gebhart/patrepeval huggingface dataset:
Predicting Scattering From Complex Nano-Structures via Deep Learning (2020)

Existing numerical electromagnetic (EM) solvers are usually computationally expensive, time consuming, and memory demanding. Recent advances in deep learning (DL) techniques have demonstrated superior efficiency and provide an alternative pathway for speeding up simulations by serving as effective computational tools. In this paper, we propose a DL framework for real-time predictions of the scattering from an isolated nano-structure in the near-field regime. We find that, to achieve precise approximation of the optical response obtained from numerical simulations, the proposed DL framework only requires a small training data set. The fully trained framework can be three orders of magnitude faster than a conventional EM solver based on the finite difference frequency domain method (FDFD). Furthermore, the proposed DL framework has demonstrated robustness to changes in design variables which govern the nano-structure geometry and material selection as well as properties of the incident wave, shedding light on universal scattering predictions at the nano scale via deep learning techniques. This framework increases the viability of the design and analysis of complex nanostructures, offering great potential for applications pertaining to complex light-matter interaction between electromagnetic fields and nanomaterials.
Large Scale Personalized Categorization of Financial Transactions (2019)

A major part of financial accounting involves tracking and organizing business transactions over and over each month and hence automation of this task is of significant value to the users of accounting software. In this paper we present a large-scale recommendation system that successfully recommends company specific categories for several million small businesses in US, UK, Australia, Canada, India and France and handles billions of financial transactions each year. Our system uses machine learning to combine fragments of information from millions of users in a manner that allows us to accurately recommend user-specific Chart of Accounts categories. Accounts are handled even if named using abbreviations or in a foreign language. Transactions are handled even if a given user has never categorized a transaction like that before. The development of such a system and testing it at scale over billions of transactions is a first in the financial industry.
A Soft Computing Approach to Controlling Emissions Under Imperfect Sensors (2013)

NOx emissions from commercial equipment vehicles can be controlled by the introduction of cleansing agents into output of the equipment. This process requires a monitoring of the output by sensors. Typically, these sensors can be of two types, physical and virtual, each of which can be imperfect in their readings. Physical sensors gradually deteriorate in time while virtual sensors have limit range of reliability. We provide an approach for fusing these imperfect sensor readings using the ordered weighted averaging (OWA) operator. The use of the OWA operator allows users to easily provide their preferred tradeoff between costly introductions of too much cleansing agent versus the possibility of penalization for emission violation. We also provide a methodology for determining the state of the physical sensor. We observe that the system described in this paper has been operationally implemented.
Efficient 3D cell tracking using adaptive scanning OCT (2023)

Optical coherence tomography (OCT) has wide application in medicine, particularly ophthalmology. In the anterior chamber of the eye, OCT can potentially image blood cells to monitor cellular response to injury or inflammation. However, low volumetric refresh rates limit OCT in applications that require the tracking of individual, moving cells. Therefore, we propose an efficient 3D cell tracking using adaptive scanning OCT. Adaptive scanning prioritizes capturing regions of interest that change from volume to volume. Using depth information from OCT A-scans, our cell tracking method successfully localized simulated cells across multiple OCT volumes.
A Dynamic Method to Analyze Cold-Start First Cycles Engine-Out Emissions at Elevated Cranking Speed Conditions of a Hybrid Electric Vehicle Including a Gasoline Direct Injection Engine (2022)

&lt;div&gt;The cold crank-start stage, including the first three engine cycles, is responsible for a significant amount of the cold-start phase emissions in a Gasoline Direct Injection (GDI) engine. The engine crank-start is highly transient due to substantial engine speed changes, Manifold Absolute Pressure (MAP) dynamics, and in-cylinder temperatures. Combustion characteristics change depending on control inputs variations, including throttle angle and spark timing. Fuel injection strategy, timing, and vaporization dynamics are other parameters causing cold-start first cycles analysis to be more complex. Hybrid Electric Vehicles (HEVs) provide elevated cranking speed, enabling technologies such as cam phasing to adjust the valve timing and throttling, and increased fuel injection pressure from the first firings. To analyze the engine-out emissions, including unburnt Hydrocarbon (HC), Nitrogen Oxides (NOx), Carbon monoxide (CO), and Carbon dioxide (CO&lt;sub&gt;2&lt;/sub&gt;), the measured emissions in mole fraction need to be quantified in mass per cycle per cylinder considering all dynamics mentioned above. This study proposes a new method to quantify individual-cylinder engine-out emissions event by event dynamically. The method consists of the individual-cylinder GT-Power Three Pressure Analysis (TPA), in-cylinder parameters estimation, fuel vaporization Computational Fluid Dynamics (CFD) analysis, and exhaust gas dynamics in the exhaust manifold. Experimental MAP, cylinder and exhaust pressures, injection pulse width, GT-Power estimated parameters, and air mass flow meter data are used for the new method calibration and validation. The estimated trapped air charge and the equivalent combusted fuel masses are the most critical parameters affecting the precision of calculating engine-out emissions on a mass basis. The results show that the trapped air charge is estimated with a 2.7 mg average error. In addition, the simulated Indicated Mean Effective Pressure (IMEP) as representative of the mass of fuel contributed to the combustion during the same event was validated with a 0.06 bar average error. Furthermore, the fuel path analysis is carried out to validate the post-oxidization coefficient and lost fuel portion calibrated values, showing 75.3% and 15.8% post-oxidization rate of unburnt HC and 18.5% and 20% lost fuel portion for high cranking speed/highly retarded and low cranking speed/advanced spark timing conditions, respectively.&lt;/div&gt;
Interferon β-1b–neutralizing antibodies 5 years after clinically isolated syndrome (2011)

Although NAb positivity was associated with increased brain MRI activity, no discernible effects on clinical outcomes were found. This finding may reflect the greater power of MRI compared with clinical outcomes to detect the treatment effects of IFNβ-1b and may also result from temporal changes in NAb titers and biology.
Intraclonal Complexity in Chronic Lymphocytic Leukemia: Fractions Enriched in Recently Born/Divided and Older/Quiescent Cells (2011)

The failure of chemotherapeutic regimens to eradicate cancers often results from the outgrowth of minor subclones with more dangerous genomic abnormalities or with self-renewing capacity. To explore such intratumor complexities in B-cell chronic lymphocytic leukemia (CLL), we measured B-cell kinetics in vivo by quantifying deuterium ((2)H)-labeled cells as an indicator of a cell that had divided. Separating CLL clones on the basis of reciprocal densities of chemokine (C-X-C motif) receptor 4 (CXCR4) and cluster designation 5 (CD5) revealed that the CXCR4(dim)CD5(bright) (proliferative) fraction contained more (2)H-labeled DNA and hence divided cells than the CXCR4(bright)CD5(dim) (resting) fraction. This enrichment was confirmed by the relative expression of two cell cycle-associated molecules in the same fractions, Ki-67 and minichromosome maintenance protein 6 (MCM6). Comparisons of global gene expression between the CXCR4(dim)CD5(bright) and CXCR4(bright)CD5(dim) fractions indicated higher levels of pro-proliferation and antiapoptotic genes and genes involved in oxidative injury in the proliferative fraction. An extended immunophenotype was also defined, providing a wider range of surface molecules characteristic of each fraction. These intraclonal analyses suggest a model of CLL cell biology in which the leukemic clone contains a spectrum of cells from the proliferative fraction, enriched in recently divided robust cells that are lymphoid tissue emigrants, to the resting fraction enriched in older, less vital cells that need to immigrate to lymphoid tissue or die. The model also suggests several targets preferentially expressed in the two populations amenable for therapeutic attack. Finally, the study lays the groundwork for future analyses that might provide a more robust understanding of the development and clonal evolution of this currently incurable disease.
Genetic targeting for cardiovascular therapeutics: are we near the summit or just beginning the climb? (2001)

This article is based on an Experimental Biology symposium held in April 2001 and presents the current status of gene therapy for cardiovascular diseases in experimental studies and clinical trials. Evidence for the use of gene therapy to limit neointimal hyperplasia and confer myocardial protection was presented, and it was found that augmenting local nitric oxide (NO) production using gene transfer (GT) of NO synthase or interruption of cell cycle progression through a genetic transfer of cell cycle regulatory genes limited vascular smooth muscle hyperplasia in animal models and infra-inguinal bypass patients. The results of application of vascular endothelial growth factor (VEGF) GT strategies for therapeutic angiogenesis in critical limb and myocardial ischemia in pilot clinical trials was reviewed. In addition, experimental evidence was presented that genetic manipulation of peptide systems (i.e., the renin-angiotensin II system and the kallikrein-kinin system) was effective in the treatment of systemic cardiovascular diseases such as hypertension, heart failure, and renal failure. Although, as of yet, there are no well controlled human trials proving the clinical benefits of gene therapy for cardiovascular diseases, the data presented here in animal models and in human subjects show that genetic targeting is a promising and encouraging modality, not only for the treatment and long-term control of cardiovascular diseases, but for their prevention as well.
Association of an Endoribonuclease with the Avian Myeloblastosis Virus Deoxyribonucleic Acid Polymerase (1972)

Abstract A ribonuclease degrading only RNA complexed to DNA is found associated with the avian myeloblastosis virus DNA polymerase. A convenient and sensitive assay for the enzyme is degradation of [3H]poly(A) complexed to poly(dT). Using this assay, nuclease and DNA polymerase activities are inseparable by DEAE-Sephadex or phosphocellulose ion exchange chromatography or by glycerol gradient centrifugation. Poly(A) labeled selectively at each end can be used to demonstrate that the nuclease is an endonuclease, and chromatography of the digestion products of poly(A) confirms this result. The oligonucleotide digestion products can be further digested to 5'-AMP by venom phosphodiesterase, indicating that they are terminated by 3'-OH groups.
Altered cytotoxicity of ROS-inducing compounds by sodium pyruvate in cell culture medium depends on the location of ROS generation (2015)

Induction of oxidative stress by drugs and other xenobiotics is an important mechanism of cytotoxicity. However, in vitro studies on the relationship between oxidative stress and cytotoxicity in cultured cells is frequently complicated by the fact that cell culture medium components affect reactive oxygen species (ROS) exposures in ways that vary with the mode of ROS production. The objectives of this study were to first determine the mode of ROS induction by certain model compounds when they are applied to cultured cells, and then to determine how ROS induction and cytotoxicity were affected by the ROS-quenching medium component pyruvate. Three compounds, eseroline, benserazide, and pyrogallol induced H2O2 in cell culture media independent of cells. However, another compound, menadione, induced H2O2 in a manner largely dependent on the MDA-MB-231 breast cancer cells used in this study, which is consistent with its known mechanism of inducing ROS through intracellular redox cycling. 1 mM pyruvate, as well as catalase, reduced the H2O2 in culture wells with each ROS inducer tested but it only reduced the cytotoxicity of cell-independent inducers. It reduced the cytotoxicity of benserazide and pyrogallol >10-fold and of eseroline about 2.5-fold, but had no effect on menadione cytotoxicity. From this data, it was concluded that depending on the mechanism of ROS induction, whether intra- or extracellular, a ROS-quenching medium component such as pyruvate will differentially affect the net ROS-induction and cytotoxicity of a test compound.
Appendix B: The Scalar Theory of Diffraction (2009)

This appendix contains sections titled: Full Scalar Theory Scalar Diffraction Models for Digital Optics Extended Scalar Models References
Transkriptionsabhängige und -unabhängige Regulation von Mcl-1 durch die p53-Familie (2011)

Die p53-Familie, besteht aus den transkriptionell aktiven (TA-) Isoformen p53, TAp63 und TAp73, die Apoptose induzieren, und dominant negativen (DN-) Isoformen, die die TA-vermittelte Apoptose inhibieren. Wir konnten zeigen, dass die Imbalance der TA- und DN-Isoformen der p53-Familie bei Überwiegen der DN-Isoformen zu Entstehung, Progression und Therapieresistenz des Hepatozellulären Karzinoms (HCC) führt. Darüber hinaus konnten wir zeigen, dass die Expression von Myeloid cell leukemia-1 (Mcl-1), ein anti-apoptotisches Mitglied der Bcl-2 Familie, mit einer verminderten Apoptosesensitivität und Chemoresistenz im HCC einhergeht.
Synthesis of titania embedded silica hollow nanospheres via sonication mediated etching and re-deposition (2011)

Titania embedded silica hollow nanospheres were synthesized from sonication-mediated etching and re-deposition of silica/titania core/shell nanospheres. The designed structure of the hollow nanospheres was proved to be a key factor for the charge trapping/detrapping and resulting bistability in non-volatile organic bistable memory devices (OBDs).
Abstract 739: Preclinical and clinical activity of SAR439859, Amcenestrant, a next generation SERD (2021)

Abstract Primary treatment for estrogen receptor-positive (ER+) breast cancer is endocrine therapy. Selective estrogen receptor degraders (SERDs), such as fulvestrant, induce effective ER signaling inhibition, although clinical studies with fulvestrant report insufficient blockade of ER signaling, possibly due to suboptimal pharmaceutical properties. Here we describe the discovery of SAR439859 (Amcenestrant), a novel, orally bioavailable SERD with potent antagonist and degradation activities against both wild-type and mutant Y537S ER. Driven by its fluoropropyl pyrrolidinyl side chain, SAR439859 has demonstrated broader and superior ER antagonist and degrader activities across a large panel of ER+ cells, compared with other SERDs including improved inhibition of ER signaling and tumor cell growth. Similarly, in vivo treatment with SAR439859 demonstrated significant tumor regression in ER+ breast cancer models including MCF7-ESR1 mutant-Y537S mouse tumors and HCI013, a patient-derived tamoxifen-resistant xenograft tumor. Importantly, in these mutant ESR1 models, we demonstrate that the efficacy of SAR439859 was increased when coadministered with palbociclib, an inhibitor of cyclin-dependent kinase 4 and 6. In the clinical setting, SAR439859 also demonstrated a high level of target engagement, ER degradation and inhibition of ER signaling as well as encouraging anti-tumor activity in heavily pretreated patients with advanced or metastatic ER-positive breast cancer. These findings indicate that SAR439859 would provide therapeutic benefit to patients with ER+ breast cancer, including those who are resistant to endocrine therapy with both wild-type and mutant ER. Citation Format: Maysoun Shomali, Fangxian Sun, Laurent Besret, Anne Caron, Joon Sang Lee, Youssef El-Ahmed, Laurent Schio, Jack Pollard, Vasiliki Pelekanou, Patrick Cohen, Marina Celanovic, Christina Herold, Chris Soria, Laurent Debussche, Monsif Bouaboula. Preclinical and clinical activity of SAR439859, Amcenestrant, a next generation SERD [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 739.
LINE-1 retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5′ single-cell RNA-Seq (2023)

LINE-1 retrotransposons are sequences capable of copying themselves to new genomic loci via an RNA intermediate. New studies implicate LINE-1 in a range of diseases, especially in the context of aging, but without an accurate understanding of where and when LINE-1 is expressed, a full accounting of its role in health and disease is not possible. We therefore developed a method-5' scL1seq-that makes use of a widely available library preparation method (10x Genomics 5' single cell RNA-seq) to measure LINE-1 expression in tens of thousands of single cells. We recapitulated the known pattern of LINE-1 expression in tumors-present in cancer cells, absent from immune cells-and identified hitherto undescribed LINE-1 expression in human epithelial cells and mouse hippocampal neurons. In both cases, we saw a modest increase with age, supporting recent research connecting LINE-1 to age related diseases.
The Road from Panama to Keccak via RadioGatún (2009)

In this presentation, we explain the design choices of Panama [1] and RadioGatun [2], which lead to Keccak [3]. After a brief recall of Panama, RadioGatun and the trail backtracking cost, we focus on three important aspects. First, we explain the role of the belt in the light of differential trails. Second, we discuss the relative advantages of a block mode hash function compared to a stream mode one. Finally, we point out why Panama and RadioGatun are not sponge functions and why their design philosophy differs from that of Keccak. [1] J. Daemen and C. S. K. Clapp, FSE 1998 [2] G. Bertoni et al., NIST Hash Workshop 2006 [3] G. Bertoni et al., SHA-3 submission, 2008
Genetic control of experimental autoimmune encephalomyelitis at the level of cytotoxic lymphocytes in guinea pigs (1982)

To analyze immunologic mechanisms involved in experimental autoimmune encephalomyelitis (EAE), a system for studying the cytotoxic reaction of guinea pig lymphocytes against syngeneic macrophages pulsed with myelin basic protein (BP) was developed. It was found that both EAE-susceptible strain 13 and EAE-resistant strain 2 animals developed cytotoxicity directed against whole BP. However, only strain 13 guinea pigs developed such cells in response to immunization with the encephalitogenic nonapeptide determinant of BP. Strain 2 macrophages appeared able to present the nonapeptide determinant to strain 13 lymphocytes. Anti-BP cytotoxic lymphocytes were found to be recruited by anti-BP initiator lymphocytes.
Silicon-Directed Oxa-Pictet−Spengler Cyclization and an Unusual Dimerization of 2-Trimethylsilanyl Tryptophols (2005)

The tetrahydro-pyrano[3,4-b]indoles 6 were synthesized from 2-(2-trimethylsilanyl-1H-indol-3-yl)-ethanols 5 and various ketones or aldehydes through silicon-directed oxa-Pictet-Spengler cyclizations. An unusual reaction led to the dimeric products 7 when some of 5 was treated with acetone using BF(3) as the catalyst.
Constant depth, near constant depth, and subcubic size threshold circuits for linear algebraic calculations (2023)

A method of increasing an efficiency at which a plurality of threshold gates arranged as neuromorphic hardware is able to perform a linear algebraic calculation having a dominant size of N. The computer-implemented method includes using the plurality of threshold gates to perform the linear algebraic calculation in a manner that is simultaneously efficient and at a near constant depth. “Efficient” is defined as a calculation algorithm that uses fewer of the plurality of threshold gates than a naïve algorithm. The naïve algorithm is a straightforward algorithm for solving the linear algebraic calculation. “Constant depth” is defined as an algorithm that has an execution time that is independent of a size of an input to the linear algebraic calculation. The near constant depth comprises a computing depth equal to or between O(log(log(N)) and the constant depth.
Coding-adaptive transforms (2004)

Transform coding plays a central role in image and video coding technologies. Various transforms, whether fixed or adaptive, have been utilized for video compression. However, these transforms are inherently sub-optimal in a coding-efficiency sense, given that their design does not explicitly take into account the entire transform coding model. Thus, commonly used transforms such as the DCT have desirable properties, but were designed without the full consideration of the other transform coding elements including quantization and entropy coding. Although these transforms have good performance in a rate-distortion sense, as demonstrated by today's image and video coding standards, we show that superior transforms can be designed based on the complete transform coding model. We present a new class of transforms called coding-adaptive transforms, that are derived under an optimality criterion which incorporates the elements of transform coding and is formulated for coding efficiency. Additionally, characteristics of the new transforms such as adaptivity, generalization, and robustness are discussed.
Providing Geo-Elasticity in Geographically Distributed Clouds (2018)

Geographically distributed cloud platforms are well suited for serving a geographically diverse user base. However, traditional cloud provisioning mechanisms that make local scaling decisions are not adequate for delivering the best possible performance for modern web applications that observe both temporal and spatial workload fluctuations. We propose GeoScale, a system that provides geo-elasticity by combining model-driven proactive and agile reactive provisioning approaches. GeoScale can dynamically provision server capacity at any location based on workload dynamics. We conduct a detailed evaluation of GeoScale on Amazon’s geo-distributed cloud and show up to 40% improvement in the 95th percentile response time when compared to traditional elasticity techniques.
Readout-Signal Amplification by Homodyne Detection Scheme (2007)

Optical signal amplification by using homodyne detection scheme was newly proposed and demonstrated experimentally. We estimated that the scheme improved S/N for an 8-layer and 3x-read-speed Blu-ray Disc by more than 20 dB.
ChemInform Abstract: Z,Z‐DIENES VIA ACETYLENE CARBOCUPRATION: SYNTHESIS OF NAVEL ORANGEWORM PHEROMONE (1985)

Abstract Durch zweifache Umsetzung von Cupraten mit Acetylen und anschließende Abfangreaktion mit Elektrophilen werden Z,Z‐Diene wie (IV) gut zugänglich.