expression (HR 0.55, p = 0.04). Conclusions: APNG measured by qIHC was found to be an independent significant prognostic factor for OS in GBMs, This was supported by IF measurements. Removing bias associated with APNG expression in non-tumor cells in both assays has, in this study contributed substantially to analyze the prognostic value of APNG in GBM patients. We expect that APNG qIHC can potentially identify patients who will not benefit from treatment with TMZ.
An EM approach for dynamic battery management systems (2012)

In this paper we propose an expectation maximization (EM) type algorithm for online system identification and tracking of prognostic states as applied to battery management systems (BMS). The objective of BMS is to adaptively estimate state of charge (SOC) - a crucial battery state information. We find that the existing approaches in the literature need enhancement because (i) they lack battery equivalent models that accurately model the actual physical and chemical properties of the batteries, and (ii) they fail to utilize powerful state and parameter estimation techniques for system identification and tracking. It is often noticed throughout the literature that (ii) is a precursor to (i). In this paper, first we model the dynamic equivalent model of batteries as a series of m parallel RC circuits and derive the relationship between the time-varying battery states and the current, voltage output observations as a non-linear state space model. Then, we derive an expectation maximization (EM) type algorithm for identification of the so-derived statespace model and for the adaptive tracking of SOC. Finally we discuss the performance evaluation of the proposed algorithm through simulation and by testing them on experimental data obtained from Li-ion based cellphone batteries. © 2012 ISIF (Intl Society of Information Fusi).
Quantifying and Verifying Reachability for Access Controlled Networks (2012)

Quantifying and querying network reachability is important for security monitoring and auditing as well as many aspects of network management such as troubleshooting, maintenance, and design. Although attempts to model network reachability have been made, feasible solutions to computing network reachability have remained unknown. In this paper, we propose a suite of algorithms for quantifying reachability based on network configurations [mainly Access Control Lists (ACLs)] as well as solutions for querying network reachability. We present a network reachability model that considers connectionless and connection-oriented transport protocols, stateless and stateful routers/firewalls, static and dynamic NAT, PAT, IP tunneling, etc. We implemented the algorithms in our network reachability tool called Quarnet and conducted experiments on a university network. Experimental results show that the offline computation of reachability matrices takes a few hours, and the online processing of a reachability query takes 0.075 s on average.
Tunable Optomechanical Cavity Filters (2019)

Cavity optomechanics enables large-scale index tuning (Δneff). However, most demonstrations exhibited small Δneff or have not considered optical loss at large Δneff. We demonstrate Δnefrtuning using gradient electric forces and analyze optomechanically-induced loss and mitigation. © 2019 The Author(s)