gebhart/patrepeval huggingface dataset:
Capillary-tube package devices for the quantitative performance evaluation of nuclear magnetic resonance spectrometers and pulse sequences (2018)

With the increased sensitivity of modern nuclear magnetic resonance (NMR) spectrometers, the minimum amount needed for chemical-shift referencing of NMR spectra has decreased to a point where a few microliters can be sufficient to observe a reference signal. The reduction in the amount of required reference material is the basis for the NMR Capillary-tube Package (CapPack) platform that utilizes capillary tubes with inner diameters smaller than 150 <i>µ</i>m as NMR-tube inserts for external reference standards. It is shown how commercially available electrophoresis capillary tubes with outer diameters of 360 <i>µ</i>m are filled with reference liquids or solutions and then permanently sealed by the arc discharge plasma of a commercially available fusion splicer normally employed for joining optical fibers. The permanently sealed capillaries can be used as external references for chemical-shift, signal-to-noise, resolution, and concentration calibration. Combining a number of permanently sealed capillaries to form CapPack devices leads to additional applications such as performance evaluation of NMR spectrometers and NMR pulse sequences. A 10-capillary-tube side-by-side Gradient CapPack device is used in combination with one or two constant gradients, produced by room-temperature shim coils, to monitor the excitation profiles of shaped pulses. One example illustrates the performance of hyperbolic secant (sech) pulses in the EXponentially Converging Eradication Pulse Train (EXCEPT) solvent suppression sequence. The excitation profile of the pulse sequence is obtained in a single gradient NMR experiment. A clustered <i>T</i> <sub>1</sub> CapPack device is introduced consisting of a coaxial NMR-tube insert that holds seven capillary tubes filled with aqueous solutions of different concentrations of the paramagnetic relaxation agent copper(ii) sulfate (CuSO<sub>4</sub>). The different CuSO<sub>4</sub> concentrations lead to spin-lattice relaxation times in the seven capillary tubes that cover a range which extends to more than an order of magnitude. Clustered <i>T</i> <sub>1</sub> CapPack devices are best suited to quantify the effects that relaxation has on magnetizations and coherences during the execution of NMR experiments, which is demonstrated for the order-of-magnitude <i>T</i> <sub>1</sub> insensitivity of signal suppression with EXCEPT.
Selected data(s) from : Five-dimensional optical data storage based on ellipse orientation and fluorescence intensity in a silver-sensitized commercial glass (2022)

The data selected is based on the figures below, published in the linked article (see the doi). - Figure 1. (a) Femtosecond laser tight focusing in the silver-containing glass, leading to the production of fluorescent silver clusters at its periphery. (b) SLM holographic phase masks with an additional cylindrical profile leading to an elliptical pattern by DLW. (c) Oriented elliptical patterns obtained by SLM phase mask manipulation, corresponding to 24 = 16 orientation-encoded levels. (Only picture) - Figure 2. Fabricated fluorescence calibration matrix. (a) Confocal image of all basic storage units composed by 16 intensity levels and 16 orientation levels. (b) Measured fluorescence intensity versus incident DLW intensity for the 5D decoding process. (Pictures, opj file, csv datas) - Figure 3. (a,b) are the encoded images of two Nobel laureates in 16 orientation levels and 16 intensity levels, respectively. (c) 100 × 100 entangled patterns among 16 × 16 intensity and orientation levels. (d) The fluorescence calibration matrix was fabricated for decoding (fluorescence excitation at 405 nm). (Pictures, cvs datas) ANR_ ARCHIFLUO_ICMCB_Article_Micromachines_Figure3_2020-10-21_V01 : Figure 3 ANR_ ARCHIFLUO_ICMCB_Article_Micromachines_Figure3a_2020-10-21_V01 : Original image oritentation ANR_ ARCHIFLUO_ICMCB_Article_Micromachines_Figure3b_2020-10-21_V01 : Original image intensity ANR_ ARCHIFLUO_ICMCB_Article_Micromachines_Figure3c_Figure3d_2020-10-21_V01 : DLW image ANR_ ARCHIFLUO_ICMCB_Article_Micromachines_Figure3_datas_IICT4BF_2020-10-21_V01 : Intensity image converted to 4 bit format ANR_ ARCHIFLUO_ICMCB_Article_Micromachines_Figure3_datas_OICT4BF_T2020-10-21_V01 : Orientation image converted to 4 bit format ANR_ ARCHIFLUO_ICMCB_Article_Micromachines_Figure3_datas_OICT4BFL_2020-10-21_V01 : Orientation image converted to 4 bit format level - Figure 4. (a,b) Retrieved images from the initial images of Figure 3a,b, respectively. (c,d) Histograms of the level difference between original and decoded levels for the orientation direction and the fluorescence intensity, respectively. (Picture and csv datas) - Figure 5. (a) Confocal top-view image of one single elliptically-shaped storage unit fabricated by using type A DLW. (b) Fluorescence intensity profile along the horizontal and vertical cross section at focal plane. (c) Fluorescence intensity profile and Gaussian fitting along the z-axis (depth). (Picture, opj file, csv datas)
Numerical Model of Fluid Flow and Oxygen Transport in a Radial-Flow Microchannel Containing Hepatocytes (1999)

The incorporation of monolayers of cultured hepatocytes into an extracorporeal perfusion system has become a promising approach for the development of a temporary bioartificial liver (BAL) support system. In this paper we present a numerical investigation of the oxygen tension, shear stress, and pressure drop in a bioreactor for a BAL composed of plasma-perfused chambers containing monolayers of porcine hepatocytes. The chambers consist of microfabricated parallel disks with center-to-edge radial flow. The oxygen uptake rate (OUR), measured in vitro for porcine hepatocytes, was curve-fitted using Michaelis–Menten kinetics for simulation of the oxygen concentration profile. The effect of different parameters that may influence the oxygen transport inside the chambers, such as the plasma flow rate, the chamber height, the initial oxygen tension in the perfused plasma, the OUR, and Km was investigated. We found that both the plasma flow rate and the initial oxygen tension may have an important effect upon oxygen transport. Increasing the flow rate and/or the inlet oxygen tension resulted in improved oxygen transport to cells in the radial-flow microchannels, and allowed significantly greater diameter reactor without oxygen limitation to the hepatocytes. In the range investigated in this paper (10 μm &lt; H &lt; 100 μm), and for a constant plasma flow rate, the chamber height, H, had a negligible effect on the oxygen transport to hepatocytes. On the contrary, it strongly affected the mechanical stress on the cells that is also crucial for the successful design of the BAL reactors. A twofold decrease in chamber height from 50 to 25 μm produced approximately a fivefold increase in maximal shear stress at the inlet of the reactor from 2 to 10 dyn/cm2. Further decrease in chamber height resulted in shear stress values that are physiologically unrealistic. Therefore, the channel height needs to be carefully chosen in a BAL design to avoid deleterious hydrodynamic effects on hepatocytes.
Abstract 603: O-GlcNAcylation of Runx2 is Essential for Vascular Calcification (2014)

Osteogenic differentiation of vascular smooth muscle cells (VSMC) contribute predominantly to vascular calcification, a characteristic of advanced atherosclerosis, chronic kidney disease, and diabetes. Using Runx2 shRNA and SMC-specific Runx2 deletion mice, we have demonstrated an essential role of Runx2 in regulating vascular calcification in vitro and in vivo. The present studies aim to pinpoint the Runx2 functional domain that is critical for its osteogenic function in VSMC and to elucidate the underlying molecular mechanisms. A series of Runx2 deletion mutants were generated and stably transfected into VSMC. Full-length Runx2 protein and Runx2 deletion mutants containing amino acids 1-495 or 1-432, but not Runx2 1-391, induced VMC calcification, indicating that the Runx2 osteogenic functional domain is located between amino acids 391-432. Site-directed mutagenesis analysis identified that mutations at the amino acids 412, 413, 425 and 426-428 markedly reduced Runx2 transactivity and inhibited Runx2-induced VSMC calcification. Mutations at amino acids 412, 413 and 425 were found to inhibit Runx2 post-translational modification by O-GlcNAcylation. Immunoprecipitation revealed that Runx2 O-GlcNAcylation at 412, at 413, and proximal to 425 was critical for its binding to Smad 1/5/8 and Smad 4, but not Smad 2/3. Using lentivirus-mediated shRNA, we determined that knockdown of Smad1/5/8, but not Smad 2/3, inhibited Runx2-induced VSMC calcification, suggesting that BMP but not TGF-beta signaling is critical for the osteogenic function of Runx2 in VSMC. Taken together, these data demonstrate that Runx2 amino acids 412, 413, 425 and 426-428 are key for its osteogenic function in VSMC, and Runx2 O-GlcNAcylation at 412, 413 and 425 is essential for its interaction with Smad proteins to determine Runx2 transactivity and VSMC calcification. We have identified a novel Runx2 post-translational modification by O-GlcNAcylation at key residues that are essential for its osteogenic function. Our studies provide molecular insights into the function of Runx2 in regulating VSMC calcification, which may shed light on novel targets that are amenable to drug discovery for vascular calcification.
Assessment of Blood Glucose Predictors: The Prediction-Error Grid Analysis (2011)

We propose a new CG-EGA, the PRED-EGA, for the assessment of glucose predictors. The presented analysis shows that, compared with the straightforward application of the CG-EGA, the PRED-EGA gives a significant reduction of the misclassification cases. A reduction by a factor of at least 4 was observed in the study. Moreover, the PRED-EGA is much more robust against uncertainty in the input and references.
On a Particular Family of Differential Beamformers With Cardioid-Like and No-Null Patterns (2020)

Differential microphone arrays (DMAs), which are responsive to the differential acoustic pressure fields, have been used in a wide range of applications related to audio and speech. The core part of a DMA is the so-called differential beamformer, which is generally designed by placing a number of nulls in its beampattern to attenuate noise from some directions. But the presence of these nulls may cause some great issues, e.g., leading to suboptimal performance if the interference/noise is incident from directions other than the nulls' directions, and making the beamformer less robust to sensors' self noise and array imperfections. To overcome these problems, this letter is devoted to the design of differential beamformers with no nulls in its beampattern. A design method and its multistage implementation are presented and analyzed. An improved solution is then developed, which is able to form frequency-invariant beampatterns with no nulls in the frequency range of speech signals. Simulations are provided to illustrate the properties of the developed methods.
Comparative Evaluation of Three-Phase AC–AC Matrix Converter and Voltage DC-Link Back-to-Back Converter Systems (2011)

This paper introduces the methodology and the results of a comprehensive comparison of a direct matrix converter (MC), an indirect MC, and a voltage dc-link back-to-back converter for a 15-kW permanent magnet synchronous motor drive. The comparison involves the investigation of the passive components, including the EMI input filter, the required silicon chip area for a defined maximum admissible thermal loading of the power semiconductors, the total losses and/or achievable efficiency, a prediction of the resulting volume and weight of the passive components, and, finally, a tradeoff study between the efficiency, volume, and weight of the converters. Different performance indicators that ultimately allow a systematic determination of the application area of each converter topology are provided with this comparative evaluation.
Relationship between Forskolin and Calcium‐Calmodulin Stimulation of Rat Cerebral Cortex Adenylate Cyclase: Enzyme Activation Modulates Substrate (MgATP) Affinity (1988)

In membranes prepared from the rat cerebral cortex EGTA 0.4-100 mumol/l was found to dose-dependently inhibit adenylate cyclase activity, both during basal conditions and when the cyclase activity had been stimulated with 10 mumol/l forskolin. Addition of calcium 2-30 mumol/l (in excess of EGTA) totally prevented the inhibition induced by EGTA, both in the absence and presence of forskolin. These data are consistent with the notion that in the absence of EGTA the rat cortex adenylate cyclase is considerably stimulated by endogenous calcium-calmodulin. The data also show that stimulation with endogenous calcium-calmodulin is more than additive with that of forskolin indicating an action on identical cyclase units. The kinetics of the rat cortex adenylate cyclase for its substrate (MgATP) was also investigated. Activation of the cyclase with endogenous calcium-calmodulin, induced a marked increase in the Vmax of the enzyme and a concomitant almost 2-fold increase in the Km. Stimulation with 10 microM forskolin also induced a marked increase in the Vmax as well as an almost 3-fold increase in the Km. A combination of the two stimulants caused a further increase in Vmax as well as Km; the Vmax being increased more than 17-fold and the Km being increased 3.5-fold over the basal. The data indicates that both calcium-calmodulin and forskolin induces a similar type of activation of the adenylate cyclase which is associated with a lowered affinity for its substrate.
SNEED: Enhancing Network Security Services Using Network Coding and Joint Capacity (2011)

Network security protocols depend mainly on developing cryptographic schemes and using biometric methods. These have led to several security protocols that are unbreakable based on difficulty of solving untractable mathematical problems such as factoring large integers. In this paper, Securing Networks by Employing Encoding and Decoding (SNEED) is developed to mitigate single and multiple link attacks. Network coding and shared capacity among the working paths are used to provide data protection and data integrity against network attackers and eavesdroppers. It is shown that SNEED can be implemented easily where there are k link disjoint paths between two core nodes (routers or switches) in an enterprise network. Finally, SNEED can be incorporated into various applications such as on-demand TV, satellite communications, and multimedia security.
TNFα and IL-17 alkalinize airway surface liquid through CFTR and pendrin (2020)

The pH of airway surface liquid (ASL) is a key factor that determines respiratory host defense; ASL acidification impairs and alkalinization enhances key defense mechanisms. Under healthy conditions, airway epithelia secrete base ([Formula: see text]) and acid (H<sup>+</sup>) to control ASL pH (pH<sub>ASL</sub>). Neutrophil-predominant inflammation is a hallmark of several airway diseases, and TNFα and IL-17 are key drivers. However, how these cytokines perturb pH<sub>ASL</sub> regulation is uncertain. In primary cultures of differentiated human airway epithelia, TNFα decreased and IL-17 did not change pH<sub>ASL</sub>. However, the combination (TNFα+IL-17) markedly increased pH<sub>ASL</sub> by increasing [Formula: see text] secretion. TNFα+IL-17 increased expression and function of two apical [Formula: see text] transporters, CFTR anion channels and pendrin Cl<sup>-</sup>/[Formula: see text] exchangers. Both were required for maximal alkalinization. TNFα+IL-17 induced pendrin expression primarily in secretory cells where it was coexpressed with CFTR. Interestingly, significant pendrin expression was not detected in CFTR-rich ionocytes. These results indicate that TNFα+IL-17 stimulate [Formula: see text] secretion via CFTR and pendrin to alkalinize ASL, which may represent an important defense mechanism in inflamed airways.
An open-source method for simulating atrial fibrillation using ECGSYN (2005)

A method for simulating atrial fibrillation has been developed using the open source simulator ECGSYN (available at physionet.org). In this method episodes of atrial fibrillation are simulated by combining data streams generated by two ECGSYN engines driven from a correlated stochastic process. The underlying process represents atrial activity during fibrillation. This process generates a series of atrial inter-beat intervals with the same statistical properties as those found in the MIT-BIH atrial fibrillation database (afdb). The atrial beats from this process are then selected to be either conducting beats that generate subsequent ventricular activity or nonconducting beats that generate only atrial activity. The intervals for conducting beats are processed by an ECGSYN engine with appropriate parameters to create PQRS and T waves while the nonconducting intervals are processed by a second ECGSYN engine with parameters to generate only P waves. The data streams from the two engines are superimposed to create an artificial atrial fibrillation waveform. This waveform generator has been made into an operator and has been incorporated into a stream based ECG simulator. The simulator uses a timing operator to switch from generating normal ECG morphologies to atrial fibrillation.
Saccharomyces cerevisiae SPT3 gene is required for transposition and transpositional recombination of chromosomal Ty elements. (1986)

Mutations in the Saccharomyces cerevisiae SPT3 gene have dramatic effects on the expression of Ty elements and genes adjacent to the element. The SPT3 gene is essential for Ty transposition, because transposition of chromosomal Ty elements ceased when the SPT3 gene was replaced with the frameshift mutation spt3-101. Presumably, the elimination of transposition was due to the effect of the SPT3 gene product on Ty transcription; the transcripts of chromosomal Ty elements were largely abolished in the spt3-101 strain (F. Winston, K. J. Durbin, and G. R. Fink, Cell 39:675-682, 1984). Ty transcription in an spt3-101 strain could be reestablished by introduction of the pGTyH3 plasmid, in which transcription of the Ty element TyH3 is under the control of the GAL1 promoter; these plasmid-derived Ty transcripts were SPT3-independent. Ty transposition resumed after galactose induction in spt3-101 strains containing the pGTyH3 plasmid. In spt3 mutants nearly all of the resulting transposition events derived from pGTyH3 plasmids and not from chromosomal elements.
Multidimensional Constellations for Power-Efficient and Flexible Optical Networks (2014)

Multidimensional constellations and time domain hybrid QAM both realize a non-integer ratio of bits per complex 2D symbol in order to allow for flexibility of spectral efficiency. We compare both approaches in terms of symbol error probability, asymptotic power efficiency, and bit error probability. In order to achieve 400G transmission, as an example for a non-integer ratio, an average number of 3.33 bits per complex 2D symbol was chosen, resulting in a symbol rate of 67.2 GBd including 12% FEC overhead. We show a 0.34-dB gain of multidimensional 16-QAM modulation over a hybrid 8-QAM/16-QAM scheme in terms of asymptotic power efficiency.
About This Special Issue (1979)

Technical Forum About This Special Issue Masayoshi Tomizuka, Masayoshi Tomizuka Department of Mechanical Engineering, University of California, Berkeley, Calif. 94720 Search for other works by this author on: This Site PubMed Google Scholar David M. Auslander David M. Auslander Department of Mechanical Engineering, University of California, Berkeley, Calif. 94720 Search for other works by this author on: This Site PubMed Google Scholar Author and Article Information Masayoshi Tomizuka Department of Mechanical Engineering, University of California, Berkeley, Calif. 94720 David M. Auslander Department of Mechanical Engineering, University of California, Berkeley, Calif. 94720 J. Dyn. Sys., Meas., Control. Jun 1979, 101(2): 89-90 (2 pages) https://doi.org/10.1115/1.3426419 Published Online: June 1, 1979 Article history Online: July 13, 2010
DPFEE: A High Performance Scalable Pre-Processor for Network Security Systems (2017)

Network Intrusion Detection Systems (NIDS) and Anti-Denial-of-Service (DoS) employ Deep Packet Inspection (DPI) which provides visibility to the content of payload to detect network attacks. All DPI engines assume a pre-processing step that extracts the various protocol-specific fields. However, application layer (L7) field extraction is computationally expensive. We propose a novel Deep Packet Field Extraction Engine (DPFEE) for application layer field extraction to hardware. DPFEE is a content-aware, grammar-based, Layer 7 programmable field extraction engine for text-based protocols. Our prototype DPFEE implementation for the Session Initiation Protocol (SIP) and HTTP protocol on a single FPGA, achieves a bandwidth of 408.5 Gbps and this can be scaled beyond 500 Gbps. Single DPFEE exhibits a speedup of 24X-89X against widely used preprocessors. Even against 12 multi-instances of a preprocessor, single DPFEE demonstrated a speedup of 4.7-7.4X. Single DPFEE achieved 3.14X higher bandwidth, 1020X lower latency, and 106X lower power consumption, when compared with 200 parallel streams of GPU accelerated preprocessor.
Mitigating Storage Side Channels Using Statistical Privacy Mechanisms (2015)

A storage side channel occurs when an adversary accesses data objects influenced by another, victim computation and infers information about the victim that it is not permitted to learn directly. We bring advances in privacy for statistical databases to bear on storage side-channel defense, and specifically demonstrate the feasibility of applying differentially private mechanisms to mitigate storage side channels in procfs, a pseudo file system broadly used in Linux and Android kernels. Using a principled design with quantifiable security, our approach injects noise into kernel data-structure values that are used to generate procfs contents, but also reestablishes invariants on these noised values so as to not violate assumptions on which procfs or its clients depend. We show that our modifications to procfs can be configured to mitigate known storage side channels while preserving its utility for monitoring and diagnosis.