gebhart/patrepeval huggingface dataset:
Efficient Subspace Methods-Based Algorithms for Performing Sensitivity, Uncertainty, and Adaptive Simulation of Large-Scale Computational Models (2008)

This paper introduces the concepts and derives the mathematical theory of efficient subspace methods (ESMs) applied to the simulation of large-scale complex models, of which nuclear reactor simulation will serve as a test basis. ESMs are intended to advance the capabilities of predictive simulation to meet the functional requirements of future energy system simulation and overcome the inadequacies of current design methods. Some of the inadequacies addressed by ESM include lack of rigorous approach to perform comprehensive validation of the multitudes of models and input data used in the design calculations and lack of robust mathematical approaches to enhance fidelity of existing and advanced computational codes. To accomplish these tasks, the computational tools must be capable of performing the following three applications with both accuracy and efficiency: (a) sensitivity analysis of key system attributes with respect to various input data; (b) uncertainty quantification for key system attributes; and (c) adaptive simulation, also known as data assimilation, for adapting existing models based on the assimilated body of experimental information to achieve the best possible prediction accuracy. These three applications, involving large-scale computational models, are now considered computationally infeasible if both the input data and key system attributes or experimental information fields are large. This paper will develop the mathematical theory of ESM-based algorithms for these three applications. The treatment in this paper is based on linearized approximation of the associated computational models. Extension to higher-order approximations represents the focus of our ongoing research.
Design of microcantilever sensors using SLM based holographic lithography (2013)

A holographic multiphoton fabrication technique is applied to the development of a microcantilever based analyte sensor. Holograms generated using a spatial light modulator (SLM) initiate the fabrication of sub-micron three-dimensional structures. Chemically functional microstructures are patterned onto the surface of commercially available piezoelectric microcantilevers using this holographic lithography technique. Controlling the form and location of the added structure enables the resonant frequency of the cantilever to be regulated with a higher accuracy than is currently available using bulk lithography techniques and without the inclusion of additional electronic feedback control components. A potential analyte sensor is then developed by patterning on an array of multiple piezoelectric microcantilevers, which are initially identical within manufacturing tolerances. The resonant frequency, was adjusted such that cantilevers, which were initially separated by 2.82 kHz, are tuned to be within 0.13 kHz of each other. Connecting the piezoelectric microcantilevers in series enables the response of each sensor element to be measured simultaneously using a single frequency based data acquisition system and allowing rapid data collection.
1401 Visualization and Numerical Simulation on the Jet of Liear Shaped Charges (2007)

The jet of linear shaped charges (LSC) has been utilized separation of space rocket's components or cutting of large steel constructions. The behavior of the jet still remains unexplained. We experimented with visualization of the jet using the flash X-ray shooting system. We also conducted numerical simulation using the AUTODYN, applied the multi-material Euler solver. Some X-ray photos indicate that the velocity of the jet is approximately 3,000m/s at the tip of the jet. Although the number of meshes on the calculation model was not enough to get an accurate result, we decided that the multi-material Euler solver is useful for evaluating the performance of the LSC jet.
Microelectronic systems engineering (1961)

Several general requirements for microelectronic systems are most likely to influence the nature of the future product of the components engineer. These requirements are grouped under three main headings: power dissipation, topology, and reliability.
Voicing feature integration in SRI's decipher LVCSR system (2004)

We augment the Mel cepstral (MFCC) feature representation with voicing features from an independent front end. The voicing feature front end parameters are optimized for recognition accuracy. The voicing features computed are the normalized autocorrelation peak and a newly proposed entropy of the high-order cepstrum. We explored several alternatives to integrate the voicing features into SRI's DECIPHER system. Promising early results were obtained in a simple system concatenating the voicing features with MFCC features and optimizing the voicing feature window duration. Best results overall came from a more complex system combining a multiframe voicing feature window with the MFCC plus third differential features using linear discriminant analysis and optimizing the number of voicing feature frames. The best integration approach from the single-pass system experiments was implemented in a multi-pass system for large vocabulary testing on the Switchboard database. An average WER reduction of 2% relative was obtained on the NIST Hub-5 dev2001 and eval2002 databases.
Identification of Splicing Changes in the Blood and Muscle in Congenital Myotonic Dystrophy (P4.110) (2015)

OBJECTIVE: Evaluate RNA splicing changes in the peripheral blood and skeletal muscle of patients with congenital myotonic dystrophy (CDM). BACKGROUND: Congenital myotonic dystrophy is a severe, infantile-onset form of myotonic dystrophy (DM1). Splicing changes leading to disruptions in gene regulation have been demonstrated in DM1, but it is unknown if patients with CDM experience the same changes in splicing. Furthermore, the splicing changes associated with myotonic dystrophy have not been examined in the peripheral blood of children or adults. DESIGN/METHODS: Peripheral blood lymphocytes were isolated from two patients with CDM (ages 3 and 8) and two healthy controls (ages 5 and 10) using PAXgene tubes. cDNA libraries were prepared with poly-A selection. Skeletal muscle was collected from the 3 year-old CDM patient and compared with skeletal muscle obtained from a Duchenne muscular dystrophy patient. RNA was prepared with ribosomal depletion and RNA sequencing was performed using the Illumina HiSeq 2500 sequencer in random blocks of 6. Samples were aligned using TopHat. Splicing differences were analyzed with Miso. RESULTS: MBNL1 and DMPK, are known to cause splicing changes in skeletal muscle of DM1 patients. Both are expressed in the peripheral blood of CDM and control patients. Comparing CDM to control blood samples we identified 80 different transcripts with differential inclusion of exons. These transcripts include NDRG1, whose splicing has been shown to be MBNL1 dependent. Other MBNL1 dependent transcripts were also identified. In skeletal muscle, known splicing changes associated with DM1, such as in MBNL1 (exon 5), were identified. CONCLUSIONS: This work demonstrates the presence of known myotonic dystrophy associated RNA splicing changes in the skeletal muscle of a CDM patient. Furthermore, there is a suggestion of splicing changes in the peripheral blood that may serve as potential biomarkers. Additional samples obtained longitudinally will be required to confirm these findings.
Spinning of hydroalcoholic chitosan solutions: Mechanical behavior and multiscale microstructure of resulting fibers (2018)

ABSTRACT The morphology and mechanical properties of chitosan fibers obtained by spinning of hydroalcoholic (1,2propanediol/water) chitosan solutions of low DA and high molecular mass are reported. The impact of processing parameters on final fiber properties, such as fiber stretching at different steps of the spinning process, is investigated. A stretching ratio applied during the fiber coagulation appeared to have no significant effect on mechanical properties, whereas fiber drawing after the coagulation step, that is, during the washing step was a key parameter for the control of macromolecular orientation, fiber tenacity, and Young's modulus. The microstructure and morphology of the various as‐spun chitosan fibers were studied by means of wide‐angle and small‐angle X‐ray scattering and scanning electron microscopy. Microstructure impacts mechanical properties from the interplay of different deformation mechanisms acting at different length scales of the microstructure, namely the macromolecular orientation, the semicrystalline morphology, and the core–shell structure. The obtained monofilament fibers (45–70D) can be knitted. © 2018 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019 , 136 , 47130.
Targeted Learning in Healthcare Research (2015)

The increasing availability of Big Data in healthcare encourages investigators to seek answers to big questions. However, nonparametric approaches to analyzing these data can suffer from the curse of dimensionality, and traditional parametric modeling does not necessarily scale. Targeted learning (TL) combines semiparametric methodology with advanced machine learning techniques to provide a sound foundation for extracting information from data. Predictive models, variable importance measures, and treatment benefits and risks can all be addressed within this framework. TL has been applied in a broad range of healthcare settings, including genomics, precision medicine, health policy, and drug safety. This article provides an introduction to the two main components of TL, targeted minimum loss-based estimation and super learning, and gives examples of applications in predictive modeling, variable importance ranking, and comparative effectiveness research.
Correctness and parallelism in composite systems (1997)

Article Correctness and parallelism in composite systems Share on Authors: Gustavo Alonso Database Research Group, Institute of Inf. Systems, ETH Zentrum, Zürich CH-8092, Switzerland Database Research Group, Institute of Inf. Systems, ETH Zentrum, Zürich CH-8092, SwitzerlandView Profile , Stephen Blott Lucent Technologies (Bell Labs) 600 Mountain Avenue, Murray Hill, NJ Lucent Technologies (Bell Labs) 600 Mountain Avenue, Murray Hill, NJView Profile , Armin Fessler Database Research Group, Institute of Inf. Systems, ETH Zentrum, Zürich CH-8092, Switzerland Database Research Group, Institute of Inf. Systems, ETH Zentrum, Zürich CH-8092, SwitzerlandView Profile , Hans-Jörg Schek Database Research Group, Institute of Inf. Systems, ETH Zentrum, Zürich CH-8092, Switzerland Database Research Group, Institute of Inf. Systems, ETH Zentrum, Zürich CH-8092, SwitzerlandView Profile Authors Info & Claims PODS '97: Proceedings of the sixteenth ACM SIGACT-SIGMOD-SIGART symposium on Principles of database systemsMay 1997 Pages 197–208https://doi.org/10.1145/263661.263683Published:01 May 1997 15citation267DownloadsMetricsTotal Citations15Total Downloads267Last 12 Months3Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Has Improvement in PTCA Intervention Affected Long-term Prognosis? (1995)

Compared with registry 1, the management of the registry 2 cohort resulted in lower 5-year morbid event rates and reduced CABG operations. Mortality rates remained similar. When symptomatic status was considered in combination with events, a significantly better outcome was seen overall and in the initially successful cohort. In registry 2, repeated PTCA was used with much greater frequency early after the initial procedure.
Magnetooptical memory experiments on a rotating Mn-Cu-Bi disk medium (1977)

A thin film of a new magnetooptical memory medium, Mn-Cu-Bi, was prepared on a glass disk and their dynamic memory characteristics were examined with an experimental rotating disk exerciser. The Curie temperature of the medium was about 200°C. Curie-point writing was made on it. The written information was read by the Kerr effect. The Kerr rotation was ±1.3° at an Ar ion laser wavelength of 5145 Å, where the Kerr rotation of the medium was made maximum by an SiO overcoating. For track selection, a moving coil with a linear motion air bearing, whose shaft was rectangular in form, was used. By utilizing a laser for the light source of a moiré fringe measurement technique, an accurate track access was made possible. The accuracy was within 1 μm and the track-to-track transfer time was about 5 ms. Writing and reading were accomplished under computer control with the direct memory access mode. A 5.09 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-6</sup> medium error rate without error correction was obtained for a 2.5 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> bit/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> packing density at a data transfer rate of 0.5 MHz.
Label-free photoacoustic expansion histopathology with enhanced temporal and spatial resolution (2021)

Ultraviolet photoacoustic microscopy (UV-PAM) provides label-free imaging of cell nuclei with the superior optical absorption of DNAs and RNAs. UV-PAM does not require any additional staining process to visualize the structures of tissues and cells. However, conventional UV-PAM is limited in imaging speed to be used in real pre-clinical and clinical situations. To overcome this limitation, we developed an UV-PAM adopting a high-speed scanning module. We demonstrated the applicability of the system as an intraoperative surgical margin assessment tool by imaging formalinfixed paraffine-embedded (FFPE) sections of human colon cancer tissues and comparing these results to conventional optical microscopic images. Additionally, three more types of cancerous tissue such as liver, uterus, and kidney were photoacoustically examined. The imaging results successfully showed the characteristic features of cancerous and normal tissues, allowing rapid diagnosis of cancer. UV-PAM has achieved sufficient spatial resolution to distinguish the individual nuclei in human tissue, but it is challenging to resolve the closely adjacent nuclei. Therefore, we applied tissue expansion technology, which enables nanoscale imaging of subcellular components beyond the resolution of optical microscopy, to our developed system. A mouse brain section was physically expanded by hydrogel-tissue hybridization, and consequently distances between cell nuclei in the tissue increased. We could separate densely distributed nuclei in the hippocampus of mouse brain better compared to conventional UV-PAM. In short, we developed a novel PA imaging system with the enhanced temporal and spatial resolution by combining fast scanning modality and tissue expansion technology with UV-PAM.
The Use of Logarithmic and Density Units for Pixels (1991)

The use of logarithmic representation for pixel data may provide maximum flexibility in several areas. The logarithmic representation seems to be an optimum coding for digital brightness representation and also allows easy conversion to and from the linear brightness domain, which is necessary for proper spatial filtering. The ability to provide latitude by simply “sliding” up and down the logarithmic curve can also provide the crucial capability to print-up or print-down or color-correct scenes after initial capture. Density units are a natural analogy to logarithmic units for digital input scanning of motion-picture film. The film itself, however, will have introduced a toe and shoulder to the dark and light parts of the image. The natural relationship between film density and logarithmic units, as well as the ability to provide latitude and correction capabilities, makes the logarithmic pixel representation a significant candidate for high-definition television (HDTV) and computer graphics.
Novel, near-infrared spectroscopic, label-free, techniques to assess bone abnormalities such as Paget's disease, osteoporosis and bone fractures (2015)

Near- infrared (NIR) light with wavelengths from 650 nm to 950 nm (known as the first NIR window) has conventionally been used as a non-invasive technique that can reach deeper penetration depths through media than light at shorter wavelengths. Recently, several novel, NIR, label-free, techniques have been developed to assess Paget’s disease of bone, osteoporosis and bone microfractures. We designed a Bone Optical Analyzer (BOA) which utilizes the first window to measure changes of Hb and HbO<sub>2</sub>. Paget’s disease is marked by an increase in vascularization in bones, and this device can enable easy diagnosis and more frequent monitoring of the patient’s condition, without exposing him to a high cumulative dose of radiation. We have also used inverse imaging algorithms to reconstruct 2D and 3D maps of the bone’s structure. This device could be used to assess diseases such as osteoporosis. Using 800 nm femtosecond excitation with two-photon (2P) microscopy, we acquired 2PM images of the periosteum and spatial frequency spectra (based on emission of collagen) from the periosteal regions. This technique can provide information on the structure of the periosteum and can detect abnormalities which may be an indication of disease. Most recently, we showed that longer NIR wavelengths in the second and third NIR windows (1100 nm-1350 nm, 1600 nm-1870 nm), could be used to image bone microfractures. Use of NIR light could allow for repeated studies in patients with diseases such as Paget’s and osteoporosis quickly and non-invasively, and could impact the current management for these diseases.
Modeling parameters for the spectral behavior of infrared frequency-selective surfaces (2001)

Comparisons of experiment and theory are presented for transmission spectra over the range 2-15 mum of a set of frequency-selective surfaces consisting of arrays of simple dipole patches of aluminum on or in silicon. The arrays are fabricated by direct-write electron-beam lithography. Important parameters controlling the spectral shape are identified, such as dipole length, spacing, resistance, and dielectric surroundings. The separate influence of these variables is exhibited. Encouraging agreement between simple model calculations and the measurements is found.
Generalizable links between symptoms of borderline personality disorder and functional connectivity (2023)

Individual differences in functional connectivity in developmentally-sensitive regions are associated with the symptoms of BPD.
Consistent Pilot Designs for Frequency Offset Estimation in Mimo OFDM Systems (2007)

This paper presents pilot designs for consistent frequency offset estimation of MIMO OFDM systems in frequency-selective fading channels. We derive the sufficient consistency condition for the pilots in MIMO OFDM systems to yield unambiguous estimation, and present corresponding consistent pilot designs. We develop pilot designs which satisfy both consistency over a limited CFO estimation range and the optimal channel estimation condition in MIMO OFDM systems. Simulation results corroborate that the consistent pilot design condition is efficient in choosing pilot patterns yielding better frequency offset estimation performance.
Engineered Microvasculature in PDMS Networks Using Endothelial Cells Derived from Human Induced Pluripotent Stem Cells (2017)

In this study, we used a polydimethylsiloxane (PDMS)-based platform for the generation of intact, perfusion-competent microvascular networks in vitro. COMSOL Multiphysics, a finite-element analysis and simulation software package, was used to obtain simulated velocity, pressure, and shear stress profiles. Transgene-free human induced pluripotent stem cells (hiPSCs) were differentiated into partially arterialized endothelial cells (hiPSC-ECs) in 5 d under completely chemically defined conditions, using the small molecule glycogen synthase kinase 3β inhibitor CHIR99021 and were thoroughly characterized for functionality and arterial-like marker expression. These cells, along with primary human umbilical vein endothelial cells (HUVECs), were seeded in the PDMS system to generate microvascular networks that were subjected to shear stress. Engineered microvessels had patent lumens and expressed VE-cadherin along their periphery. Shear stress caused by flowing medium increased the secretion of nitric oxide and caused endothelial cells s to align and to redistribute actin filaments parallel to the direction of the laminar flow. Shear stress also caused significant increases in gene expression for arterial markers Notch1 and EphrinB2 as well as antithrombotic markers Kruppel-like factor 2 (KLF-2)/4. These changes in response to shear stress in the microvascular platform were observed in hiPSC-EC microvessels but not in microvessels that were derived from HUVECs, which indicated that hiPSC-ECs may be more plastic in modulating their phenotype under flow than are HUVECs. Taken together, we demonstrate the feasibly of generating intact, engineered microvessels in vitro, which replicate some of the key biological features of native microvessels.
A Novel Compound, “FA-1” Isolated from Prunus mume, Protects Human Bronchial Epithelial Cells and Keratinocytes from Cigarette Smoke Extract-Induced Damage (2018)

Extract of the Japanese apricot (JAE) has biological properties as an antioxidant and anti-inflammatory agent. We hypothesized that JAE might exert therapeutic effects on cigarette smoke (CS)-induced DNA damage and cytotoxicity. In this study, we found that concentrated JAE protects against cigarette smoke extract (CSE)-induced cytotoxicity and DNA damage accompanied by increased levels of aldehyde dehydrogenase (ALDH)2, 3A1, and Werner's syndrome protein (WRN) in immortalized human bronchial epithelial cells (HBEC2) and normal human epidermal keratinocytes (NHEK). Using the centrifugal partition chromatography (CPC) method, we identified an undescribed compound, 5-hydroxymethyl-2-furaldehyde bis(5-formylfurfuryl) acetal (which we named FA-1), responsible for the protective effects against CSE. This chemical structure has not been reported from a natural source to date. Protective effects of isolated FA-1 against CSE were observed in both HBEC2 and NHEK cells. The studies described herein suggest that FA-1 isolated from JAE protects against CSE-induced DNA damage and apoptosis by augmenting multiple isozymes of ALDH and DNA repair and reducing oxidative stress.