cssi/SciSciGPT-SciSciNet huggingface dataset:
Bacteriophage Resistance Alters Antibiotic-Mediated Intestinal Expansion of Enterococci.

ABSTRACT Enterococcus faecalis is a human intestinal pathobiont with intrinsic and acquired resistance to many antibiotics, including vancomycin. Nature provides a diverse and virtually untapped repertoire of bacterial viruses, or bacteriophages (phages), that could be harnessed to combat multidrug-resistant enterococcal infections. Bacterial phage resistance represents a potential barrier to the implementation of phage therapy, emphasizing the importance of investigating the molecular mechanisms underlying the emergence of phage resistance. Using a cohort of 19 environmental lytic phages with tropism against E. faecalis, we found that these phages require the enterococcal polysaccharide antigen (Epa) for productive infection. Epa is a surface-exposed heteroglycan synthesized by enzymes encoded by both conserved and strain-specific genes. We discovered that exposure to phage selective pressure favors mutation in nonconserved epa genes both in culture and in a mouse model of intestinal colonization. Despite gaining phage resistance, epa mutant strains exhibited a loss of resistance to cell wall-targeting antibiotics. Finally, we show that an E. faecalisepa mutant strain is deficient in intestinal colonization, cannot expand its population upon antibiotic-driven intestinal dysbiosis, and fails to be efficiently transmitted to juvenile mice following birth. This study demonstrates that phage therapy could be used in combination with antibiotics to target enterococci within a dysbiotic microbiota. Enterococci that evade phage therapy by developing resistance may be less fit at colonizing the intestine and sensitized to vancomycin, preventing their overgrowth during antibiotic treatment.
Liquid-Liquid Phase Separation of Patchy Particles Illuminates Diverse Effects of Regulatory Components on Protein Droplet Formation.

Recently many cellular functions have been associated with membraneless organelles, or protein droplets, formed by liquid-liquid phase separation (LLPS). Proteins in these droplets often contain RNA-binding domains, but the effects of RNA on LLPS have been controversial. To gain better understanding on the roles of RNA and other macromolecular regulators, here we used Gibbs-ensemble simulations to determine phase diagrams of two-component patchy particles, as models for mixtures of proteins with regulatory components. Protein-like particles have four patches, with attraction strength ePP; regulatory particles experience mutual steric repulsion but have two attractive patches toward proteins, with the strength ePR tunable. At low ePR, the regulator, due to steric repulsion, preferentially partitions in the dispersed phase, thereby displacing the protein into the droplet phase and promoting LLPS. At moderate ePR, the regulator starts to partition and displace the protein in the droplet phase, but only to weaken bonding networks and thereby suppress LLPS. At ePR > ePP, the enhanced bonding ability of the regulator initially promotes LLPS, but at higher amounts, the resulting displacement of the protein suppresses LLPS. These results illustrate how RNA can have disparate effects on LLPS, thus able to perform diverse functions in different organelles.
Reactive dications: The superacid-catalyzed reactions of alkynes bearing adjacent N-heterocycles or amine groups

A variety of aminoalkynes and related heterocycles are reacted in the Bronsted superacid CF3SO3H (triflic acid), and products are obtained in generally good yields (69−99%) from Friedel−Crafts-type reactions. The reactions are consistent with the formation of novel dicationic intermediates having a vinyl cationic site and an adjacent protonated N-heterocycle or ammonium cation.
Total Synthesis of (-)-Muscoride A.

The recently isolated cyanobacterium metabolite muscoride A was synthesized in 15 steps and in 4.3% overall yield. Novel structural features of this peptide antibiotic include the presence of a threonine-derived bioxazole core and an N-(1,1-dimethyl)allyl (“reverse prenyl”) valine residue. In the context of our synthesis, efficient new strategies for the preparation of these segments were developed. The synthesis of two epimers of muscoride A allowed the unambiguous assignment of the relative and absolute configuration of the natural product by NMR and optical rotation analyses.
Pinetree: a step-wise gene expression simulator with codon-specific translation rates.

Motivation Stochastic gene expression simulations often assume steady-state transcript levels, or they model transcription in more detail than translation. Moreover, they lack accessible programing interfaces, which limit their utility. Results We present Pinetree, a step-wise gene expression simulator with codon-specific translation rates. Pinetree models both transcription and translation in a stochastic framework with individual polymerase and ribosome-level detail. Written in C++ with a Python front-end, any user familiar with Python can specify a genome and simulate gene expression. Pinetree was designed to be efficient and scale to simulate large plasmids or viral genomes. Availability and implementation Pinetree is available on GitHub (https://github.com/benjaminjack/pinetree) and the Python Package Index (https://pypi.org/project/pinetree/).
Stereochemical models for rh-catalyzed amination reactions of chiral sulfamates.

Oxidative C−H amination of chiral sulfamate esters using achiral Rh-carboxylate catalysts, PhI(OAc)2, and MgO occurs in high yield and with good to excellent diastereocontrol. A number of examples are included to support a proposed transition state model that accounts for the observed stereoinduction. In addition, stereoselective intramolecular aziridination with substituted homoallyl sulfamates is demonstrated and is rationalized through an analogous stereochemical construct.
Ammonia synthesis kinetics: Surface chemistry, rate expressions, and kinetic analysis

The results of surface science studies of nitrogen adsorption and desorption on iron single crystals are summarized with respect to ammonia synthesis reaction kinetics. Analytical rate expressions for ammonia synthesis on high surface iron catalysts at industrial reaction conditions are presented and compared to the behavior of microkinetic models based on the surface science results. Microkinetic models based on uniform surfaces are successful in extrapolating results from surface science studies at low surface coverages to describe the performance of iron catalysts at industrial ammonia synthesis reaction conditions. We suggest that the value of rate constant for recombination of nitrogen atoms on the surface is a weak function of surface coverage. Furthermore, modest variations in the heat of N2 adsorption are sufficient to achieve fractional ammonia orders that are relatively insensitive to the ammonia pressure.
Synthesis of 2H-1-benzopyrans via palladacycles with a metal-bonded stereogenic carbon.

Stable oxapalladacycles have been prepared and converted into a series of highly functionalized 2H-1-benzopyrans via regioselective insertion of activated alkynes.
Preparation of a variety of macrocyclic Di‐ and tetraamides and their peraza‐crown analogs using the crab‐like cyclization reaction

Twelve new macrocyclic di- and tetraamides have been synthesized from the reaction of a bis(α-chloroamide) with a primary amine or with a diamine. Some of these cyclic di- and tetraamides contained pendant aminoalkyl groups attached on one or more ring nitrogen atoms. Two macrocyclic dithiadiamides were prepared from the reaction of a bis(α-chloroamide) and a dimercaptan. In every case, 12-, 14- and 15-membered cyclic di- and tetraamides were isolated in good yields. The 9-, 17- and 18-membered macrocycles were prepared in lower yields. Four of the amide-containing macrocycles were reduced by diborane to the perazacrown compounds.
Hypomethylation of STAT1 and HLA-DRB1 is associated with type-I interferon-dependent HLA-DRB1 expression in lupus CD8+ T cells.

Objective We examined genome-wide DNA methylation changes in CD8+ T cells from patients with lupus and controls and investigated the functional relevance of some of these changes in lupus. Methods Genome-wide DNA methylation of lupus and age, sex and ethnicity-matched control CD8+ T cells was measured using the Infinium MethylationEPIC arrays. Measurement of relevant cell subsets was performed via flow cytometry. Gene expression was quantified by qPCR. Inhibiting STAT1 and CIITA was performed using fludarabine and CIITA siRNA, respectively. Results Lupus CD8+ T cells had 188 hypomethylated CpG sites compared with healthy matched controls. Among the most hypomethylated were sites associated with HLA-DRB1. Genes involved in the type-I interferon response, including STAT1, were also found to be hypomethylated. IFNα upregulated HLA-DRB1 expression on lupus but not control CD8+ T cells. Lupus and control CD8+ T cells significantly increased STAT1 mRNA levels after treatment with IFNα. The expression of CIITA, a key interferon/STAT1 dependent MHC-class II regulator, is induced by IFNα in lupus CD8+ T cells, but not healthy controls. CIITA knockdown and STAT1 inhibition experiments revealed that HLA-DRB1 expression in lupus CD8+ T cells is dependent on CIITA and STAT1 signalling. Coincubation of naive CD4+ T cells with IFNα-treated CD8+ T cells led to CD4+ T cell activation, determined by increased expression of CD69 and cytokine production, in patients with lupus but not in healthy controls. This can be blocked by neutralising antibodies targeting HLA-DR. Conclusions Lupus CD8+ T cells are epigenetically primed to respond to type-I interferon. We describe an HLA-DRB1+ CD8+ T cell subset that can be induced by IFNα in patients with lupus. A possible pathogenic role for CD8+ T cells in lupus that is dependent on a high type-I interferon environment and epigenetic priming warrants further characterisation.
Stereoselective synthesis of E-β,β-disubstituted alkenylsilanes from α-(mesyloxy)allylsilanes.

Abstract Cross-coupling reactions of various organocopper reagents with α-(mesyloxy)allylsilanes have been evaluated for stereoselective β,β-disubstituted vinylsilane synthesis. S N 2′ displacements with RMgBr/CuCN(cat.) reagents proceeded in high yields (84»94%) and E -selectivities (10:1 » 38:1) in THF at −78°C.
Syntrophic co-culture amplification of production phenotype for high-throughput screening of microbial strain libraries

Microbes can be engineered to synthesize a wide array of bioproducts, yet production phenotype evaluation remains a frequent bottleneck in the design-build-test cycle where strain development requires iterative rounds of library construction and testing. Here, we present Syntrophic Co-culture Amplification of Production phenotype (SnoCAP). Through a metabolic cross-feeding circuit, the production level of a target molecule is translated into highly distinguishable co-culture growth characteristics, which amplifies differences in production into highly distinguishable growth phenotypes. We demonstrate SnoCAP with the screening of Escherichia coli strains for production of two target molecules: 2-ketoisovalerate, a precursor of the drop-in biofuel isobutanol, and L-tryptophan. The dynamic range of the screening can be tuned by employing an inhibitory analog of the target molecule. Screening based on this framework requires compartmentalization of individual producers with the sensor strain. We explore three formats of implementation with increasing throughput capability: confinement in microtiter plates (102-104 assays/experiment), spatial separation on agar plates (104-105 assays/experiment), and encapsulation in microdroplets (105-107 assays/experiment). Using SnoCAP, we identified an efficient isobutanol production strain from a random mutagenesis library, reaching a final titer that is 5-fold higher than that of the parent strain. The framework can also be extended to screening for secondary metabolite production using a push-pull strategy. We expect that SnoCAP can be readily adapted to the screening of various microbial species, to improve production of a wide range of target molecules.
CO J=1-0 observations of molecular gas interacting with galactic supernova remnants G5.4-1.2, G5.55+0.32 and G5.71-0.08

Aims. We searched for signs of interaction of radio supernova remnants with ambient molecular gas in the sky field just West of the SNR W28. Methods. We analyze a datacube of CO J = 1−0 emission having 1 � and 1.2 km s −1 resolution, made with on-the-fly mapping over the region 5 o ≤ l ≤ 6 o , −1 o ≤ b ≤ 0.5 o . Results. Although broad CO lines characteristic of shocked gas were not seen in this kinematically complex region, a bright (14 K), new, marginally-resolved ± 9k m s −1 outflow source G5.638+0.233 and a comparably bright rim of CO emission were found at/around the periphery of SNR G5.55+0.12. Most of the periphery of SNR G5.71-0.08 is surrounded by a bright rim of CO emission. CO emission at the 7 km s −1 velocity of a 1720 OH maser spot near SNR G5.70-0.12 is very bright, 19 K, but gas at −21 km s −1 is widespread over the region and CO emission is rather weak toward the OH maser spots at this velocity north of G5.4-1.2. Other very bright CO lines in the region are associated with H II regions, i.e. 27 K toward W28A2 = G5.89-0.39 and 15 K toward an MSX-IR source at l = 5.9 o , b = −0.13 o which is probably the exciting agent of a separate, classical HII region just north of W28A2.
Political Institutions and Pollution: Evidence from Coal‐Fired Power Generation

What is the relationship between political institutions and air pollution generated by the power sector? Here we focus on the association between democracy and power generated from coal, the most polluting of all fossil fuels. Using a new dataset on coal‐fired power plants commissioned between 1980 and 2016 in 71 countries, we find that the relationship between democracy and coal varies according to the environmental Kuznets curve logic. Democratic political institutions at lower levels of economic development are correlated with increased commissioning of coal power plants, as governments seek to appeal to an electorate prioritizing economic growth and affordable energy access. As a country becomes richer, democracy comes to have a negative association with coal power, as clean air becomes a more salient issue for the public. 政治制度和污染：燃煤发电提供的证据 政治制度和由电力部门制造的空气污染之间存在何种关系？笔者在文中聚焦于民主和煤电之间的联系，煤电在所有化石燃料中最具污染性。通过使用1980‐2016年间由71个国家批准生产的燃煤发电厂所得出的数据集，笔者发现，民主和煤电之间的关系随环境库兹涅茨曲线的逻辑发生变化。经济发展程度较低的国家中，民主政治制度与煤电厂批准数量的增加相关，因为政府试图吸引那些希望将经济增长和可支付能源获取作为优先事项的选民。当一个国家变得更加富裕时，民主与煤电的关系呈负相关，因为洁净的空气对大众而言是一个更为突出的问题。 Instituciones politicas y contaminacion: evidencia de la generacion de energia de carbon ?Cual es la relacion entre las instituciones politicas y la contaminacion del aire generada por el sector electrico? Aqui nos centramos en la asociacion entre la democracia y el poder generado por el carbon, el mas contaminante de todos los combustibles fosiles. Al utilizar un nuevo conjunto de datos sobre centrales electricas de carbon comisionadas entre 1980 y 2016 en 71 paises, encontramos que la relacion entre democracia y carbon varia segun la logica de la curva ambiental de Kuznets. Las instituciones politicas democraticas en niveles mas bajos de desarrollo economico estan correlacionadas con una mayor puesta en servicio de las centrales electricas de carbon, ya que los gobiernos buscan apelar a un electorado que prioriza el crecimiento economico y el acceso a energia asequible. A medida que un pais se vuelve mas rico, la democracia tiene una asociacion negativa con el poder del carbon, ya que el aire limpio se convierte en un tema mas importante para el publico.
Cardiolipin-Dependent Properties of Model Mitochondrial Membranes from Molecular Simulations

Cardiolipin is an anionic lipid found in the mitochondrial membranes of eukaryotes ranging from unicellular microorganisms to metazoans. This unique lipid contributes to various mitochondrial functions, including metabolism, mitochondrial membrane fusion and/or fission dynamics, and apoptosis. However, differences in cardiolipin content between the two mitochondrial membranes, as well as dynamic fluctuations in cardiolipin content in response to stimuli and cellular signaling events, raise questions about how cardiolipin concentration affects mitochondrial membrane structure and dynamics. Although cardiolipin's structural and dynamic roles have been extensively studied in binary mixtures with other phospholipids, the biophysical properties of cardiolipin in higher number lipid mixtures are still not well resolved. Here, we used molecular dynamics simulations to investigate the cardiolipin-dependent properties of ternary lipid bilayer systems that mimic the major components of mitochondrial membranes. We found that changes to cardiolipin concentration only resulted in minor changes to bilayer structural features but that the lipid diffusion was significantly affected by those alterations. We also found that cardiolipin position along the bilayer surfaces correlated to negative curvature deflections, consistent with the induction of negative curvature stress in the membrane monolayers. This work contributes to a foundational understanding of the role of cardiolipin in altering the properties in ternary lipid mixtures composed of the major mitochondrial phospholipids, providing much-needed insights to help understand how cardiolipin concentration modulates the biophysical properties of mitochondrial membranes.
Quantifying heart valve interstitial cell contractile state using highly tunable poly(ethylene glycol) hydrogels.

Abstract Valve interstitial cells (VIC) are the primary cell type residing within heart valve tissues. In many valve pathologies, VICs become activated and will subsequently profoundly remodel the valve tissue extracellular matrix (ECM). A primary indicator of VIC activation is the upregulation of α -smooth muscle actin ( α SMA) stress fibers, which in turn increase VIC contractility. Thus, contractile state reflects VIC activation and ECM biosynthesis levels. In general, cell contraction studies have largely utilized two-dimensional substrates, which are a vastly different micro mechanical environment than 3D native leaflet tissue. To address this limitation, hydrogels have been a popular choice for studying cells in a three-dimensional environment due to their tunable properties and optical transparency, which allows for direct cell visualization. In the present study, we extended the use of hydrogels to study the active contractile behavior of VICs. Aortic VICs (AVIC) were encapsulated within poly(ethylene glycol) (PEG) hydrogels and were subjected to flexural-deformation tests to assess the state of AVIC contraction. Using a finite element model of the experimental setup, we determined the effective shear modulus μ of the constructs. An increase in μ resulting from AVIC active contraction was observed. Results further indicated that AVIC contraction had a more pronounced effect on μ in softer gels (72 ± 21% increase in μ within 2.5 kPa gels) and was dependent upon the availability of adhesion sites (0.5–1 mM CRGDS). The transparency of the gel allowed us to image AVICs directly within the hydrogel, where we observed a time-dependent decrease in volume (time constant τ = 3.04 min) when the AVICs were induced into a hypertensive state. Our results indicated that AVIC contraction was regulated by both the intrinsic (unseeded) gel stiffness and the CRGDS peptide concentrations. This finding suggests that AVIC contractile state can be profoundly modulated through their local micro environment using modifiable PEG gels in a 3D micromechanical-emulating environment. Moving forward, this approach has the potential to be used towards delineating normal and diseased VIC biomechanical properties using highly tunable PEG biomaterials. Statement of Significance 1. Hydrogels are a popular choice for studying cells in a 3D environment due to their tunable properties and optical transparency, which allows for direct cell visualization. In this study, we extended the use of hydrogels to study the active contractile behavior of VICs in 3D. 2. Results indicated that AVIC contraction has a more pronounced effect on macroscale properties in softer gels (72 ± 21% increase in shear moduli within 2.5 kPa gels) and is dependent upon the availability of adhesion sites (0.5–1 mM CRGDS). 3. Our results indicate that AVIC contraction is regulated by both the intrinsic (unseeded) gel stiffness and the CRGDS peptide concentration. This finding suggests that AVIC contraction can be modulated through their local micro environment.
Epigenetic Effects of Polybrominated Diphenyl Ethers on Human Health.

Disruption of epigenetic regulation by environmental toxins is an emerging area of focus for understanding the latter’s impact on human health. Polybrominated diphenyl ethers (PBDEs), one such group of toxins, are an environmentally pervasive class of brominated flame retardants that have been extensively used as coatings on a wide range of consumer products. Their environmental stability, propensity for bioaccumulation, and known links to adverse health effects have evoked extensive research to characterize underlying biological mechanisms of toxicity. Of particular concern is the growing body of evidence correlating human exposure levels to behavioral deficits related to neurodevelopmental disorders. The developing nervous system is particularly sensitive to influence by environmental signals, including dysregulation by toxins. Several major modes of actions have been identified, but a clear understanding of how observed effects relate to negative impacts on human health has not been established. Here, we review the current body of evidence for PBDE-induced epigenetic disruptions, including DNA methylation, chromatin dynamics, and non-coding RNA expression while discussing the potential relationship between PBDEs and neurodevelopmental disorders.
Symmetrical Peripheral Gangrene Associated with Low Output Cardiac Failure

Symmetrical peripheral gangrene (SPG) is a rare entity characterized by ischemic changes of the distal extremities with maintained vascular integrity. We present the case of a 64-year-old man with bilateral necrotic toes and deranged liver function tests. This was thought to be related to severely depressed ejection fraction from non-ischemic etiology, presumably chronic alcohol ingestion. We hope that awareness of SPG and association with a low output state will aid in early detection and prevention.
On the Interplay between Social and Topical Structure

People’s interests and people’s social relationships are intuitively connected, but understanding their interplay and whether they can help predict each other has remained an open question. We examine the interface of two decisive structures forming the backbone of online social media: the graph structure of social networks — who connects with whom — and the set structure of topical affiliations — who is interested in what. In studying this interface, we identify key relationships whereby each of these structures can be understood in terms of the other. The context for our analysis is Twitter, a complex social network of both follower relationships and communication relationships. On Twitter, “hashtags” are used to label conversation topics, and we examine hashtag usage alongside these social structures. We find that the hashtags that users adopt can predict their social relationships, and also that the social relationships between the initial adopters of a hashtag can predict the future popularity of that hashtag. By studying weighted social relationships, we observe that while strong reciprocated ties are the easiest to predict from hashtag structure, they are also much less useful than weak directed ties for predicting hashtag popularity. Importantly, we show that computationally simple structural determinants can provide remarkable performance in both tasks. While our analyses focus on Twitter, we view our findings as broadly applicable to topical affiliations and social relationships in a host of diverse contexts, including the movies people watch, the brands people like, or the locations people frequent.
When to Reset Your Keys: Optimal Timing of Security Updates via Learning

Cybersecurity is increasingly threatened by advanced and persistent attacks. As these attacks are often designed to disable a system (or a critical resource, e.g., a user account) repeatedly, it is crucial for the defender to keep updating its security measures to strike a balance between the risk of being compromised and the cost of security updates. Moreover, these decisions often need to be made with limited and delayed feedback due to the stealthy nature of advanced attacks. In addition to targeted attacks, such an optimal timing policy under incomplete information has broad applications in cybersecurity. Examples include key rotation, password change, application of patches, and virtual machine refreshing. However, rigorous studies of optimal timing are rare. Further, existing solutions typically rely on a pre-defined attack model that is known to the defender, which is often not the case in practice. In this work, we make an initial effort towards achieving optimal timing of security updates in the face of unknown stealthy attacks. We consider a variant of the influential FlipIt game model with asymmetric feedback and unknown attack time distribution, which provides a general model to consecutive security updates. The defender's problem is then modeled as a time associative bandit problem with dependent arms. We derive upper confidence bound based learning policies that achieve low regret compared with optimal periodic defense strategies that can only be derived when attack time distributions are known.
The SYZ Conjecture via Homological Mirror Symmetry

These are expanded notes based on a talk given at the Superschool on Derived Categories and D-branes held at the University of Alberta in July of 2016. The goal of these notes is to give a motivated introduction to the Strominger-Yau-Zaslow (SYZ) conjecture from the point of view of homological mirror symmetry.
On the crystalline period map

The paper contains a proof of the Fontaine-Jannsen conjecture based on a crystalline version of the p-adic Poincar'e lemma (different proofs were found earlier by Faltings, Niziol and Tsuji).
Results of UBV photoelectric observations of the early-type eclipsing binary system XZ Cep

Results of the three-colour photoelectric observation of the close binary system XZ Cep, obtained at the Abastumani Astrophysical observatory, are presented.
Solving systems of phaseless equations via Kaczmarz methods: a proof of concept study

We study the Kaczmarz methods for solving systems of phaseless equations, i.e., the generalized phase retrieval problem. The methods extend the Kaczmarz methods for solving systems of linear equations by integrating a phase selection heuristic in each iteration and overall have the same per iteration computational complexity. Extensive empirical performance comparisons establish the computational advantages of the Kaczmarz methods over other state-of-the-art phase retrieval algorithms both in terms of the number of measurements needed for successful recovery and in terms of computation time. Preliminary convergence analysis is presented for the randomized Kaczmarz methods.
Equilibria Interchangeability in Cellular Games

The notion of interchangeability has been introduced by John Nash in one of his original papers on equilibria. This paper studies properties of Nash equilibria interchangeability in cellular games that model behavior of infinite chain of homogeneous economic agents. The paper shows that there are games in which a strategy of any given player is interchangeable with strategies of players in an arbitrary large neighborhood of the given player, but is not interchangeable with the strategy of a remote player outside of the neighborhood. The main technical result is a sound and complete logical system describing universal properties of interchangeability common to all cellular games.
Evasion and hardening of tree ensemble classifiers

Classifier evasion consists in finding for a given instance x the "nearest" instance x′ such that the classifier predictions of x and x′ are different. We present two novel algorithms for systematically computing evasions for tree ensembles such as boosted trees and random forests. Our first algorithm uses a Mixed Integer Linear Program solver and finds the optimal evading instance under an expressive set of constraints. Our second algorithm trades off optimality for speed by using symbolic prediction, a novel algorithm for fast finite differences on tree ensembles. On a digit recognition task, we demonstrate that both gradient boosted trees and random forests are extremely susceptible to evasions. Finally, we harden a boosted tree model without loss of predictive accuracy by augmenting the training set of each boosting round with evading instances, a technique we call adversarial boosting.
A spanning tree cohomology theory for links

Abstract In their recent preprint, Baldwin, Ozsvath and Szabo defined a twisted version (with coefficients in a Novikov ring) of a spectral sequence, previously defined by Ozsvath and Szabo, from Khovanov homology to Heegaard–Floer homology of the branched double cover along a link. In their preprint, they give a combinatorial interpretation of the E 3 -term of their spectral sequence. The main purpose of the present paper is to prove directly that this E 3 -term is a link invariant. We also give some concrete examples of computation of the invariant.
Buoyancy instability of homologous implosions

With this study, I consider the hydrodynamic stability of imploding ideal gases as an idealized model for inertial confinement fusion capsules, sonoluminescent bubbles and the gravitational collapse of astrophysical gases. For oblate modes (short-wavelength incompressive modes elongated in the direction of the mean flow), a second-order ordinary differential equation is derived that can be used to assess the stability of any time-dependent flow with planar, cylindrical or spherical symmetry. Upon further restricting the analysis to homologous flows, it is shown that a monatomic gas is governed by the Schwarzschild criterion for buoyant stability. Under buoyantly unstable conditions, both entropy and vorticity fluctuations experience power-law growth in time, with a growth rate that depends upon mean flow gradients and, in the absence of dissipative effects, is independent of mode number. If the flow accelerates throughout the implosion, oblate modes amplify by a factor (2C)|N0|ti, where C is the convergence ratio of the implosion, N0 is the initial buoyancy frequency and ti is the implosion time scale. If, instead, the implosion consists of a coasting phase followed by stagnation, oblate modes amplify by a factor exp(π|N0|ts), where N0 is the buoyancy frequency at stagnation and ts is the stagnation time scale. Evenmore » under stable conditions, vorticity fluctuations grow due to the conservation of angular momentum as the gas is compressed. For non-monatomic gases, this additional growth due to compression results in weak oscillatory growth under conditions that would otherwise be buoyantly stable; this over-stability is consistent with the conservation of wave action in the fluid frame. The above analytical results are verified by evolving the complete set of linear equations as an initial value problem, and it is demonstrated that oblate modes are the fastest-growing modes and that high mode numbers are required to reach this limit (Legendre mode l ≳ 100 for spherical flows). Finally, comparisons are made with a Lagrangian hydrodynamics code, and it is found that a numerical resolution of ~30 zones per wavelength is required to capture these solutions accurately. This translates to an angular resolution of ~(12/l)°, or ≲ 0.1° to resolve the fastest-growing modes.« less
Learning Fuzzy Set Representations of Partial Shapes on Dual Embedding Spaces

Modeling relations between components of 3D objects is essential for many geometry editing tasks. Existing techniques commonly rely on labeled components, which requires substantial annotation effort and limits components to a dictionary of predefined semantic parts. We propose a novel framework based on neural networks that analyzes an uncurated collection of 3D models from the same category and learns two important types of semantic relations among full and partial shapes: complementarity and interchangeability. The former helps to identify which two partial shapes make a complete plausible object, and the latter indicates that interchanging two partial shapes from different objects preserves the object plausibility. Our key idea is to jointly encode both relations by embedding partial shapes as fuzzy sets in dual embedding spaces. We model these two relations as fuzzy set operations performed across the dual embedding spaces, and within each space, respectively. We demonstrate the utility of our method for various retrieval tasks that are commonly needed in geometric modeling interfaces.
Simplices and sets of positive upper density in $\mathbb{R}^d$

We prove an extension of Bourgain's theorem on pinned distances in measurable subset of $\mathbb{R}^2$ of positive upper density, namely Theorem $1^\prime$ in [Bourgain, 1986], to pinned non-degenerate $k$-dimensional simplices in measurable subset of $\mathbb{R}^{d}$ of positive upper density whenever $d\geq k+2$ and $k$ is any positive integer.
Approximation Results for Reflectionless Jacobi Matrices

We study spaces of reflectionless Jacobi matrices. The main theme is the following type of question: Given a reflectionless Jacobi matrix, is it possible to approximate it by other reflectionless and, typically, simpler Jacobi matrices of a special type? For example, can we approximate by periodic operators?
The Global Dimension of the full Transformation Monoid (with an Appendix by V. Mazorchuk and B. Steinberg)

The representation theory of the symmetric group has been intensively studied for over 100 years and is one of the gems of modern mathematics. The full transformation monoid \(\mathfrak {T}_{n}\) (the monoid of all self-maps of an n-element set) is the monoid analogue of the symmetric group. The investigation of its representation theory was begun by Hewitt and Zuckerman in 1957. Its character table was computed by Putcha in 1996 and its representation type was determined in a series of papers by Ponizovskiĭ, Putcha and Ringel between 1987 and 2000. From their work, one can deduce that the global dimension of \(\mathbb {C}\mathfrak {T}_{n}\) is n−1 for n = 1, 2, 3, 4. We prove in this paper that the global dimension is n−1 for all n ≥ 1 and, moreover, we provide an explicit minimal projective resolution of the trivial module of length n−1. In an appendix with V. Mazorchuk we compute the indecomposable tilting modules of \(\mathbb {C}\mathfrak T_{n}\) with respect to Putcha’s quasi-hereditary structure and the Ringel dual (up to Morita equivalence).
The measure problem in no-collapse (many worlds) quantum mechanics

We explain the measure problem (cf. origin of the Born probability rule) in no-collapse quantum mechanics. Everett defined maverick branches of the state vector as those on which the usual Born probability rule fails to hold — these branches exhibit highly improbable behaviors, including possibly the breakdown of decoherence or even the absence of an emergent semi-classical reality. Derivations of the Born rule which originate in decision theory or subjective probability (i.e. the reasoning of individual observers) do not resolve this problem, because they are circular: they assume, a priori, that the observer occupies a non-maverick branch. An ab initio probability measure is sometimes assumed to explain why we do not occupy a maverick branch. This measure is constrained by, e.g. Gleason’s theorem or envariance to be the usual Hilbert measure. However, this ab initio measure ultimately governs the allocation of a self or a consciousness to a particular branch of the wave function, and hence invokes primi...
Forbidden directed minors and Kelly-width

Abstract Partial k -DAGs are generalizations of partial k -trees. Partial k -trees are undirected graphs with bounded treewidth, whereas partial k -DAGs are digraphs with bounded Kelly-width. It is well-known that an undirected graph is a partial 1-tree if and only if it has no K 3 minor. In this paper, we prove that partial 1-DAGs are characterized by three forbidden directed minors, K 3 , N 4 and M 5 .
Modeling and simulation of a fluttering cantilever in channel flow

Abstract Characterizing the dynamics of a cantilever in channel flow is relevant to applications ranging from snoring to energy harvesting. Aeroelastic flutter induces large oscillating amplitudes and sharp changes with frequency that impact the operation of these systems. The fluid–structure mechanisms that drive flutter can vary as the system parameters change, with the stability boundary becoming especially sensitive to the channel height and Reynolds number, especially when either or both are small. In this paper, we develop a coupled fluid–structure model for viscous, two-dimensional channel flow of arbitrary shape. Its flutter boundary is then compared to results of two-dimensional direct numerical simulations to explore the model’s validity. Provided the non-dimensional channel height remains small, the analysis shows that the model is not only able to replicate DNS results within the parametric limits that ensure the underlying assumptions are met, but also over a wider range of Reynolds numbers and fluid–structure mass ratios. Model predictions also converge toward an inviscid model for the same geometry as Reynolds number increases.
A generalized LDPC framework for robust and sublinear compressive sensing

Compressive sensing aims to recover a high-dimensional sparse signal from a relatively small number of measurements. In this paper, a novel design of the measurement matrix is proposed. The design is inspired by the construction of generalized low-density parity-check codes, where the capacity-achieving point-to-point codes serve as subcodes to robustly estimate the signal support. In the case that each entry of the n-dimensional ft-sparse signal lies in a known discrete alphabet, the proposed scheme requires only O(k log n) measurements and arithmetic operations. In the case of arbitrary, possibly continuous alphabet, an error propagation graph is proposed to characterize the residual estimation error. With O(k log2 n) measurements and computational complexity, the reconstruction error can be made arbitrarily small with high probability.
Cortical computations via metastable activity

Metastable brain dynamics are characterized by abrupt, jump-like modulations so that the neural activity in single trials appears to unfold as a sequence of discrete, quasi-stationary ‘states’. Evidence that cortical neural activity unfolds as a sequence of metastable states is accumulating at fast pace. Metastable activity occurs both in response to an external stimulus and during ongoing, self-generated activity. These spontaneous metastable states are increasingly found to subserve internal representations that are not locked to external triggers, including states of deliberations, attention and expectation. Moreover, decoding stimuli or decisions via metastable states can be carried out trial-by-trial. Focusing on metastability will allow us to shift our perspective on neural coding from traditional concepts based on trial-averaging to models based on dynamic ensemble representations. Recent theoretical work has started to characterize the mechanistic origin and potential roles of metastable representations. In this article we review recent findings on metastable activity, how it may arise in biologically realistic models, and its potential role for representing internal states as well as relevant task variables.
REPRESENTATIONS OF POINTED HOPF ALGEBRAS AND THEIR DRINFEL'D QUANTUM DOUBLES

Abstract We study representations of nontrivial liftings of nilpotent type of quantum linear spaces and their Drinfel'd quantum doubles. We construct a family of Verma-type modules in both cases and prove a parametrization theorem for simple modules. We compute the Loewy and socle series of Verma modules under a mild restriction on the datum of a lifting. We find bases and dimensions of simple modules.
CRAFT: ClusteR-specific Assorted Feature selecTion

We present a framework for clustering with cluster-specific feature selection. The framework, CRAFT, is derived from asymptotic log posterior formulations of nonparametric MAP-based clustering models. CRAFT handles assorted data, i.e., both numeric and categorical data, and the underlying objective functions are intuitively appealing. The resulting algorithm is simple to implement and scales nicely, requires minimal parameter tuning, obviates the need to specify the number of clusters a priori, and compares favorably with other methods on real datasets.
Variation of the Canonical Height for Polynomials in Several Variables

Let K be a number field, X/K a curve, and f/X a family of endomorphisms of projective N-space. It follows from a result of Call and Silverman that the canonical height associated to the family f, evaluated along a section, differs from a Weil height on the base by little-o of a Weil height. In the case where f is a family with an invariant hyperplane, whose restriction to this invariant hyperplane is isotrivial, we improve this by showing that the canonical height along a section differs from a Weil height on the base by a bounded amount.
Iteratively Reweighted $\ell_1$ Approaches to Sparse Composite Regularization

Motivated by the observation that a given signal ${x}$ admits sparse representations in multiple dictionaries ${\Psi}_d$ but with varying levels of sparsity across dictionaries, we propose two new algorithms for the reconstruction of (approximately) sparse signals from noisy linear measurements. Our first algorithm, Co-L1, extends the well-known lasso algorithm from the L1 regularizer $\Vert{\Psi x}\Vert_1$ to composite regularizers of the form $\sum_d \lambda_d \Vert{\Psi}_d {x}\Vert_1$ while self-adjusting the regularization weights $\lambda_d$ . Our second algorithm, Co-IRW-L1, extends the well-known iteratively reweighted L1 algorithm to the same family of composite regularizers. We provide several interpretations of both algorithms: 1) majorization-minimization (MM) applied to a non-convex log-sum-type penalty; 2) MM applied to an approximate $\ell_0$ -type penalty; 3) MM applied to Bayesian MAP inference under a particular hierarchical prior; and 4) variational expectation maximization (VEM) under a particular prior with deterministic unknown parameters. A detailed numerical study suggests that our proposed algorithms yield significantly improved recovery SNR when compared to their noncomposite L1 and IRW-L1 counterparts.
Optimal Transport for Gaussian Mixture Models

We introduce an optimal mass transport framework on the space of Gaussian mixture models. These models are widely used in statistical inference. Specifically, we treat the Gaussian mixture models as a submanifold of probability densities equipped with the Wasserstein metric. The topology induced by optimal transport is highly desirable and natural because, in contrast to total variation and other metrics, the Wasserstein metric is weakly continuous (i.e., convergence is equivalent to the convergence of moments). Thus, our approach provides natural ways to compare, interpolate, and average Gaussian mixture models. Moreover, the approach has low computational complexity. Different aspects of the framework are discussed, and examples are presented for illustration purposes.
Asymptotic Normality of Degree Counts in a Preferential Attachment Model

S. Resnick and G. Samorodnitsky were supported by Army MURI grant W911NF-12-1-0385 to Cornell University
Anisotropic nonlocal means denoising

It has recently been proved that the popular nonlocal means (NLM) denoising algorithm does not optimally denoise images with sharp edges. Its weakness lies in the isotropic nature of the neighborhoods it uses to set its smoothing weights. In response, in this paper we introduce several theoretical and practical anisotropic nonlocal means (ANLM) algorithms and prove that they are near minimax optimal for edge-dominated images from the Horizon class. On real-world test images, an ANLM algorithm that adapts to the underlying image gradients outperforms NLM by a significant margin.
Strong test ideals associated to Cartier algebras

In this note, we use the theory of test ideals and Cartier algebras to examine the interplay between the tight and integral closures in a local ring of positive characteristic. Using work of Schwed...
Product-type non-commutative polynomial states

In math/0702157, arXiv:0712.4185, we investigated monic multivariate non-commutative orthogonal polynomials, their recursions, states of orthogonality, and corresponding continued fraction expansions. In this note, we collect a number of examples, demonstrating what these general results look like for the most important states on non-commutative polynomials, namely for various product states. In particular, we introduce a notion of a product-type state on polynomials, which covers all the non-commutative universal products and excludes some other familiar non-commutative products, and which guarantees a number of nice properties for the corresponding polynomials.
Machine Learning-Based Prototyping of Graphical User Interfaces for Mobile Apps

It is common practice for developers of user-facing software to transform a mock-up of a graphical user interface (GUI) into code. This process takes place both at an application's inception and in an evolutionary context as GUI changes keep pace with evolving features. Unfortunately, this practice is challenging and time-consuming. In this paper, we present an approach that automates this process by enabling accurate prototyping of GUIs via three tasks: detection , classification , and assembly . First, logical components of a GUI are detected from a mock-up artifact using either computer vision techniques or mock-up metadata. Then, software repository mining, automated dynamic analysis, and deep convolutional neural networks are utilized to accurately classify GUI-components into domain-specific types (e.g., toggle-button). Finally, a data-driven, K-nearest-neighbors algorithm generates a suitable hierarchical GUI structure from which a prototype application can be automatically assembled . We implemented this approach for Android in a system called ReDraw . Our evaluation illustrates that ReDraw achieves an average GUI-component classification accuracy of 91 percent and assembles prototype applications that closely mirror target mock-ups in terms of visual affinity while exhibiting reasonable code structure. Interviews with industrial practitioners illustrate ReDraw's potential to improve real development workflows.