283 results on '"So Yokomori"'
Search Results
2. Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy
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Chen, Lujia, Kong, Xiangduo, Johnston, Kevin G., Mortazavi, Ali, Holmes, Todd C., Tan, Zhiqun, Yokomori, Kyoko, and Xu, Xiangmin
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Facioscapulohumeral muscular dystrophy (FSHD) is linked to abnormal derepression of the transcription activator DUX4. This effect is localized to a low percentage of cells, requiring single-cell analysis. However, single-cell/nucleus RNA-seq cannot fully capture the transcriptome of multinucleated large myotubes. To circumvent these issues, we use multiplexed error-robust fluorescent in situ hybridization (MERFISH) spatial transcriptomics that allows profiling of RNA transcripts at a subcellular resolution. We simultaneously examined spatial distributions of 140 genes, including 24 direct DUX4 targets, in in vitro differentiated myotubes and unfused mononuclear cells (MNCs) of control, isogenic D4Z4 contraction mutant and FSHD patient samples, as well as the individual nuclei within them. We find myocyte nuclei segregate into two clusters defined by the expression of DUX4 target genes, which is exclusively found in patient/mutant nuclei, whereas MNCs cluster based on developmental states. Patient/mutant myotubes are found in “FSHD-hi” and “FSHD-lo” states with the former signified by high DUX4 target expression and decreased muscle gene expression. Pseudotime analyses reveal a clear bifurcation of myoblast differentiation into control and FSHD-hi myotube branches, with variable numbers of DUX4 target-expressing nuclei found in multinucleated FSHD-hi myotubes. Gene coexpression modules related to extracellular matrix and stress gene ontologies are significantly altered in patient/mutant myotubes compared with the control. We also identify distinct subpathways within the DUX4 gene network that may differentially contribute to the disease transcriptomic phenotype. Taken together, our MERFISH-based study provides effective gene network profiling of multinucleated cells and identifies FSHD-induced transcriptomic alterations during myoblast differentiation.
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- 2024
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3. Clinical landscape of TP73structural variants in ATL patients
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Hiramatsu, Hiroaki, Yokomori, Rui, Shengyi, Liu, Tanaka, Norio, Mori, Seiichi, Kiyotani, Kazuma, Gotoh, Osamu, Kusumoto, Shigeru, Nakano, Nobuaki, Suehiro, Youko, Ito, Asahi, Choi, Ilseung, Ohtsuka, Eiichi, Hidaka, Michihiro, Nosaka, Kisato, Yoshimitsu, Makoto, Imaizumi, Yoshitaka, Iida, Shinsuke, Utsunomiya, Atae, Noda, Tetsuo, Nishikawa, Hiroyoshi, Ueda, Ryuzo, Sanda, Takaomi, and Ishida, Takashi
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- 2023
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4. Detailed unsteady dynamics of flame-flow interactions during combustion instability and its transition scenario for lean-premixed low-swirl hydrogen turbulent flames.
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Shoji, Takeshi, Tachibana, Shigeru, Nakazumi, Yoshihiro, Fujii, Ryota, Masugi, Judai, and Yokomori, Takeshi
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This experimental study elucidates the unsteady dynamics of flame-flow interactions during unique thermoacoustic instability (TI) and the transition mechanism from stable combustion to TI for lean-premixed hydrogen turbulent jet flames in a low-swirl combustor (LSC), where a swirler assembly consists of an unswirled central region (CR) and an annular swirler region (SR). Simultaneous 200-kHz pressure fluctuation p' measurements and 10-kHz OH* chemiluminescence imaging, as well as 40-kHz stereoscopic particle image velocimetry (SPIV) and two-dimensional PIV measurements for steady-state and transient data acquisitions, respectively, were conducted. The SPIV was performed in multiple planes to explore three-dimensional velocity fields. During TI, periodic flashback was possibly caused by significant axial velocity oscillations, resulting in the local mixture velocity falling below the turbulent flame speed. The large-scale vortex ring generated by the velocity oscillations caused axisymmetric radial velocity V r oscillations with switching signs during the TI period. Similar to a typical low-swirl flow, the positive V r away from the combustor axis created diverging flow, whereas unlike the typical flowfield, the negative V r toward the combustor axis generated converging flow while flattening the axial velocity distributions, which was the signature phenomenon for this TI. Using the transient data and dynamic mode decomposition, variations in delay times between the mixture injection and its convection to a region with positive local Rayleigh indices were investigated. During stable combustion, the mixture jet from the SR predominantly induced thermoacoustic coupling (TC). As the combustion transitioned into the TI, the mixture jet from the CR began to induce TC and, eventually, achieved predominance in inducing TC during fully evolved TI. The transition from the SR jet- into CR jet-dominant TI arising from the dynamic flame-flow interactions resulted from the inherent physical characteristics of hydrogen flames, thereby yielding the larger p' amplitude compared to typical TIs. [ABSTRACT FROM AUTHOR]
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- 2023
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5. TAL1 hijacks MYCN enhancer that induces MYCN expression and dependence on mevalonate pathway in T-cell acute lymphoblastic leukemia
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Tan, Shi Hao, Tan, Tze King, Yokomori, Rui, Liao, Minghui, Huang, Xiao Zi, Yeoh, Allen Eng Juh, and Sanda, Takaomi
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A hallmark of T-cell acute lymphoblastic leukemia (T-ALL) is the dysregulated expression of oncogenic transcription factors (TFs), including TAL1, NOTCH1 and MYC. Rewiring of the transcriptional program disrupts the tightly controlled spatiotemporal expression of downstream target genes, thereby contributing to leukemogenesis. In this study, we first identify an evolutionarily conserved enhancer element controlling the MYCNoncogene (named enhMYCN) that is aberrantly activated by the TAL1 complex in T-ALL cells. TAL1-positive T-ALL cells are highly dependent on MYCN expression for their maintenance in vitro and in xenograft models. Interestingly, MYCN drives the expression of multiple genes involved in the mevalonate pathway, and T-ALL cells are sensitive to inhibition of HMG-CoA reductase (HMGCR), a rate-limiting enzyme of this pathway. Importantly, MYC and MYCN regulate the same targets and compensate for each other. Thus, MYCN-positive T-ALL cells display a dual dependence on the TAL1-MYCN and NOTCH1-MYC pathways. Together, our results demonstrate that enhMYCN-mediated MYCN expression is required for human T-ALL cells and implicate the TAL1-MYCN-HMGCR axis as a potential therapeutic target in T-ALL.
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- 2023
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6. Laminar flame speed of methane/air stratified flames under elevated temperature and pressure.
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Tomidokoro, Takuya, Yokomori, Takeshi, and Im, Hong G.
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Flame propagation under mixture stratification is relevant to a wide range of applications including gas turbine combustors and internal combustion engines. One of the local stratification effects is known as the back-support effect, where the laminar flame speed is modified when a premixed flame propagates into gradually richer or leaner mixtures. A majority of previous studies have focused on the propagation of methane/air stratified flames under standard temperature and pressure. However, stratified combustion often occurs under elevated temperature and pressure in practical applications, which may influence the characteristics of the back support effect through modified reaction pathways. This study performs numerical simulations of stratified laminar counterflow flames under an Atmospheric Temperature and Pressure (ATP) condition and an Elevated Temperature and Pressure (ETP) condition and examines the influence of elevated temperature and pressure on the back-support effect. Reaction flow analyses were extensively conducted to elucidate the difference in the primary reaction pathway between the two conditions. When scaled by the stratification Damköhler number, the back-support effect on the rich-to-lean stratified flame is weaker under the ETP condition than the ATP condition in the stoichiometric to lean region. This is due to increased contribution from reactions involved with OH radicals under the ETP condition, which leads to lower H 2 reproduction in the reaction zone than under the ATP condition. The contribution from OH radicals is increased under the ETP condition because the conversion of H into OH is enhanced. These results suggest that the back-support effect may become negligibly small in practical combustors operating under elevated temperature and pressure due to (1) the flame being less sensitive to stratification because of the thinner flame, and (2) the lower H 2 reproduction that deteriorates the radical production that drives the back-support effect. [ABSTRACT FROM AUTHOR]
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- 2023
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7. Ambipolar Nickel Dithiolene Complex Semiconductors: From One- to Two-Dimensional Electronic Structures Based upon Alkoxy Chain Lengths.
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Ito, Masatoshi, Fujino, Tomoko, Zhang, Lei, Yokomori, So, Higashino, Toshiki, Makiura, Rie, Takeno, Kanokwan Jumtee, Ozaki, Taisuke, and Mori, Hatsumi
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- 2023
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8. Ambipolar Nickel Dithiolene Complex Semiconductors: From One- to Two-Dimensional Electronic Structures Based upon Alkoxy Chain Lengths
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Ito, Masatoshi, Fujino, Tomoko, Zhang, Lei, Yokomori, So, Higashino, Toshiki, Makiura, Rie, Takeno, Kanokwan Jumtee, Ozaki, Taisuke, and Mori, Hatsumi
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Air-stable single-component ambipolar organic semiconductors that conduct both holes and electrons are highly desired but have been rarely realized. Neutral nickel bis(dithiolene) complexes are promising candidates that fulfill the stringent electronic requirements of shallow HOMO levels and deep LUMO levels, which can reduce the carrier injection barrier to overcome the work function of gold electrodes and ensure air stability. However, most nickel bis(dithiolene) analogs that have been characterized as ambipolar semiconductors have twisted molecular structures that hinder the effective intermolecular interactions required for carrier conduction. To address this issue, we synthesized planar alkoxy-substituted nickel bis(dithiolene) analogs that facilitate dense packing with effective intermolecular interactions. Remarkably, changing the methoxy substituents to ethoxy or propoxy groups led to a dramatic change in the packing mode, from one-dimensional to herringbone-like, while maintaining effective intermolecular interactions. These materials overcome the usual trade-off between crystallinity and solubility; they are highly crystalline, even in their film forms, and are highly soluble in organic solvents. They are therefore readily solution-processable to form semiconducting layers with well-defined and well-ordered structures in field-effect transistors. Devices based on these compounds exhibited efficient ambipolar characteristics, even after several months of exposure to air, achieving high carrier mobilities of up to 10–2cm2V–1s–1and large on/off ratios of up to 105, which are the top-class performances achieved for a single-component ambipolar semiconductor material driven in air.
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- 2023
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9. Neutral Radical Molecular Conductors Based on a Gold Dimethoxybenzenedithiolene Complex with and without Crystal Solvent
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Yokomori, So, Dekura, Shun, Ueda, Akira, Higashino, Toshiki, and Mori, Hatsumi
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Two new neutral radical molecular conductors consisting of a gold dimethoxybenzenedithiolene complex have been successfully synthesized. In these crystals, the p–p stacking manners were significantly altered by the formation of weak hydrogen bonds upon the inclusion of a crystal solvent. Reflecting the structural changes, transport and magnetic properties above transition temperatures were modulated by reduced spin dimerization.Two new neutral radical molecular conductors of a gold dimethoxybenzene complex have been successfully synthesized by changing crystallization conditions. The inclusion of the crystal solvent and the formation of weak hydrogen bonds change the p–p stacking manners, which lead to the modulation of transport and magnetic properties by reduced spin dimerization above transition temperatures.
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- 2023
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10. Loss of METTL3 attenuates blastic plasmacytoid dendritic cell neoplasm response to PRMT5 inhibition via IFN signaling
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Rethnam, Malini, Tan, Darren Qiancheng, Tan, Shi Hao, Li, Jia, Yokomori, Rui, Li, Ying, Yang, Henry, Sanda, Takaomi, and Suda, Toshio
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Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and aggressive hematologic malignancy with poor clinical outcomes. Dysregulated MYC expression, which is associated with protein arginine methyltransferase 5 (PRMT5) dependency, is a recurrent feature of BPDCN. Although recent studies have reported a PRMT5 gene signature in BPDCN patient samples, the role of PRMT5 in BPDCN remains unexplored. Here, we demonstrate that BPDCN is highly sensitive to PRMT5 inhibition. Consistent with the upregulation of PRMT5 in BPDCN, we show that pharmacological inhibition (GSK3326595) of PRMT5 inhibits the growth of the patient-derived BPDCN cell line CAL-1 in vitro and mitigated tumor progression in our mouse xenograft model. Interestingly, RNA-sequencing (RNA-seq) analysis revealed that PRMT5 inhibition increases intron retention in several key RNA methylation genes, including METTL3, which was accompanied by a dose-dependent decrease in METTL3 expression. Notably, the function of cellular m6A RNA modification of METTL3 was also affected by PRMT5 inhibition in CAL-1 cells. Intriguingly, METTL3 depletion in CAL-1 caused a significant increase in interferon (IFN) signaling, which was further elevated upon PRMT5 inhibition. Importantly, we discovered that this increase in IFN signaling attenuated the sensitivity of METTL3-depleted CAL-1 cells to PRMT5 inhibition. Correspondingly, stimulation of IFN signaling via TLR7 agonists weakened CAL-1 cell sensitivity to PRMT5 inhibition. Overall, our findings implicate PRMT5 as a therapeutic target in BPDCN and provide insight into the involvement of METTL3 and the IFN pathway in regulating the response to PRMT5 inhibition.
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- 2022
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11. Loss of METTL3 attenuates blastic plasmacytoid dendritic cell neoplasm response to PRMT5 inhibition via IFN signaling
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Rethnam, Malini, Tan, Darren Qiancheng, Tan, Shi Hao, Li, Jia, Yokomori, Rui, Li, Ying, Yang, Henry, Sanda, Takaomi, and Suda, Toshio
- Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and aggressive hematologic malignancy with poor clinical outcomes. Dysregulated MYCexpression, which is associated with protein arginine methyltransferase 5 (PRMT5) dependency, is a recurrent feature of BPDCN. Although recent studies have reported a PRMT5gene signature in BPDCN patient samples, the role of PRMT5 in BPDCN remains unexplored. Here, we demonstrate that BPDCN is highly sensitive to PRMT5 inhibition. Consistent with the upregulation of PRMT5in BPDCN, we show that pharmacological inhibition (GSK3326595) of PRMT5 inhibits the growth of the patient-derived BPDCN cell line CAL-1 in vitro and mitigated tumor progression in our mouse xenograft model. Interestingly, RNA-sequencing (RNA-seq) analysis revealed that PRMT5 inhibition increases intron retention in several key RNA methylation genes, including METTL3, which was accompanied by a dose-dependent decrease in METTL3 expression. Notably, the function of cellular m6A RNA modification of METTL3was also affected by PRMT5 inhibition in CAL-1 cells. Intriguingly, METTL3 depletion in CAL-1 caused a significant increase in interferon (IFN) signaling, which was further elevated upon PRMT5 inhibition. Importantly, we discovered that this increase in IFN signaling attenuated the sensitivity of METTL3-depleted CAL-1 cells to PRMT5 inhibition. Correspondingly, stimulation of IFN signaling via TLR7 agonists weakened CAL-1 cell sensitivity to PRMT5 inhibition. Overall, our findings implicate PRMT5 as a therapeutic target in BPDCN and provide insight into the involvement of METTL3 and the IFN pathway in regulating the response to PRMT5 inhibition.
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- 2022
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12. Requirement for TP73and genetic alterations originating from its intragenic super-enhancer in adult T-cell leukemia
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Ong, Jolynn Zu Lin, Yokomori, Rui, Wong, Regina Wan Ju, Tan, Tze King, Ueda, Ryuzo, Ishida, Takashi, Iida, Shinsuke, and Sanda, Takaomi
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Adult T-cell leukemia/lymphoma (ATL) is a genetically complex hematological malignancy derived from mature T cells. Using an integrative approach, we previously identified genes recurrently associated with super-enhancers in ATL. One of those genes was TP73, a TP53family gene; however, the roles and function of TP73 and its super-enhancer in ATL pathogenesis are poorly understood. Our study demonstrates that TP73 is highly activated under the control of a super-enhancer in ATL cells but not in normal T cells or other hematological malignancies examined. Full-length TP73 is required for ATL cell maintenance in vitro and in vivo via the regulation of cell proliferation and DNA damage response pathways. Notably, recurrent deletions of TP73exons 2–3 were observed in a fraction of primary ATL cases that harbored the super-enhancer, while induction of this deletion in cell lines further increased proliferation and mutational burden. Our study suggests that formation of the TP73intragenic super-enhancer and genetic deletion are likely sequentially acquired in relation to intracellular state of ATL cells, which leads to functional alteration of TP73 that confers additional clonal advantage.
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- 2022
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13. Correction to: TAL1 hijacks MYCN enhancer that induces MYCN expression and dependence on mevalonate pathway in T-cell acute lymphoblastic leukemia
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Tan, Shi Hao, Tan, Tze King, Yokomori, Rui, Liao, Minghui, Huang, Xiao Zi, Yeoh, Allen Eng Juh, and Sanda, Takaomi
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- 2024
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14. Effect of Alkyl Chain Length on Charge Transport Property of Anthracene-Based Organic Semiconductors.
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Zhang, Dongwei, Yokomori, So, Kameyama, Ryohei, Zhao, Changbin, Ueda, Akira, Zhang, Lei, Kumai, Reiji, Murakami, Youichi, Meng, Hong, and Mori, Hatsumi
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- 2021
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15. A computational analysis of strained laminar flame propagation in a stratified CH4/H2/air mixture.
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Tomidokoro, Takuya, Yokomori, Takeshi, Ueda, Toshihisa, and Im, Hong G.
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Propagation of a H 2 -added strained laminar CH 4 /air flame in a rich-to-lean stratified mixture is numerically studied. The back-support effect , which is known to enhance the consumption speed of a flame propagating into a leaner mixture compared to that into a homogeneous mixture, is evaluated. A new method is devised to characterize unsteady reactant-to-reactant counterflow flames under transiently decreasing equivalence ratio, in order to elucidate the influence of flow strain on the back-support effect. In contrast to the conventional reactant-to-product configurations, the current configuration is more relevant to unsteady stratified flames back-supported by their own combustion products. Moreover, since H 2 distribution downstream of the flame is known to play a crucial role in back-supported CH 4 /air flames, the influence of H 2 addition in the upstream mixture is examined. The results suggest that a larger strain rate leads to a larger equivalence ratio gradient at the reaction zone through increased flow divergence, which amplifies the back-support. Meanwhile, since H 2 addition in the upstream mixture does not affect the downstream H 2 content, the relative increase in the consumption speed, i.e. the back-support, is suppressed with larger H 2 addition. Especially, when the upstream H 2 content decreases with the equivalence ratio, the H 2 preferentially diffuses toward the unburned gas, which mitigates H 2 accumulation in the preheat zone and further weakens the back-support. [ABSTRACT FROM AUTHOR]
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- 2020
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16. A new pattern of flame/flow dynamics for lean-premixed, low-swirl hydrogen turbulent jet flames under thermoacoustic instability.
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Shoji, Takeshi, Tachibana, Shigeru, Suzuki, Terukazu, Nakazumi, Yoshihiro, and Yokomori, Takeshi
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This paper presents a phenomenological investigation of a new pattern of lean-premixed hydrogen-flame and flowfield dynamics under thermoacoustic instabilities (TIs) observed inside a low-swirl combustor (LSC) with two combustion chamber lengths of 300 and 500 mm. In this study, the initial bulk inlet velocity was set to V m = 15 m/s. The fuel flow rate was linearly increased while the air flow rate was kept constant, causing a transition from stable operation to TI. Simultaneous time-resolved electronically excited hydroxyl radical (OH*) chemiluminescence imaging and two-dimensional particle image velocimetry were performed along with pressure-fluctuation measurements to investigate spatiotemporal relationships between fluctuating quantities, i.e., OH* chemiluminescence, velocity fields, and pressure, before and after TI onset. A typical TI pattern characterized by a lifted, inverted conical flame caused by diverging, decelerating flow near the injector exit was observed in the long combustor. In contrast, the flame/flow dynamics pattern under TI in the short combustor had strong pressure oscillations and anomalous LSC flame structures which were characterized by a radially flat flame region and counter-rotating vortex pair (CVP) flame structures. In this case, the radial profile of the axial velocity assumed an atypical top-hat-like shape. This feature resulted in thermoacoustic coupling that satisfied the Rayleigh criterion over an almost entirely flat flame region and further strengthened the TI. Thermal expansions of CVP structures served as "converging nozzles" constricting the central flow region. Periodic appearances of this Venturi-like effect caused an alternating diverging (decelerating) and converging (accelerating) flowfield, with a significant peak-to-peak velocity-oscillation amplitude of 15 m/s, equivalent to V m. These pioneering observations regarding LSCs provide further insights into TI mechanisms in hydrogen-fueled gas turbine combustors. [ABSTRACT FROM AUTHOR]
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- 2020
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17. Effect of Alkyl Chain Length on Charge Transport Property of Anthracene-Based Organic Semiconductors
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Zhang, Dongwei, Yokomori, So, Kameyama, Ryohei, Zhao, Changbin, Ueda, Akira, Zhang, Lei, Kumai, Reiji, Murakami, Youichi, Meng, Hong, and Mori, Hatsumi
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Anthracene, a simple planar building block for organic semiconductors, shows strong intermolecular interactions and exhibits strong blue fluorescence. Thus, its derivatives have a great potential to integrate considerable charge carrier mobility and strong emission within a molecule. Here, we systematically studied the influence of alkyl chain length on the crystal structures, thermal properties, photophysical characteristics, electrochemical behaviors, and mobilities for a series of 2,6-di(4-alkyl-phenyl)anthracenes (Cn-Ph-Ants, where nrepresents the alkyl chain length). Among them, Cn-Ph-Ants (n= 0, 1, 2, and 3) display similar layered herringbone (LHB) packing motifs, which facilitate two-dimensional charge transport and thereby enables high-performance organic field-effect transistors (OFETs). All Cn-Ph-Ants exhibit similar work functions and show strong blue fluorescence with photoluminescence quantum yields (PLQY) of approximately 40% in toluene. In addition, the absolute powder PLQYs of C0-, C2-, C3-, C4-, and C6-Ph-Ants are 24.6, 8.2, 5.7, 10.9, and 8.6%, respectively. Note that the alkyl chain length shows a significant effect on the charge mobilities of Cn-Ph-Ants. Our newly synthesized C1-, C3-, and C4-Ph-Ants show hole mobilities of up to 2.40, 1.34, and 1.00 cm2V–1s–1, respectively, with mobilities of 3.40, 1.57, and 0.82 cm2V–1s–1for C0-, C2-, and C6-Ph-Ants, indicating an increasing tendency of mobility with shorter alkyl chain length. This feature is related to the microstructures of the thin films, which reveal the enhanced film order, crystallinity, and grain size with a decrease in the alkyl chain length. Moreover, we theoretically analyze the intermolecular transfer integrals of HOMOs, which increase at T-shaped contacts as the alkyl chain length decreases, which improves the intermolecular charge transport properties, leading to the increases in mobility. Interestingly, the anisotropy of the transfer integral tends to decrease upon substitution with longer alkyl chains, suggesting that alkyl chain adjustments may facilitate isotropic charge transport property in 2,6-alkylated anthracenes.
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- 2021
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18. Prostaglandin E-major urinary metabolite as a noninvasive surrogate marker for infantile necrotizing enterocolitis.
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Konishi, Ken-ichiro, Yoshida, Mariko, Nakao, Atsushi, Tsuchiya, Keiji, Tsurisawa, Chisa, Ichiki, Kunihiko, Takeda, Tomohiro, Hisaeda, Yoshiya, Hirota, Atsushi, Amagata, Shusuke, Odashima, Takayuki, Yokomori, Kinji, Ishida, Kazuo, Matsuura, Masaaki, Ito, Satoru, Fujiwara, Mutsunori, and Nakahara, Saori
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Early definitive diagnosis of necrotizing enterocolitis (NEC) based on Bell's staging criteria is difficult because there are few observable changes on abdominal imaging and blood chemistry tests at the onset of the disease. To investigate whether prostaglandin E-2 major urinary metabolite (PGE-MUM) can be a useful surrogate marker reflecting the disease state and severity of NEC in infants. Infants were enrolled in this study between January 2014 and December 2016. NEC diagnosis was based on Bell's staging criteria > Stage II or necrotic bowel observed at surgery. After diagnosis, PGE-MUM level was measured and compared with that of the other disease and healthy infant groups. Median PGE-MUM value was highest in the NEC group (576 [65–3672] μg/g•Cre/BSA × 1000), followed by the other disease group (94 [57–296] μg/g•Cre/BSA × 1000) and the healthy infant group (19 [10–44] μg/g•Cre/BSA × 1000) (sensitivity: 92.3%, specificity: 81.5%, accuracy: 85.0%; p < 0.01). PGE-MUM level correlated with improved status of NEC, length of necrotic intestine, and Bell's staging criteria. PGE-MUM level may be a useful surrogate biomarker reflecting the disease state of NEC. The method of urine sample collection is also advantageous, being noninvasive for infants. This is the first study reporting PGE-MUM level in NEC. Study of diagnostic test. LEVEL II. [ABSTRACT FROM AUTHOR]
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- 2019
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19. Study of a thermo-acoustic instability triggering in a low-swirl burner using simultaneous time-resolved acetone and OH-PLIF.
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Renaud, Antoine, Yokomori, Takeshi, and Tachibana, Shigeru
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Abstract A low-swirl burner operating in premixed mode with methane and air is studied using high-speed acetone and OH-PLIF and advanced post-processing methods. In a transient operating point where the equivalence ratio is slowly increased while keeping the bulk velocity constant, a thermo-acoustic instability is found to grow and generate large pressure fluctuations in the combustion chamber. The instability is maintained by bursts of flame in phase with the pressure fluctuation cycle. It is found that these bursts are amplified by the fact that the boundaries of the flame arms are fluctuating in phase. This phasing of the arms' boundaries is due to the change in flame speed coming from the increase of equivalence ratio. [ABSTRACT FROM AUTHOR]
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- 2019
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20. Triplet-Mediator Ligand-Protected Metal Nanocluster Sensitizers for Photon Upconversion
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Arima, Daichi, Hidaka, Shion, Yokomori, So, Niihori, Yoshiki, Negishi, Yuichi, Oyaizu, Ryuichi, Yoshinami, Takumi, Kobayashi, Kenji, and Mitsui, Masaaki
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Triplet–triplet annihilation photon upconversion (TTA-UC) is attracting a great deal of attention as a viable approach to exploit unutilized wavelengths of light in solar-driven devices. Recently, ligand-protected metal nanoclusters have emerged as a compelling platform for serving as triplet sensitizers for TTA-UC. In this study, we developed an atomically precise, triplet-mediator ligand (TL)-protected metal nanocluster, Au2Cu6(S-Adm)6[P(DPA)3]2(Au2Cu6DPA; S-Adm = 1-adamanthanethiolate, DPA = 9,10-diphenylanthracene). In Au2Cu6DPA, the excitation of the Au2Cu6core rapidly generates a metal-to-ligand charge transfer state, followed by the formation of the long-lived triplet state (approximately 150 μs) at a DPA site in the TL. By combining Au2Cu6DPAwith a DPA annihilator, we achieved a red-to-blue upconversion quantum yield (ΦUCg) of 20.7 ± 0.4% (50% max.) with a low threshold excitation intensity of 36 mW cm–2at 640 nm. This quantum yield almost reaches the maximum limit achievable using a DPA annihilator and establishes a record-setting value, outperforming previously reported nanocrystal and nanocluster sensitizers. Furthermore, strong upconversion emission based on a pseudo-first-order TTA process was observed under 1 sun illumination, indicating that the Au2Cu6DPAsensitizer holds promise for applications in solar-energy-based systems.
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- 2024
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21. Deciphering the regulatory landscape of murine splenic response to anemic stress at single-cell resolution
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Yang, Chong, Yokomori, Rui, Chua, Lee Hui, Tan, Shi Hao, Koh, Mun Yee, Totani, Haruhito, Sanda, Takaomi, and Suda, Toshio
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•Distinct developmental phases and a "hiatus" quiescent subpopulation were identified in emerging erythroid cells under anemic stress.•CD81, identified as a novel marker for central macrophages in erythroblastic islands, is functionally required for combating anemic stress.
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- 2024
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22. Whole Exome Sequencing Analysis of Diffuse Large B-Cell Lymphoma That Progressed to Central Nervous System
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Suzuki, Tomotaka, Yokomori, Rui, Sanda, Takaomi, Yano, Hiroki, Kikuchi, Takaki, Kanamori, Takashi, Inagaki, Atsushi, Yoshida, Takashi, Kayukawa, Satoshi, Oshima, Yoshiko, Sasaki, Hirokazu, Kinoshita, Shiori, Narita, Tomoko, Masaki, Ayako, Ri, Masaki, Kusumoto, Shigeru, Komatsu, Hirokazu, Inagaki, Hiroshi, and Iida, Shinsuke
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Background: Recent sequencing analyses have identified distinct genetic subtypes of diffuse large B-cell lymphoma (DLBCL). The MCD subtype, characterized by MYD88L265P and CD79Bgene mutations, is frequently found in DLBCL that progresses to the central nervous system (CNS), known as secondary CNS lymphoma (sCNSL) (Ollila, Blood 2021). In addition, the MCD subtype is also frequently found in primary CNS lymphoma (PCNSL) (Radke, Nat commun 2022). Therefore, we hypothesized that specific genetic alterations that are present in the initial DLBCL tumors are associated with their progression to the CNS. We aimed to investigate i) the clinical impact of genetic subtypes of DLBCL and ii) genomic mutations that may be associated with sCNSL. To this end, genetic alterations in DLBCL samples at diagnosis that later developed into sCNSL were evaluated using whole-exome sequencing (WES).
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- 2023
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23. NAD+ consumption by PARP1 in response to DNA damage triggers metabolic shift critical for damaged cell survival
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Murata, Michael M., Kong, Xiangduo, Moncada, Emmanuel, Chen, Yumay, Imamura, Hiromi, Wang, Ping, Berns, Michael W., Yokomori, Kyoko, and Digman, Michelle A.
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We show that the phasor-FLIM approach serves as a unique tool to monitor damage-induced metabolic changes in real time, revealing cell-wide NADH dynamics in response to nuclear DNA damage and that NAD+ consumption by PARP1 triggers an increase in metabolic reliance to oxidative phosphorylation, which is critical for damaged cell survival.
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- 2019
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24. Roles of the SWI/SNF Chromatin Remodelling Factors in Sustaining Oncogenic Transcription Program in T-Cell Acute Lymphoblastic Leukaemia
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Kim, Hyoju, Tan, Tze King, Huang, Xiao Zi, Ong, Jolynn, Yokomori, Rui, Yeoh, Allen Eng Juh, Sanda, Takaomi, and Tan, Shi Hao
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- 2022
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25. Roles of the SWI/SNF Chromatin Remodelling Factors in Sustaining Oncogenic Transcription Program in T-Cell Acute Lymphoblastic Leukaemia
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Kim, Hyoju, Tan, Tze King, Huang, Xiao Zi, Ong, Jolynn, Yokomori, Rui, Yeoh, Allen Eng Juh, Sanda, Takaomi, and Tan, Shi Hao
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- 2022
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26. The effect of Nipped-B-like (Nipbl) haploinsufficiency on genome-wide cohesin binding and target gene expression: modeling Cornelia de Lange syndrome.
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Newkirk, Daniel A., Yen-Yun Chen, Richard Chien, Weihua Zeng, Biesinger, Jacob, Flowers, Ebony, Kawauchi, Shimako, Santos, Rosaysela, Calof, Anne L., Lander, Arthur D., Xiaohui Xie, and Kyoko Yokomori
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- 2017
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27. Exploration into a New Dicarboxylic Acid Derived from Ricinoleic Acid for High-Performance Aluminum Electrolytic Capacitors
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Mizota, Isao, Umeshima, Satoshi, Matsunaga, Sei, Isomura, Rinpei, Nakahama, Kenta, Shimizu, Makoto, Yokomori, Yorozu, Umemura, Tokihiro, Kuroki, Noburo, Kiyosawa, Junich, and Tanaka, Hiroyuki
- Abstract
New dicarboxylic acids were synthesized from ricinoleic acid in 3–8 steps in good overall yields, and they were found to be effective as an electrolyte in aluminum electrolytic capacitors. These types of dicarboxylic acids show good heat-resistance and higher withstand voltage than conventional electrolytes.New dicarboxylic acids were synthesized from ricinoleic acid in 3–8 steps in good overall yields, and they were found to be effective as an electrolyte in aluminum electrolytic capacitors. These types of dicarboxylic acids show good heat resistance and a higher withstand voltage than conventional electrolytes.
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- 2016
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28. Cancer-associated fibroblasts promote venous thrombosis through podoplanin/CLEC-2 interaction in podoplanin-negative lung cancer mouse model
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Shirai, Toshiaki, Tsukiji, Nagaharu, Sasaki, Tomoyuki, Oishi, Saori, Yokomori, Ryohei, Takano, Katsuhiro, and Suzuki-Inoue, Katsue
- Abstract
Cancer-associated thrombosis (CAT) is the leading cause of morbidity and mortality. Cancer-associated fibroblasts (CAFs) are a prominent component of the tumor microenvironment that contributes to cancer progression through direct cell–cell interactions and the release of extracellular vesicles (EVs). However, the role of CAFs in CAT remains unclear.
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- 2023
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29. Mitochondria transfer mediates stress erythropoiesis by altering the bioenergetic profiles of early erythroblasts through CD47
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Yang, Chong, Yokomori, Rui, Chua, Lee Hui, Tan, Shi Hao, Tan, Darren Qiancheng, Miharada, Kenichi, Sanda, Takaomi, and Suda, Toshio
- Abstract
Intercellular mitochondria transfer is a biological phenomenon implicated in diverse biological processes. However, the physiological role of this phenomenon remains understudied between erythroblasts and their erythroblastic island (EBI) macrophage niche. To gain further insights into the mitochondria transfer functions, we infused EBI macrophages in vivo into mice subjected to different modes of anemic stresses. Interestingly, we observed the occurrence of mitochondria transfer events from the infused EBI macrophages to early stages of erythroblasts coupled with enhanced erythroid recovery. Single-cell RNA-sequencing analysis on erythroblasts receiving exogenous mitochondria revealed a subset of highly proliferative and metabolically active erythroid populations marked by high expression of CD47. Furthermore, CD47 or Sirpα blockade leads to a decline in both the occurrence of mitochondria transfer events and their mediated erythroid recovery. Hence, these data indicate a significant role of mitochondria transfer in the enhancement of erythroid recovery from stress through the alteration of the bioenergetic profiles via CD47–Sirpα interaction in the early stages of erythroblasts.
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- 2022
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30. Acute Anemic Stress Is Modulated By Intercellular Mitochondria Transport from Erythroblastic Island Macrophages to Early Erythroblasts Via CD47-Sirpα Interactions
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Yang, Chong, Yokomori, Rui, Chua, Lee Hui, Sanda, Takaomi, and Suda, Toshio
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- 2022
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31. Acute Anemic Stress Is Modulated By Intercellular Mitochondria Transport from Erythroblastic Island Macrophages to Early Erythroblasts Via CD47-Sirpα Interactions
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Yang, Chong, Yokomori, Rui, Chua, Lee Hui, Sanda, Takaomi, and Suda, Toshio
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- 2022
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32. Automating the DNA Computer: Solving n-Variable 3-SAT Problems.
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Chengde Mao, Yokomori, Takashi, and Johnson, Clifford R.
- Abstract
In the decade since the first molecular computation was performed, it has been shown that DNA molecules can perform sophisticated, massively parallel computations avoiding the Von Neumann bottleneck. However, progress in the field has been slow. The largest problem solved to date is an instance of the 20-variable 3-CNF SAT problem. Performing the computation took more than two man-weeks to complete because every aspect of the computation was performed by hand. Molecular computations are extremely labor intensive and error prone-automation is necessary for further progress. The next step, (the second generation DNA computer - that of taking the laborious, laboratory bench protocols performed by hand, and automating them), has been achieved with the construction of an automated DNA computer dubbed EDNAC. It employs the same paradigm that was used to solve the labor-intensive instance of the 20-variable 3-CNF SAT problem. Using a combinatorial DNA library and complementary probes, EDNAC solves instances of the n-variable 3-CNF SAT problem. A 10 variable instance of the 3-CNF SAT problem was essayed. The computation took 28 hours to perform. EDNAC correctly computed nine of the ten variables, with a tenth variable remaining ambiguous. This result is comparable to current results in the molecular computation community. This research tested the critical properties, such as complexity, robustness, reliability, and repeatability necessary for the successful automation of a molecular computer. [ABSTRACT FROM AUTHOR]
- Published
- 2006
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33. Local Area Manipulation of DNA Molecules for Photonic DNA Memory.
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Chengde Mao, Yokomori, Takashi, Shogenji, Rui, Tate, Naoya, Beppu, Taro, Ogura, Yusuke, and Tanida, Jun
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The address space in DNA memory can be extended by combining information of spatial position and base sequences. Controlling the states of DNA in a local area is an essential technique to use positional information. In this paper, we focus on a photonic DNA memory, which uses optical techniques for addressing on the basis of positional information. We present the concept of photonic DNA memory and describe the read out method using local area manipulation of DNA molecules. [ABSTRACT FROM AUTHOR]
- Published
- 2006
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34. A New Readout Approach in DNA Computing Based on Real-Time PCR with TaqMan Probes.
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Chengde Mao, Yokomori, Takashi, Ibrahim, Zuwairie, Rose, John A., Tsuboi, Yusei, Ono, Osamu, and Khalid, Marzuki
- Abstract
A new readout approach for the Hamiltonian Path Problem (HPP) in DNA computing based on the real-time polymerase chain reaction (PCR) is investigated. Several types of fluorescent probes and detection mechanisms are currently employed in real-time PCR, including SYBR Green, molecular beacons, and hybridization probes. In this study, real-time amplification performed using the TaqMan probes is adopted, as the TaqMan detection mechanism can be exploited for the design and development of the proposed readout approach. Double-stranded DNA molecules of length 120 base-pairs are selected as the input molecules, which represent the solving path for an HPP instance. These input molecules are prepared via the self-assembly of 20-mer and 30-mer single-stranded DNAs, by parallel overlap assembly. The proposed readout approach consists of two steps: real-time amplification in vitro using TaqMan-based real-time PCR, followed by information processing in silico to assess the results of real-time amplification, which in turn, enables extraction of the Hamiltonian path. The performance of the proposed approach is compared with that of conventional graduated PCR. Experimental results establish the superior performance of the proposed approach, relative to graduated PCR, in terms of implementation time. [ABSTRACT FROM AUTHOR]
- Published
- 2006
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35. Experimental Validation of the Statistical Thermodynamic Model for Prediction of the Behavior of Autonomous Molecular Computers Based on DNA Hairpin Formation.
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Chengde Mao, Yokomori, Takashi, Komiya, Ken, Yaegashi, Satsuki, Hagiya, Masami, Suyama, Akira, and Rose, John A.
- Abstract
Due to the multi-state nature of autonomous computing systems, it is important to develop a simulation model which accounts for process coupling, and allows the precise prediction of the behavior of a composite system formed by a series of competing reactions, in which each intermediate step is difficult to probe. In this work, the statistical thermodynamic apparatus for predicting the efficiency of DNA hairpin-based computers is validated experimentally. The model system employed is a simple competitive folding system, formed by two competing hairpin structures (sub-optimal vs. optimal), with the intent of testing the ability to predict the efficiency of target structure formation in the presence of a non-target structure. System behavior was characterized via a set of fluorescence measurement experiments, to directly determine the fractional occupancy of target structures versus temperature. Predicted and experimental behaviors are compared for both the melting of each of the two isolated hairpin structures (control), and the efficiency of the competitive composite system. Results indicate that the applied equilibrium model provides predictions which consistently agree with experimental results, supporting design for the control and programming of DNA-based systems. [ABSTRACT FROM AUTHOR]
- Published
- 2006
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36. Development of DNA Relational Database and Data Manipulation Experiments.
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Chengde Mao, Yokomori, Takashi, Yamamoto, Masahito, Kita, Yutaka, Kashiwamura, Satoshi, Kameda, Atsushi, and Ohuchi, Azuma
- Abstract
An enormous amount of data such as genomic data can be stored into DNA molecules as base sequences. DNA database is important for organizing and maintaining these data, because extracted data from DNA database can be directly manipulated by chemical reactions. In this paper, we develop a DNA relational database with a simple data model and realize a computational model (relational algebra) of data manipulation as a sequence of chemical experiments. By using the developed database, it is shown that we can execute query operations based on the contents of data (the values of attributes). Furthermore, we propose a conversion scheme of query input to a series of experiment operations. [ABSTRACT FROM AUTHOR]
- Published
- 2006
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37. MethyLogic: Implementation of Boolean Logic Using DNA Methylation.
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Chengde Mao, Yokomori, Takashi, Dimitrova, Nevenka, and Gal, Susannah
- Abstract
The MethyLogic method performs flexible and reversible modification of DNA in order to establish the logical value of true or false for a set of clauses. It combines both the biological meaning and experimental procedure with the logical implementation of the basic Boolean operators: OR, AND, and NOT. The original feature of methylation logic, MethyLogic, is the use of the reversibility of DNA methylation of cytosine and adenine. Logic variables can be negated by reversing the DNA methylation status. We introduce four implementation scenarios: three of them use methyl-sensitive restriction enzymes and the fourth uses methyl-binding proteins. Encoding can use either single or double-stranded DNA. In addition, we show how to solve a three variable SAT problem and how to implement a logic circuit. [ABSTRACT FROM AUTHOR]
- Published
- 2006
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38. Displacement Whiplash PCR: Optimized Architecture and Experimental Validation.
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Chengde Mao, Yokomori, Takashi, Rose, John A., Komiya, Ken, Yaegashi, Satsuki, and Hagiya, Masami
- Abstract
Whiplash PCR-based methods of biomolecular computation (BMC), while highly-versatile in principle, are well-known to suffer from a simple but serious form of self-poisoning known as back-hybridization. In this work, an optimally re-engineered WPCR-based architecture, Displacement Whiplash PCR (DWPCR) is proposed and experimentally validated. DWPCR's new rule protect biostep, which is based on the primer-targeted strand-displacement of back-hybridized hairpins, renders the most recently implemented rule-block of each strand unavailable, abolishing back-hybridization after each round of extension. In addition to attaining a near-ideal efficiency, DWPCR's ability to support isothermal operation at physiological temperatures eliminates the need for thermal cycling, and opens the door for potential biological applications. DWPCR should also be capable of supporting programmable exon shuffling, allowing XWPCR, a proposed method for programmable protein evolution, to more closely imitate natural evolving systems. DWPCR is expected to realize a highly-efficient, versatile platform for routine and efficient massively parallel BMC. [ABSTRACT FROM AUTHOR]
- Published
- 2006
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39. Unravel Four Hairpins!
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Chengde Mao, Yokomori, Takashi, Kameda, Atsushi, Yamamoto, Masahito, Ohuchi, Azuma, Yaegashi, Satsuki, and Hagiya, Masami
- Abstract
DNA machines consisting of consecutive hairpins, which we have previously described, have various potential applications in DNA computation. In the present study, a 288-base DNA machine containing four consecutive hairpins was successfully constructed by ligation and PCR. PAGE and fluorescence spectroscopy experiments verified that all four hairpins were successfully opened by four opener oligomers, and that hairpin opening was dependent on the proper openers added in the correct order. Quantitative analysis of the final results by fluorescence spectroscopy indicated that all four hairpins were open in about 1/4 to 1/3 of the DNA machines. [ABSTRACT FROM AUTHOR]
- Published
- 2006
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- View/download PDF
40. "Reasoning" and "Talking" DNA: Can DNA Understand English?
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Chengde Mao, Yokomori, Takashi, Bobba, Kiran C., Neel, Andrew J., Phan, Vinhthuy, and Garzon, Max H.
- Abstract
Memory is a fundamental challenge in computing, particularly if they are to store large amounts of interrelated data based on content and be queried associatively to retrieve information useful to the owners of the storage, such as self-assembled DNA structures, cells, and biological organisms. New methods to encode large data sets compactly on DNA chips have been recently proposed in (Garzon & Deaton, 2004) [6]. The method consists of shredding the data into short oligonucleotides and pouring it over a DNA chip with spots populated by copies of a basis set of noncrosshybridizing strands. In this paper, we probe into the capacity of these memories in terms of their ability to discern semantic relationships and discriminate information in complex contexts in two applications, as opposed to their raw capacity to store volumes of uncorrelated data. First, we show that DNA memories can be designed to store information about English texts so that they can "conduct a conversation" about their content with an interlocutor who wants to learn about the subject contained in the memories. In this preliminary approach, the results are competitive, if not better, with state-of-the-art methods in conventional artificial intelligence. In a second application in biology, we show how a biomolecular computing analysis based on similar techniques can be used to re-design DNA microarrays in order to increase their sensitivity to the level required for successful discrimination of conditions that may escape detection by standard methods. Finally, we briefly discuss the scalability of the common technique to large amounts of data given recent advances in the design of noncrosshybridizing DNA oligo sets, as well other applications in bioinformatics and medical diagnosis. Keywords: Semantic analysis and information retrieval; DNA chips and microarrays; question answering; sensitivy analysis; data classification and discrimination. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
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41. Abstraction Layers for Scalable Microfluidic Biocomputers.
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Chengde Mao, Yokomori, Takashi, Thies, William, Urbanski, John Paul, Thorsen, Todd, and Amarasinghe, Saman
- Abstract
Microfluidic devices are emerging as an attractive technology for automatically orchestrating the reactions needed in a biological computer. Thousands of microfluidic primitives have already been integrated on a single chip, and recent trends indicate that the hardware complexity is increasing at rates comparable to Moore's Law. As in the case of silicon, it will be critical to develop abstraction layers—such as programming languages and Instruction Set Architectures (ISAs)—that decouple software development from changes in the underlying device technology. Towards this end, this paper presents BioStream, a portable language for describing biology protocols, and the Fluidic ISA, a stable interface for microfluidic chip designers. A novel algorithm translates microfluidic mixing operations from the BioStream layer to the Fluidic ISA. To demonstrate the benefits of these abstraction layers, we build two microfluidic chips that can both execute BioStream code despite significant differences at the device level. We consider this to be an important step towards building scalable biological computers. [ABSTRACT FROM AUTHOR]
- Published
- 2006
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42. Fuzzy Forecasting with DNA Computing.
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Chengde Mao, Yokomori, Takashi, Jeng, Don Jyh-Fu, Watada, Junzo, Berlin Wu, and Jui-Yu Wu
- Abstract
There are many forecasting techniques including: exponential smoothing, ARIMA model, GARCH model, neural networks and genetic algorithm, etc. Since financial time series may be influenced by many factors, conventional model based techniques and hard computing methods seem inadequate in the prediction. Those methods, however, have their drawbacks and advantages. In recent years, the innovation and improvement of forecasting techniques have caught more attention, and also provides indispensable information in decision-making process. In this paper, a new forecasting technique, named DNA forecasting, is developed. This may be of use to a nonlinear time series forecasting. The methods combined the mathematical, computational, and biological sciences. In the empirical study, we demonstrated a novel approach to forecast the exchange rates through DNA. The mean absolute forecasting accuracy method is defined and used in evaluating the performance of linguistic forecasting. The comparison with ARIMA model is also illustrated. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
- View/download PDF
43. DNA Hypernetworks for Information Storage and Retrieval.
- Author
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Chengde Mao, Yokomori, Takashi, Byoung-Tak Zhang, and Joo-Kyung Kim
- Abstract
Content-addressability is a fundamental feature of human memory underlying many associative information retrieval tasks. In contrast to location-based memory devices, content-addressable memories require complex interactions between memory elements, which makes conventional computation paradigms difficult. Here we present a molecular computational model of content-addressable information storage and retrieval which makes use of the massive interaction capability of DNA molecules in a reaction chamber. This model is based on the "hypernetwork" architecture which is an undirected hypergraph of weighted edges. We describe the theoretical basis of the hypernetwork model of associative memory and its realization in DNA-based computing. A molecular algorithm is derived for automatic storage of data into the hypernetwork, and its performance is examined on an image data set. In particular, we study the effect of the hyperedge cardinality and error tolerance on the associative recall performance. Our simulation results demonstrate that short DNA strands in a vast number can be effective in some pattern information processing tasks whose implementation is within reach of current DNA nanotechnology. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
- View/download PDF
44. Simulations of Microreactors: The Order of Things.
- Author
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Chengde Mao, Yokomori, Takashi, Ibershoff, Joseph, Jaromczyk, Jerzy W., and Noort, Danny
- Abstract
Simulations are needed to predict various parameters for chemical reactions and error propagation in microfluidic networks. This paper studies the impact of the order of microreactors implementing a fluidic network on the error in solutions for Boolean expressions. Additionally, we present a computer program that augments the software toolkit introduced in our previous work. The program is useful for simulating microfluidics; we present an example from DNA computing. It monitors the concentration of every molecule throughout the fluidic network and assists in predicting how the layout of the network contributes to the error in the DNA computation. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
- View/download PDF
45. A Probabilistic Model of the DNA Conformational Change.
- Author
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Chengde Mao, Yokomori, Takashi, Shiozaki, Masashi, Ono, Hirotaka, Sadakane, Kunihiko, and Yamashita, Masafumi
- Abstract
Predicting the behavior of DNA molecules in vitro is one of the most fundamental issues on DNA computing, but is also known to be quite difficult. Shiozaki et al. proposed a probabilistic model that can simulate many features of biochemical experiments in terms of the reaction rate [7], although there are several differences between the biochemical experiments and the computational simulations on the model. In this paper, we extend the model to support base pairs construction among k DNA sequences, which plays an essential role in realizing branch migrations. The simulation results have much more similarities to the biochemical experiments results than ones on the previous model, which implies that the analysis of the model may give some insight about the reaction rate. Through the analysis, we conclude this paper by giving a guideline for designing DNA sequences that can quickly react. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
- View/download PDF
46. Uniquimer: A de Novo DNA Sequence Generation Computer Software for DNA Self-assembly.
- Author
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Chengde Mao, Yokomori, Takashi, Bryan Wei, Zhengyu Wang, and Yongli Mi
- Abstract
We developed a computer-software with graphic interfaces for generating de novo DNA sequences of various DNA motifs for DNA nanotechnology research. The software is free of charge for academic and non-profit organizations. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
- View/download PDF
47. A Mathematical Approach to Cross-Linked Structures in Viral Capsids: Predicting the Architecture of Novel Containers for Drug Delivery.
- Author
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Chengde Mao, Yokomori, Takashi, and Keef, Thomas
- Abstract
Understanding the structure of viruses is an important first step in terms of many applications in virology, including the protein engineering of containers to enable more effective drug delivery. In particular, the viral capsids, i.e. the protective shells on the exterior of viruses containing the important genetic code, play an important role in the context of gene therapy, where small amounts of therapeutic DNA is packaged into a capsid which then penetrates the cell membrane and delivers its payload. Cross-linking structures are particular additional covalent bonds that can occur in addition to the already present hydrophobic interactions and hydrogen bonds between the proteins. Their importance lies in the fact that they render the capsid particularly stable. Here we shall introduce a mathematical method to predict possible locations for these additional bonds of cross-linking. We will give examples of failed cases as well as of cases where cross-linking structures are possible. These results serve as a pointer for experimentalists as to which types of cross-linking structures may possibly be engineered and exploited in the framework of drug delivery. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
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48. A Framework for Modeling DNA Based Molecular Systems.
- Author
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Chengde Mao, Yokomori, Takashi, Sahu, Sudheer, Wang, Bei, and Reif, John H.
- Abstract
In this paper, we propose a framework for a discrete event simulator for simulating the DNA based nano-robotical systems. We describe a physical model that captures the conformational changes of the solute molecules. We also present methods to simulate various chemical reactions due to the molecular collisions, including hybridization, dehybridization and strand displacement. The feasibility of such a framework is demonstrated by some preliminary results. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
- View/download PDF
49. Capabilities and Limits of Compact Error Resilience Methods for Algorithmic Self-assembly in Two and Three Dimensions.
- Author
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Chengde Mao, Yokomori, Takashi, Sahu, Sudheer, and Reif, John H.
- Abstract
Winfree's pioneering work led the foundations in the area of error-reduction in algorithmic self-assembly[26], but the construction resulted in increase of the size of assembly. Reif et. al. contributed further in this area with compact error-resilient schemes [15] that maintained the original size of the assemblies, but required certain restrictions on the Boolean functions to be used in the algorithmic self-assembly. It is a critical challenge to improve these compact error resilient schemes to incorporate arbitrary Boolean functions, and to determine how far these prior results can be extended under different degrees of restrictions on the Boolean functions. In this work we present a considerably more complete theory of compact error-resilient schemes for algorithmic self-assembly in two and three dimensions. First we consider two-dimensional algorithmic self-assembly. We present an error correction scheme for reduction of errors from ε to ε2 for arbitrary Boolean functions in two dimensional algorithmic self-assembly. Then we characterize the class of Boolean functions for which the error reduction can be done from ε to ε3, and present an error correction scheme that achieves this reduction. Then we prove ultimate limits on certain classes of compact error resilient schemes: in particular we show that they can not provide reduction of errors from ε to ε4 is for any Boolean functions. Further, we develop the first provable compact error resilience schemes for three dimensional tiling self-assemblies. We also extend the work of Winfree on self-healing in two-dimensional self-assembly[25] to obtain a self-healing tile-set for three-dimensional self-assembly. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
- View/download PDF
50. On Times to Compute Shapes in 2D Tile Self-assembly.
- Author
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Chengde Mao, Yokomori, Takashi, Baryshnikov, Yuliy, Coffman, Ed, and Yimwadsana, Boonsit
- Abstract
We study the times to grow structures within the tile self-assembly model proposed by Winfree, and the possible shapes that can be achieved during the self-assembly. Our earlier work was confined to the growth of rectangular structures, in which the border tiles are prefabricated. By varying the relative rates between the border-tile and rule-tile attachment, one can engineer interesting new shapes, which have been observed in the laboratory. We show that the results from an extension of our earlier stochastic models agree remarkably closely with experimental results. This is an important further demonstration of the validity and usefulness of our stochastic models, which have also been used successfully in studies of error correction in DNA self assembly. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
- View/download PDF
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