gebhart/patrepeval huggingface dataset:
Adeno-Associated Virus Rep78 Protein Interacts with Protein Kinase A and Its Homolog PRKX and Inhibits CREB-Dependent Transcriptional Activation (1998)

Adeno-associated virus (AAV) is a human parvovirus of the genus Dependovirus. AAV replication is largely restricted to cells which are coinfected with a helper virus. In the absence of a helper virus, the AAV genome can integrate into a specific chromosomal site where it remains latent until reactivated by superinfection of the host cell with an appropriate helper virus. Replication functions of AAV have been mapped to the Rep68 and Rep78 gene products. Rep proteins demonstrate DNA binding, endonuclease, and helicase activities and are involved in regulation of transcription from both AAV and heterologous promoters. AAV has been associated with suppression of oncogenicity in a range of viral and nonviral tumors. In this study we sought to identify and study cellular protein targets of AAV Rep, in order to develop a better understanding of the various activities of Rep. We used the yeast two-hybrid system to identify HeLa cell proteins that interact with AAV type 2 Rep78. We isolated several strongly interacting clones which were subsequently identified as PRKX (previously named PKX1), a recently described homolog of the protein kinase A (PKA) catalytic subunit (PKAc). The interaction was confirmed in vitro by using pMal-Rep pull-down assays. The region of Rep78 which interacts was mapped to a C-terminal zinc finger-like domain; Rep68, which lacks this domain, did not interact with PRKX. PRKX demonstrated autophosphorylation and kinase activity towards histone H1 and a PKA oligopeptide target. Autophosphorylation was inhibited by interaction with Rep78. In transfection assays, a PRKX expression vector was shown to be capable of activating CREB-dependent transcription. This activation was suppressed by Rep78 but not by Rep68. Since PRKX is a close homolog of PKAc, we investigated whether Rep78 could interact directly with PKAc. pMal-Rep78 was found to associate with purified PKAc and inhibited its kinase activity. Cotransfection experiments demonstrated that Rep78 could block the activation of CREB by a PKAc expression vector. These experiments suggest that AAV may perturb normal cyclic AMP response pathways in infected cells.
Orthostatic Hypotension in the Elderly (1989)

ORTHOSTATIC hypotension is often observed in elderly people and may result in substantial morbidity and mortality from associated falls and syncope. Studies of elderly people living in the community have found a prevalence of orthostatic hypotension as high as 20 percent among medical outpatients over 65 years of age1 , 2 and 30 percent among those over 75.1 However, recent epidemiologic studies of healthy, normotensive elderly subjects without known risk factors for orthostatic hypotension have found a prevalence of less than 7 percent.3 , 4 Data on blood pressure measured in the supine and sitting positions in over 8000 participants in the National Health . . .
Bio-Inspired Extreme Wetting Surfaces for Biomedical Applications (2016)

Biological creatures with unique surface wettability have long served as a source of inspiration for scientists and engineers. More specifically, materials exhibiting extreme wetting properties, such as superhydrophilic and superhydrophobic surfaces, have attracted considerable attention because of their potential use in various applications, such as self-cleaning fabrics, anti-fog windows, anti-corrosive coatings, drag-reduction systems, and efficient water transportation. In particular, the engineering of surface wettability by manipulating chemical properties and structure opens emerging biomedical applications ranging from high-throughput cell culture platforms to biomedical devices. This review describes design and fabrication methods for artificial extreme wetting surfaces. Next, we introduce some of the newer and emerging biomedical applications using extreme wetting surfaces. Current challenges and future prospects of the surfaces for potential biomedical applications are also addressed.
Microbiological transformations, part 6. Microbiological transformations of acyl derivatives of indoline, 1,2,3,4-tetrahydroquinoline, 1,2,3,4-tetrahydroisoquinoline and 2,3,4,5-tetrahydro-1H-1-benzazepine with the fungus Cunninghamella elegans (1985)

Incubation of N-benzoyl and N-(p-toluoyl)indoline with Cunninghamella elegans resulted in reductive cleavage with the formation of indoline and the corresponding benzyl alcohol. N-Acetylindoline underwent normal benzylic hydroxylation and open chain analogues of N-(p-toluoyl)indolines were hydroxylated at the aryl methyl group by C. elegans. The fungus effected benzylic oxidation at the 4-position in N-benzoyl-1,2,3,4-tetrahydroquinoline and in N-benzoyl-1,2,3,4-tetrahydroisoquinoline derivatives. N-(p-Toluoyl)-1,2,3,4-tetrahydroquinoline and N-(p-ethylbenzoyl)-1,2,3,4-tetrahy-droisoquinoline were, however, hydroxylated at the alternative 4′-benzylic position. Incubation of N-(p-toluoyl)-2,3,4,5-tetrahydro-1 H-1 -benzazepine with C. elegans gave 5-hydroxy-N-(p-toluoyl)-2,3,4,5-tetrahydro-1 H-1 -benzazepine
Conducting channel at the LaAlO<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mrow/><mml:mn>3</mml:mn></mml:msub></mml:math>/SrTiO<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mrow/><mml:mn>3</mml:mn></mml:msub></mml:math>interface (2013)

Localization of electrons in the two-dimensional electron gas at the LaAlO${}_{3}$/SrTiO${}_{3}$ interface is investigated by varying the channel thickness in order to establish the nature of the conducting channel. Layers of SrTiO${}_{3}$ were grown on NdGaO${}_{3}$ (110) substrates and capped with LaAlO${}_{3}$. When the SrTiO${}_{3}$ thickness is \ensuremath{\le}6 unit cells, most electrons at the interface are localized, but when the number of SrTiO${}_{3}$ layers is 8--16, the free carrier density approaches 3.3\ifmmode\times\else\texttimes\fi{}10${}^{14}$ cm${}^{\ensuremath{-}2}$, the value corresponding to charge transfer of 0.5 electrons per unit cell at the interface. The number of delocalized electrons decreases again when the SrTiO${}_{3}$ thickness is \ensuremath{\ge}20 unit cells. The \ensuremath{\sim}4 nm conducting channel is therefore located significantly below the interface. The results are explained in terms of Anderson localization and the position of the mobility edge with respect to the Fermi level.
The Roles of Phosphatidylinositol 3-Kinase and Protein Kinase Cζ for Thrombopoietin-induced Mitogen-activated Protein Kinase Activation in Primary Murine Megakaryocytes (2001)

Thrombopoietin (TPO) stimulates a network of intracellular signaling pathways that displays extensive cross-talk. We have demonstrated previously that the ERK/mitogen-activated protein kinase pathway is important for TPO-induced endomitosis in primary megakaryocytes (MKs). One known pathway by which TPO induces ERK activation is through the association of Shc with the penultimate phosphotyrosine within the TPO receptor, Mpl. However, several investigators found that the membrane-proximal half of the cytoplasmic domain of Mpl is sufficient to activate ERK in vitro and support base-line megakaryopoiesis in vivo. Using BaF3 cells expressing a truncated Mpl (T69Mpl) as a tool to identify non-Shc/Ras-dependent signaling pathways, we describe here novel mechanisms of TPO-induced ERK activation mediated, in part, by phosphoinositide 3-kinase (PI3K). Similar to cells expressing full-length receptor, PI3K was activated by its incorporation into a complex with IRS2 or Gab2. Furthermore, the MEK-phosphorylating activity of protein kinase Czeta (PKCzeta) was also enhanced after TPO stimulation of T69Mpl, contributing to ERK activity. PKCzeta and PI3K also contribute to TPO-induced ERK activation in MKs, confirming their physiological relevance. Like in BaF3 cells, a TPO-induced signaling complex containing p85PI3K is detectable in MKs expressing T61Mpl and is probably responsible for PI3K activation. These data demonstrate a novel role of PI3K and PKCzeta in steady-state megakaryopoiesis.
Rigid, Sterically Diverse N-Heterocyclic Carbene-Pyridine Chelates: Synthesis, Mild Palladation, and Palladium-Catalyzed Allylic Substitution (2009)

A series of four 1-(pyridin-2-yl)benzimidazolium salts was synthesized as precursors to rigid, bidentate N-heterocyclic carbene-pyridine ligands. With the goal of exploring the interplay between steric and electronic asymmetry in catalysis, the ligands are constructed with very small (H, Me) or very bulky (2,6-diisopropylphenyl, 2,4,6-triisopropylphenyl) groups adjacent to the nitrogen and carbon donor atoms. Cationic palladium-allyl complexes were synthesized under mild conditions, using triethylamine as base and potassium or silver hexafluorophosphate as counterion source. The structures of three complexes were verified using X-ray crystallography. All four palladium complexes were active catalysts for the allylic substitution reaction between allylic carbonates and either sodium diethyl-2-methylmalonate or N-methylbenzylamine, although significant ligand-controlled effects on regioselectivity were not observed under the conditions studied.
Graphene activated 3D-hierarchical flower-like Li<sub>2</sub>FeSiO<sub>4</sub> for high-performance lithium-ion batteries (2015)

Graphene activated 3D-hierarchical flower-like Li<sub>2</sub>FeSiO<sub>4</sub> exhibits a discharge capacity of 327.2 mA h g<sup>−1</sup> which approaches the theoretical capacity of 332 mA h g<sup>−1</sup> with outstanding high large-current and long-life performances.
Gas Separation Membranes Derived from High-Performance Immiscible Polymer Blends Compatibilized with Small Molecules (2015)

An immiscible polymer blend comprised of high-performance copolyimide 6FDA-DAM:DABA(3:2) (6FDD) and polybenzimidazole (PBI) was compatibilized using 2-methylimidazole (2-MI), a commercially available small molecule. Membranes were fabricated from blends of 6FDD:PBI (50:50) with and without 2-MI for H2/CO2 separations. The membranes demonstrated a matrix-droplet type microstructure as evident with scanning electron microscopy (SEM) imaging where 6FDD is the dispersed phase and PBI is the continuous phase. In addition, membranes with 2-MI demonstrated a uniform microstructure as observed by smaller and more uniformly dispersed 6FDD domains in contrast to 6FDD:PBI (50:50) blend membranes without 2-MI. This compatibilization effect of 2-MI was attributed to interfacial localization of 2-MI that lowers the interfacial energy similar to a surfactant. Upon the incorporation of 2-MI, the H2/CO2 selectivity improved remarkably, compared to the pure blend, and surpassed the Robeson's upper bound. To our knowledge, this is the first report of the use of a small molecule to compatibilize a high-performance immiscible polymer blend. This approach could afford a novel class of membranes in which immiscible polymer blends can be compatibilized in an economical and convenient fashion.
Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma (2018)

Liquid biopsies including circulating tumor cells (CTCs) and cell-free DNA (cfDNA) have enabled minimally invasive characterization of many cancers, but are rarely analyzed together. Understanding the detectability and genomic concordance of CTCs and cfDNA may inform their use in guiding cancer precision medicine. Here, we report the detectability of cfDNA and CTCs in blood samples from 107 and 56 patients with multiple myeloma (MM), respectively. Using ultra-low pass whole-genome sequencing, we find both tumor fractions correlate with disease progression. Applying whole-exome sequencing (WES) to cfDNA, CTCs, and matched tumor biopsies, we find concordance in clonal somatic mutations (~99%) and copy number alterations (~81%) between liquid and tumor biopsies. Importantly, analyzing CTCs and cfDNA together enables cross-validation of mutations, uncovers mutations exclusive to either CTCs or cfDNA, and allows blood-based tumor profiling in a greater fraction of patients. Our study demonstrates the utility of analyzing both CTCs and cfDNA in MM.
Effect of Fin Angle on Electrical Characteristics of Nanoscale Bulk FinFETs (2006)

Bulk fin-shaped field effect transistor (finFET) has been viewed as a promising candidate for sub-45 nm very largescale integrated (VLSI) circuit design and manufacturing. The structure features excellent device characteristics in comparing with the conventionally planar devices. In fabricating the bulk finFETs, the effect of a nonrectangular fin angle has to be carefully concerned that an ideal fin angle (90 degree) is not easy to be manufactured. Therefore, the short channel effect may be arisen due to the non-ideal manufacturing conditions and influence the device electrical properties. In this paper, the performance impacted by angles and heights of bulk finFETs are for the first time comprehensively investigated to draw the optimal strategy in novel VLSI circuit design.
An Advanced Load Balancing Strategy for Cloud Environment (2016)

The rapid development of cloud computing, bring great convenience to developers. Recently the resource management of the cloud platform has become a hot research topic, especially the load balancing problem in data center is very important for cloud provider. In this paper, a load balancing framework is proposed for cloud platform, it use the threshold window strategy and an advanced AR prediction model to reduce the migration of VMs. Experiments show that this method can effectively achieve load balancing, promote the utilization of the physical machines, and solve the frequent migration problem caused by high instantaneous peak values significantly.
Recovery of drawing order from scanned images of multi-stroke handwriting (1999)

Describes a method to recover the drawing order of a multi-stroke handwritten script from a binary 2D image. First, we construct a graph from the scanned image by applying a thinning process and extracting the skeletal pixels. Next, we identify the start or end vertices in the graph, and then globally analyze the graph to label it by determining the types of each vertex and each edge. Finally, we trace all the strokes using the labeling information and recover the drawing order. The method does not enumerate the possible drawing orders and does not cause a combinatorial explosion, even if the script is very complex. By recovering the drawing order of a handwritten script, the temporal information can be recovered from a scanned image. Hence, this method can be used as a bridge from the offline handwriting character recognition problem to the online one.
Pulmonary hypertension (2013)

2011 to 2012 has seen an explosion in published research in the field of pulmonary vascular disease, especially pulmonary hypertension. In conjunction with this research has been an explosion in clinical interest in treating pulmonary hypertension. This is possible because we now have three different generic classes of drug therapy: endothelin receptor antagonists, phosphodiesterase-5 inhibitors and prostacyclins. Clearly, however, we need to be careful that we are treating the correct disease with the correct drug and measuring the correct response. Herein, I will review the papers published over the last year that offer the most insight into the pathobiology, but also those that give us the clinical information we need in epidemiology, treatment and end-points so that we can treat this devastating group of disease.
How Bit Profile and Gauges Affect Well Trajectory (2003)

Summary The importance of wellbore deviation is well recognized by the drilling industry. An analysis of a drilling system's directional behavior must include the directional characteristics of the drill bit. This paper presents a comprehensive analysis of the directional behavior of polycrystalline diamond compact (PDC) bits, including the effect of bit profile, gauge cutters, and gauge length. Numerical simulations as well as laboratory tests have been carried out to better understand the mechanisms of PDC bit deviation and to evaluate the most important parameters affecting the directional behavior of PDC bits. The analysis presented in this paper shows that each part of the PDC bit (profile and active and passive gauges) plays a major role in its walking tendency and steerability. A quantitative evaluation of how these factors contribute to well trajectory (inclination and azimuth) is given. For the first time, a full-scale directional-drilling bench was built to measure the walking tendency and steerability of PDC bits. The results obtained demonstrate that the bit profile, gauge cutters, and gauge length have a significant effect. A 3D theoretical rockbit interaction model was developed to reproduce the drilling test results.
Enhanced Degradation of the Ferritin Repressor Protein During Induction of Ferritin Messenger RNA Translation (1992)

Induction of ferritin synthesis in cultured cells by heme or iron is accompanied by degradation of the ferritin repressor protein (FRP). Intermediates in the degradative pathway apparently include FRP covalently linked in larger aggregates. The effect of iron on FRP degradation is enhanced by porphyrin precursors but is decreased by inhibitors of porphyrin synthesis, which implies that heme is an active agent. These results suggest that translational induction in this system may be caused by enhanced repressor degradation. While unique among translational regulatory systems, this process is common to a variety of other biosynthetic control mechanisms.
Progress in replication of substrates for multilayer coatings (1998)

Studies are being carried out to compare the performance of several different separation materials used in the replication process. This report presents the results obtained during the second year of a program which consists of replicating smooth, thin substrates, depositing multilayer coatings upon them, and evaluating their performance. Replication smooth, thin substrates, depositing multilayer coatings upon them, and evaluating their performance. Replication and multilayer coatings are both critically important to the development of focussing hard x- ray telescopes that function up to 100 keV. The activities of the current year include extending the comparison between sputtered amorphous carbon and evaporated gold to include sputtered as well as evaporated gold. The figure of merit being the smoothness of the replica which has a direct effect on the specular reflectivity. These results were obtained with epoxy replication, but they should be applicable to electroformed nickel, the process we expect to use for the ultimate replicated optics.
Soft immobilized pH gradient gels in proteome analysis: A follow‐up (2003)

As a follow-up of a previous work on two-dimensional map analysis utilizing soft (< 4%T) immobilized pH gradient (IPG) matrices in the first dimension (Candiano et al., Electrophoresis 2002, 23, 292-297), we have further optimized the preparation of such dilute IPG gels. One important step for obtaining an even reswelling of the entire IPG strip along the pH 3-10 interval is a washing step in 100 mM citric acid. It appears as though after rinsing off the excess acid in distilled water, a gradient of this tricarboxylic acid remains trapped into the IPG matrix, from almost nil at the acidic gel region to substantially higher amounts in its basic counterpart. This gradient helps in obtaining a uniform reswelling of the IPG strip, since carboxyl groups are more heavily hydrated than amino groups. The combined effects of uniform reswelling and of diluting the gel matrix favor penetration of large macromolecules (> 200 kDa) and allow for better spot resolution and for the display of a substantially higher number of spots also in the 30-60 000 Da region. A delipidation step in tri-n-butylphosphate:acetone:methanol (1:12:1) appears to substantially improve spot focusing and greatly diminish streaking and smearing of spots in all regions of the pH gradient.
Modeling and evaluation of human-to-robot mapping of grasps (2009)

Abstract — We study the problem of human to robot grasp mapping as a basic building block of a learning by imitation system. The human hand posture, including both the grasp type and hand orientation, is first classified based on a single image and mapped to a specific robot hand. A metric for the evaluation based on the notion of virtual fingers is proposed. The first part of the experimental evaluation, performed in simulation, shows how the differences in the embodiment between human and robotic hand affect the grasp strategy. The second part, performed with a robotic system, demonstrates the feasibility of the proposed methodology in realistic applications.
Fever‐Inspired Immunotherapy Based on Photothermal CpG Nanotherapeutics: The Critical Role of Mild Heat in Regulating Tumor Microenvironment (2018)

Although there have been more than 100 clinical trials, CpG-based immunotherapy has been seriously hindered by complications in the immunosuppressive microenvironment of established tumors. Inspired by the decisive role of fever upon systemic immunity, a photothermal CpG nanotherapeutics (PCN) method with the capability to induce an immunofavorable tumor microenvironment by casting a fever-relevant heat (43 °C) in the tumor region is developed. High-throughput gene profile analysis identifies nine differentially expressed genes that are closely immune-related upon mild heat, accompanied by IL-6 upregulation, a pyrogenic cytokine usually found during fever. When treated with intratumor PCN injection enabling mild heating in the tumor region, the 4T1 tumor-bearing mice exhibit significantly improved antitumor immune effects compared with the control group. Superb efficacy is evident from pronounced apoptotic cell death, activated innate immune cells, enhanced tumor perfusion, and intensified innate and adaptive immune responses. This work highlights the crucial role of mild heat in modulating the microenvironment in optimum for improved immunotherapy, by converting the tumor into an in situ vaccine.
Distinctive regions of 3D surfaces (2007)

Selecting the most important regions of a surface is useful for shape matching and a variety of applications in computer graphics and geometric modeling. While previous research has analyzed geometric properties of meshes in isolation, we select regions that distinguish a shape from objects of a different type. Our approach to analyzing distinctive regions is based on performing a shape-based search using each region as a query into a database. Distinctive regions of a surface have shape consistent with objects of the same type and different from objects of other types. We demonstrate the utility of detecting distinctive surface regions for shape matching and other graphics applications including mesh visualization, icon generation, and mesh simplification.
Equalization &amp; carrier recovery for 112Gbps optical coherent system with HEX-16-QAM modulation (2012)

We propose and demonstrate a new 112 Gbps Polarization division Multiplexing digital optical coherent systems with hexagonal 16-QAM (HEX-16-QAM) modulation. In our proposed system we use decision directed dispersion compensation algorithm which is Least Mean Square (LMS) algorithm and single tap decision directed carrier recovery algorithm. We compare the HEX-16-QAM systems with 16-QAM system for uncompensated transmission. Our analysis result found that HEX-16-QAM can achieve bit error rate (BER) of 1.5×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> whereas square 16-QAM BER is 5×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> for uncompensated 500-km transmission at 25 dB OSNR. Propose system achieve 0.3 dB OSNR penalty with compare to square 16-QAM system.