cssi/SciSciGPT-SciSciNet huggingface dataset:
Regioselective synthesis of fluoroaldols. Studies toward fluoroepothilones syntheses via antibody catalysis

Abstract A general method for the synthesis of fluoromethyl aldols has been developed. Tributylboron enolates of fluoroacetone react with thiazole aldehydes (6) to provide fluoromethylaldols (4) regioselectively in high yields. Regioisomeric fluoroaldols (5) are produced as a 1:1 isomeric mixture of the erythro and threo products via a two-step procedure: first, aldol reaction with Weinreb amide and then Grignard reaction.
Promoter Boundaries for the luxCDABE and betIBA-proXWV Operons in Vibrio harveyi Defined by the Method Rapid Arbitrary PCR Insertion Libraries (RAIL)

ABSTRACT Experimental studies of transcriptional regulation in bacteria require the ability to precisely measure changes in gene expression, often accomplished through the use of reporter genes. However, the boundaries of promoter sequences required for transcription are often unknown, thus complicating the construction of reporters and genetic analysis of transcriptional regulation. Here, we analyze reporter libraries to define the promoter boundaries of the luxCDABE bioluminescence operon and the betIBA-proXWV osmotic stress operon in Vibrio harveyi. We describe a new method called rapid arbitrary PCR insertion libraries (RAIL) that combines the power of arbitrary PCR and isothermal DNA assembly to rapidly clone promoter fragments of various lengths upstream of reporter genes to generate large libraries. To demonstrate the versatility and efficiency of RAIL, we analyzed the promoters driving expression of the luxCDABE and betIBA-proXWV operons and created libraries of DNA fragments from these loci fused to fluorescent reporters. Using flow cytometry sorting and deep sequencing, we identified the DNA regions necessary and sufficient for maximum gene expression for each promoter. These analyses uncovered previously unknown regulatory sequences and validated known transcription factor binding sites. We applied this high-throughput method to gfp, mCherry, and lacZ reporters and multiple promoters in V. harveyi. We anticipate that the RAIL method will be easily applicable to other model systems for genetic, molecular, and cell biological applications. IMPORTANCE Gene reporter constructs have long been essential tools for studying gene regulation in bacteria, particularly following the recent advent of fluorescent gene reporters. We developed a new method that enables efficient construction of promoter fusions to reporter genes to study gene regulation. We demonstrate the versatility of this technique in the model bacterium Vibrio harveyi by constructing promoter libraries for three bacterial promoters using three reporter genes. These libraries can be used to determine the DNA sequences required for gene expression, revealing regulatory elements in promoters. This method is applicable to various model systems and reporter genes for assaying gene expression.
Molecular Routes to Tin Oxides

A general route to low temperature synthesis of ternary metal tin oxides with controlled stoichiometries from single component molecular metal alkoxide precursors is described. The solid state and solution structures of homoleptic tin(IV) alkoxide compounds have been investigated to establish criteria for the determination of their solution structure. Tin alkoxide compounds suitable for metathesis reactions have been synthesized and used to prepare the mixed metal alkoxide compounds [ZnSn(OEt)6] and [((COD)Rh)2Sn(OEt)6] (where Et = ethyl and COD = 1,5-cyclooctadiene). Hydrolysis of [ZnSn(OEt)6] at neutral pH results in the formation of a high surface area, mainly amorphous hydrous oxide powder which forms Zn2SnO4 and SnO2 on heating to 600°C and ZnSnO3 on heating to 1000°C.Thermolysis of [((COD)Rh}2Sn(OEt)6] results in formation of rhodium and tin(IV) oxide (cassiterite phase).
Debenzylation of complex oligosaccharides using ferric chloride

Abstract Anhydrous FeCl 3 in CH 2 Cl 2 at room temperature and 0 °C has been used to debenzylate monosaccharides and oligosaccharides in yields generally greater than 70%. Notably, alkenes, acetates, benzoates, phthalimides, acyl amides, and sensitive glycosidic linkages are unaffected by the reaction conditions.
Quantifying the risk of hemiplasy in phylogenetic inference

Convergent evolution-the appearance of the same character state in apparently unrelated organisms-is often inferred when a trait is incongruent with the species tree. However, trait incongruence can also arise from changes that occur on discordant gene trees, a process referred to as hemiplasy. Hemiplasy is rarely taken into account in studies of convergent evolution, despite the fact that phylogenomic studies have revealed rampant discordance. Here, we study the relative probabilities of homoplasy (including convergence and reversal) and hemiplasy for an incongruent trait. We derive expressions for the probabilities of the two events, showing that they depend on many of the same parameters. We find that hemiplasy is as likely-or more likely-than homoplasy for a wide range of conditions, even when levels of discordance are low. We also present a method to calculate the ratio of these two probabilities (the "hemiplasy risk factor") along the branches of a phylogeny of arbitrary length. Such calculations can be applied to any tree to identify when and where incongruent traits may be due to hemiplasy.
Liquid/Liquid Interface as a Model System for Studying Electrochemical Catalysis in Microemulsions. Reduction of trans-1,2-Dibromocyclohexane with Vitamin B12

A complex electrochemical catalytic reaction was investigated at the interface between water and benzonitrile as a model for interfacial chemistry in microemulsions. Structures similar to those between oil−water microphases in microemulsions were created by using the interface between two immiscible electrolyte solutions (ITIES). While interfacial area in a microemulsion can be uncertain, the ITIES is well-defined and can be used to evaluate relevant heterogeneous interfacial kinetics. The reaction between the Co(I) form of vitamin B12 generated electrochemically in the water phase, and trans-1,2-dibromocyclohexane (DBCH) in benzonitrile was probed directly at the ITIES by scanning electrochemical microscopy (SECM). Apparent heterogeneous rate constants for the interfacial reaction were extracted from SECM current−distance curves. Influences of reactant concentration, potential drop across the ITIES, and adsorbed surfactants were investigated. Results suggest that the kinetics of reduction of DBCH by B12 ...
The Gene Master Regulators (GMR) Approach Provides Legitimate Targets for Personalized, Time-Sensitive Cancer Gene Therapy

The dynamic and never exactly repeatable tumor transcriptomic profile of people affected by the same form of cancer requires a personalized and time-sensitive approach of the gene therapy. The Gene Master Regulators (GMRs) were defined as genes whose highly controlled expression by the homeostatic mechanisms commands the cell phenotype by modulating major functional pathways through expression correlation with their genes. The Gene Commanding Height (GCH), a measure that combines the expression control and expression correlation with all other genes, is used to establish the gene hierarchy in each cell phenotype. We developed the experimental protocol, the mathematical algorithm and the computer software to identify the GMRs from transcriptomic data in surgically removed tumors, biopsies or blood from cancer patients. The GMR approach is illustrated with applications to our microarray data on human kidney, thyroid and prostate cancer samples, and on thyroid, prostate and blood cancer cell lines. We proved experimentally that each patient has his/her own GMRs, that cancer nuclei and surrounding normal tissue are governed by different GMRs, and that manipulating the expression has larger consequences for genes with higher GCH. Therefore, we launch the hypothesis that silencing the GMR may selectively kill the cancer cells from a tissue.
Highly enantioselective syntheses of anti homoaldol products by (-)-sparteine-mediated lithiation/transmetalation/substitution of N-Boc allylic amines.

(−)-Sparteine-mediated lithiation/transmetalation/substitution of N-Boc allylic amines provides anti-configured homoaldol precursors in yields of 38−85% and enantiomeric ratios of 83:17−99:1. Subsequent O-protection and hydrolysis allows access to O-protected homoaldol adducts in good yields. The absolute configurations of the homoaldol products have been assigned by calculation of optical rotations and by X-ray crystallography of derivatives. A stereochemical course of reaction for the lithiation/transmetalation/substitution sequence is proposed.
Nickel catalyzed silane reductions of α, β - unsaturated ketones and nitriles

Abstract Activated nickel, produced by the ultrasound-promoted reduction of nickel iodide with lithium, catalyzes the 1,4 addition of phenylsilane to α, β-unsaturated ketones and α,β -unsaturated nitriles to give, after hydrolysis, high yields of the products of 1,2 hydrogenation.
Carboxamidation of Pyridines by the System of Elemental Fluorine-Carbonitrile-Water: A Useful Alternative to the Chichibabin Amination

Abstract The title reaction with pyridine, 4-methylpyridine, 3-methylpyridine, 3-bromopyridine, nicotinonitrile, and quinoline yields 2-carboxamido derivatives regioselectively. Isoquinoline is amidated at position 1.
Three-Component, Stereoselective Palladium-Catalyzed Synthesis of Functionalized Bicyclopentanoids

1,5-Cyclooctadiene can be stereoselectively transformed into a substituted bicyclo[3.3.0]octane ring system under palladium catalysis with concomitant formation of three carbon−carbon bonds. Reaction with an aryl iodide or triflate and malonate gives an exo-endo product, while the reaction with a malonate in the presence of oxygen affords a bis-endo adduct.
Syntheses of [F5TeNH3][AsF6], [F5TeN(H)Xe][AsF6], and F5TeNF2 and Characterization by Multi-NMR and Raman Spectroscopy and by Electronic Structure Calculations: The X-ray Crystal Structures of α- and β-F5TeNH2, [F5TeNH3][AsF6], and [F5TeN(H)Xe][AsF6]

The salt, [F5TeN(H)Xe][AsF6], has been synthesized in the natural abundance and 99.5% 15N-enriched forms. The F5TeN(H)Xe+ cation has been obtained as the product of the reactions of [F5TeNH3][AsF6] with XeF2 (HF and BrF5 solvents) and F5TeNH2 with [XeF][AsF6] (HF solvent) and characterized in solution by 129Xe, 19F, 125Te, 1H, and 15N NMR spectroscopy at −60 to −30 °C. The orange [F5TeN(H)Xe][AsF6] and colorless [F5TeNH3][AsF6] salts were crystallized as a mixture from HF solvent at −35 °C and were characterized by Raman spectroscopy at −165 °C and by X-ray crystallography. The crystal structure of the low-temperature phase, α-F5TeNH2, was obtained by crystallization from liquid SO2 between −50 and −70 °C and is fully ordered. The high-temperature phase, β-F5TeNH2, was obtained by sublimation at room temperature and exhibits a 6-fold disorder. Decomposition of [F5TeN(H)Xe][AsF6] in the solid state was rapid above −30 °C. The decomposition of F5TeN(H)Xe+ in HF and BrF5 solution at −33 °C proceeded by fluor...
Free radical reactions for heterocycle synthesis. Part 3: Formation of novel spirodilactones, spirolactone-lactams, and spirolactone-thiolactones

Synthesis of spirodilactones is achieved by intramolecular free radical Michael addition of enol esters derivatized from tetronic acid. Synthesis of spirolactone-lactams and spirolactone-thiolactones is also covered by the scope of this new reaction.
Characterization of Methicillin-resistant Staphylococcus aureus Isolates from Fitness Centers in Memphis Metropolitan Area, USA

Indoor skin-contact surfaces of public fitness centers may serve as reservoirs of potential human transmission of methicillin-resistant Staphylococcus aureus (MRSA). We found a high prevalence of multi-drug resistant (MDR)-MRSA of CC59 lineage harboring a variety of extracellular toxin genes from surface swab samples collected from inanimate surfaces of fitness centers in Memphis metropolitan area, USA. Our findings underscore the role of inanimate surfaces as potential sources of transmission of MDR-MRSA strains with considerable genetic diversity.
Determination of the enantiomeric purity and absolute configuration of α-hydroxy phosphonates

Abstract The absolute configuration of α-hydroxy phosphonates was determined by NMR spectroscopy of the O-methyl mandelate ester derivatives. The O-methyl mandelate ester diastereoisomers are distinguishable by their 1 H and 31 P NMR spectra and the observed chemical shifts allow assignment of the absolute configuration of the phosphonate C-1. The crystal structure of (1R) dimethyl 1-[(2′R)-2′-methoxy-2′-phenylacetoxy]-3-phenyl-2 E -propenyl phosphonate was determined by X-ray diffraction. The enatiomers were separable by HPLC on a chiral stationery phase and therefore the enantiomeric purity of the hydroxy phosphonates could accurately be determined.
Resources for Interpreting Variants in Precision Genomic Oncology Applications.

Precision genomic oncology–applying high throughput sequencing (HTS) at the point-of-care to in- form clinical decisions–is a developing precision medicine paradigm that is seeing increasing adoption. Simultaneously, new developments in targeted agents and immunotherapy, when informed by rich ge- nomic characterization, offer potential benefit to a growing subset of patients. Multiple previous studies have commented on methods for identifying both germline and somatic variants. However, interpreting individual variants remains a significant challenge, relying in large part on the integration of observed variants with biological knowledge. A number of data and software resources have been developed to assist in interpreting observed variants, determining their potential clinical actionability, and augmenting them with ancillary information that can inform clinical decisions and even generate new hypotheses for exploration in the laboratory. Here, we review available variant catalogs, variant and functional an- notation software and tools, and databases of clinically actionable variants that can be used in an ad hoc approach with research samples or incorporated into a data platform for interpreting and formally reporting clinical results.
Effect of external shear flow on sperm motility

The trajectory of sperm in the presence of background flow is of utmost importance for the success of fertilization, as sperm encounter background flow of different magnitude and direction on their way to the egg. Here, we have studied the effect of an unbounded simple shear flow as well as a Poiseuille flow on the sperm trajectory. In the presence of a simple shear flow, the sperm moves on an elliptical trajectory in the reference frame advecting with the local background flow. The length of the major-axis of this elliptical trajectory decreases with the shear rate. The flexibility of the flagellum and consequently the length of the major axis of the elliptical trajectories increases with the sperm number. The sperm number is a dimensionless number representing the ratio of viscous force to elastic force. The sperm moves downstream or upstream depending on the strength of background Poiseuille flow. In contrast to the simple shear flow, the sperm also moves toward the centerline in a Poiseuille flow. Far away from the centerline, the cross-stream migration velocity of the sperm increases as the transverse distance of the sperm from the centerline decreases. Close to the centerline, on the other hand, the cross-stream migration velocity decreases as the sperm further approaches the center. The cross-stream migration velocity of the sperm also increases with the sperm number.
SoPhie: An Attentive GAN for Predicting Paths Compliant to Social and Physical Constraints

This paper addresses the problem of path prediction for multiple interacting agents in a scene, which is a crucial step for many autonomous platforms such as self-driving cars and social robots. We present SoPhie; an interpretable framework based on Generative Adversarial Network (GAN), which leverages two sources of information, the path history of all the agents in a scene, and the scene context information, using images of the scene. To predict a future path for an agent, both physical and social information must be leveraged. Previous work has not been successful to jointly model physical and social interactions. Our approach blends a social attention mechanism with physical attention that helps the model to learn where to look in a large scene and extract the most salient parts of the image relevant to the path. Whereas, the social attention component aggregates information across the different agent interactions and extracts the most important trajectory information from the surrounding neighbors. SoPhie also takes advantage of GAN to generates more realistic samples and to capture the uncertain nature of the future paths by modeling its distribution. All these mechanisms enable our approach to predict socially and physically plausible paths for the agents and to achieve state-of-the-art performance on several different trajectory forecasting benchmarks.
Bayesian optimization with unknown constraints

Recent work on Bayesian optimization has shown its effectiveness in global optimization of difficult black-box objective functions. Many real-world optimization problems of interest also have constraints which are unknown a priori. In this paper, we study Bayesian optimization for constrained problems in the general case that noise may be present in the constraint functions, and the objective and constraints may be evaluated independently. We provide motivating practical examples, and present a general framework to solve such problems. We demonstrate the effectiveness of our approach on optimizing the performance of online latent Dirichlet allocation subject to topic sparsity constraints, tuning a neural network given test-time memory constraints, and optimizing Hamiltonian Monte Carlo to achieve maximal effectiveness in a fixed time, subject to passing standard convergence diagnostics.
Objective Variables for Probabilistic Revenue Maximization in Second-Price Auctions with Reserve

Many online companies sell advertisement space in second-price auctions with reserve. In this paper, we develop a probabilistic method to learn a profitable strategy to set the reserve price. We use historical auction data with features to fit a predictor of the best reserve price. This problem is delicate - the structure of the auction is such that a reserve price set too high is much worse than a reserve price set too low. To address this we develop objective variables, an approach for combining probabilistic modeling with optimal decision-making. Objective variables are "hallucinated observations" that transform the revenue maximization task into a regularized maximum likelihood estimation problem, which we solve with the EM algorithm. This framework enables a variety of prediction mechanisms to set the reserve price. As examples, we study objective variable methods with regression, kernelized regression, and neural networks on simulated and real data. Our methods outperform previous approaches both in terms of scalability and profit.
Stability and convergence of a second-order mixed finite element method for the Cahn–Hilliard equation

In this paper we devise and analyze an unconditionally stable, second-order-in-time numerical scheme for the Cahn-Hilliard equation in two and three space dimensions. We prove that our two-step scheme is unconditionally energy stable and unconditionally uniquely solvable. Furthermore, we show that the discrete phase variable is bounded in $L^\infty (0,T;L^\infty)$ and the discrete chemical potential is bounded in $L^\infty (0,T;L^2)$, for any time and space step sizes, in two and three dimensions, and for any finite final time $T$. We subsequently prove that these variables converge with optimal rates in the appropriate energy norms in both two and three dimensions. We include in this work a detailed analysis of the initialization of the two-step scheme.
Monitoring Variability of the Sky

Variability in the sky has been known for centuries, even millennia, but our knowledge of it is very incomplete even at the bright end. Current technology makes it possible to built small, robotic optical instruments, to record images and to process data in real time, and to archive them on-line, all at a low cost. In addition to obtaining complete catalogs of all kinds of variable objects, spectacular discoveries can be made, like the optical flash associated with GRB 990123 and a planetary transit in front of HD 209458. While prototypes of such robotic instruments have been in operation for several years, it is not possible to purchase a complete system at this time. I expect (hope) that complete systems will become available `off the shelf' in the near future, as monitoring bright sky for variability has a great scientific, educational and public outreach potential.
Eliminating dual spaces

Macaulay dual spaces provide a local description of an affine scheme and give rise to computational machinery that is compatible with the methods of numerical algebraic geometry. We introduce eliminating dual spaces, use them for computing dual spaces of quotient ideals, and develop an algorithm for detection of embedded points on an algebraic curve.
Decomposing manifolds into Cartesian products

The decomposability of a Cartesian product of two nondecomposable manifolds into products of lower dimensional manifolds is studied. For 3-manifolds we obtain an analog of a result due to Borsuk for surfaces, and in higher dimensions we show that similar analogs do not exist unless one imposes further restrictions such as simple connectivity.
Efficient Training of Very Deep Neural Networks for Supervised Hashing

In this paper, we propose training very deep neural networks (DNNs) for supervised learning of hash codes. Existing methods in this context train relatively "shallow" networks limited by the issues arising in back propagation (e.g. vanishing gradients) as well as computational efficiency. We propose a novel and efficient training algorithm inspired by alternating direction method of multipliers (ADMM) that overcomes some of these limitations. Our method decomposes the training process into independent layer-wise local updates through auxiliary variables. Empirically we observe that our training algorithm always converges and its computational complexity is linearly proportional to the number of edges in the networks. Empirically we manage to train DNNs with 64 hidden layers and 1024 nodes per layer for supervised hashing in about 3 hours using a single GPU. Our proposed very deep supervised hashing (VDSH) method significantly outperforms the state-of-theart on several benchmark datasets.
Pointwise estimates and regularity in geometric optics and other Generated Jacobian Equations

The study of reflector surfaces in geometric optics necessitates the analysis of certain nonlinear equations of Monge-Amp\`ere type known as generated Jacobian equations. These equations, whose general existence theory has been recently developed by Trudinger go beyond the framework of optimal transport. We obtain pointwise estimates for weak solutions of such equations under a condition analogous to the A3w condition of Ma, Trudinger and Wang. Estimates of this type have played an important role in the regularity theory for optimal transport maps and were previously unknown in this context, including the important case of the near field reflector problem.
Goodness-of-fit for log-linear network models: Dynamic Markov bases using hypergraphs

Social networks and other sparse data sets pose significant challenges for statistical inference, since many standard statistical methods for testing model/data fit are not applicable in such settings. Algebraic statistics offers a theoretically justified approach to goodness-of-fit testing that relies on the theory of Markov bases. Most current practices require the computation of the entire basis, which is infeasible in many practical settings. We present a dynamic approach to explore the fiber of a model, which bypasses this issue, and is based on the combinatorics of hypergraphs arising from the toric algebra structure of log-linear models. We demonstrate the approach on the Holland–Leinhardt $$p_1$$ model for random directed graphs that allows for reciprocation effects.
Convergent iteration in Sobolev space for time dependent closed quantum systems

Abstract Time dependent quantum systems have become indispensable in science and its applications, particularly at the atomic and molecular levels. Here, we discuss the approximation of closed time dependent quantum systems on bounded domains, via iterative methods in Sobolev space based upon evolution operators. Recently, existence and uniqueness of weak solutions were demonstrated by a contractive fixed point mapping defined by the evolution operators. Convergent successive approximation is then guaranteed. This article uses the same mapping to define quadratically convergent Newton and approximate Newton methods. Estimates for the constants used in the convergence estimates are provided. The evolution operators are ideally suited to serve as the framework for this operator approximation theory, since the Hamiltonian is time-dependent. In addition, the hypotheses required to guarantee quadratic convergence of the Newton iteration build naturally upon the hypotheses used for the existence/uniqueness theory.
Electronic transport in a two-dimensional superlattice engineered via self-assembled nanostructures

Nanoscience offers a unique opportunity to design modern materials from the bottom up via low-cost, solution processed assembly of nanoscale building blocks. These systems promise electronic band structure engineering using not only the nanoscale structural modulation, but also the mesoscale spatial patterning, although experimental realization of the latter has been challenging. Here, we design and fabricate a new type of artificial solid by stacking graphene on a self-assembled, nearly periodic array of nanospheres, and experimentally observe superlattice miniband effects. We find conductance dips at commensurate fillings of charge carriers per superlattice unit cell, which are key features of minibands that are induced by the quasi-periodic deformation of the graphene lattice. These dips become stronger when the lattice strain is larger. Using a tight-binding model, we simulate the effect of lattice deformation as a parameter affecting the inter-atomic hopping integral, and confirm the superlattice transport behavior. This 2D material-nanoparticle heterostructure enables facile band structure engineering via self-assembly, promising for large-area electronics and optoelectronics applications. A hybrid heterostructure of self-assembled nanoparticles on graphene displays conductance dips due to superlattice miniband effects. A team led by Yingjie Zhang and Nadya Mason at the University of Illinois designed and fabricated a large-area artificial solid combining self-assembled dielectric nanospheres and graphene grown by chemical vapor deposition. Taking advantage of the structural versatility of SiO2 nanoparticle assembly and the high mobility of graphene, the resulting heterostructure displays miniband effects in the electronic transport characteristics as a result of superlattice formation. Due to the size variability and imperfect ordering of the nanospheres, a broadening was observed in the miniband density of states. This effect can find an application in optoelectronic devices, such as optical modulators and sensor, requiring broadband modulation of their optical spectrum.
Dynamics on Grassmannians and resolvents of cone operators

The paper proves the existence and elucidates the structure of the asymptotic expansion of the trace of the resolvent of a closed extension of a general elliptic cone operator on a compact manifold with boundary as the spectral parameter tends to infinity. The hypotheses involve only minimal conditions on the symbols of the operator. The results combine previous investigations by the authors on the subject with an analysis of the asymptotics of a family of projections related to the domain. This entails a fairly detailed study of the dynamics of a flow on the Grassmannian of domains.
On the reconstruction problem in mirror symmetry

Abstract Let π : M → B be a Lagrangian torus fibration with singularities such that the fibers are of Maslov index zero, and unobstructed. The paper constructs a rigid analytic space M 0 ∨ over the Novikov field which is a deformation of the semi-flat complex structure of the dual torus fibration over the smooth locus B 0 ⊂ B of π. Transition functions of M 0 ∨ are obtained via A ∞ homomorphisms which capture the wall-crossing phenomenon of moduli spaces of holomorphic disks.
Growth tradeoffs produce complex microbial communities without direct interactions

The distribution of fitness effects for mutations is often believed to be key to predicting microbial evolution. However, fitness effects alone may be insufficient to predict evolutionary dynamics if mutations produce nontrivial ecological effects which depend on the composition of the population. Here we show that variation in multiple growth traits, such as lag times and growth rates, creates higher-order effects such the relative competition between two strains is fundamentally altered by the presence of a third strain. These effects produce a range of ecological phenomena: an unlimited number of strains can coexist, potentially with a single keystone strain stabilizing the community; strains that coexist in pairs do not coexist all together; and the champion of all pairwise competitions may not dominate in a mixed community. This occurs with competition for only a single finite resource and no other interactions. Since variation in multiple growth traits is ubiquitous in microbial populations due to pleiotropy and non-genetic variation, these higher-order effects may also be widespread, especially in laboratory ecology and evolution experiments. Our results underscore the importance of considering the distribution of ecological effects from mutations in predicting microbial evolution.
Inference in Probabilistic Logic Programs Using Lifted Explanations.

In this paper, we consider the problem of lifted inference in the context of Prism-like probabilistic logic programming languages. Traditional inference in such languages involves the construction of an explanation graph for the query and computing probabilities over this graph. When evaluating queries over probabilistic logic programs with a large number of instances of random variables, traditional methods treat each instance separately. For many programs and queries, we observe that explanations can be summarized into substantially more compact structures, which we call lifted explanation graphs. In this paper, we define lifted explanation graphs and operations over them. In contrast to existing lifted inference techniques, our method for constructing lifted explanations naturally generalizes existing methods for constructing explanation graphs. To compute probability of query answers, we solve recurrences generated from the lifted graphs. We show examples where the use of our technique reduces the asymptotic complexity of inference.
Synchronization of Kuramoto oscillators in networks of networks

We study synchronization of Kuramoto oscillators in strongly modular networks in which the structure of the network inside each community is averaged. We find that the dynamics of the interacting communities can be described as an ensemble of coupled planar oscillators. In the limit of a large number of communities, we find a low dimensional description of the level of synchronization between the communities. In this limit, we describe bifurcations between incoherence, local synchrony, and global synchrony. We compare the predictions of this simplified model with simulations of heterogeneous networks in which the internal structure of each community is preserved and find excellent agreement. Finally, we investigate synchronization in networks where several layers of communities within communities may be present.
CYLINDRICAL HOMOMORPHISMS AND LAWSON HOMOLOGY

We use the cylindrical homomorphism and a geometric construction introduced by J. Lewis to study the Lawson homology groups of certain hypersurfaces XP n+1 of degree dn + 1. As an application, we compute the rational semi- topological K-theory of a generic cubic of dimension 5, 6 and 8 and, using the Bloch-Kato conjecture, we prove Suslin's conjecture for these varieties. Using the generic cubic sevenfolds, we show that there are smooth projective varieties with the lowest non-trivial step in their s-filtration infinitely generated and undetected by the Abel-Jacobi map.
Polynomial relations between matrices of graphs

We derive a correspondence between the eigenvalues of the adjacency matrix $A$ and the signless Laplacian matrix $Q$ of a graph $G$ when $G$ is $(d_1,d_2)$-biregular by using the relation $A^2=(Q-d_1I)(Q-d_2I)$. This motivates asking when it is possible to have $X^r=f(Y)$ for $f$ a polynomial, $r>0$, and $X,\ Y$ matrices associated to a graph $G$. It turns out that, essentially, this can only happen if $G$ is either regular or biregular.
Lip Movements Generation at a Glance

In this paper, we consider the task: given an arbitrary audio speech and one lip image of arbitrary target identity, generate synthesized lip movements of the target identity saying the speech. To perform well, a model needs to not only consider the retention of target identity, photo-realistic of synthesized images, consistency and smoothness of lip images in a sequence, but more importantly, learn the correlations between audio speech and lip movements. To solve the collective problems, we devise a network to synthesize lip movements and propose a novel correlation loss to synchronize lip changes and speech changes. Our full model utilizes four losses for a comprehensive consideration; it is trained end-to-end and is robust to lip shapes, view angles and different facial characteristics. Thoughtful experiments on three datasets ranging from lab-recorded to lips in-the-wild show that our model significantly outperforms other state-of-the-art methods extended to this task.
Modular representations and indicators for bismash products

Abstract We introduce Brauer characters for representations of the bismash products of groups in characteristic p > 0 , p ≠ 2 and study their properties analogous to the classical case of finite groups. We then use our results to extend to bismash products a theorem of Thompson on lifting Frobenius–Schur indicators from characteristic p to characteristic 0.
Automorphisms of higher rank lamplighter groups

Let Γd(q) denote the group whose Cayley graph with respect to a particular generating set is the Diestel–Leader graph DLd(q), as described by Bartholdi, Neuhauser and Woess. We compute both Aut(Γd(q)) and Out(Γd(q)) for d ≥ 2, and apply our results to count twisted conjugacy classes in these groups when d ≥ 3. Specifically, we show that when d ≥ 3, the groups Γd(q) have property R∞, that is, every automorphism has an infinite number of twisted conjugacy classes. In contrast, when d = 2 the lamplighter groups Γ2(q) = Lq = ℤq ≀ ℤ have property R∞ if and only if (q, 6)≠1.
Obfuscated Gradients Give a False Sense of Security: Circumventing Defenses to Adversarial Examples

We identify obfuscated gradients, a kind of gradient masking, as a phenomenon that leads to a false sense of security in defenses against adversarial examples. While defenses that cause obfuscated gradients appear to defeat iterative optimization-based attacks, we find defenses relying on this effect can be circumvented. We describe characteristic behaviors of defenses exhibiting the effect, and for each of the three types of obfuscated gradients we discover, we develop attack techniques to overcome it. In a case study, examining non-certified white-box-secure defenses at ICLR 2018, we find obfuscated gradients are a common occurrence, with 7 of 9 defenses relying on obfuscated gradients. Our new attacks successfully circumvent 6 completely, and 1 partially, in the original threat model each paper considers.
Distribution of the nodal sets of eigenfunctions on analytic manifolds

The nodal set of the Laplacian eigenfunction has co-dimension one and has finite hypersurface measure on a compact Riemannian manifold. In this paper, we investigate the distribution of the nodal sets of eigenfunctions, when the metric on the manifold is analytic. We prove that if the eigenfunctions are equidistributed at a small scale, then the weak limits of the hypersurface volume form of their nodal sets are comparable to the volume form on the manifold. In particular, on the negatively curved manifolds with analytic metric and on the tori, we show that in any eigenbasis, there is a full density subsequence of eigenfunctions such that the weak limits of the hypersurface volume form of their nodal sets are comparable to the volume form on the manifold.
Predicting Phase Behavior Of Grain Boundaries With Evolutionary Search And Machine Learning

The study of grain boundary phase transitions is an emerging field until recently dominated by experiments. The major bottleneck in the exploration of this phenomenon with atomistic modeling has been the lack of a robust computational tool that can predict interface structure. Here we develop a computational tool based on evolutionary algorithms that performs efficient grand-canonical grain boundary structure search and we design a clustering analysis that automatically identifies different grain boundary phases. Its application to a model system of symmetric tilt boundaries in Cu uncovers an unexpected rich polymorphism in the grain boundary structures. We find new ground and metastable states by exploring structures with different atomic densities. Our results demonstrate that the grain boundaries within the entire misorientation range have multiple phases and exhibit structural transitions, suggesting that phase behavior of interfaces is likely a general phenomenon. The atomic structure of grain boundary phases remains unknown and is difficult to investigate experimentally. Here, the authors use an evolutionary algorithm to computationally explore interface structures in higher dimensions and predict low-energy configurations, showing interface phases may be ubiquitous.