gebhart/patrepeval huggingface dataset:
Investigation of Tryptic Protein Digestion in Microdroplets and in Bulk Solution (2022)

Recent studies have shown that ultrafast enzymatic digestion of proteins can be achieved in microdroplet within 250 μs. Further investigation of peptides resulting from microdroplet digestion (MD) would be necessary to evaluate it as an alternative to the conventional bulk digestion for bottom-up and biotherapeutic protein characterization. Herein we examined and compared protein tryptic digestion in both MD and bulk solution. In the case of MD of β-lactoglobulin B, the preservation of long peptides was observed due to the short digestion time. In addition, MD is applicable to digest both high- and low-abundance proteins in mixture. In the case of digesting NIST 8671 mAb antibody containing a low level of commonly encountered host cell protein (HCP) PLBL2 (mAb:PLBL2 = 100:1 by weight), MD produced lower levels of digestion-induced chemical modifications of asparagine/glutamine deamidation, compared with overnight digestion. No significant difference between MD and bulk digestion was observed in terms of trypsin digestion specificity based on examination of semi- and unspecific-cleaved peptides. Our study suggests that MD, a fast digestion approach, could be adopted for bottom-up proteomics research and for peptide mapping of mAbs to characterize site-specific deamidation and glycosylation, for the purpose of development of biopharmaceuticals.
A New Control Architecture With Enhanced ARP, Burst-Based Transmission, and Hop-Based Wavelength Allocation for Ethernet-Supported (2004)

This paper focuses on the control architecture and the enabling technologies for the Ethernet-supported Internet protocol-over-wavelength-division-multiplexing metropolitan area networks. We present the general architecture of an access node of such networks and propose solutions to facilitate the es- sential system functionalities. The aim is to render the flexible and high-capacity metropolitan network, which provides service pro- visioning improvement and resource utilization efficiency for the packet-dominated data traffic. Specifically, an enhanced address resolution protocol is proposed to reduce the call setup latency and the signaling overhead associated with the address probing procedure, a burst-based transmission mechanism is adopted to improve the network throughput and resource utilization effi- ciency, and a wavelength allocation algorithm is investigated to provide flexible bandwidth multiplexing with fairness and high scalability. Theoretical analysis and simulations are conducted to evaluate the performance of our algorithms, demonstrating that the proposed architecture and technologies deliver substan- tial transport performance improvement with efficient network resource utilization.
High mobility III&#x2013;V-on-insulator MOSFETs on Si with ALD-Al<inf>2</inf>O<inf>3</inf> BOX layers (2010)

We have successfully demonstrated III–V-semiconductor-on-insulator (III–V-OI) MOSFETs with ALD-Al <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> buried oxide (BOX) layers under front-gate operation, for the first time. The high electron mobilities of ∼3000 and ∼2000 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Vs were achieved for i-InGaAs and p-InGaAs channels, respectively, formed on Al <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> /Si. Also, we have found that the InGaAs-OI channel bottom condition (the InGaAs-OI/BOX interface) is quite important for the device performance through improvements by adapting ALD-Al <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> and S passivation, resulting in high electron mobility of ∼4000 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Vs under back-gate operation.
Potent Synergistic Interactions between Lopinavir and Azole Antifungal Drugs against Emerging Multidrug-Resistant Candida auris (2020)

The limited therapeutic options and the recent emergence of multidrug-resistant <i>Candida</i> species present a significant challenge to human medicine and underscore the need for novel therapeutic approaches. Drug repurposing appears as a promising tool to augment the activity of current azole antifungals, especially against multidrug-resistant <i>Candida auris</i> In this study, we evaluated the fluconazole chemosensitization activities of 1,547 FDA-approved drugs and clinical molecules against azole-resistant <i>C. auris</i> This led to the discovery that lopinavir, an HIV protease inhibitor, is a potent agent capable of sensitizing <i>C. auris</i> to the effect of azole antifungals. At a therapeutically achievable concentration, lopinavir exhibited potent synergistic interactions with azole drugs, particularly with itraconazole against <i>C. auris</i> (fractional inhibitory concentration index [ΣFICI] ranged from 0.04 to 0.09). Additionally, the lopinavir/itraconazole combination enhanced the survival rate of <i>C. auris</i>-infected <i>Caenorhabditis elegans</i> by 90% and reduced the fungal burden in infected nematodes by 88.5% (<i>P < </i>0.05) relative to that of the untreated control. Furthermore, lopinavir enhanced the antifungal activity of itraconazole against other medically important <i>Candida</i> species, including <i>C. albicans</i>, <i>C. tropicalis</i>, <i>C. krusei</i>, and <i>C. parapsilosis</i> Comparative transcriptomic profiling and mechanistic studies revealed that lopinavir was able to significantly interfere with the glucose permeation and ATP synthesis. This compromised the efflux ability of <i>C. auris</i> and consequently enhanced the susceptibility to azole drugs, as demonstrated by Nile red efflux assays. Altogether, these findings present lopinavir as a novel, potent, and broad-spectrum azole-chemosensitizing agent that warrants further investigation against recalcitrant <i>Candida</i> infections.
Histologic scoring indices for evaluation of disease activity in Crohn’s disease (2017)

Currently there is no fully validated histological scoring index for evaluation of Crohn's disease activity. Development of a validated histological scoring index for Crohn's disease is a clinical and research priority.
Computer simulation of radio frequency confinement of a plasma near critical density (1977)

The time evolution of an initially uniform slightly underdense (ωe≲ω) plasma in a resonant cavity has been studied using two-dimensional electromagnetic simulations. The ponderomotive force compresses plasma into the nodes of the applied radio frequency field. The plasma buildup at the nodes terminates either when the plasma pressure increases to equal the field pressure or when phase space breaking occurs. Explanations of the density buildup and tail formation of the particle distribution functions are provided.
Layered Electrode Architectures Enabled By Holey Graphene Hosts (2020)

Battery electrodes are typically prepared using a slurry-based method, where high boiling point organic solvents are typically used with a polymer binder to disperse active electrode materials and conductive carbon additives followed by casting onto current collector sheets. In this process, the use of organic solvents are environmentally hazardous, energy intensive, and time-consuming, while polymeric binders add weight and can undergo parasitic reactions during battery cycling. Here we discuss the use of a unique conductive carbon nanomaterial, namely holey graphene, as a multifunctional host that can be processed via a facile, solvent-free, binder-free, cold pressing method to prepare electrodes with unique architectures. This approach can accommodate a broad range of battery chemistries, such as lithium oxygen/carbon dioxide (Li-O 2 /CO 2 ), lithium sulfur/selenium (Li-S/Se), and various lithium ion chemistries. The successful use of dry, cold compression allows the convenient modification of electrode mass loading with unique architectures containing active materials randomly mixed or layered with single or multiple layers of one or more active materials. In the conventional slurry-based electrode fabrication method, it is difficult, if not impossible, to achieve such layered architectures. In particular, the layered electrode architectures from the dry, cold press approach are easy to fabricate without significantly sacrificing device performance, and are amenable to continuous roll-to-roll dry processing. In addition, these architectures offer unprecedented perspectives on the battery material loading vs. utilization efficiency, as well as enabling unique characterization opportunities to advance mechanistic understanding of various battery chemistries. Potential applications of this unique electrode fabrication approach for solid-state batteries will also be discussed.
Observing the Effects of Shaping on Gas Adsorption in Metal‐Organic Frameworks (2016)

A series of four micro‐ or mesoporous metal‐organic frameworks [UiO‐66(Zr), UiO‐66(Zr)_NH 2 , MIL‐100(Fe), MIL‐127(Fe)] were synthesized in powder form and pelletized in the form of spheres by using a polyvinyl‐based binder. The effect of pelletization on the adsorption of a series of gasses (N 2 , CO, CO 2 , CH 4 , C 2 H 6 , C 3 H 8 , C 3 H 6 , C 4 H 10 ) at 303 K was evidenced in the adsorption isotherms and the enthalpies of adsorption measured by using microcalorimetric analysis. As expected, uptakes of gas per gram of material were lower for the spheres than for the powder. However, taking into account the bulk density, this tendency was inverted, suggesting that the spherical materials are of distinct interest for gas‐based applications. Nevertheless, other effects including partial pore restriction and active site “protection” may equally be evidenced for some pelletized materials, suggesting that the polyvinyl binder may play a more complex role.
Fast and Interactive Analytics over Hadoop Data with Spark (2012)

Matei Zaharia is a fifth­ year PhD student at UC Berkeley, working with Scott Shenker and Ion Stoica on topics in computer systems, networks, cloud computing, and big data. He is also a committer on Apache Hadoop and Apache
A Multiband Shared Aperture MIMO Antenna for Millimeter-Wave and Sub-6GHz 5G Applications (2022)

A shared aperture 2-element multiple-input-multiple-output (MIMO) antenna design for 5G standards is presented in this study, one which uses the same radiating structure to cover both the sub-6GHz and millimeter-wave (millimeter-wave) bands. The proposed antenna comprises four concentric pentagonal slots that are uniformly separated from one another. For the sub-6GHz band, the antenna is excited by a single open-end microstrip transmission-line, while a 1 × 8 power divider (PD) connected via a T-junction structure excites the millimeter-wave band. Both the sub-6GHz and mm-wave antennas operate in a MIMO configuration. The proposed antenna design was fabricated on a 120 × 60 mm<sup>2</sup> substrate with an edge-to-edge distance of 49 mm. The proposed sub-6GHz antenna covers the following frequency bands: 4-4.5 GHz, 3.1-3.8 GHz, 2.48-2.9 GHz, 1.82-2.14 GHz, and 1.4-1.58 GHz, while the millimeter-wave antenna operates at 28 GHz with at least 500 MHz of bandwidth. A complete antenna analysis is provided via a step-by-step design procedure, an equivalent circuit diagram showing the operation of the shared aperture antenna, and current density analysis at both millimeter-wave and sub-6GHz bands. The proposed antenna design is also characterized in terms of MIMO performance metrics with a good MIMO operation with maximum envelop correlation coefficient value of 0.113. The maximum measured gain and efficiency values obtained were 91% and 8.5 dBi over the entire band of operation. The antenna is backward compatible with 4G bands and also encompasses the sub-6GHz and 28 GHz bands for future 5G wireless communcation systems.
Asymmetric Electrical Structure in the Mantle Beneath the East Pacific Rise at 17°S (1999)

The magnetotelluric component of the Mantle Electromagnetic and Tomography (MELT) Experiment measured the electrical resistivity structure of the mantle beneath the fast-spreading southern East Pacific Rise (EPR). The data reveal an asymmetric resistivity structure, with lower resistivity to the west of the ridge. The uppermost 100 kilometers of mantle immediately to the east of the ridge is consistent with a dry olivine resistivity structure indicating a mantle depleted of melt and volatiles. Mantle resistivities to the west of the ridge are consistent with a low-melt fraction (about 1 to 2 percent interconnected melt) distributed over a broad region and extending to depths of about 150 kilometers. The asymmetry in resistivity structure may be the result of asymmetric spreading rates and a westward migration of the ridge axis and suggests distinct styles of melt formation and delivery in the mantle beneath the two plates.
@An automated self-service multi-cloud HPC platform applied to the simulation of cardiac valve disease with machine learning (2021)

The team's Living Heart Abaqus 2020 workflow from Dassault Systèmes Simulia has been implemented in UberCloud's HPC containers on the fully automated UberCloud Platform on Google Cloud's c2 instances. The team ran more than 1,500 simulations needed to train the ML algorithm. The whole simulation process took place as a multi-cloud approach, with all computations running on Google GCP, and management, monitoring, and health-checks orchestrated from Azure Cloud performed through SUSE's Kubernetes management platform Rancher implemented in UberCloud's own Azure account.
Analysis of Retinal Nonperfusion Using Depth-Integrated Optical Coherence Tomography Images in Eyes With Branch Retinal Vein Occlusion (2015)

Depth-integrated OCT images with automated layer segmentation showed a two-dimensional honeycomb-like structure in retinal nonperfusion with retinal edema. In eyes with BRVO, the thickness of retina did not decrease but increased due to retinal cyst in spite of neural retinal thinning.
Preparation of Transparent Nanocomposite Microspheres via Dispersion of High-Concentration TiO2 and BaTiO3 Nanoparticles in Acrylic Monomer (2008)

Functional nanoparticle-dispersed composite polymer materials were prepared. Metal oxide nanoparticles such as BaTiO3 (primary diameter: 20nm) and three sizes of TiO2 (primary diameter: 7, 15, 20nm) were dispersed into acrylic monomer by means of beads mill filled with fine beads (50μm in diameter), and the nanoparticle-dispersed monomers were polymerized to obtain nanocomposite polymers by the suspension polymerization. The morphology, the nanoparticle dispersibility and the compressive strength of prepared polymer were evaluated. As a result, the TiO2-dispersed acrylic polymer spheres were fairly uniform in size with the diameter of several micrometers, and had relatively high compressive strength of 257MPa. It was also confirmed from the transmission electron microscope that the nanoparticles were well-dispersed in the polymer matrix.
Real-Time Shape Evolution of Nanoimprinted Polymer Structures during Thermal Annealing (2006)

The real-time shape evolution of nanoimprinted polymer patterns is measured as a function of annealing time and temperature using critical dimension small-angle X-ray scattering (CD-SAXS). Periodicity, line width, line height, and sidewall angle are reported with nanometer resolution for parallel line/space patterns in poly(methyl methacrylate) (PMMA) both below and above the bulk glass transition temperature (T(G)). Heating these patterns below T(G) does not produce significant thermal expansion, at least to within the resolution of the measurement. However, above T(G) the fast rate of loss in pattern size at early times transitions to a reduced rate in longer time regimes. The time-dependent rate of polymer flow from the pattern into the underlying layer, termed pattern "melting", is consistent with a model of elastic recovery from stresses induced by the molding process.
Evaluation of a shock wave induced cavitation activity bothin vitroandin vivo (2007)

This study evaluated the cavitation activity induced by shock wave (SW) pulses, both in vitro and in vivo, based on the area measurements of echogenic regions observed in B-mode ultrasound images. Residual cavitation bubble clouds induced by SW pulses were detected as echogenic regions in B-mode images. The temporal evolution of residual bubble clouds, generated by SWs with varying lithotripter charging voltage and pulse repetition frequency (PRF), was analyzed by measuring the time-varying behaviors of the echogenic region areas recorded in B-mode images. The results showed that (1) the area of SW-induced echogenic regions enlarged with increased SW pulse number; (2) echogenic regions in the B-mode images dissipated gradually after ceasing the SWs, which indicated the dissolution of the cavitation bubbles; and (3) larger echogenic regions were generated with higher charging voltage or PRF.
CURRENT STATUS AND RIGHT-CENSORED DATA STRUCTURES WHEN OBSERVING A MARKER AT THE CENSORING TIME. (2003)

We study nonparametric estimation with two types of data structures. In the first data structure n i.i.d. copies of (C, N(C)) are observed, where N is a finite state counting process jumping at time-variables of interest and C a random monitoring time. In the second data structure n i.i.d. copies of (C ∧ T, I (T ≤ C), N(C ∧ T)) are observed, where N is a counting process with a final jump at time T (e.g., death). This data structure includes observing right-censored data on T and a marker variable at the censoring time.In these data structures, easy to compute estimators, namely (weighted)-pool-adjacent-violator estimators for the marginal distributions of the unobservable time variables, and the Kaplan-Meier estimator for the time T till the final observable event, are available. These estimators ignore seemingly important information in the data. In this paper we prove that, at many continuous data generating distributions the ad hoc estimators yield asymptotically efficient estimators of [Formula: see text]-estimable parameters.
44-ns Continuously Tunable Dispersionless Optical Delay Element Using a PPLN Waveguide With Two-Pump Configuration, DCF, and a Dispersion Compensator (2007)

This letter presents an optically controlled, continuously tunable, dispersionless optical delay element in fiber based on a selective wavelength converter using a periodically poled lithium-niobate waveguide with two-pump configuration, dispersion-compensated fiber, and a dispersion compensator. Optical phase information is preserved in this technique, and there is no fundamental limitation on pulsewidth or bit rate. A Continuous optical delay up to 44-ns is shown for 10-Gb/s nonreturn-to-zero applications, which is equal to a 440-bit slot
Toward ML-centric cloud platforms (2020)

Exploring the opportunities to use ML, the possible designs, and our experience with Microsoft Azure.
Enhanced Precoding Design with Adaptive Beam Width for 5G New Radio Systems (2017)

Multiple-Input Multiple-Output (MIMO) is considered as a key technology for next generation wireless cellular systems. Depending on the scenario and propagation environment the optimal beamwidth of the precoding vectors in MIMO systems can be different. Precoding vectors corresponding to narrow beams are most appropriate in several scenarios, as they provide maximum beamforming gain in the desired direction and generate less interference in other directions. However, in some cases the use of only narrow beams for precoding is not optimal. For example, to increase the spatial multiplexing gains and the number of transmitted MIMO layers, the precoding vectors corresponding to wider beams should be also considered. Moreover, for open-loop transmission schemes, the use of precoding with wider beamwidth results in better diversity and, therefore, improved performance. To accommodate the variable beamwidth requirement for MIMO beamforming, this paper proposes an enhanced precoding approach with adaptive beamwidth of the precoding vectors for 5G New Radio (NR) systems. System-level and link- level performance evaluation results show that the proposed precoding vector structure with adaptive beamwidth of the precoding vectors outperforms conventional DFT-based precoding with narrow beamwidth supported in LTE-A systems.
A 4D Statistical Model of Wrist Bone Motion Patterns (2011)

Direct imaging of ligament damage in the wrist remains a challenge. Still, such damage can be assessed indirectly through the analysis of changes in wrist pose and motion pattern. For this purpose we built a statistical reference model that describes healthy motion patterns. We show that such a model can also be used to detect and quantify pathologies. A model that only describes the global translations and rotations of the carpal bones is insufficiently accurate due to size and shape variations of the bones. We present a local statistical motion model that minimizes the influence of size and shape differences by analyzing the coordinate differences of pairs of points on adjacent bone surfaces. These differences are determined in a set of 14 healthy example wrists imaged in a range of poses by means of 4D-RX imaging. The distribution of the differences as a function of the pose form the local statistical motion model (LSMM). Translations of 2 mm and rotations of 20° with respect to the healthy example wrists are detected as outliers in the point pair distributions. An evaluation involving wrists with a damaged ligament between scaphoid and lunate shows that not only joint space widenings can be detected, but also shifts of congruent bone surfaces. The LSMM is also used to perform a virtual reconstruction of the most likely healthy wrist after a simulated perturbation of bones. The reconstruction precision is shown to be about 1 mm. Therefore, the presented 4D statistical model of wrist bone movement may become a valuable clinical tool for diagnosis and surgical planning.
Functional characterization and immunomodulatory properties of Lactobacillus helveticus strains isolated from Italian hard cheeses (2021)

Lactobacillus helveticus carries many properties such as the ability to survive gastrointestinal transit, modulate the host immune response, accumulate biopeptides in milk, and adhere to the epithelial cells that could contribute to improving host health. In this study, the applicability as functional cultures of four L. helveticus strains isolated from Italian hard cheeses was investigated. A preliminary strain characterization showed that the ability to produce folate was generally low while antioxidant, proteolytic, peptidase, and β-galactosidase activities resulted high, although very variable, between strains. When stimulated moDCs were incubated in the presence of live cells, a dose-dependent release of both the pro-inflammatory cytokine IL-12p70 and the anti-inflammatory cytokine IL-10, was shown for all the four strains. In the presence of cell-free culture supernatants (postbiotics), a dose-dependent, decrease of IL-12p70 and an increase of IL-10 was generally observed. The immunomodulatory effect took place also in Caciotta-like cheese made with strains SIM12 and SIS16 as bifunctional (i.e., immunomodulant and acidifying) starter cultures, thus confirming tests in culture media. Given that the growth of bacteria in the cheese was not necessary (they were killed by pasteurization), the results indicated that some constituents of non-viable bacteria had immunomodulatory properties. This study adds additional evidence for the positive role of L. helveticus on human health and suggests cheese as a suitable food for delivering candidate strains and modulating their anti-inflammatory properties.