gebhart/patrepeval huggingface dataset:
Structure and properties of sodium aluminosilicate glasses from molecular dynamics simulations (2013)

Addition of alumina to sodium silicate glasses considerably improves the mechanical properties and chemical durability and changes other properties such as ionic conductivity and melt viscosity. As a result, aluminosilicate glasses find wide industrial and technological applications including the recent Corning(®) Gorilla(®) Glass. In this paper, the structures of sodium aluminosilicate glasses with a wide range of Al∕Na ratios (from 1.5 to 0.6) have been studied using classical molecular dynamics simulations in a system containing around 3000 atoms, with the aim to understand the structural role of aluminum as a function of chemical composition in these glasses. The short- and medium-range structures such as aluminum coordination, bond angle distribution around cations, Q(n) distribution (n bridging oxygen per network forming tetrahedron), and ring size distribution have been systematically studied. In addition, the mechanical properties including bulk, shear, and Young's moduli have been calculated and compared with experimental data. It is found that aluminum ions are mainly four-fold coordinated in peralkaline compositions (Al∕Na < 1) and form an integral part of the rigid silicon-oxygen glass network. In peraluminous compositions (Al∕Na > 1), small amounts of five-fold coordinated aluminum ions are present while the concentration of six-fold coordinated aluminum is negligible. Oxygen triclusters are also found to be present in peraluminous compositions, and their concentration increases with increasing Al∕Na ratio. The calculated bulk, shear, and Young's moduli were found to increase with increasing Al∕Na ratio, in good agreement with experimental data.
Compoweb (2008)

In this paper, client-site Web mashups are studied from component-oriented perspective, and CompoWeb, a component-oriented Web architecture, is proposed. In CompoWeb, a Web application is decomposed into Web components called gadgets. A gadget is an abstraction of functional or logical Web component. It is isolated from other gadgets for security and reliability. Contract-based channels are the only way to interact with each other. An abstraction of contract-based channels supported or required by a gadget is also presented. It enables binding of gadgets at deployment, and promotes interchangeable gadgets. Unlike the model of a normal function call where the function logic is executed in caller's context, CompoWeb ensures that the function logic is executed in callee's context so that both the caller and callee are protected. Implementation of a prototype CompoWeb system and its performance are also presented.
Identification and Characterization of Aluminum Tolerance Loci in Arabidopsis (Landsberg <i>erecta</i> × Columbia) by Quantitative Trait Locus Mapping. A Physiologically Simple But Genetically Complex Trait (2003)

Aluminum (Al) toxicity, which is caused by the solubilization of Al3+ in acid soils resulting in inhibition of root growth and nutrient/water acquisition, is a serious limitation to crop production, because up to one-half of the world's potentially arable land is acidic. To date, however, no Al tolerance genes have yet been cloned. The physiological mechanisms of tolerance are somewhat better understood; the major documented mechanism involves the Al-activated release of Al-binding organic acids from the root tip, preventing uptake into the primary site of toxicity. In this study, a quantitative trait loci analysis of Al tolerance in Arabidopsis was conducted, which also correlated Al tolerance quantitative trait locus (QTL) with physiological mechanisms of tolerance. The analysis identified two major loci, which explain approximately 40% of the variance in Al tolerance observed among recombinant inbred lines derived from Landsberg erecta (sensitive) and Columbia (tolerant). We characterized the mechanism by which tolerance is achieved, and we found that the two QTL cosegregate with an Al-activated release of malate from Arabidopsis roots. Although only two of the QTL have been identified, malate release explains nearly all (95%) of the variation in Al tolerance in this population. Al tolerance in Landsberg erecta x Columbia is more complex genetically than physiologically, in that a number of genes underlie a single physiological mechanism involving root malate release. These findings have set the stage for the subsequent cloning of the genes responsible for the Al tolerance QTL, and a genomics-based cloning strategy and initial progress on this are also discussed.
A mixed-precision fused multiply and add (2011)

The floating-point fused multiply and add, computing R=AB+C with a single rounding, is now an IEEE-754 standard operator. This article investigates variants in which the addend C and the result R are of a larger format, for instance binary64 (double precision), while the multiplier inputs A and B are of a smaller format, for instance binary32 (single precision). Like the standard FMA operator, the proposed mixed-precision operator computes AB+C with a single rounding, and fully support subnormals. With minor modifications, it is also able to perform the standard FMA in the smaller format, and the standard addition in the larger format. For sum-of-product applications, the proposed mixed-precision FMA provides the accumulation accuracy of the larger format at a cost that is shown to be only one third more than that of a classical FMA in the smaller format. Besides, we show that such a mixed-precision FMA, although not mentioned in existing standard (IEEE 754, C and Fortran), is perfectly compliant to these standards. For DSP and embedded applications, a mixed binary32/binary64 FMA will enable binary64 computing where it is most needed, at a small cost overhead with respect to current binary32 FMAs, and with fewer data transfers, hence lower power than a pure binary64 approach. In high-end processors, a mixed binary64/binary128 FMA could provide an adequate solution to the binary128 requirements of very large scale computing applications.
Superpixel-Based Multitask Learning Framework for Hyperspectral Image Classification (2017)

Due to the high spectral dimensionality of hyperspectral images as well as the difficult and time-consuming process of collecting sufficient labeled samples in practice, the small sample size scenario is one crucial problem and a challenging issue for hyperspectral image classification. Fortunately, the structure information of materials, reflecting region of homogeneity in the spatial domain, offers an invaluable complement to the spectral information. Assuming some spatial regularity and locality of surface materials, it is reasonable to segment the image into different homogeneous parts in advance, called superpixel, which can be used to improve the classification performance. In this paper, a superpixel-based multitask learning framework has been proposed for hyperspectral image classification. Specifically, a set of 2-D Gabor filters are first applied to hyperspectral images to extract discriminative features. Meanwhile, a superpixel map is generated from the hyperspectral images. Second, a superpixel-based spatial-spectral Schroedinger eigenmaps (S <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> E) method is adopted to effectively reduce the dimensions of each extracted Gabor cube. Finally, the classification is carried out by a support vector machine (SVM)-based multitask learning framework. The proposed approach is thus termed Gabor S <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> E and SVM-based multitask learning (GS <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> E-MTLSVM). A series of experiments is conducted on three real hyperspectral image data sets to demonstrate the effectiveness of the proposed GS <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> E-MTLSVM approach. The experimental results show that the performance of the proposed GS <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> E-MTLSVM is better than those of several state-of-the-art methods, while the computational complexity has been greatly reduced, compared with the pixel-based spatial-spectral Schroedinger eigenmaps method.
Efficient Production of Alkanolamides from Microalgae (2014)

Fatty acid alkanolamides (FAAA) are lipid derivatives with industrial applications as biosurfactants and biolubricants. Although conventionally produced from vegetable oils, use of alternative renewable sources that do not compete with the food supply chain, such as microalgae, is desirable. We studied the production of FAAA through direct in situ amidation of algal biomass or by amidation of fatty acid methyl esters (FAME) recovered from in situ transesterification of algae. In situ transesterification resulted in spontaneous formation of a distinct FAME phase, which could be easily recovered and converted to FAAA. With this two-step transesterification-followed-by-amidation method, >95% of algal lipids were recovered as FAAA products. In situ amidation did not result in a separate product phase, likely because of the amphiphilic nature of the product. However, extraction with ethyl acetate allowed recovery of nearly 90% of the biomass lipids as FAAA after in situ amidation.
A New High-performance Interface for Capillary Electrophoresis/Electrospray Ionization Mass Spectrometry (1996)

A novel capillary electrophoresis electrospray ionization mass spectrometry (CE/ESI-MS) interface has been developed based upon an alternative means of establishing electrical contact at the CE capillary terminus. In this design, the terminus of the CE separation capillary and a short ESI emitter capillary are connected and sheathed by polysulphone micro-dialysis tubing. The electrical connection, to close the CE circuit and simultaneously establish the electrospray voltage, is provided outside the membrane via an electrode in a small liquid reservoir. In contrast to the sheath flow and liquid junction interfaces, the flow rate of liquid to the ESI source consists of the CE eluent and is not increased. The use of a "micro-spray' type emitter produces a stable electrospray at the very low flow rates typical of CE, providing a highly sensitive, efficient interface. Post-separation acidification of analytes via the dialysis junction is also demonstrated.
A Shallow-Etched Distributed-Grating Wavelength Demultiplexer in SOI (2006)

A shallow-etched, distributed grating is proposed as a wavelength demultiplexer. Modeling results predict up to 94% efficiency over a 120nm wavelength range. Early fabrication results, using electron-beam lithography and electron-cyclotron-resonance single-step etching, are presented.
Restoration of female fertility in Trichoderma reesei QM6a provides the basis for inbreeding in this industrial cellulase producing fungus (2015)

The finding that Trichoderma reesei is generally capable of undergoing sexual reproduction even under laboratory conditions raised hope for the applicability of classical breeding techniques with this fungus as known for plants and certain yeasts. The discovery that the wild-type isolate QM6a was female sterile, however, precluded any progress along that line. With the discovery of the genetic cause of female sterility and the creation of an engineered fertile strain we now provide the basis to establish sexual crossing in this fungus and herald a new era of strain improvement in T. reesei.
Cloning and sequencing of LlaDCHI [corrected] restriction/modification genes from Lactococcus lactis and relatedness of this system to the Streptococcus pneumoniae DpnII system (1995)

The natural 7.8-kb plasmid pSRQ700 was isolated from Lactococcus lactis subsp. cremoris DCH-4. It encodes a restriction/modification system named LlaDCHI [corrected]. When introduced into a phage-sensitive L. lactis strain, pSRQ700 confers strong phage resistance against the three most common lactococcal phage species, namely, 936, c2, and P335. The LlaDCHI [corrected] endonuclease was purified and found to cleave the palindromic sequence 5'-GATC-3'. It is an isoschizomer of Streptococcus pneumoniae DpnII. The plasmid pSRQ700 was mapped, and the genetic organization of LlaDCHI [corrected] was localized. Cloning and sequencing of the entire LlaDCHI [corrected] system allowed the identification of three open reading frames. The three genes (llaIIA, llaIIB, and llaIIC) overlapped and are under one putative promoter. A putative terminator was found at the end of llaIIC. The genes llaIIA and llaIIB coded for m6A methyltransferases, and llaIIC coded for an endonuclease. The LlaDCHI [corrected] system shares strong genetic similarities with the DpnII system. The deduced amino acid sequence of M.LlaIIA was 75% identical with that of M.DpnII, whereas M.LlaIIB was 88% identical with M.DpnA. However, R.LlalII shared only 31% identity with R.DpnII.
Implementation of subharmonic imaging (2003)

Ultrasound contrast agents promise to improve the sensitivity and specificity of diagnostic ultrasound imaging. It is of great importance to adapt ultrasound equipment for optimal use with contrast agents e.g., by exploiting the nonlinear properties of the contrast microbubbles. Harmonic Imaging is known to be associated with problems, due to second harmonic generation and accumulation within the tissue itself. Given the lack of subharmonic generation in tissue, one alternative is the creation of subharmonic images with better blood-to-tissue contrast. Here, the implementation of grayscale subharmonic imaging is presented.
Learning-Assisted Multimodality Dielectric Imaging (2019)

We introduce a convolutional neural network (CNN)-assisted dielectric imaging method, which uses CNN to incorporate the abundant image information from magnetic resonance (MR) images into the model-based microwave inverse scattering imaging process and generate high-fidelity dielectric images. A CNN is designed and trained to learn the complex mapping function from MR T1 images to dielectric images. Once trained, the new patients' MR T1 images are fed into the CNN to generate predicted dielectric images, which are used as the starting image for the microwave inverse scattering imaging. The CNN-predicted dielectric image, containing abundant prior information from MR images, significantly reduces the non-linearity and ill-posedness of the inverse scattering problem. We demonstrate the application of the proposed method to recover human brain dielectric images at 4 and 2 mm resolution with single-frequency and multifrequency microwave measurements. The reconstructed brain dielectric images with the proposed method show significant improvements in image quality compared with images reconstructed with no assistance from MR and CNN.
Safety, radiation dosimetry and tumor uptake of 68Ga-NOTA-AE105: a first-in-humans phase I study of a novel PET ligand for uPAR-PET imaging. (2016)

585 Objectives Overexpression of urokinase-type plasminogen activator receptors (uPAR) represents an established biomarker for poor prognosis in many common malignant diseases including breast (BC) and prostate cancer (PC). Accordingly, uPAR is an important target for new therapeutic and diagnostic strategies. In this first-in-human clinical phase I trial, uPAR Positron Emission Tomography (PET) imaging using a 68Ga-labelled version of a uPAR targeting peptide (AE105) was applied in patients with BC, PC and urinary bladder cancer (UBC). The aim was to establish safety, dosimetry and biodistribution as well as obtain preliminary data on tumor uptake. Methods Ten patients (6 PC, 2 BC and 2 UBC) received a single intravenous dose of 68Ga-NOTA-AE105 (200 MBq). The biodistribution and radiation dosimetry were assessed by serial PET/CT scans (10 minutes, 1 and 2 hours post injection). Safety assessment included measurements of vital signs with regular intervals during the imaging sessions and laboratory blood screening tests performed before and after injection. In a subgroup of patients the in vivo stability of 68Ga-NOTA-AE105 was determined in collected blood and urine. Quantitative assessment of 68Ga-NOTA-AE105 uptake in tumor lesions (SUVs) were obtained by manually drawing volumes of interest (VOIs). Results are given as tumor-to-background (psoas muscle) ratios. Results No adverse events or clinically detectable pharmacologic effects were found. The radioligand, 68Ga-NOTA-AE105, exhibited good in vivo stability and fast clearance from tissue compartments primarily by renal excretion. The effective dose was 0.015 mSv/MBq. Both BC patients had visible tracer accumulation above background in primary tumors and lymph node metastases. In 4 newly diagnosed PC patients a heterogenous pattern of 68Ga-NOTA-AE105 uptake in the prostate gland was found. Two of 6 PC patients had disseminated disease with significant uptake in primary prostate cancer lesions and several bone metastases. Tumor-to-background ratios at 1 hour p.i. were as follows: primary BC: 6.9, BC lymph node metastases: 4.4, Primary PC 3.6 and PC bone metastases: 4.9. Patients with UBC had no visible tumor uptake. Conclusions This first-in-human study demonstrates the safe use and clinical potential of 68Ga-NOTA-AE105 as a promising ligand for PET imaging of uPAR-mediated tumor invasiveness in cancer patients.
Video Stabilization and Completion Using Two Cameras (2011)

Video stabilization is important in many application fields, such as visual surveillance. Video stabilization and completion based on a single camera have been well studied in recent years, but it remains a very challenging problem. In this paper, we propose a novel framework to produce a stable high-resolution video for visual surveillance by using two cameras, in which one static camera serves to capture low-resolution wide-view-angle images, and the other is a pan-tilt-zoom camera to capture high-resolution images. Different with using a single camera, the interesting target can be detected and tracked more effectively and much more high-resolution information can be utilized for the stabilization and completion by using two videos from two cameras. A three-step stabilization approach is designed to deal with the resolution's discrepancy between two synchro videos and a four-stage completion strategy is taken to utilize more high-resolution information. Experimental results show that the proposed algorithm has a satisfying performance.
Regenerative synchronous electrical charge extraction for highly coupled piezoelectric generators (2017)

This paper proposes a new strategy for vibration harvesting using piezoelectric material. This work relies on an adaptation of the classical Synchronous Electrical Charge Extraction (SECE). Instead of harvesting the energy at every displacement extremum, we choose to wait a certain number of extremum before harvesting the accumulated energy. This technique extends the harvested power compared to SECE, especially with highly coupled piezoelectric generators. It is notably shown that this strategy largely increases the harvested power as the product km <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> Qm gets greater, and at the same time optimizes the switching losses. Measurements on a piezoelectric energy harvester (PEH) exhibiting a relatively large global coupling coefficient have been realized and have proven the efficiency and potential of this technique (193% harvested power improvement at resonance compared with a standard SECE strategy).
Abstract 5309: Determining EGFR and STK11 mutational status in lung adenocarcinoma histopathology images using deep learning (2018)

Abstract To characterize a tumor and suggest appropriate treatments, pathologists rely on the visual assessment of histopathology slides as well as molecular profiling of the tumors. This is especially true in lung adenocarcinoma cases where targeted therapies exist for tumors with EGFR mutations. In this work, we studied the use of deep learning approaches to classify lung cancer histopathology images and predict the mutational status of frequently mutated genes. To achieve these tasks, more than 1600 scanned histopathology slides, obtained from TCGA, were separated into independent training, validation and test sets. They were then tiled into 512x512 pixel windows, and the training set was used to feed the inception v3 convolutional neural network developed by Google. The resulting model was evaluated on the test set, and the generated per-tile probabilities were aggregated to generate a per-slide classification score. We based our study on whole-slide images of adenocarcinoma, squamous cells carcinoma and normal lung tissues and the neural network was trained on several tasks: first, the goal was to identify normal from tumor regions, and then, once the tumor regions were identified, it was trained to identify adenocarcinoma versus squamous cell carcinoma. Finally, the neural network was trained predict the mutational status of the most frequently mutated genes in lung adenocarcinoma. After verifying that the trained network properly identifies tumor slides compared to normal tissue (AUC=0.99) and distinguishes adenocarcinomas from squamous cell carcinomas (AUC=0.95), the network was trained to simultaneously identify different mutations. It achieved AUC scores of 0.82 and 0.86 for STK11 and EGFR respectively, showing that mutations in these two genes may confer specific macroscopic features, visible in histopathology images, and that a deep convolutional neural network can be trained to recognize those features. Our results demonstrate that, given the availability of sufficient data, convolutional neural networks learn to perform complex diagnoses and thus assist pathologists in their work. Citation Format: Nicolas Coudray, Andre L. Moreira, Theodore Sakellaropoulos, David Fenyö, Narges Razavian, Aristotelis Tsirigos. Determining EGFR and STK11 mutational status in lung adenocarcinoma histopathology images using deep learning [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5309.
Study of the thermal effects of a five-phase permanent magnet assisted synchronous reluctance motor under fault tolerant control (2017)

This paper presents a study on the thermal effects of a five-phase permanent magnet assisted synchronous reluctance motor (PMa-SynRM) under various fault conditions. The major advantage of a five-phase system is the additional number of phases which make it suitable for fault tolerant control in critical service applications. However, under the fault tolerant control (FTC), to maintain maximum torque, the phase currents are changed (magnitude and phase) in the remaining healthy phases. This change results in higher copper losses and heat generated in the healthy phases. Additionally, under FTC, the temperature rises unevenly inside the machine which leads to unbalanced magnetic pull. Due to this unbalanced magnetic pull, the actual torque capability of the machine reduces which may seem counterproductive to the fault tolerant advantage of the system. In this study, the temperature sensitivity of a five-phase PMaSynRM under FTC has been investigated through finite element (FE) analysis. The experimental analysis has been conducted on a 5 hp five-phase motor drive system.