gebhart/patrepeval huggingface dataset:
Polarity Sampling: Quality and Diversity Control of Pre-Trained Generative Networks via Singular Values (2022)

We present Polarity Sampling, a theoretically justified plug-and-play method for controlling the generation quality and diversity of any pre-trained deep generative network (DGN). Leveraging the fact that DGNs are, or can be ap-proximated by, continuous piecewise affine splines, we derive the analytical DGN output space distribution as a function of the product of the DGN's Jacobian singular values raised to a power p. We dub p the polarity param-eter and prove that p focuses the DGN sampling on the modes (p < 0) or anti-modes (p > 0) of the DGN output-space probability distribution. We demonstrate that nonzero polarity values achieve a better precision-recall (quality-diversity) Pareto frontier than standard methods, such as truncation, for a number of state-of-the-art DGNs. We also present quantitative and qualitative results on the improve-ment of overall generation quality (e.g., in terms of the Fréchet Inception Distance) for a number of state-of-the-art DGNs, including StyleGAN3, BigGAN-deep, NVAE, for different conditional and unconditional image generation tasks. In particular, Polarity Sampling redefines the state-of-the-art for StyleGAN2 on the FFHQ Dataset to FID 2.57, StyleGAN2 on the LSUN Car Dataset to FID 2.27 and Style-GAN3 on the AFHQv2 Dataset to FID 3.95. Colab Demo.
An Official American Thoracic Society Clinical Practice Guideline: Classification, Evaluation, and Management of Childhood Interstitial Lung Disease in Infancy (2013)

After common causes of DLD are excluded, neonates and infants with childhood ILD syndrome should be evaluated by a knowledgeable subspecialist. The evaluation may include echocardiography, controlled ventilation high-resolution computed tomography, infant pulmonary function testing, bronchoscopy with bronchoalveolar lavage, genetic testing, and/or lung biopsy. Preventive care, family education, and support are essential.
The Three-Sided PyramidWavefront Sensor. I. Simulations and Analysis for Astronomical Adaptive Optics (2021)

For ExAO instruments for the Giant Segmented Mirror Telescopes (GSMTs), alternative architectures of WFS are under consideration because there is a tradeoff between detector size, speed, and noise that reduces the performance of GSMT-ExAO wavefront control. One option under consideration for a GSMT-ExAO wavefront sensor is a three-sided PWFS (3PWFS). The 3PWFS creates three copies of the telescope pupil for wavefront sensing, compared to the conventional four-sided PWFS (4PWFS) which uses four pupils. The 3PWFS uses fewer detector pixels than the 4PWFS and should therefore be less sensitive to read noise. Here we develop a mathematical formalism based on the diffraction theory description of the Foucault knife edge test that predicts the intensity pattern after the PWFS. Our formalism allows us to calculate the intensity in the pupil images formed by the PWFS in the presence of phase errors corresponding to arbitrary Fourier modes. We then use the Object Oriented MATLAB Adaptive Optics toolbox (OOMAO) to simulate an end-to-end model of an adaptive optics system using a PWFS with modulation and compare the performance of the 3PWFS to the 4PWFS. In the case of a low read noise detector, the Strehl ratios of the 3PWFS and 4PWFS are within 0.01. When we included higher read noise in the simulation, we found a Strehl ratio gain of 0.036 for the 3PWFS using Raw Intensity over the 4PWFS using Slopes Maps at a stellar magnitude of 10. At the same magnitude, the 4PWFS RI also outperformed the 4PWFS SM, but the gain was only 0.012 Strehl. This is significant because 4PWFS using Slopes Maps is how the PWFS is conventionally used for AO wavefront sensing. We have found that the 3PWFS is a viable wavefront sensor that can fully reconstruct a wavefront and produce a stable closed-loop with correction comparable to that of a 4PWFS, with modestly better performance for high read-noise detectors.
Semi-automatic contour analysis of the optic nerve head (2004)

Keywords: LTS5 Reference EPFL-CONF-87114 Record created on 2006-06-14, modified on 2017-05-10
Hybrid Organic—Inorganic Materials Based on Organophosphorus Derivatives (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Biosynthesis of Phage-specific Initiation Dipeptides (1971)

Abstract This report describes the properties of a purified Escherichia coli protein synthetic system which accurately translates the initial codons of the bacteriophage f2 maturation, coat, and RNA synthetase cistrons. In order to assay cistron recognition easily and to accumulate specific intermediates in the translation of a natural message, we have restricted in vitro synthesis to the formation of the initial formyldipeptides corresponding to the three f2 cistrons. This is accomplished by preventing the initial, G factor-requiring translocation reaction through the use of small amounts of monospecific anti-G factor antibody or the antibiotic fusidic acid. The reaction requires initiation-competent ribosomes which are depleted of elongation factors by repeated washings in low ionic strength buffer. Initiation in this system is quite specific. The initial f2 coat dipeptide, N-formylmethionylalanine, is readily converted into the expected coat tripeptide, N-formylmethionylalanylserine, if translocation is permitted. In addition, synthesis of the initial f2 RNA synthetase dipeptide, N-formylmethionylserine, is specifically repressed in the presence of f2 coat protein, indicating that this purified system is sensitive to translational control.
Quantitative in vivo X-ray dark-field radiography for early pulmonary emphysema diagnosis (2014)

Aims: Using conventional chest X-ray imaging it is hardly possible to visualize early stages of emphysema. The aim of this study was to evaluate whether mild to moderate emphysema can be diagnosed in vivo using X-ray dark-field radiography. Materials/Methods: Female C57Bl/6N mice were used for the experiments. Emphysema was induced by orotracheal injection of elastase. Control mice received orotracheal injection of PBS. To ensure the development of different stages of emphysema anesthetized and freely breathing mice were scanned 7, 14 and 21 days after application of elastase or PBS. Images were acquired with a prototype grating-based small animal scanner and processed using Fourier decomposition to generate transmission as well as dark-field radiographs. In vivo pulmonary function tests were performed before sacrificing the animals. Lungs were obtained for further histopathological analysis (e.g. mean cord length (MCL-) quantification). Three blinded readers, all of them experienced radiologists who are familiar with dark-field imaging, were asked to stage the severity of emphysema for dark-field and transmission images. Results: As confirmed by MCL-quantifications lungs in the elastase group had developed different stages of emphysema. Correlation of MCL and dark-field signal intensity (r=0,86) was significantly better than correlation of MCL and transmission signal intensity (r=0,37). Visual ratings for dark-field intensity correlated better with MCL (r=0,82) than those for transmission images (r=0,55). Conclusion: Using X-ray dark-field radiography it is possible to visualize and diagnose mild to moderate emphysema in vivo with a conventional imaging method for the first time.
Optimizing Coverage and Capacity in Cellular Networks using Machine Learning (2021)

Wireless cellular networks have many parameters that are normally tuned upon deployment and re-tuned as the network changes. Many operational parameters affect reference signal received power (RSRP), reference signal received quality (RSRQ), signal-to-interference-plus-noise-ratio (SINR), and, ultimately, throughput. In this paper, we develop and compare two approaches for maximizing coverage and minimizing interference by jointly optimizing the transmit power and downtilt (elevation tilt) settings across sectors. To evaluate different parameter configurations offline, we construct a realistic simulation model that captures geographic correlations. Using this model, we evaluate two optimization methods: deep deterministic policy gradient (DDPG), a reinforcement learning (RL) algorithm, and multi-objective Bayesian optimization (BO). Our simulations show that both approaches significantly outperform random search and converge to comparable Pareto frontiers, but that BO converges with two orders of magnitude fewer evaluations than DDPG. Our results suggest that data-driven techniques can effectively self-optimize coverage and capacity in cellular networks.
Abstract 1920: miR-211 directly targets pyruvate dehydrogenase kinase 4 to inhibit cellular growth and glucose metabolism in triple negative breast cancer (2016)

Abstract Deregulated metabolism and aerobic glycolysis are common to many kinds of tumors including, breast cancers driven by a plethora of transcription factors. One such is hypoxia-inducible factor-1α (HIF-1α) known to drive the expression of glycolytic target genes. Here, we identify PDK4 (pyruvate dehydrogenase kinase 4) as a key regulator of HIF-1α signaling. In triple-negative human breast cancer (TNBC) cell lines, we investigated the contribution of PDK4 and HIF-1α to experimental tumor growth, core glucose metabolism and ionizing radiation effects. When these TNBC cells were exposed to 4, 6 and 8Gy treatment, we observed a linear increase in the expression levels of PDK4 and HIF-1α genes. In this study we also report that miR-211, a microRNA predicted to target PDK4 is suppressed in TNBC patient specimens as evidenced by in situ hybridization analysis. The expression levels of PDK4, HIF-1α and RICTOR were reduced with miR-211 over expression while the levels of PDH and FH were observed to be increased. Further, we observed that miR-211 conjugated to cerium oxide nanoparticles (nanoceria) showed increased cytotoxicity. Similar effects were observed when these TNBCs were treated with 5mM DCA, a potent metabolic inhibitor of PDK. Combinatory suppression of PDK4 and HIF-1α exerted synergistic inhibition of lactate released suggesting of reversal of aerobic glycolysis. Alternatively, TCGA datasets were predictive of patient survival, with a PDK4/miR-211 signature robustly predicting poor patient prognosis. Overall, our findings suggest that combined targeting of PDK4 signaling cascade with miR-211 and DCA in combination specifically regulate core glucose metabolism in TNBC. Citation Format: Maheedhara R. Guda, Swapna Asuthkar, Soumen Das, Sudipta Seal, Andrew J. Tsung, Kiran K. Velpula. miR-211 directly targets pyruvate dehydrogenase kinase 4 to inhibit cellular growth and glucose metabolism in triple negative breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1920.
Inhibition of substrate synthesis: a pharmacological approach for glycosphingolipid storage disease therapy (2004)

Abstract The neuronopathic lysosomal storage diseases are not currently amenable to therapy due to the difficulties of delivering functional enzyme/protein to the brain. Over two decades ago, an alternative strategy was suggested by Radin based on small-molecule enzyme inhibitors for treating a subset of these disorders, the glycosphingolipidoses. Recently, the efficacy of this approach has been demonstrated in animal disease models and in the clinic. This chapter discusses these studies. It begins with a brief background on glycosphingolipids (GSLs) and GSL storage diseases, as it provides insights into the potentials and the limitations of drug-based strategies for treating this family of predominantly neurodegenerative disorders.
Stochastic MPC with Multi-modal Predictions for Traffic Intersections (2022)

We propose a Stochastic MPC (SMPC) formu-lation for autonomous driving at traffic intersections which incorporates multi-modal predictions of surrounding vehicles given by Gaussian Mixture Models (GMM) for collision avoid-ance constraints. Our main theoretical contribution is a SMPC formulation that optimizes over a novel feedback policy class designed to exploit additional structure in the GMM predictions, and that is amenable to convex programming. The use of feedback policies for prediction is motivated by the need for reduced conservatism in handling multi-modal predictions of the surrounding vehicles, especially prevalent in traffic intersection scenarios. We evaluate our algorithm along axes of mobility, comfort, conservatism and computational efficiency at a simulated intersection in CARLA. Our simulations use a kinematic bicycle model and multimodal predictions trained on a subset of the Lyft Level 5 prediction dataset. To demonstrate the impact of optimizing over feedback policies, we compare our algorithm with two SMPC baselines that handle multi-modal collision avoidance chance constraints by optimizing over open-loop sequences.
A Scalable Successive-Cancellation Decoder for Polar Codes (2014)

Polar codes are the first error-correcting codes to provably achieve channel capacity, asymptotically in code length, with an explicit construction. However, under successive-cancellation decoding, polar codes require very long code lengths to compete with existing modern codes. Nonetheless, the successive cancellation algorithm enables very-low-complexity implementations in hardware, due to the regular structure exhibited by polar codes. In this paper, we present an improved architecture for successive-cancellation decoding of polar codes, making use of a novel semi-parallel, encoder-based partial-sum computation module. We also provide quantization results for realistic code length N=2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">15</sup> , and explore various optimization techniques such as a chained processing element and a variable quantization scheme. This design is shown to scale to code lengths of up to N=2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">21</sup> , enabled by its low logic use, low register use and simple datapaths, limited almost exclusively by the amount of available SRAM. It also supports an overlapped loading of frames, allowing full-throughput decoding with a single set of input buffers.
Graphene-based Wireless Agile Interconnects for Massive Heterogeneous Multi-chip Processors (2020)

The main design principles in computer architecture have recently shifted from a monolithic scaling-driven approach to the development of heterogeneous architectures that tightly co-integrate multiple specialized processor and memory chiplets. In such data-hungry multi-chip architectures, current Networks-in-Package (NiPs) may not be enough to cater to their heterogeneous and fast-changing communication demands. This position paper makes the case for wireless in-package nanonetworking as the enabler of efficient and versatile wired-wireless interconnect fabrics for massive heterogeneous processors. To that end, the use of graphene-based antennas and transceivers with unique frequency-beam reconfigurability in the terahertz band is proposed. The feasibility of such a nanonetworking vision and the main research challenges towards its realization are analyzed from the technological, communications, and computer architecture perspectives.
Measurement of Leadframe Strain in Electrically Active Power Semiconductors (2015)

In this work, thermal-mechanical leadframe strain in an electrically active IGBT was measured using electronic speckle pattern interferometry (ESPI). ESPI is a non-contact optical technique capable of high resolution surface displacement measurements. The significant contribution of this paper is an experimental methodology by which strain can be measured in electrically active devices. A 3-D ESPI test stand was developed, combining two cameras to simultaneously capture the local (interconnect level) and global (device level) displacements. Through the combination of incremental sub-loads and mathematical recorrelation of speckle patterns, device power loads have been measured (which would have been otherwise impossible due to speckle decorrelation, which limits measurement of large deformations). A model-based tracking technique was developed from coupled experimental noise measurements and FE modeling — allowing for optimal strain solution to be extracted from noisy displacement results. The developed and experimentally-validated thermal-mechanical FE strain model agreed to within 7% of ESPI strain measurements.
Constructing and solving variational image registration problems (2009)

Nonrigid image registration has received much attention in the medical imaging and computer vision research communities, because it enables a wide variety of applications. Feature tracking, segmentation, classification, temporal image differencing, tumour growth estimation, and pharmacokinetic modeling are examples of the many tasks that are enhanced by the use of aligned imagery. Over the years, the medical imaging and computer vision communties have developed and refined image registration techniques in parallel, often based on similar assumptions or underlying paradigms. This thesis focuses on variational registration, which comprises a subset of nonrigid image registration. It is divided into chapters that are based on fundamental aspects of the variational registration problem: image dissimilarity measures, changing overlap regions, regularizers, and computational solution strategies. Key contributions include the development of local versions of standard dissimilarity measures, the handling of changing overlap regions in a manner that is insensitive to the amount of non-interesting background information, the combination of two standard taxonomies of regularizers, and the generalization of solution techniques based on Fourier methods and the Demons algorithm for use with many regularizers. To illustrate and validate the various contributions, two sets of example imagery are used: 3D CT, MR, and PET images of the brain as well as 3D CT images of lung cancer patients.
Creation of mouse TNFR2-selective agonistic TNF mutants using a phage display technique (2016)

Tumor necrosis factor-α (TNF), which is an immuno-modulatory cytokine, has been suggested to cause inflammatory responses as well as protection against tissue dysfunction by binding two types of TNF receptor (TNFR1/TNFR2). However, the physiological effects of TNFR2-specific activation remain unclear. We therefore aimed to generate a TNF mutant with full TNFR2-selective agonist activity as a functional analytical tool. In this study, we utilized a phage display technique to create mouse TNFR2 (mTNFR2)-selective TNF mutants that bind specifically to mTNFR2 and show full bioactivity compared with wild-type TNF. A new phage library displaying TNF mutants was created, in which nine amino acid residues at the predicted receptor-binding site were randomized. From this library, an agonistic TNF mutant exhibiting high binding selectivity and bioactivity to mTNFR2 was isolated. We propose that this TNF mutant would be a powerful tool with which to elucidate the functional roles of mTNFR2.
Actions of somatostatins on gastric smooth muscle cells (1992)

The effects of somatostatin-28, somatostatin-14, and a synthetic somatostatin octapeptide analogue, D-Phe-Cys-Tyr-D-Trp-Lys-Thr-Cys-Nal-NH2 (cyclo SS-8) were examined on contraction of dispersed gastric smooth muscle cells from guinea pigs. The somatostatins did not cause contraction of gastric smooth muscle cells, nor did they inhibit carbachol-stimulated contraction. However, they reversed vasoactive intestinal peptide (VIP)-induced inhibition (relaxation) of carbachol-stimulated contraction. Somatostatin-28 had a half-maximal effect (EC50) at 1.6 +/- 0.8 nM, cyclo SS-8 at 0.6 +/- 0.3 nM, but somatostatin-14 had no effect even when used in concentrations as high as 1 microM. Incubation of muscle cells with peptidase inhibitors phosphoramidon (1 microM) plus amastatin (10 microM) had no effect on the EC50 of somatostatin-28 or cyclo SS-8 but increased the potency of somatostatin-14 greater than 1,000-fold. When peptides were incubated with muscle cells and the products applied to high-performance liquid chromatography, cyclo SS-8 was not degraded, but somatostatin-14 was rapidly degraded when present alone, and the addition of peptidase inhibitors partially inhibited the degradation. Cyclo SS-8 had its maximal effect at 0.5-1 min and inhibited relaxation induced by VIP, isoproterenol, glucagon, or dibutyryl adenosine 3',5'-cyclic monophosphate (DBcAMP). Cyclo SS-8 partially inhibited the increase in VIP-stimulated cAMP. Preincubation with pertussis toxin blocked the inhibitory action of cyclo SS-8 on VIP or DBcAMP-induced relaxation. These results indicate that gastric smooth muscle cells rapidly degrade somatostatin-14 and suggest that muscle cell peptidases could have a major effect on the actions of somatostatin-14.(ABSTRACT TRUNCATED AT 250 WORDS)
Pathophysiology of T akotsubo syndrome – a joint scientific statement from the Heart Failure Association T akotsubo Syndrome Study Group and Myocardial Function Working Group of the E uropean Society of Cardiology – Part 1: overview and the central role for catecholamines and sympathetic nervous system (2021)

This is the first part of a scientific statement from the Heart Failure Association (HFA) of the European Society of Cardiology focused upon the pathophysiology of Takotsubo syndrome and is complimentary to the previous HFA position statement on Takotsubo syndrome which focused upon clinical management. In part 1 we provide an overview of the pathophysiology of Takotsubo syndrome and fundamental questions to consider. We then review and discuss the central role of catecholamines and the sympathetic nervous system in the pathophysiology, and the direct effects of high surges in catecholamines upon myocardial biology including β-adrenergic receptor signalling, G-protein coupled receptor kinases, cardiomyocyte calcium physiology, myofilament physiology, cardiomyocyte gene expression, myocardial electrophysiology and arrhythmogenicity, myocardial inflammation, metabolism and energetics. The integrated effects upon ventricular haemodynamics are discussed and integrated into the pathophysiological model.
Modulating the Biological Function of Protein by Tailoring the Adsorption Orientation on Nanoparticles (2020)

&lt;div&gt;&lt;div&gt;&lt;div&gt;&lt;p&gt;Protein orientation in nanoparticle-protein conjugates plays a crucial role in binding to cell receptors and ultimately, defines their targeting efficiency. Therefore, understanding fundamental aspects of the role of protein orientation upon adsorption on the surface of nanoparticles (NPs) is vital for the development of clinically important protein-based nanomedicine. In this work, new insights on the effect of the different orientation of cytochrome c (cyt c) bound to gold nanoparticles (GNPs) using various ligands on its apoptotic activity is reported. Time-of-Flight Secondary-Ion Mass Spectrometry (ToF- SIMS), electrochemical and circular dichroism (CD) analyses are used to investigate the characteristics of cyt c orientation and structure on functionalized GNPs. These studies indicate that the orientation and position of the heme ring inside the cyt c structure can be altered by changing the surface chemistry on the NPs. A difference in the apoptosis inducing capability because of different orientation of cyt c bound to the GNPs is observed. These findings indicate that the biological activity of a protein can be modulated on the surface of NPs by varying its adsorption orientation. This study will impact on the rational design of new nanoscale biosensors, bioelectronics, and nanoparticle-protein based drugs.&lt;/p&gt;&lt;/div&gt;&lt;/div&gt;&lt;/div&gt;
MTF Full-Field Displays for Camera Lenses (2017)

Modern optical systems achieve record resolution and require more thorough testing. We outline a method of measuring the performance of camera lenses across the entire rectangular field of view and presenting the results.