| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Hong, Yuanyuan, et al.
(author)
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A Multi-Floor Arrayed Waveguide Grating Based Architecture with Grid Topology for Datacenter Networks
- 2020
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In: IEEE Access. - 2169-3536 .- 2169-3536. ; 8, s. 107134-107145
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Journal article (peer-reviewed)abstract
- This paper proposes a grid topology based passive optical interconnect (POI) architecture that is composed of multiple floors of arrayed waveguide grating routers (AWGRs) to offer high connectivity and scalability for datacenter networks. In the proposed POI signal only needs to pass one AWGR, and thus can avoid the crosstalk accumulation and cascaded filtering effects, which exist in many existing POI architectures based on cascaded AWGRs. Meanwhile, due to high connectivity, the proposed grid topology based POI also has the potential advantage of high reliability. Simulation results validate the network performance. With a proper node degree, the proposed grid topology can achieve acceptable blocking probability. Besides, steady performance is kept when the number of floors increases, indicating good scalability of the proposed POI.
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| 3. |
- Hong, Yuanyuan, et al.
(author)
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Elastic all-optical multi-hop interconnection in data centers with adaptive spectrum allocation
- 2017
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In: Optics Communications. - : Elsevier. - 0030-4018 .- 1873-0310. ; 383, s. 478-484
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Journal article (peer-reviewed)abstract
- In this paper, a novel flex-grid all-optical interconnect scheme that supports transparent multi-hop connections in data centers is proposed. An inter-rack all-optical multi-hop connection is realized with an optical loop employed at flex-grid wavelength selective switches (WSSs) in an intermediate rack rather than by relaying through optical-electric-optical (O-E-O) conversions. Compared with the conventional O-E-O based approach, the proposed all-optical scheme is able to off-load the traffic at intermediate racks, leading to a reduction of the power consumption and cost. The transmission performance of the proposed flex-grid multi-hop all-optical interconnect scheme with various modulation formats, including both coherently detected and directly detected approaches, are investigated by Monte-Carlo simulations. To enhance the spectrum efficiency (SE), number-of-hop adaptive bandwidth allocation is introduced. Numerical results show that the SE can be improved by up to 33.3% at 40 Gbps, and by up to 25% at 100 Gbps. The impact of parameters, such as targeted bit error rate (BER) level and insertion loss of components, on the transmission performance of the proposed approach are also explored. The results show that the maximum SE improvement of the adaptive approach over the non-adaptive one is enhanced with the decrease of the targeted BER levels and the component insertion loss.
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| 4. |
- Hong, Yuanyuan, et al.
(author)
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Hybrid Routing and Adaptive Spectrum Allocation for Flex-Grid Optical Interconnects
- 2018
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In: Journal of Optical Communications and Networking. - : Optical Society of America. - 1943-0620 .- 1943-0639. ; 10:5, s. 506-514
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Journal article (peer-reviewed)abstract
- A hybrid routing scheme with an adaptive spectrum assignment is proposed for flex-grid all-optical core switch supporting multihop transparent paths in data center networks. Compared with conventional spectrum assignment algorithms (RSA) developed for a multihop network with optical-electric-optical (OEO) conversion in every hop (i.e., RSA for EO) and that devised for an all-optical multihop network (i.e., RSA for AO), the present RSA algorithm provides better utilization of network resources. Being aware of the all-optical bypass path in hopping, the proposed RSA reduces the blocking probability due to lack of bandwidth-tunable transceivers, which is the major reason for blocking for an RSA for the EO. Similar to the RSA for the AO, the proposed RSA is compatible with the number-of-hops adaptive spectrum assignment, which improves spectrum efficiency. On the other hand, the new algorithm enhances connectivity by eliminating the number-of-hops limitation, which severely constrains the performance of RSA for the AO. Simulations for the system are carried out to investigate the performance of the new algorithm. The impacts of various parameters, such as traffic load, ratio of connection requests with different data rates, and resource configuration on the link cost, are studied in terms of network blocking probability (BP). The achievable traffic load of the proposed RSA under varied connection degrees (i.e., the maximum number of ports that one rack has in order to connect to the core switch) and number of racks is also assessed to keep BP no more than 0.1. The results show that the proposed RSA with appropriate cost functions outperforms the EO and AO, which implies that it has the highest scalability.
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| 5. |
- Hong, Yuanyuan, et al.
(author)
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Neural network-assisted decision-making for adaptive routing strategy in optical datacenter networks
- 2022
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In: Optical Switching and Networking. - : Elsevier BV. - 1573-4277. ; 45
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Journal article (peer-reviewed)abstract
- To improve the blocking probability (BP) performance and enhance the resource utilization, a correct decision of routing strategy which is most adaptable to the network configuration and traffic dynamics is essential for adaptive routing in optical datacenter networks (DCNs). A neural network (NN)-assisted decision-making scheme is proposed to find the optimal routing strategy in optical DCNs by predicting the BP performance for various candidate routing strategies. The features of an optical DCN architecture (i.e., the rack number N, connection degree D, spectral slot number S and optical transceiver number M) and the traffic pattern (i.e., the ratio of requests of various capacities R, and the load of arriving request) are used as the input to the NN to estimate the optimal routing strategy. A case of two-strategy decision in the transparent optical multi-hop interconnected DCN is studied. Three metrics are defined for performance evaluation, which include (a) the ratio of the load range with wrong decision over the whole load range of interest (i.e., decision error E), (b) the maximum BP loss (BPL) and (c) the resource utilization loss (UL) caused by the wrong decision. Numerical results show that the ratio of error-free cases over tested cases always surpasses 83% and the average values of E, BPL and UL are less than 3.0%, 4.0% and 1.2%, respectively, which implies the high accuracy of the proposed scheme. The results validate the feasibility of the proposed scheme which facilitates the autonomous implementation of adaptive routing in optical DCNs.
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| 6. |
- Hong, Yuanyuan, et al.
(author)
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Neural network-assisted routing strategy selection for optical datacenter networks
- 2020
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In: Optics InfoBase Conference Papers. - 2162-2701. - 9781943580828
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Conference paper (peer-reviewed)abstract
- This paper proposes the neural network-assisted routing strategy selection for the optical datacenter networks. Results reveal the high accuracy of strategy selection within the range of interested traffic load, validating feasibility of the proposed scheme.
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| 7. |
- Bi, Meihua, et al.
(author)
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Client scheduling and bandwidth slicing for multiple federated learning tasks over multiple passive optical networks
- 2024
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In: Computer Networks. - 1389-1286. ; 243
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Journal article (peer-reviewed)abstract
- Federated Learning (FL) has attracted extensive attention in facilitating emerging edge intelligence applications for its inherent advantages of ensuring data security and privacy. Especially in the edge computing networks connected by Passive Optical Network (PON) system, FL is introduced to enable applications like autonomous driving, intelligent manufacturing, and precision medicine. However, in this system, the FL deployment over PON inevitably faces challenges induced by the conflict between a large volume of model data with the restrict latency limitation and the confined bandwidth resource of PON, especially for the multiple FL tasks. To address these issues, a novel scheme is proposed for tackling the client distribution and bandwidth allocation problems under the scenario of multiple simultaneous FL tasks supported by the multiple interconnected PON systems, which is consisted of the client scheduling and bandwidth slicing processes. To be specific, an easy-to-implement heuristic algorithm is first performed to assign the client numbers to PONs based on iterative method, with which certain operations are repetitively executed to achieve optimal solutions. And then, the serial bandwidth slicing which adapts the traditional policy, i.e., one-task-per-cycle, to the situation with multiple FL tasks, and parallel slicing with the multi-task-per-cycle, are designed for the investigated system. Furthermore, the simulation system is constructed to verify our method. The corresponding results exhibit that, the largest 43.2 % round time reduction is achieved by client scheduling compared to benchmark without the scheduling. Compared to the benchmark with serial slicing, our scheme can achieve a maximum 50.11 % of the round time decrease. It's also validated that, our proposed client scheduling and parallel bandwidth slicing method can improve the learning efficiency by reducing communication delay, especially for the situation with less client number and smaller FL threshold.
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| 8. |
- Lin, Yuanyuan, et al.
(author)
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Investigation of the Reynolds number independence of cavity flow in 2D street canyons by wind tunnel experiments and numerical simulations
- 2021
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In: Building and Environment. - : Elsevier. - 0360-1323 .- 1873-684X. ; 201
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Journal article (peer-reviewed)abstract
- The Reynolds number independence (Re independence) criterion of Re > 11,000 is widely adopted to fulfill the dynamic similarity between the urban flow modeling and the down-scale measurements. However, for 2D street canyons with H/W ≥ 1.5, experiments, numerical simulations, and in-situ observations have reported different vortex-flow regimes with similar building configurations but at different scales. This study uses both wind tunnel experiments and numerical simulations to revisit the Re-independent flow regimes and Re independence criteria with an extensive Re range for idealized 2D street canyons with various aspect ratios (H/W = 1.1, 2.4, 3, 4, and 5). We introduced an optimized ratio of relative changes (RRCs) to evaluate the flow regimes’ similarity. The wind tunnel experiment confirms that the cavity flow with H/W = 1.1 meets the Re independence when reference building Re (Reref) exceeds 11,000. Simulations validated by the experiment results are conducted to investigate detailed flow regimes and the critical Re (Rec) range for each aspect ratio. The canyons with H/W = 2.4, 3, and 4 are dominated by a single asymmetric vortex when the Re independence is satisfied, while there are two vertically-stacked counter-rotating vortices in the canyon with H/W = 5. The value range of Rec increases with aspect ratio from 1.9 × 104–2.6 × 104 (H/W = 2.4) to 1.3 × 105–2.1 × 105 (H/W = 3), and 2.1 × 106–6.4 × 106 (H/W = 4 and 5). Our results indicate that the fully Re-independent flow regimes in deep canyons have fewer vortices than the literature value with down-scale experiments and simulations. The variant Rec with different aspect ratios suggests the requirement to conduct the Re-independence test for different model configurations.
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| 9. |
- Schweinsberg, Martin, et al.
(author)
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Same data, different conclusions : Radical dispersion in empirical results when independent analysts operationalize and test the same hypothesis
- 2021
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In: Organizational Behavior and Human Decision Processes. - : Elsevier BV. - 0749-5978 .- 1095-9920. ; 165, s. 228-249
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Journal article (peer-reviewed)abstract
- In this crowdsourced initiative, independent analysts used the same dataset to test two hypotheses regarding the effects of scientists' gender and professional status on verbosity during group meetings. Not only the analytic approach but also the operationalizations of key variables were left unconstrained and up to individual analysts. For instance, analysts could choose to operationalize status as job title, institutional ranking, citation counts, or some combination. To maximize transparency regarding the process by which analytic choices are made, the analysts used a platform we developed called DataExplained to justify both preferred and rejected analytic paths in real time. Analyses lacking sufficient detail, reproducible code, or with statistical errors were excluded, resulting in 29 analyses in the final sample. Researchers reported radically different analyses and dispersed empirical outcomes, in a number of cases obtaining significant effects in opposite directions for the same research question. A Boba multiverse analysis demonstrates that decisions about how to operationalize variables explain variability in outcomes above and beyond statistical choices (e.g., covariates). Subjective researcher decisions play a critical role in driving the reported empirical results, underscoring the need for open data, systematic robustness checks, and transparency regarding both analytic paths taken and not taken. Implications for orga-nizations and leaders, whose decision making relies in part on scientific findings, consulting reports, and internal analyses by data scientists, are discussed.
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| 10. |
- Wang, Linqin, et al.
(author)
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Design and synthesis of dopant-free organic hole-transport materials for perovskite solar cells
- 2018
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In: Chemical Communications. - : ROYAL SOC CHEMISTRY. - 1359-7345 .- 1364-548X. ; 54:69, s. 9571-9574
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Journal article (peer-reviewed)abstract
- Two novel dopant-free hole-transport materials (HTMs) with spiro[dibenzo[c,h]xanthene-7,9-fluorene] (SDBXF) skeletons were prepared via facile synthesis routes. A power conversion efficiency of 15.9% in perovskite solar cells is attained by using one HTM without dopants, which is much higher than undoped Spiro-OMeTAD-based devices (10.8%). The crystal structures of both new HTMs were systematically investigated to reveal the reasons behind such differences in performance and to indicate the design principles of more advanced HTMs.
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