gebhart/patrepeval huggingface dataset:
Relative roles of CCAAT/enhancer-binding protein beta and cAMP regulatory element-binding protein in controlling transcription of the gene for phosphoenolpyruvate carboxykinase (GTP). (1993)

The gene for phosphoenolpyruvate carboxykinase (GTP) (EC 4.1.1.32) (PEPCK) is expressed in a tissue-specific manner in the liver, kidney, and adipose tissue and is regulated by hormones including cAMP and insulin. Previous studies have shown that the CCAAT/enhancer-binding protein alpha (C/EBP alpha) binds to several sites on the PEPCK promoter and activates transcription from the promoter in hepatoma cells. Here, we report that a second member of the C/EBP family, C/EBP beta, bound to the same sites on the PEPCK promoter. However, C/EBP beta stimulated transcription primarily through the cAMP-responsive element (CRE), which maps between positions -77 to -94, but not at the more 5'-binding sites. In addition, the nuclear factor-1 site, which is immediately adjacent to the CRE in the PEPCK promoter, was also required for the full response of the promoter to cotransfected C/EBP beta. In gel mobility assays, antibodies to both C/EBP beta and the cAMP regulatory element-binding protein (CREB), but not to C/EBP alpha, "supershifted" DNA-protein complexes formed between a synthetic CRE oligomer and proteins prepared from rat liver nuclei. C/EBP beta mRNA was expressed at low levels in both the periportal and pericentral regions of the liver lobule, whereas expression of the gene for C/EBP alpha was confined to the pericentral region of the liver lobule. PEPCK gene transcription is greatest in the periportal region of the liver. CREB also bound to the CRE and stimulated transcription of a PEPCK-CAT vector in the presence of an expression vector for the catalytic subunit of protein kinase A. C/EBP beta and CREB bound to the CRE with similar affinities, both of which were greater than the affinity of C/EBP alpha. Within 90 min after the administration of dibutyryl cAMP to rats, there was a marked increase in the hepatic concentration of C/EBP beta mRNA and a decrease in the level of mRNA for C/EBP alpha. These studies indicate that C/EBP beta can regulate PEPCK gene transcription by acting through the CRE and that C/EBP beta, together with CREB, may contribute to the cAMP responsiveness of the PEPCK promoter.
Long-Term Recreational Football Training and Health in Aging (2020)

This narrative review aims to critically analyze the effects of exercise on health in aging. Here we discuss the main clinical and biomolecular modifications induced by long-term recreational football training in older subjects. In particular, the effects induced by long-term recreational football training on cardiovascular, metabolic and musculo-skeletal fitness, together with the modifications in the muscle expression of hallmarks related to oxidative metabolism, DNA repair and senescence suppression pathways and protein quality control mechanisms will be provided. All these topics will be debated also in terms of preventing non-communicable metabolic diseases, in order to achieve successful aging over time.
Design of authentication schemes based on graphical password and analysis of its security (2009)

To solve the conflict of security and memorability of password in authentication method.According to the significant drawbacks of alphanumerical passwords,new authentication schemes based on graphical password are proposed.Under the design requirement of graphical password,the recognition-based and recall-based graphical password authentication schemes are proposed.In addition,it's illustrated that graphical password has better memorability and security than text password.And it's shown graphical password has better resistance to most password attacks.Indicated that most graphical password authentication schems are better then traditional password.
Rejection of disk drive vibration and shock disturbances with a disturbance observer (1999)

Improving the position control of the disk drive read/write heads is an important step in increasing the storage capacity of a drive, especially in the presence of internal and external disturbances. To address this problem, the typical feedback loop of a disk drive servo system was augmented with a disturbance observer. The disturbance observer uses the position error signal and a nominal model of the plant to create an estimate of the disturbance. This estimate is then used to compensate for the disturbance effects. The effectiveness of the disturbance observer in rejecting shock and vibration disturbances is demonstrated in simulation and shake table experiments. The effects of noise in the position error signal are also discussed.
Induction of the Angiogenic Modulator Fibroblast Growth Factor-binding Protein by Epidermal Growth Factor Is Mediated through Both MEK/ERK and p38 Signal Transduction Pathways (2000)

Fibroblast growth factor-binding protein (FGF-BP) is a secreted protein that binds and activates fibroblast growth factors (FGF-1 and FGF-2) and induces angiogenesis in some human cancers. FGF-BP is expressed at high levels in squamous cell carcinoma (SCC) cell lines and tumor samples and has been shown to be rate-limiting for the growth of SCC tumors in vivo. In this study, we examine the regulation of FGF-BP by epidermal growth factor (EGF) and the signal transduction mechanisms that mediate this effect. We found that EGF treatment of the ME-180 SCC cell line caused a rapid induction of FGF-BP gene expression. This induction was mediated transcriptionally through the AP-1 (c-Fos/JunD) and CCAAT/enhancer-binding protein elements as well as through an E-box repressor site in the proximal regulatory region of the FGF-BP promoter. Pharmacological inhibition of protein kinase C and mitogen-activated protein kinase/extracellular signal-regulated kinase kinase 1/2 (MEK1/2) completely blocked EGF induction of FGF-BP mRNA, whereas inhibition of phosphatidylinositol 3-kinase had no effect. Additionally, both EGF- and anisomycin-induced FGF-BP mRNA was abrogated by inhibition of p38 mitogen-activated protein kinase, demonstrating a role for p38 in the regulation of FGF-BP. Co-transfection of the FGF-BP promoter with dominant negative forms of MEK2, extracellular signal-regulated kinase 2, and p38 significantly decreased the level of EGF induction, whereas expression of a dominant negative c-Jun N-terminal kinase mutant or expression of c-Jun N-terminal kinase inhibitory protein had no effect. Similarly, activation of the p38 pathway by overexpression of wild-type p38 or MKK6 enhanced FGF-BP transcription. These results demonstrate that EGF induction of FGF-BP occurs selectively through dual activation of the stress-activated p38 and the MEK/extracellular signal-regulated kinase mitogen-activated protein kinase pathways, which ultimately leads to activation of the promoter through AP-1 and CCAAT/enhancer-binding protein sites.
Narrow‐Width Single‐Phase Power Rail (I‐type) (2017)

In this chapter, an advanced version of on-line electric vehicles (OLEVs) is introduced as an introductory example of road-powered electric vehicles (RPEVs). Because the author is heavily involved in the development of OLEVs, this chapter will guide readers to how practical problems are dealt with. This chapter is based on the paper by J. Huh, S.W. Lee, W.Y. Lee, G.H. Cho, and C.T. Rim, “Narrow-width inductive power transfer system for on-line electrical vehicles,” IEEE Trans. on Power Electronics, vol. 26, no. 12, pp. 3666–3679, December 2011. The inductive power transfer system (IPTS) with a narrow rail width, a small pick-up size, and a large airgap is explained, as an extension of previous research on OLEVs, in this chapter. By introducing a new core structure, the orientation of the magnetic flux alternates along with the road; hence, an inductive power transfer system with a narrow rail width of 10 cm, a large airgap of 20 cm, and a large lateral displacement of about 24 cm was implemented. The resonant circuit of the inductive power transfer system, driven by a current source, was fully characterized. The experimental results showed that the maximum output power was 35 kW and that the maximum efficiency was 74% at 27 kW.
Impact of self-assembled monolayer on low frequency noise of organic thin film transistors (2008)

Bottom-contact organic field-effect transistors (FETs) based on regioregular poly(3-hexylthiophene) were fabricated with different surface treatments and were evaluated using a low frequency noise (LFN) spectroscopy. The oxygen-plasma (OP) treated device shows the highest mobility with the lowest current fluctuation. Octadecyltrichlorosilane and perfluorodecyldimetylchlorosilane treated device gives a higher noise compared with the OP treated device. Hexamethyldisilazane treated devices show the highest noise but the lowest mobility. The LFN results are correlated with organic FET device mobility and stability, proved by channel material crystallinity and degree of dislocations analysis. LFN measurement provides a nondisruptive and direct methodology to characterize device performance.
Dendrite-Free Potassium–Oxygen Battery Based on a Liquid Alloy Anode (2017)

The safety issue caused by the dendrite growth is not only a key research problem in lithium-ion batteries but also a critical concern in alkali metal (i.e., Li, Na, and K)-oxygen batteries where a solid metal is usually used as the anode. Herein, we demonstrate the first dendrite-free K-O<sub>2</sub> battery at ambient temperature based on a liquid Na-K alloy anode. The unique liquid-liquid connection between the liquid alloy and the electrolyte in our alloy anode-based battery provides a homogeneous and robust anode-electrolyte interface. Meanwhile, we manage to show that the Na-K alloy is only compatible in K-O<sub>2</sub> batteries but not in Na-O<sub>2</sub> batteries, which is mainly attributed to the stronger reducibility of potassium and relatively more favorable thermodynamic formation of KO<sub>2</sub> over NaO<sub>2</sub> during the discharge process. It is observed that our K-O<sub>2</sub> battery based on a liquid alloy anode shows a long cycle life (over 620 h) and a low discharge-charge overpotential (about 0.05 V at initial cycles). Moreover, the mechanism investigation into the K-O<sub>2</sub> cell degradation shows that the O<sub>2</sub> crossover effect and the ether-electrolyte instability are the critical problems for K-O<sub>2</sub> batteries. In a word, this study provides a new route to solve the problems caused by the dendrite growth in alkali metal-oxygen batteries.
Circulating cancer‐associated extracellular vesicles as early detection and recurrence biomarkers for pancreatic cancer (2022)

Early detection of pancreatic ductal adenocarcinoma (PDAC) is essential for improving patient survival rates, and noninvasive biomarkers are urgently required to identify patients who are eligible for curative surgery. Here, we examined extracellular vesicles (EVs) from the serum of PDAC patients to determine their ability to detect early-stage disease. EV-associated proteins purified by ultracentrifugation and affinity columns underwent proteomic analysis to identify novel PDAC markers G protein-coupled receptor class C group 5 member C (GPRC5C) and epidermal growth factor receptor pathway substrate 8 (EPS8). To verify the potency of GPRC5C- or EPS8-positive EVs as PDAC biomarkers, we analyzed EVs from PDAC patient blood samples using ultracentrifugation in two different cohorts (a total of 54 PDAC patients, 32 healthy donors, and 22 pancreatitis patients) by immunoblotting. The combination of EV-associated GPRC5C and EPS8 had high accuracy, with area under the curve values of 0.922 and 0.946 for distinguishing early-stage PDAC patients from healthy controls in the two cohorts, respectively, and could detect PDAC patients who were negative for CA19-9. Moreover, we analyzed 30 samples taken at three time points from 10 PDAC patients who underwent surgery: before surgery, after surgery, and recurrence as an early-stage model. These proteins were detected in EVs derived from preoperative and recurrence samples. These results indicated that GPRC5C- or EPS8-positive EVs were biomarkers that have the potential to detect stage I early pancreatic cancer and small recurrent tumors detected by computed tomography.
Generation of coherent phonons by coherent extreme ultraviolet radiation in a transient grating experiment (2019)

We investigate the excitation of coherent acoustic and optical phonons by ultrashort extreme ultraviolet (EUV) pulses produced by a free electron laser. Two crossed femtosecond EUV (wavelength 12.7 nm) pulses are used to excite coherent phonons at a wavelength of 280 nm, which are detected via diffraction of an optical probe beam. Longitudinal and surface acoustic waves are measured in BK-7 glass, diamond, and Bi4Ge3O12; in the latter material, the excitation of a coherent optical phonon mode is also observed. We discuss probing different acoustic modes in reflection and transmission geometries and frequency mixing of surface and bulk acoustic waves in the signal. The use of extreme ultraviolet radiation will allow the creation of tunable GHz to THz acoustic sources in any material without the need to fabricate transducer structures. The contribution by the MIT group was supported by the U.S. Department of Energy, Office of Basic Energy Sciences under Award No. DE-FG02-00ER15087. The JILA group graciously acknowledges support from the Department of Energy BES Award No. DE-FG02-99ER14982 and the Gordon and Betty Moore Foundation's EPiQS Initiative through Grant No. GBMF: 4538, and J.K. acknowledges support from an SRC Fellowship. The Elettra group acknowledges the European Research Council Grant No. 202804-TIMER. A.C. and T.F. acknowledge the Swiss NSF through the NCCR-MUST.
Properties of network polynomials (2012)

It is well known that transfer polynomials play an important role in the network code design problem. In this paper we provide a graph theoretical description of the terms of such polynomials. We consider acyclic networks with arbitrary number of receivers and min-cut h between each source-receiver pair. We show that the associated polynomial can be described in terms of certain subgraphs of the network.
Direct molecular mimicry enables off-target cardiovascular toxicity by an enhanced affinity TCR designed for cancer immunotherapy (2016)

Natural T-cell responses generally lack the potency to eradicate cancer. Enhanced affinity T-cell receptors (TCRs) provide an ideal approach to target cancer cells, with emerging clinical data showing significant promise. Nevertheless, the risk of off target reactivity remains a key concern, as exemplified in a recent clinical report describing fatal cardiac toxicity, following administration of MAGE-A3 specific TCR-engineered T-cells, mediated through cross-reactivity with an unrelated epitope from the Titin protein presented on cardiac tissue. Here, we investigated the structural mechanism enabling TCR cross-recognition of MAGE-A3 and Titin, and applied the resulting data to rationally design mutants with improved antigen discrimination, providing a proof-of-concept strategy for altering the fine specificity of a TCR towards an intended target antigen. This study represents the first example of direct molecular mimicry leading to clinically relevant fatal toxicity, mediated by a modified enhanced affinity TCR designed for cancer immunotherapy. Furthermore, these data demonstrate that self-antigens that are expressed at high levels on healthy tissue should be treated with extreme caution when designing immuno-therapeutics.
ChemInform Abstract: Intramolecular Carbonyl Oxide‐Ester Cycloaddition. Structure of a Novel Alkoxy Ozonide. (1987)

Abstract Treatment of the ester (Ia) with ozone affords the ozonide (IIa) which can be reduced with PPh 3 to the ketone (IIIa).
Acoustically Induced Increase of Bragg Grating Bandwidth in Four Holes Suspended Core Fiber (2014)

The acousto-optic induced modulation of fiber Bragg gratings in a suspended core fiber is experimentally demonstrated. The grating bandwidth is increased by up to 57%, which is tunable by 10 V of an electric signal.
Fromthe ‡ DepartmentofAnatomyandCellBiology, ¶ DepartmentofInternalMedicine,and § CenterforGeneTherapyofCystic FibrosisandOtherGeneticDiseases,UniversityofIowaCollegeofMedicine,IowaCity, Iowa 52242 (2006)

The choice of adeno-associated virus serotypes for clinical applications is influenced by the animal model and model system used to evaluate various serotypes. In the present study, we sought to compare the biologic properties of rAAV2/1, rAAV2/2, and rAAV2/5 transduction in polarized human airway epithelia using viruses purified by a newly developed common column chromatography method. Results demonstrated that apical transduction of human airway epithelia with rAAV2/1 was 100-fold more efficient than rAAV2/2 and rAAV2/5. This transduction profile in human airway epithelia (rAAV2/1 rAAV2/2 rAAV2/5) was significantly different from that seen following nasal administration of these vectors to mouse lung (rAAV2/5 > rAAV2/1 rAAV2/2), emphasizing differences in transduction of these serotypes between these two species. In stark contrast to rAAV2/2 and rAAV2/5, rAAV2/1 transduced both the apical and basolateral membrane of human airway epithelia with similar efficiency. However, the overall level of transduction across serotypes did not correlate with vector internalization. We hypothesized that differences in post-entry processing of these serotypes might influence the efficiency of apical transduction. To this end, we tested the effectiveness of proteasome inhibitors to augment nuclear translocation and gene expression from the three serotypes. Augmentation of rAAV2/1 apical transduction of human polarized airway epithelia was 10-fold lower than that for rAAV2/2 and rAAV2/5. Cellular fractionation studies demonstrated that proteasome inhibitors more significantly enhanced rAAV2/2 and rAAV2/5 translocation to the nucleus than rAAV2/1. These results demonstrate that AAV1 transduction biology in human airway epithelia differs from that of AAV2 and AAV5 by virtue of altered ubiquitin/ proteasome sensitivities that influence nuclear translocation.
Spectral Color Reproduction Based on a Six-Color InkJet Output System (2001)

The accuracy of a six-color inkjet printing system was tested using object-color spectral datasets known to both span and exceed the system's spectral gamut. The theoretical basis of the system is the Yule-Nielsen modified spectral Neugebauer equation implemented in an iterative optimization process minimizing spectral RMS error. Results of the end-to-end system based on the reproduction of 170 object colors compiled by Vrhel, et al. show a mean &#x394;E*94 of 3.2 while 384 randomly selected printed color samples (in-gamut) were reproduced with a mean &#x394;E*94 of 0.9.
Incorrect focus cues in stereo displays (2008)

Stereoscopic displays have become important for many applications including vision research, operation of remote devices, medical imaging, surgical training, scientific visualization, virtual prototyping, and more. In many of these applications, it is important for the graphic image to create a faithful impression of the 3d structure of the portrayed object or scene. Unfortunately, 3d displays often yield distortions in perceived 3d structure compared with the percepts of the real scenes the displays depict. A likely cause of such distortions is the fact that computer displays present images on one surface. Thus, focus cues---accommodation and blur in the retinal image---specify the depth of the display rather than the depths in the depicted scene. Additionally, such displays require the viewer to override the normal coupling of vergence and accommodation. I will discuss the development of displays that present focus cues that are correct or nearly correct for the depicted scene. Such displays can create retinal images that are a reasonable approximation to the images formed in natural viewing of depth-varying scenes. Research with these displays has shown that presenting correct or nearly correct focus cues allows a much larger percentage of viewers to fuse binocular images, reduces the time required to identify a stereoscopic stimulus, reduces distortions in perceived depth, and decreases viewer fatigue and discomfort. I will discuss the implications of this work for basic vision research and applications of stereoscopic presentation.
Identification of human and rodent thymic epithelium using tetanus toxin and monoclonal antibody A2B5. (1983)

Using a monoclonal antibody (A2B5), which binds to GQ ganglioside, and tetanus toxin, which binds to GD and GT gangliosides, distinct regions of human and rodent thymic epithelial cells have been identified. The lymphoid elements of the thymus do not bind A2B5 or tetanus toxin. The A2B5 and tetanus toxin-binding cells form a network of thymic epithelial cells throughout the thymic subcapsular cortex and thymic medulla and contain thymopoietin and thymosin alpha-1.
Dendrimer-based chemically amplified resists for sub-100-nm lithography (2000)

Several new poly(benzyl ether) and poly(benzyl ester) dendrimers that incorporate acid- and thermally- labile peripheral groups have been synthesized. Tertiary butyl ester terminated poly(benzyl ether) dendrimers were synthesized using (alpha) -bromo-t-butyl acetate in the preliminary protection step to afford the first generation alcohol. A standard bromination of the focal point benzylic alcohol was used for the activation step, while standard Williamson ether conditions were used for the coupling steps to afford higher generation poly(benzyl ether) dendrons. Tertiary butyl ester terminated dendrons were then coupled to a difunctional core to produce the [G-3] dendrimer. Tertiary butyl carbonate (t-Boc) terminated poly(benzyl ester) dendrimers were also synthesized. This class of dendrimers was synthesized by first protecting monomeric building block 3,5-dihydroxybenzaldehyde with di-t-butyl dicarbonate. A reductive activation step afforded the [G-1] alcohol. The growth steps were accomplished by either Mitsunobu etherification with 3,5- dihydroxybenzaldehyde or by esterification with 5- hydroxymethylisophthalic acid. Finally, coupling of the benzyl alcohol dendrons to a polyfunctional core afforded second and third generation dendrimers. Chemically amplified resists formulated from both t-butyl ester and t-Boc terminated dendrimers show high sensitivity to DUV and e-beam irradiation. Feature sizes well below 100 nm have been routinely patterned using e-beam lithography.
Meta-Analysis in Human Neuroimaging: Computational Modeling of Large-Scale Databases (2014)

Spatial normalization--applying standardized coordinates as anatomical addresses within a reference space--was introduced to human neuroimaging research nearly 30 years ago. Over these three decades, an impressive series of methodological advances have adopted, extended, and popularized this standard. Collectively, this work has generated a methodologically coherent literature of unprecedented rigor, size, and scope. Large-scale online databases have compiled these observations and their associated meta-data, stimulating the development of meta-analytic methods to exploit this expanding corpus. Coordinate-based meta-analytic methods have emerged and evolved in rigor and utility. Early methods computed cross-study consensus, in a manner roughly comparable to traditional (nonimaging) meta-analysis. Recent advances now compute coactivation-based connectivity, connectivity-based functional parcellation, and complex network models powered from data sets representing tens of thousands of subjects. Meta-analyses of human neuroimaging data in large-scale databases now stand at the forefront of computational neurobiology.