gebhart/patrepeval huggingface dataset:
Autophagy Limited Role In Mitigating Ubiquitin Proteasome Pathway Inhibition Induced ER Stress and mTORC1 Signaling. (2015)

The regulation of muscle mass is dictated by a balance between the rates of muscle protein synthesis (MPS) and muscle protein breakdown (MPB). The absolute rate of both measures fluctuates during catabolic and anabolic conditions. Decreasing the rate of MPB can but has not always resulted in increased muscle mass. This disparity may be the result of interactions between the ubiquitin proteasome pathway (UPP), autophagy, and endoplasmic reticulum (ER) stress pathways along with crosstalk with the mTORC1 signaling pathway, a primary mediator of MPS. PURPOSE: To determine how the inhibition of the ubiquitin proteasome alters autophagy, ER stress, mTORC1 signaling, and MPS within cultured myotubes. METHODS: MG132 was selected as a primary inhibitor of the UPP. Differentiated C2C12’s, were treated with 50μM of MG132 for 6 or 12hours(h), with DMSO volume and time match controls (n=3 per experiment). Cells were incubated with 1μM puromycin for 5min prior to collection, for determination of MPS via SuNSET. Equal aliquots of protein were separated by SDS-PAGE and protein levels determined by western blot. The effect of treatment was compared using a one way ANOVA with tukeys post hoc test. RESULTS: Inhibition of the ubiquitin proteasome pathway resulted in a 0.75- and 4.24-fold increase in total ubiquitinated protein following 6 and 12h of MG132 treatment respectively (P<0.05). Puromycin incorporation decreased ∼0.5-fold at both 6 and 12h (P<0.05). Phospho (Ser473)/total Akt increased 1.9- and 3-fold over corresponding controls at 6 and 12h (P<0.05). Phospho-S6K (Thr 389) increased 1.8 and 3.4 fold with MG132 treatment. Phospho-S6 (Ser 244/240) showed no increase in phosphorylation with treatment. Autophagy markers including Atg7, Beclin or LC3B exhibited no significant effect of treatment. However, Phospho (Ser575)/Total ULK decreased 0.33-fold at 12h, (P<0.05). The ER stress markers BIP and CHOP, exhibited marked increases in expression with a 2.4-fold increase at 12h (P<0.05) and a 2.2- and 4.9-fold increase in expression at 6 and 12h of treatment, respectively (P<0.05). CONCLUSION: Inhibition of the UPP decreased total protein synthesis in C2C12 myotubes even though Akt/mTORC1 signaling were partially activated. The changes in proteosomal activity did not immediately result in a compensatory increase in autophagy. More work will need to be done to determine the interconnection between these pathways.
Measuring the nonlinear elastic properties of tissue-like phantoms (2004)

A direct mechanical system simultaneously measuring external force and deformation of samples over a wide dynamic range is used to obtain force-displacement curves of tissue-like phantoms under plain strain deformation. These measurements, covering a wide deformation range, then are used to characterize the nonlinear elastic properties of the phantom materials. The model assumes incompressible media, in which several strain energy potentials are considered. Finite-element analysis is used to evaluate the performance of this material characterization procedure. The procedures developed allow calibration of nonlinear elastic phantoms for elasticity imaging experiments and finite-element simulations.
The Iterative Learning Gain That Optimizes Real-Time Torque Tracking for Ankle Exoskeletons in Human Walking Under Gait Variations (2021)

Lower-limb exoskeletons often use torque control to manipulate energy flow and ensure human safety. The accuracy of the applied torque greatly affects how well the motion is assisted and therefore improving it is always of interest. Feed-forward iterative learning, which is similar to predictive stride-wise integral control, has proven an effective compensation to feedback control for torque tracking in exoskeletons with complicated dynamics during human walking. Although the intention of iterative learning was initially to benefit average tracking performance over multiple strides, we found that, after proper gain tuning, it can also help improve real-time torque tracking. We used theoretical analysis to predict an optimal iterative-learning gain as the inverse of the passive actuator stiffness. Walking experiments resulted in an optimum gain equal to 0.99 ± 0.38 times the predicted value, confirming our hypothesis. The results of this study provide guidance for the design of torque controllers in robotic legged locomotion systems and will help improve the performance of robots that assist gait.
T1 mapping and survival in systemic light-chain amyloidosis (2014)

Myocardial ECV (bolus or infusion technique) and pre-contrast T1 are biomarkers for cardiac AL amyloid and they predict mortality in systemic amyloidosis.
A comparison of autoregressive spectral estimation algorithms and order determination methods in ultrasonic tissue characterization (1995)

Several autoregressive (AR) methods for spectral estimation were applied toward the task of estimating ultrasonic backscatter coefficients from small volumes of tissue. Data were acquired from a homogeneous tissue-mimicking phantom and from a normal human liver in vivo. AR methods performed better at short record lengths than the traditional DFT (discrete Fourier Transform) approach. The DFT method consistently underestimated backscatter coefficients at small gate lengths. Burg's algorithm, the Modified Covariance algorithm, and the Recursive Maximum Likelihood Estimation algorithm performed comparably. The Yule-Walker algorithm did not perform as well as these but offered a slight improvement over the DFT. Several order determination methods were tested. These included residual variance (RV), final prediction error (FPE), Akaike information criterion (AIC), and Minimum Description Length (MDL). The AIC and MDL produced misleading results at higher orders. The RV and FPE yielded better results. The autoregressive method offers promise for enhanced spatial resolution and accuracy in ultrasonic tissue characterization and nondestructive evaluation of materials.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A search for prompt lepton-jets in pp collisions at s = 8 $$ \sqrt{\mathrm{s}}=8 $$ TeV with the ATLAS detector (2016)

A search is presented for a new, light boson with a mass of about 1 GeV and decaying promptly to jets of collimated electrons and/or muons (lepton-jets). The analysis is performed with 20.3 fb -1 of data collected by the ATLAS detector at the Large Hadron Collider in proton-proton collisions at a centre-of-mass energy of 8 TeV. Events are required to contain at least two lepton-jets. This study finds no statistically significant deviation from predictions of the Standard Model and places 95% confidence-level upper limits on the contribution of new phenomena beyond the SM, incuding SUSY-portal and Higgs-portal models, on the number of events with lepton-jets.
EFFECTS OF INTERDIALYTIC CHANGES IN SERUM NA+ CONCENTRATION ON WHOLE BODY AND SEGMENTAL CALF ELECTRICAL RESISTANCE MEASURED BY MULTIFREQUENCY BIOIMPEDANCE SPECTROSCOPY (2005)

Multifrequency Bioimpedance analysis (BIA) measures whole body or segmental tissue electrical resistance (R) and is considered a useful tool for assessing body composition, ECV and ICV in HD pts. Tissue resistance depends on tissue conductivity, which is assumed to remain stable during dialysis, but may be affected by changes in intracellular Na+ concentration. We investigated whether pre/post-HD changes in whole body (ΔRw) and segmental calf R (ΔRc) are affected by changes in serum sodium (ΔNa+). Pre/post-HD whole body BIA and intradialytic segmental calf BIA were recorded (Xitron 4200) during 44 HD treatments in 9 pts and serum Na+ was determined pre- and post-HD for each treatment. The ratio of ΔR to ultrafiltration volume (ΔR/UFV) was used to express changes in resistance per unit of fluid removed. Mean ΔNa+ was 2.5 ± 1.9 mmol/l, mean ΔRw 145.0 ± 30.8 Ohm, mean ΔRc 14.9 ± 4.6 Ohm. And mean ΔRw/UFV 0.044 ± 0.012 Ohm/L and mean ΔRc/UFV 0.0043 ± 0.0013 Ohm/L. The correlation between ΔNa+ and ΔRw/UFV (r2 = 0.247, p = <0.05) was weak and there was no correlation between ΔNa+ and ΔRc/UFV (r2 = 0.002, p = n.s.). These data indicate that changes in whole body and calf resistance of BIA are not substantially affected by changes in serum Na+ concentration occurring during dialysis. Intradialytic changes in whole body and calf electrical resistance, as measured by BIA, thus merely reflect changes in extracellular fluid volumes.
Mathematical Modeling and Microbiological Verification of Ohmic Heating of a Multicomponent Mixture of Particles in a Continuous Flow Ohmic Heater System with Electric Field Parallel to Flow (2013)

To accomplish continuous flow ohmic heating of a low-acid food product, sufficient heat treatment needs to be delivered to the slowest-heating particle at the outlet of the holding section. This research was aimed at developing mathematical models for sterilization of a multicomponent food in a pilot-scale ohmic heater with electric-field-oriented parallel to the flow and validating microbial inactivation by inoculated particle methods. The model involved 2 sets of simulations, one for determination of fluid temperatures, and a second for evaluating the worst-case scenario. A residence time distribution study was conducted using radio frequency identification methodology to determine the residence time of the fastest-moving particle from a sample of at least 300 particles. Thermal verification of the mathematical model showed good agreement between calculated and experimental fluid temperatures (P > 0.05) at heater and holding tube exits, with a maximum error of 0.6 °C. To achieve a specified target lethal effect at the cold spot of the slowest-heating particle, the length of holding tube required was predicted to be 22 m for a 139.6 °C process temperature with volumetric flow rate of 1.0 × 10(-4) m3/s and 0.05 m in diameter. To verify the model, a microbiological validation test was conducted using at least 299 chicken-alginate particles inoculated with Clostridium sporogenes spores per run. The inoculated pack study indicated the absence of viable microorganisms at the target treatment and its presence for a subtarget treatment, thereby verifying model predictions.
Fluid-Structure Interaction and Applications to Screening Pipeline Span VIV and Subsea Piping FIV (2014)

Flow-induced vibrations (FIV) of subsea piping due to external flow (e.g., vortex-induced vibrations of pipeline spans) or internal flow (e.g., high velocity multiphase flow in subsea piping) may pose structural integrity concerns due to cyclic stressing at critical welds and, over time, a threat of fatigue failure. Assets in the design stage or in the operating stage which fail a screening based on published guidelines, may undergo a comprehensive screening based on numerical simulation. This paper gives an overview of such a screening methodology, based on computational fluid dynamics (CFD), structural finite element analysis (FEA), and associated fluid-structure interaction (FSI). In the context of pipeline span VIV, seabed proximity effects and flow blockage effects may have a significant effect on the pipeline span response. High-level screenings based on DNV-RP-F105 may not account for these effects appropriately and result in overly conservative fatigue life estimates. We present a couple of application cases where the comprehensive screening makes evident these conservatisms. In the context of FIV (due to internal flow) a high-level screening approach exists as part of the Energy Institute (EI) Guidelines on the Avoidance of Vibration Induced Fatigue Failure (AVIFF). However, the EI AVIFF guideline does not provide a framework for the direct estimation of vibration levels, stress levels, or fatigue life. The comprehensive screening methodology addresses this gap and is illustrated with an application case. Vibration measurements and piping remediation are much more costly subsea than they are on topsides. Hence, advanced simulation techniques are valuable tools in determining the integrity status as well as the safe operating limits of subsea piping.
Comparison of transduction efficiency of recombinant AAV serotypes 1, 2, 5, and 8 in the rat nigrostriatal system (2009)

Enhanced delivery and expression of genes in specific neuronal systems is critical for the development of genetic models of neurodegenerative disease and potential gene therapy. Recent discovery of new recombinant adeno-associated viral (rAAV) capsid serotypes has resulted in improved transduction efficiency, but expression levels, spread of transgene, and potential toxicity can differ depending on brain region and among species. We compared the transduction efficiency of titer-matched rAAV 2/1, 2/5, and 2/8 to the commonly used rAAV2/2 in the rat nigrostriatal system via expression of the reporter transgene, enhanced green fluorescent protein. Newer rAAV serotypes 2/1, 2/5, and 2/8 demonstrated marked increase in transduction and spread of enhanced green fluorescent protein expression in dopaminergic nigrostriatal neurons and projections to the striatum and globus pallidus compared to rAAV2/2 at 2 weeks post-injection. The number of nigral cells transduced was greatest for rAAV2/1, but for serotypes 2/5 and 2/8 was still two- to threefold higher than that for 2/2. Enhanced transduction did not cause an increase in glial cell response or toxicity. New rAAV serotypes thus promise improved gene delivery to nigrostriatal system with the potential for better models and therapeutics for Parkinson disease and other neurodegenerative disorders.
Language Issues for Cognitive Radio Computer languages that may be useful for expressing cognitive radio concepts are identified and evaluated in this tutorial paper. (2009)

This paper discusses various aspects of formal languages in the context of cognitive radio. A bottom up approach is taken in which an example of a specification of a feature of cognitive radio in a selected language is shown, followed by an example of a feature that cannot be expressed in the language and the identification of a capability that needs to be added to the language in order to cover the identified gap in the expressiveness. Following this pattern, we start with a language based on description logics and add the capability of expressing rules, then functions, and finally behavioral aspects. The running example used in this paperVconveying the description of a component to be synthesized by another radioVcovers two major aspects of a cognitive radio: an ability to express own capabilities and an ability to interoperate with other cognitive radios.
Paclitaxel: Application in Modern Oncology and Nanomedicine‐Based Cancer Therapy (2021)

Paclitaxel is a broad-spectrum anticancer compound, which was derived mainly from a medicinal plant, in particular, from the bark of the yew tree <i>Taxus brevifolia</i> Nutt. It is a representative of a class of diterpene taxanes, which are nowadays used as the most common chemotherapeutic agent against many forms of cancer. It possesses scientifically proven anticancer activity against, e.g., ovarian, lung, and breast cancers. The application of this compound is difficult because of limited solubility, recrystalization upon dilution, and cosolvent-induced toxicity. In these cases, nanotechnology and nanoparticles provide certain advantages such as increased drug half-life, lowered toxicity, and specific and selective delivery over free drugs. Nanodrugs possess the capability to buildup in the tissue which might be linked to enhanced permeability and retention as well as enhanced antitumour influence possessing minimal toxicity in normal tissues. This article presents information about paclitaxel, its chemical structure, formulations, mechanism of action, and toxicity. Attention is drawn on nanotechnology, the usefulness of nanoparticles containing paclitaxel, its opportunities, and also future perspective. This review article is aimed at summarizing the current state of continuous pharmaceutical development and employment of nanotechnology in the enhancement of the pharmacokinetic and pharmacodynamic features of paclitaxel as a chemotherapeutic agent.
Supplementary Table S1-S3 Legends and Supplementary Figure S1-S6 Legends from Selective Inhibition of HDAC1 and HDAC2 as a Potential Therapeutic Option for B-ALL (2023)

&lt;p&gt;Supplementary Table S1-S3 Legends and Supplementary Figure S1-S6 Legends. Legends for supplementary tables S1-S3 and supplementary figures S1-S6 which support data in the manuscript, but could not be included due to space constraints.&lt;/p&gt;
Activation of a transfected FGFR‐1 receptor in Madin‐Darby epithelial cells results in a reversible loss of epithelial properties (1995)

Basic fibroblast growth factor (bFGF) is a potent mitogen for a wide variety of cell types derived from mesoderm and neuroectoderm. The activity of bFGF is mediated by several types of closely related receptors belonging to the tyrosine-kinase family of receptors. We have found that Madin-Darby epithelial cells (MDCK) do not seem to produce bFGF or bFGF receptors. High level expression of human bFGF cDNA in these cells did not produce any mitogenic or morphological effects. Expression of the mouse-derived cDNA encoding FGF receptor-1 (FGFR-1) in MDCK cells resulted in the acquisition of a fibroblast-like morphology when the transfected cells were cultured at low density in the presence of 0.6% fetal calf serum and 20 ng/ml bFGF. Acidic fibroblast growth factor (aFGF) also induced these morphological changes but not keratinocyte growth factor. The morphological effect was not accompanied by increased bFGF-induced cell proliferation and did not result in the loss of epithelial cell markers such as cytokeratins. However, the morphological transition was accompanied by changes in the intracellular distribution of actin. In spite of these changes the transfected cells formed monolayers even in the presence of bFGF. Coexpression of bFGF and FGFR-1 in the MDCK cells resulted in similar morphological effects that were not dependent upon exogenous bFGF. These morphological effects were mimicked by exposure of MDCK cells to either orthovanadate or phorbol ester. Parental and FGFR-1-expressing MDCK cells formed monolayers that displayed high electrical resistance. Incubation of monolayers of FGFR-1-transfected cells with bFGF resulted in the loss of trans-epithelial resistance. Monolayers of parental MDCK cells did not lose their trans-epithelial resistance in response to bFGF, although exposure to phorbol ester did result in the loss of their trans-epithelial resistance, indicating that the effects on the trans-epithelial resistance are mediated by protein kinase C activation. Interestingly, orthovanadate did not cause a loss of transepithelial resistance, suggesting that the loss of trans-epithelial resistance is separable from the morphological transition.
High-dose vitamin E supplementation normalizes retinal blood flow and creatinine clearance in patients with type 1 diabetes. (1999)

Oral vitamin E treatment appears to be effective in normalizing retinal hemodynamic abnormalities and improving renal function in type 1 diabetic patients of short disease duration without inducing a significant change in glycemic control. This suggests that vitamin E supplementation may provide an additional benefit in reducing the risks for developing diabetic retinopathy or nephropathy.
Integrative structural and functional analysis of human malic enzyme 3: A potential therapeutic target for pancreatic cancer (2022)

Malic enzymes (ME1, ME2, and ME3) are involved in cellular energy regulation, redox homeostasis, and biosynthetic processes, through the production of pyruvate and reducing agent NAD(P)H. Recent studies have implicated the third and least well-characterized isoform, mitochondrial NADP<sup>+</sup>-dependent malic enzyme 3 (ME3), as a therapeutic target for pancreatic cancers. Here, we utilized an integrated structure approach to determine the structures of ME3 in various ligand-binding states at near-atomic resolutions. ME3 is captured in the open form existing as a stable tetramer and its dynamic Domain C is critical for activity. Catalytic assay results reveal that ME3 is a non-allosteric enzyme and does not require modulators for activity while structural analysis suggests that the inner stability of ME3 Domain A relative to ME2 disables allostery in ME3. With structural information available for all three malic enzymes, the foundation has been laid to understand the structural and biochemical differences of these enzymes and could aid in the development of specific malic enzyme small molecule drugs.
<title>Brain imaging registration by correlation of first-order geometry</title> (1999)

A new method is introduced for the registration of MRI and CT scans of the head, based on the first order geometry of the images. Registration is accomplished by optimal alignment of gradient vector fields between respective MRI and CT images. We show that the summation of the squared inner products of gradient vectors between images is well-behaved, having a strongly peaked maximum when images are exactly registered. This supports our premise that both magnitude and orientation of edge information are important features for image registration. A number of experimental results are presented demonstrating the accuracy of our performance.
ChemInform Abstract: Synthesis and PTP1B Inhibition of Novel 4‐Aryl‐1‐oxa‐9‐thiacyclopenta[b]fluorenes. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
120 Gb/s Optical Card-to-Card Interconnect Link Demonstrator with Embedded Waveguides (2007)

We report on a card-to-card optical interconnect demonstrator with passively aligned butt-coupled optoelectronic modules onto waveguides embedded into the printed circuit board (PCB). After describing selected building blocks, we will present experimental results obtained with the demonstrator hardware consisting of a parallel 12-channel at 10 Gb/s (120 Gb/s) optical card-to-card link.
Phosphorylation of the 5-hydroxytryptamine3 (5-HT3) receptor expressed in HEK293 cells. (2000)

The 5-hydroxytrptamine3 (5-HT3) receptor is a pentameric complex belonging to the family of ligand-gated ion channels. A variety of studies have suggested that phosphorylation regulates the rate of desensitisation and the size of amplitude of the receptor current. In this study we have examined the phosphorylation of the myc-tagged wild-type 5-HT3A receptor subunits from guinea-pig expressed in HEK293 cells (human embryonic kidney). Stably transfected cells were metabolically labelled with 32P-phosphoric acid. The results of immunoprecipitation and autoradiography demonstrate that both splicc variants of the 5-HT3A receptor subunit are phosphorylated in HEK293 cells. Site-specific mutagenesis revealed that phosphorylation occurs at serine 409, a potential target of protein kinase A. Thus the 5-HT3 receptor might be modulated by intracellular pathways, that allow variable 5-hydroxytryptamine action as responses to different extracellular stimuli.