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1. A gap-free genome assembly of Fusarium oxysporum f. sp. conglutinans, a vascular wilt pathogen

Author

Huan Wang, Gang Yao, Weikai Chen, Dilay Hazal Ayhan, Xiangfeng Wang, Jie Sun, Shu Yi, Tan Meng, Shaoying Chen, Xin Geng, Dian Meng, Lili Zhang, and Li Guo

Subjects
Science
Abstract

Abstract Fusarium oxysporum is an asexual filamentous fungus that causes vascular wilt in hundreds of crop plants and poses a threat to public health through Fusariosis. F. oxysporum f. sp. conglutinans strain Fo5176, originally isolated from Brassica oleracea, is pathogenic to Arabidopsis, making it a model pathosystem for dissecting the molecular mechanisms underlying host-pathogen interactions. Assembling the F. oxysporum genome is notoriously challenging due to the presence of repeat-rich accessory chromosomes. Here, we report a gap-free genome assembly of Fo5176 using PacBio HiFi and Hi-C data. The 69.56 Mb assembly contained 18 complete chromosomes, including all centromeres and most telomeres (20/36), representing the first gap-free genome sequence of a pathogenic F. oxysporum strain. In total, 21,460 protein-coding genes were annotated, a 26.3% increase compared to the most recent assembly. This high-quality reference genome for F. oxysporum f. sp. conglutinans Fo5176 provides a valuable resource for further research into fungal pathobiology and evolution.

Published
2024
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2. Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis

Author

Weikai Chen, Xiangfeng Wang, Jie Sun, Xinrui Wang, Zhangsheng Zhu, Dilay Hazal Ayhan, Shu Yi, Ming Yan, Lili Zhang, Tan Meng, Yu Mu, Jun Li, Dian Meng, Jianxin Bian, Ke Wang, Lu Wang, Shaoying Chen, Ruidong Chen, Jingyun Jin, Bosheng Li, Xingping Zhang, Xing Wang Deng, Hang He, and Li Guo

Subjects
Science
Abstract

Abstract Chili pepper (Capsicum) is known for its unique fruit pungency due to the presence of capsaicinoids. The evolutionary history of capsaicinoid biosynthesis and the mechanism of their tissue specificity remain obscure due to the lack of high-quality Capsicum genomes. Here, we report two telomere-to-telomere (T2T) gap-free genomes of C. annuum and its wild nonpungent relative C. rhomboideum to investigate the evolution of fruit pungency in chili peppers. We precisely delineate Capsicum centromeres, which lack high-copy tandem repeats but are extensively invaded by CRM retrotransposons. Through phylogenomic analyses, we estimate the evolutionary timing of capsaicinoid biosynthesis. We reveal disrupted coding and regulatory regions of key biosynthesis genes in nonpungent species. We also find conserved placenta-specific accessible chromatin regions, which likely allow for tissue-specific biosynthetic gene coregulation and capsaicinoid accumulation. These T2T genomic resources will accelerate chili pepper genetic improvement and help to understand Capsicum genome evolution.

Published
2024
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3. De novo chromosome-level genome assembly of Chinese motherwort (Leonurus japonicus)

Author

Xinrui Wang, Lili Zhang, Gang Yao, Xiangfeng Wang, Shu Yi, Tan Meng, Dian Meng, Weikai Chen, and Li Guo

Subjects
Science
Abstract

Abstract Chinese motherwort (Leonurus japonicus), a member of Lamiaceae family, is a commonly used medicinal herb for treating obstetrical and gynecological diseases, producing over 280 officinal natural products. Due to limited genomic resources, little progress has been made in deciphering the biosynthetic pathway of valuable natural products in L. japonicus. Here, we de novo assembled the L. japonicus genome using high-coverage ONT long reads and Hi-C reads. The chromosome-level genome assembly contained ten chromosomes representing 99.29% of 489.34 Mb genomic sequence with a contig and scaffold N50 of 7.27 Mb and 50.86 Mb, respectively. Genome validations revealed BUSCO and LAI score of 99.2% and 21.99, respectively, suggesting high quality of genome assembly. Using transcriptomic data from various tissues, 22,531 protein-coding genes were annotated. Phylogenomic analysis of 13 angiosperm plants suggested L. japonicus had 58 expanded gene families functionally enriched in specialized metabolism such as diterpenoid biosynthesis. The genome assembly, annotation, and sequencing data provide resources for the elucidation of biosynthetic pathways behind natural products of pharmaceutical applications in L. japonicus.

Published
2024
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5. Gapless genome assembly of Fusarium verticillioides, a filamentous fungus threatening plant and human health

Author

Gang Yao, Weikai Chen, Jie Sun, Xiangfeng Wang, Huan Wang, Tan Meng, Lili Zhang, and Li Guo

Subjects
Science
Abstract

Abstract Fusarium verticillioides is a filamentous fungus that causes plant diseases and harms human health through cancer-inducing mycotoxin and life-threatening Fusariosis. Given its threat to agriculture and public health, genome assembly of this fungus is critical to our understanding of its pathobiology and developing antifungal drugs. Here, we report a gap-free genome assembly of F. verticillioides using PacBio HiFi data and high-throughput chromosome capture (Hi-C) sequencing data. The assembled 42.0 Mb sequence contains eleven gapless chromosomes capturing all centromeres and 19 of all 22 telomeres. This assembly represents a significant improvement over previous version on contiguity (contig N50: 4.3 Mb), completeness (BUSCO score: 99.0%) and correctness (QV: 88.8). A total of 15,230 protein-coding genes were predicted, 6.2% of which are newly annotated genes. In addition, we identified three-dimension chromatin structures such as TADs-like structures and chromatin loops based on Hi-C data of ultra-high coverage. This gap-free genome of F. verticillioides is an excellent resource for further panoramic understanding mechanisms of fungal genome evolution, mycotoxin production and pathogenesis on plant and human host.

Published
2023
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6. Validating the effectiveness of game-based learning approach in the form of video game for assessing computational thinking

Author

Tan Meng Joo and Wong Yoke Seng

Subjects
game-based learning, computational thinking, learning assessment, video games, Education
Abstract

This research aims to validate the effectiveness of students’ understanding in four aspects of computational thinking with the game-based learning assessment. The four aspects of computational thinking involved in this research are decomposition, pattern recognition, abstraction, and algorithm. This research will use a mixed method design approach with a quasi-experiment using a pre-test and post-test nonequivalent group design. The quasi-experiment will validate the effectiveness of students’ understanding on the decomposition, pattern recognition, abstraction, and algorithm aspects of computational thinking with the game-based learning assessment. The qualitative data gathered will be analyzed using thematic analysis. It is expected that the students’ understanding in four aspects of computational thinking with the game-based learning assessment will vary in terms of the effectiveness.

Published
2021
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7. Topological 8d $\mathcal{N}=1$ Gauge Theory: Novel Floer Homologies, and $A_\infty$-categories of Six, Five, and Four-Manifolds

Author

Er, Arif and Tan, Meng-Chwan

Subjects
High Energy Physics - Theory, Mathematics - Algebraic Geometry, Mathematics - Differential Geometry, Mathematics - Geometric Topology, Mathematics - Symplectic Geometry
Abstract

This work is a continuation of the program initiated in [arXiv:2311.18302]. We show how one can define novel gauge-theoretic (holomorphic) Floer homologies of seven, six, and five-manifolds, from the physics of a topologically-twisted 8d $\mathcal{N}=1$ gauge theory on a Spin$(7)$-manifold via its supersymmetric quantum mechanics interpretation. They are associated with $G_2$ instanton, Donaldson-Thomas, and Haydys-Witten configurations on the seven, six, and five-manifolds, respectively. We also show how one can define hyperk\"ahler Floer homologies specified by hypercontact three-manifolds, and symplectic Floer homologies of instanton moduli spaces. In turn, this will allow us to derive Atiyah-Floer type dualities between the various gauge-theoretic Floer homologies and symplectic intersection Floer homologies of instanton moduli spaces. Via a 2d gauged Landau-Ginzburg model interpretation of the 8d theory, one can derive novel Fukaya-Seidel type $A_\infty$-categories that categorify Donaldson-Thomas, Haydys-Witten, and Vafa-Witten configurations on six, five, and four-manifolds, respectively, where an Atiyah-Floer type correspondence for the Donaldson-Thomas case can be established. Last but not least, topological invariance of the theory suggests a relation amongst these Floer homologies and Fukaya-Seidel type $A_\infty$-categories for certain Spin$(7)$-manifolds. Our work therefore furnishes purely physical proofs and generalizations of the conjectures by Donaldson-Thomas [2], Donaldson-Segal [3], Cherkis [4], Hohloch-Noetzel-Salamon [5], Salamon [6], Haydys [7], and Bousseau [8], and more., Comment: 82 pp

Published
2024

10. Topological 5d $\mathcal {N} = 2$ Gauge Theory: Novel Floer Homologies, their Dualities, and an $A_\infty$-category of Three-Manifolds

Author

Er, Arif, Ong, Zhi-Cong, and Tan, Meng-Chwan

Subjects
High Energy Physics - Theory, Mathematics - Algebraic Geometry, Mathematics - Differential Geometry, Mathematics - Geometric Topology, Mathematics - Symplectic Geometry
Abstract

We show how one can define novel gauge-theoretic Floer homologies of four, three and two-manifolds from the physics of a certain topologically-twisted 5d ${\cal N}=2$ gauge theory via its supersymmetric quantum mechanics interpretation. They are associated with Vafa-Witten, Hitchin and $G_{\mathbb{C}}$-BF configurations on the four, three and two-manifolds, respectively. We also show how one can define novel symplectic Floer homologies of Hitchin spaces, which in turn will allow us to derive novel Atiyah-Floer correspondences that relate our gauge-theoretic Floer homologies to symplectic intersection Floer homologies of Higgs bundles. Furthermore, topological invariance and 5d "S-duality" suggest a web of relations and a Langlands duality amongst these novel Floer homologies and their loop/toroidal group generalizations. Last but not least, via a 2d gauged Landau-Ginzburg model interpretation of the 5d theory, we derive, from the soliton string theory that it defines and the 5d partition function, a Fukaya-Seidel type $A_\infty$-category of Hitchin configurations on three-manifolds and its novel Atiyah-Floer correspondence. Our work therefore furnishes purely physical proofs and generalizations of the mathematical conjectures of Haydys [1], Abouzaid-Manolescu [2], and Bousseau [3], and more., Comment: 61 pp. Additional material in Section 9 which physically proves and generalizes Bousseau's mathematical conjecture in [3]

Published
2023

11. Topological-Holomorphic ${\mathcal N} =4$ Gauge Theory: From Langlands Duality of Holomorphic Invariants to Mirror Symmetry of Quasi-topological Strings

Author

Ong, Zhi-Cong and Tan, Meng-Chwan

Subjects
High Energy Physics - Theory, Mathematics - Algebraic Geometry, Mathematics - Differential Geometry, Mathematics - Quantum Algebra, Mathematics - Representation Theory
Abstract

We perform a topological-holomorphic twist of $\mathcal{N}=4$ supersymmetric gauge theory on a four-manifold of the form $M_4=\Sigma_1 \times \Sigma_2$ with Riemann surfaces $\Sigma_{1,2}$, and unravel the mathematical implications of its physics. In particular, we consider different linear combinations of the resulting scalar supercharges under $S$-duality, where this will allow us to derive novel topological and holomorphic invariants of $M_4$ and their Langlands duals. As the twisted theory can be topological along $\Sigma_1$ whence we can dimensionally reduce it to 2d, via the effective sigma-model on $\Sigma_2$, we can also relate these 4d invariants and their Langlands duals to the mirror symmetry of Higgs bundles and that of quasi-topological strings described by the sheaf of chiral differential operators. As an offshoot, we would be able to obtain a fundamental understanding from 4d gauge theory, why chiral differential operators are purely perturbative objects., Comment: 30 pp. Further clarifications

Published
2023

12. Vafa-Witten Theory: Invariants, Floer Homologies, Higgs Bundles, a Geometric Langlands Correspondence, and Categorification (String Math 2022 Proceedings)

Author

Tan, Meng-Chwan

Subjects
High Energy Physics - Theory, Mathematics - Algebraic Geometry, Mathematics - Differential Geometry, Mathematics - Geometric Topology, Mathematics - Representation Theory
Abstract

This is a concise version of the original article in [arXiv:2203.17115] that will be published in the String Math 2022 Proceedings by the American Mathematical Society., Comment: 16 pp. References updated to match publication version. arXiv admin note: substantial text overlap with arXiv:2203.17115

Published
2023
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13. Vafa-Witten Theory: Invariants, Floer Homologies, Higgs Bundles, a Geometric Langlands Correspondence, and Categorification

Author

Ong, Zhi-Cong and Tan, Meng-Chwan

Subjects
High Energy Physics - Theory, Mathematics - Algebraic Geometry, Mathematics - Differential Geometry, Mathematics - Geometric Topology, Mathematics - Representation Theory
Abstract

We revisit Vafa-Witten theory in the more general setting whereby the underlying moduli space is not that of instantons, but of the full Vafa-Witten equations. We physically derive (i) a novel Vafa-Witten four-manifold invariant associated with this moduli space, (ii) their relation to Gromov-Witten invariants, (iii) a novel Vafa-Witten Floer homology assigned to three-manifold boundaries, (iv) a novel Vafa-Witten Atiyah-Floer correspondence, (v) a proof and generalization of a conjecture by Abouzaid-Manolescu in [1] about the hypercohomology of a perverse sheaf of vanishing cycles, (vi) a Langlands duality of these invariants, Floer homologies and hypercohomology, and (vii) a quantum geometric Langlands correspondence with purely imaginary parameter that specializes to the classical correspondence in the zero-coupling limit, where Higgs bundles feature in (ii), (iv), (vi) and (vii). We also explain how these invariants and homologies will be categorified in the process, and discuss their higher categorification. We therefore relate differential and enumerative geometry, topology and geometric representation theory in mathematics, via a maximally-supersymmetric topological quantum field theory with electric-magnetic duality in physics., Comment: 44 pp. Additional acknowledgments. Presented at "String Math 2022". To appear in ATMP

Published
2022
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17. The $u$-plane integral, mock modularity and enumerative geometry

Author

Aspman, Johannes, Furrer, Elias, Korpas, Georgios, Ong, Zhi-Cong, and Tan, Meng-Chwan

Subjects
High Energy Physics - Theory, Mathematics - Algebraic Geometry, Mathematics - Differential Geometry, Mathematics - Number Theory
Abstract

We revisit the low-energy effective $U(1)$ action of topologically twisted $\mathcal N=2$ SYM theory with gauge group of rank one on a generic oriented smooth 4-manifold $X$ with nontrivial fundamental group. After including a specific new set of $\mathcal Q$-exact operators to the known action, we express the integrand of the path integral of the low-energy $U(1)$ theory as an anti-holomorphic derivative. This allows us to use the theory of mock modular forms and indefinite theta functions for the explicit evaluation of correlation functions of the theory, including but not restricted to those that physically reproduce Donaldson invariants, thus facilitating the computations compared to previously used methods. As an explicit check of our results, we compute the path integral for the product ruled surfaces $X=\Sigma_g \times \mathbb{CP}^1$ for the reduction on either factor and compare the results with existing literature. In the case of reduction on the Riemann surface $\Sigma_g$, via an equivalent topological A-model on $\mathbb{CP}^1$, we will be able to express the generating function of genus zero Gromov-Witten invariants of the moduli space of flat rank one connections over $\Sigma_g$ in terms of an indefinite theta function, whence we would be able to make concrete numerical predictions of these enumerative invariants in terms of modular data, thereby allowing us to derive results in enumerative geometry from number theory., Comment: 31 pages + appendices. Minor changes to title, abstract, introduction and section 5 after reviewer comments. To appear in Lett.Math.Phys

Published
2021
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22. Matrix Quantization of Classical Nambu Brackets and Super $p$-Branes

Author

Ashwinkumar, Meer, Schmidt, Lennart, and Tan, Meng-Chwan

Subjects
High Energy Physics - Theory, Mathematical Physics, Quantum Physics
Abstract

We present an explicit matrix algebra quantization of the algebra of volume-preserving diffeomorphisms of the $n$-torus. That is, we approximate the corresponding classical Nambu brackets using $\mathfrak{sl}(N^{\lceil\frac{n}{2}\rceil},\mathbb{C})$-matrices equipped with the finite bracket given by the completely anti-symmetrized matrix product, such that the classical brackets are retrieved in the $N\rightarrow \infty$ limit. We then apply this approximation to the super $4$-brane in $9$ dimensions and give a regularized action in analogy with the matrix quantization of the supermembrane. This action exhibits a reduced gauge symmetry that we discuss from the viewpoint of $L_\infty$-algebras in a slight generalization to the construction of Lie $2$-algebras from Bagger--Lambert $3$-algebras., Comment: 36 pages. Updated title and refined presentation. Published in JHEP

Published
2021
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23. Cardiovascular Outcomes in GRADE (Glycemia Reduction Approaches in Type 2 Diabetes: A Comparative Effectiveness Study)

Author

Green, Jennifer B., Everett, Brendan M., Ghosh, Alokananda, Younes, Naji, Krause-Steinrauf, Heidi, Barzilay, Joshua, Desouza, Cyrus, Inzucchi, Silvio E., Pokharel, Yashashwi, Schade, David, Scrymgeour, Alexandra, Tan, Meng H., Utzschneider, Kristina M., Mudaliar, Sunder, Crandall, J.P., McKee, M.D., Behringer-Massera, S., Brown-Friday, J., Xhori, E., Ballentine-Cargill, K., Duran, S., Estrella, H., Gonzalez de la Torre, S., Lukin, J., Phillips, L.S., Burgess, E., Olson, D., Rhee, M., Wilson, P., Raines, T.S., Boers, J., Costello, J., Maher-Albertelli, M., Mungara, R., Savoye, L., White, C.A., Gullett, C., Holloway, L., Morehead, F., Person, S., Sibymon, M., Tanukonda, S., Adams, C., Ross, A., Balasubramanyam, A., Gaba, R., Gonzalez Hattery, E., Ideozu, A., Jimenez, J., Montes, G., Wright, C., Hollander, P., Roe, E., Jackson, A., Smiley, A., Burt, P., Estrada, L., Chionh, K., Ismail-Beigi, F., Falck-Ytter, C., Sayyed Kassem, L., Sood, A., Tiktin, M., Kulow, T., Newman, C., Stancil, K.A., Cramer, B., Iacoboni, J., Kononets, M.V., Sanders, C., Tucker, L., Werner, A., Maxwell, A., McPhee, G., Patel, C., Colosimo, L., Krol, A., Goland, R., Pring, J., Alfano, L., Kringas, P., Hausheer, C., Tejada, J., Gumpel, K., Kirpitch, A., Schneier, H., AbouAssi, H., Chatterjee, R., Feinglos, M.N., English Jones, J., Khan, S.A., Kimpel, J.B., Zimmer, R.P., Furst, M., Satterwhite, B.M., Thacker, C.R., Evans Kreider, K., Mariash, C.N., Mather, K.J., Ismail, H.M., Lteif, A., Mullen, M., Hamilton, T., Patel, N., Riera, G., Jackson, M., Pirics, V., Aguillar, D., Howard, D., Hurt, S., Bergenstal, R., Carlson, A., Martens, T., Johnson, M., Hill, R., Hyatt, J., Jensen, C., Madden, M., Martin, D., Willis, H., Konerza, W., Yang, S., Kleeberger, K., Passi, R., Fortmann, S., Herson, M., Mularski, K., Glauber, H., Prihoda, J., Ash, B., Carlson, C., Ramey, P.A., Schield, E., Torgrimson-Ojerio, B., Arnold, K., Kauffman, B., Panos, E., Sahnow, S., Bays, K., Berame, K., Cook, J., Ghioni, D., Gluth, J., Schell, K., Criscola, J., Friason, C., Jones, S., Nazarov, S., Rassouli, N., Puttnam, R., Ojoawo, B., Nelson, R., Curtis, M., Hollis, B., Sanders-Jones, C., Stokes, K., El-Haqq, Z., Kolli, A., Tran, T., Wexler, D., Larkin, M.E., Meigs, J., Chambers, B., Dushkin, A., Rocchio, G., Yepes, M., Steiner, B., Dulin, H., Cayford, M., Chu, K., DeManbey, A., Hillard, M., Martin, K., Thangthaeng, N., Gurry, L., Kochis, R., Raymond, E., Ripley, V., Stevens, C., Park, J., Aroda, V., Ghazi, A., Magee, M., Ressing, A., Loveland, A., Hamm, M., Hurtado, M., Kuhn, A., Leger, J., Manandhar, L., Mwicigi, F., Sanchez, O., Young, T., Garg, R., Lagari-Libhaber, V., Florez, H.J., Valencia, W.M., Marks, J., Casula, S., Oropesa-Gonzalez, L., Hue, L., Cuadot, A., Nieto-Martinez, R., Riccio Veliz, A.K., Gutt, M., Kendal, Y.J., Veciana, B., Ahmann, A., Aby-Daniel, D., Joarder, F., Morimoto, V., Sprague, C., Yamashita, D., Cady, N., Rivera-Eschright, N., Kirchhoff, P., Morales Gomez, B., Adducci, J., Goncharova, A., Hox, S.H., Petrovitch, H., Matwichyna, M., Jenkins, V., Broadwater, L., Ishii, R.R., Bermudez, N.O., Hsia, D.S., Cefalu, W.T., Greenway, F.L., Waguespack, C., King, E., Fry, G., Dragg, A., Gildersleeve, B., Arceneaux, J., Haynes, N., Thomassie, A., Pavlionis, M., Bourgeois, B., Hazlett, C., Henry, R., Boeder, S., Pettus, J., Diaz, E., Garcia-Acosta, D., Maggs, S., DeLue, C., Stallings, A., Castro, E., Hernandez, S., Krakoff, J., Curtis, J.M., Killean, T., Khalid, M., Joshevama, E., Diaz, E., Martin, D., Tsingine, K., Karshner, T., Albu, J., Pi-Sunyer, F.X., Frances, S., Maggio, C., Ellis, E., Bastawrose, J., Gong, X., Banerji, M.A., August, P., Lee, M., Lorber, D., Brown, N.M., Josephson, D.H., Thomas, L.L., Tsovian, M., Cherian, A., Jacobson, M.H., Mishko, M.M., Kirkman, M.S., Buse, J.B., Diner, J., Dostou, J., Machineni, S., Young, L., Bergamo, K., Goley, A., Kerr, J., Largay, J.F., Guarda, S., Cuffee, J., Culmer, D., Fraser, R., Almeida, H., Coffer, S., Debnam, E., Kiker, L., Morton, S., Josey, K., Fuller, G., Garvey, W.T., Cherrington, A.L., Dyer, D., Lawson, M.C.R., Griffith, O., Agne, A., McCullars, S., Cohen, R.M., Craig, J., Rogge, M.C., Burton, K., Kersey, K., Wilson, C., Lipp, S., Vonder Meulen, M.B., Adkins, C., Onadeko, T., Rasouli, N., Baker, C., Schroeder, E., Razzaghi, M., Lyon, C., Penaloza, R., Underkofler, C., Lorch, R., Douglass, S., Steiner, S., Sivitz, W.I., Cline, E., Knosp, L.K., McConnell, J., Lowe, T., Herman, W.H., Pop-Busui, R., Martin, C., Waltje, A., Katona, A., Goodhall, L., Eggleston, R., Kuo, S., Bojescu, S., Bule, S., Kessler, N., LaSalle, E., Whitley, K., Seaquist, E.R., Bantle, A., Harindhanavudhi, T., Kumar, A., Redmon, B., Bantle, J., Coe, M., Mech, M., Taddese, A., Lesne, L., Smith, S., Kuechenmeister, L., Shivaswamy, V., Burbach, S., Rodriguez, M.G., Seipel, K., Alfred, A., Morales, A.L., Eggert, J., Lord, G., Taylor, W., Tillson, R., Adolphe, A., Burge, M., Duran-Valdez, E., Martinez, J., Bancroft, A., Kunkel, S., Ali Jamaleddin Ahmad, F., Hernandez McGinnis, D., Pucchetti, B., Scripsick, E., Zamorano, A., DeFronzo, R.A., Cersosimo, E., Abdul-Ghani, M., Triplitt, C., Juarez, D., Mullen, M., Garza, R.I., Verastiqui, H., Wright, K., Puckett, C., Raskin, P., Rhee, C., Abraham, S., Jordan, L.F., Sao, S., Morton, L., Smith, O., Osornio Walker, L., Schnurr-Breen, L., Ayala, R., Kreymer, R.B., Sturgess, D., Kahn, S.E., Alarcon-Casas Wright, L., Boyko, E.J., Tsai, E.C., Trence, D.L., Trikudanathan, S., Fattaleh, B.N., Montgomery, B.K., Atkinson, K.M., Kozedub, A., Concepcion, T., Moak, C., Prikhodko, N., Rhothisen, S., Elasy, T.A., Martin, S., Shackelford, L., Goidel, R., Hinkle, N., Lovell, C., Myers, J., Lipps Hogan, J., McGill, J.B., Salam, M., Schweiger, T., Kissel, S., Recklein, C., Clifton, M.J., Tamborlane, W., Camp, A., Gulanski, B., Pham, K., Alguard, M., Gatcomb, P., Lessard, K., Perez, M., Iannone, L., Magenheimer, E., Montosa, A., Cefalu, W.T., Fradkin, J., Burch, H.B., Bremer, A.A., Nathan, D.M., Lachin, J.M., Buse, J.B., Kahn, S.E., Larkin, M.E., Tiktin, M., Wexler, D., Burch, H.B., Bremer, A.A., Lachin, J.M., Bebu, I., Butera, N., Buys, C.J., Fagan, A., Gao, Y., Gramzinski, M.R., Hall, S.D., Kazemi, E., Legowski, E., Liu, H., Suratt, C., Tripputi, M., Arey, A., Backman, M., Bethepu, J., Lund, C., Mangat Dhaliwal, P., McGee, P., Mesimer, E., Ngo, L., Steffes, M., Seegmiller, J., Saenger, A., Arends, V., Gabrielson, D., Conner, T., Warren, S., Day, J., Huminik, J., Soliman, E.Z., Zhang, Z.M., Campbell, C., Hu, J., Keasler, L., Hensley, S., Li, Y., Herman, W.H., Kuo, S., Martin, C., Waltje, A., Mihalcea, R., Min, D.J., Perez-Rosas, V., Prosser, L., Resnicow, K., Ye, W., Shao, H., Zhang, P., Luchsinger, J., Sanchez, D., Assuras, S., Groessl, E., Sakha, F., Chong, H., Hillery, N., Abdouch, I., Bahtiyar, G., Brantley, P., Broyles, F.E., Canaris, G., Copeland, P., Craine, J.J., Fein, W.L., Gliwa, A., Hope, L., Lee, M.S., Meiners, R., Meiners, V., O’Neal, H., Park, J.E., Sacerdote, A., Sledge Jr, E., Soni, L., Steppel-Reznik, J., and Turchin, A.

Published
2024
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25. 4d Chern-Simons Theory as a 3d Toda Theory, and a 3d-2d Correspondence

Author

Ashwinkumar, Meer, Png, Kee-Seng, and Tan, Meng-Chwan

Subjects
High Energy Physics - Theory, Mathematics - Quantum Algebra, Mathematics - Representation Theory, Mathematics - Symplectic Geometry
Abstract

We show that the four-dimensional Chern-Simons theory studied by Costello, Witten and Yamazaki, is, with Nahm pole-type boundary conditions, dual to a boundary theory that is a three-dimensional analogue of Toda theory with a novel 3d W-algebra symmetry. By embedding four-dimensional Chern-Simons theory in a partial twist of the five-dimensional maximally supersymmetric Yang-Mills theory on a manifold with corners, we argue that this three-dimensional Toda theory is dual to a two-dimensional topological sigma model with A-branes on the moduli space of solutions to the Bogomolny equations. This furnishes a novel 3d-2d correspondence, which, among other mathematical implications, also reveals that modules of the 3d W-algebra are modules for the quantized algebra of certain holomorphic functions on the Bogomolny moduli space., Comment: 28 pages. Presented at "String Math 2020". Further clarifications. To appear in JHEP

Published
2020
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28. Microarray data mining: A novel optimization-based approach to uncover biologically coherent structures

Author

Broach James R, Smith Erin N, Tan Meng P, and Floudas Christodoulos A

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background DNA microarray technology allows for the measurement of genome-wide expression patterns. Within the resultant mass of data lies the problem of analyzing and presenting information on this genomic scale, and a first step towards the rapid and comprehensive interpretation of this data is gene clustering with respect to the expression patterns. Classifying genes into clusters can lead to interesting biological insights. In this study, we describe an iterative clustering approach to uncover biologically coherent structures from DNA microarray data based on a novel clustering algorithm EP_GOS_Clust. Results We apply our proposed iterative algorithm to three sets of experimental DNA microarray data from experiments with the yeast Saccharomyces cerevisiae and show that the proposed iterative approach improves biological coherence. Comparison with other clustering techniques suggests that our iterative algorithm provides superior performance with regard to biological coherence. An important consequence of our approach is that an increasing proportion of genes find membership in clusters of high biological coherence and that the average cluster specificity improves. Conclusion The results from these clustering experiments provide a robust basis for extracting motifs and trans-acting factors that determine particular patterns of expression. In addition, the biological coherence of the clusters is iteratively assessed independently of the clustering. Thus, this method will not be severely impacted by functional annotations that are missing, inaccurate, or sparse.

Published
2008
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29. Unifying Lattice Models, Links and Quantum Geometric Langlands via Branes in String Theory

Author

Ashwinkumar, Meer and Tan, Meng-Chwan

Subjects
High Energy Physics - Theory, Condensed Matter - Statistical Mechanics, Mathematics - Geometric Topology, Mathematics - Quantum Algebra, Mathematics - Representation Theory
Abstract

We explain how, starting with a stack of D4-branes ending on an NS5-brane in type IIA string theory, one can, via T-duality and the topological-holomorphic nature of the relevant worldvolume theories, relate (i) the lattice models realized by Costello's 4d Chern-Simons theory, (ii) links in 3d analytically-continued Chern-Simons theory, (iii) the quantum geometric Langlands correspondence realized by Kapustin-Witten using 4d N = 4 gauge theory and its quantum group modification, and (iv) the Gaitsgory-Lurie conjecture relating quantum groups/affine Kac-Moody algebras to Whittaker D-modules/W-algebras. This furnishes, purely physically via branes in string theory, a novel bridge between the mathematics of integrable systems, geometric topology, geometric representation theory, and quantum algebras., Comment: 31 pages. Minor improvements, typos corrected, and reference added

Published
2019
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31. Boundary N=2 Theory, Floer Homologies, Affine Algebras, and the Verlinde Formula

Author

Ashwinkumar, Meer, Png, Kee-Seng, and Tan, Meng-Chwan

Subjects
High Energy Physics - Theory, Mathematics - Differential Geometry, Mathematics - Geometric Topology, Mathematics - Quantum Algebra, Mathematics - Symplectic Geometry
Abstract

Generalizing our ideas in [arXiv:1006.3313], we explain how topologically-twisted N=2 gauge theory on a four-manifold with boundary, will allow us to furnish purely physical proofs of (i) the Atiyah-Floer conjecture, (ii) Munoz's theorem relating quantum and instanton Floer cohomology, (iii) their monopole counterparts, and (iv) their higher rank generalizations. In the case where the boundary is a Seifert manifold, one can also relate its instanton Floer homology to modules of an affine algebra via a 2d A-model with target the based loop group. As an offshoot, we will be able to demonstrate an action of the affine algebra on the quantum cohomology of the moduli space of flat connections on a Riemann surface, as well as derive the Verlinde formula., Comment: 44 pp. Typos corrected. To appear in ATMP

Published
2019
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35. Optimization of Metformin in the GRADE Cohort: Effect on Glycemia and Body Weight

Author

Sivitz, William I, Phillips, Lawrence S, Wexler, Deborah J, Fortmann, Stephen P, Camp, Anne W, Tiktin, Margaret, Perez, Magalys, Craig, Jacqueline, Hollander, Priscilla A, Cherrington, Andrea, Aroda, Vanita R, Tan, Meng Hee, Krakoff, Jonathan, Rasouli, Neda, Butera, Nicole M, Younes, Naji, Crandall, Jill P, Diane McKee, Melissa, Brown-Friday, Janet, Xhori, Entila, Ballentine-Cargill, Keisha, Duran, Sally, Lukin, Jennifer, Beringher, Stephanie, Gonzalez de la torre, Susana, Phillips, Lawrence, Burgess, Elizabeth, Olson, Darin, Rhee, Mary, Wilson, Peter, Stephanie Raines, Tasha, Costello, Julie, Gullett, Chona, Maher-Albertelli, Maxine, Morehead, Folayan, Mungara, Radhika, Person, Saranjit, Savoye, Louise, Sibymon, Mabil, Tanukonda, Sridhar, Ann White, Carol, Holloway, Leah, Adams, Cynthia, Ross, April, Balasubramanyam, Ashok, Gonzalez, Erica, Wright, Charlyne, Hollander, Priscilla, Roe, Erin, Uy, Analyn, Burt, Polly, Estrada, Lorie, Chionh, Kris, Ismail-Beigi, Faramarz, Falck-Ytter, Corinna, Sayyed Kassem, Laure, Sood, Ajay, Cramer, Bethany, Iacoboni, Jacalyn, Kononets, Maria V, Kulow, Tanya, Newman, Cynthia, Stancil, Katherine A, Sanders, Cristina, Tucker, Lisa, Werner, Amanda, Krol, Adrienne, McPhee, Gloria, Patel, Christine, Colosimo, Linda, Goland, Robin, Pring, James, Kringas, Patricia, Tejada, Jessica, Hausheer, Camille, Schneier, Harvey, Gumpel, Kelly, Kirpitch, Amanda, Green, Jennifer B, AbouAssi, Hiba, Chatterjee, Ranee, Feinglos, Mark N, English Jones, Jennifer, Khan, Shubi A, Kimpel, Jeanne B, Zimmer, Ronna P, Furst, Mary, Satterwhite, Barbara M, Thacker, Connie R, Evans Kreider, Kathryn, Mather, Kieren J, Lteif, Amale, Hamilton, Tonya, Patel, Nick, Riera, Gabriela, Jackson, Marcia, Pirics, Vivian, Howard, Devin, and Aguillar, Danielle

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Prevention, Clinical Research, Diabetes, Nutrition, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Metabolic and endocrine, Adult, Aged, Blood Glucose, Body Weight, Calibration, Comparative Effectiveness Research, Diabetes Mellitus, Type 2, Dose-Response Relationship, Drug, Drug Therapy, Combination, Female, Glycated Hemoglobin, Humans, Hypoglycemic Agents, Insulin, Liraglutide, Male, Maximum Tolerated Dose, Metformin, Middle Aged, Sitagliptin Phosphate, Sulfonylurea Compounds, Weight Loss, GRADE Research Group, Medical and Health Sciences, Endocrinology & Metabolism, Biomedical and clinical sciences, Health sciences
Abstract

ObjectiveWe evaluated the effect of optimizing metformin dosing on glycemia and body weight in type 2 diabetes.Research design and methodsThis was a prespecified analysis of 6,823 participants in the Glycemia Reduction Approaches in Diabetes: A Comparative Effectiveness Study (GRADE) taking metformin as the sole glucose-lowering drug who completed a 4- to 14-week (mean ± SD 7.9 ± 2.4) run-in in which metformin was adjusted to 2,000 mg/day or a maximally tolerated lower dose. Participants had type 2 diabetes for

Published
2020

45. Direct identification of A-to-I editing sites with nanopore native RNA sequencing

Author

Nguyen, Tram Anh, Heng, Jia Wei Joel, Kaewsapsak, Pornchai, Kok, Eng Piew Louis, Stanojević, Dominik, Liu, Hao, Cardilla, Angelysia, Praditya, Albert, Yi, Zirong, Lin, Mingwan, Aw, Jong Ghut Ashley, Ho, Yin Ying, Peh, Kai Lay Esther, Wang, Yuanming, Zhong, Qixing, Heraud-Farlow, Jacki, Xue, Shifeng, Reversade, Bruno, Walkley, Carl, Ho, Ying Swan, Šikić, Mile, Wan, Yue, and Tan, Meng How

Published
2022
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47. Branes and Categorifying Integrable Lattice Models

Author

Ashwinkumar, Meer, Tan, Meng-Chwan, and Zhao, Qin

Subjects
High Energy Physics - Theory, Condensed Matter - Statistical Mechanics, Mathematical Physics
Abstract

We elucidate how integrable lattice models described by Costello's 4d Chern-Simons theory can be realized via a stack of D4-branes ending on an NS5-brane in type IIA string theory, with D0-branes on the D4-brane worldvolume sourcing a meromorphic RR 1-form, and fundamental strings forming the lattice. This provides us with a nonperturbative integration cycle for the 4d Chern-Simons theory, and by applying T- and S-duality, we show how the R-matrix, the Yang-Baxter equation and the Yangian can be categorified, that is, obtained via the Hilbert space of a 6d gauge theory., Comment: 19 pp. Minor improvements and typos corrected. To appear in ATMP

Published
2018
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