cssi/SciSciGPT-SciSciNet huggingface dataset:
Phosphine-mediated addition of 1,2-dicarbonyls to diazenes: an umpolung approach toward N-acyl hydrazone synthesis

Abstract Using a Kukhtin–Ramirez-like condensation employing hexamethylphosphorous triamide, the addition of 1,2-dicarbonyls to diazenes affords direct access to N-acyl hydrazones in moderate to excellent yields. The strategic assembly of this ubiquitous functional group proceeds through an umpolung disconnect in which an in situ generated acyl anion equivalent reacts with an electrophilic azodicarboxylate to form a new C–N bond. The method presented herein complements traditional condensation approaches toward hydrazone synthesis to access important synthetic intermediates and potentially biologically relevant architectures.
A new series of dendrimers containing two ferrocenyl units and a Fréchet dendron around a triazine nucleus.

The preparation and characterization of a new series of dendrimers containing two identical aminoferrocenyl units and a Frechet dendron around a triazine nucleus is described. A sizable degree of electronic communication between the two redox active ferrocenyl residues was detected in dichloromethane solution containing tetrabutylammonium tetra(pentafluorophenyl)borate as the supporting electrolyte. Binding of glutarimide via hydrogen bonding interactions to all the dendrimers was easily detected by using (1)H NMR spectroscopic and voltammetric techniques.
The genetic architecture of local adaptation I: the genomic landscape of foxtail pine ( Pinus balfouriana Grev. & Balf.) as revealed from a high-density linkage map

Explaining the origin and evolutionary dynamics of the genetic architecture of adaptation is a major research goal of evolutionary genetics. Despite controversy surrounding success of the attempts to accomplish this goal, a full understanding of adaptive genetic variation necessitates knowledge about the genomic location and patterns of dispersion for the genetic components affecting fitness-related phenotypic traits. Even with advances in next-generation sequencing technologies, the production of full genome sequences for non-model species is often cost-prohibitive, especially for tree species such as pines where genome size often exceeds 20 to 30 Gbp. We address this need by constructing a dense linkage map for foxtail pine (Pinus balfouriana Grev. & Balf.), with the ultimate goal of uncovering and explaining the origin and evolutionary dynamics of adaptive genetic variation in natural populations of this forest tree species. We utilized megagametophyte arrays (n = 76–95 megagametophytes/tree) from four maternal trees in combination with double digest restriction-site associated DNA sequencing (ddRADseq) to produce a consensus linkage map covering 98.58 % of the foxtail pine genome, which was estimated to be 1276 cM in length (95 % CI, 1174 to 1378 cM). A novel bioinformatic approach using iterative rounds of marker ordering and imputation was employed to produce single-tree linkage maps (507–17,066 contigs/map; lengths, 1037.40–1572.80 cM). These linkage maps were collinear across maternal trees, with highly correlated marker orderings (Spearman’s ρ>0.95). A consensus linkage map derived from these single-tree linkage maps contained 12 linkage groups along which 20,655 contigs were non-randomly distributed across 901 unique positions (n=23 contigs/position), with an average spacing of 1.34 cM between adjacent positions. Of the 20,655 contigs positioned on the consensus linkage map, 5627 had enough sequence similarity to contigs contained within the most recent build of the loblolly pine (Pinus taeda L.) genome to identify them as putative homologues containing both genic and non-genic loci. Importantly, all 901 unique positions on the consensus linkage map had at least one contig with putative homology to loblolly pine. When combined with the other biological signals that predominate in our data (e.g., correlations of recombination fractions across single trees), we show that dense linkage maps for non-model forest tree species can be efficiently constructed using next-generation sequencing technologies. We subsequently discuss the usefulness of these maps as community-wide resources and as tools with which to test hypotheses about the genetic architecture of local adaptation.
Conformational Studies of Oxacyclodecan-2-one and Oxacycloundecan-2-one by Dynamic NMR Spectroscopy and Computational Methods

The ten-membered lactone, oxacyclodecan-2-one (1), was found by low-temperature 1H and 13C NMR spectroscopy to have two conformations with populations of 95.2 and 4.8% at −133.8 °C. Free-energy barriers of 9.09 ± 0.15 and 8.26 ± 0.15 kcal/mol for interconversion of conformations at −110.7 °C were calculated from 13C NMR spectra, and a free-energy barrier of 9.1 ± 0.2 kcal/mol at −70.8 °C was determined for another process, observed only in the 1H NMR spectra. The barrier for the process observed in the proton NMR spectra was suggested to be a lower limit for the barrier to rotation of the lactone group through the ring. Oxacycloundecan-2-one (2) has two conformations at −139.3 °C, with populations of 64.3 and 35.7% at this temperature and free-energy barriers to interconversion of 7.83 ± 0.15 and 7.67 ± 0.15 kcal/mol at −109.1 °C. The NMR results for both compounds are discussed in terms of the conformations predicted by Allinger's MM3 program. Ab initio calculations of electronic energies for three confo...
Structural and bonding investigation of the donor—acceptor complex 1-Sn(phenanthroline)-2, 3-[Si(CH3)]3]2-2,3-C2B4H4: A comparative study of the group 14 metallacarborane-Lewis base complexes

Closo-1-Sn-2,3-[Si(CH3)3]2-2,3-C2B4H4 (1) reacts with 1,10-phenanthroline to form the complex 1-(C12H8N2)Sn-2, 3-[Si(CH3)3]2-2,3-C2B4H4. When crystals of this complex were grown slowly from benzene, a crystalline modification (2) was obtained in which the unit cell consisted of four identical molecules of the base-stannacarborane and six benzene molecules of solvation. When the complex was sublimed, a second crystalline modification (3) was obtained whose unit cell consisted of two crystaliographically different molecules (3-1 and3-2). In all three forms the tin was not symmetrically bonded to the carborane but was slipped toward the boron side of the C2B3 face, and the phenanthroline molecules were oriented opposite to the cage carbons so that the plane of the base and the carborane faces gave acute dihedral angles. However, the three forms showed a great deal of variation in the extent of slippage and the magnitudes of the base-carborane dihedral angles. Since these distortions are common structural features of base-group 14-carborane and cyclopentadienyl systems, MNDO-SCF molecular orbital calculations were carried out on the model compounds 1-(C12H8N2)Sn-2,3-C2B4H6, 1-[C10H8N2)Sn-2, 3-C2B9H11, and [(C10H8N2)-SnC5(CH3)5]+ to determine what factors dictate the structures of these complexes. The results showed that competing bonding interactions give rise to a very broad minimum in energy as a function of slippage and base orientation. Small energy variations, such as those produced by crystal packing forces, could produce large structural changes. Complex2 crystallizes in the monoclinic space group P21/n witha=11.096 (9) A,b=26.51(2) A,c=11.729 (7) A,β=107.43 (6) ∘,U=3291 (4) A3, andZ=4. Full-matrix least-squares analysis converged atR=0.044 andRw=0.055. Complex3 crystallizes in the triclinic space group P¯1 witha=10.251 (3) A,b= 13.845(9) A;c=19.168 (9) A,α=71.12 (5) ∘,β=89.29 (3) ∘,γ=84.62 (4) ∘,U=2562 (2) A3, andZ=4. The structure refined atR=0.079 andRw=0.125.
Enantiomeric Synthesis of l-(or 1‘R,2‘S)-Carbocyclic Cyclopropyl Nucleosides

The enantiomeric synthesis of carbocyclic cyclopropyl L-nucleosides has been accomplished from L-gulonic gamma-lactone. The key intermediate 3 was stereoselectively synthesized by DIBAL-H reduction and silyl protection followed by cyclopropanation from ester 2, which was in turn prepared from L-gulonic gamma-lactone (1) in five steps. Desilylation of cyclopropyl intermediate 3 gave alcohol 4, which was then converted to the urea derivative 5 and cyclopropylamine 7 by Curtius rearrangement of an acyl azide. The urea intermediate 5 was utilized to prepare thymine 10, uracil 11, and cytosine 14 derivatives. The hypoxanthine, adenine, and guanine nucleosides 21, 22, and 24 were synthesized from the amino intermediate 7.
Practical Synthesis of 1-Aryl-6-(hydroxymethyl)-2-ketopiperazines via a 6-exo Amide−Epoxide Cyclization

Chiral 1-aryl-6-(hydroxymethyl)-2-ketopiperazines can be prepared via an operationally simple, 6-exo epoxide ring-opening cyclization to form the ketopiperazine C6−N1 bond in high yields and with excellent enantiomeric purity.
Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease

ABSTRACT Small molecules are the primary communication media of the microbial world. Recent bioinformatic studies, exploring the biosynthetic gene clusters (BGCs) which produce many small molecules, have highlighted the incredible biochemical potential of the signaling molecules encoded by the human microbiome. Thus far, most research efforts have focused on understanding the social language of the gut microbiome, leaving crucial signaling molecules produced by oral bacteria and their connection to health versus disease in need of investigation. In this study, a total of 4,915 BGCs were identified across 461 genomes representing a broad taxonomic diversity of oral bacteria. Sequence similarity networking provided a putative product class for more than 100 unclassified novel BGCs. The newly identified BGCs were cross-referenced against 254 metagenomes and metatranscriptomes derived from individuals either with good oral health or with dental caries or periodontitis. This analysis revealed 2,473 BGCs, which were differentially represented across the oral microbiomes associated with health versus disease. Coabundance network analysis identified numerous inverse correlations between BGCs and specific oral taxa. These correlations were present in healthy individuals but greatly reduced in individuals with dental caries, which may suggest a defect in colonization resistance. Finally, corroborating mass spectrometry identified several compounds with homology to products of the predicted BGC classes. Together, these findings greatly expand the number of known biosynthetic pathways present in the oral microbiome and provide an atlas for experimental characterization of these abundant, yet poorly understood, molecules and socio-chemical relationships, which impact the development of caries and periodontitis, two of the world’s most common chronic diseases. IMPORTANCE The healthy oral microbiome is symbiotic with the human host, importantly providing colonization resistance against potential pathogens. Dental caries and periodontitis are two of the world’s most common and costly chronic infectious diseases and are caused by a localized dysbiosis of the oral microbiome. Bacterially produced small molecules, often encoded by BGCs, are the primary communication media of bacterial communities and play a crucial, yet largely unknown, role in the transition from health to dysbiosis. This study provides a comprehensive mapping of the BGC repertoire of the human oral microbiome and identifies major differences in health compared to disease. Furthermore, BGC representation and expression is linked to the abundance of particular oral bacterial taxa in health versus dental caries and periodontitis. Overall, this study provides a significant insight into the chemical communication network of the healthy oral microbiome and how it devolves in the case of two prominent diseases.
An Unusual Ruthenium-Catalyzed Cycloisomerization of Alkynes and Propargyl Alcohols

CpRu(NCCH3)3+PF6- catalyzes the cycloisomerization of diyne-ols to α,β,γ,δ-unsaturated aldehydes and ketones in good-to-excellent yields. 1-Hydroxy-2,7-diynes and 1-hydroxy-2,8-diynes can be utilized to form highly functionalized five- and six-membered rings, respectively. Tertiary as well as secondary propargyl alcohols are cycloisomerized to a single isomeric product. A wide variety of tether substitution can be tolerated. Even totally unsubstituted tethers can be employed, as geminal disubstituents are not required for cyclization. Additional hydroxyl substituents at an alternative “internal" propargylic position are eliminated during the reactiona feature that leads to a convenient cyclopentadiene synthesis. Furthermore, 3-hydroxy-1,6-diynes also can be cyclized to form cross-conjugated aldehydes.
Associations Between Ambient Air Pollutant Concentrations and Birth Weight: A Quantile Regression Analysis.

Introduction:We investigated the extent to which associations of ambient air pollutant concentrations and birth weight varied across birth weight quantiles.Methods:We analyzed singleton births ≥27 weeks of gestation from 20-county metropolitan Atlanta with conception dates between January 1, 2002 an
Development of High-Throughput Screening Assays for Inhibitors of ETS Transcription Factors:

ETS transcription factors from the ERG and ETV1/4/5 subfamilies are overexpressed in the majority of prostate cancer patients and contribute to disease progression. Here, we have developed two in vitro assays for the interaction of ETS transcription factors with DNA that are amenable to high-throughput screening. Using ETS1 as a model, we applied these assays to screen 110 compounds derived from a high-throughput virtual screen. We found that the use of lower-affinity DNA binding sequences, similar to those that ERG and ETV1 bind to in prostate cells, allowed for higher inhibition from many of these test compounds. Further pilot experiments demonstrated that the in vitro assays are robust for ERG, ETV1, and ETV5, three of the ETS transcription factors that are overexpressed in prostate cancer.
A rapid and direct access to symmetrical/unsymmetrical 3,4-diarylmaleimides and pyrrolin-2-ones

Abstract 1,8-Diazabicyclo[5.4.0]undec-7ene (DBU) facilitated the oxidative cyclization of phenacyl amide in the presence of atmospheric oxygen under environmentally friendly conditions. The reaction has been studied under various conditions and a plausible mechanism is proposed. This ‘green’ reaction proceeds via intramolecular ring closure of the amide followed by subsequent reaction with molecular oxygen where DBU played a crucial role. A variety of phenacyl amides were treated with DBU in acetonitrile under an oxygen atmosphere to give the symmetrical/unsymmetrical 3,4-diarylsubstituted maleimides in good yields. Corresponding pyrrolin-2-ones however, were obtained in good to excellent yields when K 2 CO 3 was used in place of DBU affording a practical synthesis of these compounds of potential biological interest.
The Ruthenium Acetylide Catalyzed Cross-Coupling Reaction of Terminal and Internal Alkynes: Isolation of a Catalytically Active β-Agostic Intermediate Species

The in situ generated ruthenium acetylide complex C5Me5(PPh3)RuC⋮CPh (1) was found to catalyze the cross-coupling reaction of terminal and internal alkynes to yield functionalized enynes. An intermediate β-agostic species was isolated from the reaction of C5Me5(PPh3)(Cl)RuCCHBu-t (2b) with 2-butyne in the presence of NaOMe.
Aromatic Annulation: Two New Methods for the Synthesis of Chiral Bicyclic Phenols

Abstract Two selective and mild aromatic annulation procedures are described for the synthesis of chiral substituted tetrahydronaphthalene derivatives from ( − )-menthone and ( + )-dihydrocarvone . © 1997 Elsevier Science Ltd.
Characterization of a Human-Specific Tandem Repeat Associated with Bipolar Disorder and Schizophrenia.

Bipolar disorder (BD) and schizophrenia (SCZ) are highly heritable diseases that affect more than 3% of individuals worldwide. Genome-wide association studies have strongly and repeatedly linked risk for both of these neuropsychiatric diseases to a 100 kb interval in the third intron of the human calcium channel gene CACNA1C. However, the causative mutation is not yet known. We have identified a human-specific tandem repeat in this region that is composed of 30 bp units, often repeated hundreds of times. This large tandem repeat is unstable using standard polymerase chain reaction and bacterial cloning techniques, which may have resulted in its incorrect size in the human reference genome. The large 30-mer repeat region is polymorphic in both size and sequence in human populations. Particular sequence variants of the 30-mer are associated with risk status at several flanking single-nucleotide polymorphisms in the third intron of CACNA1C that have previously been linked to BD and SCZ. The tandem repeat arrays function as enhancers that increase reporter gene expression in a human neural progenitor cell line. Different human arrays vary in the magnitude of enhancer activity, and the 30-mer arrays associated with increased psychiatric disease risk status have decreased enhancer activity. Changes in the structure and sequence of these arrays likely contribute to changes in CACNA1C function during human evolution and may modulate neuropsychiatric disease risk in modern human populations.
Mild conditions for Pd-catalyzed conversion of aryl bromides to primary anilines using benzophenone imine

Abstract Mild (30 °C) and efficient (53–91%) conversion of aryl bromides to primary anilines using a Pd-catalyzed amination strategy is described. A detailed account of the ligand optimization, base and solvent selection, and general substrate scope of this methodology is described herein.
Synthesis and Characterization of N-Arylsulfonylazetidines

A convenient method for the synthesis of N-arylsulfonyl azetidines using N-(3-bromopropyl)-arylsulfonamide with cesium carbonate and potassium iodide in DMF is reported. The reaction conditions are optimized and seven N-arylsulfonyl azetidines have been synthesized in good yield using this method. The structures of compounds 2a and 2e were determined by X-ray crystallography.
On the Complexity and Typology of Inflectional Morphological Systems

We quantify the linguistic complexity of different languages’ morphological systems. We verify that there is a statistically significant empirical trade-off between paradigm size and irregularity: ...
Functionalization of saturated fluorocarbons

Abstract A method is described for transforming perfluoroalkanes and perfluorocycloalkanes bearing tertiary fluorine into perfluoroenolates, which can be variously derivatized.
Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status.

ABSTRACT Factors that contribute to enhanced susceptibility to severe bacterial disease after influenza virus infection are not well defined but likely include the microbiome of the respiratory tract. Vaccination against influenza, while having variable effectiveness, could also play a role in microbial community stability. We collected nasopharyngeal samples from 215 individuals infected with influenza A/H3N2 or influenza B virus and profiled the microbiota by target sequencing of the 16S rRNA gene. We identified signature taxonomic groups by performing linear discriminant analysis and effective size comparisons (LEfSe) and defined bacterial community types using Dirichlet multinomial mixture (DMM) models. Influenza infection was shown to be significantly associated with microbial composition of the nasopharynx according to the virus type and the vaccination status of the patient. We identified four microbial community types across the combined cohort of influenza patients and healthy individuals with one community type most representative of the influenza virus-infected group. We also identified microbial taxa for which relative abundance was significantly higher in the unvaccinated elderly group; these taxa include species known to be associated with pneumonia. IMPORTANCE Our results suggest that there is a significant association between the composition of the microbiota in the nasopharynx and the influenza virus type causing the infection. We observe that vaccination status, especially in more senior individuals, also has an association with the microbial community profile. This indicates that vaccination against influenza, even when ineffective to prevent disease, could play a role in controlling secondary bacterial complications.
Inference of differential gene regulatory networks based on gene expression and genetic perturbation data

Motivation Gene regulatory networks (GRNs) of the same organism can be different under different conditions, although the overall network structure may be similar. Understanding the difference in GRNs under different conditions is important to understand condition-specific gene regulation. When gene expression and other relevant data under two different conditions are available, they can be used by an existing network inference algorithm to estimate two GRNs separately, and then to identify the difference between the two GRNs. However, such an approach does not exploit the similarity in two GRNs, and may sacrifice inference accuracy. Results In this paper, we model GRNs with the structural equation model (SEM) that can integrate gene expression and genetic perturbation data, and develop an algorithm named fused sparse SEM (FSSEM), to jointly infer GRNs under two conditions, and then to identify difference of the two GRNs. Computer simulations demonstrate that the FSSEM algorithm outperforms the approaches that estimate two GRNs separately. Analysis of a dataset of lung cancer and another dataset of gastric cancer with FSSEM inferred differential GRNs in cancer versus normal tissues, whose genes with largest network degrees have been reported to be implicated in tumorigenesis. The FSSEM algorithm provides a valuable tool for joint inference of two GRNs and identification of the differential GRN under two conditions. Availability and implementation The R package fssemR implementing the FSSEM algorithm is available at https://github.com/Ivis4ml/fssemR.git. It is also available on CRAN. Supplementary information Supplementary data are available at Bioinformatics online.
Evaluation of the Assumptions in the Steady-State Tropical Cyclone Self-Stratified Outflow Using Three-Dimensional Convection-Allowing Simulations

AbstractThe criteria and assumptions that were used to derive the steady-state tropical cyclone intensity and structure theory of Emanuel and Rotunno are assessed using three-dimensional convection...
Algebraic geometry over hyperrings

Abstract We develop basic notions and methods of algebraic geometry over the algebraic objects called hyperrings. Roughly speaking, hyperrings generalize rings in such a way that an addition is ‘multi-valued’. This paper largely consists of two parts; algebraic aspects and geometric aspects of hyperrings. We first investigate several technical algebraic properties of a hyperring. In the second part, we begin by giving another interpretation of a tropical variety as an algebraic set over the hyperfield which canonically arises from a totally ordered semifield. Then we define a notion of an integral hyperring scheme ( X , O X ) and prove that Γ ( X , O X ) ≃ R for any integral affine hyperring scheme X = Spec R .
Entity-Augmented Distributional Semantics for Discourse Relations.

Discourse relations bind smaller linguistic elements into coherent texts. However, automatically identifying discourse relations is difficult, because it requires understanding the semantics of the linked sentences. A more subtle challenge is that it is not enough to represent the meaning of each sentence of a discourse relation, because the relation may depend on links between lower-level elements, such as entity mentions. Our solution computes distributional meaning representations by composition up the syntactic parse tree. A key difference from previous work on compositional distributional semantics is that we also compute representations for entity mentions, using a novel downward compositional pass. Discourse relations are predicted not only from the distributional representations of the sentences, but also of their coreferent entity mentions. The resulting system obtains substantial improvements over the previous state-of-the-art in predicting implicit discourse relations in the Penn Discourse Treebank.
Sharp Bounds on Random Walk Eigenvalues via Spectral Embedding

Spectral embedding of graphs uses the top k non-trivial eigenvectors of the random walk matrix to embed the graph into R^k. The primary use of this embedding has been for practical spectral clustering algorithms [SM00,NJW02]. Recently, spectral embedding was studied from a theoretical perspective to prove higher order variants of Cheeger's inequality [LOT12,LRTV12]. We use spectral embedding to provide a unifying framework for bounding all the eigenvalues of graphs. For example, we show that for any finite graph with n vertices and all k >= 2, the k-th largest eigenvalue is at most 1-Omega(k^3/n^3), which extends the only other such result known, which is for k=2 only and is due to [LO81]. This upper bound improves to 1-Omega(k^2/n^2) if the graph is regular. We generalize these results, and we provide sharp bounds on the spectral measure of various classes of graphs, including vertex-transitive graphs and infinite graphs, in terms of specific graph parameters like the volume growth. As a consequence, using the entire spectrum, we provide (improved) upper bounds on the return probabilities and mixing time of random walks with considerably shorter and more direct proofs. Our work introduces spectral embedding as a new tool in analyzing reversible Markov chains. Furthermore, building on [Lyo05], we design a local algorithm to approximate the number of spanning trees of massive graphs.
Density Evolution in the Degree-correlated Stochastic Block Model

There is a recent surge of interest in identifying the sharp recovery thresholds for cluster recovery under the stochastic block model. In this paper, we address the more refined question of how many vertices that will be misclassified on average. We consider the binary form of the stochastic block model, where n vertices are partitioned into two clusters with edge probability a/n within the first cluster, c/n within the second cluster, and b/n across clusters. Suppose that as n → ∞, a = b + μ √ b, c = b + ν √ b for two fixed constants μ, ν, and b → ∞ with b = n. When the cluster sizes are balanced and μ 6= ν, we show that the minimum fraction of misclassified vertices on average is given by Q( √ v∗), where Q(x) is the Q-function for standard normal, v∗ is the unique fixed point of v = (μ−ν) 2 16 + (μ+ν) 16 E[tanh(v + √ vZ)], and Z is standard normal. Moreover, the minimum misclassified fraction on average is attained by a local algorithm, namely belief propagation, in time linear in the number of edges. Our proof techniques are based on connecting the cluster recovery problem to tree reconstruction problems, and analyzing the density evolution of belief propagation on trees with Gaussian approximations.
Quantum vertex F((t))-algebras and their modules

This is a paper in a series to study vertex algebra-like structures arising from various algebras including quantum affine algebras and Yangians. In this paper, we develop a theory of what we call (weak) quantum vertex F((t))-algebras with F a field of characteristic zero and t a formal variable, and we give a conceptual construction of (weak) quantum vertex F((t))-algebras and their modules. As an application, we associate weak quantum vertex F((t))-algebras to quantum affine algebras, providing a solution to a problem posed by Frenkel and Jing. We also explicitly construct an example of quantum vertex F((t))-algebras from a certain quantum βγ-system.
Learning Infinite RBMs with Frank-Wolfe

In this work, we propose an infinite restricted Boltzmann machine (RBM), whose maximum likelihood estimation (MLE) corresponds to a constrained convex optimization. We consider the Frank-Wolfe algorithm to solve the program, which provides a sparse solution that can be interpreted as inserting a hidden unit at each iteration, so that the optimization process takes the form of a sequence of finite models of increasing complexity. As a side benefit, this can be used to easily and efficiently identify an appropriate number of hidden units during the optimization. The resulting model can also be used as an initialization for typical state-of-the-art RBM training algorithms such as contrastive divergence, leading to models with consistently higher test likelihood than random initialization.
The toggle group, homomesy, and the Razumov-Stroganov correspondence

The Razumov-Stroganov correspondence, an important link between statistical physics and combinatorics proved in 2011 by L. Cantini and A. Sportiello, relates the ground state eigenvector of the $ O(1)$ dense loop model on a semi-infinite cylinder to a refined enumeration of fully-packed loops, which are in bijection with alternating sign matrices. This paper reformulates a key component of this proof in terms of posets, the toggle group, and homomesy, and proves two new homomesy results on general posets which we hope will have broader implications.
Recovery Guarantees for Quadratic Tensors with Limited Observations

We consider the tensor completion problem of predicting the missing entries of a tensor. The commonly used CP model has a triple product form, but an alternate family of quadratic models which are the sum of pairwise products instead of a triple product have emerged from applications such as recommendation systems. Non-convex methods are the method of choice for learning quadratic models, and this work examines their sample complexity and error guarantee. Our main result is that with the number of samples being only linear in the dimension, all local minima of the mean squared error objective are global minima and recover the original tensor. We substantiate our theoretical results with experiments on synthetic and real-world data.
Energy-dependent orbital phases in NGC 300 X-1

NGC~300 X-1 is a Wolf Rayet + black hole binary that exhibits periodic decreases in X-ray flux. We present two new observations of NGC~300 X-1 from the Chandra X-ray Observatory (totaling $\sim$130 ks) along with ACS imaging data from the Hubble Space Telescope. We observe significant short-term variability in the X-ray emission that is inconsistent with an occultation by the donor star, but is consistent with structure in the outer accretion disk or the wind of the donor star. We simultaneously fit a partially-covered disk blackbody and Comptonized corona model to the eclipse egress and non-eclipsing portions of the X-ray spectrum. We find that the only model parameters that varied between the eclipse egress and non-eclipsing portions of the spectra were the partial covering fraction ($\sim$86% during eclipse egress and $\sim$44% during non-eclipse) and absorbing column ($\sim$12.3$\times10^{22}$ cm$^{-2}$ during eclipse egress, compared to $\sim$1.4$\times10^{22}$ cm$^{-2}$ during non-eclipse). The X-ray spectra are consistent with the movement of the X-ray source through the dense stellar winds of the companion star. From our new HST imaging, we find the WR star within the X-ray error circle, along with additional optical sources including an AGB star and an early-type main sequence star. Finally, we use our egress measurement to rephase previous radial velocity measurements reported in the literature, and find evidence that the velocities are strongly affected by the ionization of the wind by the compact object. Thus, we argue the inferred mass of the black hole may not be reliable.
Magnetism in Compact Ultra Dense Objects

In spin-0 color superconductivity (CS), the electromagnetism is not the conventional one. In the color superconducting medium the conventional electromagnetic field is not a real eigenfield. Instead, in the presence of the diquark ground state the conventional electromagnetic field mixes with one gluon field leading to two new mass eigenmodes. The massless resultant eigenmode is the new electromagnetic field in the medium, which is often called the rotated electromagnetic field. Hence, even though the original electromagnetic U(1)em symmetry is broken by the formation of the electrically charged quark Cooper pairs, a residual Ũ(1) symmetry still remains. The massless gauge field associated with this symmetry in the colorflavor-locked (CFL) phase of CS, for example, is given by the linear combination of the conventional photon field and the 8th gluon field, Aμ = cos θAμ − sin θG 8
Staleness-aware async-SGD for distributed deep learning

Deep neural networks have been shown to achieve state-of-the-art performance in several machine learning tasks. Stochastic Gradient Descent (SGD) is the preferred optimization algorithm for training these networks and asynchronous SGD (ASGD) has been widely adopted for accelerating the training of large-scale deep networks in a distributed computing environment. However, in practice it is quite challenging to tune the training hyperparameters (such as learning rate) when using ASGD so as achieve convergence and linear speedup, since the stability of the optimization algorithm is strongly influenced by the asynchronous nature of parameter updates. In this paper, we propose a variant of the ASGD algorithm in which the learning rate is modulated according to the gradient staleness and provide theoretical guarantees for convergence of this algorithm. Experimental verification is performed on commonly-used image classification benchmarks: CIFAR10 and Imagenet to demonstrate the superior effectiveness of the proposed approach, compared to SSGD (Synchronous SGD) and the conventional ASGD algorithm.
Identifying centromeric satellites with dna-brnn

Summary Human alpha satellite and satellite 2/3 contribute to several percent of the human genome. However, identifying these sequences with traditional algorithms is computationally intensive. Here we develop dna-brnn, a recurrent neural network to learn the sequences of the two classes of centromeric repeats. It achieves high similarity to RepeatMasker and is times faster. Dna-brnn explores a novel application of deep learning and may accelerate the study of the evolution of the two repeat classes. Availability and implementation https://github.com/lh3/dna-nn.
Some Forms of Exceptional Lie Algebras

Some forms of Lie algebras of types E 6, E 7, and E 8 are constructed using the exterior cube of a rank 9 finitely generated projective module.
Statistical state dynamics of vertically sheared horizontal flows in two-dimensional stratified turbulence

Simulations of strongly stratified turbulence often exhibit coherent large-scale structures called vertically sheared horizontal flows (VSHFs). VSHFs emerge in both two-dimensional (2D) and three-dimensional (3D) stratified turbulence with similar vertical structure. The mechanism responsible for VSHF formation is not fully understood. In this work, the formation and equilibration of VSHFs in a 2D Boussinesq model of stratified turbulence is studied using statistical state dynamics (SSD). In SSD, equations of motion are expressed directly in the statistical variables of the turbulent state. Restriction to 2D turbulence facilitates application of an analytically and computationally attractive implementation of SSD referred to as S3T, in which the SSD is expressed by coupling the equation for the horizontal mean structure with the equation for the ensemble mean perturbation covariance. This second-order SSD produces accurate statistics, through second order, when compared with fully nonlinear simulations. In particular, S3T captures the spontaneous emergence of the VSHF and associated density layers seen in simulations of turbulence maintained by homogeneous large-scale stochastic excitation. An advantage of the S3T system is that the VSHF formation mechanism, which is wave–mean flow interaction between the emergent VSHF and the stochastically excited large-scale gravity waves, is analytically understood in the S3T system. Comparison with fully nonlinear simulations verifies that S3T solutions accurately predict the scale selection, dependence on stochastic excitation strength, and nonlinear equilibrium structure of the VSHF. These results constitute a theory for VSHF formation applicable to interpreting simulations and observations of geophysical examples of turbulent jets such as the ocean’s equatorial deep jets.
Dissociation and propagation for approximate lifted inference with standard relational database management systems

Probabilistic inference over large data sets is a challenging data management problem since exact inference is generally #P-hard and is most often solved approximately with sampling-based methods today. This paper proposes an alternative approach for approximate evaluation of conjunctive queries with standard relational databases: In our approach, every query is evaluated entirely in the database engine by evaluating a fixed number of query plans, each providing an upper bound on the true probability, then taking their minimum. We provide an algorithm that takes into account important schema information to enumerate only the minimal necessary plans among all possible plans. Importantly, this algorithm is a strict generalization of all known PTIME self-join-free conjunctive queries: A query is in PTIME if and only if our algorithm returns one single plan. Furthermore, our approach is a generalization of a family of efficient ranking methods from graphs to hypergraphs. We also adapt three relational query optimization techniques to evaluate all necessary plans very fast. We give a detailed experimental evaluation of our approach and, in the process, provide a new way of thinking about the value of probabilistic methods over non-probabilistic methods for ranking query answers. We also note that the techniques developed in this paper apply immediately to lifted inference from statistical relational models since lifted inference corresponds to PTIME plans in probabilistic databases.
Nonparametric Detection of Anomalous Data Streams

A nonparametric anomalous hypothesis testing problem is investigated, in which there are totally $n$ observed sequences out of which $s$ anomalous sequences are to be detected. Each typical sequence consists of $m$ independent and identically distributed (i.i.d.) samples drawn from a distribution $p$ , whereas each anomalous sequence consists of $m$ i.i.d. samples drawn from a distribution $q$ that is distinct from $p$ . The distributions $p$ and $q$ are assumed to be unknown in advance. Distribution-free tests are constructed by using the maximum mean discrepancy as the metric, which is based on mean embeddings of distributions into a reproducing kernel Hilbert space. The probability of error is bounded as a function of the sample size $m$ , the number $s$ of anomalous sequences, and the number $n$ of sequences. It is shown that with $s$ known, the constructed test is exponentially consistent if $m$ is greater than a constant factor of $\log n$ , for any $p$ and $q$ , whereas with $s$ unknown, $m$ should have an order strictly greater than $\log n$ . Furthermore, it is shown that no test can be consistent for arbitrary $p$ and $q$ if $m$ is less than a constant factor of $\log n$ . Thus, the order-level optimality of the proposed test is established. Numerical results are provided to demonstrate that the proposed tests outperform (or perform as well as) tests based on other competitive approaches under various cases.
A Precision Environment-Wide Association Study of Hypertension via Supervised Cadre Models

We consider the problem in precision health of grouping people into subpopulations based on their degree of vulnerability to a risk factor. These subpopulations cannot be discovered with traditional clustering techniques because their quality is evaluated with a supervised metric: The ease of modeling a response variable for observations within them. Instead, we apply the more appropriate supervised cadre model (SCM). We extend the SCM formalism so that it may be applied to multivariate regression and binary classification problems and develop a way to use conditional entropy to assess the confidence in the process by which a subject is assigned their cadre. Using the SCM, we generalize the environment-wide association study (EWAS) to be able to model heterogeneity in population risk. In our EWAS, we consider more than 200 environmental exposure factors and find their association with diastolic blood pressure, systolic blood pressure, and hypertension. This requires adapting the SCM to be applicable to data generated by a complex survey design. After correcting for false positives, we found 25 exposure variables that had a significant association with at least one of our response variables. Eight of these were significant for a discovered subpopulation but not for the overall population. Some of these associations have been identified by previous researchers, whereas others appear to be novel. We examine discovered subpopulations in detail, finding that they are interpretable and suggestive of further research questions.
Maximum likelihood for dual varieties

Maximum likelihood estimation (MLE) is a fundamental computational problem in statistics. In this paper, MLE for statistical models with discrete data is studied from an algebraic statistics viewpoint. A reformulation of the MLE problem in terms of dual varieties and conormal varieties will be given. With this description, we define the dual likelihood equations and the dual MLE problem. We show that solving the dual MLE problem yields solutions to the MLE problem, and that we can solve the dual MLE problem even if we do not have the defining equations of the model itself.
Poincaré linearizers in higher dimensions

It is well-known that a holomorphic function near a repelling fixed point may be conjugated to a linear function. The function which conjugates is called a Poincar\'e linearizer and may be extended to a transcendental entire function in the plane. In this paper, we study the dynamics of a higher dimensional generalization of Poincar\'e linearizers. These arise by conjugating a uniformly quasiregular mapping in $\R^m$ near a repelling fixed point to the mapping $x\mapsto 2x$. In particular, we show that the fast escaping set of such a linearizer has a spider's web structure.
Sobolev regularity for first order mean field games.

Abstract In this paper we obtain Sobolev estimates for weak solutions of first order variational Mean Field Game systems with coupling terms that are local functions of the density variable. Under some coercivity conditions on the coupling, we obtain first order Sobolev estimates for the density variable, while under similar coercivity conditions on the Hamiltonian we obtain second order Sobolev estimates for the value function. These results are valid both for stationary and time-dependent problems. In the latter case the estimates are fully global in time, thus we resolve a question which was left open in [23] . Our methods apply to a large class of Hamiltonians and coupling functions.
Groupoid C*-algebras with Hausdorff Spectrum

Suppose $G$ is a second countable, locally compact Hausdorff groupoid with abelian stabilizer subgroups and a Haar system. We provide necessary and sufficient conditions for the groupoid $C^*$-algebra to have Hausdorff spectrum. In particular we show that the spectrum of $C^*(G)$ is Hausdorff if and only if the stabilizers vary continuously with respect to the Fell topology, the orbit space $G\unit/G$ is Hausdorff, and, given convergent sequences $\chi_i\to \chi$ and $\gamma_i\cdot\chi_i \to \omega$ in the dual stabilizer groupoid $\widehat{S}$ where the $\gamma_i\in G$ act via conjugation, if $\chi$ and $\omega$ are elements of the same fiber then $\chi = \omega$. 10.1017/S0004972713000129
Cascaded lattice Boltzmann method based on central moments for axisymmetric thermal flows including swirling effects

Abstract A cascaded lattice Boltzmann (LB) approach based on central moments and multiple relaxation times to simulate thermal convective flows, which are driven by buoyancy forces and/or swirling effects, in the cylindrical coordinate system with axial symmetry is presented. In this regard, the dynamics of the axial and radial momentum components along with the pressure are represented by means of the 2D Navier-Stokes equations with geometric mass and momentum source terms in the pseudo Cartesian form, while the evolutions of the azimuthal momentum and the temperature field are each modeled by an advection-diffusion type equation with appropriate local source terms. Based on these, cascaded LB schemes involving three distribution functions are formulated to solve for the fluid motion in the meridian plane using a D2Q9 lattice, and to solve for the azimuthal momentum and the temperature field each using a D2Q5 lattice. The geometric mass and momentum source terms for the flow fields and the energy source term for the temperature field are included using a new symmetric operator splitting technique, via pre-collision and post-collision source steps around the cascaded collision step for each distribution function. These result in a particularly simple and compact formulation to directly represent the effect of various geometric source terms consistently in terms of changes in the appropriate zeroth and first order moments. Simulations of several complex buoyancy-driven thermal flows and including rotational effects in cylindrical geometries using the new axisymmetric cascaded LB schemes show good agreement with prior benchmark results for the structures of the velocity and thermal fields as well as the heat transfer rates given in terms of the Nusselt numbers. Furthermore, the method is shown to be second order accurate and significant improvements in numerical stability with the use of the cascaded LB formulation when compared to other collision models for axisymmetric flow simulations are demonstrated.
Polynomial relations among principal minors of a 4x4-matrix

Abstract The image of the principal minor map for n × n -matrices is shown to be closed. In the 19th century, Nanson and Muir studied the implicitization problem of finding all relations among principal minors when n = 4 . We complete their partial results by constructing explicit polynomials of degree 12 that scheme-theoretically define this affine variety and also its projective closure in P 15 . The latter is the main component in the singular locus of the 2 × 2 × 2 × 2 -hyperdeterminant.
Multi-criteria Anomaly Detection using Pareto Depth Analysis

We consider the problem of identifying patterns in a data set that exhibit anomalous behavior, often referred to as anomaly detection. In most anomaly detection algorithms, the dissimilarity between data samples is calculated by a single criterion, such as Euclidean distance. However, in many cases there may not exist a single dissimilarity measure that captures all possible anomalous patterns. In such a case, multiple criteria can be defined, and one can test for anomalies by scalarizing the multiple criteria using a linear combination of them. If the importance of the different criteria are not known in advance, the algorithm may need to be executed multiple times with different choices of weights in the linear combination. In this paper, we introduce a novel non-parametric multi-criteria anomaly detection method using Pareto depth analysis (PDA). PDA uses the concept of Pareto optimality to detect anomalies under multiple criteria without having to run an algorithm multiple times with different choices of weights. The proposed PDA approach scales linearly in the number of criteria and is provably better than linear combinations of the criteria.
Algebraization and Tannaka duality

Our goal in this paper is to identify certain naturally occurring colimits of schemes and algebraic spaces. To do so, we use (and prove) some new Tannaka duality theorems for maps of algebraic spaces.