gebhart/patrepeval huggingface dataset:
Development of small molecule mitochondria-targeted antioxidants for radioprotection (2006)

4410 We have previously demonstrated that overexpression of MnSOD protects cells from irradiation damage by reduction of superoxide and inhibition of subsequent production of peroxynitrite resulting in stabilization of the mitochondria. To develop new compounds for radioprotection we have attached a gramicidin (GS)-peptide isotere linker that facilitates transportation of proteins into the mitochondria to the antioxidant 4-amino-Tempo (4-AT) and the nitric oxide synthase (NOS) inhibitor 2-amino-5,6-dihydro-6-methyl-4H-1,3-thiazine (AMT) to concentrate the inhibitions in the mitochondria. Initial experiments were performed with two GS-Tempo derivatives (XJB-5-125 or XJB-5-131) or two AMT derivatives (XJB-5-127 or XJB-5-133). To demonstrate concentration of the compounds into the mitochondria, 32D cl 3 cells were incubated in the presence of 100 μM of XJB-5-125, XJB-5-127, XJB-5-131, XJB-5-133, tempol or AMT for 1 hour at which time the mitochondria were isolated and analyzed by mass spectrometry. There was no detectable uptake of 4-AT or AMT into the mitochondria but there was significant uptake of XJB-5-125, 127, 131 or 133 in the mitochondria. Localization of 4-AT to the mitochondria using the mitochondrial leader sequence resulted in increased radiation resistance. Irradiation survival curves were performed on 32D cl 3 cells incubated in 100 μM XJB-5-125, 10 μM XJB-5-131 or 100 μM 4-AT for 1 hour and irradiated to doses ranging from 0 to 800 cGy. The cells were plated in methylcellulose and colonies of greater than 50 cells were counted 7 days later. Cells incubated in XJB-5-125 or XJB-5-131 had increased radiation resistance as shown by an increased shoulder on the survival curve (n=18.24) compared to 32D cl 3 cells only or cells incubated in 4-AT (n=7.47 or 5.82, respectively). The mitochondrial localized AMT (XJB-5-127 or XJB-5-133) also exhibited increased radiation resistance. Irradiation survival curves were performed by incubating 32D cl 3 cells for 1 hour in 10 or 100 μM AMT, XJB-5-127 or XJB-5-133 and irradiating the cells at doses ranging from 0 to 800 cGy. Radiation survival curves at 10 μM revealed no significant change in the D0 between AMT and the mitochondrial linked XJB-5-125 or XJB-5-133. At 100 μM there was a significant increase in the D0 of 1.925 Gy for AMT compared to 1.281 for control 32D cl 3. The two AMT conjugates with the mitochondria linker had a higher D0 of 2.771 or 3.317 Gy compared to the AMT of 1.925 and the 32D cl 3 at 1.281. Using probes specific for peroxynitrite, 32D cl 3 cells incubated in 10 μM or 100 μM of XJB-5-127 or XJB-5-133 produced no peroxynitrite following irradiation while control cells or cells incubated in AMT produced peroxynitrite. The mitochondrial localization was necessary in preventing production of peroxynitrite. These results demonstrate the importance of localization of antioxidants or NOS inhibitors to the mitochondria in protecting cells from irradiation.
Algorithms to evaluate the reliability of a network (2006)

We consider problems of network reliability: the two-terminal network reliability consists, given an undirected graph G/spl equiv/(V, E), and a series of independent edge failure events, in computing the probability that two nodes remain connected. The all-terminal network reliability is the probability that the whole network remains connected. We present in the following two different approaches to compute two-terminal and all-terminal reliability, with various characteristics on the precision level of the result. We give an exact algorithm to compute the reliability in O([V]f(w)/sup 2/ + [E]f(w)) with f(x)/spl equiv/ and w is the tree-width of G. We also present polynomial methods to give bounds on the reliability. We discuss methods to optimize the mean time to repair of the components.
Systems analysis of subjects acutely infected with the Chikungunya virus (2019)

The largest ever recorded epidemic of the Chikungunya virus (CHIKV) broke out in 2004 and affected four continents. Acute symptomatic infections are typically associated with the onset of fever and often debilitating polyarthralgia/polyarthritis. In this study, a systems biology approach was adopted to analyze the blood transcriptomes of adults acutely infected with the CHIKV. Gene signatures that were associated with viral RNA levels and the onset of symptoms were identified. Among these genes, the putative role of the Eukaryotic Initiation Factor (eIF) family genes and apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC3A) in the CHIKV replication process were displayed. We further compared these signatures with signatures induced by the Dengue virus infection and rheumatoid arthritis. Finally, we demonstrated that the CHIKV in vitro infection of murine bone marrow-derived macrophages induced IL-1 beta production in a mechanism that is significantly dependent on the inflammasome NLRP3 activation. The observations provided valuable insights into virus-host interactions during the acute phase and can be instrumental in the investigation of new and effective therapeutic interventions.
Analytical Model of the Effects of a Nonuniform Distribution of Stored Charge on the Electrical Characteristics of Discrete-Trap Nonvolatile Memories (2005)

We propose an analytical model of the effects of a nonuniform distribution of trapped charge on the electrical characteristics and on the perspectives of 2-bit operation of discrete-trap memories. To keep the model tractable, we consider an idealized nonuniform distribution, represented by a step function, so that the concentration of trapped charge can assume only two possible values in two different regions. Notwithstanding the simplicity of our assumptions, which limits the range of validity of our model to the subthreshold and weak inversion regions of the I-V characteristics, we can investigate a series of important aspects for 2-bit storage of nonvolatile memories. Our model is then validated through comparison with detailed numerical simulations performed with a commercial technology computer-aided design tool, and with the experimental electrical characteristics of nanocrystal flash memories under different bias conditions. Finally, we provide a method, based on our model, to extract an "effective" distribution of trapped charge, in which all charge is uniformly distributed in a localized region close to the drain.
Attosecond Science at the Future ELI-ALPS Facility in Hungary (2011)

ELI-ALPS will offer record breaking attosecond pulses optimized for time-resolved experiments in valence and core electron science, plasma physics and 4D-imaging. Additional sources spanning the THz…X-ray range will constitute a versatile facility.
Early alterations in the brown adipose tissue adenylate cyclase system of pre-obese Zucker rat fa/fa pups: decreased G-proteins and β3-adrenoceptor activities (1995)

This study was undertaken to determine whether receptor and non-receptor components of the adenylate cyclase (AC) cascade were altered in brown adipose tissue (BAT) of 14-day-old pre-obese (fa/fa) rats, before endocrine status is strongly modified by fa gene expression. Activity of the AC catalytic subunit did not differ between the two genotypes. In fa/fa rats compared with control Fa/fa rats, there was a 50% decrease in the activity of alpha Gs (stimulated by NaF or guanosine 5'-[gamma-thio]triphosphate) but no change in protein content (Western blotting). alpha Gi function, assessed by the inhibitory action of low concentrations of guanosine 5'-[beta gamma-imido]triphosphate upon 10(-4) M forskolin-stimulated AC activity, was equally low in both genotypes. Analysis of dose-response curves for different beta-agonists revealed that (i) both the basal and the maximally stimulated activity of AC were 2-fold lower in fa/fa rats than in Fa/fa rats; (ii) BRL37344 and CGP12177 (beta 3 agonists) were less potent in fa/fa than in Fa/fa rats (Kact. multiplied by 2); (iii) noradrenaline and isoprenaline (Iso), at the low-affinity site (beta 3-AR), were less potent in fa/fa than in Fa/fa pups (Kact. increased by 30 and 20% respectively). At the high-affinity site (mainly beta 1) these two agonists were more potent in fa/fa than in Fa/fa rats (Kact. decreased by 40 and 80% respectively). In good agreement with the latter result, the beta 1-adrenergic receptor (beta 1-AR)-selective antagonist CGP20712A had more effect on the Iso-stimulated AC activity in pre-obese than in lean pups (2-fold decreased in IC50). Binding experiments with [3H]CGP12177 show that in BAT of suckling rats, beta 3-ARs represent 80% of the total beta-ARs. Bmax values for the two sites were not affected by the genotype, although the beta 3-AR mRNA concentration in BAT (quantitative reverse-transcriptase PCR) was 3-fold lower in fa/fa rats than in Fa/fa pups. In conclusion, these results provide evidence for alterations in beta 1- and beta 3-AR signalling in BAT of 14-day-old suckling pre-obese Zucker rats with a decreased activity of alpha Gs. The impaired AC responsiveness to catecholamines might be a primary contributor to the development of this genetic obesity.
The Role of Trichoderma Species in Plants Response to Salt Stress (2021)

Soil salinity is a pending threat to global agricultural sustainability and food security. The natural means of alleviating this stress have become the major concern as to which methods, mechanisms, and organisms to be used. Soil-borne fungi Trichoderma has proven to alleviate salinity stress in plants. This review aimed to shed light on the roles and mechanisms of some species of Trichoderma in response to salt stress and other merits to plant growth and development. Detailed of this research reviewed the level of growth promotion induced by Trichoderma species with an estimated increase of 200% of total plant biomass compared with control plants from literature. The defined mechanisms of Trichoderma in combating salinity stress in plants are; formation of ion channels in host plants, activation of ion exchange (K+/N+), increase Reactive Oxygen Species (ROS) scavenging enzymes, antioxidants, and genes, production of phytohormones and their signal pathways, stimulates root formation and developments, regulate stomata conductance through the increment of carotenoids in host plants which corresponds to the functions of the photosystems.
Liquid Membrane Technology (1987)

Liquid membrane technology is introduced and is identified as a subset of membrane science. A tutorial section discusses configurations, transport mechanisms, experimental techniques, and a survey of basic theoretical approaches. The concepts of reactive liquid membranes which combine traditional unit operations such as extraction or absorption with stripping are discussed. The chapters to follow in this volume are summarized and the subject of each is placed in perspective to the field of liquid membrane technology.
The Effect of Hypoxia and Hypoxia-Associated Pathways in the Regulation of Antitumor Response: Friends or Foes? (2022)

Hypoxia is an environmental stressor that is instigated by low oxygen availability. It fuels the progression of solid tumors by driving tumor plasticity, heterogeneity, stemness and genomic instability. Hypoxia metabolically reprograms the tumor microenvironment (TME), adding insult to injury to the acidic, nutrient deprived and poorly vascularized conditions that act to dampen immune cell function. Through its impact on key cancer hallmarks and by creating a physical barrier conducive to tumor survival, hypoxia modulates tumor cell escape from the mounted immune response. The tumor cell-immune cell crosstalk in the context of a hypoxic TME tips the balance towards a cold and immunosuppressed microenvironment that is resistant to immune checkpoint inhibitors (ICI). Nonetheless, evidence is emerging that could make hypoxia an asset for improving response to ICI. Tackling the tumor immune contexture has taken on an <i>in silico</i>, digitalized approach with an increasing number of studies applying bioinformatics to deconvolute the cellular and non-cellular elements of the TME. Such approaches have additionally been combined with signature-based proxies of hypoxia to further dissect the turbulent hypoxia-immune relationship. In this review we will be highlighting the mechanisms by which hypoxia impacts immune cell functions and how that could translate to predicting response to immunotherapy in an era of machine learning and computational biology.
Microporous 3D-Structured Hierarchically Entangled Graphene-Supported Pt3Co Alloy Catalyst for PEMFC Application with Process-Friendly Features (2023)

To improve the oxygen reduction reaction (ORR) performance in a proton-exchange membrane fuel cell (PEMFC) cathode with respect to mass activity and durability, a suitable electrocatalyst design strategy is essentially needed. Here, we have prepared a sub-three nm-sized platinum (Pt)-cobalt (Co) alloy (Pt<sub>3</sub>Co)-supported N-doped microporous 3D graphene (Pt<sub>3</sub>Co/pNEGF) by using the polyol synthesis method. A microwave-assisted synthesis method was employed to prepare the catalyst based on the 3D porous carbon support with a large pore volume and dense micro-/mesoporous surfaces. The ORR performance of Pt<sub>3</sub>Co/pNEGF closely matches with the <i>state-of-the-art</i> commercial Pt/C catalyst in 0.1 M HClO<sub>4</sub>, with a small overpotential of 10 mV. The 3D microporous structure of the N-doped graphene significantly improves the mass transport of the reactant and thus the overall ORR performance. As a result of the lower loading of Pt in Pt<sub>3</sub>Co/pNEGF as compared to that in Pt/C, the alloy catalyst achieved 1.5 times higher mass activity than Pt/C. After 10,000 cycles, the difference in the electrochemically active surface area (ECSA) and half-wave potential (<i>E</i><sub>1/2</sub>) of Pt<sub>3</sub>Co/pNEGF is found to be 5 m<sup>2</sup> g<sub>Pt</sub><sup>-1</sup> (ΔECSA) and 24 mV (Δ<i>E</i><sub>1/2</sub>), whereas, for Pt/C, these values are 9 m<sup>2</sup> g<sub>Pt</sub><sup>-1</sup> and 32 mV, respectively. Finally, in a realistic perspective, single-cell testing of a membrane electrode assembly (MEA) was made by sandwiching the Pt<sub>3</sub>Co/pNEGF-coated gas diffusion layers as the cathode displayed a maximum power density of 800 mW cm<sup>-2</sup> under H<sub>2</sub>-O<sub>2</sub> feed conditions with a clear indication of helping the system in the mass-transfer region (i.e., the high current dragging condition). The nature of the <i>I</i>-<i>V</i> polarization shows a progressively lower slope in this region of the polarization plot compared to a similar system made from its Pt/C counterpart and a significantly improved performance throughout the polarization region in the case of the system made from the Pt<sub>3</sub>Co/NEGF catalyst (without the microwave treatment) counterpart. These results validate the better process friendliness of Pt<sub>3</sub>Co/pNEGF as a PEMFC electrode-specific catalyst owing to its unique texture with 3D architecture and well-defined porosity with better structural endurance.
Electrical, thermal, and elastic properties of theMAX-phase Ti2SC (2008)

We report on the electronic, thermal, and elastic properties of the layered ternary, Ti2SC. Resistivity, Hall effect, and magnetoresistance were measured as a function of temperature between 2 and 300 K and at fields up to 9 T. The Hall coefficient is negative and roughly temperature independent. The transport results were analyzed within a two-band framework, with electrons as the dominant charge carrier. The room-temperature thermal conductivity (≈60 W/m K) is the highest of any MAX phase measured to date, with a substantial phonon contribution. The specific heat was measured from 2 to 300 K, yielding a Debye temperature of 765 K and in agreement with the Debye temperature of 745 K found from ultrasonic time-of-flight measurements. Young’s, shear, and bulk moduli from the latter measurements were 290, 125, and 145 GPa, respectively. The calculated values of the lattice parameters (a=3.2051 Å and c=11.2636 Å), and Young’s, shear, and bulk moduli (329, 138, and 179 GPa, respectively), based on the results of density functional theoretical simulations, compare favorably with measurements.
A Budget of Paradoxes (1955)

By Augustus de Morgan. Two volumes bound as one. (New York : Dover Publications Inc.). Pp. xiii + 402 + 387. Price $4.95. With a new introduction by Professor Earnes Nagel.
Model-Based Design and System on Chip Implementation of DTC and PWM Techniques (2022)

This paper presents the implementation procedure of three Pulse Width Modulation (PWM) techniques and a closed-loop motor control method using a model-based design approach. The implemented PWM techniques are the Sinusoidal Pulse Width Modulation (SPWM), Space Vector Pulse Width Modulation (SVPWM), and Selective Harmonic Elimination Pulse Width Modulation (SHEPWM), whereas the closed-loop motor control method is the Direct Torque Control (DTC). These techniques are implemented using a ZedBoard development board which contains a System on a Chip (SoC) Xilinx Zynq-7000. The procedure of implementing these techniques on the ZedBoard and required considerations are discussed. The model-based design approach facilitates rapid implementation without prior knowledge of HDL and ARM programming, which makes it advantageous for students and research work. To verify the integrity of the implemented designs, the ZedBoard is used to control an induction machine (IM), and the results are presented.
Role of endogenous adenine in kidney failure and mortality with diabetes (2023)

Diabetic kidney disease (DKD) can lead to end-stage kidney disease (ESKD) and mortality, however, few mechanistic biomarkers are available for high risk patients, especially those without macroalbuminuria. Urine from participants with diabetes from Chronic Renal Insufficiency Cohort (CRIC), Singapore Study of Macro-Angiopathy and Reactivity in Type 2 Diabetes (SMART2D), and the Pima Indian Study determined if urine adenine/creatinine ratio (UAdCR) could be a mechanistic biomarker for ESKD. ESKD and mortality were associated with the highest UAdCR tertile in CRIC (HR 1.57, 1.18, 2.10) and SMART2D (HR 1.77, 1.00, 3.12). ESKD was associated with the highest UAdCR tertile in patients without macroalbuminuria in CRIC (HR 2.36, 1.26, 4.39), SMART2D (HR 2.39, 1.08, 5.29), and Pima Indian study (HR 4.57, CI 1.37-13.34). Empagliflozin lowered UAdCR in non-macroalbuminuric participants. Spatial metabolomics localized adenine to kidney pathology and transcriptomics identified ribonucleoprotein biogenesis as a top pathway in proximal tubules of patients without macroalbuminuria, implicating mammalian target of rapamycin (mTOR). Adenine stimulated matrix in tubular cells via mTOR and stimulated mTOR in mouse kidneys. A specific inhibitor of adenine production was found to reduce kidney hypertrophy and kidney injury in diabetic mice. We propose that endogenous adenine may be a causative factor in DKD.
Temporal Change in Human Nicotinic Acetylcholine Receptor After Smoking Cessation: 5IA SPECT Study (2007)

Because the upregulation of the nAChRs of the smokers after chronic exposure of the nicotine was downregulated to the nonsmokers' level by around 21 d after smoking cessation, the upregulation is a temporary effect. The decrease in nicotinic receptors to nonsmoker levels may be the breaking point during the nicotine withdrawal period.
Synergistic Targeting of PI3K/AKT Pathway and Androgen Receptor Axis Significantly Delays Castration-Resistant Prostate Cancer Progression In Vivo (2013)

The progression to castration-resistant prostate cancer (CRPC) correlates with gain-of-function of the androgen receptor (AR) and activation of AKT. However, as single agents, AR or AKT inhibitors result in a reciprocal feedback loop. Therefore, we hypothesized that combination of an AKT inhibitor with an antiandrogen might result in a more profound, long-lasting remission of CRPC. Here, we report that the AKT inhibitor AZD5363 potently inhibits proliferation and induces apoptosis in prostate cancer cell lines expressing the AR and has anticancer activity in vivo in androgen-sensitive and castration-resistant phases of the LNCaP xenograft model. However, we found that the effect of castration-resistant tumor growth inhibition and prostate-specific antigen (PSA) stabilization is transient and resistance occurs with increasing PSA after approximately 30 days of treatment. Mechanistically, we found that single agent AZD5363 induces increase of AR binding to androgen response element, AR transcriptional activity, and AR-dependent genes such as PSA and NKX3.1 expression. These effects were overcome by the combination of AZD5363 with the antiandrogen bicalutamide, resulting in synergistic inhibition of cell proliferation and induction of apoptosis in vitro, and prolongation of tumor growth inhibition and PSA stabilization in CRPC in vivo. This study provides a preclinical proof-of-concept that combination of an AKT inhibitor with antiandrogen results in prolonged disease stabilization in a model of CRPC.
High-stability ultrathin spin-on benzocyclobutene gate dielectric for polymer field-effect transistors (2004)

Using a thermal-crosslinkable siloxane bisbenzocyclobutene, high quality spin-on (solutionprocessable) gate dielectric layers as thin as 50 nm have been fabricated over the semiconductor layer for polymer field-effect transistors. This was demonstrated on a poly(9,9-dialkylfluorene-alt-triarylamine) as p-channel semiconductor, with a surfactantion-exchanged poly(3,4-ethylenedioxythiophene)-polystyrenesulfonate complex as top-gate electrode. The devices operate at a low voltage with a field-effect mobility of few 10−4 cm2/Vs, and can be continuously operated at 120 °C.
Ellipsoidal Toolbox (ET) (2006)

Ellipsoidal Toolbox is the first free MATLAB package that implements the operations of ellipsoidal calculus: geometric (Minkowski) sums and differences of ellipsoids, intersections of ellipsoids, and ellipsoids with hyperplanes and polyhedra. The toolbox uses ellipsoidal methods to compute forward and backward reach sets of continuous- and discrete-time piecewise affine systems. Forward and backward reach sets can be also computed for continuous-time piece-wise linear systems with disturbances
Utilization of Formic Acid as C1 Building Block for the Ruthenium‐Catalyzed Synthesis of Formaldehyde Surrogates (2020)

Abstract Dialkoxymethanes are becoming increasingly important as fuel additives, formaldehyde surrogates, and chemical intermediates, but the effective synthesis remains challenging. Herein, the catalytic synthesis of dialkoxymethane products using a molecular catalyst is reported. The catalytic system, comprising the [Ru(triphos)(tmm)] in combination with the Lewis acid Al(OTf) 3 , enables the direct synthesis of dialkoxymethane products with formic acid as C1 building block in high to excellent turnover numbers.