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1. CellularResolutions M2 Package

Author

Sobieska, Aleksandra and Yang, Jay

Subjects
Mathematics - Commutative Algebra
Abstract

Cellular resolutions are a technique for constructing resolutions of monomial ideals by giving a cell complex labeled by monomials, or more generally, by monomial modules. This \verb|Macaulay2| package allows us to work with cellular resolutions in a natural way.

Published
2023

2. Olutasidenib (FT-2102) induces durable complete remissions in patients with relapsed or refractory IDH1-mutated AML.

Author

de Botton, Stéphane, Fenaux, Pierre, Yee, Karen, Récher, Christian, Wei, Andrew, Montesinos, Pau, Taussig, David, Pigneux, Arnaud, Braun, Thorsten, Curti, Antonio, Grove, Carolyn, Khwaja, Asim, Legrand, Ollivier, Peterlin, Pierre, Arnan, Montserrat, Blum, William, Cilloni, Daniela, Hiwase, Devendra, Jurcic, Joseph, Krauter, Jürgen, Thomas, Xavier, Watts, Justin, Yang, Jay, Polyanskaya, Olga, Brevard, Julie, Sweeney, Jennifer, Barrett, Emma, Cortes, Jorge, and Jonas, Brian

Subjects
Humans, Adult, Middle Aged, Aged, Aged, 80 and over, Pyridines, Quinolines, Leukemia, Myeloid, Acute, Prognosis, Isocitrate Dehydrogenase
Abstract

Olutasidenib (FT-2102) is a potent, selective, oral, small-molecule inhibitor of mutant isocitrate dehydrogenase 1 (mIDH1). Overall, 153 IDH1 inhibitor-naive patients with mIDH1R132 relapsed/refractory (R/R) acute myeloid leukemia (AML) received olutasidenib monotherapy 150 mg twice daily in the pivotal cohort of this study. The median age of participants was 71 years (range, 32-87 years) and the median number of prior regimens received by patients was 2 (1-7). The rate of complete remission (CR) plus CR with partial hematologic recovery (CRh) was 35%, and the overall response rate was 48%. Response rates were similar in patients who had, and who had not, received prior venetoclax. With 55% of patients censored at the time of data cut-off, the median duration of CR/CRh was 25.9 months. The median duration of overall response was 11.7 months, and the median overall survival was 11.6 months. Of 86 patients who were transfusion dependent at baseline, a 56-day transfusion independence was achieved in 29 (34%), which included patients in all response groups. Grade 3 or 4 treatment-emergent adverse events (≥10%) were febrile neutropenia and anemia (n = 31; 20% each), thrombocytopenia (n = 25; 16%), and neutropenia (n = 20; 13%). Differentiation syndrome adverse events of special interest occurred in 22 (14%) patients, with 14 (9%) grade ≥3 and 1 fatal case reported. Overall, olutasidenib induced durable remissions and transfusion independence with a well-characterized and manageable side effect profile. The observed efficacy represents a therapeutic advance in this molecularly defined, poor-prognostic population of patients with mIDH1 R/R AML. This trial was registered at www.clinicaltrials.gov as #NCT02719574.

Published
2023

3. Hadamard Products and Binomial Ideals

Author

Atar, Büşra, Bhaskara, Kieran, Cook, Adrian, Da Silva, Sergio, Harada, Megumi, Rajchgot, Jenna, Van Tuyl, Adam, Wang, Runyue, and Yang, Jay

Subjects
Mathematics - Commutative Algebra, Mathematics - Algebraic Geometry, 13F65, 14N05, 14M99
Abstract

We study the Hadamard product of two varieties $V$ and $W$, with particular attention to the situation when one or both of $V$ and $W$ is a binomial variety. The main result of this paper shows that when $V$ and $W$ are both binomial varieties, and the binomials that define $V$ and $W$ have the same binomial exponents, then the defining equations of $V \star W$ can be computed explicitly and directly from the defining equations of $V$ and $W$. This result recovers known results about Hadamard products of binomial hypersurfaces and toric varieties. Moreover, as an application of our main result, we describe a relationship between the Hadamard product of the toric ideal $I_G$ of a graph $G$ and the toric ideal $I_H$ of a subgraph $H$ of $G$. We also derive results about algebraic invariants of Hadamard products: assuming $V$ and $W$ are binomial with the same exponents, we show that $\text{deg}(V\star W) = \text{deg}(V)=\text{deg}(W)$ and $\dim(V\star W) = \dim(V)=\dim(W)$. Finally, given any (not necessarily binomial) projective variety $V$ and a point $p \in \mathbb{P}^n \setminus \mathbb{V}(x_0x_1\cdots x_n)$, subject to some additional minor hypotheses, we find an explicit binomial variety that describes all the points $q$ that satisfy $p \star V = q\star V$., Comment: 24 pages, comments welcome

Published
2022

4. Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser.

Author

Jernigan, Rebecca J, Logeswaran, Dhenugen, Doppler, Diandra, Nagaratnam, Nirupa, Sonker, Mukul, Yang, Jay-How, Ketawala, Gihan, Martin-Garcia, Jose M, Shelby, Megan L, Grant, Thomas D, Mariani, Valerio, Tolstikova, Alexandra, Sheikh, Michelle Z, Yung, Mimi Cho, Coleman, Matthew A, Zaare, Sahba, Kaschner, Emily K, Rabbani, Mohammad Towshif, Nazari, Reza, Zacks, Michele A, Hayes, Brandon, Sierra, Raymond G, Hunter, Mark S, Lisova, Stella, Batyuk, Alexander, Kupitz, Christopher, Boutet, Sebastien, Hansen, Debra T, Kirian, Richard A, Schmidt, Marius, Fromme, Raimund, Frank, Matthias, Ros, Alexandra, Chen, Julian J-L, Botha, Sabine, and Fromme, Petra

Subjects
Humans, Crystallography, X-Ray, Lasers, Temperature, Electrons, COVID-19, SARS-CoV-2, NSP15, NendoU, X-ray free-electron laser, serial femtosecond crystallography, Prevention, Infectious Diseases, Emerging Infectious Diseases, Vaccine Related, Biodefense, Infection, Chemical Sciences, Biological Sciences, Information and Computing Sciences, Biophysics
Abstract

NendoU from SARS-CoV-2 is responsible for the virus's ability to evade the innate immune system by cleaving the polyuridine leader sequence of antisense viral RNA. Here we report the room-temperature structure of NendoU, solved by serial femtosecond crystallography at an X-ray free-electron laser to 2.6 Å resolution. The room-temperature structure provides insight into the flexibility, dynamics, and other intrinsic properties of NendoU, with indications that the enzyme functions as an allosteric switch. Functional studies examining cleavage specificity in solution and in crystals support the uridine-purine cleavage preference, and we demonstrate that enzyme activity is fully maintained in crystal form. Optimizing the purification of NendoU and identifying suitable crystallization conditions set the benchmark for future time-resolved serial femtosecond crystallography studies. This could advance the design of antivirals with higher efficacy in treating coronaviral infections, since drugs that block allosteric conformational changes are less prone to drug resistance.

Published
2023

8. Enhancing anti-AML activity of venetoclax by isoflavone ME-344 through suppression of OXPHOS and/or purine biosynthesis in vitro

Author

Hurrish, Katie H., Su, Yongwei, Patel, Shraddha, Ramage, Cassandra L., Zhao, Jianlei, Temby, Brianna R., Carter, Jenna L., Edwards, Holly, Buck, Steven A., Wiley, Sandra E., Hüttemann, Maik, Polin, Lisa, Kushner, Juiwanna, Dzinic, Sijana H., White, Kathryn, Bao, Xun, Li, Jing, Yang, Jay, Boerner, Julie, Hou, Zhanjun, Al-Atrash, Gheath, Konoplev, Sergej N., Busquets, Jonathan, Tiziani, Stefano, Matherly, Larry H., Taub, Jeffrey W., Konopleva, Marina, Ge, Yubin, and Baran, Natalia

Published
2024
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9. Syzygies of $\mathbb{P}^{1}\times \mathbb{P}^{1}$: data and conjectures

Author

Bruce, Juliette, Corey, Daniel, Erman, Daniel, Goldstein, Steve, Laudone, Robert P., and Yang, Jay

Subjects
Mathematics - Commutative Algebra, Mathematics - Algebraic Geometry, 13D02
Abstract

We provide a number of new conjectures and questions concerning the syzygies of $\mathbb{P}^1\times \mathbb{P}^1$. The conjectures are based on computing the graded Betti tables and related data for large number of different embeddings of $\mathbb{P}^1\times \mathbb{P}^1$. These computations utilize linear algebra over finite fields and high-performance computing.

Published
2021

10. Phase I First-in-Human Dose Escalation Study of the oral SF3B1 modulator H3B-8800 in myeloid neoplasms.

Author

Steensma, David, Wermke, Martin, Klimek, Virginia, Greenberg, Peter, Font, Patricia, Komrokji, Rami, Yang, Jay, Brunner, Andrew, Carraway, Hetty, Ades, Lionel, Al-Kali, Aref, Alonso-Dominguez, Juan, Alfonso-Piérola, Ana, Coombs, Catherine, Deeg, H, Flinn, Ian, Foran, James, Garcia-Manero, Guillermo, Maris, Michael, McMasters, Malgorzata, Micol, Jean-Baptiste, De Oteyza, Jaime, Thol, Felicitas, Wang, Eunice, Watts, Justin, Taylor, Justin, Stone, Richard, Gourineni, Vikram, Marino, Alyssa, Yao, Huilan, Destenaves, Benoit, Yuan, Xiaobin, Yu, Kun, Dar, Sara, Ohanjanian, Lernik, Kuida, Keisuke, Xiao, Jianjun, Scholz, Catherine, Gualberto, Antonio, and Platzbecker, Uwe

Subjects
Administration, Oral, Aged, Aged, 80 and over, Biomarkers, Tumor, Dose-Response Relationship, Drug, Female, Humans, Leukemia, Myeloid, Acute, Male, Middle Aged, Mutation, Missense, Myelodysplastic Syndromes, Patient Safety, Phosphoproteins, Piperazines, Pyridines, RNA Splicing Factors, Treatment Outcome
Abstract

We conducted a phase I clinical trial of H3B-8800, an oral small molecule that binds Splicing Factor 3B1 (SF3B1), in patients with MDS, CMML, or AML. Among 84 enrolled patients (42 MDS, 4 CMML and 38 AML), 62 were red blood cell (RBC) transfusion dependent at study entry. Dose escalation cohorts examined two once-daily dosing regimens: schedule I (5 days on/9 days off, range of doses studied 1-40 mg, n = 65) and schedule II (21 days on/7 days off, 7-20 mg, n = 19); 27 patients received treatment for ≥180 days. The most common treatment-related, treatment-emergent adverse events included diarrhea, nausea, fatigue, and vomiting. No complete or partial responses meeting IWG criteria were observed; however, RBC transfusion free intervals >56 days were observed in nine patients who were transfusion dependent at study entry (15%). Of 15 MDS patients with missense SF3B1 mutations, five experienced RBC transfusion independence (TI). Elevated pre-treatment expression of aberrant transcripts of Transmembrane Protein 14C (TMEM14C), an SF3B1 splicing target encoding a mitochondrial porphyrin transporter, was observed in MDS patients experiencing RBC TI. In summary, H3B-8800 treatment was associated with mostly low-grade TAEs and induced RBC TI in a biomarker-defined subset of MDS.

Published
2021

11. Whole Exome Sequencing Identifies a Novel Homozygous Missense Mutation in the CSB Protein-Encoding ERCC6 Gene in a Taiwanese Boy with Cockayne Syndrome.

Author

Lin, Ching-Ming, Yang, Jay-How, Lee, Hwei-Jen, Lin, Yu-Pang, Tsai, Li-Ping, Hsu, Chih-Sin, Luxton, G, and Hu, Chih-Fen

Subjects
Cockayne syndrome B, ERCC6, progeroid, transcription-coupled nucleotide excision repair (TC-NER), whole exome sequencing
Abstract

BACKGROUND: Cockayne syndrome (CS) is a rare form of dwarfism that is characterized by progressive premature aging. CS is typically caused by mutations in the excision repair cross-complementing protein group 6 (ERCC6) gene that encodes the CS group B (CSB) protein. Using whole exome sequencing, we recently identified a novel homozygous missense mutation (Leu536Trp) in CSB in a Taiwanese boy with CS. Since the current database (Varsome) interprets this variant as likely pathogenic, we utilized a bioinformatic tool to investigate the impact of Leu536Trp as well as two other variants (Arg453Ter, Asp532Gly) in similar articles on the CSB protein structure stability. METHODS: We used iterative threading assembly refinement (I-TASSER) to generate a predictive 3D structure of CSB. We calculated the change of mutation energy after residues substitution on the protein stability using I-TASSER as well as the artificial intelligence program Alphafold. RESULTS: The Asp532Gly variant destabilized both modeled structures, while the Leu536Trp variant showed no effect on I-TASSERs model but destabilized the Alphafolds modeled structure. CONCLUSIONS: We propose here the first case of CS associated with a novel homozygous missense mutation (Leu536Trp) in CSB. Furthermore, we suggest that the Asp532Gly and Leu536Trp variants are both pathogenic after bioinformatic analysis of protein stability.

Published
2021

12. Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography

Author

Pandey, Suraj, Calvey, George, Katz, Andrea M, Malla, Tek Narsingh, Koua, Faisal HM, Martin-Garcia, Jose M, Poudyal, Ishwor, Yang, Jay-How, Vakili, Mohammad, Yefanov, Oleksandr, Zielinski, Kara A, Bajt, Sasa, Awel, Salah, Doerner, Katarina, Frank, Matthias, Gelisio, Luca, Jernigan, Rebecca, Kirkwood, Henry, Kloos, Marco, Koliyadu, Jayanath, Mariani, Valerio, Miller, Mitchell D, Mills, Grant, Nelson, Garrett, Olmos, Jose L, Sadri, Alireza, Sato, Tokushi, Tolstikova, Alexandra, Xu, Weijun, Ourmazd, Abbas, Spence, John CH, Schwander, Peter, Barty, Anton, Chapman, Henry N, Fromme, Petra, Mancuso, Adrian P, Phillips, George N, Bean, Richard, Pollack, Lois, and Schmidt, Marius

Subjects
Tuberculosis, Rare Diseases, Good Health and Well Being, substrate diffusion in crystals, antibiotic resistance, beta-lactamases, enzyme kinetics, irreversible inhibition, mix-and-inject serial crystallography, serial femtosecond crystallography, European X-ray Free-Electron Laser, megahertz pulse-repetition rate, protein structure determination, drug discovery, ceftriaxone, sulbactam, X-ray crystallography, enzyme mechanisms, β-lactamases, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Condensed Matter Physics, Physical Chemistry (incl. Structural)
Abstract

Here, we illustrate what happens inside the catalytic cleft of an enzyme when substrate or ligand binds on single-millisecond timescales. The initial phase of the enzymatic cycle is observed with near-atomic resolution using the most advanced X-ray source currently available: the European XFEL (EuXFEL). The high repetition rate of the EuXFEL combined with our mix-and-inject technology enables the initial phase of ceftriaxone binding to the Mycobacterium tuberculosis β-lactamase to be followed using time-resolved crystallography in real time. It is shown how a diffusion coefficient in enzyme crystals can be derived directly from the X-ray data, enabling the determination of ligand and enzyme-ligand concentrations at any position in the crystal volume as a function of time. In addition, the structure of the irreversible inhibitor sulbactam bound to the enzyme at a 66 ms time delay after mixing is described. This demonstrates that the EuXFEL can be used as an important tool for biomedically relevant research.

Published
2021

13. Homological and combinatorial aspects of virtually Cohen--Macaulay sheaves

Author

Berkesch, Christine, Klein, Patricia, Loper, Michael C., and Yang, Jay

Subjects
Mathematics - Commutative Algebra, Mathematics - Algebraic Geometry, Mathematics - Combinatorics, 13D02 (Primary), 14M25, 13F55, 05E40 (Secondary)
Abstract

When studying a graded module $M$ over the Cox ring of a smooth projective toric variety $X$, there are two standard types of resolutions commonly used to glean information: free resolutions of $M$ and vector bundle resolutions of its sheafification. Each approach comes with its own challenges. There is geometric information that free resolutions fail to encode, while vector bundle resolutions can resist study using algebraic and combinatorial techniques. Recently, Berkesch, Erman, and Smith introduced virtual resolutions, which capture desirable geometric information and are also amenable to algebraic and combinatorial study. The theory of virtual resolutions includes a notion of a virtually Cohen--Macaulay property, though tools for assessing which modules are virtually Cohen--Macaulay have only recently started to be developed. In this paper, we continue this research program in two related ways. The first is that, when $X$ is a product of projective spaces, we produce a large new class of virtually Cohen--Macaulay Stanley--Reisner rings, which we show to be virtually Cohen--Macaulay via explicit constructions of appropriate virtual resolutions reflecting the underlying combinatorial structure. The second is that, for an arbitrary smooth projective toric variety $X$, we develop homological tools for assessing the virtual Cohen--Macaulay property. Some of these tools give exclusionary criteria, and others are constructive methods for producing suitably short virtual resolutions. We also use these tools to establish relationships among the arithmetically, geometrically, and virtually Cohen--Macaulay properties., Comment: Accepted to Transactions of the London Mathematical Society

Published
2020
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16. Asymptotic Degree of Random Monomial Ideals

Author

Silverstein, Lily, Wilburne, Dane, and Yang, Jay

Subjects
Mathematics - Commutative Algebra, Mathematics - Combinatorics
Abstract

One of the fundamental invariants connecting algebra and geometry is the degree of an ideal. In this paper we derive the probabilistic behavior of degree with respect to the versatile Erd\H{o}s-R\'enyi-type model for random monomial ideals defined in \cite{rmi}. We study the staircase structure associated to a monomial ideal, and show that in the random case the shape of the staircase diagram is approximately hyperbolic, and this behavior is robust across several random models. Since the discrete volume under this staircase is related to the summatory higher-order divisor function studied in number theory, we use this connection and our control over the shape of the staircase diagram to derive the asymptotic degree of a random monomial ideal. Another way to compute the degree of a monomial ideal is with a standard pair decomposition. This paper derives bounds on the number of standard pairs of a random monomial ideal indexed by any subset of the ring variables. The standard pairs indexed by maximal subsets give a count of degree, as well as being a more nuanced invariant of the random monomial ideal., Comment: 16 pages, 2 figures

Published
2020

17. Characteristic dependence of syzygies of random monomial ideals

Author

Booms, Caitlyn, Erman, Daniel, and Yang, Jay

Subjects
Mathematics - Commutative Algebra, Mathematics - Algebraic Geometry, Mathematics - Combinatorics
Abstract

When do syzygies depend on the characteristic of the field? Even for well-studied families of examples, very little is known. For a family of random monomial ideals, namely the Stanley--Reisner ideals of random flag complexes, we prove that the Betti numbers asymptotically almost always depend on the characteristic. Using this result, we also develop a heuristic for characteristic dependence of asymptotic syzygies of algebraic varieties., Comment: We have reworked the title, abstract, and introduction to reflect the paper's primary focus on homological behavior of random flag complexes. Further, Section 1.1 was added, which tries to more clearly explain how questions about asymptotic syzygies provided motivation for this work and how we see our new results as providing motivation for new conjectures about syzygies in geometric settings

Published
2020

20. Virtual Resolutions of Monomial Ideals on Toric Varieties

Author

Yang, Jay

Subjects
Mathematics - Commutative Algebra, Mathematics - Algebraic Geometry
Abstract

We use cellular resolutions of monomial ideals to prove an analog of Hilbert's syzygy theorem for virtual resolutions of monomial ideals on smooth toric varieties., Comment: Section 6 has been rewritten to correct a flaw in the original proof

Published
2019

21. The Schur-Veronese package in Macaulay2

Author

Bruce, Juliette, Erman, Daniel, Goldstein, Steve, and Yang, Jay

Subjects
Mathematics - Commutative Algebra
Abstract

This note introduces the Macaulay2 package SchurVeronese, which gathers together data about Veronese syzygies and makes it readily accessible in Macaulay2. In addition to standard Betti tables, the package includes information about the Schur decompositions of the various spaces of syzygies. The package also includes a number of functions useful for manipulating and studying this data., Comment: Minor revisions

Published
2019
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22. Author Correction: Membrane protein megahertz crystallography at the European XFEL

Author

Gisriel, Chris, Coe, Jesse, Letrun, Romain, Yefanov, Oleksandr M, Luna-Chavez, Cesar, Stander, Natasha E, Lisova, Stella, Mariani, Valerio, Kuhn, Manuela, Aplin, Steve, Grant, Thomas D, Dörner, Katerina, Sato, Tokushi, Echelmeier, Austin, Villarreal, Jorvani Cruz, Hunter, Mark S, Wiedorn, Max O, Knoska, Juraj, Mazalova, Victoria, Roy-Chowdhury, Shatabdi, Yang, Jay-How, Jones, Alex, Bean, Richard, Bielecki, Johan, Kim, Yoonhee, Mills, Grant, Weinhausen, Britta, Meza, Jose D, Al-Qudami, Nasser, Bajt, Saša, Brehm, Gerrit, Botha, Sabine, Boukhelef, Djelloul, Brockhauser, Sandor, Bruce, Barry D, Coleman, Matthew A, Danilevski, Cyril, Discianno, Erin, Dobson, Zachary, Fangohr, Hans, Martin-Garcia, Jose M, Gevorkov, Yaroslav, Hauf, Steffen, Hosseinizadeh, Ahmad, Januschek, Friederike, Ketawala, Gihan K, Kupitz, Christopher, Maia, Luis, Manetti, Maurizio, Messerschmidt, Marc, Michelat, Thomas, Mondal, Jyotirmoy, Ourmazd, Abbas, Previtali, Gianpietro, Sarrou, Iosifina, Schön, Silvan, Schwander, Peter, Shelby, Megan L, Silenzi, Alessandro, Sztuk-Dambietz, Jolanta, Szuba, Janusz, Turcato, Monica, White, Thomas A, Wrona, Krzysztof, Xu, Chen, Abdellatif, Mohamed H, Zook, James D, Spence, John CH, Chapman, Henry N, Barty, Anton, Kirian, Richard A, Frank, Matthias, Ros, Alexandra, Schmidt, Marius, Fromme, Raimund, Mancuso, Adrian P, Fromme, Petra, and Zatsepin, Nadia A

Subjects
Biochemistry and Cell Biology, Biological Sciences
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

23. Olutasidenib alone or with azacitidine in IDH1-mutated acute myeloid leukaemia and myelodysplastic syndrome: phase 1 results of a phase 1/2 trial

Author

Watts, Justin M, Baer, Maria R, Yang, Jay, Prebet, Thomas, Lee, Sangmin, Schiller, Gary J, Dinner, Shira N, Pigneux, Arnaud, Montesinos, Pau, Wang, Eunice S, Seiter, Karen P, Wei, Andrew H, De Botton, Stephane, Arnan, Montserrat, Donnellan, Will, Schwarer, Anthony P, Récher, Christian, Jonas, Brian A, Ferrell, P Brent, Jr, Marzac, Christophe, Kelly, Patrick, Sweeney, Jennifer, Forsyth, Sanjeev, Guichard, Sylvie M, Brevard, Julie, Henrick, Patrick, Mohamed, Hesham, and Cortes, Jorge E

Published
2023
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24. Domain-based analysis of RUNX1somatic mutations in myeloid neoplasms.

Author

Padmanabhan, Dakshin Sitaram, primary, Aguilar, Jeff Justin, additional, Dhillon, Vikram, additional, Potluri, Lakshmi Bhavani, additional, Nanja Reddy, Sushmitha, additional, Dhiman, Sandhya, additional, Kim, Paul, additional, Boerner, Julie, additional, Carr, David, additional, Yang, Jay, additional, Maciejewski, Jaroslaw P., additional, and Balasubramanian, Suresh Kumar, additional

Published
2024
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25. Conjectures and computations about Veronese syzygies

Author

Bruce, Juliette, Erman, Daniel, Goldstein, Steve, and Yang, Jay

Subjects
Mathematics - Commutative Algebra, Mathematics - Algebraic Geometry
Abstract

We formulate several conjectures which shed light on the structure of Veronese syzygies of projective spaces. Our conjectures are based on experimental data that we derived by developing a numerical linear algebra and distributed computation technique for computing and synthesizing new cases of Veronese embeddings for $\mathbb{P}^2$., Comment: 25 pages

Published
2017

26. Membrane protein megahertz crystallography at the European XFEL

Author

Gisriel, Chris, Coe, Jesse, Letrun, Romain, Yefanov, Oleksandr M, Luna-Chavez, Cesar, Stander, Natasha E, Lisova, Stella, Mariani, Valerio, Kuhn, Manuela, Aplin, Steve, Grant, Thomas D, Dörner, Katerina, Sato, Tokushi, Echelmeier, Austin, Cruz Villarreal, Jorvani, Hunter, Mark S, Wiedorn, Max O, Knoska, Juraj, Mazalova, Victoria, Roy-Chowdhury, Shatabdi, Yang, Jay-How, Jones, Alex, Bean, Richard, Bielecki, Johan, Kim, Yoonhee, Mills, Grant, Weinhausen, Britta, Meza, Jose D, Al-Qudami, Nasser, Bajt, Saša, Brehm, Gerrit, Botha, Sabine, Boukhelef, Djelloul, Brockhauser, Sandor, Bruce, Barry D, Coleman, Matthew A, Danilevski, Cyril, Discianno, Erin, Dobson, Zachary, Fangohr, Hans, Martin-Garcia, Jose M, Gevorkov, Yaroslav, Hauf, Steffen, Hosseinizadeh, Ahmad, Januschek, Friederike, Ketawala, Gihan K, Kupitz, Christopher, Maia, Luis, Manetti, Maurizio, Messerschmidt, Marc, Michelat, Thomas, Mondal, Jyotirmoy, Ourmazd, Abbas, Previtali, Gianpietro, Sarrou, Iosifina, Schön, Silvan, Schwander, Peter, Shelby, Megan L, Silenzi, Alessandro, Sztuk-Dambietz, Jolanta, Szuba, Janusz, Turcato, Monica, White, Thomas A, Wrona, Krzysztof, Xu, Chen, Abdellatif, Mohamed H, Zook, James D, Spence, John CH, Chapman, Henry N, Barty, Anton, Kirian, Richard A, Frank, Matthias, Ros, Alexandra, Schmidt, Marius, Fromme, Raimund, Mancuso, Adrian P, Fromme, Petra, and Zatsepin, Nadia A

Subjects
Biochemistry and Cell Biology, Biological Sciences, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Crystallography, Cyanobacteria, Electrons, Lasers, Membrane Proteins, Models, Molecular, Photosystem I Protein Complex, Static Electricity, Synchrotrons, Thermosynechococcus, X-Rays
Abstract

The world's first superconducting megahertz repetition rate hard X-ray free-electron laser (XFEL), the European XFEL, began operation in 2017, featuring a unique pulse train structure with 886 ns between pulses. With its rapid pulse rate, the European XFEL may alleviate some of the increasing demand for XFEL beamtime, particularly for membrane protein serial femtosecond crystallography (SFX), leveraging orders-of-magnitude faster data collection. Here, we report the first membrane protein megahertz SFX experiment, where we determined a 2.9 Å-resolution SFX structure of the large membrane protein complex, Photosystem I, a > 1 MDa complex containing 36 protein subunits and 381 cofactors. We address challenges to megahertz SFX for membrane protein complexes, including growth of large quantities of crystals and the large molecular and unit cell size that influence data collection and analysis. The results imply that megahertz crystallography could have an important impact on structure determination of large protein complexes with XFELs.

Published
2019

28. EZH2 inhibitor tazemetostat in patients with relapsed or refractory, BAP1-inactivated malignant pleural mesothelioma: a multicentre, open-label, phase 2 study

Author

Zauderer, Marjorie G, Szlosarek, Peter W, Le Moulec, Sylvestre, Popat, Sanjay, Taylor, Paul, Planchard, David, Scherpereel, Arnaud, Koczywas, Marianna, Forster, Martin, Cameron, Robert B, Peikert, Tobias, Argon, Evren Kocabaş, Michaud, Neil R, Szanto, Attila, Yang, Jay, Chen, Yingxue, Kansra, Vikram, Agarwal, Shefali, and Fennell, Dean A

Published
2022
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31. Random Flag Complexes and Asymptotic Syzygies

Author

Erman, Daniel and Yang, Jay

Subjects
Mathematics - Commutative Algebra, Mathematics - Algebraic Geometry, Mathematics - Combinatorics, 13D02, 13F55, 14J40, 05C80
Abstract

We use the probabilistic method to construct examples of conjectured phenomenon about asymptotic syzygies. In particular, we use the Stanley-Reisner ideals of random flag complexes to construct new examples of Ein and Lazarsfeld's nonvanishing for asymptotic syzygies and of Ein, Erman, and Lazarsfeld's conjectural on the asymptotic normal distribution of Betti numbers., Comment: 15 pages

Published
2017
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32. Multi-institutional study evaluating clinical outcome with allogeneic hematopoietic stem cell transplantation after blinatumomab in patients with B-cell acute lymphoblastic leukemia: real-world data

Author

Badar, Talha, Szabo, Aniko, Litzow, Mark, Burkart, Madelyn, Yurkiewicz, Ilana, Dinner, Shira, Hefazi, Mehrdad, Shallis, Rory M., Podoltsev, Nikolai, Patel, Anand A., Curran, Emily, Wadleigh, Martha, Balasubramanian, Suresh, Yang, Jay, Arslan, Shukaib, Aldoss, Ibrahim, Mattison, Ryan, Cenin, Danielle, Siebenaller, Caitlin, Advani, Anjali, Liedtke, Michaela, and Atallah, Ehab

Published
2021
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33. Random Toric Surfaces and a Threshold for Smoothness

Author

Yang, Jay

Subjects
Mathematics - Algebraic Geometry, Mathematics - Commutative Algebra, Mathematics - Combinatorics
Abstract

We present a notion of a random toric surface modeled on a notion of a random graph. We then study some threshold phenomena related to the smoothness of the resulting surfaces.

Published
2016
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34. Tazemetostat for patients with relapsed or refractory follicular lymphoma: an open-label, single-arm, multicentre, phase 2 trial

Author

Morschhauser, Franck, Tilly, Hervé, Chaidos, Aristeidis, McKay, Pamela, Phillips, Tycel, Assouline, Sarit, Batlevi, Connie Lee, Campbell, Phillip, Ribrag, Vincent, Damaj, Gandhi Laurent, Dickinson, Michael, Jurczak, Wojciech, Kazmierczak, Maciej, Opat, Stephen, Radford, John, Schmitt, Anna, Yang, Jay, Whalen, Jennifer, Agarwal, Shefali, Adib, Deyaa, and Salles, Gilles

Published
2020
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35. Enhancing anti-AML activity of venetoclax by isoflavone ME-344 through suppression of OXPHOS and/or purine biosynthesis in vitro

Author

Hurrish, Katie H., primary, Su, Yongwei, additional, Patel, Shraddha, additional, Ramage, Cassandra L., additional, Zhao, Jianlei, additional, Temby, Brianna R., additional, Carter, Jenna L., additional, Edwards, Holly, additional, Buck, Steven A., additional, Wiley, Sandra E., additional, Hüttemann, Maik, additional, Polin, Lisa, additional, Kushner, Juiwanna, additional, Dzinic, Sijana H., additional, White, Kathryn, additional, Bao, Xun, additional, Li, Jing, additional, Yang, Jay, additional, Boerner, Julie, additional, Hou, Zhanjun, additional, Al-Atrash, Gheath, additional, Konoplev, Sergej N., additional, Busquets, Jonathan, additional, Tiziani, Stefano, additional, Matherly, Larry H., additional, Taub, Jeffrey W., additional, Konopleva, Marina, additional, Ge, Yubin, additional, and Baran, Natalia, additional

Published
2023
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36. HJKC3-0006: Outcome of Patients with CML Treated on Second Line or Later Therapy in Routine Clinical Practice

Author

Thompson, James E, primary, Gao, Yan, additional, Visotcky, Alexis, additional, Flynn, Kathryn E, additional, Mauro, Michael, additional, Giever, Emily, additional, Baim, Arielle, additional, Akinola, Idayat, additional, Larson, Richard, additional, Jamy, Omer, additional, Hunter, Anthony M., additional, Kota, Vamsi K., additional, Cortes, Jorge, additional, Druker, Brian J., additional, Shah, Neil P., additional, Pinilla-Ibarz, Javier, additional, Yang, Jay, additional, Ritchie, Ellen K., additional, Rein, Lindsay A.M, additional, Smith, B. Douglas, additional, Tantravahi, Srinivas K., additional, Badar, Talha, additional, Deininger, Michael W., additional, and Atallah, Ehab L., additional

Published
2023
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47. Pemvidutide, a glp-1/glucagon dual receptor agonist, significantly reduces liver fat, fibro-inflammation, and body weight in patients with non-alcoholic fatty liver disease: a 24-week multicenter, randomized, double-blind, placebo-controlled trial

Author

Harrison, Stephen, primary, Tomah, Shaheen, additional, Suschak, John, additional, Roberts, Scot, additional, Yang, Jay, additional, He, Liang, additional, Georges, Bertrand, additional, Rodwell-Green, Lakisha, additional, Brown, Randy, additional, Harris, M. Scott, additional, and Browne, Sarah, additional

Published
2023
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