gebhart/patrepeval huggingface dataset:
Kinetic and Cross-Linking Studies on the Interactions of Negative Patch Mutant Plastocyanin from Silene pratensis with Photosystem I Complexes from Cyanobacteria, Green Algae, and Plants (1996)

The site-directed mutants of negative patches on silene plastocyanin (PC) were used to investigate the change of interactions between photosystem I (PSI) and PC during the course of evolution from cyanobacteria to plants. The net charges of two highly conserved negative patches (#42-45 and #59-61) on silene PC were systematically modified from -4 to +1. PSI complexes from cucumber and Chlamydomonas reinhardtii were efficient electron acceptors for silene PC. The increase of net charge on the negative patch (#42-45) of silene PC decreased the reduction rates of PSI from cucumber and Chlamydomonas, while the modification of the other negative patch (#59-61) had no effect. Though the addition of MgCl2 decreased the reduction rate of cucumber PSI, the decrease was severely diminished in the case of Chlamydomonas PSI, and the reduction rate increased with increasing concentration of MgCl2 when the net charge of the negative patch (#42-45) was modified to +1. The PSI complexes from Anabaena variabilis and Synechosystis sp. PCC 6803 were inefficient electron acceptors for silene PC and their rates were almost independent of the net charge of the negative patches, as well as the ionic strength of the reaction mixtures. Silene PC specifically cross-linked to the PsaF subunit of PSI complexes from cucumber, Chlamydomonas, Anabaena, and Synechosystis sp. PCC 6803. Modification of the negative patch (#42-45) inhibited the formation of cross-linked adducts in all the cases examined, whereas modification of the other negative patch (#59-61) had essentially no effect. Based on these results, the changes of electrostatic interactions between PC and PSI during the course of evolution from cyanobacteria to plants are discussed.
Single cell analysis of population-wide nuclear and cytosolic drug responses using high-content FRET imaging: measuring protein kinase activation in rat primary striatal neurons (2021)

Abstract Genetically-encoded biosensors are used to track biochemical activities in living cells by measuring changes in fluorescence emitted by one or more fluorescent proteins. In the present article, we describe the application of genetically-encoded FRET biosensors with high content microscopy to image the signaling responses of thousands of neurons in response to drug treatments. We applied this approach to reveal intercellular variation in signaling responses among cultured striatal neurons stimulated with multiple drugs. The striatum is largely composed of medium-spiny GABAergic neurons which are divided into two broad sub-types based in part on their expression of dopamine D1 vs. D2 receptors. Using high content FRET imaging and immunofluorescence, we identified neuronal sub-populations with unique responses to pharmacological manipulation. Focusing on dopamine- and glutamate-regulated PKA and ERK1/2 signaling in both the cytoplasm and nucleus, we identified pronounced intercellular differences, in both the magnitude and kinetics of signaling responses to drug application. Importantly, we found that a conventional “bulk” analysis that included all cells in culture yielded a different rank order of drug potency than that revealed by our single-cell analysis. The high degree of heterogeneity that we observed at the single cell level would not have been detectable using common population-level analyses, derived for example from western blotting or plate reader-based measurements. In conclusion, our single-cell analytical approach highlights the limitations of population-level analyses, and provides a novel way to study signaling biology.
Syntheses of 24,25-dihydroxyvitamin D2, 24,25-dihydroxy-22-dehydrovitamin D3, 25-hydroxy-24-oxo-22-dehydrovitamin D3 and 22,24,25-trihydroxyvitamin D3. (1987)

Four vitamin D2 and D3 metabolites, 24, 25-dihydroxyvitamin D2 (8), 24, 25-dihydroxy-22-dehydrovitamin D3 (10). 25-hydroxy-24-oxo-22-dehydrovitamin D3 (12) and 22, 24, 25-trihydroxy-vitamin D3 (14), were synthesized from ergosterol (1) via the hydroxyketone (4) as a common key intermediate.
Kindlin-2 Inhibits the Hippo Signaling Pathway by Promoting Degradation of MOB1 (2019)

The Hippo signaling pathway plays a key role in development and cancer progression. However, molecules that intrinsically inhibit this pathway are less well known. Here, we report that the focal adhesion molecule Kindlin-2 inhibits Hippo signaling by interacting with and degrading MOB1 and promoting the interaction between MOB1 and the E3 ligase praja2. Kindlin-2 thus inhibits the phosphorylation of LATS1 and YAP and promotes YAP translocation into the nucleus, where it activates downstream Hippo target gene transcription. Kindlin-2 depletion activates Hippo/YAP signaling and alleviates renal fibrosis in Kindlin-2 knockout mice with unilateral ureteral occlusion (UUO). Moreover, Kindlin-2 levels are negatively correlated with MOB1 and phosphorylated (p) YAP in samples from patients with renal fibrosis. Altogether, these results demonstrate that Kindlin-2 inhibits Hippo signaling through degradation of MOB1. A specific long-lasting siRNA against Kindlin-2 effectively alleviated UUO-induced renal fibrosis and could be a potential therapy for renal fibrosis.
Mechanical properties of CN x coatings obtained by carbon arc sputtering (2007)

Internal stresses σ0, friction coefficients fand microhardness were measured in diamond-like coatings obtained by vacuum-arc sputtering of carbon target at different nitrogen pressures in a work chamber during deposition on metallic substrates. The dependence of these parameters on nitrogen concentration in coatings can be used in practical deposition of strengthening and friction coatings for improvement of their tribological properties. The correlation between mechanical properties of diamond-like and CN x coatings was established.
Vibration-based structural health monitoring using large sensor networks (2010)

Recent advances in hardware and instrumentation technology have allowed the possibility of deploying very large sensor arrays on structures. Exploiting the huge amount of data that can result in order to perform vibration-based structural health monitoring (SHM) is not a trivial task and requires research into a number of specific problems. In terms of pressing problems of interest, this paper discusses: the design and optimisation of appropriate sensor networks, efficient data reduction techniques, efficient and automated feature extraction methods, reliable methods to deal with environmental and operational variability, efficient training of machine learning techniques and multi-scale approaches for dealing with very local damage. The paper is a result of the ESF-S3T Eurocores project "Smart Sensing For Structural Health Monitoring" (S3HM) in which a consortium of academic partners from across Europe are attempting to address issues in the design of automated vibration-based SHM systems for structures.
Liquid movements in ventilated and perfused isolated lungs of fetal sheep at 0.87, 0.90, and 0.95 of term (1995)

To study lung liquid movements, an isolated lung model, adapted from adult physiology, was developed to measure pulmonary weight changes after the onset of artificial ventilation of lungs from 16 fetal sheep at 0.87 (n = 5), 0.90 (n = 6), and 0.95 (n = 5) of gestation. The fetuses were delivered by Caesarean section. After tracheotomy and thoracotomy under general anaesthesia, a blocked air-free tracheal cannula and a pulmonary arterial catheter were inserted and secured to ensure in situ perfusion of the pulmonary circulation (Krebs-Henseleit buffer) without ventilation before the lungs were removed from the chest and mounted in a specially designed apparatus. Lung weight and pulmonary perfusion pressure were recorded continuously before, during and after the onset of ventilation. After 50 min of ventilation the perfusate was allowed to recirculate and samples were taken at 10-min intervals to determine the concentrations of sodium and the activity of lactate dehydrogenase (LDH) as a marker for cell destruction. In all lungs studied there was a significant removal of lung liquid after the onset of ventilation as assessed by lung weight loss. However, there was a positive correlation between lung weight loss and gestational age of the donor fetuses. These changes were accompanied by a rise in sodium concentrations in the perfusate, possibly suggesting that active sodium transport across the pulmonary epithelium facilitates alveolar liquid removal. As the experiments progressed the lungs regained weight while LDH concentrations increased, indicating that lung cell destruction causing pulmonary oedema may be involved. This pulmonary weight gain was inversely related to gestational age. It is concluded that in isolated ventilated and perfused lungs from fetal sheep, lung liquid removal is an age-related phenomenon that might involve an active sodium transport mechanism. It is further concluded that the development of pulmonary oedema during ventilation is also age related.
Experimental Colonic Obstruction Increases Collagen Degradation by Matrix Metalloproteinases in the Bowel Wall (2003)

Colonic obstruction and trauma up-regulated matrix metalloproteinases and decreased collagen concentration in colonic wall.
Operations, Administration and Maintenance (OAM) Requirements for Bit Index Explicit Replication (BIER) Layer (1999)

This document describes a list of functional requirement toward
Operations, Administration and Maintenance (OAM) toolset in Bit Index
Explicit Replication (BIER) layer of a network.
Cardiac Submembrane [Na + ] Transients Sensed by Na + -Ca 2+ Exchange Current (2003)

Na+ influx via INa during cardiac action potentials can raise bulk [Na+]i by 10 to 15 micromol/L. However, larger rises in submembrane [Na+] ([Na+]sm) local to Na+-Ca2+ exchangers (NCX) could enhance Ca2+ influx via NCX (and Ca2+-induced Ca2+ release). We tested whether INa could increase [Na+]sm, using NCX current (INCX) as a biosensor in rabbit ventricular myocytes (with [Ca2+]i buffered, [Na+]i=10 mmol/L, and other currents blocked). We measured INCX as early as 5 ms after INa. Prior INa activation did not affect INCX at physiological membrane potentials (Em=-100 to +50 mV), but for Em >+50 mV (where INCX is especially sensitive to [Na+]i), INCX shifted outward. At 5 ms and +100 mV, INa shifted INCX outward by 0.23 A/F (corresponding to Delta[Na+]sm=0.24 mmol/L). The effect of INa dissipated with a time constant of approximately 15 ms. Thus, the impact of INa on NCX is almost undetectable at physiological Em and short lived. This suggests that INa effects on excitation-contraction coupling (via outward INCX) are minimal and limited to early during the action potential. However, local Delta[Na+]sm during INa may be 60 times higher than bulk Delta[Na+]i.
Uncatalyzed Click Reaction between Phenyl Azides and Acrolein: 4-Formyl-1,2,3-Triazolines as “Clicked” Markers for Visualizations of Extracellular Acrolein Released from Oxidatively Stressed Cells (2016)

Acrolein, a highly toxic α,β-unsaturated aldehyde, has been a longstanding key biomarker associated with a range of disorders related to oxidative stresses. Currently available analytical methods rely on the indirect protocols, e.g., derivatization/HPLC or mAb detection of the lysine adducts. Consequently, developing new analytical tools for acrolein detection that are straightforward, cost-effective, selective, and preferably feasible using live cells remains a highly essential pursuit in the diagnosis and therapeutic treatment of oxidative stress-related diseases. We demonstrated that for the first time aryl azides can rapidly and selectively react with acrolein in a “click” manner to provide 4-formyl-1,2,3-triazolines and 4-formyl-1,2,3-triazoles, which represents an unexplored reactivity of aryl azides. When treating a fluorescently labeled phenyl azide with oxidatively stressed or smoking-associated cell models, these heterocyclic compounds could be selectively taken up by the cells and preferably localized at the endoplasmic reticulum (ER) and lysosome, leading to a new tool for both effectively detecting acrolein level and directly imaging live cells that are under stress. The detection method developed here is convenient: target cells may be treated with fluorescently labeled azides to enable the direct and efficient detection of acrolein in live system. The simple stuctures of the azide probes allows for functional groups other than fluorescent groups to be readily linked to aryl azides to image, examine, or target cells associated with oxidative stress processes. We developed a new method for detecting and imaging acrolein extracellularly released by cells in the context of oxidative stress processes or introduced via environmental exposure.
Blind Multiuser Adaptive Combining For Asynchronous Cdma Systems (1996)

Publication in the conference proceedings of EUSIPCO, Trieste, Italy, 1996
Generation of Lung Cancer Cell Line Variants by Drug Selection or Cloning (2011)

Clonal variants or subpopulations have been isolated from every major histological type of cancer, and cellular heterogeneity in lung cancer is a common occurrence. These subpopulations may exhibit differences in drug resistance and invasive potential. One therefore needs to consider the subpopulations as well as the tumour to overcome the barriers of drug resistance and metastasis for successful treatment. Isogenic variants of cancer cell lines can be very valuable in providing controlled human experimental systems to study clinically relevant parameters such as drug resistance and invasiveness. These variants can be established by selection based on a characteristic of the subpopulation or by isolating clonal subpopulations from a heterogeneous population. Drug-resistant variants can be generated by pulse selection, which usually generates low-level resistance, which may as well be clinically relevant, or by continuous exposure, which can be used to obtain high-level resistant variants. Clonal subpopulations may also be isolated based on morphological differences using simple cell-culture-based techniques.
Robust Convex Optimization (1998)

We study convex optimization problems for which the data is not specified exactly and it is only known to belong to a given uncertainty set U, yet the constraints must hold for all possible values of the data from U. The ensuing optimization problem is called robust optimization. In this paper we lay the foundation of robust convex optimization. In the main part of the paper we show that if U is an ellipsoidal uncertainty set, then for some of the most important generic convex optimization problems (linear programming, quadratically constrained programming, semidefinite programming and others) the corresponding robust convex program is either exactly, or approximately, a tractable problem which lends itself to efficient algorithms such as polynomial time interior point methods.
Modificaciones estructurales de un suelo sometido a distintos usos forestales (1993)

An evaluation of the effect of management (native forest, pasture, afforestation with Pinus radiata) in first and second rotation on volumetric properties of Hapludand soil profiles located in Loncoche, Southern Chile was carried out. The reference to evaluate the amount and course of changes was the soil under the native forest. Undisturbed soil samples were taken for to determine volumetric soil components. Settlement of the soil was detected through the decrease of pore volume after the native forest was eliminated. The pasture presented the highest settlement of increase with the number of afforestations. The effects of soil management were reflected in pore size distribution. The loss of pore volume goes together with a decrease of large pores and an increase of small pores. The structural degradation of afforestation sites involves intermedate soil layers. On the site under pasture the coarse pores diminish in the upper layers. Recently incorporate soil sites to production use, show primary consolidation curves. With an increment of soil management intensity the consolidation curves were secondary and marked an increase of bearing capacity.
Macrocyclic lathyrane diterpenes as antitumor promoters. (2007)

Human cytomegalovirus (CMV) preferentially infects tumor tissues and the accumulated CMV immediate-early (IE) antigen may lead to tumor promotion and progression. The development of strategies to inhibit human CMV IE antigen expression and/or function is an important goal to prevent and treat certain forms of cancers associated with human CMV. The aim of this study was to search for antitumor promoters from plant sources. The effect of six macrocyclic lathyrane-type diterpenoids, latilagascenes A-E (1-5) and jolkinol B (6), isolated from the methanol extract of Euphorbia lagascae, on the expression of IE antigen in lung cancer cells (A549) infected by CMV was studied. All the compounds, except latilagascene D (4), decreased IE antigen expression of CMV.
Design and Analysis of DC Solid-State Circuit Breakers Using SiC JFETs (2016)

Protection against short-circuit faults remains a major technical challenge in increasingly popular dc power networks. This paper describes a new concept of a self-powered dc solid-state circuit breaker (SSCB) with one or more normally on SiC JFETs as the main static switch and a fast-starting isolated dc/dc converter as the protection driver. The new SSCB detects short-circuit faults by sensing its terminal voltage rise and draws power from the fault condition itself to turn and hold off the SiC switch. The new two-terminal SSCB can be directly placed in a circuit branch without requiring any external power supply or extra wiring. A low-power isolated dc/dc converter is designed and optimized to provide a fast reaction to a short-circuit fault. Unidirectional and bidirectional SSCB prototypes based on this design concept have been built. Repeated interruption of fault currents up to 180 A at a dc bus voltage of 400 V within 0.8 μs was experimentally demonstrated. DC circuit protection applications provide a unique market opportunity for wide-bandgap semiconductors, which are outside the conventional focus on power electronic converters.
New axially aryloxy substituted gallium phthalocyanines for nonlinear optics (2003)

The ability to control reductions in the saturation energy density is important from the point of view of realizing applications where one would require successive layers in the practical limiter to be fabricated from materials of decreasing saturation energy density. In this paper, two new axially aryloxy substituted gallium phthalocyanine compounds: tBu4PcGa(p-CPO) and [tBu4PcGa]2·SDPO, have been prepared and structurally characterized. Their nonlinear optical (NLO) properties are described.
Parkin, a large common fragile site gene, is a potential tumor suppressor gene involved in cancer development. (2004)

3450 The Parkin gene was originally identified due to gene mutations in patients with autosomal recessive juvenile Parkinsonism (AJRP). We recently found that Parkin is an extremely large gene (1.4 Mb) within the highly unstable FRA6E common fragile site (CFS) region. Parkin /FRA6E has genomic similarities to Fhit/FRA3B and WWOX/FRA16D, two other large tumor suppressor genes that are located within highly active CFSs. Fhit and WWOX, although not typical tumor suppressor genes, have both been demonstrated to play important roles in cancer development due to their loss of expression in many different cancers. We were therefore very interested in characterizing Parkin gene alterations and its possible association with cancer. After analyzing over 50 cancer-derived cell lines including 11 hepatocellular carcinoma (HCC) cell lines, we found one HCC cell line, PLC/PRF/5, with a detectable homozygous deletion encompassing exon 3. Using quantitative duplex PCR and fluorescent in situ hybridization (FISH) analysis to characterize the copy number changes of Parkin exons in HCC cell lines, we found 4 out of 12 cell lines with heterozygous deletion of Parkin exons (PLC5, SNU398, SK-Hep1 and Hep3B), and one cell line, Hep3, with a heterozygous duplication of an exon. Parkin protein expression was significantly diminished or absent in all the HCC cell lines and primary tumors examined. We also detected loss of Parkin in ovarian cancer and other types of cancer. To examine the role that the loss of Parkin plays in the development of HCC we generated stable transfectants with Parkin and Parkin-myc in two HCC cell lines, pLC5 and Hep3B. Examination of growth rates revealed that expression of Parkin was associated with slightly slower growth rates. In addition, cells expressing Parkin were more sensitive to apoptosis with certain apoptotic-inducing agents. We also utilized the Parkin-myc transfectants to identify other proteins in epithelial cells that might be interacting with Parkin. This analysis revealed that the cytokeratins CK8 and CK18 are associated with Parkin in epithelial cells. In addition, we demonstrate that Parkin can ubiquitinylate CK8 both in vitro and in vivo. Our results suggest that Parkin may be involved with the cytoskeleton in epithelial cells. We hypothesize that Parkin functions to monitor cytoskeletal stress in these cells and that the loss of Parkin expression, presumably due to instability within the highly unstable FRA6E common fragile site, results in cells that grow more quickly and are less sensitive to apoptotic induction. Our overall hypothesis for the common fragile sites, and the genes contained within them, is that they all function to monitor cells for different types of stress and to help the cells respond appropriately. What we observe in cancer cells may actually represent the distintegration of this system caused by the genomic instability present in developing cancer cells.
Early trajectories of skin thickening are associated with severity and mortality in systemic sclerosis (2020)

Early identification of clinical phenotype based on skin thickening trajectories could predict morbi-mortality in SSc. This study suggested that mRSS trajectories characterization might be pivotal for clinical practice and future trial designs.
A High Performance Leadframe Design For Memory Application (2008)

Memory is widely used in most applications. It has the trend for larger storage and higher speed operation, but lower prices. Leadframe based package is a low cost solution for memory applications, but it always has the problem of high lead inductance. Higher power and ground pins inductance design will result in big bouncing noise and make products malfunction. Therefore, how to reduce the lead inductance is a key issue for a successful leadframe design. Traditional power and ground pins are individually arranged from inner die pad to outer leads. Here we proposed connection type leadframe design to reduce power and ground nets inductance. Wire length impact and lead width impact are included in this study. In this paper, we even discuss the impact of different gold wire diameters. According to the simulation results for all these impacts, we will come out the low inductance and resistance design guideline for designer's reference.