gebhart/patrepeval huggingface dataset:
Disease-free survival as a surrogate for overall survival in neoadjuvant trials of gastroesophageal adenocarcinoma: Pooled analysis of individual patient data from randomized controlled trials. (2020)

4533 Background: Disease-free survival (DFS) is an appealing surrogate endpoint for overall survival (OS) in trials on neoadjuvant or adjuvant cancer therapy, because it is available faster and with less follow-up effort. The aim of this study was to assess if DFS can be a valid surrogate endpoint for OS when comparing neoadjuvant treatment followed by surgery to surgery alone for gastroesophageal adenocarcinoma. Methods: Individual patient data (IPD) from eight randomized controlled trials (n = 1,126 patients) which compared neoadjuvant therapy followed by surgery with surgery alone for gastroesophageal adenocarcinoma were used for the analysis. Correlation between OS-time and DFS-time was calculated. Kaplan-Meier survival curves and corresponding hazard ratios (HRs) for treatment effects were separately determined for each trial. Subsequently, HRs were pooled in a meta-analysis using a random-effects model. An error-in-variables linear regression model was used to compare observed and predicted values. The minimum treatment effect on DFS necessary to predict a non-zero treatment effect on OS was estimated by calculating the surrogate threshold effect. Results: OS-time correlated strongly with DFS-time. HRs for OS and DFS were highly similar for all single trials. The meta-analysis yielded almost identical overall HRs for treatment effects on OS and DFS. The determination coefficient for the association between HRs for OS and DFS was 0.912 (95% confidence interval 0.75-1.0), indicating a strong trial-level surrogacy between OS and DFS. The surrogate threshold effect was calculated at 0.79, indicating that a future trial yielding a hazard ratio for the treatment effect on DFS &lt; 0.79 could be expected with a 95% probability to yield a hazard ratio for the treatment effect on OS &lt; 1. Conclusions: DFS and OS strongly correlate both after neoadjuvant therapy followed by surgery and after surgery alone for gastroesophageal adenocarcinoma. Likewise, the treatment effects on the two endpoints are very similar. Consequently, DFS can be regarded an appropriate surrogate endpoint for OS in trials on neoadjuvant therapy for gastroesophageal adenocarcinoma.
Alzheimer’s β‐amyloid peptide blocks vascular endothelial growth factor mediated signaling via direct interaction with VEGFR‐2 (2009)

Beta-amyloid peptides (Abeta) are the major constituents of senile plaques and cerebrovascular deposits in the brains of Alzheimer's disease patients. We have shown previously that soluble forms of Abeta are anti-angiogenic both in vitro and in vivo. However, the mechanism of the anti-angiogenic activity of Abeta peptides is unclear. In this study, we examined the effects of Abeta1-42 on vascular endothelial growth factor receptor 2 (VEGFR-2) signaling, which plays a key role in angiogenesis. Abeta inhibited VEGF-induced migration of endothelial cells, as well as VEGF-induced permeability of an in vitro model of the blood brain barrier. Consistently, exogenous VEGF dose-dependently antagonized the anti-angiogenic activity of Abeta in a capillary network assay. Abeta1-42 also blocked VEGF-induced tyrosine phosphorylation of VEGFR-2 in two types of primary endothelial cells, suggesting an antagonistic action of Abeta toward VEGFR-2 signaling in cells. Moreover, Abeta was able to directly interact with the extracellular domain of VEGFR-2 and to compete with the binding of VEGF to its receptor in a cell-free assay. Co-immunoprecipitation experiments confirmed that Abeta can bind VEGFR-2 both in vitro and in vivo. Altogether, our data suggest that Abeta acts as an antagonist of VEGFR-2 and provide a mechanism explaining the anti-angiogenic activity of Abeta peptides.
Intact glycosphingolipidomic analysis of the cell membrane during differentiation yields extensive glycan and lipid changes (2018)

Glycosphingolipids (GSLs) are found in cellular membranes of most organisms and play important roles in cell-cell recognition, signaling, growth, and adhesion, among others. A method based on nanoflow high performance liquid chromatography-chip-quadrupole-time-of-flight mass spectrometry (nanoHPLC Chip-Q-TOF MS) was applied towards identifying and quantifying intact GSLs from a variety of samples, including cultured cell lines and animal tissue. The method provides the composition and sequence of the glycan, as well as variations in the ceramide portion of the GSL. It was used to profile the changes in the glycolipidome of Caco-2 cells as they undergo differentiation. A total of 226 unique GSLs were found among Caco-2 samples from five differentiation time-points. The method provided a comprehensive glycolipidomic profile of a cell during differentiation to yield the dynamic variation of intact GSL structures.
Electro-Thermal Co-design of a High-Density Power-Stage for a Reconfigurable-Battery-Assisted Electric-Vehicle Fast-Charger using Multi-Physics Co-simulation and Topology Optimization (2023)

This paper presents an electro-thermal co-design and co-simulation methodology for power-electronic applications. Previous works have used co-simulation approaches to adapt thermal designs to predefined electrical loads, or vice versa. In contrast, the presented work exploits the interdependence between the domains to develop a compact thermal-management solution that leverages power-electronic control to enhance heat extraction in the presence of heat sources with different material and thermal properties. This process is shown to provide great benefit in designs that combine different power-electronic devices with different materials and thermal properties on a compact shared heatsink. The proposed methodology is applied to the design of a multi-phase current-controlled Linear Regulator (LR) as part of a custom Battery-Assisted DC Fast-Charger (BA-DCFC) architecture for electric vehicles. A topologically optimized heatsink is developed for the two different power MOS-FETs comprising the LR, which leverages electrically controlled thermal balancing. A co-simulation process combining domain-specific simulation tools to obtain high-fidelity results in both electrical and thermal realms is proposed, and demonstrated for the LR system. Through co-simulation, the optimal number of parallel phases for the LR <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$\text{is}$</tex> chosen, by accurately determining the waste-heat distribution across the LR MOSFETs with the optimized heatsink for different numbers of phases. Experimental results show that the heatsink design and thermal-balance control work together to reduce the average and differences in device junction temperatures by 15% and 83%, respectively.
Nonlinear Gradient Mappings and Stochastic Optimization: A General Framework with Applications to Heavy-Tail Noise (2023)

.We introduce a general framework for nonlinear stochastic gradient descent (SGD) for the scenarios when gradient noise exhibits heavy tails. The proposed framework subsumes several popular nonlinearity choices, like clipped, normalized, signed, or quantized gradient, but we also consider novel nonlinearity choices. We establish for the considered class of methods strong convergence guarantees assuming a strongly convex cost function with Lipschitz continuous gradients under very general assumptions on the gradient noise. Most notably, we show that, for a nonlinearity with bounded outputs and for the gradient noise that may not have finite moments of order greater than one, the nonlinear SGD's mean squared error (MSE), or equivalently, the expected cost function's optimality gap, converges to zero at rate \(O(1/t^\zeta )\) , \(\zeta \in (0,1)\) . In contrast, for the same noise setting, the linear SGD generates a sequence with unbounded variances. Furthermore, for general nonlinearities that can be decoupled componentwise and a class of joint nonlinearities, we show that the nonlinear SGD asymptotically (locally) achieves an \(O(1/t)\) rate in the weak convergence sense and explicitly quantify the corresponding asymptotic variance. Experiments show that, while our framework is more general than existing studies of SGD under heavy-tail noise, several easy-to-implement nonlinearities from our framework are competitive with state-of-the-art alternatives on real datasets with heavy-tail noises.Keywordsstochastic optimizationstochastic gradient descentnonlinear mappingheavy-tail noiseconvergence ratemean square analysisasymptotic normalitystochastic approximationMSC codes90C1590C2565K0562L2068T05
Moving costs, security of tenure and eviction (2004)

We contrast equilibrium and welfare analysis in the rental housing market under two property rights regimes – eviction rights and security of tenure – when tenants face moving costs. A tenant’s idiosyncratic benefit from his unit and a landlord’s idiosyncratic profit from conversion are treated as private information. The two regimes differ when a tenant wants to stay in his unit but the landlord wants to redevelop it. North American housing markets have been characterized by eviction rights and many European housing markets by security of tenure. Under eviction rights, a landlord who evicts a tenant imposes a negative externality on him, which can be imperfectly internalized through a demolition (conversion) tax. Similarly, under security of tenure efficiency can be improved by subsidizing the moving costs of tenants.
Formation and Reduction of NO<sub>2</sub> in Fixed Bed Combustion of Coal Char under Oxy–Fuel Conditions: Experimental and Density Functional Theory Analysis (2020)

Nitrogen dioxide (NO2) has been attracting a lot of attention because of its toxicity and potential in contaminating land, air, and water. However, research on NO2 release behavior under oxy–fuel conditions is still insufficient. This paper aims to explore the formation and reduction mechanisms of NO2 during oxy–fuel combustion of char by using both experimental and density functional theory (DFT) methods. Results showed that with the increase of temperature, the energy barrier of the NO oxidation reaction increases, while that of the NO2 reduction reaction decreases. These facts lead to a higher peak concentration of NO and lower NO2 emissions. Because of a larger effect of temperature on the rate constant of the NO2 reduction reaction than that of the NO oxidation reaction, the NO2 concentration decreases dramatically and rapidly even if the temperature increases only slightly. As the temperature increases to above 1273 K, the equilibrium constant of the NO oxidation reaction falls to below 105. That is, the oxidation of NO to NO2 is incomplete and reversible over the temperature range of 1273–1673 K. By contrast, the reduction of NO2 to NO is complete and irreversible over this temperature range. As a result, almost no NO2 is observed at high temperatures. In the presence of H2O, DFT calculations show that the water-gas-shift reaction is less important in contrast to the H2O–carbon reaction, which is consistent with previous research. In this case, NOx emissions under an O2/CO2/H2O atmosphere are lower than those under an O2/CO2 atmosphere. Overall, combined experiments with DFT calculations offer a new approach to study the microcosmic mechanisms of NO2 formation and reduction under oxy–fuel conditions during isothermal combustion of char.
Biochemistry and Biomedical Applications of Spherical Nucleic Acids (SNAs) (2012)

Careful observation of cellular processes has revealed exquisite examples of how the architecture of DNA and RNA can confer unique and complex functionality upon nucleic acid sequences. DNA superhelices, tRNA, and other intracellular ribozymes are essential components of life processes which require higher ordered structure for proper function. The realization that higher order nucleic acid architectures can afford unique functionality has ignited a new field of research that attempts to exploit such structures for a vast array of applications. In this chapter, we describe a novel three-dimensional nucleic acid architecture, referred to as the spherical nucleic acid (SNA), which possesses a number of exceptional properties not observed with any other nucleic acid structural motif. We then discuss how the unique properties of SNAs are being exploited in many next generation extra- and intra- cellular diagnostic and therapeutic applications.
Colorization and Automated Segmentation of Human T2 MR Brain Images for Characterization of Soft Tissues (2012)

Characterization of tissues like brain by using magnetic resonance (MR) images and colorization of the gray scale image has been reported in the literature, along with the advantages and drawbacks. Here, we present two independent methods; (i) a novel colorization method to underscore the variability in brain MR images, indicative of the underlying physical density of bio tissue, (ii) a segmentation method (both hard and soft segmentation) to characterize gray brain MR images. The segmented images are then transformed into color using the above-mentioned colorization method, yielding promising results for manual tracing. Our color transformation incorporates the voxel classification by matching the luminance of voxels of the source MR image and provided color image by measuring the distance between them. The segmentation method is based on single-phase clustering for 2D and 3D image segmentation with a new auto centroid selection method, which divides the image into three distinct regions (gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) using prior anatomical knowledge). Results have been successfully validated on human T2-weighted (T2) brain MR images. The proposed method can be potentially applied to gray-scale images from other imaging modalities, in bringing out additional diagnostic tissue information contained in the colorized image processing approach as described.
Stilbenoid molecules: An experimental and theoretical study of <i>trans</i>-1-(2-pyridyl)-2-(4-pyridyl)-ethylene and the parent molecule (1997)

Free-jet absorption millimeter-wave spectroscopy and gradient-corrected density-functional calculations are combined to study trans-1-(2-pyridyl)-2-(4-pyridyl)-ethylene, 2,4-DPE, a stilbenelike molecule. The interplay between experiments and computational theory backed by the large amount of data and modeling already available for stilbene allows us to establish the parameters of the two-dimensional potential of the pyridyl torsions which well reproduce the experimental defect of inertia (−1.295 uÅ2). The large difference between the defects of inertia of 2,4-DPE and stilbene (≈−15 uÅ2) and further computer simulations suggest that the latter may warrant a reinvestigation. The effect of introducing a weakly binding N⋯H interaction in the stilbene frame is discussed and a very simple model based on the ab initio calculations is found to rationalize the energetics and structural differences of the two conformers of 2,4-DPE.
Voltage‐Control of Magnetism in All‐Solid‐State and Solid/Liquid Magnetoelectric Composites (2019)

The control of magnetism by means of low-power electric fields, rather than dissipative flowing currents, has the potential to revolutionize conventional methods of data storage and processing, sensing, and actuation. A promising strategy relies on the utilization of magnetoelectric composites to finely tune the interplay between electric and magnetic degrees of freedom at the interface of two functional materials. Albeit early works predominantly focused on the magnetoelectric coupling at solid/solid interfaces; however, recently there has been an increased interest related to the opportunities offered by liquid-gating techniques. Here, a comparative overview on voltage control of magnetism in all-solid-state and solid/liquid composites is presented within the context of the principal coupling mediators, i.e., strain, charge carrier doping, and ionic intercalation. Further, an exhaustive and critical discussion is carried out, concerning the suitability of using the common definition of coupling coefficient <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow><mml:msub><mml:mi>α</mml:mi> <mml:mi>C</mml:mi></mml:msub> <mml:mo>=</mml:mo> <mml:mfrac><mml:mrow><mml:mi>Δ</mml:mi> <mml:mi>M</mml:mi></mml:mrow> <mml:mrow><mml:mi>Δ</mml:mi> <mml:mi>E</mml:mi></mml:mrow> </mml:mfrac> <mml:mo> </mml:mo></mml:mrow> </mml:math> to compare the strength of the interaction between electricity and magnetism among different magnetoelectric systems.
Highly Stable Intermetallic FeSn<sub>2</sub>‐Graphite Composite Anode for Sodium‐Ion Batteries (2017)

Abstract The development of anodes with high capacity, long cycle life and good rate capability is essential to expedite the commercialization of sodium‐ion batteries for practical applications, including grid storage and electric vehicles (EV). Herein, we report the facile solvothermal synthesis of nanostructured iron distannide (FeSn 2 ) intermetallic particles as an alloy‐type anode and the improvement of its cycle life by fabricating FeSn 2 ‐graphite composites by a ball‐milling process. The influence of graphite concentration on the sodium storage properties is studied. The composite anode delivered over 400 mAh g −1 sodiation capacity over 200 cycles at a specific current of 100 mA g −1 . In addition, the composite anode exhibited excellent rate performance at higher current rates. This result would certainly pave the way for the development of high‐performance anodes that would realize low‐cost sodium‐ion batteries with a longer calendar life.
Hydraulic Design Optimization and Performance Analysis of a Centrifugal Blood Pump (2006)

This paper presents the hydrodynamic design and performance analysis method for a miniaturized centrifugal blood pump using three-dimensional computational fluid dynamics (CFD) code. In order to obtain the hydraulically high efficient configuration of a miniaturized centrifugal blood pump for cardiopulmonary circulation, a well-established commercial CFD code was incorporated considering detailed flow dynamic phenomena in the blood pump system. A prototype of centrifugal blood pump developed by the present design and analysis method has been tested in the mock circulatory system. Predicted results by the CFD code agree very well with in vitro hydraulic performance data for a centrifugal blood pump over the entire operating conditions. Preliminary in vivo animal testing has also been conducted to demonstrate the hemodynamic feasibility for use of centrifugal blood pump as a mechanical circulatory support. A miniaturized centrifugal blood pump developed by the hydraulic design optimization and performance prediction method presented herein shows the possibility of a good candidate for intra and extracorporeal cardiopulmonary circulation pump in the near future.
Simplified inverse Fourier transform technique to measure optical nonlinearity profiles using reference sample (2004)

A new Maker-fringe technique based on the use of a known reference sample to measure the second-order nonlinearity profile of thin films is described and demonstrated experimentally. Advantages over previous techniques include greater accuracy, simpler measurement, and much simpler and faster data processing.
A Stabilizing Influence: CAL PDZ Inhibition Extends the Half‐Life of ΔF508‐CFTR (2010)

Recycling lohnt sich! Die am häufigsten auftretende Mutation bei Mukoviszidose verhindert die Reifung und beschleunigt den Abbau des Ionenkanals CFTR. Ein Stabilisator wird vorgestellt, der eine für den CFTR-Abbau verantwortliche PDZ-Domäne blockiert. Der Hemmstoff iCAL36 verlängert die Halbwertszeit des Chloridkanals in bronchialen Epithelzellen. Er ergänzt außerdem die Aktivität eines Faltungskorrektors und erfüllt damit eine Voraussetzung für kombinierte Mukoviszidosetherapien. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Bipolar Room Temperature Ferromagnetic Semiconductor LaMnOP (2005)

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Supplementary Figure Legends 1-2 from Elucidating the Function of Secreted Maspin: Inhibiting Cathepsin D–Mediated Matrix Degradation (2023)

Supplementary Figure Legends 1-2 from Elucidating the Function of Secreted Maspin: Inhibiting Cathepsin D–Mediated Matrix Degradation
Table S1 from Abiraterone Acetate Induces CREB1 Phosphorylation and Enhances the Function of the CBP-p300 Complex, Leading to Resistance in Prostate Cancer Cells (2023)

&lt;p&gt;Table S1. Differential-express genes enrichment analysis in LNCaP-AAr and LNCaP.ES= enrichment score, NES= normalized enrichment score, NOM = nominal, FDR = false discovery rate. The significant related genes were defined with an NOM p-val less than 0.01 and FDR q-val less than 0.25.&lt;/p&gt;
Systematic separation of electrical power systems for hardware-in-the-loop simulation (2017)

The increasing complexity of power grids makes hardware-in-the-loop simulations of electrical power systems more and more interesting for the industry. The simulation models are typically large. They often have to be split and used on several hardware platforms to allow efficient computations. Finding an appropriate position for splitting the simulation model requires expert knowledge about the electrical power system itself and about the functionality and limitations of the simulation hardware. In this paper, we present criteria that have to be taken into account when splitting an electrical power system model into subsystems. These criteria can serve as a basis for a systematic model splitting algorithm, which requires no special expert knowledge.
Computationally Efficient Optimization Method to Quantify the Required Surgical Accuracy for a Ligament Balanced TKA (2021)

Towards the research society, the proposed method allows for a computationally efficient uncertainty quantification on a complex model. Towards surgical technique developers, six critical implant position parameters were identified, which should be the focus when refining surgical accuracy of TKA, leveraging better patient satisfaction.
The Microglial Component (2006)

This chapter contains sections titled: Microglia: Intrinsic Immune Sensor Cells of the CNS Development Microglial Activation Antigen Presentation/Cytotoxicity Terminology: Subtypes and Their Location in Regard to Brain Vessels Perivascular Macrophages Juxtavascular and Other Microglia Turnover of Brain Mononuclear Cells by Precursor Recruitment Across the BBB Perivascular Cells Microglia Turnover Used by “Trojan Horses” Microglial Impact on BBB Function Concept of the BBB Chemokines – an Overview GAG/Duffy Chemokine Expression in the CNS CCL2 and CCR2 CCL3 and CCL5 CXCR3 and CXCL10 Microglia-Endothelial Cell Dialogue Microglial Effects on Tight Junctions Concluding Remarks References
Asymmetric Ruthenium Catalysis Enables Fluorophores with Point Chirality Displaying CPL Properties** (2022)

A novel enantiopure π-allylruthenium(IV) precatalyst allowed the enantioselective and stereospecific allylations of indoles and gave access to indolin-3-ones, containing vicinal stereogenic centers. Facile separation of diastereoisomers exhibiting opposite circularly polarized luminescence (CPL) activities in diverse solvents, including water, demonstrated the potential of these sustainable transformations and of the newly prepared molecules.