gebhart/patrepeval huggingface dataset:
Selection-free, high frequency genome editing by homologous recombination of human pluripotent stem cells using Cas9 RNP and AAV6 (2018)

Abstract Combination of genome editing and human pluripotent stem cells (hPSCs) offers a platform for in vitro disease modeling, drug discovery and personalized stem cell therapeutics. However, incorporation of large modifications using CRISPR/Cas9-based genome editing in hPSCs typically requires the use of selection markers due to low editing efficiencies. Here we report a novel editing technology in hPSCs using Cas9 protein complexed with chemically modified single guide RNA (sgRNA) and recombinant AAV6 (rAAV6) vectors for donor delivery without marker selection. With these components, we demonstrate targeted integration of a 2.2 kb DNA expression cassette in hPSCs at frequencies up to 94% and 67% at the HBB and MYD88 loci, respectively. We used this protocol to correct the homozygous sickle cell disease (SCD) mutation in an iPSC line derived from a SCD patient with a frequency of 63%. This Cas9/AAV6 system allows for both the integration of large gene cassettes and the creation of single nucleotide changes in hPSCs at high frequencies, eliminating the need for multiple editing steps and marker selection, thus increasing the potential of editing human pluripotent cells for both research and translational applications.
Isolation of Blood-vessel-derived Multipotent Precursors from Human Skeletal Muscle (2014)

Since the discovery of mesenchymal stem/stromal cells (MSCs), the native identity and localization of MSCs have been obscured by their retrospective isolation in culture. Recently, using fluorescence-activated cell sorting (FACS), we and other researchers prospectively identified and purified three subpopulations of multipotent precursor cells associated with the vasculature of human skeletal muscle. These three cell populations: myogenic endothelial cells (MECs), pericytes (PCs), and adventitial cells (ACs), are localized respectively to the three structural layers of blood vessels: intima, media, and adventitia. All of these human blood-vessel-derived stem cell (hBVSC) populations not only express classic MSC markers but also possess mesodermal developmental potentials similar to typical MSCs. Previously, MECs, PCs, and ACs have been isolated through distinct protocols and subsequently characterized in separate studies. The current isolation protocol, through modifications to the isolation process and adjustments in the selective cell surface markers, allows us to simultaneously purify all three hBVSC subpopulations by FACS from a single human muscle biopsy. This new method will not only streamline the isolation of multiple BVSC subpopulations but also facilitate future clinical applications of hBVSCs for distinct therapeutic purposes.
Magnetic structure of Co1/3NbS2and Co1/3TaS2 (1983)

The authors have examined the magnetic structures of the antiferromagnetic layered compounds Co1/3NbS2 and Co1/3TaS2 using single-crystal neutron photographic and counting methods. The magnetic structure of Co1/3NbS2 has been determined in detail, and has an orthohexagonal unit cell, containing two Co atoms, arranged on the 'hexagonal ordering of the first kind' scheme. The different symmetries of the crystallographic and magnetic unit cells leads to a complicated domain structure. A large part of the magnetisation in this material is localised on the Co atoms, although the magnetic moment of the Co2+ ion is approximately 10% lower than that of the corresponding spin-only moment. The magnetic structure of the related material, Co1/3TaS2, which has the same crystal structure as Co1/3NbS2, is very different, and is a triangular antiferromagnetic structure although for this material only the unit cell has been determined.
A Generalized Gossip Algorithm on Convex Metric Spaces (2014)

A consensus problem consists of a group of dynamic agents who seek to agree upon certain quantities of interest. This problem can be generalized in the context of convex metric spaces that extend the standard notion of convexity. In this paper we introduce and analyze a randomized gossip algorithm for solving the generalized consensus problem on convex metric spaces, where the communication between agents is controlled by a set of Poisson counters. We study the convergence properties of the algorithm using stochastic calculus. In particular, we show that the distances between the states of the agents converge to zero with probability one and in the r <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> mean sense. In the special case of complete connectivity and uniform Poisson counters, we give upper bounds on the dynamics of the first and second moments of the distances between the states of the agents. In addition, we introduce instances of the generalized consensus algorithm for several examples of convex metric spaces together with numerical simulations.
Three‐dimensional streamlined finite elements: Design of extrusion dies (1992)

Abstract A method to determine three‐dimensional die shapes from extrudate swell and vice versa is presented using a three‐dimensional Galerkin finite element method based on a streamlined formulation with the fluid velocities and pressures represented by triquadratic and trilinear basis functions respectively. The three‐dimensional streamlined method, an extension of the two‐dimensional formulation, uses successive streamsurfaces to form a boundary‐conforming co‐ordinate system. This produces a fixd, computational domain leaving the spatial location of the elements as unknowns to be determined with the standard primary variables ( u , v , w , p ). The extrudate produced by a die of a given shape is considered for moderate Reynolds numbers. Finally, the method is extended to address the problem of die design, where a die profile is sought to produce a target extrudate shape.
Multi-core leakage-channel fibers with up to 26000 µm2 combined effective mode-field area (2009)

Hexagonally stacked all-glass multi-core leakage-channel fibers consisting of seven fused silica cores of up to 100µm in diameter were fabricated. Simultaneous fundamental mode propagation in all cores and their active coherent combination was demonstrated.
Verification of a neuromorphic computing network simulator using experimental traffic data (2022)

Simulations are a powerful tool to explore the design space of hardware systems, offering the flexibility to analyze different designs by simply changing parameters within the simulator setup. A precondition for the effectiveness of this methodology is that the simulation results accurately represent the real system. In a previous study, we introduced a simulator specifically designed to estimate the network load and latency to be observed on the connections in neuromorphic computing (NC) systems. The simulator was shown to be especially valuable in the case of large scale heterogeneous neural networks (NNs). In this work, we compare the network load measured on a SpiNNaker board running a NN in different configurations reported in the literature to the results obtained with our simulator running the same configurations. The simulated network loads show minor differences from the values reported in the ascribed publication but fall within the margin of error, considering the generation of the test case NN based on statistics that introduced variations. Having shown that the network simulator provides representative results for this type of -biological plausible-heterogeneous NNs, it also paves the way to further use of the simulator for more complex network analyses.
Spectrum Sensing for Cognitive Radio : State-of-the-Art and Recent Advances (2012)

The ever-increasing demand for higher data rates in wireless communications in the face of limited or underutilized spectral resources has motivated the introduction of cognitive radio. Traditionally, licensed spectrum is allocated over relatively long time periods and is intended to be used only by licensees. Various measurements of spectrum utilization have shown substantial unused resources in frequency, time, and space [1], [2]. The concept behind cognitive radio is to exploit these underutilized spectral resources by reusing unused spectrum in an opportunistic manner [3], [4]. The phrase cognitive radio is usually attributed to Mitola [4], but the idea of using learning and sensing machines to probe the radio spectrum was envisioned several decades earlier (cf., [5]).
Significance of Pairing In/Ga Precursor Structures on PEALD InGaOx Thin-Film Transistor (2021)

Atomic layer deposition (ALD) is a promising deposition method to precisely control the thickness and metal composition of oxide semiconductors, making them attractive materials for use in thin-film transistors because of their high mobility and stability. However, multicomponent deposition using ALD is difficult to control without understanding the growth mechanisms of the precursors and reactants. Thus, the adsorption and surface reactivity of various precursors must be investigated. In this study, InGaO (IGO) semiconductors were deposited by plasma-enhanced atomic layer deposition (PEALD) using two sets of In and Ga precursors. The first set of precursors consisted of In(CH<sub>3</sub>)<sub>3</sub>[CH<sub>3</sub>OCH<sub>2</sub>CH<sub>2</sub>NHtBu] (TMION) and Ga(CH<sub>3</sub>)<sub>3</sub>[CH<sub>3</sub>OCH<sub>2</sub>CH<sub>2</sub>NHtBu]) (TMGON), denoted as TM-IGO; the other set of precursors was (CH<sub>3</sub>)<sub>2</sub>In(CH<sub>2</sub>)<sub>3</sub>N(CH<sub>3</sub>)<sub>2</sub> (DADI) and (CH<sub>3</sub>)<sub>3</sub>Ga (TMGa), denoted as DT-IGO. We varied the number of InO subcycles between 3 and 19 to control the chemical composition of the ALD-processed films. The indium compositions of TM-IGO and DT-IGO thin films increased as the InO subcycles increased. However, the indium/gallium metal ratios of TM-IGO and DT-IGO were quite different, despite having the same InO subcycles. The steric hindrance of the precursors and different densities of the adsorption sites contributed to the different TM-IGO and DT-IGO metal ratios. The electrical properties of the precursors, such as Hall characteristics and device parameters of the thin-film transistors, were also different, even though the same deposition process was used. These differences might have resulted from the growth behavior, anion/cation ratios, and binding states of the IGO thin films.
A Season of Giving to Science (2016)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTA Season of Giving to ScienceCarolyn R. Bertozzi and Miranda A. PaleyView Author Information Department of Chemistry, Stanford University American Chemical SocietyE-mail: [email protected]Cite this: ACS Cent. Sci. 2016, 2, 12, 872–873Publication Date (Web):December 28, 2016Publication History Published online28 December 2016Published inissue 28 December 2016https://doi.org/10.1021/acscentsci.6b00382Copyright © 2016 American Chemical SocietyRIGHTS & PERMISSIONSACS AuthorChoiceArticle Views1934Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (227 KB) Get e-Alerts Get e-Alerts
Measurement of Intrasound from the Marine Environment (2015)

Abstract : The objective of the Measurement Ultrasound from the Maritime Environment project team at Space and Naval Warfare Systems Center Pacific (SSC Pacific) is to develop an infrasound sensing capability that can operate from the maritime environment. Infrasound monitoring stations are normally situated on land-based sites. Because two thirds of the earths surface is composed of oceans, a functional maritime-based infrasound sensing capability would greatly enhance the ability to monitor natural and anthropogenic sources of infrasound around the world. Ocean heave, as measured by the sea surface spectrum, is shown to occupy a significant portion of the infrasound receive frequency band. Measurements were taken with a microbarometer fielded on board a ship during an at-sea experiment. The collected sound pressure data shows the interference effects of ocean heave, which are due to the change in the background atmospheric pressure as the sensor moves up and down. An external inertial measurement unit (IMU) was used to estimate the heave, and was highly correlated with the pressure interference signal.
RNN-Based On-Line Continuous Gait Phase Estimation from Shank-Mounted IMUs to Control Ankle Exoskeletons (2019)

Several research groups have developed and studied powered ankle exoskeletons to improve energetics of healthy subjects and the mobility of elderly subjects, or to reduce asymmetry in gaits induced by strokes. To achieve optimal effect, the timing of assistive torque has been proved to be of crucial importance. Previous studies estimated the onset timings mostly by extrapolating the time horizon from past gait events observed with sensors. Such methods have inherently limited performance when subjects are not walking at steady frequencies. To overcome such limitation and allow the use of exoskeletons in various scenarios in a daily life, we propose to estimate the gait phase as a continuous variable progressing over a gait cycle, hence allowing immediate response to frequency changes rather than iteratively correcting it after each cycle. Our method uses recurrent neural networks to estimate gait phases out of an inertial measurement unit (IMU) every 10 ms. By replacing foot sensors with an IMU we can obtain rich enough information to estimate gait phase continuously as well as avoid physical damage in sensors from ground impacts. Our preliminary tests with 2 healthy subjects showed qualitatively positive outcomes regarding the gait phase estimation and the assistive torque control.
Cross-modal preparatory attention is reduced in amblyopes: An ERP Study (2013)

Previous evidence of attention deficits in individuals with amblyopia (Popple & Levi, 2008; Secen et al., 2011) has relied on studies that were conducted purely in the visual domain. However, it is unknown whether amblyopes are also impaired when visual attention is cued within the auditory domain. To test this, we recorded event-related potentials (ERPs) to examine differences in attentional orienting to an auditory cue when observing with an amblyopic (AE) vs. dominant eye (DE). While fixating, a brief auditory cue prompted observers to attend to one of two locations in the left and right visual field, where stimuli were later bilaterally presented following a 800ms cue-target-interval. The target stimulus was a tilted Gabor patch that appeared on the cued side in 5% of the trials, and on the uncued side in another 5%. In all other cases, stimuli were horizontally-oriented Gabor patches. Observers were instructed to respond via key press only when the target stimulus appeared in the cued location. Contrast and orientation of targets were adjusted prior to recordings such that each individual could achieve 75-90% accuracy on the task while viewing monocularly with each eye. To isolate cued-attention effects, ERPs recorded for contralaterally-cued events were subtracted from ipsilaterally-cued events for the AE and DE. Our preliminary results indicate that during the cue-target-interval, anterior electrodes (F7, F5, F3) showed greater modulation to the auditory cue in the DE in comparison to the AE, with two contralateral positivity peaks at 100-180ms and 200-450ms. The observed differences in event-related lateralization effects provide initial evidence of decreased attentional orienting when viewing with the AE, even when driven by cues in the auditory domain. As directing attention to a visual stimulus can boost the speed and accuracy of its processing, increasing this orienting response may help improve other aspects of amblyopic viewing. Meeting abstract presented at VSS 2013
Populating Web-Scale Knowledge Graphs Using Distantly Supervised Relation Extraction and Validation (2021)

In this paper, we propose a fully automated system to extend knowledge graphs using external information from web-scale corpora. The designed system leverages a deep-learning-based technology for relation extraction that can be trained by a distantly supervised approach. In addition, the system uses a deep learning approach for knowledge base completion by utilizing the global structure information of the induced KG to further refine the confidence of the newly discovered relations. The designed system does not require any effort for adaptation to new languages and domains as it does not use any hand-labeled data, NLP analytics, and inference rules. Our experiments, performed on a popular academic benchmark, demonstrate that the suggested system boosts the performance of relation extraction by a wide margin, reporting error reductions of 50%, resulting in relative improvement of up to 100%. Furthermore, a web-scale experiment conducted to extend DBPedia with knowledge from Common Crawl shows that our system is not only scalable but also does not require any adaptation cost, while yielding a substantial accuracy gain.
Techno-Economic Feasibility Study of Battery- Powered Ferries (2018)

The move towards incorporating more-electric solutions in the transportation sector has gained increased momentum during the last decade. Cost of fossil fuels and environmental impacts of emissions are the main driving factors behind this growing trend. Nevertheless, advancements in battery technologies are the key enablers for the wide- spread application of electric alternatives in a more realistic manner. This paper looks into this trend from electric ferries perspective and presents a technical and economic feasibility assessment. The technical study includes sizing of the battery storage system based on Depth-of- Discharge (DOD) and maximum load scenario. The proposed sizing is validated against the measured load profile. The economic study includes initial investment, operational cost and maintenance cost of a battery powered electric ferry. The economic analysis considered the payback period (PBP) and battery lifecycles as assessment factors. The technical assessment results revealed that the proposed battery system can efficiently power the ferry within the stipulated DOD range. The maximum DOD achieved is 70 %, which provided a reasonable lifetime of 10.7 years. The economic analysis revealed that the battery's DOD has significant effects on the investment cost of the system and the PBP. The PBP is found to be 6.7 years which is 37 % less than the lifetime of the battery. Overall, the battery-powered ferry is found to be feasible with 51.3% operational costs saving compared to the diesel-electric alternative.
Modeling Spatial-Temporal Clues in a Hybrid Deep Learning Framework for Video Classification (2015)

Classifying videos according to content semantics is an important problem with a wide range of applications. In this paper, we propose a hybrid deep learning framework for video classification, which is able to model static spatial information, short-term motion, as well as long-term temporal clues in the videos. Specifically, the spatial and the short-term motion features are extracted separately by two Convolutional Neural Networks (CNN). These two types of CNN-based features are then combined in a regularized feature fusion network for classification, which is able to learn and utilize feature relationships for improved performance. In addition, Long Short Term Memory (LSTM) networks are applied on top of the two features to further model longer-term temporal clues. The main contribution of this work is the hybrid learning framework that can model several important aspects of the video data. We also show that (1) combining the spatial and the short-term motion features in the regularized fusion network is better than direct classification and fusion using the CNN with a softmax layer, and (2) the sequence-based LSTM is highly complementary to the traditional classification strategy without considering the temporal frame orders. Extensive experiments are conducted on two popular and challenging benchmarks, the UCF-101 Human Actions and the Columbia Consumer Videos (CCV). On both benchmarks, our framework achieves very competitive performance: 91.3% on the UCF-101 and 83.5% on the CCV.
Glycan-dependent HIV-specific neutralizing antibodies bind to cells of uninfected individuals (2019)

A number of highly potent and broadly neutralizing antibodies (bNAbs) against the human immunodeficiency virus (HIV) have recently been shown to prevent transmission of the virus, suppress viral replication, and delay plasma viral rebound following discontinuation of antiretroviral therapy in animal models and infected humans. However, the degree and extent to which such bNAbs interact with primary lymphocytes have not been fully delineated. Here, we show that certain glycan-dependent bNAbs, such as PGT121 and PGT151, bind to B, activated T, and natural killer (NK) cells of HIV-infected and -uninfected individuals. Binding of these bNAbs, particularly PGT121 and PGT151, to activated CD4+ and CD8+ T cells was mediated by complex-type glycans and was abrogated by enzymatic inhibition of N-linked glycosylation. In addition, a short-term incubation of PGT151 and primary NK cells led to degranulation and cellular death. Our data suggest that the propensity of certain bNAbs to bind uninfected/bystander cells has the potential for unexpected outcomes in passive-transfer studies and underscore the importance of antibody screening against primary lymphocytes.