cssi/SciSciGPT-SciSciNet huggingface dataset:
Controlling Neutral Mixtures: Thin Film Deposition via Laser Ablation and Selective Ionization of K4In4Sb6

We present experimental results on a technique that combines laser ablation with selective ionization in order to generate and subsequently separate neutral mixtures. For example, in the laser ablation (λ = 308 nm) of K4In4Sb6, irradiation of the ablation plume with 248 nm laser light induces selective ionization of potassium. Subsequent electric field extraction leads to macroscopic depletion of potassium from the ablation plume. Quantification via scanning Auger electron spectroscopy of thin films deposited from such ablation plumes reveals that even without optimization of the spatial overlap between the ablation plume and the ionization laser, the technique leads to ∼60% removal of potassium. While at present it is not clear whether conditions exist for full quantitative removal of the potassium, it is apparent that control over the neutral plume has been exerted.
Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale.

The rapidly expanding body of available genomic and protein structural data provides a rich resource for understanding protein dynamics with biomolecular simulation. While computational infrastructure has grown rapidly, simulations on an omics scale are not yet widespread, primarily because software infrastructure to enable simulations at this scale has not kept pace. It should now be possible to study protein dynamics across entire (super)families, exploiting both available structural biology data and conformational similarities across homologous proteins. Here, we present a new tool for enabling high-throughput simulation in the genomics era. Ensembler takes any set of sequences—from a single sequence to an entire superfamily—and shepherds them through various stages of modeling and refinement to produce simulation-ready structures. This includes comparative modeling to all relevant PDB structures (which may span multiple conformational states of interest), reconstruction of missing loops, addition of missing atoms, culling of nearly identical structures, assignment of appropriate protonation states, solvation in explicit solvent, and refinement and filtering with molecular simulation to ensure stable simulation. The output of this pipeline is an ensemble of structures ready for subsequent molecular simulations using computer clusters, supercomputers, or distributed computing projects like Folding@home. Ensembler thus automates much of the time-consuming process of preparing protein models suitable for simulation, while allowing scalability up to entire superfamilies. A particular advantage of this approach can be found in the construction of kinetic models of conformational dynamics—such as Markov state models (MSMs)—which benefit from a diverse array of initial configurations that span the accessible conformational states to aid sampling. We demonstrate the power of this approach by constructing models for all catalytic domains in the human tyrosine kinase family, using all available kinase catalytic domain structures from any organism as structural templates. Ensembler is free and open source software licensed under the GNU General Public License (GPL) v2. It is compatible with Linux and OS X. The latest release can be installed via the conda package manager, and the latest source can be downloaded from https://github.com/choderalab/ensembler.
The synthesis of a potential cross-linking reagent: 2,2'-sulfonylbis[3-benzylamino-E,E)-N-(2-oxoethyl) propenamide]

Abstract The synthesis of the title bis-aldehydic reagent (3) with potential applications in biomacromolecular cross-linking is reported.
Synthesis of bifunctional phosphonates and phosphine oxides. Structural studies of 1-N,N-diethyl-carbamoyl-2-(4-hydroxylbenzene)-ethyl phosphonic acid and diphenyl[1-(N,N-diethyl-carbamoyl)-2-(phenyl)ethyl]phosphine oxide uranyl nitrate

Abstract Syntheses of the bifunctional ligands Ph2P(O)CH[CH2C6H4X][C(O)NEt2] (XH, OCH3, OH), (EtO)2P(O)CH[CH2C6H4X][C(O)NEt2] (XH, OCH3) and (HO)2P(O)CH[CH2C6H4OH][C(O)NEt2] from the corresponding carbanions [Ph2P(O)CHC(O)NEt2−] and [(EtO)2P(O)CHC(O)NEt2−] are described. The molecular structures of the phosphonic acid, (HO)2P(O)CH[CH2C6H4OH][C(O)NEt2] (4c), and of one complex, {Ph2P(O)CH[CH2C6H5][C(O)NEt2]}UO2(NO3)2 (5a), were determined by single crystal X-ray diffraction techniques. The phosphonic acid 4c crystallizes in the monoclinic space group P21/c with a = 10.347(2), b = 11.403(2), c = 12.427(1) A, β = 90.95(1)o, Z = 4, V = 1465.8(5) A3 and ϱcalc = 1.36 g cm−3. The structure was solved by direct methods, and blocked least-squares refinement converged at RF=6.37% and RwF=5.63%. The uranyl complex 5a crystallizes in the triclinic space group P 1 with a = 10.323(3), b = 11.204(3), c = 13.639(4) A, α = 100.96(2), β = 95.21(2), γ = 98.68(2)o, Z = 2, V = 1519.3(8) A3 and ϱcalc = 1.748 g cm−3. The structure was solved by Patterson methods, and blocked least-squares refinement converged at RF = 5.42% and RwF = 3.89%. The ligand binds to the uranyl group in a bidentate fashion with no unusual steric congestion presented by the phenyl substituent groups. Selected bond distances include: U  Oav = 1.740, UO(P) 2.347(5), UO(C) 2.525(6), P  O 1.501(4), C  O 1.258(8) A.
Generation and trapping of alkene radical cations under nonoxidizing conditions: formation of six-membered rings by exo- and endo-mode cyclizations.

It is demonstrated that alkene radical cations generated by the radical ionic fragmentation of β-(phosphatoxy)alkyl radicals undergo efficient nucleophilic capture by amines in either the 6-exo or 6-endo modes, leading to six-membered nitrogen heterocycles. Suitable placement of an alkene enables the juxtaposition of a radical cyclization resulting in the formation of both the indolizidine and 1-azabicyclo[3.2.1]octane skeleta.
Synthesis and characterization of Er3SmQ6 (Q=S, Se) and Er1.12Sm0.88Se3

The interlanthanide compounds Er{sub 3}SmS{sub 6}, Er{sub 3}SmSe{sub 6}, and Er{sub 1.12}Sm{sub 0.88}Se{sub 3} have been synthesized from stoichiometric reactions of the elements in a KI salt flux at 1273, 1173, and 1123 K, respectively. Er{sub 3}SmS{sub 6} and Er{sub 3}SmSe{sub 6}, which are isostructural and ordered, crystallize in space group P2{sub 1}/m in the ScEr{sub 3}S{sub 6} structure type whereas Er{sub 1.12}Sm{sub 0.88}Se{sub 3}, in which the Er and Sm atoms are disordered, crystallizes in space group Pnma in the U{sub 2}S{sub 3} structure type. Er{sub 3}SmS{sub 6} is a paramagnet with a {mu} {sub eff}=11.25(1) {mu}{sub B}/mol. From optical measurements a direct band gap of 2.0 eV for light perpendicular to the (100) crystal face of Er{sub 3}SmSe{sub 6} is derived whereas for isostructural Er{sub 3}SmS{sub 6} an optical transition at 2.2-2.4 eV and a broad absorption peak at lower energies are observed. - Graphical abstract: The structure of Er{sub 3}SmSe{sub 6} viewed approximately down [010].
Structures and Stabilities of B2H2n2+ Dications (n = 1−4)

Structures of B2H2n2+ dications (n = 1−4) were investigated at the QCISD(T)/6-311G** level of theory. Thermodynamic and kinetic stabilities of the dications were also estimated. Although deprotonations of the dications are exothermic (except the dication B2H22+), they show considerable kinetic barriers. The charge distributions and Wiberg bond indices were calculated by the NBO method. 11B NMR chemical shifts were also calculated by GIAO-MP2 and GIAO-DFT methods.
Conclusive evidence of the trapping of primary ozonides.

Anomalous ozonolysis of strained bicyclic allylic alcohols yields α-hydroxymethyl ketones. The proposed mechanism involves an unusual trapping of the primary ozonide that undergoes a Grob-like fragmentation instead of dissociating into the Criegee intermediates.
A one-pot method for the synthesis of 2-aminobenzimidazoles and related heterocycles

A rapid and efficient one-pot method for the synthesis of 2-aminobenzimidazoles and related heterocycles is described. The reaction is mediated by a polymer-supported carbodiimide, which simplifies product isolation. The scope and limitations of this method are described.
Upconversion in Er3+:ZrO2 Nanocrystals

Erbium-doped ZrO2 nanoparticles are prepared by a sol−emulsion−gel technique. The effects of the Er3+ concentration and different codopants (Yb3+ and Y3+) in the ZrO2 matrix on the upconverted emission are reported. Green and red upconversion emission at 550 and 670 nm were observed from these oxide nanocrystals with 980 nm excitation. The overall intensity decreases with an increasing concentration of erbium in zirconia. The presence of codopants (Y3+ and Yb3+) also increases the overall intensity of the upconverted emission. The emission spectra and the pump intensity dependence of the luminescence intensities are used to understand the excitation mechanism. These results confirm that upconverted emission in these materials is due to a two-photon excited-state absorption (ESA)/energy transfer upconversion (ETU) process.
SYNTHESIS OF 2-AMINOQUINAZOLINES FROM ORTHO-FLUOROBENZALDEHYDES

The reaction of guanidine carbonate with various ortho-fluorobenzaldehydes in N,N-diinethylacetamide was investigated as a potential route for preparing 2-aminoquinazolines. Eleven new 2-aminoquinazolines were elaborated in this manner in low to moderate yields. In general the best results were obtained with ortho-fluorobenzaldehydes possessing an electron withdrawing substituent at the other ortho position. Complex mixtures were obtained using 2-fluorobenzaldehyde, 2,5-difluorobenzaldehyde and 2-fluoro-5-methoxybenzaldehyde which were not resolved.
Sexual conflict through mother’s curse and father’s curse

In contrast with autosomes, lineages of sex chromosomes reside for different amounts of time in males and females, and this transmission asymmetry makes them hotspots for sexual conflict. Similarly, the maternal inheritance of the mitochondrial genome (mtDNA) means that mutations that are beneficial in females can spread in a population even if they are deleterious in males, a form of sexual conflict known as Mother's Curse. While both Mother's Curse and sex chromosome induced sexual conflict have been well studied on their own, the interaction between mitochondrial genes and genes on sex chromosomes is poorly understood. Here, we use analytical models and computer simulations to perform a comprehensive examination of how transmission asymmetries of nuclear, mitochondrial, and sex chromosome-linked genes may both cause and resolve sexual conflicts. For example, the accumulation of male-biased Mother's Curse mtDNA mutations will lead to selection in males for compensatory nuclear modifier loci that alleviate the effect. We show how the Y chromosome, being strictly paternally transmitted provides a particularly safe harbor for such modifiers. This analytical framework also allows us to discover a novel kind of sexual conflict, by which Y chromosome-autosome epistasis may result in the spread of male beneficial but female deleterious mutations in a population. We christen this phenomenon Father's Curse. Extending this analytical framework to ZW sex chromosome systems, where males are the heterogametic sex, we also show how W-autosome epistasis can lead to a novel kind of nuclear Mother's Curse. Overall, this study provides a comprehensive framework to understand how genetic transmission asymmetries may both cause and resolve sexual conflicts.
Towards the Standard Model spectrum from elliptic Calabi-Yau

We show that it is possible to construct supersymmetric three-generation models with the Standard Model gauge group in the framework of non-simply-connected elliptically fibered Calabi–Yau threefolds, without section but with a bi-section. The fibrations on a cover Calabi–Yau threefold, where the model has six generations of SU(5) and the bundle is given via the spectral cover description, use a different description of the elliptic fiber which leads to more than one global section. We present two examples of a possible cover Calabi–Yau threefold with a free involution: one is a fiber product of rational elliptic surfaces dP9; another example is an elliptic fibration over a Hirzebruch surface. We compute the necessary amount of chiral matter by "turning on" a further parameter which is related to singularities of the fibration and the branching of the spectral cover.
Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence.

ABSTRACT Permafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the class Bacilli were more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of the Clostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost. IMPORTANCE Permafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.
The transcription factor Tfap2e/AP-2ε plays a pivotal role in maintaining the identity of basal vomeronasal sensory neurons.

Abstract The identity of individual neuronal cell types is defined and maintained by the expression of specific combinations of transcriptional regulators that control cell type–specific genetic programs. The epithelium of the vomeronasal organ of mice contains two major types of vomeronasal sensory neurons (VSNs): 1) the apical VSNs which express vomeronasal 1 receptors (V1r) and the G-protein subunit Gαi2 and; 2) the basal VSNs which express vomeronasal 2 receptors (V2r) and the G-protein subunit Gαo. Both cell types originate from a common pool of progenitors and eventually acquire apical or basal identity through largely unknown mechanisms. The transcription factor AP-2e, encoded by the Tfap2e gene, plays a role in controlling the development of GABAergic interneurons in the main and accessory olfactory bulb (AOB), moreover AP-2e has been previously described to be expressed in the basal VSNs. Here we show that AP-2e is expressed in post-mitotic VSNs after they commit to the basal differentiation program. Loss of AP-2e function resulted in reduced number of basal VSNs and in an increased number of neurons expressing markers of the apical lineage. Our work suggests that AP-2e, which is expressed in late phases of differentiation, is not needed to initiate the apical-basal differentiation dichotomy but for maintaining the basal VSNs’ identity. In AP-2e mutants we observed a large number of cells that entered the basal program can express apical genes, our data suggest that differentiated VSNs of mice retain a notable level of plasticity.
Extending the scope of chromium-manganese redox-coupled reactions: a one-pot synthesis of benzoxazoles.

A critically important strategy for synthetic chemistry is the development of “domino” processes: those capable of concatenating multiple transformations into a single step. Such transformations not only provide an increase in synthetic efficiency, but also imply the development of a significant degree of mechanistic understanding. We report herein a new domino reaction, in which a chromium−manganese redox couple is employed both to catalytically reduce an o-hydroxy nitroarene and to oxidatively cyclize a subsequently formed imine. We find that the reaction is most effective for starting o-hydroxy nitroarenes with a strongly electron-withdrawing group at the para position.
SYNTHESIS AND STABILITIES OF THE GA(III) AND IN(III) CHELATES OF A NEW DIAMINODITHIOL BIFUNCTIONAL LIGAND

Abstract The synthesis of a new bifunctional ligand 1-(4-carboxymethoxybenzyl)-N-N′-bis[(2-mercapto-2,2-dimethyl)ethyl]-1,2-ethylenediamine-N,N′-diacetic acid (B6SS) is described. It consists of substitution of a side-chain, a 4-carboxymethoxybenzyl group on a carbon atom of the ethylenediamine moiety of a hexadentate ligand, 6SS, which has been found to have a very high affinity for In(III). Potentiometric determination of Ga(III) and In(III) chelate stabilities of the bifunctional ligand show that the side-chain on the ligand reduces the pM values about 2–4 log values.
A one-step method to synthesize N,N′-bis(4′-aminophenyl)-1,4-quinonenediimine and its derivatives

A convenient, one-step method has been developed for the synthesis of N,N′-bis(4′-aminophenyl)-1,4-quinonenediimine and its derivatives from the oxidation of p-phenyl-enediamine in the presence of aniline or substituted anilines in an acidic aqueous medium. These diimine compounds can be readily reduced to afford their corresponding diamine derivatives.
Reversal of enantioselectivity using tethered bisguanidine catalysts in the aza-Henry reaction

A series of chiral guanidines were synthesized and shown to efficiently catalyze the aza-Henry reaction. Modifications of the catalyst structure revealed important selectivity trends as well as an intriguing reversal in stereoselectivity with bisguanidine variants. These compounds were applied to the aza-Henry reaction between N-Boc imines and nitroalkanes generating the β-nitroamines in up to 77% ee and up to 20:1 diastereoselectivity.
Biomolecular hydration dynamics probed with 2D-IR spectroscopy: From dilute solution to a macromolecular crowd

Abstract Although it is well known that water is essential for biological function, it has been a challenge to determine how water behaves near biomacromolecular interfaces, and what role water plays in influencing the dynamics of the biochemical machinery. By adopting a vibrational labeling strategy coupled with ultrafast two-dimensional infrared (2D-IR) spectroscopy, it has recently become possible to study hydration dynamics, site specifically at the surface of proteins and model membranes. We review our recent progress in measuring hydration dynamics in contexts ranging from small-molecule solutes to biomacromolecules in dilute, viscous, and crowded environments.
Beyond clines: lineages and haplotype blocks in hybrid zones

Hybrid zones formed between recently diverged populations offer an opportunity to study the mechanisms underlying reproductive isolation and the process of speciation. Here, we use a combination of analytical theory and explicit forward simulations to describe how selection against hybrid genotypes impacts patterns of introgression across genomic and geographic space. By describing how lineages move across the hybrid zone, in a model without coalescence, we add to modern understanding of how clines form and how parental haplotypes are broken up during introgression. Working with lineages makes it easy to see that clines form in about 1/s generations, where s is the strength of selection against hybrids, and linked clines persist over a genomic scale of 1/T, where T is the age, in generations, of the hybrid zone. Locally disadvantageous alleles tend to exist as small families, whose lineages trace back to the side from which they originated at speed s dispersal distances per generation. The lengths of continuous tracts of ancestry provide an additional source of information: blocks of ancestry surrounding incompatibilities can be substantially longer than the genomewide average block length at the same spatial location, an observation that might be used to identify candidate targets of selection.
A new approach to bounds on mixing

We consider mixing by incompressible flows. In 2003, Bressan stated a conjecture concerning a bound on the mixing achieved by the flow in terms of an L1 norm of the velocity field. Existing results...
Leveraging Network Dynamics for Improved Link Prediction

The aim of link prediction is to forecast connections that are most likely to occur in the future, based on examples of previously observed links. A key insight is that it is useful to explicitly model network dynamics, how frequently links are created or destroyed when doing link prediction. In this paper, we introduce a new supervised link prediction framework, RPM (Rate Prediction Model). In addition to network similarity measures, RPM uses the predicted rate of link modifications, modeled using time series data; it is implemented in Spark-ML and trained with the original link distribution, rather than a small balanced subset. We compare the use of this network dynamics model to directly creating time series of network similarity measures. Our experiments show that RPM, which leverages predicted rates, outperforms the use of network similarity measures, either individually or within a time series.
A quasi-isometric embedding into the group of Hamiltonian diffeomorphisms with Hofer's metric

We construct an embedding Φ of [0, 1]∞ into Ham(M, ω), the group of Hamiltonian diffeomorphisms of a suitable closed symplectic manifold (M, ω). We then prove that Φ is in fact a quasi-isometry. After imposing further assumptions on (M, ω), we adapt our methods to construct a similar embedding of ℝ ⊕ [0, 1]∞ into either Ham(M, ω) or , the universal cover of Ham(M, ω). Along the way, we prove results related to the filtered Floer chain complexes of radially symmetric Hamiltonians. Our proofs rely heavily on a continuity result for barcodes (as presented in [28]) associated to filtered Floer homology viewed as a persistence module.
The density of primes dividing a particular non-linear recurrence sequence

Define the sequence $\{b_n\}$ by $b_0=1,b_1=1, b_2=2,b_3=1$, and $$b_n=\begin{cases} \frac{b_{n-1}b_{n-3}-b_{n-2}^2}{b_{n-4}}&\textrm{if}~ n\not\equiv 0\pmod 3, \frac{b_{n-1}b_{n-3}-3b_{n-2}^2}{b_{n-4}}&\textrm{if}~ n\equiv 0\pmod 3. We relate this sequence $\{b_n\}$ to the coordinates of points on the elliptic curve $E:y^2+y=x^3-3x+4$. We use Galois representations attached to $E$ to prove that the density of primes dividing a term in this sequence is equal to $\frac{179}{336}$. Furthermore, we describe an infinite family of elliptic curves whose Galois images match that of $E$.
Sewing Riemannian Manifolds with Positive Scalar Curvature

We explore to what extent one may hope to preserve geometric properties of three-dimensional manifolds with lower scalar curvature bounds under Gromov–Hausdorff and Intrinsic Flat limits. We introduce a new construction, called sewing, of three-dimensional manifolds that preserves positive scalar curvature. We then use sewing to produce sequences of such manifolds which converge to spaces that fail to have nonnegative scalar curvature in a standard generalized sense. Since the notion of nonnegative scalar curvature is not strong enough to persist alone, we propose that one pair a lower scalar curvature bound with a lower bound on the area of a closed minimal surface when taking sequences as this will exclude the possibility of sewing of manifolds.
Robust Stereo Visual Inertial Odometry for Fast Autonomous Flight

In recent years, vision-aided inertial odometry for state estimation has matured significantly. However, we still encounter challenges in terms of improving the computational efficiency and robustness of the underlying algorithms for applications in autonomous flight with microaerial vehicles, in which it is difficult to use high-quality sensors and powerful processors because of constraints on size and weight. In this letter, we present a filter-based stereo visual inertial odometry that uses the multistate constraint Kalman filter. Previous work on the stereo visual inertial odometry has resulted in solutions that are computationally expensive. We demonstrate that our stereo multistate constraint Kalman filter (S-MSCKF) is comparable to state-of-the-art monocular solutions in terms of computational cost, while providing significantly greater robustness. We evaluate our S-MSCKF algorithm and compare it with state-of-the-art methods including OKVIS, ROVIO, and VINS-MONO on both the EuRoC dataset and our own experimental datasets demonstrating fast autonomous flight with a maximum speed of 17.5 m/s in indoor and outdoor environments. Our implementation of the S-MSCKF is available at https://github.com/KumarRobotics/msckf_vio.
Parity of the partition function p(n,k)

Let p(n,k) denote the number of partitions of n into parts less than or equal to k. We show several properties of this function modulo 2. First, we prove that for fixed positive integers k and m, p...
Axion dark matter and the 21-cm signal

Abstract It was shown in Erken et al. (2012) that cold dark matter axions reach thermal contact with baryons, and therefore cool them, shortly after the axions thermalize among themselves and form a Bose–Einstein condensate. The recent observation by the EDGES collaboration of a baryon temperature at cosmic dawn lower than expected under “standard” assumptions is interpreted as new evidence that the dark matter is axions, at least in part. Baryon cooling by dark matter axions is found to be consistent with the observation of baryon acoustic oscillations.
Heavy flavor results at RHIC - A comparative overview

I review the latest heavy flavor measurements at RHIC experiments. Measurements from RHIC together with preliminary results from LHC offer us an opportunity to systematically study the sQGP medium properties. In the end, I will outlook a prospective future on precision heavy flavor measurements with detector upgrades at RHIC.
Improved Sum-of-Squares Lower Bounds for Hidden Clique and Hidden Submatrix Problems.

Given a large data matrix A ∈ Rn×n, we consider the problem of determining whether its entries are i.i.d. from some known marginal distribution Aij ∼ P0, or instead A contains a principal submatrix AQ,Q whose entries have marginal distribution Aij ∼ P1 6= P0. As a special case, the hidden (or planted) clique problem is finding a planted clique in an otherwise uniformly random graph. Assuming unbounded computational resources, this hypothesis testing problem is statistically solvable provided |Q| ≥ C log n for a suitable constant C. However, despite substantial effort, no polynomial time algorithm is known that succeeds with high probability when |Q| = o( √ n). Recently, Meka and Wigderson (2013) proposed a method to establish lower bounds for the hidden clique problem within the Sum of Squares (SOS) semidefinite hierarchy. Here we consider the degree-4 SOS relaxation, and study the construction of Meka and Wigderson (2013) to prove that SOS fails unless k ≥ C n/ log n. An argument presented by Barak (2014) implies that this lower bound cannot be substantially improved unless the witness construction is changed in the proof. Our proof uses the moment method to bound the spectrum of a certain random association scheme, i.e. a symmetric random matrix whose rows and columns are indexed by the edges of an Erdos-Renyi random graph.
Area and Perimeter of the Convex Hull of Stochastic Points

Given a set $P$ of $n$ points in the plane, we study the computation of the probability distribution function of both the area and perimeter of the convex hull of a random subset $S$ of $P$. The random subset $S$ is formed by drawing each point $p$ of $P$ independently with a given rational probability $\pi_p$. For both measures of the convex hull, we show that it is \#P-hard to compute the probability that the measure is at least a given bound $w$. For $\varepsilon\in(0,1)$, we provide an algorithm that runs in $O(n^{6}/\varepsilon)$ time and returns a value that is between the probability that the area is at least $w$, and the probability that the area is at least $(1-\varepsilon)w$. For the perimeter, we show a similar algorithm running in $O(n^{6}/\varepsilon)$ time. Finally, given $\varepsilon,\delta\in(0,1)$ and for any measure, we show an $O(n\log n+ (n/\varepsilon^2)\log(1/\delta))$-time Monte Carlo algorithm that returns a value that, with probability of success at least $1-\delta$, differs at most $\varepsilon$ from the probability that the measure is at least $w$.
Compactness of Hankel Operators with Symbols Continuous on the Closure of Pseudoconvex Domains

Let $\Omega$ be a bounded pseudoconvex domain in $\mathbb{C}^2$ with Lipschitz boundary or a bounded convex domain in $\mathbb{C}^n$ and $\phi\in C(\overline{\Omega})$ such that $H_{\phi}$ is compact on $A^2(\Omega)$. Then $\phi\circ f$ is holomorphic for any holomorphic $f:\mathbb{D}\rightarrow b\Omega$.
COARSE REDUCIBILITY AND ALGORITHMIC RANDOMNESS

A coarse description of a set A ⊆ ω is a set D ⊆ ω such that the symmetric difference of A and D has asymptotic density 0. We study the extent to which noncomputable information can be effectively recovered from all coarse descriptions of a given set A, especially when A is effectively random in some sense. We show that if A is 1-random and B is computable from every coarse description D of A, then B is K-trivial, which implies that if A is in fact weakly 2-random then B is computable. Our main tool is a kind of compactness theorem for cone-avoiding descriptions, which also allows us to prove the same result for 1-genericity in place of weak 2-randomness. In the other direction, we show that if is a 1-random set, then there is a noncomputable c.e. set computable from every coarse description of A, but that not all K-trivial sets are computable from every coarse description of some 1-random set. We study both uniform and nonuniform notions of coarse reducibility. A set Y is uniformly coarsely reducible to X if there is a Turing functional Φ such that if D is a coarse description of X, then Φ D is a coarse description of Y. A set B is nonuniformly coarsely reducible to A if every coarse description of A computes a coarse description of B. We show that a certain natural embedding of the Turing degrees into the coarse degrees (both uniform and nonuniform) is not surjective. We also show that if two sets are mutually weakly 3-random, then their coarse degrees form a minimal pair, in both the uniform and nonuniform cases, but that the same is not true of every pair of relatively 2-random sets, at least in the nonuniform coarse degrees.
Maximum Entropy Flow Networks

Maximum entropy modeling is a flexible and popular framework for formulating statistical models given partial knowledge. In this paper, rather than the traditional method of optimizing over the continuous density directly, we learn a smooth and invertible transformation that maps a simple distribution to the desired maximum entropy distribution. Doing so is nontrivial in that the objective being maximized (entropy) is a function of the density itself. By exploiting recent developments in normalizing flow networks, we cast the maximum entropy problem into a finite-dimensional constrained optimization, and solve the problem by combining stochastic optimization with the augmented Lagrangian method. Simulation results demonstrate the effectiveness of our method, and applications to finance and computer vision show the flexibility and accuracy of using maximum entropy flow networks.
C⁎-algebras from planar algebras II: The Guionnet–Jones–Shlyakhtenko C⁎-algebras

Abstract We study the C ⁎ -algebras arising in the construction of Guionnet–Jones–Shlyakhtenko (GJS) for a planar algebra. In particular, we show they are pairwise strongly Morita equivalent, we compute their K -groups, and we prove many properties, such as simplicity, unique trace, and stable rank 1. Interestingly, we see a K -theoretic obstruction to the GJS C ⁎ -algebra analog of Goldman-type theorems for II 1 -subfactors. This is the second article in a series studying canonical C ⁎ -algebras associated to a planar algebra. This is the published version of arXiv:1401.2486 .
Deep Painterly Harmonization

Copying an element from a photo and pasting it into a painting is a challenging task. Applying photo compositing techniques in this context yields subpar results that look like a collage --- and existing painterly stylization algorithms, which are global, perform poorly when applied locally. We address these issues with a dedicated algorithm that carefully determines the local statistics to be transferred. We ensure both spatial and inter-scale statistical consistency and demonstrate that both aspects are key to generating quality results. To cope with the diversity of abstraction levels and types of paintings, we introduce a technique to adjust the parameters of the transfer depending on the painting. We show that our algorithm produces significantly better results than photo compositing or global stylization techniques and that it enables creative painterly edits that would be otherwise difficult to achieve.
PARITY, SKEIN POLYNOMIALS AND CATEGORIFICATION

We investigate an application of crossing parity for the bracket expansion of the Jones polynomial for virtual knots. In addition we consider an application of parity for the arrow polynomial as well as for the categorifications of both polynomials. We present a number of examples found through our calculations. We provide tables of calculations for these invariants on virtual knots with at most four real crossings.
Properties of the Secondary Hochschild Homology

In this paper we study properties of the secondary Hochschild homology of the triple (A, B, e) with coefficients in M. We establish a type of Morita equivalence between two triples and show that H•...
Predicting Wireless Channel Features Using Neural Networks

We investigate the viability of using machine-learning techniques for estimating user-channel features at a large-array base station (BS). In the scenario we consider, user-pilot broadcasts are observed and processed by the BS to extract angle-of-arrival (AoA) specific information about propagation-channel features, such as received signal strength and relative path delay. The problem of interest involves using this information to predict the angle-of-departure (AoD) of the dominant propagation paths in the user channels, i.e., channel features not directly observable at the BS. To accomplish this task, the data collected in the same propagation environment are used to train neural networks. Our studies rely on ray-tracing channel data that have been calibrated against measurements from Shinjuku Square, a famous hotspot in Tokyo, Japan. We demonstrate that the observed features at the BS side are correlated with the angular features at the user side. We train neural networks that exploit different combinations of measured features at the BS to infer the unknown parameters at the users. The evaluation based on standard statistical performance metrics suggests that such data-driven methods have the potential to predict unobserved channel features from observed ones.
Fillings of genus-1 open books and 4-braids

We show that there are contact 3-manifolds of support genus one which admit infinitely many Stein fillings, but do not admit arbitrarily large ones. These Stein fillings arise from genus-1 allowable Lefschetz fibrations with distinct homology groups, all filling a fixed minimal genus open book supporting the boundary contact 3-manifold. In contrast, we observe that there are only finitely many possibilities for the homology groups of Stein fillings of a given contact 3-manifold with support genus zero. We also show that there are 4-strand braids which admit infinitely many distinct Hurwitz classes of quasipositive factorizations, yielding in particular an infinite family of knotted complex analytic annuli in the 4-ball bounding the same transverse link up to transverse isotopy. These realize the smallest possible examples in terms of the number of boundary components a genus-1 mapping class and the number of strands a braid can have with infinitely many positive/quasipositive factorizations.
Characterizing domains by the limit set of their automorphism group

Abstract In this paper we study the automorphism group of smoothly bounded convex domains. We show that such a domain is biholomorphic to a “polynomial ellipsoid” (that is, a domain defined by a weighted homogeneous balanced polynomial) if and only if the limit set of the automorphism group intersects at least two closed complex faces of the set. The proof relies on a detailed study of the geometry of the Kobayashi metric and ideas from the theory of non-positively curved metric spaces. We also obtain a number of other results including the Greene–Krantz conjecture in the case of uniform non-tangential convergence, new results about continuous extensions (of biholomorphisms and complex geodesics), and a new Wolff–Denjoy theorem.
Estimating the spectrum in computed tomography via Kullback–Leibler divergence constrained optimization

Purpose We study the problem of spectrum estimation from transmission data of a known phantom. The goal is to reconstruct an x-ray spectrum that can accurately model the x-ray transmission curves and reflects a realistic shape of the typical energy spectra of the CT system. Methods Spectrum estimation is posed as an optimization problem with x-ray spectrum as unknown variables, and a Kullback-Leibler (KL)-divergence constraint is employed to incorporate prior knowledge of the spectrum and enhance numerical stability of the estimation process. The formulated constrained optimization problem is convex and can be solved efficiently by use of the exponentiated-gradient (EG) algorithm. We demonstrate the effectiveness of the proposed approach on the simulated and experimental data. The comparison to the expectation-maximization (EM) method is also discussed. Results In simulations, the proposed algorithm is seen to yield x-ray spectra that closely match the ground truth and represent the attenuation process of x-ray photons in materials, both included and not included in the estimation process. In experiments, the calculated transmission curve is in good agreement with the measured transmission curve, and the estimated spectra exhibits physically realistic looking shapes. The results further show the comparable performance between the proposed optimization-based approach and EM. Conclusions Our formulation of a constrained optimization provides an interpretable and flexible framework for spectrum estimation. Moreover, a KL-divergence constraint can include a prior spectrum and appears to capture important features of x-ray spectrum, allowing accurate and robust estimation of x-ray spectrum in CT imaging.
Sparse low rank approximation of potential energy surfaces with applications in estimation of anharmonic zero point energies and frequencies

We propose a method that exploits sparse representation of potential energy surfaces (PES) on a polynomial basis set selected by compressed sensing. The method is useful for studies involving large numbers of PES evaluations, such as the search for local minima, transition states, or integration. We apply this method for estimating zero point energies and frequencies of molecules using a three step approach. In the first step, we interpret the PES as a sparse tensor on polynomial basis and determine its entries by a compressed sensing based algorithm using only a few PES evaluations. Then, we implement a rank reduction strategy to compress this tensor in a suitable low-rank canonical tensor format using standard tensor compression tools. This allows representing a high dimensional PES as a small sum of products of one dimensional functions. Finally, a low dimensional Gauss–Hermite quadrature rule is used to integrate the product of sparse canonical low-rank representation of PES and Green’s function in the second-order diagrammatic vibrational many-body Green’s function theory (XVH2) for estimation of zero-point energies and frequencies. Numerical tests on molecules considered in this work suggest a more efficient scaling of computational cost with molecular size as compared to other methods.
Linear scaling solution of the all-electron Coulomb problem in solids

We present a linear scaling formulation for the solution of the all-electron Coulomb problem in crystalline solids. The resulting method is systematically improvable and well suited to large-scale quantum mechanical calculations in which the Coulomb potential and energy of a continuous electronic density and singular nuclear density are required. Linear scaling is achieved by introducing smooth, strictly local neutralizing densities to render nuclear interactions strictly local, and solving the remaining neutral Poisson problem for the electrons in real space. While the formulation includes singular nuclear potentials without smearing approximations, the required Poisson solution is in Sobolev space $H^1$, as required for convergence in the energy norm. We employ enriched finite elements, with enrichments from isolated atom solutions, for an efficient solution of the resulting Poisson problem in the interacting solid. We demonstrate the accuracy and convergence of the approach by direct comparison to standard Ewald sums for a lattice of point charges, and demonstrate the accuracy in all-electron quantum mechanical calculations with an application to crystalline diamond.
A Flexible ADMM Algorithm for Big Data Applications

We present a Flexible Alternating Direction Method of Multipliers (F-ADMM) algorithm for solving optimization problems involving a strongly convex objective function that is separable into $$n \ge 2$$nź2 blocks, subject to (non-separable) linear equality constraints. The F-ADMM algorithm uses a Gauss---Seidel scheme to update blocks of variables, and a regularization term is added to each of the subproblems. We prove, under common assumptions, that F-ADMM is globally convergent and that the iterates converge linearly. We also present a special case of F-ADMM that is partially parallelizable, which makes it attractive in a big data setting. In particular, we partition the data into groups, so that each group consists of multiple blocks of variables. By applying F-ADMM to this partitioning of the data, and using a specific regularization matrix, we obtain a hybrid ADMM (H-ADMM) algorithm: the grouped data is updated in a Gauss---Seidel fashion, and the blocks within each group are updated in a Jacobi (parallel) manner. Convergence of H-ADMM follows directly from the convergence properties of F-ADMM. Also, we describe a special case of H-ADMM that may be applied to functions that are convex, rather than strongly convex. Numerical experiments demonstrate the practical advantages of these new algorithms.
Tidal Response of Preliminary Jupiter Model

NASA's Juno project; National Science Foundation (astronomy and astrophysics research grant) [1412646]
Better Streaming Algorithms for the Maximum Coverage Problem

We study the classic NP-Hard problem of finding the maximum k-set coverage in the data stream model: given a set system of m sets that are subsets of a universe $\{1,\ldots ,n \}$ , find the k sets that cover the most number of distinct elements. The problem can be approximated up to a factor $1-1/e$ in polynomial time. In the streaming-set model, the sets and their elements are revealed online. The main goal of our work is to design algorithms, with approximation guarantees as close as possible to $1-1/e$ , that use sublinear space $o(mn)$ . Our main results are: We also study the maximum k-vertex coverage problem in the dynamic graph stream model. In this model, the stream consists of edge insertions and deletions of a graph on N vertices. The goal is to find k vertices that cover the most number of distinct edges.
Relative Fourier transforms and expectations on coideal subalgebras

Abstract For an algebraic compact quantum group H we establish a bijection between the set of right coideal ⁎-subalgebras A → H and that of left module quotient ⁎-coalgebras H → C . It turns out that the inclusion A → H always splits as a map of right A-modules and right H-comodules, and the resulting expectation E : H → A is positive (and lifts to a positive map on the full C ⁎ completion on H) if and only if A is invariant under the squared antipode of H. The proof proceeds by Tannaka-reconstructing the coalgebra C corresponding to A → H by means of a fiber functor from H-equivariant A-modules to Hilbert spaces, while the characterization of those A → H which admit positive expectations makes use of a Fourier transform turning elements of H into functions on C.
Correlated states of electrons in wide quantum wells at low fillings: the role of charge distribution symmetry.

Magnetotransport measurements on electrons confined to a 57-nm-wide, GaAs quantum well reveal that the correlated electron states at low Landau level fillings ($\ensuremath{\nu}$) display a remarkable dependence on the symmetry of the electron charge distribution. At a density of $1.93\ifmmode\times\else\texttimes\fi{}{10}^{11}\text{ }\text{ }{\mathrm{cm}}^{\ensuremath{-}2}$, a developing fractional quantum Hall state is observed at the even-denominator filling $\ensuremath{\nu}=1/4$ when the distribution is symmetric, but it quickly vanishes when the distribution is made asymmetric. At lower densities, as we make the charge distribution asymmetric, we observe a rapid strengthening of the insulating phases that surround the $\ensuremath{\nu}=1/5$ fractional quantum Hall state.
Affine-compact functors

Several well known polytopal constuctions are examined from the functorial point of view. A naive analogy between the Billera-Sturmfels fiber polytope and the abelian kernel is disproved by an infinite explicit series of polytopes. A correct functorial formula is provided in terms of the affine-compact kernel. The dual cokernel object is almost always the natural affine projection. The Mond-Smith-van Straten space of sandwiched simplices, useful in stochastic factorizations, leads to a different kind of affine-compact functors and new challenges in polytope theory.