cssi/SciSciGPT-SciSciNet huggingface dataset:
Energetic, structural and mechanical properties of terraced interfaces

Abstract Taking the well-understood Cu-Ni {111} semi-coherent interface as a prototype, we demonstrate an important, yet long-been-overlooked, size effect on the properties of terraced interfaces — i.e. the facet length scale effect. Interfacial facets are considered as super interface disconnections (SIDs). We then studied the SID's size effect on the energy, structure, and mechanical response of terraced interfaces by using atomistic simulations and defect theories. We found that the specific facet energy — therefore the specific energy of the terraced interface — exhibits a periodic change with the SID's size. The periodic change is associated with the quantized transitions in their dislocation structures. Correspondingly, the mechanical response of terraced interfaces also exhibits clear regime shifts, as reflected in changes in the nucleation and emission mechanisms for lattice dislocations.
Assessment of equilibrium field coil misalignments on the divertor footprints in NSTX-U

The presence of error fields in a tokamak device is inevitable, so it is of fundamental importance to understand their impact on the operation of the device and up to what level they can be tolerated. In this paper a prediction of the impact on the magnetic footprints on the divertor plates due to the misalignment of NSTX-U equilibrium coils is presented. Resistive MHD simulations are used to predict the magnetic field perturbations experienced by the field lines due to the presence of error fields. A linear relation between the magnitude of the misalignment and the area of the magnetic footprints is found, as well as an inverse proportionality between the size of a magnetic footprint and the plasma penetration of the field lines composing the footprint. This study is intended as a starting point in the process of investigating divertor footprints associated with the plasma response to intrinsic error fields with resistive MHD codes. A basic interpretation of the results suggests that large footprints resulting from equilibrium coils misalignment may be desirable, to some extent, to decrease the peak heat load on the divertor components. A more complete interpretation of the results presented here will involve a number of complex physics issues, for example pedestal transport and stability, along with the role of various scrape-off layer and divertor processes, as well as experimental data to confirm the predictions.
Allylindation of 6-Substituted 2-Hydroxy-1-tetralones in Aqueous and Organic Media. Stereochemistry and Competition Studies

A systematic investigation of the stereoselectivity associated with coupling reactions involving the allylindium reagent and 6-substituted 2-hydroxy-1-tetralones is presented. In each instance, the allylations were carried out in water, 50% aqueous THF, and dry THF. The extent of 1,2-induction was found to be highest in THF−H2O (1:1) and to favor the trans diol isomer. Somewhat lower levels of stereochemical bias in the same direction were observed in pure water. However, further erosion of this trend was noted for those reactions performed in THF, such that a modest crossover in product distribution became apparent in certain examples. On the basis of competition experiments, both reaction trajectories give evidence of proceeding via chelated intermediates. The extent of stereoinduction was found to be in line with the normal predilection of 2-cyclohexenones for axial attack, which is the process believed to be beset with minimal torsional effects. The substituents situated para to the ketone carbonyl do...
Synthesis of 2,2',6,6'-Tetramethylbiphenyl-4,4'-Dibenzthiazole

Abstract For the synthesis of 2,2',6,6'-tetramethylbiphenyl-4,4'-dibenzthiazole 2 , first 2,2',6,6'-tetramethylbiphenyl-4,4'-dicarboxylic acid 1 was synthesized by the selective oxidation reaction of bimesityl. 2 was prepared by reaction of 1 with 2-aminothiophenol.
GToTree: a user-friendly workflow for phylogenomics.

Summary Genome-level evolutionary inference (i.e. phylogenomics) is becoming an increasingly essential step in many biologists' work. Accordingly, there are several tools available for the major steps in a phylogenomics workflow. But for the biologist whose main focus is not bioinformatics, much of the computational work required-such as accessing genomic data on large scales, integrating genomes from different file formats, performing required filtering, stitching different tools together etc.-can be prohibitive. Here I introduce GToTree, a command-line tool that can take any combination of fasta files, GenBank files and/or NCBI assembly accessions as input and outputs an alignment file, estimates of genome completeness and redundancy, and a phylogenomic tree based on a specified single-copy gene (SCG) set. Although GToTree can work with any custom hidden Markov Models (HMMs), also included are 13 newly generated SCG-set HMMs for different lineages and levels of resolution, built based on searches of ∼12 000 bacterial and archaeal high-quality genomes. GToTree aims to give more researchers the capability to make phylogenomic trees. Availability and implementation GToTree is open-source and freely available for download from: github.com/AstrobioMike/GToTree. It is implemented primarily in bash with helper scripts written in python. Supplementary information Supplementary data are available at Bioinformatics online.
Volkensinin: A new limonoid from Melia volkensii

Abstract Bioactivity-directed fractionation of the root bark of M. volkensii Gurke (Meliaceae) resulted in the isolation of a new compound: volkensinin ( 1 ). The structure of 1 , which contains a unique 5-membered C ring, has been elucidated by the analysis of spectral data. Compound 1 showed weak cytotoxicities against six human tumor cell lines.
Key Insulation and Intrusion Resilience Over a Public Channel.

Key insulation (KI) and Intrusion resilience (IR) are methods to protect a user’s key against exposure by utilizing periodic communications with an auxiliary helper. But existing work assumes a secure channel between user and helper. If we want to realize KI or IR in practice we must realize this secure channel. This paper looks at the question of how to do this when the communication is over what we are more likely to have in practice, namely a public channel such as the Internet or a wireless network. We explain why this problem is not trivial, introduce models and definitions that capture the desired security in a public channel setting, and provide a complete (and surprising) answer to the question of when KI and IR are possible over a public channel. The information we provide is important to guide practitioners with regard to the usage of KI and IR and also to guide future research in this area. ∗Dept. of Computer Science & Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. E-Mail: mihir@cs.ucsd.edu. URL: http://www-cse.ucsd.edu/users/mihir. Supported in part by NSF grant CNS 0524765 and CNS 0627779 and a gift from Intel corporation. †Dept. of Computer Science & Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. E-Mail: shduan@cs.ucsd.edu. URL: http://www-cse.ucsd.edu/users/shduan. Supported in part by the grants of the first author. ‡Computer Science Department, Bowdoin College, 8650 College Station, Brunswick, ME 04011-8486, USA. EMail: apalacio@bowdoin.edu. URL: http://academic.bowdoin.edu/faculty/A/apalacio/.
An enantioselective synthesis of differentially protected erythro-α, β-diamino acids and its application to the synthesis of an analogue of rhodopeptin B5

Methodology for the enantioselective synthesis of differentially protected erythro-α,β-diamino acids from N-tosyloxy β-lactams is reported. The requisite N-tosyloxy β-lactams are readily available from simple β-keto esters. The reported approach is flexible and compatible with a variety of functional groups. The synthetic utility of the method is demonstrated through its application to the preparation of an analogue of the antifungal cyclic peptide rhodopeptin B5.
Optimal Point Placement for Mesh Smoothing

We study the problem of moving a vertex in an unstructured mesh of triangular, quadrilateral, or tetrahedral elements to optimize the shapes of adjacent elements. We show that many such problems can be solved in linear time using generalized linear programming. We also give efficient algorithms for some mesh smooth ing problems that do not fit into the generalized linear programming paradigm.
Evolution of Endothelin signaling and diversification of adult pigment pattern in Danio fishes.

Fishes of the genus Danio exhibit diverse pigment patterns that serve as useful models for understanding the genes and cell behaviors underlying the evolution of adult form. Among these species, zebrafish D. rerio exhibit several dark stripes of melanophores with sparse iridophores that alternate with light interstripes of dense iridophores and xanthophores. By contrast, the closely related species D. nigrofasciatus has an attenuated pattern with fewer melanophores, stripes and interstripes. Here we demonstrate species differences in iridophore development that presage the fully formed patterns. Using genetic and transgenic approaches we identify the secreted peptide Endothelin-3 (Edn3)—a known melanogenic factor of tetrapods—as contributing to reduced iridophore proliferation and fewer stripes and interstripes in D. nigrofasciatus. We further show the locus encoding this factor is expressed at lower levels in D. nigrofasciatus owing to cis-regulatory differences between species. Finally, we show that functions of two paralogous loci encoding Edn3 have been partitioned between skin and non-skin iridophores. Our findings reveal genetic and cellular mechanisms contributing to pattern differences between these species and suggest a model for evolutionary changes in Edn3 requirements for pigment patterning and its diversification across vertebrates.
Reaction of organolithiums with fluoro-N,N-diallylanilines: A benzyne-mediated anionic cascade leading to 3,4-disubstituted indolines

Abstract Regioselective ortho-lithiation of either 2-fluoro- (2) or 3-fluoro-N,N-diallylaniline (3) initiates an anionic cascade leading to an N-allyl-3,4-disubstituted indoline. The transformation involves loss of LiF from the ortho-lithiated species, regioselective intermolecular addition of the organolithium to the benzyne intermediate, and cyclization of the resulting [6-substituted-2-(N,N-diallylamino)phenyl]lithium.
Solubilized zirconocene dihydride as a promotor of alkene coupling reactions

Abstract The THF-soluble bis(methoxyethyl)zirconocene dihydride 3 displayed novel reactivity patterns and was used to reductively couple alkenes, dienes, and enynes. A plausible mechanism involves the formation of a 14-electron zirconium(II) and zirconacyclopentane species.
Foliar fungi alter reproductive timing and allocation in Arabidopsis under normal and water-stressed conditions

Abstract Microbes influence plant phenotypes but most known examples of this are from the study of below-ground microbes and plant disease modification. To examine the potential importance of phyllosphere microbes on non-disease related plant traits, we used sterile Arabidopsis clones to test the effects of foliar fungi on flowering phenology and reproductive allocation under conditions of varying water stress. We inoculated the sterile plants with fully-factorial combinations of four fungal isolates, then measured flowering time and reproductive allocation for each treatment group under normal and water-stressed conditions. All plants inoculated with foliar fungi had significantly later flowering and greater seed mass than the sterile control groups. The magnitude of this effect depended on the specific fungi present, but individual fungal effects diminished as inoculum richness increased. Above-ground microbes likely influence other plant traits as well and should be considered in any study measuring plant phenotypes.
Tau Internalization is Regulated by 6-O Sulfation on Heparan Sulfate Proteoglycans (HSPGs).

The misfolding and accumulation of tau protein into intracellular aggregates known as neurofibrillary tangles is a pathological hallmark of neurodegenerative diseases such as Alzheimer’s disease. However, while tau propagation is a known marker for disease progression, exactly how tau propagates from one cell to another and what mechanisms govern this spread are still unclear. Here, we report that cellular internalization of tau is regulated by quaternary structure and have developed a cellular assay to screen for genetic modulators of tau uptake. Using CRISPRi technology we have tested 3200 genes for their ability to regulate tau entry and identified enzymes in the heparan sulfate proteoglycan biosynthetic pathway as key regulators. We show that 6-O-sulfation is critical for tau-heparan sulfate interactions and that this modification regulates uptake in human central nervous system cell lines, iPS-derived neurons, and mouse brain slice culture. Together, these results suggest novel strategies to halt tau transmission.
High-throughput synthesis of substituted hydrazine derivatives

Regioselective alkylations of the hydrazine derivatives are achieved by using the (2,6-dichloro-4-methoxyphenyl)(2,4-dichlorophenyl)methoxycarboxyl resin. High-throughput synthesis of monosubstituted and 1,1-disubstituted hydrazine building blocks is described.
Distributed Uplink Power Control in an Ultra-Dense Millimeter Wave Network: A Mean-Field Game Approach

In this letter, a novel mean-field game (MFG) framework is proposed for uplink power control in an ultra-dense millimeter wave network. The proposed MFG considers the time evolution of the mobile users’ (MUs) orientations as well as the energy available in their batteries, under adaptive user association. The objective of each MU is then to find the optimal transmission power that maximizes its energy efficiency. The expression of the energy efficiency is analytically derived for the realistic case of a finite size network. Simulation results show that the proposed approach yields gains of up to 24%, in terms of energy efficiency, compared to a baseline in which the nodes transmit according to the path loss compensating power control policy.
New formulas relating the masses of some baryons and mesons

Abstract Sum rules relating the masses of ground-state baryons and mesons obtained in a constituent quark model, but it is argued that the formulas are more general than the model that motivates them. The relation of one of the formulas to heavy quark theory is discussed. Where precise data are available, the sum rules agree with experiment to better than 1%. One of the sum rules agrees with new preliminary measurements of masses of b -quark baryons.
Rb4Sn2Ag4(P2Se6)3: First Example of a Quinary Selenophosphate and an Unusual Sn−Ag s2−d10 Interaction

The flux synthesis of the layered compound Rb4Sn2Ag4P6Se18 is reported. Multiply bonded [P2Se6]4- ligands hold together Sn2+ and Ag+ atoms, stabilizing a novel Sn−Ag s2−d10 bonding interaction at 2...
Thermodynamic constraints on the regulation of metabolic fluxes

Nutrition and metabolism are fundamental to cellular function. Metabolic activity (i.e. rates of flow, most commonly referred to as flux) is constrained by thermodynamics and regulated by the activity of enzymes. The general principles that relate biological and physical variables to metabolic control are incompletely understood. Using metabolic control analysis and computer simulations in several models of simplified metabolic pathways, we derive analytical expressions that define relationships between thermodynamics, enzyme activity, and flux control. The relationships are further analyzed in a mathematical model of glycolysis as an example of a complex biochemical pathway. We show that metabolic pathways that are very far from equilibrium are controlled by the activity of upstream enzymes. However, in general, regulation of metabolic fluxes by an enzyme has a more adaptable pattern, which relies more on distribution of free energy among reaction steps in the pathway than on the thermodynamic properties of the given enzyme. These findings show how the control of metabolic pathways is shaped by thermodynamic constraints of the given pathway.
Free Radical-Mediated Intermolecular Conjugate Additions. Effect of the Lewis Acid, Chiral Auxiliary, and Additives on Diastereoselectivity

We have developed a highly diastereoselective method for the conjugate addition of carbon radicals to chiral α,β-unsaturated N-enoyloxazolidinones using Bu3SnH as chain carrier and Et3B/O2 as radical initiator. Lewis acids have been screened, and Yb(OTf)3 proved to give optimized results for both chemical yield (88% for 1a and 94% for 1b) and diastereoselectivity (25:1 for 1a and 46:1 for 1b). The selectivity is solvent-dependent, CH2Cl2-THF being an ideal combination. Scrupulously dry solvents or reaction conditions were not required. Substoichiometric amounts of Yb(OTf)3 provided efficient reaction with minimal sacrifice in diastereoselectivity. Carbon radicals with reasonable nucleophilicity were generally successful, including functionalized radicals such as acetyl or methoxymethyl. Electrophilic radicals were not successful. A model which accounts for most of our observations is presented.
Syntheses, structures, and physical properties of LnAsTe (Ln = La, Pr, Sm, Gd, Dy, Er).

Six rare-earth arsenic tellurides have been synthesized by the reactions of the rare-earth elements (Ln) with As and Te at 1123 K. LaAsTe (a = 7.8354(11) A, b = 4.1721(6) A, c = 10.2985(14) A, T = 153 K), PrAsTe (a = 7.728(2) A, b = 4.1200(11) A, c = 10.137(3) A, T = 153 K), SmAsTe (a = 7.6180(16) A, b = 4.0821(9) A, c = 9.991(2) A, T = 153 K), GdAsTe (a = 7.5611(15) A, b = 4.0510(8) A, c = 9.920(2) A, T = 153 K), DyAsTe (a = 7.4951(13) A, b = 4.0246(7) A, c = 9.8288(17) A, T = 153 K), and ErAsTe (a = 7.4478(1) A, b = 4.0078(1) A, c = 9.7552(2) A, T = 153 K) crystallize with four formula units in the orthorhombic space group D2h16-Pnma. These compounds are isostructural and belong to the β-ZrSb2 structure type. In each compound, the Ln atoms are coordinated by a tricapped trigonal prism of four As atoms and five Te atoms. The entire three-dimensional structure is built up by the motif of the LnAs4Te5 tricapped trigonal prisms. Infinite nonalternating zigzag As chains are found along the b axis, with As−As...
A convergent total synthesis of the marine sponge alkaloid ageladine A via a strategic 6π-2-azatriene electrocyclization

Abstract A second generation total synthesis of the marine sponge metabolite ageladine A utilizing a biogenetically inspired 6π-2-azaelectrocyclization of triene 34 as the key step is performed to construct the imidazopyridine core of the metabolite.
A simple aza wittig‐mediated pyrimidine annulation reaction

Treatment of heterocyclic o-aminonitriles and o-aminoesters 1a-5a with dibromotriphenylphosphorane gives iminophosphoranes 1b-5b which undergo a facile aza-Wittig reaction at room temperature with phenyl isocyanate to provide the carbodiimides 1c-5c. Treatment of the latter intermediates with ammonia leads to intramolecular ring closure of the initially formed guanidines to provide the fused 4-aminopyrimidines and 4(3H)-pyrimidinones 1d-Sd.
An efficient and practical chemoenzymatic preparation of optically active secondary amines.

An efficient and practical chemoenzymatic method was developed for the preparation of a variety of chiral secondary amines. Here, oxalamic esters were identified as unique derivatives amenable to the enzyme-catalyzed kinetic resolution of racemic secondary amines. Both enantiomers of the amines were produced in high optical purity and yields after the cleavage of the oxalamic groups.
A Concise Route to β-Cyclopropyl Amino Acids Utilizing 1,2-Dioxines and Stabilized Phosphonate Nucleophiles

1,2-Dioxines react with glycine-derived phosphonate nucleophiles via a multistep cascade reaction to give beta-cyclopropyl amino acid derivatives in good yield with excellent control of the cyclopropane stereocentres. The cyclopropyl ketones were oxidized to the corresponding carboxylic esters using Baeyer-Villiger conditions. Standard deprotection protocols produced a series of known beta-cyclopropyl amino acids that are selective and potent agonists or antagonists of the metabotropic glutamate receptors in excellent yields.
A Repetitive Mutation and Selection System for Bacterial Evolution to Increase the Specific Affinity to Pancreatic Cancer Cells

It is difficult to target and kill cancer cells. One possible approach is to mutate bacteria to enhance their binding to cancer cells. In the present study, Gram-negative Escherichia coli and Gram-positive Bacillus subtilis were randomly mutated, and then were positively and negatively selected for binding cancer vs normal cells. With repetitive mutation and selection both bacteria successfully evolved to increase affinity to the pancreatic cancer cell line (Mia PaCa-2) but not normal cells (HPDE: immortalized human pancreatic ductal epithelial cells). The mutant E. coli and B. subtilis strains bound to Mia PaCa-2 cells about 10 and 25 times more than to HPDE cells. The selected E. coli strain had mutations in biofilm-related genes and the regulatory region for a type I pilus gene. Consistent with type I pili involvement, mannose could inhibit the binding to cells. The results suggest that weak but specific binding is involved in the initial step of adhesion. To test their ability to kill Mia PaCa-2 cells, hemolysin was expressed in the mutant strain. The hemolysin released from the mutant strain was active and could kill Mia PaCa-2 cells. In the case of B. subtilis, the initial binding to the cells was a weak interaction of the leading pole of the motile bacteria. The frequency of this interaction to Mia PaCa-2 cells dramatically increased in the evolved mutant strain. This mutant strain could also specifically invade beneath Mia PaCa-2 cells and settle there. This type of mutation/selection strategy may be applicable to other combinations of cancer cells and bacterial species.
Control of Staphylococcus aureus Quorum Sensing by a Membrane-Embedded Peptidase

Gram-positive bacteria process and release small peptides, or pheromones, that act as signals for the induction of adaptive traits, including those involved in pathogenesis. One class of small signaling pheromones is the cyclic autoinducing peptides (AIPs), which regulate expression of genes that orchestrate virulence and persistence in a range of microbes, including staphylococci, listeriae, clostridia, and enterococci. In a genetic screen for Staphylococcus aureus secreted virulence factors, we identified an S. aureus mutant containing an insertion in the gene SAUSA300_1984 (mroQ), which encodes a putative membrane-embedded metalloprotease. A ΔmroQ mutant exhibited impaired induction of Toll-like receptor 2-dependent inflammatory responses from macrophages but elicited greater production of the inflammatory cytokine interleukin-1β and was attenuated in a murine skin and soft tissue infection model. The ΔmroQ mutant phenocopies an S. aureus mutant containing a deletion of the accessory gene regulatory system (Agr), wherein both strains have significantly reduced production of secreted toxins and virulence factors but increased surface protein A abundance. The Agr system controls virulence factor gene expression in S. aureus by sensing the accumulation of AIP via the histidine kinase AgrC and the response regulator AgrA. We provide evidence to suggest that MroQ acts within the Agr pathway to facilitate the optimal processing or export of AIP for signal amplification through AgrC/A and induction of virulence factor gene expression. Mutation of MroQ active-site residues significantly reduces AIP signaling and attenuates virulence. Altogether, this work identifies a new component of the Agr quorum-sensing circuit that is critical for the production of S. aureus virulence factors.
Dynamic network partnerships and social contagion drive cooperation.

Both reciprocity and positive assortment (like with like) are predicted to promote the evolution of cooperation, yet how partners influence each other's behaviour within dynamic networks is not wel...
Single-cell transcriptome profiling of the Ciona larval brain

The tadpole-type larva of Ciona has emerged as an intriguing model system for the study of neurodevelopment. The Ciona intestinalis connectome has been recently mapped, revealing the smallest central nervous system (CNS) known in any chordate, with only 177 neurons. This minimal CNS is highly reminiscent of larger CNS of vertebrates, sharing many conserved developmental processes, anatomical compartments, neuron subtypes, and even specific neural circuits. Thus, the Ciona tadpole offers a unique opportunity to understand the development and wiring of a chordate CNS at single-cell resolution. Here we report the use of single-cell RNAseq to profile the transcriptomes of single cells isolated by fluorescence-activated cell sorting (FACS) from the whole brain of Ciona robusta (formerly intestinalis Type A) larvae. We have also compared these profiles to bulk RNAseq data from specific subsets of brain cells isolated by FACS using cell type-specific reporter plasmid expression. Taken together, these datasets have begun to reveal the compartment- and cell-specific gene expression patterns that define the organization of the Ciona larval brain.
Simplified preparations of trialkylsilyl- and bis(trialkylsilyl) dihalomethanes via the deprotonation of dihalomethanes

Abstract Simple, high-yield routes to trialkylsilyl- and bis(trialkylsilyI)dihalomethanes are described. These compounds are prepared by the deprotonation of dibromomethane or dichloromethane by lithium diisopropylamide in the presence of a chlorosilane. The reactions are carried out at temperatures below −70°C in THF/hexane solvent mixtures. After aqueous workup, the air- and water-stable products are isolated by either distillation or crystallization. Further reactions on these compounds are possible, as illustrated by one example.
Synthesis of fused bicyclic imidazoles by ring-closing metathesis

Abstract The preparation of a number of dienylimidazole via chemoselective metal–halogen exchange and their utility in ring-closing metathesis is described. Essentially all regioisomeric permutations participate in metathesis with the notable exception of 4-vinyl-5-allylimidazoles, provided that the imidazole N3 atom is protonated.
Toxoplasma Controls Host Cyclin E Expression through the Use of a Novel MYR1-Dependent Effector Protein, HCE1.

ABSTRACT Toxoplasma gondii is an obligate intracellular parasite that establishes a favorable environment in the host cells in which it replicates. We have previously reported that it uses MYR-dependent translocation of dense granule proteins to elicit a key set of host responses related to the cell cycle, specifically, E2F transcription factor targets, including cyclin E. We report here the identification of a novel Toxoplasma effector protein that is exported from the parasitophorous vacuole in a MYR1-dependent manner and localizes to the host’s nucleus. Parasites lacking this inducer of host cyclin E (HCE1) are unable to modulate E2F transcription factor target genes and exhibit a substantial growth defect. Immunoprecipitation of HCE1 from infected host cells showed that HCE1 efficiently binds elements of the cyclin E regulatory complex, namely, DP1 and its partners E2F3 and E2F4. Expression of HCE1 in Neospora caninum, or in uninfected human foreskin fibroblasts (HFFs), showed localization of the expressed protein to the host nuclei and strong cyclin E upregulation. Thus, HCE1 is a novel effector protein that is necessary and sufficient to impact the E2F axis of transcription, resulting in co-opting of host functions to the advantage of Toxoplasma. IMPORTANCE Like most Apicomplexan parasites, Toxoplasma gondii has the remarkable ability to invade and establish a replicative niche within another eukaryotic cell, in this case, any of a large number of cell types in almost any warm-blooded animals. Part of the process of establishing this niche is the export of effector proteins to co-opt host cell functions in favor of the parasite. Here we identify a novel effector protein, HCE1, that the parasites export into the nucleus of human cells, where it modulates the expression of multiple genes, including the gene encoding cyclin E, one of the most crucial proteins involved in controlling when and whether a human cell divides. We show that HCE1 works through binding to specific transcription factors, namely, E2F3, E2F4, and DP1, that normally carefully regulate these all-important pathways. This represents a new way in which these consummately efficient infectious agents co-opt the human cells that they so efficiently grow within.
Evidence for cryptand-like behavior in bibracchial lariat ether (BiBLE) complexes obtained from X-ray crystallography and solution thermodynamic studies

[diaza-4,13-18-crown-6(bis-N,N'-methoxy-2 ethyl)]NaI•H 2 O cristallise dans le systeme trialinique avec le groupe d'espace P1. Affinement de la structure jusqu'a 0,033
Muscarinic antagonist activity of 3-(5-alkoxy-oxazol-2-yl)-1,2,5,6-tetrahydropyridines.

Abstract A series of 3-(5-alkoxy-oxazol-2-yl)-1,2,5,6-tetrahydropyridines (OXTP) were found to have high affinity for muscarinic receptors and to be potent muscarinic antagonists as measured by blockade of acetylcholine stimulated PI hydrolysis in rat cortex or by blockade of oxotremorine induced tremors in mice.
Impacts of white-tailed deer on regional patterns of forest tree recruitment.

Abstract Local, short- to medium-term studies make clear that white-tailed deer can greatly suppress tree growth and survival in palatable tree species. To assess how deer have broadly affected patterns of tree recruitment across northern Wisconsin, we analyzed recruitment success in 11 common trees species that vary in palatability across 13,105 USFS - FIA plots sampled between 1983 and 2013. We also examined how recruitment in these species covaried with estimated deer densities here. Saplings of five palatable species were scarce relative to less palatable species and showed highly skewed distributions. Scarcity and skew provide reliable signals of deer impacts even when deer have severely reduced recruitment and/or no reliable deer density data are available. Deer densities ranged from 2.3 to 23 deer per km 2 over a 30 year period. Sapling numbers in two maples ( Acer ) and aspen ( Populus ) with intermediate palatability declined sharply in apparent response to higher deer density. Path analysis also reveals that deer act to cumulatively depress sapling recruitment in these species over successive decades. Together, these approaches show that deer have strongly depressed sapling recruitment in all taxa except Abies and Picea . As these impacts are now propagating into larger sized trees, deer are also altering canopy composition and dynamics. The tools developed here provide efficient and reliable indicators for monitoring deer impacts on forest tree recruitment using consistent data collected by public agencies.
An efficient procedure for the preparation of chiral β-substituted (E)-crotylsilanes: Application of a rhodium(II) catalyzed silylformylation of terminal alkynes

Abstract Functionalized β-substituted ( E )-crotylsilanes ( R )-7 and ( S )-8, bearing an alkyl or aryl group adjacent to the stereogenic C-Si center have been synthesized in an efficient four-step procedure initiated with a regio- and stereoselective silylformylation of a terminal alkyne catalyzed by dirhodium(II) perfluorobutyrate.
Difunctional heterocycles : a convenient one pot synthesis of novel bis(benzoxazoles) from bis(o-aminophenols)

New bis(benzoxazoles) 14 and 17 have been synthesized in excellent yields from the corresponding bis(o-aminophenols) by refluxing with triethyl orthoformate. 6,6′-Bis(benzoxazole) (14) has also been prepared utilizing Gold's reagent. Compound 14 is inert to Reissert reaction conditions. However, the Reissert reaction on 5,5′-bis(benzoxazole) (17) led to ring opened product 20.
Geology of the northeastern flank of Apollinaris Mons, Mars: Constraints on the erosional history from morphology, topography, and crater populations

Abstract We have utilized THEMIS, MOLA, CTX and HiRISE data sets to investigate the morphologic and topographic characteristics of the northeast flank of Apollinaris Mons, a region with evidence for significant erosion of volcanic deposits. Using ArcGIS software, we mapped the geology of the northeast flank and obtained age estimates using crater size-frequency distributions from crater counts. Of the eight mapped units, three (Apollinaris Mons upper, mid-, and lower flank units) represent volcanic flank materials in various states of preservation. The Late Noachian-Early Hesperian upper flank unit is massive and contains joint-like vertical structures along the scarp faces of two large plateaus whose upper surfaces likely represent the original surface or near-surface deposits of Apollinaris Mons. Downslope-facing plateau scarps have up to 500 m of relief. Positioned below this unit are the mid-flank and lower flank units, each representing eroded surfaces within Apollinaris Mons flank materials that have stabilization ages between the Late Hesperian to Early Amazonian. Mantling material in the region contains cavities and boxwork-like textures that resemble patterns in terrestrial eroded pyroclastic flow deposits. Dome-shaped mounds west of the mapping region have morphologic similarities to terrestrial fumarolic mounds or possibly inverted impact craters. Both the texture and features suggest widespread pyroclastic deposits adjacent to Apollinaris Mons. Using MOLA gridded topography, we estimate that ~308 km3 of materials have been eroded along the flanks of the volcano. Statistical and histogram data from the thickness values of eroded materials shows that up to ~300 m of material has been removed from the majority of flank surfaces. Assuming steady state erosion of flank surfaces, we estimate an area-normalized loss rate of ~0.859 nm/yr for northeast Apollinaris Mons. This erosion rate is within the long-term range for Mars (~0.01–10 nm/yr) as estimated from MER landing site geology by Golombek et al. [2006].
Robustness of neural networks: a probabilistic and practical approach

Neural networks are becoming increasingly prevalent in software, and it is therefore important to be able to verify their behavior. Because verifying the correctness of neural networks is extremely challenging, it is common to focus on the verification of other properties of these systems. One important property, in particular, is robustness. Most existing definitions of robustness, however, focus on the worst-case scenario where the inputs are adversarial. Such notions of robustness are too strong, and unlikely to be satisfied by---and verifiable for---practical neural networks. Observing that real-world inputs to neural networks are drawn from non-adversarial probability distributions, we propose a novel notion of robustness: probabilistic robustness, which requires the neural network to be robust with at least (1 - 'e) probability with respect to the input distribution. This probabilistic approach is practical and provides a principled way of estimating the robustness of a neural network. We also present an algorithm, based on abstract interpretation and importance sampling, for checking whether a neural network is probabilistically robust. Our algorithm uses abstract interpretation to approximate the behavior of a neural network and compute an overapproximation of the input regions that violate robustness. It then uses importance sampling to counter the effect of such overapproximation and compute an accurate estimate of the probability that the neural network violates the robustness property.
Scheduled-Asynchronous Distributed Algorithm for Optimal Power Flow

Optimal power flow (OPF) problems are nonconvex and large-scale optimization problems with important applications in power networks. This paper proposes the scheduled-asynchronous algorithm to solve a distributed semidefinite programming formulation of the OPF problem. In this formulation, every agent seeks to solve a local optimization with its own cost function, physical constraints on its nodal power injection, voltage, and power flow of the lines it is connected to, and decision constraints on variables shared with neighbors to ensure consistency of the obtained solution. In the scheduled-asynchronous algorithm, every pair of connected nodes in the electrical network update their local variables in an alternating fashion. This strategy is asynchronous, in the sense that no clock synchronization is required, and relies on an orientation of the electrical network that prescribes the precise ordering of node updates. We establish the asymptotic convergence properties to the primal-dual optimizer when the orientation is acyclic. Given the dependence of the convergence rate on the network orientation, we also develop a distributed graph coloring algorithm that finds an orientation with diameter at most five for electrical networks. Simulations illustrate our results on various IEEE bus test cases.
IONIZED GAS IN THE SMITH CLOUD

We present Wisconsin Hα Mapper observations of ionized gas in the Smith Cloud, a high-velocity cloud which Lockman et al. have recently suggested is interacting with the Galactic disk. Our Hα map shows the brightest Hα emission, 0.43 ± 0.04 R, coincident with the brightest Hi, while slightly fainter Hα emission (0.25 ± 0.02 R) is observed in a region with Hi intensities < 0.1 times as bright as the brightest Hi. We derive an ionized mass of 3 × 10 6 M� , comparable to the Hi mass, with the H + mass spread over a considerably larger area than that of Hi. An estimated Galactic extinction correction could adjust these values upward by 40%. Hα and [Sii] line widths toward the region of brightest emission constrain the electron temperature of the gas to be between 8000 K and 23,000 K. A detection of [Nii] λ6583 in the same direction with a line ratio [Nii]/Hα = 0.32 ± 0.05 constrains the metallicity of the cloud: for typical photoionization temperatures of 8000–12,000 K, the nitrogen abundance is 0.15–0.44 times solar. These results lend further support to the claim that the Smith Cloud is new material accreting onto the Galaxy.
On the Azumaya locus of almost commutative algebras

We prove a general statement which implies the coincidence of the Azumaya and smooth loci of the center of an algebra in positive characteristic, provided that the spectrum of its associated graded algebra has a large symplectic leaf. In particular, we show that for a symplectic reflection algebra, the smooth and the Azumaya loci coincide.
VARTOOLS: A Program for Analyzing Astronomical Time-Series Data

Abstract This paper describes the Vartools program, which is an open-source command-line utility, written in C, for analyzing astronomical time-series data, especially light curves. The program provides a general-purpose set of tools for processing light curves including signal identification, filtering, light curve manipulation, time conversions, and modeling and simulating light curves. Some of the routines implemented include the Generalized Lomb–Scargle periodogram, the Box-Least Squares transit search routine, the Analysis of Variance periodogram, the Discrete Fourier Transform including the CLEAN algorithm, the Weighted Wavelet Z-Transform, light curve arithmetic, linear and non-linear optimization of analytic functions including support for Markov Chain Monte Carlo analyses with non-trivial covariances, characterizing and/or simulating time-correlated noise, and the TFA and SYSREM filtering algorithms, among others. A mechanism is also provided for incorporating a user’s own compiled processing routines into the program. Vartools is designed especially for batch processing of light curves, including built-in support for parallel processing, making it useful for large time-domain surveys such as searches for transiting planets. Several examples are provided to illustrate the use of the program.
Noncommutative Schur functions, switchboards, and Schur positivity

We review and further develop a general approach to Schur positivity of symmetric functions based on the machinery of noncommutative Schur functions. This approach unifies ideas of Assaf, Lam, and Greene and the second author.
A randomized tensor singular value decomposition based on the t-product

The tensor Singular Value Decomposition (t-SVD) for third order tensors that was proposed by Kilmer and Martin~\cite{2011kilmer} has been applied successfully in many fields, such as computed tomography, facial recognition, and video completion. In this paper, we propose a method that extends a well-known randomized matrix method to the t-SVD. This method can produce a factorization with similar properties to the t-SVD, but is more computationally efficient on very large datasets. We present details of the algorithm, theoretical results, and provide numerical results that show the promise of our approach for compressing and analyzing datasets. We also present an improved analysis of the randomized subspace iteration for matrices, which may be of independent interest to the scientific community.
The local low-dimensionality of natural images

Abstract: We develop a new statistical model for photographic images, in which the local responses of a bank of linear filters are described as jointly Gaussian, with zero mean and a covariance that varies slowly over spatial position. We optimize sets of filters so as to minimize the nuclear norms of matrices of their local activations (i.e., the sum of the singular values), thus encouraging a flexible form of sparsity that is not tied to any particular dictionary or coordinate system. Filters optimized according to this objective are oriented and bandpass, and their responses exhibit substantial local correlation. We show that images can be reconstructed nearly perfectly from estimates of the local filter response covariances alone, and with minimal degradation (either visual or MSE) from low-rank approximations of these covariances. As such, this representation holds much promise for use in applications such as denoising, compression, and texture representation, and may form a useful substrate for hierarchical decompositions.
A greedy link scheduler for wireless networks with fading channels

We consider the problem of link scheduling for wireless networks with fading channels, where the link rates are varying with time. Due to the high computational complexity of the throughput optimal scheduler, we provide a low complexity greedy link scheduler GFS, with provable performance guarantees. We show that the performance of our greedy scheduler can be analyzed using the Local Pooling Factor (LPF) of a network graph, which has been previously used to characterize the stability of the Greedy Maximal Scheduling (GMS) policy for networks with static channels. We conjecture that the performance of GFS is a lower bound on the performance of GMS for wireless networks with fading channels.
Large Scale Empirical Risk Minimization via Truncated Adaptive Newton Method

We consider large scale empirical risk minimization (ERM) problems, where both the problem dimension and variable size is large. In these cases, most second order methods are infeasible due to the high cost in both computing the Hessian over all samples and computing its inverse in high dimensions. In this paper, we propose a novel adaptive sample size second-order method, which reduces the cost of computing the Hessian by solving a sequence of ERM problems corresponding to a subset of samples and lowers the cost of computing the Hessian inverse using a truncated eigenvalue decomposition. We show that while we geometrically increase the size of the training set at each stage, a single iteration of the truncated Newton method is sufficient to solve the new ERM within its statistical accuracy. Moreover, for a large number of samples we are allowed to double the size of the training set at each stage, and the proposed method subsequently reaches the statistical accuracy of the full training set approximately after two effective passes. In addition to this theoretical result, we show empirically on a number of well known data sets that the proposed truncated adaptive sample size algorithm outperforms stochastic alternatives for solving ERM problems.
On k-visibility graphs

We examine several types of visibility graphs in which sightlines can pass through k objects. For k 1 we bound the maximum thickness of semi-bar k-visibility graphs between d 2 (k + 1)e and 2k. In addition we show that the maximum number of edges in arc and circle k-visibility graphs on n vertices is at most (k +1)(3n k 2) for n > 4k +4 and n for n 4k + 4, while the maximum chromatic number is at most 6k + 6. In semi-arc k-visibility graphs on n vertices, we show that the maximum number of edges is n 2 for n 3k + 3 and at most (k + 1)(2n k+2 2 ) for n > 3k + 3, while the maximum chromatic number is at most 4k + 4.
Stable rationality of quadric surface bundles over surfaces

We study rationality properties of quadric surface bundles over the projective plane. We exhibit families of smooth projective complex fourfolds of this type over connected bases, containing both rational and non-rational fibers.
A short proof of the existence of the solution to elliptic boundary problem

There are several methods for proving the existence of the solution to the elliptic boundary problem \(Lu=f \text{in} D,\quad u|_S=0,\quad (*)\). Here L is an elliptic operator of second order, f is a given function, and uniqueness of the solution to problem (*) is assumed. The known methods for proving the existence of the solution to (*) include variational methods, integral equation methods, method of upper and lower solutions. In this paper a method based on functional analysis is proposed. This method is conceptually simple. It requires some a priori estimates and a continuation in a parameter method, which is well-known.
Late-time spectroscopy of SN 2002hh: a continued visible light echo with no shock interaction yet

Supernova (SN) 2002hh was unusual among core-collapse SNe because it was highly reddened, and displayed a bright infrared (IR) excess due to radiatively heated dust in its circumstellar medium (CSM). Estimates for the mass of dust responsible for the IR echo suggested the presence of a massive shell within 0.26 pc of the star. For a velocity of 5000 - 10000 km/s, this material should be hit by the SN blast wave at late times, starting at roughly 12 years post-explosion. We have obtained deep late-time spectra with the MMT Blue Channel spectrograph to search for any spectral signatures of ongoing shock interaction. Interaction with a strength comparable to SN 1987A's collision with the equatorial ring would be detected in our data. However, in the spectra reported here, we do not detect clear signs of strong CSM interaction, contrary to expectations based on the reported radii of the dust shell. We do, however, detect emission associated with the old SN, and we find that the broad lines in the spectrum indicate a continuation of an ongoing reflected light echo, which appears similar to the spectrum at peak luminosity for this Type II-P event.
Escape Room: A Configurable Testbed for Hierarchical Reinforcement Learning

Recent successes in Reinforcement Learning have encouraged a fast growing network of RL researchers and a number of breakthroughs in RL research. As the RL community and body of work grows, so does the need for widely applicable benchmarks that can fairly and effectively evaluate a variety of RL algorithms. In this paper we present the Escape Room Domain (ERD), a new flexible, scalable, and fully implemented testing domain for Hierarchical RL that bridges the "moderate complexity" gap left behind by existing alternatives. ERD is open-source and freely available through GitHub, and conforms to widely-used public testing interfaces for simple integration and testing with a variety of public RL agent implementations.