gebhart/patrepeval huggingface dataset:
Attenuation of Phosphate Starvation Responses by Phosphite in Arabidopsis (2001)

When inorganic phosphate is limiting, Arabidopsis has the facultative ability to metabolize exogenous nucleic acid substrates, which we utilized previously to identify insensitive phosphate starvation response mutants in a conditional genetic screen. In this study, we examined the effect of the phosphate analog, phosphite (Phi), on molecular and morphological responses to phosphate starvation. Phi significantly inhibited plant growth on phosphate-sufficient (2 mM) and nucleic acid-containing (2 mM phosphorus) media at concentrations higher than 2.5 mM. However, with respect to suppressing typical responses to phosphate limitation, Phi effects were very similar to those of phosphate. Phosphate starvation responses, which we examined and found to be almost identically affected by both anions, included changes in: (a) the root-to-shoot ratio; (b) root hair formation; (c) anthocyanin accumulation; (d) the activities of phosphate starvation-inducible nucleolytic enzymes, including ribonuclease, phosphodiesterase, and acid phosphatase; and (e) steady-state mRNA levels of phosphate starvation-inducible genes. It is important that induction of primary auxin response genes by indole-3-acetic acid in the presence of growth-inhibitory Phi concentrations suggests that Phi selectively inhibits phosphate starvation responses. Thus, the use of Phi may allow further dissection of phosphate signaling by genetic selection for constitutive phosphate starvation response mutants on media containing organophosphates as the only source of phosphorus.
High performance 32nm logic technology featuring 2<sup>nd</sup> generation high-k + metal gate transistors (2009)

A 32 nm logic technology for high performance microprocessors is described. 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> generation high-k + metal gate transistors provide record drive currents at the tightest gate pitch reported for any 32 nm or 28 nm logic technology. NMOS drive currents are 1.62 mA/um Idsat and 0.231 mA/um Idlin at 1.0 V and 100 nA/um I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</sub> . PMOS drive currents are 1.37 mA/um Idsat and 0.240 mA/um Idlin at 1.0 V and 100 nA/um I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</sub> . The impact of SRAM cell and array size on Vccmin is reported.
Halofunctionalization of alkenes by vanadium chloroperoxidase from Curvularia inaequalis (2017)

The vanadium-dependent chloroperoxidase from Curvularia inaequalis is a stable and efficient biocatalyst for the hydroxyhalogenation of a broad range of alkenes into halohydrins. Up to 1 200 000 TON with 69 s<sup>-1</sup> TOF were observed for the biocatalyst. A bienzymatic cascade to yield epoxides as reaction products is presented.
Cytokine profile and prognostic significance of high neutrophil-lymphocyte ratio in colorectal cancer (2015)

High NLR is an independent poor prognostic marker in CRC and correlates with a distinct cytokine profile related to key biological processes involved in carcinogenesis. A composite NLR-cytokine stratification has enhanced prognostic value in mCRC.
A multiplex DNA methylation assay for noninvasive early detection of gastric cancer. (2023)

300 Background: Gastric cancer (GC) is the fifth leading cancer that ranked fourth in cancer mortality worldwide. Early screening and detection can significantly improve patients’ prognosis and survival. Although in standard GC diagnosis, gastroscopy provides sufficient diagnostic power for identifying GC in early stages, the invasive and costly procedure is not suitable for screening and has low compliance in countries with high GC incidence and large populations. Furthermore, the serum-based GC related biomarkers and non-invasive tests (serum pepsinogen I and II, gastrin-17, and anti-Helicobacter pylori IgG antibody tests) showed insufficient evidence as cost-effective GC screening approaches. A non-invasive DNA methylation assay with high sensitivity was aimed to develop and validate as a potential alternative for GC early detection. Methods: A multiplex quantitative PCR (qPCR) assay for detecting GC-specific DNA methylation markers in plasma was developed, in which the markers were further optimized from a reported seven-marker panel based on a pilot case-control study with 63 GC and 130 non-GC samples. The GC detection model of the assay was developed and locked down in the first cohort consisting of 54 GC and 79 non-GC samples. The second validation cohort with 117 GC and 309 non-GC samples was used to evaluate the assay performance. All plasma samples used in the two cohorts were prospectively collected from patients diagnosed with GC or other gastrointestinal diseases or from healthy donors. Results: The multiplex DNA methylation assay showed an overall sensitivity and specificity of 80% (95% CI: 77–83%) and 65% (95% CI: 63–66%) in the model development cohort, respectively, with a sensitivity of 80% (95% CI: 65–95%, n=10) in the detection of stage I GC. The assay revealed similar performance characteristics in the validation cohort, with an overall sensitivity of 82% (95% CI: 80–83%), a specificity of 69% (95% CI: 68–69%), and a sensitivity of 78% (95% CI: 74–82%, n=41) for the stage I GC detection. The DNA methylation assay outperformed the reported serum-based GC related biomarkers and non-invasive tests (sensitivity of 69.6-70.7% and specificity of 66.8-67.8%) with higher sensitivity, particularly in the stage I GC with a comparable specificity. Conclusions: The multiplex DNA methylation assay provides a potential cost-effective tool that features high sensitivity for GC early detection.
Dialects in short songs of yellow-rumped (Cacicus cela) and red-rumped caciques (Cacicus haemorrhous): evolution and discrimination at the colony level (2013)

International audience
Near‐Room‐Temperature Production of Diameter‐Tunable ZnO Nanorod Arrays through Natural Oxidation of Zinc Metal (2005)

A simple, low-temperature strategy has been developed for the low-cost and large-area fabrication of ZnO nanoarrays on a zinc substrate by the natural oxidation of zinc metal in formamide/water mixtures. The one-step, wet-chemical approach has exhibited well-controlled growth of highly oriented and densely packed ZnO nanoarrays with large-area homogeneity and consisting of nanorods or nanowires with predictable morphologies, such as tunable diameters and identical lengths. The chemical-liquid-deposition process, an analogue to the widely used chemical-vapor-deposition technique, has been used for the near-room-temperature production of ZnO nanoarrays through continuous supply, transport, and thermal decomposition of zinc complexes in a liquid phase.
Nonlocal incoherent solitons in materials with a logarithmic nonlinearity (2004)

We study the propagation of partially coherent beams in spatially nonlocal nonlinear materials with a logarithmic nonlinearity. We describe analytically the beam evolution and find conditions for the formation of nonlocal incoherent solitons.
INCREMENT-BASED ESTIMATORS OF FRACTAL DIMENSION FOR TWO-DIMENSIONAL SURFACE DATA (2000)

This paper is concerned with estimating the fractal dimension of a surface, given the surface height at locations on a two-dimensional rectangular grid. Some new estimators are proposed and their properties, both numerical and theoretical, are examined. However, before describing the contents of this paper in more detail, we shall briefly review some earlier work on the (simpler) case of one-dimensional sampling.
Multiphase Designer Droplets for Liquid‐Liquid Extraction (2012)

Multiphase liquid droplets consisting of three connected but immiscible liquid phases are demonstrated. The droplets have designer geometries stabilized by surface energy patterns; aqueous phases prefer contact with hydrophilic surface while organic phases prefer contact with hydrophobic areas. The multiphase droplets are applied for liquid-liquid-liquid extraction.
The Importance of Proteins in Defense Against Oxidation (2001)

Free radicals are a normal feature of cellular oxygen metabolism. However, free radical-associated damage is an important factor in many pathological and toxicological processes. For a long time, lipid peroxidation, mediated by oxygen-derived free radicals, was probably the most extensively investigated process. From more recent studies, it has become evident that proteins are also the targets of free radicals, and this has important implication for their activity, unfolding, and degradation, as well as in cell functioning. After giving a brief overview of the key role of proteins in the overall antioxidant defense, this review examines their role as targets of oxidation reactions, taking into account the reactivity of amino acid residues and some of their oxidation products. In light of recent data, we then consider the specific role of sulfur-containing amino acids in protein degradation and their possible interplay with the reversal of limited oxidative lesions. The participation of proteins in the overall antioxidant defense is also discussed, specifically the role of metallothionein as an intracellular antioxidant and that of albumin as a circulating antioxidant.
Climate change: how can primary health care practitioners and researchers make a bigger difference? (2010)

Aims &amp; rationale/Objectives: The climate change research industry has been dominating Methods: The presentation uses literature reviews of the climate change and healthPrincipal findings: As a number of leading climate change researchers have suggestImplications: This paper shows how climate change research could be
Thrust Measurements and Flow Field Analysis of a Piezoelectrically Actuated Oscillating Cantilever (2012)

Although not identical to the motion employed by nature’s swimmers and flyers, the simple harmonic oscillations of cantilever-like structures have been shown to provide efficient low power solutions for applications ranging from thermal management to propulsion. However, in order to quantify their true potential, the resulting flow field and corresponding thrust must be better understood. In this work, a thin, flexible cantilever is actuated via a piezoelectric patch mounted near its base and caused to vibrate in its first resonance mode in air. The flow field is experimentally measured with Particle Image Velocimetry while the thrust produced from the oscillatory motion is quantified using a high resolution scale. The trends observed in the data are captured using an oscillating Reynolds number and a clear relationship is defined between the operating parameters and the resulting thrust. Two dimensional flow fields are extracted from the x-y and y-z planes, and are primarily used to motivate future geometry and sidewall configurations that could greatly enhance the thrust capabilities of the cantilever by directing the flow downstream in a more effective manner.
SOAP: Structural optimization of arithmetic expressions for high-level synthesis (2013)

This paper introduces SOAP, a new tool to automatically optimize the structure of arithmetic expressions for FPGA implementation as part of a high level synthesis flow, taking into account axiomatic rules derived from real arithmetic, such as distributivity, associativity and others. We explicitly target an optimized area/accuracy trade-off, allowing arithmetic expressions to be automatically re-written for this purpose. For the first time, we bring rigorous approaches from software static analysis, specifically formal semantics and abstract interpretation, to bear on source-to-source transformation for high-level synthesis. New abstract semantics are developed to generate a computable subset of equivalent expressions from an original expression. Using formal semantics, we calculate two objectives, the accuracy of computation and an estimate of resource utilization in FPGA. The optimization of these objectives produces a Pareto frontier consisting of a set of expressions. This gives the synthesis tool the flexibility to choose an implementation satisfying constraints on both accuracy and resource usage. We thus go beyond existing literature by not only optimizing the precision requirements of an implementation, but changing the structure of the implementation itself. Using our tool to optimize the structure of a variety of real world and artificially generated examples in single precision, we improve either their accuracy or the resource utilization by up to 60%.
Genetic polymorphisms and ethnic difference in outcome of adjuvant FOLFOX chemotherapy in Korean patients with colon cancer. (2012)

623 Background: Ethnic diversity of genetic polymorphism can result in individual differences in the efficacy and toxicity of cancer chemotherapy. Methods: A total of 292 Korean patients (183 men and 109 women) from six hospitals in Korea were prospectively enrolled. Patients had resected stage III or high-risk stage II colon cancer and were treated with 12 cycles of adjuvant oxaliplatin plus leucovorin plus 5-fluorouracil (FOLFOX) chemotherapy. 20 germline polymorphisms in 10 genes (TS, MTHFR, ERCC1, XPD, XRCC1, ABCC2, AGXT, GSTP1, GSTT1 and GSTM1) were analyzed from peripheral blood. TS genotype in 5’UTR was classified as ‘high’ (2R/3G, 3C/3G, and 3G/3G) or ‘low’ (2R/2R, 2R/3C, and 3C/3C). Results: Most patients (86.3%) received 12 complete cycles of FOLFOX chemotherapy. In contrast to previous studies in Caucasians, neutropenia (grade 3–4, 60.5%) was frequently observed in our Korean patients, whereas only 16.4% experienced grade 2 or more sensory neuropathy. Neutropenia was more frequent in MTHFR 677TT [adjusted odds ratio (OR) 2.32, 95% confidence interval (CI) 1.19–4.55] and ERCC1 19007TT (adjusted OR 4.58, 95% CI 1.20–17.40) genotypes. Patients harboring XRCC1 23885GG had lower risk of neuropathy (adjusted hazard ratio 0.56, 95% CI 0.32-0.99) and longer time to the onset of grade 2-4 neuropathy. MTHFR 677TT and XRCC1 23885GG genotype was also more prevalent in Koreans compared to Caucasians, and the difference of genotypic frequency could partly explain the ethnically different toxicity profile. After median 49.4 months of follow-up, there were 58 (19.9%) relapses and 19 (6.5%) deaths. TS ‘low’ genotype [adjusted hazard ratio (OR) 1.83, 95% CI 1.003–3.34] was significantly related to shorter disease-free survival. Overall survival was not significantly different according to the polymorphisms. Conclusions: Polymorphisms in MTHFR, XRCC1 and TS are related to toxicities and disease-free survival in patients with colon cancer. These polymorphisms may explain the ethnic difference in toxicity profile following adjuvant FOLFOX chemotherapy.
Hazards and risks of process related contaminants in feed and foods of animal origin formed as a result of heating (2018)

Heating of feed and food at high temperatures is known to result in the formation of process related contaminants that may raise health concerns for the consumer. These processes related contaminants formed during heating of feed and food include acrylamide, furans, polycyclic aromatic hydrocarbons (PAHs), heterocyclic amines (HCAs), acrolein, 3-monochloropropanediol (3-MCPD) esters and glycidyl esters. The present chapter provides an overview of the hazards and risks of these process related contaminants from heating, focussing on feed and food of animal origin. Acrylamide, furans, PAHs, HCAs and glycidyl esters are of concern because they are genotoxic and carcinogenic. Risk assessment of the levels of these process related contaminants in food in general as well as in food from animal origin was done using the margin of exposure approach. The results obtained indicate that for acrylamide, current exposure levels are of concern, although the risks for the consumer of acrylamide in food may originate mainly from other food categories than from food of animal origin. Also exposure to glycidol and its esters may raise a concern with fried and roast meat being among the major contributors to current levels of exposure. Exposure of the consumer to furans is also estimated to occur at levels that raise a health concern, but major dietary exposure is likely to come from other food products than food from animal origin. For PAHs, especially high level exposure raises a concern, with seafood and seafood products and also meat products contributing substantially to current exposure levels. HCAs and 3-MCPD and its esters are present in processed fish and meat but not at levels that give rise to a safety concern. Finally, exposure to acrolein may be at levels below the currently established tolerable daily intake (TDI). Intake from foods with high acrolein content may increase exposure to levels above the TDI, but this is not likely as a result of consumption of food of animal origin. It is concluded that of all process related contaminants from heating and present in food of animal origin, especially PAHs and glycidol and its esters may require risk management actions.
Nonlinear Propagation of Orbit Uncertainty Using Non-Intrusive Polynomial Chaos (2013)

This paper demonstrates the use of polynomial chaos expansions for the nonlinear, non-Gaussian propagation of orbit state uncertainty. Using linear expansions in tensor products of univariate orthogonal polynomial bases, polynomial chaos expansions approximate the stochastic solution of the ordinary differential equation describing the propagated orbit, and include information on covariance, higher moments, and the spatial density of possible solutions. Results presented in this paper use non-intrusive, i.e., sampling-based, methods in combination with either least-squares regression or pseudospectral collocation to estimate the polynomial chaos expansion coefficients at any future point in time. Such methods allow for the usage of existing orbit propagators. Samples based on sun-synchronous and Molniya orbit scenarios are propagated for up to ten days using two-body and higher-fidelity force models. Tests demonstrate that the presented methods require the propagation of orders of magnitude fewer samples than Monte Carlo techniques, and provide an approximation of the a posteriori probability density function that achieves the desired accuracy. Results also show that Poincaré-based polynomial chaos expansions require fewer samples to achieve a given accuracy than Cartesian-based solutions. In terms of probability density function accuracy, the polynomial chaos expansion-based solutions represent an improvement over the linear propagation and unscented transformation techniques.
Nitrogen Leaching From Agricultural Soils Under Imposed Freeze-Thaw Cycles: A Column Study With and Without Fertilizer Amendment (2022)

Cold regions are warming faster than the rest of the planet, with the greatest warming occurring during the winter and shoulder seasons. Warmer winters are further predicted to result in more frequent soil freezing and thawing events. Freeze-thaw cycles affect biogeochemical soil processes and alter carbon and nutrient export from soils, hence impacting receiving ground and surface waters. Cold region agricultural management should therefore consider the possible effects on water quality of changing soil freeze-thaw dynamics under future climate conditions. In this study, soil column experiments were conducted to assess the leaching of fertilizer nitrogen (N) from an agricultural soil during the non-growing season. Identical time series temperature and precipitation were imposed to four parallel soil columns, two of which had received fertilizer amendments, the two others not. A 15-30-15 N-P-K fertilizer (5.8% ammonium and 9.2% urea) was used for fertilizer amendments. Leachates from the soil columns were collected and analyzed for major cations and anions. The results show that thawing following freezing caused significant export of chloride (Cl − ), sulfate (SO 4 2− ) and nitrate (NO 3 − ) from the fertilizer-amended soils. Simple plug flow reactor model calculations indicated that the high NO 3 − concentrations produced during the fertilized soil thawing events were due to nitrification of fertilizer N in the upper oxidized portion of the soil. The very low concentrations of NO 3 − and ammonium in the non-fertilized soils leachates implied that the freeze-thaw cycles had little impact on the mineralization of soil organic N. The findings, while preliminary, indicate that unwanted N enrichment of aquifers and rivers in agricultural areas caused by fall application of N fertilizers may be exacerbated by changing freeze-thaw activity.
Some conceptual problems in the CCU 2016 draft of the New SI (2016)

After a short introduction to the present SI (Système International des Unités), this poster presentation illustrates a digest of the basics of the proposed New SI and of its difference with respect to the present SI. This involves a review of some unresolved problems in the CCU 2016 draft, concerning: the role of the constants of physics in it and their role in the conceptual construction of this international standard; the implications for science of the New SI implementation. Consequences and new duties for the users are illustrated, involving a possible hierarchy between countries that would be installed by the new definition.
Aspect determination using a transducer with a spiral wavefront: Basic concept and numerical modeling. (2009)

A circular cylindrical acoustic transducer whose direction of motion is radial produces an outgoing signal whose wavefronts are concentric circles. A similar transducer can be designed to generate spiral wavefronts where the phase of the outgoing wave changes by 360 deg in one revolution around the transducer. If these two transducers are used in tandem as a beacon, short tone bursts fired consecutively from each transducer can be used to determine the aspect angle to a receiver relative to the beacon. This is an acoustic version of the VHF omnidirectional ranging systems currently in use in airplane navigation. There are several ways of designing a transducer to produce the spiral wavefront required for the beacon. Several of these designs have been modeled numerically to understand the details of the outgoing field and their impact on aspect determination. [Work supported by ONR.]
Interactive Tools for Teaching Fourier Transforms (2020)

ABSTRACT Fourier transforms (FT) are universal in chemistry, physics, and biology. Despite FTs being a core component of multiple experimental techniques, undergraduate courses typically approach FTs from a mathematical perspective, leaving students with a lack of intuition on how an FT works. Here, I introduce interactive teaching tools for upper-level undergraduate courses and describe a practical lesson plan for FTs. The materials include a computer program to capture video from a webcam and display the original images side-by-side with the corresponding plot in the Fourier domain. Several patterns are included to be printed on paper and held up to the webcam as input. During the lesson, students are asked to predict the features observed in the FT and then place the patterns in front of the webcam to test their predictions. This interactive approach enables students with limited mathematical skills to achieve a certain level of intuition for how FTs translate patterns from real space into the corresponding Fourier space.