gebhart/patrepeval huggingface dataset:
Electrorotation and dielectrophoresis (1999)

Using microelectrode structures, various forms of electric fields, such as non-uniform, rotating and travelling wave, can be imposed on particles of sizes ranging from proteins and viruses to micro-organisms and cells. Each type of particle responds to the forces exerted on them in a unique way, allowing for their controlled and selective manipulation as well as their characterization. Moreover, particles of the same type but of different viability can be distinguished in a simple, reliable manner. This review outlines the principles that govern the way in which bioparticles respond to these various field types, and how they can be exploited. Examples of current and potential biotechnological and biomedical applications are given, along with a critical comparison of current techniques.
Protecting groups (1998)

K. Jarowicki and P. Kocienski, J. Chem. Soc., Perkin Trans. 1, 1998, 4005 DOI: 10.1039/A803688H
Phosphatidylserine (PS) induces PS receptor–mediated macropinocytosis and promotes clearance of apoptotic cells (2001)

Efficient phagocytosis of apoptotic cells is important for normal tissue development, homeostasis, and the resolution of inflammation. Although many receptors have been implicated in the clearance of apoptotic cells, the roles of these receptors in the engulfment process have not been well defined. We developed a novel system to distinguish between receptors involved in tethering of apoptotic cells versus those inducing their uptake. Our results suggest that regardless of the receptors engaged on the phagocyte, ingestion does not occur in the absence of phosphatidylserine (PS). Further, recognition of PS was found to be dependent on the presence of the PS receptor (PSR). Both PS and anti-PSR antibodies stimulated membrane ruffling, vesicle formation, and "bystander" uptake of cells bound to the surface of the phagocyte. We propose that the phagocytosis of apoptotic cells requires two events: tethering followed by PS-stimulated, PSR-mediated macropinocytosis.
Radio-Wave Propagation and Electromagnetic Surface Waves (1947)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Generation and confinement of microwave gas-plasma in photonic dielectric microstructure (2013)

We report on a self-guided microwave surface-wave induced generation of ~60 μm diameter and 6 cm-long column of argon-plasma confined in the core of a hollow-core photonic crystal fiber. At gas pressure of 1 mbar, the micro-confined plasma exhibits a stable transverse profile with a maximum gas-temperature as high as 1300 ± 200 K, and a wall-temperature as low as 500 K, and an electron density level of 10¹⁴ cm⁻³. The fiber guided fluorescence emission presents strong Ar⁺ spectral lines in the visible and near UV. Theory shows that the observed combination of relatively low wall-temperature and high ionisation rate in this strongly confined configuration is due to an unprecedentedly wide electrostatic space-charge field and the subsequent ion acceleration dominance in the plasma-to-gas power transfer.
Ligation of Prostate Cancer Cell Surface GRP78 Activates a Proproliferative and Antiapoptotic Feedback Loop (2010)

GRP78, a well characterized chaperone in the endoplasmic reticulum, is critical to the unfolded protein response. More recently, it has been identified on the cell surface, where it has many roles. On cancer cells, it functions as a signaling receptor coupled to proproliferative/antiapoptotic and promigratory mechanisms. In the current study, we demonstrate that ligation of prostate cancer cell surface GRP78 by its natural ligand, activated α(2)-macroglobulin (α(2)M*), results in a 2-3-fold up-regulation in the synthesis of prostate-specific antigen (PSA). The PSA is secreted into the medium as an active proteinase, where it binds to native α(2)M. The resultant α(2)M·PSA complexes bind to GRP78, causing a 1.5-2-fold increase in the activation of MEK1/2, ERK1/2, S6K, and Akt, which is coupled with a 2-3-fold increase in DNA and protein synthesis. PSA is a marker for the progression of prostate cancer, but its mechanistic role in the disease is unclear. The present studies suggest that PSA may be involved in a signal transduction-dependent feedback loop, whereby it promotes a more aggressive behavior by human prostate cancer cells.
Deferred Neural Rendering: Image Synthesis using Neural Textures (2019)

The modern computer graphics pipeline can synthesize images at remarkable visual quality; however, it requires well-defined, high-quality 3D content as input. In this work, we explore the use of imperfect 3D content, for instance, obtained from photo-metric reconstructions with noisy and incomplete surface geometry, while still aiming to produce photo-realistic (re-)renderings. To address this challenging problem, we introduce Deferred Neural Rendering, a new paradigm for image synthesis that combines the traditional graphics pipeline with learnable components. Specifically, we propose Neural Textures, which are learned feature maps that are trained as part of the scene capture process. Similar to traditional textures, neural textures are stored as maps on top of 3D mesh proxies; however, the high-dimensional feature maps contain significantly more information, which can be interpreted by our new deferred neural rendering pipeline. Both neural textures and deferred neural renderer are trained end-to-end, enabling us to synthesize photo-realistic images even when the original 3D content was imperfect. In contrast to traditional, black-box 2D generative neural networks, our 3D representation gives us explicit control over the generated output, and allows for a wide range of application domains. For instance, we can synthesize temporally-consistent video re-renderings of recorded 3D scenes as our representation is inherently embedded in 3D space. This way, neural textures can be utilized to coherently re-render or manipulate existing video content in both static and dynamic environments at real-time rates. We show the effectiveness of our approach in several experiments on novel view synthesis, scene editing, and facial reenactment, and compare to state-of-the-art approaches that leverage the standard graphics pipeline as well as conventional generative neural networks.
Complete lack of NF-κB activity in IKK1 and IKK2 double-deficient mice: additional defect in neurulation (2000)

NF-kappaB activity is induced by cytokines, stress, and pathogens. IKK1 and IKK2 are critical IkappaB kinases in NF-kappaB activation. In this study mice lacking IKK1 and IKK2 died at E12. Additional defect in neurulation associated with enhanced apoptosis in the neuroepithelium was also observed. MEF cells from IKK1(-/-)/IKK2(-/-) embryos did not respond to NF-kappaB inducers. Upon crossing with kappaB-lacZ transgenic mice, double-deficient embryos also lost lacZ transgene expression in vascular endothelial cells during development. Our data suggest that IKK1 and IKK2 are essential for NF-kappaB activation in vivo and have an important role in protecting neurons against excessive apoptosis during development.
Investigation on Nonwovens Leukocyte Filtering Materials Treated with Amine and Alkali Solution (2002)

Filtering materials are chosen according to the mechanism of blood filtration and mathematics model,then the material is treated with amine and alkail solution. There is cooperation and synergism between alkaliand amine, and the actions are realized in three stages. After modification the material treated has accessibilitygroups-NH2, and slits appeared in the surface of fiber, so the wettability of materials is improved distinctly; the diameter and aperture of fiber have no changes basically.
P-cadherin role in normal breast development and cancer (2011)

P-cadherin is a cell-cell adhesion molecule, whose expression is highly associated with undifferentiated cells in normal adult epithelial tissues, as well as with poorly differentiated carcinomas. Its expression has been already reported in human embryonic stem cells and it is presumed to be a marker of stem or progenitor cells of some epithelial tissues. In normal breast, P-cadherin has an essential role during ductal mammary branching, being expressed by the monolayer of epithelial cap cells at the end buds. In mature mammary tissue, its expression is restricted to the myoepithelium; it has been postulated that it may also be present in early luminal progenitor cells. In breast cancer, P-cadherin is frequently overexpressed in high-grade tumours, being a well-established indicator of poor patient prognosis. It has been reported as an important inducer of cancer cell migration and invasion, with underlying molecular mechanisms involving the signalling mediated by its juxtamembrane domain, the secretion of matrix metalloproteases to the extracellular media, and the cleavage of a P-cadherin soluble form with pro-invasive activity. Intracellularly, this protein interferes with the endogenous cadherin/catenin complex, inducing p120-catenin delocalization to the cytoplasm, and the consequent activation of Rac1/Cdc42 and associated alterations in the actin cytoskeleton. Considering P-cadherin's role in cancer cell invasion and metastasis formation, a humanized monoclonal antibody was recently produced to antagonize P-cadherin-associated signalling pathways, which is currently under Phase I clinical trials. In this review, the most important findings about the role of P-cadherin in normal breast development and cancer will be illustrated and discussed, with emphasis on the most recent data.
The Jak2V617F Oncogene Associated with Polycythemia Vera Regulates G1/S-Phase Transition. (2005)

Abstract The V617F activating point mutation in Jak2 has recently been detected in a high proportion of patients with the myeloproliferative disorders polycythemia vera, essential thrombocythemia, and idiopathic myelofibrosis. Using the Jak2V617F-mutant erythroid leukemia cell line HEL as a model, potential mechanisms that contribute to transformation were investigated. Inhibition of Jak2V617F with a small molecule kinase inhibitor reduced cell growth of HEL cells in a dose dependent manner with an IC50 of 300 nM. This inhibition of growth was associated with a G1 cell cycle arrest, with minimal or delayed apoptosis. The major Jak2 target in normal hematopoietic cells, STAT5, was found to be activated by Jak2V617F. Treatment of the cells with either a Jak2 kinase inhibitor, or with a Jak2-targeted siRNA, decreased STAT5 activation, and also resulted in decreased expression of cyclin D2 and increased expression of p27Kip. Of interest, we found that Jak2V617F induced high levels of reactive oxygen species (ROS), an activity associated with several other tyrosine kinase oncogenes. Expression of a constitutively active form of STAT5 by itself was capable reducing expression of p27Kip and increasing production of ROS, suggesting that each of these signaling events are downstream of STAT5. Additionally, treatment of HEL cells with the anti-oxidant N-acetylcystein increased expression of p27Kip, suggesting that Jak2V617F regulates cell cycle progression at least in part through STAT5 activation of ROS, and ROS regulation of p27Kip. Cell growth of HEL cells was found to be blocked by anti-oxidants. Overall, our results suggest that constitutive activation of Jak2 contributes to a transforming phenotype and therefore hints at novel targets for drug development that may aid traditional therapy.
Potassium‐potassium exchange as part of the over‐all reaction mechanism of the sodium pump of the human red blood cell. (1986)

When the efflux components of the Na-K exchange and K-K exchange are measured under identical conditions, the apparent K 1/2 (the concentration of K at which the velocity is half-maximal) for external K of the two processes differ. The discrepancy diminishes when the measurements are made in solutions containing low concentrations of Na, and in these solutions the uncoupled Na efflux is also partially suppressed. It is possible to demonstrate an uncoupled K efflux into solutions free of Na and K. This uncoupled efflux is also partially inhibited by low concentrations of external Na. At high enough concentrations, intracellular Na completely inhibits the K-K exchange. Inhibition of the K-K exchange by cell Na is competitive with cell K, and inhibition of the Na-K exchange by cell K is competitive with cell Na. In each case the characteristics of the competition suggest that both ions competitively interact with sites on the same enzyme form. The Albers-Post model of the Na-K pump reaction mechanism, modified to account for the uncoupled Na and K efflux, accounts in detail for these observations. If the K-K exchange is part of the over-all Na-K exchange, as indicated by the findings, pump models in which Na must add to the pump at the inside before K is released are excluded.
L-.alpha.-glycerophosphate and L-lactate electrodes based on the electrochemical "wiring" of oxidases (1992)

The title electrodes were constructed by coimmobilizing the respective FAD oxidases on solid electrode surfaces with a poly(vinyl pyridine) polymer which was N-derivatized with bromoethylamine and Os(bpy)2Cl2. The redox-polymer-enzyme hydrogels were cross-linked on the electrode surface using poly(ethylene glycol) diglycidyl ether. As in the case of glucose oxidase, the redox polymer acts as an electron relaying "wire" transferring electrons directly from the enzymes' FADH2 centers to the electrode. This transfer competes with the natural process of reoxidation of FADH2 by molecular oxygen. The variation of the response of these electrodes with the atmosphere (N2 or air), pH, and substrate concentration was determined. The pH profile of the electrocatalytic current differs from that of the activity of the free enzymes, exhibiting a broader maximum, shifted to higher pH values. The observed sensitivities and linear ranges are respectively 2 x 10(-2) A M-1 cm-2 and 2.7 mM for L-alpha-glycerophosphate, and 0.3 A M-1 cm-2 and 0.2 mM for L-lactate that may be compared to 2 x 10(-2) A M-1 cm-2 and 10 mM for glucose. The 0-90% response time for all electrodes is 1 s or less.
New Cutter Technology for Faster Drilling in Hard/Abrasive Formations (2010)

Abstract Drilling the hard, abrasive and interbedded Travis Peak and Cotton Valley formations in East Texas creates a difficult challenge for polycrystalline diamond compact (PDC) bits. Historically, conventional PDC cutting elements dulled quickly due to abrasive wear, impact damage and thermal fatigue. Thus, cutter technology has been the limiting factor for efficient PDC bit drilling in the East Texas Basin. Recent technological developments have produced a new, highly abrasion resistant cutter that has increased rate of penetration (ROP) and total footage drilled in addition to producing better dull grades. Further, the sections that normally require two/three PDC bits can now be drilled in one fast PDC bit run. The new cutter technology is designed and manufactured utilizing an innovative process which delivers superior properties both in laboratory testing and field trials. The manufacturing process involves a two-step high pressure/high temperature (HPHT) technique. The first step is to make a polycrystalline diamond table (PCD) using conventional HPHT parameters. The second step is to re-attach the PCD synthetic diamond wafer on a new tungsten carbide (WC) substrate under extreme HPHT parameters. The advantages of this method compared to the conventional one-step process are as follows: The residual stress in the PCD table is reduced by the additional second processThe two-step HTHP process increases the microstructure strength of the PCD Laboratory tests have indicated the new type of PDC cutter has increased resistance to abrasive wear and thermal fatigue by approximately 100% over standard PDC cutters while not compromising impact resistance. Extensive field tests in the East Texas Basin have documented that drilling efficiency could be improved by 20% in the hard/abrasive application. The cutters are expected to have a positive economic impact on other hard/abrasive applications worldwide.
Bispectrum estimation: A digital signal processing framework (1987)

It is the purpose of this tutorial paper to place bispectrum estimation in a digital signal processing framework in order to aid engineers in grasping the utility of the available bispectrum estimation techniques, to discuss application problems that can directly benefit from the use of the bispectrum, and to motivate research in this area. Three general reasons are behind the use of bispectrum in signal processing and are addressed in the paper: to extract information due to deviations from normality, to estimate the phase of parametric signals, and to detect and characterize the properties of nonlinear mechanisms that generate time series.
Characterizing and engineering antibodies against the epidermal growth factor receptor (2007)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2008.
Reverse genetics studies on the filamentous morphology of influenza A virus (2003)

We have investigated the genetic determinants responsible for the filamentous morphology of influenza A viruses, a property characteristic of primary virus isolates. A plasmid-based reverse genetics system was used to transfer the M segment of influenza A/Udorn/72 (H3N2) virus into influenza A/WSN/33 (H1N1) virus. While WSN virions display spherical morphology, recombinant WSN-Mud virus acquired the ability of the parental Udorn strain to form filamentous virus particles. This was determined by immunofluorescence studies in infected MDCK cells and by electron microscopy of purified virus particles. To determine the gene product within the M segment responsible for filamentous virus morphology, we generated four recombinant viruses carrying different sets of M1 and M2 genes from WSN or Udorn strains in a WSN background. These studies revealed that the M1 gene of Udorn, independently of the origin of the M2 gene, conferred filamentous budding properties and filamentous virus morphology to the recombinant viruses. We also constructed two WSN viruses encoding chimeric M1 proteins containing the amino-terminal 1-162 amino acids or the carboxy-terminal 163-252 amino acids of the Udorn M1 protein. Neither of these two viruses acquired filamentous phenotypes, indicating that both amino- and carboxy-terminal domains of the M1 protein contribute to filamentous virus morphology. We next rescued seven mutant WSN-M1ud viruses containing Udorn M1 proteins carrying single amino acid substitutions corresponding to the seven amino acid differences with the M1 protein of WSN virus. Characterization of these recombinant viruses revealed that amino acid residues 95 and 204 are critical in determining filamentous virus particle formation.
American College of Chest Physicians/Society of Critical Care Medicine Consensus Conference (1992)

SCCM Pediatric Critical Care Medicine Critical Care Explorations SCCM Pediatric Critical Care Medicine Critical Care Explorations
SLC7A11 Overexpression in Glioblastoma Is Associated with Increased Cancer Stem Cell-Like Properties (2017)

System x<sub>c</sub><sup>-</sup> is a sodium-independent electroneutral transporter, comprising a catalytic subunit xCT (SLC7A11), which is involved in importing cystine. Certain cancers such as gliomas upregulate the expression of system x<sub>c</sub><sup>-</sup>, which confers a survival advantage against the detrimental effects of reactive oxygen species (ROS) by increasing generation of the antioxidant glutathione. However, ROS have also been shown to function as targeted, intracellular second messengers in an array of physiological processes such as proliferation. Several studies have implicated ROS in important cancer features such as migration, invasion, and contribution to a cancer stem cell (CSC)-like phenotype. The role of system x<sub>c</sub><sup>-</sup> in regulating these ROS-sensitive processes in glioblastoma multiforme (GBM), the most aggressive malignant primary brain tumor in adults, remains unknown. Stable SLC7A11 knockdown and overexpressing U251 glioma cells were generated and characterized to understand the role of redox and system x<sub>c</sub><sup>-</sup> in glioma progression. SLC7A11 knockdown resulted in higher endogenous ROS levels and enhanced invasive properties. On the contrary, overexpression of SLC7A11 resulted in decreased endogenous ROS levels as well as decreased migration and invasion. However, SLC7A11-overexpressing cells displayed actin cytoskeleton changes reminiscent of epithelial-like cells and exhibited an increased CSC-like phenotype. The enhanced CSC-like phenotype may contribute to increased chemoresistance and suggests that overexpression of SLC7A11 in the context of GBM may contribute to tumor progression. These findings have important implications for cancer management where targeting system x<sub>C</sub><sup>-</sup> in combination with other chemotherapeutics can reduce cancer resistance and recurrence and improve GBM patient survival.
Robust Uncertainty Principles: Exact Signal Reconstruction from Highly Incomplete Frequency Information (2004)

This paper considers the model problem of reconstructing an object from incomplete frequency samples. Consider a discrete-time signal $f \in \C^N$ and a randomly chosen set of frequencies $Ω$ of mean size $τN$. Is it possible to reconstruct $f$ from the partial knowledge of its Fourier coefficients on the set $Ω$? A typical result of this paper is as follows: for each $M &gt; 0$, suppose that $f$ obeys $$ # \{t, f(t) \neq 0 \} \le α(M) \cdot (\log N)^{-1} \cdot # Ω, $$ then with probability at least $1-O(N^{-M})$, $f$ can be reconstructed exactly as the solution to the $\ell_1$ minimization problem $$ \min_g \sum_{t = 0}^{N-1} |g(t)|, \quad \text{s.t.} \hat g(ω) = \hat f(ω) \text{for all} ω\in Ω. $$ In short, exact recovery may be obtained by solving a convex optimization problem. We give numerical values for $α$ which depends on the desired probability of success; except for the logarithmic factor, the condition on the size of the support is sharp. The methodology extends to a variety of other setups and higher dimensions. For example, we show how one can reconstruct a piecewise constant (one or two-dimensional) object from incomplete frequency samples--provided that the number of jumps (discontinuities) obeys the condition above--by minimizing other convex functionals such as the total-variation of $f$.
Characterisation of Epitopes on Human Tissue Plasminogen Activator Recognised by a Group of Monoclonal Antibodies (1985)

Seven mouse monoclonal antibodies have been produced against human melanoma tissue plasminogen activator (t-PA). They were specifically bound to 125I t-PA but not 125I urokinase (u-PA) and inhibited t-PA, but not u-PA, activity in plasminogen-rich 125I fibrin wells. Three of the antibodies directly inhibited the amidolytic activity of t-PA and the two most effective also bound near the active site histidine residue as determined by competition experiments using active site blocking agents. Several antibodies interfered with the fibrin binding properties of t-PA. One antibody neither interacted with the active site nor inhibited fibrin binding but still effectively quenched t-PA activity in fibrin wells suggesting that it masks another region of the molecule necessary for effective biological activity.