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Open Access Publications from the University of California

Scholarly Works (29 results)

  • Article
  • Peer Reviewed
UCLA Previously Published Works (2004)

In this paper, we design a robust scheduling algorithm to ensure worst-case optimal performance when only coarse-grained channel state information (i.e., bounds on channel errors, but not the fine-grained error pattern) is available To solve this problem, we consider two coarse-grained channel error models and take a zero-sum game theoretic approach, in which the scheduler and the channel error act as non-cooperative adversaries in the scheduling process. Our results show that in the heavy channel error case, the optimal scheduler adopts a threshold form. It does not schedule a flow if the price (the flow is willing to pay) is too small, in order to maximize the system revenue. Among the scheduled flows, the scheduler schedules a flow with a probability inversely proportional to the flow price such that the risk of being caught by the channel error adversary is minimized. We also show that in the mild channel error model, the robust scheduling policy exhibits a balanced trade-off between a greedy decision and a conservative policy. The scheduler is likely to take a greedy decision if it evaluates the risk of encountering the channel error adversary now to be small. Therefore, robust scheduling does not always imply conservative decision. The scheduler is willing to take "risks" to expect higher gain in some scenarios. Our solution also shows that probabilistic scheduling may lead to higher worst-case performance compared to traditional deterministic policies. Finally, the current efforts show the feasibility to explore a probabilistic approach to cope with dynamic channel error conditions.

    Cover page: Robust packet scheduling in wireless cellular networks
    • Article
    • Peer Reviewed
    UC Irvine Previously Published Works (2003)

    Transport protocol for supporting multimedia streaming in mobile ad hoc networks has to cope with the rich dynamics, such as mobility-induced disconnection and reconnection, high out-of-order delivery ratios, channel errors, and network congestion. In this work, we design and implementate, ADTFRC, a TCP-friendly transport protocol for ad hoc networks. ADTFRC adapts wireline TFRC protocol to ad hoc networks with improved rate adaptation behavior, the capability of application layer framing and selective retransmission. ADTFRC detects different packet loss behaviors based on end-to-end measurements of multiple metrics. This allows ADTFRC to more accurately gauge the network behavior and achieve higher throughput. Simulations show that the performance of ADTFRC is higher than standard TFRC and TCP with explicit-link-failure-notification (ELFN) support in terms of throughput, rate adaptation behavior and application level quality while still maintaining the TCP-Friendliness property.

      Cover page: TCP friendly rate adaptation for multimedia streaming in mobile ad hoc networks
      • Article
      • Peer Reviewed
      UC Riverside Previously Published Works (2005)

      The assignment of orthologous genes between a pair of genomes is a fundamental and challenging problem in comparative genomics. Existing methods that assign orthologs based on the similarity between DNA or protein sequences may make erroneous assignments when sequence similarity does not clearly delineate the evolutionary relationship among genes of the same families. In this paper, we present a new approach to ortholog assignment that takes into account both sequence similarity and evolutionary events at a genome level, where orthologous genes are assumed to correspond to each other in the most parsimonious evolving scenario under genome rearrangement. First, the problem is formulated as that of computing the signed reversal distance with duplicates between the two genomes of interest. Then, the problem is decomposed into two new optimization problems, called minimum common partition and maximum cycle decomposition, for which efficient heuristic algorithms are given. Following this approach, we have implemented a high-throughput system for assigning orthologs on a genome scale, called SOAR, and tested it on both simulated data and real genome sequence data. Compared to a recent ortholog assignment method based entirely on homology search (called INPARANOID), SOAR shows a marginally better performance in terms of sensitivity on the real data set because it is able to identify several correct orthologous pairs that are missed by INPARANOID. The simulation results demonstrate that SOAR, in general, performs better than the iterated exemplar algorithm in terms of computing the reversal distance and assigning correct orthologs.

        Cover page: Assignment of orthologous genes via genome rearrangement
        • Article
        • Peer Reviewed
        UC Irvine Previously Published Works (2022)
        Resting-state functional magnetic resonance imaging is currently the mainstay of functional neuroimaging and has allowed researchers to identify intrinsic connectivity networks (aka functional networks) at different spatial scales. However, little is known about the temporal profiles of these networks and whether it is best to model them as continuous phenomena in both space and time or, rather, as a set of temporally discrete events. Both categories have been supported by series of studies with promising findings. However, a critical question is whether focusing only on time points presumed to contain isolated neural events and disregarding the rest of the data is missing important information, potentially leading to misleading conclusions. In this work, we argue that brain networks identified within the spontaneous blood oxygenation level-dependent (BOLD) signal are not limited to temporally sparse burst moments and that these event present time points (EPTs) contain valuable but incomplete information about the underlying functional patterns. We focus on the default mode and show evidence that is consistent with its continuous presence in the BOLD signal, including during the event absent time points (EATs), i.e., time points that exhibit minimum activity and are the least likely to contain an event. Moreover, our findings suggest that EPTs may not contain all the available information about their corresponding networks. We observe distinct default mode connectivity patterns obtained from all time points (AllTPs), EPTs, and EATs. We show evidence of robust relationships with schizophrenia symptoms that are both common and unique to each of the sets of time points (AllTPs, EPTs, EATs), likely related to transient patterns of connectivity. Together, these findings indicate the importance of leveraging the full temporal data in functional studies, including those using event-detection approaches.
          Cover page: Moving beyond the 'CAP' of the Iceberg: Intrinsic connectivity networks in fMRI are continuously engaging and overlapping.
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2023)
          BACKGROUND: Recent advances in resting-state fMRI allow us to study spatial dynamics, the phenomenon of brain networks spatially evolving over time. However, most dynamic studies still use subject-specific, spatially-static nodes. As recent studies have demonstrated, incorporating time-resolved spatial properties is crucial for precise functional connectivity estimation and gaining unique insights into brain function. Nevertheless, estimating time-resolved networks poses challenges due to the low signal-to-noise ratio, limited information in short time segments, and uncertain identification of corresponding networks within and between subjects. METHODS: We adapt a reference-informed network estimation technique to capture time-resolved spatial networks and their dynamic spatial integration and segregation. We focus on time-resolved spatial functional network connectivity (spFNC), an estimate of network spatial coupling, to study sex-specific alterations in schizophrenia and their links to multi-factorial genomic data. RESULTS: Our findings are consistent with the dysconnectivity and neurodevelopment hypotheses and align with the cerebello-thalamo-cortical, triple-network, and frontoparietal dysconnectivity models, helping to unify them. The potential unification offers a new understanding of the underlying mechanisms. Notably, the posterior default mode/salience spFNC exhibits sex-specific schizophrenia alteration during the state with the highest global network integration and correlates with genetic risk for schizophrenia. This dysfunction is also reflected in high-dimensional (voxel-level) space in regions with weak functional connectivity to corresponding networks. CONCLUSIONS: Our method can effectively capture spatially dynamic networks, detect nuanced SZ effects, and reveal the intricate relationship of dynamic information to genomic data. The results also underscore the potential of dynamic spatial dependence and weak connectivity in the clinical landscape.
            Cover page: Spatial Dynamic Subspaces Encode Sex-Specific Schizophrenia Disruptions in Transient Network Overlap and its Links to Genetic RiskCreative Commons 'BY-NC-ND' version 4.0 license
            • Article
            • Peer Reviewed
            UC San Diego Previously Published Works (2024)
            Sterile inflammation after myocardial infarction is classically credited to myeloid cells interacting with dead cell debris in the infarct zone1,2. Here we show that cardiomyocytes are the dominant initiators of a previously undescribed type I interferon response in the infarct borderzone. Using spatial transcriptomics analysis in mice and humans, we find that myocardial infarction induces colonies of interferon-induced cells (IFNICs) expressing interferon-stimulated genes decorating the borderzone, where cardiomyocytes experience mechanical stress, nuclear rupture and escape of chromosomal DNA. Cardiomyocyte-selective deletion of Irf3 abrogated IFNIC colonies, whereas mice lacking Irf3 in fibroblasts, macrophages, neutrophils or endothelial cells, Ccr2-deficient mice or plasmacytoid-dendritic-cell-depleted mice did not. Interferons blunted the protective matricellular programs and contractile function of borderzone fibroblasts, and increased vulnerability to pathological remodelling. In mice that died after myocardial infarction, IFNIC colonies were immediately adjacent to sites of ventricular rupture, while mice lacking IFNICs were protected from rupture and exhibited improved survival3. Together, these results reveal a pathological borderzone niche characterized by a cardiomyocyte-initiated innate immune response. We suggest that selective inhibition of IRF3 activation in non-immune cells could limit ischaemic cardiomyopathy while avoiding broad immunosuppression.
              Cover page: Spatially clustered type I interferon responses at injury borderzones
              • Article
              • Peer Reviewed
              UC San Francisco Previously Published Works (2023)
              Despite the known benefits of data-driven approaches, the lack of approaches for identifying functional neuroimaging patterns that capture both individual variations and inter-subject correspondence limits the clinical utility of rsfMRI and its application to single-subject analyses. Here, using rsfMRI data from over 100k individuals across private and public datasets, we identify replicable multi-spatial-scale canonical intrinsic connectivity network (ICN) templates via the use of multi-model-order independent component analysis (ICA). We also study the feasibility of estimating subject-specific ICNs via spatially constrained ICA. The results show that the subject-level ICN estimations vary as a function of the ICN itself, the data length, and the spatial resolution. In general, large-scale ICNs require less data to achieve specific levels of (within- and between-subject) spatial similarity with their templates. Importantly, increasing data length can reduce an ICN's subject-level specificity, suggesting longer scans may not always be desirable. We also find a positive linear relationship between data length and spatial smoothness (possibly due to averaging over intrinsic dynamics), suggesting studies examining optimized data length should consider spatial smoothness. Finally, consistency in spatial similarity between ICNs estimated using the full data and subsets across different data lengths suggests lower within-subject spatial similarity in shorter data is not wholly defined by lower reliability in ICN estimates, but may be an indication of meaningful brain dynamics which average out as data length increases.
                Cover page: Identifying canonical and replicable multi‐scale intrinsic connectivity networks in 100k+ resting‐state fMRI datasets
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2019)
                Sub-picosecond magnetisation manipulation via femtosecond optical pumping has attracted wide attention ever since its original discovery in 1996. However, the spatial evolution of the magnetisation is not yet well understood, in part due to the difficulty in experimentally probing such rapid dynamics. Here, we find evidence of a universal rapid magnetic order recovery in ferrimagnets with perpendicular magnetic anisotropy via nonlinear magnon processes. We identify magnon localisation and coalescence processes, whereby localised magnetic textures nucleate and subsequently interact and grow in accordance with a power law formalism. A hydrodynamic representation of the numerical simulations indicates that the appearance of noncollinear magnetisation via optical pumping establishes exchange-mediated spin currents with an equivalent 100% spin polarised charge current density of 107 A cm-2. Such large spin currents precipitate rapid recovery of magnetic order after optical pumping. The magnon processes discussed here provide new insights for the stabilization of desired meta-stable states.
                  Cover page: Spin-current-mediated rapid magnon localisation and coalescence after ultrafast optical pumping of ferrimagnetic alloys
                  • Article
                  • Peer Reviewed
                  LBL Publications (2021)
                  There are many theories where a dark matter particle is part of a multiplet with an electrically charged state. If WIMP dark matter ($\chi^{0}$) is accompanied by a charged excited state ($\chi^{-}$) separated by a small mass difference, it can form a stable bound state with a nucleus. In supersymmetric models, the $\chi^{0}$ and the $\chi^{-}$ could be the neutralino and a charged slepton, such as the neutralino-stau degenerate model. The formation binding process is expected to result in an energy deposition of {\it O}(1--10 MeV), making it suitable for detection in large liquid scintillator detectors. We describe new constraints on the bound state formation with a xenon nucleus using the KamLAND-Zen 400 Phase-II dataset. In order to enlarge the searchable parameter space, all xenon isotopes in the detector were used. For a benchmark parameter set of $m_{\chi^{0}} = 100$ GeV and $\Delta m = 10$ MeV, this study sets the most stringent upper limits on the recombination cross section $\langle\sigma v\rangle$ and the decay-width of $\chi^{-}$ of $2.0 \times 10^{-31}$ ${\rm cm^3/s}$ and $1.1 \times 10^{-18}$ GeV, respectively (90\% confidence level).
                    Cover page: A Search for Charged Excitation of Dark Matter with the KamLAND-Zen Detector
                    • Article
                    • Peer Reviewed
                    LBL Publications (2023)
                    The KamLAND-Zen experiment has provided stringent constraints on the neutrinoless double-beta (0νββ) decay half-life in ^{136}Xe using a xenon-loaded liquid scintillator. We report an improved search using an upgraded detector with almost double the amount of xenon and an ultralow radioactivity container, corresponding to an exposure of 970 kg yr of ^{136}Xe. These new data provide valuable insight into backgrounds, especially from cosmic muon spallation of xenon, and have required the use of novel background rejection techniques. We obtain a lower limit for the 0νββ decay half-life of T_{1/2}^{0ν}>2.3×10^{26}  yr at 90% C.L., corresponding to upper limits on the effective Majorana neutrino mass of 36-156 meV using commonly adopted nuclear matrix element calculations.
                      Cover page: Search for the Majorana Nature of Neutrinos in the Inverted Mass Ordering Region with KamLAND-Zen
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