gebhart/patrepeval huggingface dataset:
Challenges in seismic rock physics (2022)

Research in seismic rock physics is primarily concerned with establishing the quantitative relationship between geophysical measurements and subsurface rock parameters to explain the variations in seismic responses caused by changes in reservoir rock and fluid properties. Key challenges include effectively identifying sweet spots in a variety of tight reservoirs with low reservoir abundance, detailed characterization of high-quality oil and gas resources, and accurate prediction of the spatial distribution of oil, gas and water in late-stage oil and gas production.
Demethoxycurcumin-Metal Complexes: Fragmentation and Comparison with Curcumin-Metal Complexes, as Studied by ESI-MS/MS (2013)

Two questions are asked: the first is if the lack/presence of methoxyl moiety at aromatic ring essentially affects the stability of curcuminoid-metal complexes, and the second is if it is possible that in the metal complexes one of the possible demethoxycurcumin structures predominates. To answer the first question, the ESI-MS/MS spectra were taken of ions containing demethoxycurcumin, curcumin, and metal cation (e.g., ion [dCurc + Curc-H + Pb] + ), and in order to answer the second question the ESI-MS/MS spectra were recorded of ions containing demethoxycurcumin and metal cation (e.g., ion [dCurc-H + Zn] + ). An interpretation of the mass spectra has indicated that (i) for some metals, curcumin-metal complexes are more stable than demethoxycurcumin-metal complexes and for some metals vice versa, and (ii) in demethoxycurcumin-metal complexes structure B1 [(1 E ,4 Z ,6 E )-5-hydroxy-7-(4-hydroxy-3-methoxyphenyl)-1-(4-hydroxyphenyl)hepta-1,4,6-trien-3-one] is more stable than structure B2 [(1 E ,4 Z ,6 E )-5-hydroxy-1-(4-hydroxy-3-methoxyphenyl)-7-(4-hydroxyphenyl)hepta-1,4,6-trien-3-one].
Durable alveolar engraftment of PSC-derived lung epithelial cells into immunocompetent mice (2022)

Abstract Durable reconstitution of the injured distal lung epithelium with pluripotent stem cell (PSC) derivatives, if realized, would represent a promising potential therapy for diseases that result from alveolar damage. Here we differentiate murine PSCs in vitro into self-renewing lung epithelial progenitors able to engraft into the injured distal lung epithelium of immunocompetent, syngeneic mouse recipients. Emulating the roadmap of the developing embryo, we generate transplantable PSC-derived Nkx2-1+/Sox9+ lung epithelial progenitors that are highly similar to cultured primary embryonic distal lung bud tip progenitors. These cells display a stable phenotype after frozen archiving or extensive expansion in culture, providing a nearly inexhaustible source of cells that can be engrafted into syngeneic injured mouse lungs without the need for immunosuppression. After transplantation PSC-derived tip-like progenitors downregulate Sox9 and mature in the distal lung, upregulating alveolar type 2 cell markers or assuming the flat morphology and molecular phenotype of terminally differentiated alveolar type 1 cells. After months in vivo, donor-derived cells retain their alveolar epithelial type 2-like and type 1-like phenotypes, as characterized by single cell RNA sequencing, ultrastructural analyses, in vivo histologic profiling, and ex vivo organoid assays that demonstrate continued capacity of the engrafted cells to proliferate and differentiate. These results indicate durable reconstitution of the distal lung’s facultative progenitor and differentiated epithelial cell compartments in vivo with PSC-derived cells, thus establishing a novel model for pulmonary cell therapy which can be utilized to better understand the mechanisms and utility of engraftment prior to future clinical studies.
Clock Variation Impact on Digital Control System Performance (2019)

Digital controls have become the primary form of control in numerous applications due to the advancements in semiconductor industry and lower cost. Digital control algorithms implemented on digital signal processors (DSPs) or microcontrollers execute the algorithm at a specified clock frequency. Discrete time algorithms such as digital filters and digital PID controllers require the sampling period in the controller design, which is directly related to the microcontroller clock frequency. Due to aging, manufacturing process defects and environment conditions cause the clock frequency to drift from the specification. Such variation affects the discrete time algorithm performance deviate from expected performance.
Characterization of mixing and residence time distributions in nozzle‐type reactors (1989)

Abstract Studies of flow characteristics and residence time distribution, (RTD), have been undertaken in a range of geometrically similar, laboratory nozzle‐type reactors. High‐speed cine‐photography was employed to record the complex phenomena of liquid mixing in the reactor and also to record on film the colour of an injected tracer solution leaving in the effluent. A novel atomic absorption spectrophotometric (AAS) technique was applied to transform the results of the latter film into response curves. This technique provide detailed quantitative data on the residence time distributions (RTD) for different feed rates. A multiparameter model, comprising a network of CSTR's and plug flows, was developed to simulate the experimental response data. Good agreement was obtained between model predictions and experimental results. The experimental technique and theoretical approach are recommended for analyzing the flow patterns and mixing mechanisms in such reactors.
Supplementary Table 3 from Tamoxifen Downregulates <i>Ets</i> Oncogene Family Members <i>ETV4</i> and <i>ETV5</i> in Benign Breast Tissue: Implications for Durable Risk Reduction (2023)

&lt;p&gt;PDF file - 42K, RT-PCR primer sequences.&lt;/p&gt;
IL-23 Enhances the Inflammatory Cell Response in Cryptococcus neoformans Infection and Induces a Cytokine Pattern Distinct from IL-12 (2006)

IL-23, a heterodimeric cytokine composed of the p40 subunit of IL-12 and a novel p19 subunit, has been shown to be a key player in models of autoimmune chronic inflammation. To investigate the role of IL-23 in host resistance during chronic fungal infection, wild-type, IL-12- (IL-12p35-/-), IL-23- (IL-23p19-/-), and IL-12/IL-23- (p40-deficient) deficient mice on a C57BL/6 background were infected with Cryptococcus neoformans. Following infection, p40-deficient mice demonstrated higher mortality than IL-12p35-/- mice. Reconstitution of p40-deficient mice with rIL-23 prolonged their survival to levels similar to IL-12p35-/- mice. IL-23p19-/- mice showed a moderately reduced survival time and delayed fungal clearance in the liver. Although IFN-gamma production was similar in wild-type and IL-23p19-/- mice, production of IL-17 was strongly impaired in the latter. IL-23p19-/- mice produced fewer hepatic granulomata relative to organ burden and showed defective recruitment of mononuclear cells to the brain. Moreover, activation of microglia cells and expression of IL-1beta, IL-6, and MCP-1 in the brain was impaired. These results show that IL-23 complements the more dominant role of IL-12 in protection against a chronic fungal infection by an enhanced inflammatory cell response and distinct cytokine regulation.
Photometry and Visual Assessment of Polarized Light under Realistic Conditions (1982)

The mechanisms that produce Haidinger's polarization brushes introduce a discrepancy between photoelectric and subjective assessments of luminance. Although these effects are measurable they are probably too small to be of concern to the illuminating engineer under most circumstances.
Effect of previous surgery on clinical outcome following 1-level lumbar arthroplasty (2008)

Patients indicated for 1-level lumbar arthroplasty with previous lumbar decompressive surgery can be expected to have similar clinical outcomes to patients undergoing arthroplasty without prior lumbar decompressive surgery. Similarly, candidates for anterior lumbar fusion with prior decompressive surgery may experience similar benefits from the surgical procedure as those without.
Do mammography, sonography, and MR mammography have a diagnostic benefit compared with mammography and sonography? (1997)

MR mammography as an adjunct to mammography and sonography reveals breast cancer with a higher confidence and sensitivity than do mammography and sonography only. The combined method can be recommended if the greatest possible sensitivity or negative predictive value is wanted. However, the combined method is not useful for screening or workup of suspicious lesions because of its lower specificity and accuracy.
Wide Dynamic Range Low Light Level CMOS Image Sensor (2024)

This paper describes a CMOS image sensor technology suitable for the next generation of scientific cameras. We describe a prototype sensor with 320x240 pixels based on this technology. The sensor features 8 different types of 5T pixels with pinned photodiodes. The measured peak quantum efficiency of the sensor is greater than 50% at 550nm, and the read noise is less than 1e- RMS at room temperature. The sensor also achieves an intra-scene linear dynamic range of greater than 92dB (40000:1) at room temperature.
An efficient Optical Character Recognition algorithm using artificial neural network by curvature properties of characters (2014)

Optical Character Recognition (OCR) has gained so much importance among the researchers now a day as it is an eminent sector for a Human Computer Interaction (HCI) System. For an efficient recognition system the primary need is a reliable feature extraction process. So far the feature extraction systems used are mainly based on the character pattern, enclosure or symmetry. Still another property which is based on the angular properties of the several predetermined positions can be used for the purpose of feature extraction process that is the main motivation of this work. The effectiveness of the algorithm has been discussed in the experimental result section where the performance has been compared for different number of feature used.
Apport des nouvelles biotechnologies aux programmes d'amélioration génétique du porc. (2003)

International audience
A de novo molecular generation method using latent vector based generative adversarial network (2019)

Deep learning methods applied to drug discovery have been used to generate novel structures. In this study, we propose a new deep learning architecture, LatentGAN, which combines an autoencoder and a generative adversarial neural network for de novo molecular design. We applied the method in two scenarios: one to generate random drug-like compounds and another to generate target-biased compounds. Our results show that the method works well in both cases. Sampled compounds from the trained model can largely occupy the same chemical space as the training set and also generate a substantial fraction of novel compounds. Moreover, the drug-likeness score of compounds sampled from LatentGAN is also similar to that of the training set. Lastly, generated compounds differ from those obtained with a Recurrent Neural Network-based generative model approach, indicating that both methods can be used complementarily.
Targeting granulocyte‐macrophage colony‐stimulating factor in epithelial and vascular remodeling in experimental eosinophilic esophagitis (2016)

Granulocyte-macrophage colony-stimulating factor is a potential therapeutic target to reduce esophageal eosinophilia and remodeling.
Dissolution of underground cavities: a multiple-scale view (2013)

The generation of underground cavities through dissolution processes is used favorably in many industrial applications (mining, gas storage, ...) but is also the source of hazardous phenomena due to cavity collapse. Dissolution is also fundamental in understanding karstic formations. Because of the intrinsic heterogeneous nature of geological formations, modeling dissolution processes must take into account the different multiple-scale features. Several questions are discussed in this paper to emphasize these multi-scale aspects.
	First, the mathematical nature of dissolution models for porous formations is analyzed based on the upscaling of a simple, generic, dissolution problem. It is shown that several models may arise from the upscaling process depending on the relative importance of local and non-local effects. It is also pointed out that non traditional terms may play an important quantitative role, a problem which has been often underestimated in the literature.
	Then, the question of determining effective surface conditions for describing in a smooth manner the dissolution of chemically and physically heterogeneous surfaces is discussed based on a domain decomposition technique. Such approaches are crucial if one wants to develop large-scale dissolution numerical simulations.
	It is then shown how dissolution processes may be affected by dissolution instabilities (wormholing for instance) and how the size of the domain under investigation affects the stability conditions. Another interesting problem is the dissolution patterns induced by the coupling with hydrodynamic instabilities (natural convection for example) generated in the boundary layer near the dissolving surface.
	Finally, some questions related to the numerical modeling of the dissolution of large-scale cavities are discussed: use of explicit interface tracking (such as ALE) versus diffuse interface models, the use of simplified momentum balance equations, etc...
Supplementary Methods and Materials from Chemotherapy-Induced Upregulation of Small Extracellular Vesicle-Associated PTX3 Accelerates Breast Cancer Metastasis (2023)

&lt;p&gt;Supplementary Methods and Materials&lt;/p&gt;
Control algorithm for the petal-shape segmented-mirror telescope with 18 mirrors (2012)

A 3.8 m segmented telescope is planned to be built at the Okayama Astrophysical Observatory by the joint program among Kyoto university, Nagoya university, NAOJ, and Nano-Optonics Energy Inc. This is the world’s first optical-infrared telescope whose primary mirror is composed of “petal-shaped” segment mirrors. To investigate the best layout of the displacement sensors as well as to study the control algorithm, we have developed a simulation software for the segmented petaloid mirrors. This simulator calculates the vertical position differences between the segments at the 60 displacement sensors based on the three-dimensional movements of the 54 actuators, and enables us to test the control algorithms under various conditions including random noise on the displacement sensors, random movement errors of the actuators, and unexpected lateral shifts of the segments. The outputs of the simulator are not only the phase error of the primary mirror but also the PSF image, taking the structure function of the optical surfaces into account. Using a singular value decomposition method, we found that the 18 petal-shaped segments are controllable within the required displacement errors of 15 nm under the following three conditions: 1) the displacement measurement sensors are placed in staggered fashion between segments, 2) the displacement measurement sensors are axisymmetrically placed with respect to the optical axis, and 3) the relative lateral shift and rotation of each segment are less than 500 &mu;m and 0.05 degree, respectively. In this report, the control algorithm, requirements for the layout of the displacement measurement sensors, and the simulated performance will be presented.
Distribution of left ventricular sympathetic afferents demonstrated by reflex responses to transmural myocardial ischemia and to intracoronary and epicardial bradykinin. (1993)

We conclude that cardiac receptors with sympathetic afferents are distributed equally to the IP and anterior regions of the LV.
Uncertainty Propagation in Deep Neural Networks Using Extended Kalman Filtering (2018)

Extended Kalman Filtering (EKF) can be used to propagate and quantify input uncertainty through a Deep Neural Network (DNN) assuming mild hypotheses on the input distribution. This methodology yields results comparable to existing methods of uncertainty propagation for DNNs while lowering the computational overhead considerably. Additionally, EKF allows model error to be naturally incorporated into the output uncertainty.
Arithmetics of beta-expansions (2004)

In this paper we consider representation of numbers in an irrational basis β&amp;gt; 1. We study the arithmetic operations on β-expansions and provide bounds on the number of fractional digits arising in addition and multiplication, L⊕(β) and L(β), respectively. We determine these bounds for irrational numbers β which are algebraic with at least one conjugate in modulus smaller than 1. In the case of a Pisot number β we derive the relation between β-integers and cut-and-project sequences and then use the properties of cut-and-project sequences to estimate L⊕(β) and L(β). We generalize the results known for quadratic Pisot units to other quadratic Pisot numbers. 1 Beta-expansions Let β be a real number strictly greater than 1. A real number x ≥ 0 can be represented using a sequence (xi)k≥i&amp;gt;−∞, xi ∈ Z, 0 ≤ xi &amp;lt; β, such that
Selective Calcium Ion Sensing with a Bichromophoric Squaraine Foldamer (2005)

Several squaraine tethered bichromophoric podand systems 1a-d and a monochromophoric analogue 2 were prepared and characterized. Among these, the bichromophore, 1b, containing five oxygen atoms in the flexible podand moiety was found to specifically bind Ca(2+) in the presence of other metal ions such as K(+), Na(+), and Mg(2+). The selective binding of Ca(2+) is clear from the absorption and emission spectral changes as well as by the visual color change of 1b from light-blue to an intense purple-blue. Benesi-Hildebrand and Job plots confirmed a 1:1 binding between 1b and Ca(2+). Signaling of the binding event is achieved by the cation-induced folding of the bichromophore and the resultant exciton coupling between the squaraine chromophores. The monochromophoric squaraine dye 2 failed to give optical signals upon Ca(2+) binding, due to the absence of exciton interaction in the bound complex. Titration of the folded complex 9 with EDTA released the metal ion from the complex, thereby regaining the original absorption and emission properties of the bichromophore. The squaraine foldamer 1b reported here is the first example of a selective chromogenic Ca(2+) sensor, which works on the principle of exciton interaction in the folded Ca(2+) complex of a bichromophore, the optical properties of which are similar to those of the "H"-type aggregates of analogous squaraine dyes.
Mono- and biallelic variant effects on disease at biobank scale (2023)

Identifying causal factors for Mendelian and common diseases is an ongoing challenge in medical genetics<sup>1</sup>. Population bottleneck events, such as those that occurred in the history of the Finnish population, enrich some homozygous variants to higher frequencies, which facilitates the identification of variants that cause diseases with recessive inheritance<sup>2,3</sup>. Here we examine the homozygous and heterozygous effects of 44,370 coding variants on 2,444 disease phenotypes using data from the nationwide electronic health records of 176,899 Finnish individuals. We find associations for homozygous genotypes across a broad spectrum of phenotypes, including known associations with retinal dystrophy and novel associations with adult-onset cataract and female infertility. Of the recessive disease associations that we identify, 13 out of 20 would have been missed by the additive model that is typically used in genome-wide association studies. We use these results to find many known Mendelian variants whose inheritance cannot be adequately described by a conventional definition of dominant or recessive. In particular, we find variants that are known to cause diseases with recessive inheritance with significant heterozygous phenotypic effects. Similarly, we find presumed benign variants with disease effects. Our results show how biobanks, particularly in founder populations, can broaden our understanding of complex dosage effects of Mendelian variants on disease.
Vapor-Phase Asymmetric Hydroformylation (2000)

Abstract Polystyrene-supported (R,S)-BINAPHOS–Rh complex was demonstrated to be applicable to the asymmetric hydroformylation of gaseous substrates in a non-solvent system: 3,3,3-trifluoropropene (2a) and (Z)-2-butene (2b) were converted into the corresponding branched aldehydes with 90% and 80%ee, respectively.
Avoiding and Minimizing Construction Delay Claim Disputes in Relational Contracting (2006)

Delays on construction projects, and the claims which emanate from such delays, are an integral part of the modern construction process. The overwhelming amount of time, energy, and cost devoted to delay claims does not begin when a claim is initially submitted at or near the completion of a job, rather, the construction delay claim process commences at project inception. A discussion is provided relative to how claims are generated during a construction project, the various types of delay, contract provisions which may trigger construction delay claims, methods of solidifying a party’s position, presentation, substantiation and justification of a claim, formal and informal methods to resolve claims and, most importantly, mechanisms by which to cut down on the incidence of delay claims.
Physicists' role in the climate debate (2010)

Ever since my undergraduate days, I have believed that our prestigious scientific societies are there to serve and promote science. Now, however, they appear to be set on usurping it. To quote Thomas Huxley, "Belief, in the scientific sense of the word, is a serious matter and needs strong foundation." That strong foundation can be provided only by the profound examination of nature by individual scientists and its assessment by their peers. For a committee, however distinguished its membership, to pontificate on scientific matters is not only hubris, it is also dangerous. Let individual scientists speak and let committees be silent.
Racetrack-shape fixed field induction accelerator for giant cluster ions (2015)

A novel scheme for a racetrack-shape fixed field induction accelerator (RAFFIA) capable of accelerating extremely heavy cluster ions (giant cluster ions) is described. The key feature of this scheme is rapid induction acceleration by localized induction cells. Triggering the induction voltages provided by the signals from the circulating bunch allows repeated acceleration of extremely heavy cluster ions. The given RAFFIA example is capable of realizing the integrated acceleration voltage of 50 MV per acceleration cycle. Using 90\ifmmode^\circ\else\textdegree\fi{} bending magnets with a reversed field strip and field gradient is crucial for assuring orbit stability in the RAFFIA.
Peptide nucleic acids targeting miR-221 modulate p27Kip1 expression in breast cancer MDA-MB-231 cells (2012)

The activity of a peptide nucleic acid (PNA) targeting cancer-associated microRNA-221 is described. PNAs against miR-221 were designed in order to bind very efficiently to the target RNA strand and to undergo efficient uptake in the cells. A polyarginine-PNA conjugate targeted against miR-221 (Rpep-PNA-a221) showed both very high affinity for RNA and efficient cellular uptake without the addition of transfection reagents. Unmodified PNA with the same sequence displayed RNA binding, but cellular uptake was very poor. Consistently, only Rpep-PNA-a221 strongly inhibited miR-221. Targeting miR-221 by PNA resulted in i) lowering of the hybridization levels of miR-221 measured by RT-qPCR, ii) upregulation of p27Kip1 gene expression, measured by RT-qPCR and western blot analysis. The major conclusion of this study is that efficient delivery of anti‑miR PNA through a suitable peptide carrier (Rpep‑PNA-a221) leads to inhibition of miR-221 activity, altering the expression of miR-221-regulated functions in breast cancer cells.