gebhart/patrepeval huggingface dataset:
Deep turbulence effects compensation experiments with a cascaded adaptive optics system using a 363 m telescope (2008)

Compensation of extended (deep) turbulence effects is one of the most challenging problems in adaptive optics (AO). In the AO approach described, the deep turbulence wave propagation regime was achieved by imaging stars at low elevation angles when image quality improvement with conventional AO was poor. These experiments were conducted at the U.S. Air Force Maui Optical and Supercomputing Site (AMOS) by using the 3.63 m telescope located on Haleakala, Maui. To enhance compensation performance we used a cascaded AO system composed of a conventional AO system based on a Shack-Hartmann wavefront sensor and a deformable mirror with 941 actuators, and an AO system based on stochastic parallel gradient descent optimization with four deformable mirrors (75 control channels). This first-time field demonstration of a cascaded AO system achieved considerably improved performance of wavefront phase aberration compensation. Image quality was improved in a repeatable way in the presence of stressing atmospheric conditions obtained by using stars at elevation angles as low as 15 degrees.
A new metrology technique for defect inspection via coherent Fourier scatterometry using orbital angular momentum beams (2021)

Coherent Fourier scatterometry (CFS) using laser beams with a Gaussian spatial profile is routinely used as an in-line inspection tool in semiconductor industry. Here, a set of novel defect inspection techniques are proposed and investigated numerically, which are based on bright-field CFS using coherent beams that carry orbital angular momentum (OAM). Through numerical simulations, we demonstrated that it shows up to an order of magnitude higher in signal-to-noise ratio over the conventional Gaussian beam CFS.
Follow-Up of Anti-HBc Titers in Healthy HBsAg Carriers and Patients with Chronic Inflammatory Liver Diseases (1981)

Sera of 85 asymptomatic HBsAg carriers found among blood donors were tested for anti-HBc titers and were retested 4 years later. The results were correlated with the histological findings of first and final biopsy. None of 75 HBsAg carriers with normal or minimally changed liver tissue, 71 of them anti-HBe positive, developed chronic inflammatory liver disease. 4 HBsAg carriers eliminated HBsAg from the serum after a 1-to 3-year HBsAg-carrier state and 2 developed antibody against HBsAg in the sequel. In 65 of 75 cases we found unchanged anti-HBc titers. The geometrical mean titer (GMT) was 1:7,800 in the first and 1:7,000 in the final examination with a range of 1:400 and 1:25,600 in the group of HBsAg carriers with normal liver, and was 1:14,200 and 1:10,300, respectively, with a range of 1:800 and 1:51,200 in HBsAg carriers with minimal changes. In both groups the decrease of anti-HBc concentration within 4 years was not significant. The group of 10 HBsAg carriers with chronic hepatitis did not differ from healthy HBsAg carriers in respect to anti-HBc titers. Anti-HBc titers varied between 1:6,400 and 1:25,600, the GMT was 1:13,700 and 1:12,800, respectively. It is speculated that in healthy HBsAg carriers shedding of serologically undetectable quantities of complete and/or defective HBcAg from liver cell nuclei which contain HBcAg not detectable by immunofluorescence maintain the production of anti-HBc.
Long noncoding RNA SILC1 is an upstream regulator of SOX11 in neuroblastoma (2020)

Neuroblastoma (NB) is the most common extra cranial solid tumor during early childhood, arising from progenitors of the sympathetic nervous system. We identified the adrenergic specific transcription factor SOX11 as a lineage dependency factor and a putative master regulator of epigenetic plasticity in NB. Using ChIP-seq we mapped the sites of SOX11 DNA binding and identified several genes encoding components of major epigenetic regulatory protein complexes. In order to gain more insight into the long-range control of SOX11 expression in NB cells, we analyzed H3K27ac data to map noncoding regulatory enhancer regions. We identified a super-enhancer in a large protein coding gene poor region 1.1 Mb distal to the SOX11 locus. This region coincides with the previously annotated lncRNA coined SILC1 which was shown to be implicated in neurite outgrowth and neuron regeneration. SILC1 was found to be strongly expressed in adrenergic NB cells and highly correlated to SOX11 expression levels in both NB cell lines and tumors. Also, in the normal developing sympathetic lineage and across a wide panel of cancer cell line entities and adrenergic/mesenchymal isogenic cell line pairs, the SILC1 expression pattern closely resembled that of SOX11. To investigate the chromatin conformation of the SOX11 neighbouring (super-)enhancers, we performed 4C-seq analysis and observed looping in this highly active region between the SOX11 and SILC1 promoter in adrenergic NB cells while absent in the mesenchymal NB cell line SH-EP. We are currently unraveling the role of SILC1 using ChIRP sequencing and a dCas9-KRAB silencing system. In conclusion, our data suggests that SILC1 plays a crucial role in controlling SOX11 expression levels thus offering an entry point for targeted therapy for SOX11-driven neuroblastoma.
Coordinating opportunistic interdisciplinary projects across single-discipline capstone courses (2019)

There is increasing interest in developing interdisciplinary capstone courses in which students from different majors enroll to worktogether on complex, real-world projects. Creation of new interdisciplinary capstone courses may not be feasible for somedepartments or institutions, however, due to administrative or funding complexities. As an alternative, the inclusion of interdisciplinaryprojectsengaging students enrolled in separate single-discipline capstone courses may offer the opportunity toundertake interesting projects, or engage with certain sponsors, that would not be possible without the contributions of studentsfrom diverse disciplines. Having such projects undertaken by interdisciplinary teams of students who remain in their single-discipline capstone courses does not reduce, and may amplify, the challenges found in full-fledged interdisciplinary capstone courses(e.g., misaligned schedules, differing requirements, and unfamiliar working cultures). This paper provides findings from the pilotyear of a series of opportunistic interdisciplinary capstone projects associated with NASA’s Psyche Asteroid Mission involvingstudents from computer science, computer systems engineering, engineering management, industrial design, and graphic design. Thefindings highlight the importance of close communication and flexibility between faculty and identify a novel and potentially-replicable approach of including project management capstone students on interdisciplinary teams. The paper also describeschanges that were implemented for the national expansion of the program with the 2018–2019 academic year and provides earlylessons learned associated with those changes, outlining a plan for iterative improvement.
Supplemental Tables 6-11 from Notch1 Mutations Are Drivers of Oral Tumorigenesis (2023)

&lt;p&gt;Supplemental Tables 6-11. Supp. Table 6. List of all mutations identified in each of the normal samples. Supp. Table 7. List of the mutations in the unmatched OSCC and leukoplakia samples that were filtered-out as they were present in the normal samples or in the dbSNP. Supp. Table 8. Summary of the number of mutations present in each of the sets of samples and the number that were filtered-out during analysis. Supp. Table 9. Combined list of all mutations identified in Chinese OSCC patients in this study and by Song et. al (16). Supp. Table 10. List of all NOTCH1 mutations identified in Caucasians HNSCC samples. Supp. Table 11. List of all HNSCC samples from Caucasian patients used in this study: including exact site and HPV status.&lt;/p&gt;
Editor's Note: Regulation of HMGA1 Expression by MicroRNA-296 Affects Prostate Cancer Growth and Invasion (2020)

The editors are publishing this note to alert readers to a concern about [this article][1] ([1][2]). In Fig. 1C, similarities exist in two sets of the HMGA1 (mRNA) beta actin blots: DU145 cells treated with Block-it and with anti-Let-7, and DU145 cells treated with anti-296 and PC3 cells treated
Contactless bottom-up electrodeposition of nickel for 3D integrated circuits (2015)

Electrochemical oxidation of silicon by water generates electrons and subsequent chemical etching of silicon dioxide by fluoride based species regenerates the surface. The electrons are conducted through bulk silicon and accepted by nickel ions.
Communication-Efficient Policy Gradient Methods for Distributed Reinforcement Learning (2021)

This article deals with distributed policy optimization in reinforcement learning, which involves a central controller and a group of learners. In particular, two typical settings encountered in several applications are considered: <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">multiagent reinforcement learning</i> (RL) and <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">parallel RL</i> , where frequent information exchanges between the learners and the controller are required. For many practical distributed systems, however, the overhead caused by these frequent communication exchanges is considerable, and becomes the bottleneck of the overall performance. To address this challenge, a novel policy gradient approach is developed for solving distributed RL. The novel approach adaptively skips the policy gradient communication during iterations, and can reduce the communication overhead without degrading learning performance. It is established analytically that: i) the novel algorithm has a convergence rate identical to that of the plain-vanilla policy gradient; while ii) if the distributed learners are heterogeneous in terms of their reward functions, the number of communication rounds needed to achieve a desirable learning accuracy is markedly reduced. Numerical experiments corroborate the communication reduction attained by the novel algorithm compared to alternatives.
A Wasserstein Minimax Framework for Mixed Linear Regression (2021)

Multi-modal distributions are commonly used to model clustered data in statistical learning tasks. In this paper, we consider the Mixed Linear Regression (MLR) problem. We propose an optimal transport-based framework for MLR problems, Wasserstein Mixed Linear Regression (WMLR), which minimizes the Wasserstein distance between the learned and target mixture regression models. Through a model-based duality analysis, WMLR reduces the underlying MLR task to a nonconvex-concave minimax optimization problem, which can be provably solved to find a minimax stationary point by the Gradient Descent Ascent (GDA) algorithm. In the special case of mixtures of two linear regression models, we show that WMLR enjoys global convergence and generalization guarantees. We prove that WMLR's sample complexity grows linearly with the dimension of data. Finally, we discuss the application of WMLR to the federated learning task where the training samples are collected by multiple agents in a network. Unlike the Expectation Maximization algorithm, WMLR directly extends to the distributed, federated learning setting. We support our theoretical results through several numerical experiments, which highlight our framework's ability to handle the federated learning setting with mixture models.
Targeting EGFR-TK with radiolabeled cyclam-tyrosine (2006)

2394 Purpose. The epidermal growth factor receptor (EGFR) is expressed in a variety of human solid tumors. When EGFR is triggered, EGFR tyrosine kinase (TK) is activatedand leading to initiate the receptor-mediated signal transduction, cell proliferation, survival, angiogenesis, and metastasis. This study was to develop radiolabeled cyclam-tyrosine to assess EGFR-TK activity. Method. Cyclam-tyrosine was synthesized by conjugating O-3-tosylpropyltyrosine with cyclam N,N,N-tri (trifluoroacetate), followed by hydrolysis. In vitro cell culture were conducted using epidermoid carcinoma (A431), lung papillary adenocarcinoma (H441) and lung adenocarcinoma (H3255) cells. The cells (50,000 cells/well) were incubated with ZD1839 (gefitinib, 1-20 uM) for 1 hrs and Western blot was performed. Cellular uptake of 99mTc-cyclam-tyrosine (2 uCi/well) was conducted at 1.5 hrs after the cells (50,000 cells/well) were incubated with ZD1839 (gefitinib, 1-20 uM) for 6 hrs. The cellular upatek findings were correlated Western Blot assays Cyclam-tyrosine was also labeled with 68Ga (PET isotope). PET and planar imaging studies with 68Ga/ 99mTc-cyclam-tyrosine were conducted in tumor-bearing rodents. Results. Western blot analysis showed that high EGFR-TK expression (A431, H3255) could be inhibited with ZD1839 whereas poor EGFR-TK (H441) could not be inhibited. In vitro cellular uptake assays indicated that EGFR-TK activity correlated well with 99mTc-EC-DG. PET and planar scintigraphy in animal models demonstrated the tumor could be clearly visualized by 68Ga-cyclam-tyrosine and 99mTc-cyclam-tyrosine. Conclusion.. Radiolabeled cyclam-tyrosine could assess EGFR-TK activity in tumor cells. Such compounds may be useful in selecting patients who may respond to EGFR-TK therapy.
AirCapRL: Autonomous Aerial Human Motion Capture using Deep Reinforcement Learning (2020)

In this letter, we introduce a deep reinforcement learning (RL) based multi-robot formation controller for the task of autonomous aerial human motion capture (MoCap). We focus on vision-based MoCap, where the objective is to estimate the trajectory of body pose and shape of a single moving person using multiple micro aerial vehicles. State-of-the-art solutions to this problem are based on classical control methods, which depend on hand-crafted system and observation models. Such models are difficult to derive and generalize across different systems. Moreover, the non-linearity and non-convexities of these models lead to sub-optimal controls. In our work, we formulate this problem as a sequential decision making task to achieve the vision-based motion capture objectives, and solve it using a deep neural network-based RL method. We leverage proximal policy optimization (PPO) to train a stochastic decentralized control policy for formation control. The neural network is trained in a parallelized setup in synthetic environments. We performed extensive simulation experiments to validate our approach. Finally, real-robot experiments demonstrate that our policies generalize to real world conditions. Video Link: https://bit.ly/38SJfjo Supplementary: https://bit.ly/3evfo1O
(Invited) Solution Processing and Device Integration of Two-Dimensional Black Phosphorus (2015)

Two-dimensional black phosphorus (2D BP) has emerged as a promising candidate for next-generation electronics and optoelectronics. As is common for new materials, much of the early work on 2D BP has focused on measuring and optimizing intrinsic properties on small samples under idealized conditions. However, real-world devices and systems inevitably require large-area samples that are integrated with dielectrics, contacts, and other semiconductors at standard temperature and pressure conditions. These requirements are particularly challenging to realize for 2D BP since its properties are highly sensitive to surface chemistry, defects, and the surrounding environment. This talk will thus explore methods for improving the uniformity of solution-based 2D BP with an eye toward realizing scalable processing of large-area thin-films. Specifically, methods for exfoliating black phosphorus in anhydrous organic solvents will be discussed such that the resulting 2D BP flakes show field-effect transistor mobilities and on/off ratios that are comparable to micromechanically exfoliated flakes [1]. In addition to solution processing, this talk will also report on the integration of 2D BP with dielectrics and other materials. In particular, atomic layer deposition of alumina dielectrics on 2D BP suppresses ambient degradation, thereby preserving electronic properties in field-effect transistors at atmospheric pressure conditions [2]. [1] J. Kang, J. D. Wood, S. A. Wells, J.-H. Lee, X. Liu, K.-S. Chen, and M. C. Hersam, “Solvent exfoliation of electronic-grade, two-dimensional black phosphorus,” ACS Nano , DOI: 10.1021/acsnano.5b01143 (2015). [2] J. D. Wood, S. A. Wells, D. Jariwala, K.-S. Chen, E. Cho, V. K. Sangwan, X. Liu, L. J. Lauhon, T. J. Marks, and M. C. Hersam, “Effective passivation of exfoliated black phosphorus transistors against ambient degradation,” Nano Lett. , 14 , 6964 (2014).
Wireless Power Transfer H-Bridge design with serial resonance and varying supply voltage (2013)

In this manuscript the authors discuss the issues of designing and implementing an H-Bridge circuit with respect to small switching losses, minimal hardware afford and maximal flexibility of excitation and control. The H-Bridge is targeted for a biomedical Wireless Power Transfer (WPT) application, where the receiver (RX) is small compared to the transmitter (TX) and, thus, negligible. Resonance is applied on the TX side, while the input voltage to the H-Bridge is able to vary in the range of 3V to 28V depending on a flexible relation between the TX and RX. This causes effects to the design and the gate drivers of the H-Bridge. An H-Bridge design is proposed, which includes the use of an n-channel and p-channel Metal-Oxide Semiconductor Field-Effect Transistor (MOSFET) for a direct addressing of gates with a microcontroller (μC). In addition, the switching losses are lowered by the introduction of choke inductors and non-overlapping time delayed driving signals. Furthermore, the proposed solution has been verified, since significant advancements compared to state-of-the-art H-Bridge designs can be shown.
Complexity of sea urchin embryo nuclear proteins that contain basic domains. (1992)

We describe a quantitative two-dimensional gel electrophoretic analysis of nuclear extract from 24-hr sea urchin embryos. The extract was fractionated by using a weak cation-exchange resin, and eight known DNA-binding proteins were shown to be entirely included in a salt eluate that releases proteins containing basic domains. This fraction and a lower-salt fraction containing the majority of the protein species were mapped two-dimensionally by using new algorithms that permit reproducible spot identification, storage of intensity and map-position data, and subtractive comparison of one pattern with respect to another. By reference to a previously characterized DNA-binding factor, spot intensity could be interpreted in terms of the number of molecules per embryo nucleus. A map was constructed displaying all nuclear proteins containing basic domains that are present within the concentration range per nucleus of a set of known DNA-binding factors of the sea urchin embryo. The map includes 265 spots that fulfill both of these criteria, probably representing about 100 different protein species.
Exploring and Exploiting Acceptor Preferences of the Human Polysialyltransferases as a Basis for an Inhibitor Screen (2017)

α2,8-Linked polysialic acid (polySia) is an oncofoetal antigen with high abundance during embryonic development. It reappears in malignant tumours of neuroendocrine origin. Two polysialyltransferases (polySTs) ST8SiaII and IV are responsible for polySia biosynthesis. During development, both enzymes are essential to control polySia expression. However, in tumours ST8SiaII is the prevalent enzyme. Consequently, ST8SiaII is an attractive target for novel cancer therapeutics. A major challenge is the high structural and functional conservation of ST8SiaII and -IV. An assay system that enables differential testing of ST8SiaII and -IV would be of high value to search for specific inhibitors. Here we exploited the different modes of acceptor recognition and elongation for this purpose. With DMB-DP3 and DMB-DP12 (fluorescently labelled sialic acid oligomers with a degree of polymerisation of 3 and 12, respectively) we identified stark differences between the two enzymes. The new acceptors enabled the simple comparative testing of the polyST initial transfer rate for a series of CMP-activated and N-substituted sialic acid derivatives. Of these derivatives, the non-transferable CMP-Neu5Cyclo was found to be a new, competitive ST8SiaII inhibitor.
Effect of Hematite Dosage on Water-Based Drilling Fluid and Filter Cake Properties (2022)

Abstract Drilling deep wells became common in the oil and gas sector as a result of the high demand for energy in the world. This type of wells is not trivial to drill as a result several challenges that they encounter, such as harsh conditions represented by high-pressure and high-temperature (HPHT), and the high hydrostatic column required to prevent the kick. Therefore, advanced materials are desired and accordingly higher concentration of weighting material is required to drill such resources. In this work, a systematic investigation of the hematite concentration effect on the water-based drilling fluid properties is performed. Three doses were overloaded to a constant drill fluid recipe. Then, the drilling fluid properties including density, viscosities, filtration, and filter cake properties were evaluated. The viscosities were assessed at the temperature of 120 °F, before and after aging in a hot rolling oven for 16 h at 250 °F and 500 psi. The American Petroleum Institute filtration test was performed at ambient temperature and 100 psi. The results showed that the hematite concentration has proportional relation to the apparent viscosity, plastic viscosity, and yield point before and after the hot rolling. The YP/PV ratio was decreased as the hematite dose increased in the drilling fluid. Similarly, the gel strengths at 10 s and 10 min were increased as the concentration of hematite increased. The filter cake thinness, filtration volume, and filter cake permeability were also amplified as the hematite concentration increased, where the filter cake porosity was almost kept constant. In addition, several correlations were drawn as a function of the hematite dosage for the examined drilling properties.
Solubility and Diffusivity of Polar and Non-Polar Molecules in Polyethylene-Aluminum Oxide Nanocomposites for HVDC Applications (2020)

The best commercial high-voltage insulation material of today is (crosslinked) ultra-pure low-density polyethylene (LDPE). A 100-fold decrease in electrical conductivity can be achieved by adding 1–3 wt.% of well-dispersed inorganic nanoparticles to the LDPE. One hypothesis is that the nanoparticle surfaces attract ions and polar molecules, thereby cleaning the surrounding polymer, and thus reducing the conductivity. LDPE-based nanocomposites with 1–12 wt.% octyl-coated aluminum oxide nanoparticles were prepared and the sorption and desorption of one polar compound (acetophenone, a crosslinking by-product) and one non-polar compound of a similar size (limonene) were examined. Since the uptake of acetophenone increased linearly with increasing filler content, whereas the uptake of limonene decreased, the surface attraction hypothesis was strengthened. The analytical functions for predicting composite solubility as a function of particle size and filler fraction were derived using experimental solubility measurements and Monte Carlo simulations.