gebhart/patrepeval huggingface dataset:
Overview of RFX fusion science program (2012)

This paper summarizes the main achievements of the RFX fusion science program in the period between the 2008 and 2010 IAEA Fusion Energy Conferences. RFX-mod is the largest reversed field pinch in the world, equipped with a system of 192 coils for active control of MHD stability. The discovery and understanding of helical states with electron internal transport barriers and core electron temperature &gt; 1.5 keV significantly advances the perspectives of the configuration. Optimized experiments with plasma current up to 1.8 MA have been realized, confirming positive scaling. The first evidence of edge transport barriers is presented. Progress has been made also in the control of first-wall properties and of density profiles, with initial first-wall lithization experiments. Micro-turbulence mechanisms such as ion temperature gradient and micro-tearing are discussed in the framework of understanding gradient-driven transport in low magnetic chaos helical regimes. Both tearing mode and resistive wall mode active control have been optimized and experimental data have been used to benchmark numerical codes. The RFX programme also provides important results for the fusion community and in particular for tokamaks and stellarators on feedback control of MHD stability and on three-dimensional physics. On the latter topic, the result of the application of stellarator codes to describe three-dimensional reversed field pinch physics will be presented.
Dissecting the chloride–nitrate anion transport assay (2017)

A systematic study of chloride vs. nitrate selectivity across six anion transporters has revealed a good correlation between the selectivities of their anion binding and membrane transport properties. This work reveals the limitations of the chloride-nitrate exchange assay and shows how new approaches can be used to measure anion uniport.
Examining effects of rhizobacteria in relieving abiotic crop stresses using carbon‐11 radiotracing (2022)

In agriculture, plant growth promoting bacteria (PGPB) are increasingly used for reducing environmental stress-related crop losses through mutualistic actions of these microorganisms, activating physiological and biochemical responses, building tolerances within their hosts. Here we report the use of radioactive carbon-11 (t<sub>½</sub> 20.4 min) to examine the metabolic and physiological responses of Zea mays to Azospirillum brasilense (HM053) inoculation while plants were subjected to salinity and low nitrogen stresses. Host metabolism of "new" carbon resources (as <sup>11</sup> C) and physiology including [<sup>11</sup> C]-photosynthate translocation were measured in response to imposed growth conditions. Salinity stress caused shortened, dense root growth with a 6-fold increase in foliar [<sup>11</sup> C]-raffinose, a potent osmolyte. ICP-MS analyses revealed increased foliar Na<sup>+</sup> levels at the expense of K<sup>+</sup> . HM053 inoculation relieved these effects, reinstating normal root growth, lowering [<sup>11</sup> C]-raffinose levels while increasing [<sup>11</sup> C]-sucrose and its translocation to the roots. Na<sup>+</sup> levels remained elevated with inoculation, but K<sup>+</sup> levels were boosted slightly. Low nitrogen stress yielded longer roots possessing high levels of anthocyanins. Metabolic analysis revealed significant shifts in "new" carbon partitioning into the amino acid pool under low nitrogen stress, with significant increases in foliar [<sup>11</sup> C]-glutamate, [<sup>11</sup> C]-aspartate, and [<sup>11</sup> C]-asparagine, a noted osmoprotectant. <sup>11</sup> CO<sub>2</sub> fixation and [<sup>11</sup> C]-photosynthate translocation also decreased, limiting carbon supply to roots. However, starch levels in roots were reduced under nitrogen limitation, suggesting that carbon repartitioning could be a compensatory action to support root growth. Finally, inoculation with HM053 re-instated normal root growth, reduced anthocyanin, boosted root starch, and returned <sup>11</sup> C-allocation levels back to those of unstressed plants.
Analytical CPG model driven by limb velocity input generates accurate temporal locomotor dynamics (2018)

The ability of vertebrates to generate rhythm within their spinal neural networks is essential for walking, running, and other rhythmic behaviors. The central pattern generator (CPG) network responsible for these behaviors is well-characterized with experimental and theoretical studies, and it can be formulated as a nonlinear dynamical system. The underlying mechanism responsible for locomotor behavior can be expressed as the process of leaky integration with resetting states generating appropriate phases for changing body velocity. The low-dimensional input to the CPG model generates the bilateral pattern of swing and stance modulation for each limb and is consistent with the desired limb speed as the input command. To test the minimal configuration of required parameters for this model, we reduced the system of equations representing CPG for a single limb and provided the analytical solution with two complementary methods. The analytical and empirical cycle durations were similar (<i>R</i> <sup>2</sup> = 0.99) for the full range of walking speeds. The structure of solution is consistent with the use of limb speed as the input domain for the CPG network. Moreover, the reciprocal interaction between two leaky integration processes representing a CPG for two limbs was sufficient to capture fundamental experimental dynamics associated with the control of heading direction. This analysis provides further support for the embedded velocity or limb speed representation within spinal neural pathways involved in rhythm generation.
Quantitative 1H Nuclear Magnetic Resonance Metabolite Profiling as a Functional Genomics Platform to Investigate Alkaloid Biosynthesis in Opium Poppy   (2008)

Opium poppy (Papaver somniferum) produces a diverse array of bioactive benzylisoquinoline alkaloids and has emerged as a versatile model system to study plant alkaloid metabolism. The plant is widely cultivated as the only commercial source of the narcotic analgesics morphine and codeine. Variations in plant secondary metabolism as a result of genetic diversity are often associated with perturbations in other metabolic pathways. As part of a functional genomics platform, we used (1)H nuclear magnetic resonance (NMR) metabolite profiling for the analysis of primary and secondary metabolism in opium poppy. Aqueous and chloroform extracts of six different opium poppy cultivars were subjected to chemometric analysis. Principle component analysis of the (1)H NMR spectra for latex extracts clearly distinguished two varieties, including a low-alkaloid variety and a high-thebaine, low-morphine cultivar. Distinction was also made between pharmaceutical-grade opium poppy cultivars and a condiment variety. Such phenotypic differences were not observed in root extracts. Loading plots confirmed that morphinan alkaloids contributed predominantly to the variance in latex extracts. Quantification of 34 root and 21 latex metabolites, performed using Chenomx NMR Suite version 4.6, showed major differences in the accumulation of specific alkaloids in the latex of the low-alkaloid and high-thebaine, low-morphine varieties. Relatively few differences were found in the levels of other metabolites, indicating that the variation was specific for alkaloid metabolism. Exceptions in the low-alkaloid cultivar included an increased accumulation of the alkaloid precursor tyramine and reduced levels of sucrose, some amino acids, and malate. Real-time polymerase chain reaction analysis of 42 genes involved in primary and secondary metabolism showed differential gene expression mainly associated with alkaloid biosynthesis. Reduced alkaloid levels in the condiment variety were associated with the reduced abundance of transcripts encoding several alkaloid biosynthetic enzymes.
Optimal Flight for Ground Noise Reduction in Helicopter Landing Approach: Optimal Altitude and Velocity Control (2007)

This study aims to obtain the optimal flights of a helicopter that reduce ground noise during landing approach with an optimization technique, and to conduct flight tests for confirming the effectiveness of the optimal solutions. Past experiments of Japan Aerospace Exploration Agency (JAXA) show that the noise of a helicopter varies significantly according to its flight conditions, especially depending on the flight path angle. We therefore build a simple noise model for a helicopter, in which the level of the noise generated from a point sound source is a function only of the flight path angle. Using equations of motion for flight in a vertical plane, we define optimal control problems for minimizing noise levels measured at points on the ground surface, and obtain optimal controls for specified initial altitudes, flight constraints, and wind conditions. The obtained optimal flights avoid the flight path angle which generates large noise and decrease the flight time, which are different from conventional flight. Finally, we verify the validity of the optimal flight patterns through flight experiments. The actual flights following the optimal paths resulted in noise reduction, which shows the effectiveness of the optimization.
Structure and Function of REP34 Implicates Carboxypeptidase Activity in Francisella tularensis Host Cell Invasion (2014)

Francisella tularensis is the etiological agent of tularemia, or rabbit fever. Although F. tularensis is a recognized biothreat agent with broad and expanding geographical range, its mechanism of infection and environmental persistence remain poorly understood. Previously, we identified seven F. tularensis proteins that induce a rapid encystment phenotype (REP) in the free-living amoeba, Acanthamoeba castellanii. Encystment is essential to the pathogen's long term intracellular survival in the amoeba. Here, we characterize the cellular and molecular function of REP34, a REP protein with a mass of 34 kDa. A REP34 knock-out strain of F. tularensis has a reduced ability to both induce encystment in A. castellanii and invade human macrophages. We determined the crystal structure of REP34 to 2.05-Å resolution and demonstrate robust carboxypeptidase B-like activity for the enzyme. REP34 is a zinc-containing monomeric protein with close structural homology to the metallocarboxypeptidase family of peptidases. REP34 possesses a novel topology and substrate binding pocket that deviates from the canonical funnelin structure of carboxypeptidases, putatively resulting in a catalytic role for a conserved tyrosine and distinct S1' recognition site. Taken together, these results identify REP34 as an active carboxypeptidase, implicate the enzyme as a potential key F. tularensis effector protein, and may help elucidate a mechanistic understanding of F. tularensis infection of phagocytic cells.
Gene Expression Analysis of Energy Metabolism Mutants of <i>Desulfovibrio vulgaris</i> Hildenborough Indicates an Important Role for Alcohol Dehydrogenase (2003)

Comparison of the proteomes of the wild-type and Fe-only hydrogenase mutant strains of Desulfovibrio vulgaris Hildenborough, grown in lactate-sulfate (LS) medium, indicated the near absence of open reading frame 2977 (ORF2977)-coded alcohol dehydrogenase in the hyd mutant. Hybridization of labeled cDNA to a macroarray of 145 PCR-amplified D. vulgaris genes encoding proteins active in energy metabolism indicated that the adh gene was among the most highly expressed in wild-type cells grown in LS medium. Relative to the wild type, expression of the adh gene was strongly downregulated in the hyd mutant, in agreement with the proteomic data. Expression was upregulated in ethanol-grown wild-type cells. An adh mutant was constructed and found to be incapable of growth in media in which ethanol was both the carbon source and electron donor for sulfate reduction or was only the carbon source, with hydrogen serving as electron donor. The hyd mutant also grew poorly on ethanol, in agreement with its low level of adh gene expression. The adh mutant grew to a lower final cell density on LS medium than the wild type. These results, as well as the high level of expression of adh in wild-type cells on media in which lactate, pyruvate, formate, or hydrogen served as the sole electron donor for sulfate reduction, indicate that ORF2977 Adh contributes to the energy metabolism of D. vulgaris under a wide variety of metabolic conditions. A hydrogen cycling mechanism is proposed in which protons and electrons originating from cytoplasmic ethanol oxidation by ORF2977 Adh are converted to hydrogen or hydrogen equivalents, possibly by a putative H(2)-heterodisulfide oxidoreductase complex, which is then oxidized by periplasmic Fe-only hydrogenase to generate a proton gradient.
Patient Satisfaction Measurement in the Disease Management Industry (2005)

In mid-2004, the Disease Management Association of America (DMAA) Patient Satisfaction Workgroup in association with J.D. Power and Associates (JDPA) conducted a literature review and a member survey to gain an understanding of the nature of patient satisfaction measurement as it pertains to disease management (DM) programs within the DM industry. A review of the relevant literature indicates that perhaps, with the exception of diabetes disease management, there are no prevalent, systematic, or statistically validated approaches for measuring patient satisfaction within the disease management industry. Most existing studies tend to focus on the effectiveness of a disease management program on clinical outcomes, with patient satisfaction measured only as a part of a battery of "outcome" measures. However, many of these studies do find positive associations between patient satisfaction and clinical outcomes. A majority of the 49 respondents who completed the member feedback survey hold relatively high positions in their organizations. The vast majority of respondents indicate their organizations conduct patient satisfaction surveys that assess overall satisfaction, satisfaction with materials and information provided, and with staff members. Patient satisfaction surveys are most common among the five common chronic diseases: diabetes, asthma, congestive heart failure (CHF), coronary artery disease (CAD), and chronic obstructive pulmonary disease (COPD). More than three in four respondents agree that patient satisfaction measurement is important to the long-term success of their programs. Respondents also indicate that along with intelligence on patients' overall satisfaction with the program, they would also like to gain an understanding of whether or not their programs actually help manage the patient's medical condition. Eight survey instruments currently in use and submitted by study participants were also reviewed. Most of these instruments are relatively short and basic, typically administered by mail, and vary in the types of questions and response categories presented to respondents. This research concludes that there exists an implied need for patient satisfaction measurement in the DM industry and an opportunity to develop and leverage a standardized measurement approach assessing patient satisfaction. Additionally, the authors suggest that there may be value to conceptualizing "patient satisfaction" not as an outcome in itself, but as a means to increase compliance, which, in turn, can improve medical outcomes.
Abstract P276: Tissue Primacy of Chymase as an Angiotensin II-forming Enzyme from Angiotensin-(1-12) (2016)

Breaking the prevailing acceptance of ACE primacy as the Ang II-forming enzyme, we have demonstrated that cardiac Ang II production in human and rat heart tissues are primarily mediated by chymase. In this study, we compared the affinity of cardiac chymase to generate Ang II from Ang-(1-12) or Ang I in plasma membranes (PMs) isolated from the diseased left atria of humans and SHR left ventricle. PMs (50-100 μg) were exposed to increasing concentrations of either Ang-(1-12) or Ang I substrate (0-300 μM) for 30 min at 37 o C in the presence of lisinopril (200 μM). The K m and V max of human cardiac chymase (Mean ± SE) were 29 ± 0.9 vs 87 ± 8.8 μM and 57 ± 1.4 vs 145 ± 3.7 μM/min/mg for Ang-(1-12) and Ang I substrates, respectively. Similarly, the K m and V max of rat cardiac chymase were 64 ± 6.3 vs 142 ± 17 μM and 13.2 ± 1.3 vs 1.9 ± 0.2 μM/min/mg for Ang-(1-12) and Ang I substrate, respectively. These data suggest that cardiac chymase has a higher affinity for Ang-(1-12) substrate compared to Ang I in both human and rat heart tissues. Further, our kinetic data show that the catalytic efficiency (ratio of V max /K m ) of human and rat chymase were 1.2 and 15.4-fold higher for Ang-(1-12) substrate compared to Ang I. Overall, our findings suggest that Ang-(1-12), rather than Ang I, is the preferred substrate for chymase in the generation of Ang II by human and rat heart tissue.
Annexin-A1: Therapeutic Potential in Microvascular Disease (2019)

Annexin-A1 (ANXA1) was first discovered in the early 1980's as a protein, which mediates (some of the) anti-inflammatory effects of glucocorticoids. Subsequently, the role of ANXA1 in inflammation has been extensively studied. The biology of ANXA1 is complex and it has many different roles in both health and disease. Its effects as a potent endogenous anti-inflammatory mediator are well-described in both acute and chronic inflammation and its role in activating the pro-resolution phase receptor, FPR2, has been described and is now being exploited for therapeutic benefit. In the present mini review, we will endeavor to give an overview of ANXA1 biology in relation to inflammation and functions that mediate pro-resolution that are independent of glucocorticoid induction. We will focus on the role of ANXA1 in diseases with a large inflammatory component focusing on diabetes and microvascular disease. Finally, we will explore the possibility of exploiting ANXA1 as a novel therapeutic target in diabetes and the treatment of microvascular disease.
Inhibiting Protein Prenylation with Benzoxaboroles to Target Fungal Plant Pathogens (2020)

Fungal pathogens pose an increasing threat to global food security through devastating effects on staple crops and contamination of food supplies with carcinogenic toxins. Widespread deployment of agricultural fungicides has increased crop yields but is driving increasingly frequent resistance to available agents and creating environmental reservoirs of drug-resistant fungi that can also infect susceptible human populations. To uncover non-cross-resistant modes of antifungal action, we leveraged the unique chemical properties of boron chemistry to synthesize novel 6-thiocarbamate benzoxaboroles with broad spectrum activity against diverse fungal plant pathogens. Through whole genome sequencing of <i>Saccharomyces cerevisiae</i> isolates selected for stable resistance to these compounds, we identified mutations in the protein prenylation-related genes, <i>CDC43</i> and <i>ERG20</i>. Allele-swapping experiments confirmed that point mutations in <i>CDC43</i>, which encodes an essential catalytic subunit within geranylgeranyl transferase I (GGTase I) complex, were sufficient to confer resistance to the benzoxaboroles. Mutations in <i>ERG20</i>, which encodes an upstream farnesyl pyrophosphate synthase in the geranylgeranylation pathway, also conferred resistance. Consistent with impairment of protein prenylation, the compounds disrupted membrane localization of the classical geranylgeranylation substrate Cdc42. Guided by molecular docking predictions, which favored Cdc43 as the most likely direct target, we overexpressed and purified functional GGTase I complex to demonstrate direct binding of benzoxaboroles to it and concentration-dependent inhibition of its transferase activity. Further development of the boron-containing scaffold described here offers a promising path to the development of GGTase I inhibitors as a mechanistically distinct broad spectrum fungicide class with reduced potential for cross-resistance to antifungals in current use.
Encoding Functions with Constant Online Rate, or How to Compress Garbled Circuit Keys (2015)

Randomized encodings of functions can be used to replace a “complex” function $f(x)$ by a “simpler” randomized mapping $\hat{f}(x;r)$ whose output distribution on an input $x$ encodes the value of $f(x)$ and hides any other information about $x$. One desirable feature of randomized encodings is low online complexity. That is, the goal is to obtain a randomized encoding $\hat{f}$ of $f$ in which most of the output can be precomputed and published before seeing the input $x$. When the input $x$ is available, it remains to publish only a short string $\hat{x}$, where the online complexity of computing $\hat{x}$ is independent of (and is typically much smaller than) the complexity of computing $f$. Yao's garbled circuit construction gives rise to such randomized encodings in which the online part $\hat{x}$ consists of $n$ encryption keys of length $\kappa$ each, where $n=|x|$ and $\kappa$ is a security parameter. Thus, the online rate $|\hat{x}|/|x|$ of this encoding is proportional to the security parameter $\kappa$. In this paper, we show that the online rate can be dramatically improved. Specifically, we show how to encode any polynomial-time computable function $f:\{0,1\}^n\to\{0,1\}^{m(n)}$ with online rate of $1+o(1)$ and with nearly linear online computation. More concretely, the online part $\hat{x}$ consists of an $n$-bit string and a single encryption key. These constructions can be based on the decisional Diffie--Hellman (DDH) assumption, the learning with errors (LWE) assumption, or the RSA assumption. We also present a variant of this result which applies to arithmetic formulas, where the encoding only makes use of arithmetic operations, as well as several negative results which complement our positive results. Our positive results can lead to efficiency improvements in most contexts where randomized encodings of functions are used. We demonstrate this by presenting several concrete applications. These include protocols for secure multiparty computation and for noninteractive verifiable computation in the preprocessing model which achieve, for the first time, an optimal online communication complexity, as well as noninteractive zero-knowledge proofs which simultaneously minimize the online communication and the prover's online computation.
Spectroscopic Performance of TERA: Fast Multichannel Analog Pulse Processor ASIC for X-ray Detection Applications (2019)

This work reports the spectroscopic performance of the latest release of TERA (Throughput Enhanced Readout ASIC), a multichannel analog pulse processor (APP) ASIC suitable for detectors in ultra-high rate X-ray detection applications (>1Mcps/channel). The chip has been developed to process signals coming from Silicon Drift Detectors (SDDs) coupled with resettype Charge Sensitive Amplifiers (CSA). The demonstrator chip is composed of 4 parallel readout channels, each channel is composed by 7 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> -order semi-Gaussian shaping-amplifier with adjustable shaping times and dynamic range, followed by a peak stretcher and an analog memory. Each pair of channels can be optionally digitized by 12-bit on-chip ADC, providing the maximum sampling frequency up to 2.5MHz. TERA architecture enables to achieve simultaneously high throughput and satisfactory energy resolution. In <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">55</sup> Fe spectroscopy measurements using SDD collimated to 4mm diameter, at the shortest pulse width of 200ns, FWHM Mn-Ka line of 171.5eV and 205.1eV were obtained at input rate 10kcps and 1.61Mcps, respectively. At 1.61Mcps input rate, 1.09Mcps throughput was achieved. High-rate performances are, to our knowledge, the best ones for a Spectroscopy analog ASIC and are close to the ones achievable with standard DPPs. Therefore, TERA can represent an attractive detector pulse processing solution for high-density multichannel detection systems.