@unpublished{17115,
  abstract     = {Cascades are RNA-guided multi-subunit CRISPR-Cas surveillances complexes that target foreign nucleic acids for destruction. Here, we present a 2.9-Å resolution cryo-electron (cryo-EM) structure of the <jats:italic>D. vulgaris</jats:italic> type I-C Cascade bound to a double-stranded (ds)DNA target. Our data shows how the 5’-TTC-3’ protospacer adjacent motif (PAM) sequence is recognized, and provides a unique mechanism through which the displaced, single-stranded non-target strand (NTS) is stabilized via stacking interactions with protein subunits in order to favor R-loop formation and prevent dsDNA re-annealing. Additionally, we provide structural insights into how diverse anti-CRISPR (Acr) proteins utilize distinct strategies to achieve a shared mechanism of type I-C Cascade inhibition by blocking initial DNA binding. These observations provide a structural basis for directional R-loop formation and reveal how divergent Acr proteins have converged upon common molecular mechanisms to efficiently shut down CRISPR immunity.},
  author       = {O’Brien, Roisin E. and Bravo, Jack Peter Kelly and Ramos, Delisa and Hibshman, Grace N. and Wright, Jacquelyn T. and Taylor, David W.},
  booktitle    = {bioRxiv},
  publisher    = {Cold Spring Harbor Laboratory},
  title        = {{Modes of inhibition used by phage anti-CRISPRs to evade type I-C Cascade}},
  doi          = {10.1101/2022.06.15.496202},
  year         = {2022},
}

@unpublished{17116,
  abstract     = {CRISPR (Clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems are a type of adaptive immune response in bacteria and archaea that utilize crRNA (CRISPR RNA)-guided effector complexes to target complementary RNA or DNA for destruction. The prototypical type III-A and III-B CRISPR-Cas systems utilize multi-subunit effector complexes composed of individual proteins to cleave ssRNA targets at 6-nt intervals, as well as non-specifically degrading ssDNA and activating cyclic oligoadenylate (cOA) synthesis. Recent studies have shown that type III systems can contain subunit fusions yet maintain canonical type III RNA-targeting capabilities. To understand how a multi-subunit fusion effector functions, we determine structures of a variant type III-D effector and biochemically characterize how it cleaves RNA targets. These findings provide insights into how multi-subunit fusion proteins are tethered together and assemble into an active and programmable RNA endonuclease, how the effector utilizes a novel mechanism for target RNA seeding, and the structural basis for the evolution of type III effector complexes. Furthermore, our results provide a blueprint for fusing subunits in class 1 effectors for design of user-defined effector complexes with disparate activities.</jats:p><jats:sec><jats:title>Important note</jats:title><jats:p>While this manuscript was in preparation, a manuscript describing the structure of the type III-E effector was published<jats:sup>1</jats:sup>. We reference these important findings; however, a careful comparison of the structures will follow once the coordinates have been released by the PDB.},
  author       = {Schwartz, Evan A. and Bravo, Jack Peter Kelly and Macias, Luis A. and McCafferty, Caitlyn L. and Dangerfield, Tyler L. and Walker, Jada N. and Brodbelt, Jennifer S. and Fineran, Peter C. and Fagerlund, Robert D. and Taylor, David W.},
  booktitle    = {bioRxiv},
  publisher    = {Cold Spring Harbor Laboratory},
  title        = {{Assembly of multi-subunit fusion proteins into the RNA-targeting type III-D CRISPR-Cas effector complex}},
  doi          = {10.1101/2022.06.13.496011},
  year         = {2022},
}

@unpublished{17117,
  abstract     = {Cas12a2 is a CRISPR-associated nuclease that performs RNA-guided degradation of non-specific single-stranded (ss)RNA, ssDNA and double-stranded (ds)DNA upon recognition of a complementary RNA target, culminating in abortive infection (Dmytrenko 2022). Here, we report structures of Cas12a2 in binary, ternary, and quaternary complexes to reveal a complete activation pathway. Our structures reveal that Cas12a2 is autoinhibited until binding a cognate RNA target, which exposes the RuvC active site within a large, positively charged cleft. Double-stranded DNA substrates are captured through duplex distortion and local melting, stabilized by pairs of ‘aromatic clamp’ residues that are crucial for dsDNA degradation and in <jats:italic>vivo</jats:italic> immune system function. Our work provides a structural basis for this unprecedented mechanism of abortive infection to achieve population-level immunity, which can be leveraged to create rational mutants that degrade a spectrum of collateral substrates.},
  author       = {Bravo, Jack Peter Kelly and Hallmark, Thom and Naegle, Bronson and Beisel, Chase L. and Jackson, Ryan N. and Taylor, David W.},
  booktitle    = {bioRxiv},
  publisher    = {Cold Spring Harbor Laboratory},
  title        = {{Large-scale structural rearrangements unleash indiscriminate nuclease activity of CRISPR-Cas12a2}},
  doi          = {10.1101/2022.06.13.495754},
  year         = {2022},
}

@unpublished{17157,
  abstract     = {An action of a complex reductive group G on a smooth projective variety X is regular when all regular unipotent elements in G act with finitely many fixed points. Then the complex G-equivariant cohomology ring of X is isomorphic to the coordinate ring of a certain regular fixed point scheme. Examples include partial flag varieties, smooth Schubert varieties and Bott-Samelson varieties. We also show that a more general version of the fixed point scheme allows a generalisation to GKM spaces, such as toric varieties.},
  author       = {Hausel, Tamás and Rychlewicz, Kamil P},
  booktitle    = {arXiv},
  title        = {{Spectrum of equivariant cohomology as a fixed point scheme}},
  doi          = {10.48550/arXiv.2212.11836},
  year         = {2022},
}

@article{18606,
  abstract     = {Shear thickening is an intriguing rheological behaviour which consists in a brutal increase in the viscosity above a critical shear rate. It is famously encountered in suspensions of corn starch in water. Despite having been discovered in the early 1930's, its underlying mechanisms remained a mystery for a long time. In 2013–14, numerical and theoretical works [[1], [2], [3]] put forward a frictional transition scenario to explain this phenomenon.
In this talk, I will present experimental work investigating this frictional transition scenario. In order to test the ideas of this model, one has to go further than standard rheological techniques, since they do not provide access to the frictional state of the measured suspension. I will thus focus on the techniques that we developed in order to evidence the frictional transition and link it to the presence of a shear-thickening behaviour.},
  author       = {Clavaud, Cécile},
  issn         = {2772-5693},
  journal      = {Science Talks},
  publisher    = {Elsevier},
  title        = {{Shear thickening in dense suspensions: an experimental study}},
  doi          = {10.1016/j.sctalk.2022.100038},
  volume       = {3},
  year         = {2022},
}

@inproceedings{18876,
  abstract     = {Convolutional neural networks were the standard for solving many computer vision tasks until recently, when Transformers of MLP-based architectures have started to show competitive performance. These architectures typically have a vast number of weights and need to be trained on massive datasets; hence, they are not suitable for their use in low-data regimes. In this work, we propose a simple yet effective framework to improve generalization from small amounts of data. We augment modern CNNs with fully-connected (FC) layers and show the massive impact this architectural change has in low-data regimes. We further present an online joint knowledge-distillation method to utilize the extra FC layers at train time but avoid them during test time. This allows us to improve the generalization of a CNN-based model without any increase in the number of weights at test time. We perform classification experiments for a large range of network backbones and several standard datasets on supervised learning and active learning. Our experiments significantly outperform the networks without fully-connected layers, reaching a relative improvement of up to 16% validation accuracy in the supervised setting without adding any extra parameters during inference.},
  author       = {Kocsis, Peter and Súkeník, Peter and Brasó, Guillem and Niessner, Matthias and Leal-Taixé, Laura and Elezi, Ismail},
  booktitle    = {36th Conference on Neural Information Processing Systems},
  issn         = {1049-5258},
  location     = {New Orleans, LA, United States},
  pages        = {1896--1908},
  publisher    = {Neural Information Processing Systems Foundation},
  title        = {{The unreasonable effectiveness of fully-connected layers for low-data regimes}},
  volume       = {35},
  year         = {2022},
}

@article{19490,
  abstract     = {Abstract. We study integral points on the quadratic twists ED : y2 = x3 −
D2x of the congruent number curve. We give upper bounds on the number of
integral points in each coset of 2ED(Q) in ED(Q) and show that their total is
 (3.8)rank ED(Q). We further show that the average number of non-torsion
integral points in this family is bounded above by 2. As an application we also
deduce from our upper bounds that the system of simultaneous Pell equations
aX2 − bY 2 = d, bY 2 − cZ2 = d for pairwise coprime positive integers a, b, c, d,
has at most  (3.6)ω(abcd) integer solutions.},
  author       = {Chan, Yik Tung},
  issn         = {1088-6850},
  journal      = {Transactions of the American Mathematical Society},
  number       = {9},
  pages        = {6675--6700},
  publisher    = {American Mathematical Society},
  title        = {{Integral points on the congruent number curve}},
  doi          = {10.1090/tran/8732},
  volume       = {375},
  year         = {2022},
}

@article{19491,
  abstract     = {Using a recent breakthrough of Smith [18], we improve the results of Fouvry and Klüners [4, 5] on the solubility of the negative Pell equation. Let D denote the set of positive squarefree integers having no prime factors congruent to 3 modulo 4 . Stevenhagen [19] conjectured that the density of d in D such that the negative Pell equation x2−dy2=−1 is solvable with x,y∈Z is 58.1% , to the nearest tenth of a percent. By studying the distribution of the 8 -rank of narrow class groups Cl+(d) of Q(√d) , we prove that the infimum of this density is at least 53.8% .},
  author       = {Chan, Yik Tung and Koymans, Peter and Milovic, Djordjo and Pagano, Carlo},
  issn         = {2050-5094},
  journal      = {Forum of Mathematics, Sigma},
  publisher    = {Cambridge University Press},
  title        = {{The 8-rank of the narrow class group and the negative Pell equation}},
  doi          = {10.1017/fms.2022.40},
  volume       = {10},
  year         = {2022},
}

@article{19822,
  abstract     = {>Controlling spin wave excitations in magnetic materials underpins the burgeoning field of magnonics. Yet, little is known about how magnons interact with the conduction electrons of itinerant magnets, or how this interplay can be controlled. Via a surface-sensitive spectroscopic approach, we demonstrate a strong electron–magnon coupling at the Pd-terminated surface of the delafossite oxide PdCoO2, where a polar surface charge mediates a Stoner transition to itinerant surface ferromagnetism. We show how the coupling is enhanced sevenfold with increasing surface disorder, and concomitant charge carrier doping, becoming sufficiently strong to drive the system into a polaronic regime, accompanied by a significant quasiparticle mass enhancement. Our study thus sheds light on electron–magnon interactions in solid-state materials, and the ways in which these can be controlled.},
  author       = {Mazzola, F. and Yim, C. -M. and Sunko, Veronika and Khim, S. and Kushwaha, P. and Clark, O. J. and Bawden, L. and Marković, I. and Chakraborti, D. and Kim, T. K. and Hoesch, M. and Mackenzie, A. P. and Wahl, P. and King, P. D. C.},
  issn         = {2397-4648},
  journal      = {npj Quantum Materials},
  publisher    = {Springer Nature},
  title        = {{Tuneable electron–magnon coupling of ferromagnetic surface states in PdCoO2}},
  doi          = {10.1038/s41535-022-00428-8},
  volume       = {7},
  year         = {2022},
}

@inbook{19984,
  abstract     = {The first part of this paper is a survey of mathematical results on mirror symmetry phenomena between Hitchin systems for Langlands dual groups. The second part introduces
and discusses multiplicity algebras of the Hitchin system on Lagrangians, and considers
corresponding conjectural structures on their mirror.},
  author       = {Hausel, Tamás},
  booktitle    = {International Congress of Mathematicians},
  isbn         = {9783985470587},
  location     = {virtuel},
  pages        = {2228--2249},
  publisher    = {EMS Press},
  title        = {{Enhanced mirror symmetry for Langlands dual Hitchin systems}},
  doi          = {10.4171/icm2022/164},
  year         = {2022},
}

@inbook{20062,
  abstract     = {This article presents two fine-grained complexity lower bounds with relevance to algorithmic problems in computer aided verification. We have chosen these lower bounds as the proofs are relatively simple, but the techniques can be extended to give lower bounds for many more algorithmic problems. The goal is to present the bounds with minimal notation, making the results accessible to a broad community and stimulating further research in the area.

Specifically, we first describe a lower bound on the symbolic complexity of computing strongly connected components, which can be extended to show lower bounds for fundamental model-checking questions in graphs, published in [CDHL16b]. Second we present a conditional lower bound for disjunctive safety problems on graphs from [CDHL18] in the RAM model of computation. This bound can be modified to give conditional lower bounds for disjunctive objectives for reachability, Büchi, coBüchi and Rabin objectives in MDPs. We also present various open questions.},
  author       = {Henzinger, Monika H},
  booktitle    = {Principles of Systems Design},
  editor       = {Raskin, Jean-François and Chatterjee, Krishnendu and Doyen, Laurent and Majumdar, Rupak},
  isbn         = {9783031223365},
  issn         = {1611-3349},
  pages        = {292--305},
  publisher    = {Springer Nature Switzerland},
  title        = {{Fine-Grained Complexity Lower Bounds for Problems in Computer Aided Verification}},
  doi          = {10.1007/978-3-031-22337-2_14},
  volume       = {13660},
  year         = {2022},
}

@article{20616,
  abstract     = {We establish two WDVV-style relations for the disk invariants of real symplectic fourfolds by implementing Georgieva’s suggestion to lift homology relations from the Deligne–Mumford moduli spaces of stable real curves. This is accomplished by lifting judiciously chosen cobordisms realizing these relations. The resulting lifted relations lead to the recursions for Welschinger invariants announced by Solomon in 2007 and have the same structure as his WDVV-style relations, but differ by signs from the latter. Our topological approach provides a general framework for lifting relations via morphisms between not necessarily orientable spaces.},
  author       = {Chen, Xujia},
  issn         = {1420-8970},
  journal      = {Geometric and Functional Analysis},
  number       = {3},
  pages        = {490--567},
  publisher    = {Springer Nature},
  title        = {{Steenrod pseudocycles, lifted cobordisms, and Solomon’s relations for Welschinger invariants}},
  doi          = {10.1007/s00039-022-00596-6},
  volume       = {32},
  year         = {2022},
}

@article{20617,
  abstract     = {Our previous paper describes a geometric translation of the construction of open Gromov–Witten invariants by Solomon and Tukachinsky from a perspective of $A_{\infty }$-algebras of differential forms. We now use this geometric perspective to show that these invariants reduce to Welschinger’s open Gromov–Witten invariants in dimension 6, inline with their and Tian’s expectations. As an immediate corollary, we obtain a translation of Solomon–Tukachinsky’s open WDVV equations into relations for Welschinger’s invariants.},
  author       = {Chen, Xujia},
  issn         = {1687-0247},
  journal      = {International Mathematics Research Notices},
  number       = {9},
  pages        = {7021--7055},
  publisher    = {Oxford University Press},
  title        = {{Solomon-Tukachinsky’s versus Welschinger’s open Gromov-Witten invariants of symplectic six-folds}},
  doi          = {10.1093/imrn/rnaa318},
  volume       = {2022},
  year         = {2022},
}

@article{20620,
  abstract     = {The 2016 papers of J. Solomon and S. Tukachinsky use bounding chains in Fukaya's $A_{\infty}$-algebras to define numerical disk counts relative to a Lagrangian under certain regularity assumptions on the moduli spaces of disks. We present a (self-contained) direct geometric analogue of their construction under weaker topological assumptions, extend it over arbitrary rings in the process, and sketch an extension without any assumptions over rings containing the rationals. This implements the intuitive suggestion represented by their drawing and P. Georgieva's perspective. We also note a curious relation for the standard Gromov-Witten invariants readily deducible from their work. In a sequel, we use the geometric perspective of this paper to relate Solomon-Tukachinsky's invariants to Welschinger's open invariants of symplectic sixfolds, confirming their belief and G. Tian's related expectation concerning K. Fukaya's earlier construction.},
  author       = {Chen, Xujia},
  journal      = {Peking Mathematical Journal },
  pages        = {279--348},
  publisher    = {Springer Nature},
  title        = {{A geometric depiction of Solomon-Tukachinsky's construction of open GW-invariants}},
  doi          = {10.1007/s42543-021-00044-8},
  volume       = {5},
  year         = {2022},
}

@inproceedings{20627,
  abstract     = {The modern control model of the two-wheeled balancing vehicle is established by rational simplification and linearization and selection of appropriate state space variables. The state space expressions in modern control theory are used to make up for some deficiencies in the classical inverted pendulum model. By constructing the mathematical model of the LQR controller in MATLAB, using Simulink for model design and theoretical simulation analysis according to the actual application scenario, the results show that the improved LQR controller can be used in the autonomous balance control and anti-external interference of the two-wheeled self-balancing vehicle model. Has excellent performance.},
  author       = {Yuan, Jiemin and Chen, Haiyun and Yong, Tao and Lai, Xi and Chen, Xujia},
  booktitle    = {6th Advanced Information Technology, Electronic and Automation Control Conference},
  location     = {Beijing, China},
  publisher    = {IEEE},
  title        = {{Research on two-wheeled balance car based on improved LQR controller}},
  doi          = {10.1109/iaeac54830.2022.9930026},
  year         = {2022},
}

@article{20763,
  abstract     = {Compared with peripheral late-stage transformations mainly focusing on carbon–hydrogen functionalizations, reliable strategies to directly edit the core skeleton of pharmaceutical lead compounds still remain scarce despite the recent flurry of activity in this area. Herein, we report the skeletal editing of indoles through nitrogen atom insertion, accessing the corresponding quinazoline or quinoxaline bioisosteres by trapping of an electrophilic nitrene species generated from ammonium carbamate and hypervalent iodine. This reactivity relies on the strategic use of a silyl group as a labile protecting group that can facilitate subsequent product release. The utility of this highly functional group-compatible methodology in the context of late-stage skeletal editing of several commercial drugs is demonstrated.},
  author       = {Reisenbauer, Julia and Green, Ori and Franchino, Allegra and Finkelstein, Patrick and Morandi, Bill},
  issn         = {1095-9203},
  journal      = {Science},
  number       = {6610},
  pages        = {1104--1109},
  publisher    = {American Association for the Advancement of Science},
  title        = {{Late-stage diversification of indole skeletons through nitrogen atom insertion}},
  doi          = {10.1126/science.add1383},
  volume       = {377},
  year         = {2022},
}

@article{20764,
  abstract     = {Hydrocyanation reactions enable access to synthetically valuable nitriles from readily available alkene precursors. However, hydrocyanation reactions using hydrogen cyanide (HCN) or similarly toxic reagents on laboratory scale can be particularly challenging due to their hazardous nature. In addition, such processes typically require air- and temperature-sensitive Ni(0) precatalysts, further reducing the operational simplicity of this transformation. Herein, we report a HCN-free transfer hydrocyanation of alkenes and alkynes that employs commercially available aliphatic nitriles as sacrificial HCN donors in combination with a catalytic amount of air-stable and inexpensive NiCl2 as a precatalyst and a cocatalytic Lewis acid. The scalability and robustness of the catalytic process were demonstrated by the hydrocyanation of α-methylstyrene on a 100 mmol scale (11.4 g of product obtained) using 1 mol % of the Ni catalyst. In addition, the feasibility of the dehydrocyanation protocol using the air-stable Ni(II) precatalyst and norbornadiene as a sacrificial acceptor was showcased by the selective conversion of an aliphatic nitrile into the corresponding alkene.},
  author       = {Reisenbauer, Julia and Bhawal, Benjamin N. and Jelmini, Nicola and Morandi, Bill},
  issn         = {1520-586X},
  journal      = {Organic Process Research & Development},
  number       = {4},
  pages        = {1165--1173},
  publisher    = {American Chemical Society},
  title        = {{Development of an operationally simple, scalable, and HCN-free transfer hydrocyanation protocol using an air-stable nickel precatalyst}},
  doi          = {10.1021/acs.oprd.1c00442},
  volume       = {26},
  year         = {2022},
}

@article{10016,
  abstract     = {Auxin has always been at the forefront of research in plant physiology and development. Since the earliest contemplations by Julius von Sachs and Charles Darwin, more than a century-long struggle has been waged to understand its function. This largely reflects the failures, successes, and inevitable progress in the entire field of plant signaling and development. Here I present 14 stations on our long and sometimes mystical journey to understand auxin. These highlights were selected to give a flavor of the field and to show the scope and limits of our current knowledge. A special focus is put on features that make auxin unique among phytohormones, such as its dynamic, directional transport network, which integrates external and internal signals, including self-organizing feedback. Accented are persistent mysteries and controversies. The unexpected discoveries related to rapid auxin responses and growth regulation recently disturbed our contentment regarding understanding of the auxin signaling mechanism. These new revelations, along with advances in technology, usher us into a new, exciting era in auxin research. },
  author       = {Friml, Jiří},
  issn         = {1943-0264},
  journal      = {Cold Spring Harbor Perspectives in Biology},
  number       = {5},
  publisher    = {Cold Spring Harbor Laboratory Press},
  title        = {{Fourteen stations of auxin}},
  doi          = {10.1101/cshperspect.a039859},
  volume       = {14},
  year         = {2022},
}

@article{10181,
  abstract     = {In this article we study some geometric properties of proximally smooth sets. First, we introduce a modification of the metric projection and prove its existence. Then we provide an algorithm for constructing a rectifiable curve between two sufficiently close points of a proximally smooth set in a uniformly convex and uniformly smooth Banach space, with the moduli of smoothness and convexity of power type. Our algorithm returns a reasonably short curve between two sufficiently close points of a proximally smooth set, is iterative and uses our modification of the metric projection. We estimate the length of the constructed curve and its deviation from the segment with the same endpoints. These estimates coincide up to a constant factor with those for the geodesics in a proximally smooth set in a Hilbert space.},
  author       = {Ivanov, Grigory and Lopushanski, Mariana S.},
  issn         = {1877-0541},
  journal      = {Set-Valued and Variational Analysis},
  number       = {2},
  pages        = {657--675},
  publisher    = {Springer Nature},
  title        = {{Rectifiable curves in proximally smooth sets}},
  doi          = {10.1007/s11228-021-00612-1},
  volume       = {30},
  year         = {2022},
}

@article{10182,
  abstract     = {The mitochondrial oxidative phosphorylation system is central to cellular metabolism. It comprises five enzymatic complexes and two mobile electron carriers that work in a mitochondrial respiratory chain. By coupling the oxidation of reducing equivalents coming into mitochondria to the generation and subsequent dissipation of a proton gradient across the inner mitochondrial membrane, this electron transport chain drives the production of ATP, which is then used as a primary energy carrier in virtually all cellular processes. Minimal perturbations of the respiratory chain activity are linked to diseases; therefore, it is necessary to understand how these complexes are assembled and regulated and how they function. In this Review, we outline the latest assembly models for each individual complex, and we also highlight the recent discoveries indicating that the formation of larger assemblies, known as respiratory supercomplexes, originates from the association of the intermediates of individual complexes. We then discuss how recent cryo-electron microscopy structures have been key to answering open questions on the function of the electron transport chain in mitochondrial respiration and how supercomplexes and other factors, including metabolites, can regulate the activity of the single complexes. When relevant, we discuss how these mechanisms contribute to physiology and outline their deregulation in human diseases.},
  author       = {Vercellino, Irene and Sazanov, Leonid A},
  issn         = {1471-0080},
  journal      = {Nature Reviews Molecular Cell Biology},
  pages        = {141–161},
  publisher    = {Springer Nature},
  title        = {{The assembly, regulation and function of the mitochondrial respiratory chain}},
  doi          = {10.1038/s41580-021-00415-0},
  volume       = {23},
  year         = {2022},
}