gebhart/patrepeval huggingface dataset:
Novel Phosphorylation and Ubiquitination Sites Regulate Reactive Oxygen Species-dependent Degradation of Anti-apoptotic c-FLIP Protein (2013)

The cytosolic protein c-FLIP (cellular Fas-associated death domain-like interleukin 1β-converting enzyme inhibitory protein) is an inhibitor of death receptor-mediated apoptosis that is up-regulated in a variety of cancers, contributing to apoptosis resistance. Several compounds found to restore sensitivity of cancer cells to TRAIL, a TNF family death ligand with promising therapeutic potential, act by targeting c-FLIP ubiquitination and degradation by the proteasome. The generation of reactive oxygen species (ROS) has been implicated in c-FLIP protein degradation. However, the mechanism by which ROS post-transcriptionally regulate c-FLIP protein levels is not well understood. We show here that treatment of prostate cancer PPC-1 cells with the superoxide generators menadione, paraquat, or buthionine sulfoximine down-regulates c-FLIP long (c-FLIP(L)) protein levels, which is prevented by the proteasome inhibitor MG132. Furthermore, pretreatment of PPC-1 cells with a ROS scavenger prevented ubiquitination and loss of c-FLIP(L) protein induced by menadione or paraquat. We identified lysine 167 as a novel ubiquitination site of c-FLIP(L) important for ROS-dependent degradation. We also identified threonine 166 as a novel phosphorylation site and demonstrate that Thr-166 phosphorylation is required for ROS-induced Lys-167 ubiquitination. The mutation of either Thr-166 or Lys-167 was sufficient to stabilize c-FLIP protein levels in PPC-1, HEK293T, and HeLa cancer cells treated with menadione or paraquat. Accordingly, expression of c-FLIP T166A or K167R mutants protected cells from ROS-mediated sensitization to TRAIL-induced cell death. Our findings reveal novel ROS-dependent post-translational modifications of the c-FLIP protein that regulate its stability, thus impacting sensitivity of cancer cells to TRAIL.
Selective Ethylene Production from CO2 and CO Reduction via Engineering Membrane Electrode Assembly with Porous Dendritic Copper Oxide (2022)

Gas-fed zero-gap electrolyzers have recently emerged as attractive systems for limiting ohmic losses and costs associated with electrolytes and for optimizing energy efficiencies. Here, we report that using a dendritic Cu oxide (D-CuO) material deposited on a gas diffusion layer as the cathode of a gas-fed zero-gap membrane electrode assembly (MEA) system results in a very selective conversion of CO to ethylene. More specifically, CO reduction yielded ethylene with an FE up to 68% at 100–125 mA·cm–2 with H2 as the only other gaseous product and the electrolysis could be carried out for several hours with good stability. Ethylene was also the major product during CO2 electrolysis (FE = 41%) at 125–150 mA·cm–2, reflecting the high selectivity of D-CuO for ethylene production. Such systems are relevant for tandem CO2 electroreduction processes, allowing energy efficiencies above 30%.
Trait association of genetic markers in the growth hormone and the growth hormone receptor gene in a White Leghorn strain (1997)

Alleles of the growth hormone (GH) gene and GH receptor (GHR) gene were analyzed for association with juvenile body weight (HBWT), age at first egg (AFE), the hen-day rate of egg production (HDR), egg specific gravity (SPG), and egg weight (EWT) in a strain of White Leghorns. The particular strain segregated at near equal frequencies for two GH alleles defined by differences at three restriction fragment length polymorphisms (RFLP) and for two GHR alleles defined by a single RFLP. The GH genotype was significantly associated with AFE (P < or = 0.04) as well as HDR from 274 to 385 d (P < or = 0.04) and 386 to 497 d (P < or = 0.0003). The GHR genotype (haploid in female chickens) had trends for association with HBW (P < or = 0.06) and HDR from AFE to 273 d (P < or = 0.07). The effects on the egg quality traits SPG and EWT were not significant. Regression analysis revealed that HDR was associated negatively with AFE and positively with HBWT. The slope of the regression line of HDR on AFE varied with the GH genotype, with the effect that the differences in HDR between GH genotypes was relatively small in chickens with early AFE and large in chickens with late AFE. Similarly, the slope of the regression of HDR on HBWT varied between GHR genotypes, with the result that the effect of the GHR genotype on HDR in chickens with low HBWT was opposite to its effect in chickens with high HBWT. The complex relationship between genotypes and traits may reflect gene interaction and indicates that simple models based on additive gene effects may not be adequate for the dissection of the genetic architecture of quantitative traits.
Swapping Variables for High-Dimensional Sparse Regression with Correlated Measurements (2013)

We consider the high-dimensional sparse linear regression problem of accurately estimating a sparse vector using a small number of linear measurements that are contaminated by noise. It is well known that the standard cadre of computationally tractable sparse regression algorithms---such as the Lasso, Orthogonal Matching Pursuit (OMP), and their extensions---perform poorly when the measurement matrix contains highly correlated columns. To address this shortcoming, we develop a simple greedy algorithm, called SWAP, that iteratively swaps variables until convergence. SWAP is surprisingly effective in handling measurement matrices with high correlations. In fact, we prove that SWAP outputs the true support, the locations of the non-zero entries in the sparse vector, under a relatively mild condition on the measurement matrix. Furthermore, we show that SWAP can be used to boost the performance of any sparse regression algorithm. We empirically demonstrate the advantages of SWAP by comparing it with several state-of-the-art sparse regression algorithms.
Utility distributed reactive power control using correlation techniques (2002)

The increase in the use of power electronic devices and the advent of dispersed generation in today's utility systems make power factor correction and reactive power control in general increasingly desirable. This paper introduces correlation techniques that are shown to be valuable with regard to power factor correction. The correlation control method requires no explicit parameter knowledge and only makes use of terminal voltage and current measurements. This control method is applied to the resonant converter, static VAr compensator and the power buffer with reactive control.
Control of Electric Motor Systems Considering Input/Output Saturation (2009)

Input saturation is a well-known nonlinearity in mechanical control systems; it constrains the maximum acceleration, which results in a limitation of the system response time. Input saturation has been considered in controller design in various ways, e.g., anti-windup control. In addition to the input, the state variables of mechanical systems are often subject to saturation. For example, the maximum angular velocity of electric motor systems is limited by the maximum voltage provided for the motor. In the case of electronically commutated motors (i.e. brushless DC motors) the maximum speed is additionally constrained by limitations of the servo amplifier output. If gears are utilized, further constraints are introduced due to resonances in ball bearings and/or velocity dependent friction. Although such factors are significant in practice, they have not been fully considered in controller design. This paper investigates the input and output saturations and presents how they may be considered in the controller design; a Kalman filter, a PID controller, and a disturbance observer are designed in view of input/output saturations. A case study is provided to verify the proposed methods.
Topological Distribution of Survivors in an Evolving Cellular Structure (1994)

Time-dependent correlations in the scaling state of an evolving two-dimensional soap froth are studied. In particular, we consider the topological distribution function of those cells that are destined to survive for long times. Experimental results are compared with mean-field based dynamic equations and with topological simulations.
Tunability of Subradiant Dipolar and Fano-Type Plasmon Resonances in Metallic Ring/Disk Cavities: Implications for Nanoscale Optical Sensing (2009)

Plasmonic nanocavities consisting of the concentric arrangement of a disk and a ring sustain both subradiant and superradiant dipolar plasmon modes with large associated field enhancements and high refractive index sensitivities. In structures with broken symmetry, additionally a highly tunable Fano interference feature appears, which can be explained with a simple analytical harmonic oscillator model. The spectral tunability of these resonances from the visible to the mid-infrared is investigated, highlighting a potential for applications in surface enhanced spectroscopies.
Pulse Strengthened and Laser Edge Sealed Vacuum Insulation Glazing (2022)

A scalable, low-cost processing strategy for glass strengthening and sealing is proposed to improve the thermal performance of insulating glass units and develop innovative window technologies. In this project, a combination of large area photonic processing, additive manufacturing, and laser encapsulation techniques is reported to realize a vacuum glazing technology to meet the cost, performance, reliability, and throughput demands. A modeling framework for evaluating the mechanical and thermal response was established to verify the structural deformation and thermal conductance. Micro-size glass frits in printing ink and a continuous-wave laser curing were employed to allow the formation of a hermetic bonding layer and led to improvement of glass edge sealing. Various sealing parameters, including laser traveling speed, spot diameter, and laser power were optimized. The water seepage and mechanical strength of the resulting glass-to-glass bonding were examined as well. These results showcase the development of a practical vacuum insulating glazing with several unique features through a combination of photonic processing, laser encapsulation, and additive manufacturing.
Novel inhibitors of the methicillin-resistant Staphylococcus aureus (MRSA)-pyruvate kinase (2015)

Novel bisindolyl-cycloalkane indoles resulted from the reaction of aliphatic dialdehydes and indole. As bisindolyl-natural alkaloid compounds have recently been reported as inhibitors of the methicillin-resistant Staphylococcus aureus (MRSA)-pyruvate kinase (PK), we tested our novel compounds as MRSA PK inhibitors and now report first inhibiting activities. We discuss structure-activity relationships of structurally varied compounds. Activity influencing substituents have been characterized and relations to antibacterial activities of the most active compounds have been proved.
Freeform optics design (2021)

The higher flexibility of freeforms has opened the possibility to find better solutions than classical surfaces many optical problems, especially those whose specifications (either optical or geometrical) are far from rotational symmetry. For instance, short through distance multimedia projectors cannot be placed in front of the center of the projected image without blocking the spectators’ view, and this requires the projection to be done from one side. Offset rotational symmetric solutions are suboptimal, and a freeform projector can improve the image quality on the target area with the same number of surfaces or can match the quality with fewer optical surfaces 1. Similarly, many head-worn displays are located close to the eyes of the user to make the headset sleeker. In this case, some parts of the physical display are used at very high emitting angles and rotational symmetric cannot provide optimal solutions for this configuration. In nonimaging applications, low-beam headlamps of cars also need to produce an asymmetric pattern on the road to avoid blinding the incoming drivers. Freeforms permit to solve this design problem efficiently, and match aesthetic constraints. The continuous progress in the technology to produce and test freeforms, as occurred in the past with rotational aspherics, is pushing optical designers to consider more and more the use of freeforms in their designs. However, the also higher complexity of these surfaces introduces multiple challenges in their design since traditional design methods have been focused in rotational optics. These challenges go from finding the best mathematical description of the optical surfaces to the design algorithms themselves. We’ll review the main design techniques proposed to design freeforms and illustrating its use in specific examples for several applications.
A multivariate analysis of the relationship between response and survival among patients with higher-risk myelodysplastic syndromes treated within azacitidine or conventional care regimens in the randomized AZA-001 trial (2013)

EVALUATION OF PROGNOSTIC MARKERS FOR SURVIVAL IN MDS PATIENTS TREATED WITH AZACITIDINE
Applicability of generic naming services and fault-tolerant metacomputing with FT-MPI (2005)

There is a growing interest in deploying MPI over multiple, heterogenous and geographically distributed resources for performing very large scale computations. However, increasing the amount of geographical distribution and resources creates problems with interoperability and fault-tolerance. FT-MPI presents an interesting solution for adding fault-tolerance to MPI, but suffers from interoperability limitations and potential single points of failure when crossing multiple administrative domains. We propose to overcome these limitations by adding “pluggability” for one potential single point of failure – the name service used by FT-MPI – and combining FT-MPI with the H2O metacomputing framework.
Clinical Judgment Is Paramount When Performing Cognitive Screening during COVID ‐19 (2020)

This letter comments on the letter by Rudi Coetzer
Theoretical Study of Magnesium and Zinc Tantalates and Niobates as Prospective Catalyst Supports for Water Electrolysis (2012)

There is considerable demand for identification of non noble metal based catalysts and catalyst supports for water electrolysis.Theoretical approaches provide an ideal framework for identifying such systems.In an attempt to identify new electrochemically stable catalyst supports for electrolysis of water, the electronic structures of MgNb 2 O 6 , MgTa 2 O 6 , ZnNb 2 O 6 , and ZnTa 2 O 6 compounds doped with elements from 3A, 3B, 5B, 6A groups of the Periodic table as well as F from group VII have been calculated using the Vienna ab-initio simulation package (VASP), within the projector augmented-wave (PAW) method in the general gradient approximation (GGA) for conducting the exchange-correlation corrections.The role of incorporating the additional elements in improving the electronic conductivity as well as the structural and chemical stability is discussed.Based on the calculated values of the cohesive energies for the materials and their type of electronic conductivity, we hypothesize that introduction of group 3A elements (Sc and Y) as well as F contribute drastically to the improvement of the electronic properties including the chemical stability of all four Mg and Zn tantalates/niobates based parent oxides.Results indicate that these doped compounds might serve as candidate catalyst supports proton exchange membrane (PEM) based water electrolysis.
Cell death detection and ionic homeostasis monitoring with digital holographic microscopy (2011)

Digital holographic microscopy is an interferometric technique enabling the measurement of the quantitative phase shifts induced by cell bodies. We correlate the phase signal measured on neurons with calcium imaging measured by fluorescence on cells loaded with Fluo-4, to monitor responses to glutamate challenges, which provoke well-known calcium increases through activation of various membrane receptors. A very good correspondence can be identified between the two signals, showing the links between the phase signal, being a measure of the intracellular dilution, and the calcium concentration within cells. We then check cell viability by employing propidium iodide (PI), a fluorescent indicator relying on the cell membrane integrity loss to assess cell death. Strong intracellular calcium concentration is indeed known to induce excitotoxic effects, potentially inducing cell death. This enables showing that some cells cannot sustain the calcium saturation identified in our measurements, leading to subsequent cell death.
Conversion to aflibercept for diabetic&nbsp;macular edema unresponsive to ranibizumab or bevacizumab (2015)

Eyes with DME unresponsive to multiple ranibizumab/bevacizumab injections demonstrate anatomical and visual improvement on conversion to aflibercept.
A Combination of MEF3 and NFI Proteins Activates Transcription in a Subset of Fast-Twitch Muscles (1997)

The human aldolase A pM promoter is active in fast-twitch muscles. To understand the role of the different transcription factors which bind to this promoter and determine which ones are responsible for its restricted pattern of expression, we analyzed several transgenic lines harboring different combinations of pM regulatory elements. We show that muscle-specific expression can be achieved without any binding sites for the myogenic factors MyoD and MEF2 and that a 64-bp fragment comprising a MEF3 motif and an NFI binding site is sufficient to drive reporter gene expression in some but, interestingly, not all fast-twitch muscles. A result related to this pattern of expression is that some isoforms of NFI proteins accumulate differentially in fast- and slow-twitch muscles and in distinct fast-twitch muscles. We propose that these isoforms of NFI proteins might provide a molecular basis for skeletal muscle diversity.
Single freeze per vein strategy with the second-generation cryoballoon for atrial fibrillation: a propensity score-matched study between 180- and 240-s application time in a large cohort of patients (2017)

There is no difference in acute success, rate of complications, and freedom from atrial fibrillation recurrences during the follow-up between 3-min and 4-min per vein freeze strategies. The procedural and fluoroscopy times were significantly shorter in 3-min per vein strategy.
Microscopy-Based Automated Live Cell Screening for Small Molecules That Affect Ciliation (2019)

The primary monocilium, or cilium, is a single antenna-like organelle that protrudes from the surface of most mammalian cell types, and serves as a signaling hub. Mutations of cilia-associated genes result in severe genetic disorders termed ciliopathies. Among these, the most common is autosomal dominant polycystic kidney disease (ADPKD); less common genetic diseases include Bardet-Biedl Syndrome, Joubert Syndrome, nephronophthisis, and others. Important signaling cascades with receptor systems localized exclusively or in part at cilia include Sonic Hedgehog (SHH), platelet derived growth factor alpha (PDGF), WNTs, polycystins, and others. Changes in ciliation during development or in pathological conditions such as cancer impacts signaling by these proteins. Notably, ciliation status of cells is coupled closely to the cell cycle, with cilia protruding in quiescent (G0) or early G1 cells, declining in S/G2, and absent in M phase, and has been proposed to contribute to cell cycle regulation. Because of this complex biology, the elaborate machinery regulating ciliary assembly and disassembly receives input from many cellular proteins relevant to cell cycle control, development, and oncogenic transformation, making study of genetic factors and drugs influencing ciliation of high interest One of the most effective tools to investigate the dynamics of the cilia under different conditions is the imaging of live cells. However, developing assays to observe the primary cilium in real-time can be challenging, and requires a consideration of multiple details related to the cilia biology. With the dual goals of identifying small molecules that may have beneficial activity through action on human diseases, and of identifying ciliary activities of existing agents that are in common use or development, we here describe creation and evaluation of three autofluorescent cell lines derived from the immortalized retinal pigmented epithelium parental cell line hTERT-RPE1. These cell lines stably express the ciliary-targeted fluorescent proteins L13-Arl13bGFP, pEGFP-mSmo, and tdTomatoMCHR1-N-10. We then describe methods for use of these cell lines in high throughput screening of libraries of small molecule compounds to identify positive and negative regulators of ciliary disassembly.
Non-Invasive Fluorescent Monitoring of Ovarian Cancer in an Immunocompetent Mouse Model (2018)

Ovarian cancers (OCs) are the most lethal gynaecological malignancy, with high levels of relapse and acquired chemo-resistance. Whilst the tumour⁻immune nexus controls both cancer progression and regression, the lack of an appropriate system to accurately model tumour stage and immune status has hampered the validation of clinically relevant immunotherapies and therapeutic vaccines to date. To address this need, we stably integrated the near-infrared phytochrome iRFP720 at the <i>ROSA26</i> genomic locus of ID8 mouse OC cells. Intrabursal ovarian implantation into C57BL/6 mice, followed by regular, non-invasive fluorescence imaging, permitted the direct visualization of tumour mass and distribution over the course of progression. Four distinct phases of tumour growth and dissemination were detectable over time that closely mimicked clinical OC progression. Progression-related changes in immune cells also paralleled typical immune profiles observed in human OCs. Specifically, we observed changes in both the CD8+ T cell effector (Teff):regulatory (Treg) ratio, as well as the dendritic cell (DC)-to-myeloid derived suppressor cell (MDSC) ratio over time across multiple immune cell compartments and in peritoneal ascites. Importantly, iRFP720 expression had no detectible influence over immune profiles. This new model permits non-invasive, longitudinal tumour monitoring whilst preserving host⁻tumour immune interactions, and allows for the pre-clinical assessment of immune profiles throughout disease progression as well as the direct visualization of therapeutic responses. This simple fluorescence-based approach provides a useful new tool for the validation of novel immuno-therapeutics against OC.