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Open Access Publications from the University of California

Scholarly Works (70 results)

  • Article
  • Peer Reviewed
LBL Publications (2021)
Abstract: We present ForSE (Foreground Scale Extender), a novel Python package that aims to overcome the current limitations in the simulation of diffuse Galactic radiation, in the context of cosmic microwave background (CMB) experiments. ForSE exploits the ability of generative adversarial neural networks (GANs) to learn and reproduce complex features present in a set of images, with the goal of simulating realistic and non-Gaussian foreground radiation at subdegree angular scales. This is of great importance in order to estimate the foreground contamination to lensing reconstruction, delensing, and primordial B-modes for future CMB experiments. We applied this algorithm to Galactic thermal dust emission in both total intensity and polarization. Our results show how ForSE is able to generate small-scale features (at 12′) having as input the large-scale ones (80′). The injected structures have statistical properties, evaluated by means of the Minkowski functionals, in good agreement with those of the real sky and which show the correct amplitude scaling as a function of the angular dimension. The obtained thermal dust Stokes Q and U full-sky maps as well as the ForSE package are publicly available for download.
    Cover page: ForSE: A GAN-based Algorithm for Extending CMB Foreground Models to Subdegree Angular Scales
    • Article
    LBL Publications (2000)

    A well-known approach to compute the LU factorization of a general unsymmetric matrix A is to build the elimination tree associated with the pattern of the symmetric matrix A + A rm T and use it as a computational graph to drive the numerical factorization. This approach, although very efficient on a large range of unsymmetric matrices, does not capture the unsymmetric structure of the matrices. We introduce a new algorithm which detects and exploits the structural unsymmetry of the submatrices involved during the process of the elimination tree. We show that with the new algorithm significant gains both in memory and in time to perform the factorization can be obtained.

      Cover page: An unsymmetrized multifrontal LU factorization
      • Thesis
      • Peer Reviewed
      UC Santa Barbara Electronic Theses and Dissertations (2001)

      This study was conducted to understand student and teacher perspectives of the ways on-line learning projects provide opportunities for collaborative inquiry-based learning. Towards this end, the researcher utilized text analysis to compare what “counted” to the project's designers to what “counted” to project participants. The study also used ethnographic methods to examine classroom social dynamics through microanalysis of social interactions, discourse, and texts.

      The researcher served as principal/co-teacher/participant observer and worked with a sixth grade class and their teacher as they participated in the America Dreams on-line project; an Internet based collaborative, inquiry-based learning project sponsored by the Library of Congress. Text from the America Dreams web pages, linked sources, and e-mail interviews with the project designers served as data for analyzing what “counts” as the project from the designers' point of view. Student created texts, videos of student group collaborations, teacher interviews, surveys, and field notes served as the data for analyzing what “counts” as the America Dreams project from the perspective of the students, teachers, and researcher. The researcher explored the ways that student groups negotiate and take up common tasks as well as examining various sources of discourse and texts and their relative influence on individual student opportunities for learning.

      The most significant findings pertained to the intentions of the project designers as they relate to actual usage of the project. Pedagogical, technological, and content related issues concerning the American dream were found to “count” to both the designers and users of the project. A student—centered, constructivist approach that asked students to become researchers was found to serve students and teachers as they explored their community's and their own visions of the American dream. While the project was designed to wed technology with these pedagogical concerns, several of the technological components of the project were not implemented. Internet-based research and web publishing, however, played a significant role in the actual usage of the project. Gender and social status issues among students in the classroom and group cultures emerged as significantly influential in quantities and qualities of speech during group work.

        Cover page: Understanding the Construction o f Opportunities for Learning Among Student Groups Working on Collaborative On-line Projects
        • Article
        • Peer Reviewed
        UCLA Previously Published Works (2018)
        Increasingly, cryo-electron microscopy (cryo-EM) is used to determine the structures of RNA-protein assemblies, but nearly all maps determined with this method have biologically important regions where the local resolution does not permit RNA coordinate tracing. To address these omissions, we present de novo ribonucleoprotein modeling in real space through assembly of fragments together with experimental density in Rosetta (DRRAFTER). We show that DRRAFTER recovers near-native models for a diverse benchmark set of RNA-protein complexes including the spliceosome, mitochondrial ribosome, and CRISPR-Cas9-sgRNA complexes; rigorous blind tests include yeast U1 snRNP and spliceosomal P complex maps. Additionally, to aid in model interpretation, we present a method for reliable in situ estimation of DRRAFTER model accuracy. Finally, we apply DRRAFTER to recently determined maps of telomerase, the HIV-1 reverse transcriptase initiation complex, and the packaged MS2 genome, demonstrating the acceleration of accurate model building in challenging cases.
          Cover page: De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2014)
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2022)
            Survivors of intraventricular hemorrhage are often left with significant long-term memory impairment; thus, research utilizing intraventricular hemorrhage animal models is essential. In this study, we sought out ways to measure intracranial pressure, mean arterial pressure, and cerebral perfusion pressure during nontraumatic intraventricular hemorrhage in rodents. The experimental design included three Sprague Dawley groups: sham, standard 200 µl intraventricular hemorrhage, and vehicle control groups. By introducing an intraparenchymal fiberoptic pressure sensor, precise intracranial pressure measurements were obtained in all groups. Cerebral perfusion pressures were calculated with the knowledge of intracranial pressure and mean arterial pressure values. As expected, the intraventricular hemorrhage and vehicle control groups both experienced a rise in the intracranial pressure and subsequent decline in cerebral perfusion pressure during intraventricular injection of autologous blood and artificial cerebrospinal fluid, respectively. The addition of an intraparenchymal fiberoptic pressure sensor is beneficial in monitoring precise intracranial pressure changes.
              Cover page: Intracranial Pressure Monitoring In Nontraumatic Intraventricular Hemorrhage Rodent Model.
              • Article
              UC Merced Undergraduate Research Journal, Volume 10, Issue 1 (2017)
              Our research found that the perception of cannibalism varied across cultures; it has been shown that in some cultures cannibalism can be interpreted as a mental health disorder. We reviewed a total of eight articles that explored cannibalism, antisocial personality disorder, family dysfunction, anger, population density, and cult members. The studies examined the association between mental health disorder and behavioral problems. For the purposes of this review, only one study on Christi Cleek fit the criteria, which were (a) cannibalism amongst individuals, (b) dynamics among cult members, and (c) possible mental health disorders such as antisocial personality disorder. The study was then synthesized with the Sawney Bean Clan case study, a semi-mythical folklore story that was based off an earlier tale on Christi Cleek. The results showed that anger in community members, family dysfunction, and cult behavior could have a possible correlation that is associated with a mental health disorder such as antisocial personality disorder
                Cover page: How Does Mythical Folklore Create a Framework for Mental Health?
                • Article
                • Peer Reviewed
                Adaptive Optics for Extremely Large Telescopes 4 – Conference Proceedings, Volume 1, Issue 1 (2015)
                Laser Guide Star (LGS) reference sources, articially generated at an altitude of 90 km at the atmospheric sodiumlayer, are mandatory to ensure large sky coverage of astronomical Adaptive Optics (AO) systems developed for8m and Extremely Large Telescope (ELT) class telescopes. As a result of the projection eect of an object locatedat a nite distance from the telescope, the AO wavefront sensor (WFS) perceives the LGS as elongated. Thiselongation is a few arcseconds for the 8m class telescopes and can be more than 10 arcseconds for the ELTs. Thiscan pose several challenges when using a Shack-Hartmann wavefront sensor (SHS) such as truncation eects,the requirement for large detectors, and/or the requirement for detectors with geometry that corresponds to thesource shape. In this work, we report the results of numerical simulations focused on the pyramid wavefrontsensor (PWFS) sensitivity when used with a LGS, in this case, a 2D extended object. In addition, the closed-loopperformance of both PWFS and SHS are estimated.
                  Cover page: Use of Laser Guide Star with Pyramid Wavefront Sensor
                  • Article
                  • Peer Reviewed
                  UC Berkeley Previously Published Works (2021)
                  Abstract We address in this work the instrumental systematic errors that can potentially affect the forthcoming and future Cosmic Microwave Background experiments aimed at observing its polarized emission. In particular, we focus on the systematics induced by the beam and calibration, which are considered the major sources of leakage from total intensity measurements to polarization. We simulated synthetic data sets with Time-Ordered Astrophysics Scalable Tools, a publicly available simulation and data analysis package. We also propose a mitigation technique aiming at reducing the leakage by means of a template fitting approach. This technique has shown promising results reducing the leakage by 2 orders of magnitude at the power spectrum level when applied to a realistic simulated data set of the LiteBIRD satellite mission.
                    Cover page: Simulating Calibration and Beam Systematics for a Future CMB Space Mission with the TOAST Package
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2022)
                    Mechanisms underlying memory and cognitive dysfunction following spontaneous intracranial hemorrhage are diverse. The aim of this systematic review was to provide a contemporary review of the commonly reported mechanisms responsible for memory impairment following nontraumatic intracranial hemorrhage. PubMed, Embase, and Scopus databases were systematically searched for pre-clinical studies, and results were reported according to PRISMA guidelines. Methodological quality assessment was performed according to the SYRCLE's Risk of Bias tool. Ninety studies met the inclusion criteria. Most of animal studies reported on subarachnoid hemorrhage (48%), followed by intraparenchymal hemorrhage (44%), and intraventricular hemorrhage (8%). Most of subarachnoid hemorrhage studies (30%) reported neuronal apoptosis as a mechanism for memory dysfunction, whereas the most commonly described mechanism following intraparenchymal hemorrhage (40%) and intraventricular hemorrhage (23%) was a proinflammatory response. Based on SYRCLE's Risk of Bias assessment, the average methodological risk of bias of all studies was 56.83 ± 12.77% on a 0-100% scale. There is a great need not only for more preclinical studies with improved methodology, but also for studies reporting negative treatment effects and for multicenter animal studies. In vivo studies on non-rodent animal ICH models can also be helpful.
                      Cover page: Mechanisms of memory impairment in animal models of nontraumatic intracranial hemorrhage: A systematic review of the literature
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