gebhart/patrepeval huggingface dataset:
Fetal DNA Methylation Associates with Early Spontaneous Preterm Birth and Gestational Age (2013)

Spontaneous preterm birth (PTB, <37 weeks gestation) is a major public health concern, and children born preterm have a higher risk of morbidity and mortality throughout their lives. Recent studies suggest that fetal DNA methylation of several genes varies across a range of gestational ages (GA), but it is not yet clear if fetal epigenetic changes associate with PTB. The objective of this study is to interrogate methylation patterns across the genome in fetal leukocyte DNA from African Americans with early PTB (24(1/7)-34(0/7) weeks; N = 22) or term births (39(0/7)-40(6/7)weeks; N = 28) and to evaluate the association of each CpG site with PTB and GA. DNA methylation was assessed across the genome with the HumanMethylation450 BeadChip. For each individual sample and CpG site, the proportion of DNA methylation was estimated. The associations between methylation and PTB or GA were evaluated by fitting a separate linear model for each CpG site, adjusting for relevant covariates. Overall, 29 CpG sites associated with PTB (FDR<.05; 5.7×10(-10)<p<2.9×10(-6)) independent of GA. Also, 9637 sites associated with GA (FDR<.05; 9.5×10(-16)<p<1.0×10(-3)), with 61.8% decreasing in methylation with shorter GA. GA-associated CpG sites were depleted in the CpG islands of their respective genes (p<2.2×10(-16)). Gene set enrichment analysis (GSEA) supported enrichment of GA-associated CpG sites in genes that play a role in embryonic development as well as the extracellular matrix. Additionally, this study replicated the association of several CpG sites associated with gestational age in other studies (CRHBP, PIK3CD and AVP). Dramatic differences in fetal DNA methylation are evident in fetuses born preterm versus at term, and the patterns established at birth may provide insight into the long-term consequences associated with PTB.
On PMEPR of algebraic codes (2008)

Abstract New bounds on the ratio between the discrete and continuous maxima of multicarrier (MC) signals are derived. In contrast to the earlier known results, these bounds depend on the value of the discrete maximum. Use of the bounds yields improved estimates for the peak‐to‐mean envelope power ratio (PMEPR) of trace codes. Copyright © 2008 John Wiley &amp; Sons, Ltd.
Engineered Bone Marrow Stem Cell-Sheets Alleviate Renal Damage in a Rat Chronic Glomerulonephritis Model (2023)

Although mesenchymal stem cell (MSC)-based regenerative therapy is being developed for the treatment of kidney diseases, cell delivery and engraftment still need to be improved. Cell sheet technology has been developed as a new cell delivery method, to recover cells as a sheet form retaining intrinsic cell adhesion proteins, which promotes its transplantation efficiency to the target tissue. We thus hypothesized that MSC sheets would therapeutically reduce kidney disease with high transplantation efficiency. When the chronic glomerulonephritis was induced by two injections of the anti-Thy 1.1 antibody (OX-7) in rats, the therapeutic efficacy of rat bone marrow stem cell (rBMSC) sheet transplantation was evaluated. The rBMSC-sheets were prepared using the temperature-responsive cell-culture surfaces and transplanted as patches onto the surface of two kidneys of each rat at 24 h after the first injection of OX-7. At 4 weeks, retention of the transplanted MSC-sheets was confirmed, and the animals with MSC-sheets showed significant reductions in proteinuria, glomerular staining for extracellular matrix protein, and renal production of TGFß1, PAI-1, collagen I, and fibronectin. The treatment also ameliorated podocyte and renal tubular injury, as evidenced by a reversal in the reductions of WT-1, podocin, and nephrin and by renal overexpression of KIM-1 and NGAL. Furthermore, the treatment enhanced gene expression of regenerative factors, and IL-10, Bcl-2, and HO-1 mRNA levels, but reduced TSP-1 levels, NF-kB, and NAPDH oxidase production in the kidney. These results strongly support our hypothesis that MSC-sheets facilitated MSC transplantation and function, and effectively retarded progressive renal fibrosis via paracrine actions on anti-cellular inflammation, oxidative stress, and apoptosis and promoted regeneration.
Perception and Use of Economic Thresholds Among Farmers and Agricultural Professionals: A Case Study on Soybean Aphid in Minnesota (2021)

Abstract Economic thresholds (ETs) are a foundational principle of integrated pest management but are not always widely accepted by farmers and agricultural professionals. This article reports on a survey of Minnesota farmer and agricultural professional perceptions of the ET for soybean aphid, Aphis glycines Matsumura (Hempitera: Aphididae). We discuss insights for Extension programs on how to frame the importance of thresholds and teach stakeholders to use them effectively. Key takeaways include farmers and agricultural professionals often worry about combined effects of insect, disease, and physiological pressures, whereas effects of interactions with these other stressors are seldom discussed in educational outreach. Across groups, there is a fundamental misunderstanding about the difference between ETs and economic injury level. Many survey participants reported believing in the ET but lacked the time and capacity to fully implement it. Sales agronomists and farmers were the least likely groups to trust the university-determined soybean aphid ET, whereas commercial pesticide applicators and independent consultants were the most likely groups to trust it. Based on these results, we recommend adapting communication about ETs based on the target audience to address common misconceptions and barriers to ET use that are unique to each group.
A 24 GHz reconfigurable frequency synthesizer for 60 GHz WPAN (2013)

This paper presents the design and experimental measurement of 24 GHz phase-locked loop frequency synthesizer for 60 GHz low power transceiver implemented in 0.18 μm SiGe BiCMOS process. The synthesizer employs a novel architecture with multi-coupled LC tanks for voltage controlled oscillator and injection locked frequency divide-by-2; low loss wideband power splitter and power combiner; reconfigurable divider for both integer and fractional mode of operation with choice of multiple reference frequencies. The synthesizer chip exhibits a locking range of 23.07 GHz to 26.48 GHz with a phase noise of -100.2 dBc/Hz at 1 MHz offset. The fully integrated synthesizer is controlled by slave serial peripheral interface and dissipates 42 mW from a 1.8V supply with external loop filter.
Dynamic right ventricular function response to incremental exercise in pulmonary hypertension (2020)

Pulmonary hypertension is a progressive disease whose survival is linked to adequate right ventricle adaptation to its afterload. In the current study, we performed an in-depth characterization of right ventricle function during maximum incremental exercise in patients with pulmonary hypertension and how it relates to exercise capacity. A total of 377 pulmonary hypertension patients who completed a maximum symptom-limited invasive cardiopulmonary exercise testing were evaluated to identify 45 patients with heart failure with preserved ejection fraction, 48 with exercise pulmonary hypertension, and 47 with established pulmonary arterial hypertension. These patients were compared to 17 age- and gender-matched normal controls. Load-adjusted right ventricle function was quantified as the ratio of right ventricle stroke work index to pulmonary arterial elastance. All patients with pulmonary hypertension had reduced peak VO<sub>2</sub> %predicted compared to controls. Right ventricle function deteriorated for all pulmonary hypertension groups by 50% of peak VO<sub>2</sub>. Worsening of right ventricle function during freewheeling exercise was associated with greater reduction in peak VO<sub>2</sub> compared to those whose right ventricle function deteriorated at later exercise stages (i.e. min 1, 2, and 3). On multivariate analysis, reduced ratio of right ventricle stroke work index to arterial elastance was an independent predictor of peak VO<sub>2</sub> %predicted (β-Coefficient -5.46, 95% CI: -9.47 to -1.47, <i>p</i> = 0.01). Right ventricle function deteriorates early during incremental exercise in pulmonary hypertension, occurring by 50% of peak oxygen uptake. The current study demonstrates that right ventricle dysfunction is an early phenomenon during incremental exercise in pulmonary hypertension, occurring by 50% of peak oxygen uptake. The threshold at which right ventricle function is compromised during incremental exercise in pulmonary hypertension influences aerobic capacity and may help guide exercise strategies to mitigate dynamic worsening of right ventricle function during exercise training.
A new density functional approach to nonuniform Lennard-Jones fluids (2000)

A density-functional methodology is presented for nonuniform Lennard-Jones fluids based on both a free energy density functional of nonuniform simple fluids recently proposed by the present authors and an approximate bridge function proposed in this note resulting from a combination of the hypernetted-chain closure and Verlet-modified closure. The predictions of present methodology compares well with corresponding simulation data.
Unsaturated surface in <scp>CO</scp> saturation (2017)

In this paper, density functional theory calculations are used to address the puzzle of CO saturation on Fe(100). Through a comprehensive modeling of possible local configurations, we would be able to figure out a structural model for the CO‐saturated Fe(100). The structural model is featured by forming a local structural motif of coupled on‐top and hollow CO molecules. In this model, the on‐top‐bonded CO molecules pertain to critical couplings in the next neighbor spacing, which exclude all couplings below and above the next neighbor spacing. Rather than forming tilted on‐top CO on the surface, the critical couplings align the on‐top CO molecules in the perpendicular orientation. The new model with the coverage of 0.5 ML yields even better X‐ray emission and absorption spectra calculated by using density functional theory and shows consistent agreement with all previous experiments. Copyright © 2017 John Wiley &amp; Sons, Ltd.
Conversion of oligomeric starch, cellulose, hydrolysates or sugars to hydrocarbons (2023)

Embodiments of the present invention are directed to the conversion of a source material (e.g., a depolymerized oligosaccharide mixture, a monomeric sugar, a hydrolysate, or a mixture of monomeric sugars) to intermediate molecules containing 7 to 26 contiguous carbon atoms. These intermediates may also be converted to saturated hydrocarbons. Such saturated hydrocarbons are useful as, for example, fuels.
Formation of the NO donors glyceryl mononitrate and glyceryl mononitrite from the reaction of peroxynitrite with glycerol (1997)

Peroxynitrite (ONOO-), formed from the rapid reaction of superoxide (O2-.) with NO, is known to generate stable compounds capable of donating NO on reaction with thiols and molecules containing hydroxy groups. Using glycerol as a model compound for the reactions of ONOO- with biomolecules containing hydroxy groups, we separated the products and identified them by HPLC/MS. It was shown that both glyceryl mononitrate and glyceryl mononitrite were formed and released NO on incubation with copper and l-cysteine. The compounds were stable over a period of 4h when shielded from light and kept on ice. Slow spontaneous decomposition occurred in the buffer used for the bioassay, but this was not sufficient to explain the vasorelaxing properties of these NO donors. It is concluded that the stable organic nitrate and nitrite have the capacity to be metabolized by vascular tissues, resulting in vasorelaxation.
Changes in erythrocyte ATPase activity under different pathological conditions (2018)

Na<sup>+</sup>-K<sup>+</sup>ATPase specific activity is a biomarker for the diagnosis of individuals with different physiological diseases.
Développement de la spectrométrie gamma in situ pour la cartographie de site (2012)

The high-resolution gamma spectrometry currently provides a powerful analytical tool for performing environmental measurements. In the context of radiological characterization of a site (natural or artificial radioactivity) and for the dismantling of nuclear installations, mapping of radionuclides is an important asset. The idea is to move a HPGe spectrometer to study the site and from nuclear and position data, to identify, to locate and to quantify the radionuclides present in the soil. The development of this tool follows an intercomparaison (ISIS 2007) where an intervention / crisis exercise showed the limits of current tools. The main part of this research project has focused on mapping of nuclear data. Knowledge of the parameters of an in situ spectrum helped to create a simulator modeling the response of a spectrometer moving over contaminated soil. The simulator itself helped to develop algorithms for mapping and to test them in extreme situations and not realizable. A large part of this research leads to the creation of a viable prototype providing real-time information concerning the identity and locality as possible radionuclides. The work performed on the deconvolution of data can make in post processing a map of the activity of radionuclide soil but also an indication of the depth distribution of the source. The prototype named OSCAR was tested on contaminated sites (Switzerland and Japan) and the results are in agreement with reference measurements.
Reviews (2009)

Digital Imaging and Deconvolution: The ABCs of Seismic Exploration and Processing, by E. A. Robinson and S. Treitel, ISBN 978-1-56080-18-1 (volume), 978-0-931830-47-1 (series), Society of Exploration Geophysicists, 2008, 424 p., $75, $49 (members). Seismic Methods and Applications: A Guide for the Detection of Geologic Structures, Earthquakes Zones and Hazards, Resource Exploration, and Geotechnical Engineering, by Andreas Stark, Brown Walker Press, 2008. Volcanism and Subduction: the Kamchatka Region, edited by John Eichelberger, Evgenii Gordeev, Minorou Kasahara, Pavel Izbekov, and Jonathan Lees. Geophysical Monograph 172, American Geophysical Union, 2007, 369 p.
Drag Your GAN: Interactive Point-based Manipulation on the Generative Image Manifold (2023)

Synthesizing visual content that meets users' needs often requires flexible and precise controllability of the pose, shape, expression, and layout of the generated objects. Existing approaches gain controllability of generative adversarial networks (GANs) via manually annotated training data or a prior 3D model, which often lack flexibility, precision, and generality. In this work, we study a powerful yet much less explored way of controlling GANs, that is, to "drag" any points of the image to precisely reach target points in a user-interactive manner, as shown in Fig.1. To achieve this, we propose DragGAN, which consists of two main components: 1) a feature-based motion supervision that drives the handle point to move towards the target position, and 2) a new point tracking approach that leverages the discriminative generator features to keep localizing the position of the handle points. Through DragGAN, anyone can deform an image with precise control over where pixels go, thus manipulating the pose, shape, expression, and layout of diverse categories such as animals, cars, humans, landscapes, etc. As these manipulations are performed on the learned generative image manifold of a GAN, they tend to produce realistic outputs even for challenging scenarios such as hallucinating occluded content and deforming shapes that consistently follow the object's rigidity. Both qualitative and quantitative comparisons demonstrate the advantage of DragGAN over prior approaches in the tasks of image manipulation and point tracking. We also showcase the manipulation of real images through GAN inversion.
Supplementary Methods, Tables 1-3, Figure Legends 1-9 from Oncogenicity of the Developmental Transcription Factor Sox9 (2023)

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Perioperative Glucocorticoids in Patients With Rheumatoid Arthritis Having Total Joint Replacements: Help or Harm? (2021)

A lower GC dose was not associated with increased hypotension. However, patients with higher GC exposure were more likely to have hyperglycemia and other complications. These findings suggest that harms may be associated with high perioperative GC doses. Further research is needed to determine the optimal perioperative regimen for patients with RA.
GenSyn: A Multi-stage Framework for Generating Synthetic Microdata using Macro Data Sources (2022)

Individual-level data (microdata) that characterizes a population, is essential for studying many real-world problems. However, acquiring such data is not straightforward due to cost and privacy constraints, and access is often limited to aggregated data (macro data) sources. In this study, we examine synthetic data generation as a tool to extrapolate difficult-to-obtain high-resolution data by combining information from multiple easier-to-obtain lower-resolution data sources. In particular, we introduce a framework that uses a combination of univariate and multivariate frequency tables from a given target geographical location in combination with frequency tables from other auxiliary locations to generate synthetic microdata for individuals in the target location. Our method combines the estimation of a dependency graph and conditional probabilities from the target location with the use of a Gaussian copula to leverage the available information from the auxiliary locations. We perform extensive testing on two real-world datasets and demonstrate that our approach outperforms prior approaches in preserving the overall dependency structure of the data while also satisfying the constraints defined on the different variables.
Designing robust microarchitectures (2004)

A fault-tolerant approach to microprocessor design, developed at the University of Michigan, is presented. Our approach is based on the use of in-situ checker components that validate the functional and electrical characteristics of complex microprocessor designs. Two design techniques are highlighted: a low-cost double-sampling latch design capable of eliminating power-hungry voltage margins, and a formally verifiable checker co-processor that validates all computation produced by a complex microprocessor core. By adopting a "better than worst-case" approach to system design, it is possible to address reliability and uncertainty concerns that arise during design, manufacturing and system operation.
Epitope Mapping of a 95 kDa Antigen in Complex with Antibody by Solution-Phase Amide Backbone Hydrogen/Deuterium Exchange Monitored by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (2011)

The epitopes of a homohexameric food allergen protein, cashew Ana o 2, identified by two monoclonal antibodies, 2B5 and 1F5, were mapped by solution-phase amide backbone H/D exchange (HDX) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and the results were compared to previous mapping by immunological and mutational analyses. Antibody 2B5 defines a conformational epitope, and 1F5 defines a linear epitope. Intact murine IgG antibodies were incubated with recombinant Ana o 2 (rAna o 2) to form antigen-monoclonal antibody (Ag-mAb) complexes. mAb-complexed and uncomplexed (free) rAna o 2 were then subjected to HDX. HDX instrumentation and automation were optimized to achieve high sequence coverage by protease XIII digestion. The regions protected from H/D exchange upon antibody binding overlap and thus confirm the previously identified epitope-bearing segments: the first extension of HDX monitored by mass spectrometry to a full-length antigen-antibody complex in solution.
Photon recycling characteristics of InGaAs/GaAsP multiple quantum well solar cells incorporating a spectrally selective filter and distributed Bragg reflector (2019)

Photon management plays a vital role in the power conversion efficiency of III-V semiconductor solar cells. However, the photon recycling characteristics of GaAs-based multi-quantum-well (MQW) solar cells employed different optical designs had yet been fully explored. In this work, we investigate the impact of the spectrally selective filter (SSF) and distributed Bragg reflector (DBR) on the photovoltaic characteristics of single-junction, strain-balanced In<sub>0.1</sub>Ga<sub>0.9</sub>As/ GaAs<sub>0.85</sub>P<sub>0.15</sub> MQW solar cells. Specifically, the SSFs with cutoff wavelengths of 880, 910, and 940 nm are designed and implemented on MQW solar cells with and without the incorporation of a rear DBR. Photon confinement in the vertical direction is verified based on the characterizations of reflectance, electroluminescence, and external quantum efficiency. We show that the photon confinement reduces the saturation current density, up to 26 times and 3 times for the 880 nm SSF-MQW and SSF-MQW-DBR devices, respectively, compared to that of the 940 nm devices. Furthermore, by comparing the SSF-MQW-DBR solar cells under simulated one-sun and concentrated illumination conditions, the open-circuit voltage exhibits a maximal net increase for the 910 nm SSF due to tradeoff between the short-circuit and saturation current density. The proposed SSF design may offer a viable approach to boost the performance of GaAs-based MQW solar cells.
Impact of different hemodiafiltration solutions on ionemia in long-term CRRT (2021)

Critical patients with Acute Kidney Injury (AKI) requiring renal replacement therapy are in most cases eligible only for continuous modalities where the electrolyte balance control is a critical issue. The standard solutions used for hemodiafiltration, containing potassium at 2 mmol/L and no phosphorus, determines during the extended renal replacement therapy hypokalemia and hypophosphatemia. Therefore, solutions containing potassium and phosphate in physiological concentrations were formulated to avoid electrolyte imbalances and reduce ion alterations in prolonged treatments, these solutions are not routinely used in the standard clinical practice. To avoid electrolyte imbalances, we have first introduced in our practice two different solutions and then we have retrospectively analyzed the electrolyte balance upon these two solutions in order to identity the impact of these solutions on potassium and phosphate according to our clinical practice. We retrospectively analyzed 96 patients treated with Continuous Renal Replacement Therapy (CRRT) in the intensive care units (ICU) at Padua's University Hospital to evaluate the role on electrolyte balance of Phoxilium<sup>®</sup> and Prismasol 2<sup>®</sup> that differ in their composition and the need for electrolytes infusions. In the Phoxilium group the frequency of hypokalemia, hypophosphatemia, and the need of potassium and phosphate replacement were significantly reduced resulting in a reduction in complications, workload, and clinical risk associated with infusions of electrolytes. Our data demonstrated that the use of these two different hemodiafiltration solutions can reduce the occurrence of hypokalemia and hypophosphatemia during CRRT performing personalized treatments without the use of potassium and phosphate infusions.