cssi/SciSciGPT-SciSciNet huggingface dataset:
Communicating Original Research in Chemistry and Related Sciences

The availability of scientific information in electronic form is the convergence of traditional journal publishing, electronic communications, and the widespread availability of computer technology. This revolution in scientific communication has its roots in developments that started in the mid-19th century and culminated with the extraordinary progress in telecommunications and computer technology in the latter years of the 20th century. Eighty-three percent of scientific journals are now available online. The benefits of electronic journals include rapid publication, instantaneous linking to external information sources, and the capability to deliver new types of information. To date neither electronic-only nor preprint servers have been well received by the chemical sciences community. Continued advances in telecommunications, computer technology, and acquisition of scientific data in structured formats hold promise for even greater advances in communication of scientific information.
Ring-opening/ring-closing metathesis (RORCM) reactions of 7-Azanorbornene derivatives. An entry into perhydroindolines.

7-Azanorbornenes undergo ring-opening/ring-closing metathesis upon treatment with the second-generation Grubbs catalyst to give hexahydroindoline derivatives.
The Effects of Pitch Shifts on Delay-Induced Changes in Vocal Sequencing in a Songbird

Abstract Like human speech, vocal behavior in songbirds depends critically on auditory feedback. In both humans and songbirds, vocal skills are acquired by a process of imitation whereby current vocal production is compared to an acoustic target. Similarly, performance in adulthood relies strongly on auditory feedback, and online manipulations of auditory signals can dramatically alter acoustic production even after vocalizations have been well learned. Artificially delaying auditory feedback can disrupt both speech and birdsong, and internal delays in auditory feedback have been hypothesized as a cause of vocal dysfluency in persons who stutter. Furthermore, in both song and speech, online shifts of the pitch (fundamental frequency) of auditory feedback lead to compensatory changes in vocal pitch for small perturbations, but larger pitch shifts produce smaller changes in vocal output. Intriguingly, large pitch shifts can partially restore normal speech in some dysfluent speakers, suggesting that the effects of auditory feedback delays might be ameliorated by online pitch manipulations. Although birdsong provides a promising model system for understanding speech production, the interactions between sensory feedback delays and pitch shifts have not yet been assessed in songbirds. To investigate this, we asked whether the addition of a pitch shift modulates delay-induced changes in Bengalese finch song, hypothesizing that pitch shifts would reduce the effects of feedback delays. Compared with the effects of delays alone, combined delays and pitch shifts resulted in a significant reduction in behavioral changes in one type of sequencing (branch points) but not another (distribution of repeated syllables).
A new route to benzo[4,5]cyclohepta[1,2-b]naphthalenes: synthesis of radermachol.

Condensation of 3-phenylsulfonyl-1,3-isobenzofuranone (3) with benzocyclohept-6,7-en-5-ones such as 4 and 15 provides a straightforward, general method for synthesis of functionalized benzo[4,5]cyclohepta[1,2-b]naphthalenes (e.g., 5 and 16). This finding was used to achieve a brief and efficient preparation of 6,7-benzo-3,4-(1,4-dimethoxy-2,3-naphtho)-1,5-dioxosuberane (2), an established intermediate to the naturally occurring red pigment radermachol (1).
Gold Inorganic Rings Based on Polychalcogenide Chains

Abstract The reaction of AuCN with Sex 2- and Tex 2- in dimethylformamide in the presence of organic cations forms complexes with ring structures such as (Ph4P)2[Au2Se5] (I), (Ph4P)2[Au2Se6] (II), (Ph3P N P Ph3)2 - K2[Au4Te4]·2DMF (III). The reaction of AuCl3 with Te2- yielded (Ph4P)2[Au2(Te2)2] (IV). (I) crystallizes in the triclinic space group P-1 with a=10.381(4) A, b=11.002(5) A, c=21.181(9) A, α = 75.50(4)°, β = 74.74(3)°, γ=81.40(4)°, V=2250 A3 (-93 °C). (II) crystallizes in the monoclinic space group C2/c with a=28.409(7) A, b=10.97(1) A, c=19.762(5) A, β=130.49(1)°, V=4680 A3 (-93 °C). (III) crystallizes in the orthorhombic space group Pbcn with a=29.90(2)A, b=17.39(2)A, c=17.707(8)A, V=9206A3 (23 °C). (IV) crystallizes in the triclinic space group P-1 with a=10.526(3)A, b=11.237(2)A, b=11.237(2)A, α=103.03(2)°, β=106.95(3)°, γ=81.66(2)°, V=1148 A3 (-95 °C). Single-crystal X-ray diffraction studies of (I) and (11) show that both compounds possess the same structural feature. Two linearly-coordina...
Novel and Highly Efficient Synthesis of Substituted Dibenz[b,g]1,5-oxazocines. A Direct Comparison of the Solution versus Solid-Phase Approach

Abstract We describe a novel and highly efficient synthesis of substituted dibenz[ b , g ]1,5-oxazocines. The procedure is based on the S N Ar of fluoride with the phenolic hydroxide of the properly assembled acyclic intermediate. A direct comparison of the solution-phase vs the solid-phase synthesis has been conducted. The speed of the synthesis, the purity of the desired eight-membered heterocycles (>95%), as well as the diversity of the resultant library are definite advantages of the solid-phase procedure. Yields of dibenz[ b , g ]1,5-oxazocines synthesized via the solid-phase approach were generally better, while the purity of the products synthesized by both methods were identical.
Plantarflexor moment arms estimated from tendon excursion in vivo are not strongly correlated with geometric measurements.

Abstract Geometric and tendon excursion methods have both been used extensively for estimating plantarflexor muscle moment arm in vivo . Geometric measures often utilize magnetic resonance imaging, which can be costly and impractical for many investigations. Estimating moment arm from tendon excursion measured with ultrasonography may provide a cost-effective alternative to geometric measures of moment arm, but how well such measures represent geometry-based moment arms remains in question. The purpose of this study was to determine whether moment arms from tendon excursion can serve as a surrogate for moment arms measured geometrically. Magnetic resonance and ultrasound imaging were performed on 19 young male subjects to quantify plantarflexor moment arm based on geometric and tendon excursion paradigms, respectively. These measurements were weakly correlated that approached statistical significance (R 2 = 0.21, p = 0.052), and moment arm from tendon excursion under-approximated geometric moment arm by nearly 40% ( p 2 = 0.94) in a similar study. Therefore, we performed 92,378 regression analyses (19 choose 9) to determine if such a strong correlation existed in our study population. We found that certain sub-populations of the current study generated similarly strong coefficients of determination (R 2 = 0.92), but 84% of all analyses revealed no correlation (p > 0.05). Our results suggest that the moment arms from musculoskeletal geometry cannot be otherwise obtained by simply scaling moment arms estimated from tendon excursion.
Neutron scattering—The key characterization tool for nanostructured magnetic materials

The novel properties of materials produced using nanoscale manufacturing processes often arise from interactions across interfaces between dissimilar materials. Thus, to characterize the structure and magnetism of nanoscale materials demands tools with interface specificity. Neutron scattering has long been known to provide unique and quantitative information about nuclear and magnetic structures of bulk materials. Moreover, the specialty techniques of polarized neutron reflectometry and small angle neutron scattering (SANS) with polarized neutron beams and polarization analysis, are ideally and often uniquely suited to studies of nanostructured magnetic materials. Since neutron scattering is a weakly interacting probe, it gives quantifiable and easily-interpreted information on properties of statistically representative quantities of bulk, thin film and interfacial materials. In addition, neutron scattering can provide information to complement that obtained with bulk probes (magnetization, Kerr effect) or surface measurements obtained with scanning probe microscopy or resonant soft x-ray scattering. The straightforward interpretation and the simultaneous availability of structural information, make neutron scattering the technique of choice for the structural and physical characterization of many novel materials, especially those with buried interfaces, ones allowing for isotopic substitutions to decorate buried interfaces, or cases where the magnetic response to an external stimulus can be measured. We describe recent applications of neutron scattering to important thin film materials systems and future opportunities. Unquestionably, neutron scattering has played a decisive role in the development and study of new emergent phenomena. We argue with the advent of new techniques in neutron scattering and sample environment, neutron scattering's role in such studies will become even more dominant. In particular, neutron scattering will clarify and distinguish between intrinsic vs. extrinsic origins of unusual behavior which invariably plague novel materials. Key to realizing these opportunities will be the development of sample environment capabilities especially tailored to test the origins of novel phenomena, and techniques to collect, analyze and correlate neutron event detection with time dependent perturbations to the sample's environment.
An improved resolution of (±)-cis-N-normetazocine

The optical isomers of cis-N-normetazocine are the starting materials for the synthesis of a number of pharmacologically useful compounds. An improved resolution procedure for obtaining these isomers is reported.
A Thio-Diels−Alder Route to the Azocine Ring System. Total Synthesis of (±)-Otonecine

A sulfur-based strategy for synthesis of otonecine is described. Key steps include the thio-Diels−Alder trapping of thioketone 8 by the Danishefsky diene, followed by conversion into the enone 27 a...
Octakis(dimethylammonium) hexa-μ2-chlorido-hexachloridotrinickelate(II) dichloride: a linear trinickel complex with asymmetric bridging

The title compound, (C2H8N)8[Ni3Cl12]Cl2, crystallizes as linear [Ni3Cl12]6− complex anions with inversion symmetry, separated from one another by dimethyl­ammonium cations and noncoordinated chloride ions. The gross structural arrangement of the trinickel complex is as a segment of face-sharing NiCl6 octa­hedra similar to the (NiCl3)n chains of CsNiCl3-type compounds. On closer inspection, the regular coordination geometry of the complex consists of octa­hedral NiCl6 in the center linked by two symmetrically bridging chloride ions to square-pyramidal NiCl5 on each end. A long semicoordinate bond is formed by each of the terminal NiII cations, to give a 5+1 coordination geometry and form an asymmetric bridge to the central NiII cation. The dimethyl­ammonium cations surround the complex with an extensive hydrogen-bonding network, linking the complex to the noncoordinated chloride ions. Asymmetric bridging in the complex arises from short hydrogen bonds from the same dimethyl­ammonium cation to the apical and asymmetric bridging chloride ions, causing the complex to scissor outward.
Determining the factors driving selective effects of new nonsynonymous mutations

The distribution of fitness effects (DFE) of new mutations plays a fundamental role in evolutionary genetics. However, the extent to which the DFE differs across species has yet to be systematically investigated. Furthermore, the biological mechanisms determining the DFE in natural populations remain unclear. Here, we show that theoretical models emphasizing different biological factors at determining the DFE, such as protein stability, back-mutations, species complexity, and mutational robustness make distinct predictions about how the DFE will differ between species. Analyzing amino acid-changing variants from natural populations in a comparative population genomic framework, we find that humans have a higher proportion of strongly deleterious mutations than Drosophila melanogaster. Furthermore, when comparing the DFE across yeast, Drosophila, mice, and humans, the average selection coefficient becomes more deleterious with increasing species complexity. Last, pleiotropic genes have a DFE that is less variable than that of nonpleiotropic genes. Comparing four categories of theoretical models, only Fisher's geometrical model (FGM) is consistent with our findings. FGM assumes that multiple phenotypes are under stabilizing selection, with the number of phenotypes defining the complexity of the organism. Our results suggest that long-term population size and cost of complexity drive the evolution of the DFE, with many implications for evolutionary and medical genomics.
High-throughput crystallography at an affordable cost: The TB Structural Genomics Consortium crystallization facility

The crystallization facility of the TB Structural Genomics Consortium, one of nine P50 structural genomics centers sponsored by the National Institutes of Health, provides TB consortium members with automated crystallization, data collection, and basic molecular replacement structure solution up to bias-minimized maps. In contrast to venture capital -funded commercial enterprises, the TB consortium facilities are decentralized and aim to develop high-throughput crystallography methods and automation on a comparatively small budget. In addition to financial constraints, the logistics and organization of a production environment differ considerably from academic settings. The TB Structural Genomics Consortium crystallization facility may thus provide a model for cost-effective, efficient high-throughput crystallography. Processes and methods presented in this review should assist academic institutions planning to invest in high-throughput structural biology to assess both the rewards and risks of establishing structural genomics programs.
Asymmetric Synthesis of α,β-Dialkyl-α-phenylalanines via Direct Alkylation of a Chiral Alanine Derivative with Racemic α-Alkylbenzyl Bromides. A Case of High Enantiomer Differentiation at Room Temperature

This study demonstrates that the direct alkylation of a Ni(II)-complex of the chiral Schiff base of alanine with (S)-o-[N-(N-benzylprolyl)amino]benzophenone, with racemic α-alkylbenzyl bromides, is a synthetically feasible and methodologically advantageous approach to the target α,β-dialkylphenylalanines over previously reported methods. For the first time we report and rationalize a case of a high enantiomer differentiation process at room temperature.
A cooperative allylic fluorination: combination of nucleophilic and electrophilic fluorine sources

Abstract A one step, regioselective allylic fluorination of alkenes is reported in which electrophilic and nucleophilic sources of fluorine act synergistically to afford rearranged allylic fluorides over alternative vicinal dihalides. The reaction occurs under exceptionally mild conditions and without need for prefunctionalization or transition metal catalysts. The fluorination of cyclic alkenes and monoterpenes is highlighted, and preliminary mechanistic experiments reveal that dual (radical and ionic) pathways operate simultaneously.
From the century of the rate equation to the century of the rate constants: a revolution in catalytic kinetics and assisted catalyst design

In the past, rate constants were extracted from rate equations obtained by fitting kinetic data. In the future, they will be calculated by computational chemistry or measured by surface science techniques. They will be used for the start-up of a microkinetic analysis in a combinatorial iteration for the development of optimized catalysts.
Reveel: large-scale population genotyping using low-coverage sequencing data

Motivation Population low-coverage whole-genome sequencing is rapidly emerging as a prominent approach for discovering genomic variation and genotyping a cohort. This approach combines substantially lower cost than full-coverage sequencing with whole-genome discovery of low-allele frequency variants, to an extent that is not possible with array genotyping or exome sequencing. However, a challenging computational problem arises of jointly discovering variants and genotyping the entire cohort. Variant discovery and genotyping are relatively straightforward tasks on a single individual that has been sequenced at high coverage, because the inference decomposes into the independent genotyping of each genomic position for which a sufficient number of confidently mapped reads are available. However, in low-coverage population sequencing, the joint inference requires leveraging the complex linkage disequilibrium (LD) patterns in the cohort to compensate for sparse and missing data in each individual. The potentially massive computation time for such inference, as well as the missing data that confound low-frequency allele discovery, need to be overcome for this approach to become practical. Results Here, we present Reveel, a novel method for single nucleotide variant calling and genotyping of large cohorts that have been sequenced at low coverage. Reveel introduces a novel technique for leveraging LD that deviates from previous Markov-based models, and which is aimed at computational efficiency as well as accuracy in capturing LD patterns present in rare haplotypes. We evaluate Reveel's performance through extensive simulations as well as real data from the 1000 Genomes Project, and show that it achieves higher accuracy in low-frequency allele discovery and substantially lower computation cost than previous state-of-the-art methods. Availability and implementation http://reveel.stanford.edu/ Contact : serafim@cs.stanford.edu Supplementary information Supplementary data are available at Bioinformatics online.
Synthesis of (9S,12S)-cycloisodityrosine and its unnatural (9R,12S)-diastereomer

Abstract A synthesis of the (9 S ,12 S )-cycloisodityrosine derivatives and their unnatural (9 R ,12 S )-diastereomers are disclosed. The approach is based on an intramolecular aromatic nucleophilic substitution reaction for formation of the macrocyclic biaryl ether and includes the documentation of a remarkably facile base-catalyzed epimerization.
Highly Efficient Ring Closure of Aromatic Dialdehydes to Macrocyclic Allenes

The one-pot double deoxygenation of simple alkyl- and polyether-tethered aromatic dialdehydes to give macrocyclic allenes has been accomplished in extraordinarily high yield without the need for slow-addition techniques, using a Ti(IV)-substituted ylide reagent and bis(trimethylsilyl)amide bases. Diastereoselective allene formation occurs when a binaphthyl unit is present in the substrate backbone, and the resulting cyclic allene is characterized by X-ray diffraction. Highly efficient cyclization is proposed to be the result of a combination of preorganization about the amide base counterion and a low concentration of the immediate precursor to Wittig-style olefination ring closure.
Factors Affecting Stereocontrol during Glycosidation of 2,3-Oxazolidinone-Protected 1-Tolylthio-N-acetyl-d-glucosamine

[reaction: see text] It is demonstrated that a ring-fused 2,3-oxazolidinone-protected derivative of 1-tolylthio-N-acetyl-D-glucosamine undergoes high-yield glycosidation under mild donor activation conditions. Stereoselective formation of alpha-linked or beta-linked glycosides is dependent on reactivity of acceptor alcohols, where rate of glycosidation correlates to stereochemical outcome. Evidence for the role of glycosyl triflate intermediates and the N-acetyl substituent of the 2N,3O-oxazolidinone ring in stereochemical control is presented.
Rare-earth nitrides and carbides: A new class of permanent magnet materials

The most recent and exciting development in permanent magnet research is the discovery of rare-earth nitrides and carbides with the 2:17- and l:12- type structures. Nitrogen and carbon enter the lattice interstitially, expanding the volume of the unit cell and leading to a drastic increase in the Curie temperature (up to 300 °C) and to dramatic changes in the magnetic anisotropy. Sm2Fe17N(C))x and Nd(Fe,T)12Nx now have large magnetic anisotropy fields exceeding 9 and 7 T, respectively. Large coercivities have already been obtained in mechanically alloyed powders, melt- spun ribbons, and Zn- bonded Sm2Fe17Nx magnets.
Polyfunctional pyridines from nitroacetamidine and β‐diketones. A useful synthesis of substituted imidazo [4,5‐b] pyridines and related compounds

Nitroacetamidine undergoes a useful cyclocondensation with β-diketones to produce substituted 2-amino-3-nitropyridines. Use of an acylpyruvate generates hitherto unreported 2-amino-3-nitropyridine-4-carboxylates. These may be converted easily to functionalized imidazo[4,5-b]pyridines and oxazolo-[5,4-b]pyridines.
The Meaning of the Fine Structure Constant

A possible explanation is offered for the longstanding mystery surrounding the meaning of the fine structure constant. The reasoning is based on a discrete self-similar cosmological paradigm that has shown promise in explaining the general scaling properties of nature’s global hierarchy. The discrete scale invariance of the paradigm implies that “strong gravity” dominates the dynamical interactions within atomic scale systems. A new atomic scale gravitational coupling constant G(-1) is derived with a value of roughly 10^38 G(0) , where G(0) is the conventional Newtonian gravitational constant. G(-1) is then used to calculate a revised Planck scale. Given G(-1) and the revised Planck mass, one can demonstrate that within the context of the discrete self-similar paradigm the fine structure constant is the ratio of the strengths of the unit electromagnetic interaction and the unit gravitational interaction within atomic scale systems.
TRAIL (CD253) Sensitizes Human Airway Epithelial Cells to Toxin-Induced Cell Death.

ABSTRACT Inhalation of ricin toxin is associated with the onset of acute respiratory distress syndrome (ARDS), characterized by hemorrhage, inflammatory exudates, and tissue edema, as well as the nearly complete destruction of the lung epithelium. Here we report that the Calu-3 human airway epithelial cell line is relatively impervious to the effects of ricin, with little evidence of cell death even upon exposure to microgram amounts of toxin. However, the addition of exogenous soluble tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL; CD253) dramatically sensitized Calu-3 cells to ricin-induced apoptosis. Calu-3 cell killing in response to ricin and TRAIL exposure was partially inhibited by caspase-8 and caspase-3/7 inhibitors, consistent with involvement of extrinsic apoptotic pathways in cell death. We employed nCounter Technology to define the transcriptional response of Calu-3 cells to ricin, TRAIL, and the combination of ricin plus TRAIL. An array of genes associated with inflammation and cell death were significantly upregulated upon treatment with ricin toxin and were further amplified upon addition of TRAIL. Of particular note was interleukin-6 (IL-6), whose expression in Calu-3 cells increased 300-fold upon ricin treatment and more than 750-fold upon ricin and TRAIL treatment. IL-6 secretion by Calu-3 cells was confirmed by cytometric bead array analysis. On the basis of these finding, we speculate that the severe airway epithelial cell damage observed in animal models following ricin exposure is a result of a positive-feedback loop driven by proinflammatory cytokines such as TRAIL and IL-6. IMPORTANCE Ricin toxin is a biothreat agent that is particularly damaging to lung tissue following inhalation. A hallmark of ricin exposure is widespread inflammation and concomitant destruction of the airway epithelium. In this study, we investigated the possible interaction between ricin and known proinflammatory cytokines associated with lung tissue. Using an established human airway epithelial cell line, we demonstrate that epithelial cell killing by ricin is significantly enhanced in the presence of the proinflammatory cytokine known as TRAIL (CD253). Moreover, epithelial cells that are simultaneously exposed to ricin and TRAIL produced large amounts of secondary proinflammatory signals, including IL-6, which in the context of the lung would be expected to exacerbate toxin-induced tissue damage. Our results suggest that therapies designed to neutralize proinflammatory cytokines such as TRAIL and IL-6 may limit the bystander damage associated with ricin exposure.
Orientation of Physisorbed Fluoropropenes on Cu(111)

Fourier transform infrared reflection absorption spectra (FT-IRAS) have been obtained for adsorbed monolayers of propene and a set of fluorinated propenes (CFH2CHCH2, CF3CHCH2, and CF3CFCF2) on the Cu(111) surface. These species interact weakly with the copper surface. The FT-IRAS spectra indicate that the molecules lie flat with the plane of the molecule defined by the CCC atoms essentially parallel to the surface regardless of the degree of fluorination. Quantitative analysis of the orientation of hexafluoropropene determines the tilt of the molecular plane with respect to the surface to be 11°. The results for propene indicate a molecular tilt of 20°. Where the ν(CC) mode can be identified in the spectra of the adsorbed molecules, there is no perturbation of its frequency, which indicates that there is little backdonation between the metal and the π* orbital of the propene.
Substituent effects on the reaction of trityl chlorides with Grignard reagents

Abstract The result of the substitution of trityl chlorides with Grignard reagents was found to be highly dependent on the solvent and the nature of the substituents on the trityl group. In THF, electron donating substituents were found to give high yields of Grignard addition while electron withdrawing substituents were found to give mostly reduction to the corresponding triphenyl methane via hydride abstraction from the solvent.
Microwave irradiated Pd-catalyzed C(sp)–H activation and cross-coupling with styryltrifluoroborates

Effective catalytic effect of PdCl2(dtbpf) on the C–H activation of alkynes and its ability to overcome the limitations of styryltrifluoroborates in cross-coupling reactions by avoiding the effects of the C–X bond on starting materials is developed.
Pan-cancer analysis of transcriptional metabolic dysregulation using The Cancer Genome Atlas

Understanding metabolic dysregulation in different disease settings is vital for the safe and effective incorporation of metabolism-targeted therapeutics in the clinic. Here, using transcriptomic data for 10,704 tumor and normal samples from The Cancer Genome Atlas, across 26 disease sites, we present a novel bioinformatics pipeline that distinguishes tumor from normal tissues, based on differential gene expression for 114 metabolic pathways. We confirm pathway dysregulation in separate patient populations, demonstrating the robustness of our approach. Bootstrapping simulations were then applied to assess the biological significance of these alterations. We provide distinct examples of the types of analysis that can be accomplished with this tool to understand cancer specific metabolic dysregulation, highlighting novel pathways of interest, and patterns of metabolic flux, in both common and rare disease sites. Further, we show that Master Metabolic Transcriptional Regulators explain why metabolic differences exist, can segregate patient populations, and predict responders to different metabolism-targeted therapeutics.
New facile and mild synthesis of 2-substituted oxazolopyridines

Abstract A new, two-step synthesis of oxazolopyridines is described. The synthesis involving amide formation between o -aminopyridinols and aliphatic or aromatic carboxylic acids followed by condensation with hexachloroethane/triphenylphosphine takes place at room temperature and thereby gives mild access to all regioisomeric, 2-substituted oxazolopyridines in good yields.
Are the adverse effects of stressors on amphibians mediated by their effects on stress hormones

Adverse effects of anthropogenic changes on biodiversity might be mediated by their impacts on the stress response of organisms. To test this hypothesis, we crossed exposure to metyrapone, a synthesis inhibitor of the stress hormone corticosterone, with exposure to the herbicide atrazine and the fungal pathogen Batrachochytrium dendrobatidis (Bd) to assess whether the effects of these stressors on tadpoles and post-metamorphic frogs were mediated by corticosterone. Metyrapone countered atrazine- and Bd-induced corticosterone elevations. However, atrazine- and Bd-induced reductions in body size were not mediated by corticosterone because they persisted despite metyrapone exposure. Atrazine lowered Bd abundance without metyrapone but increased Bd abundance with metyrapone for tadpoles and frogs. In contrast, atrazine reduced tolerance of Bd infections because frogs exposed to atrazine as tadpoles had reduced growth with Bd compared to solvent controls; this effect was not countered by metyrapone. Our results suggest that the adverse effects of atrazine and Bd on amphibian growth, development, and tolerance of infection are not mediated primarily by corticosterone. A possible mechanism for these effects is energy lost from atrazine detoxification, defense against Bd, or repair from damage caused by atrazine and Bd. Additional studies are needed to evaluate how often the effects of anthropogenic stressors are mediated by stress hormones.
Palladium-Induced Cyclizations for the Synthesis of cis-2,5-Disubstituted-3- methylenetetrahydrofurans: Studies of the C7−C22 Core of Amphidinolide K

[formula: see text] The diastereoselective synthesis of cis-2,5-disubstituted-3-methylenetetrahydrofurans via Pd(0)-catalyzed cyclization of 2-methylene-1,4-diols is described. Investigations into the scope of the reaction and its application toward the synthesis of amphidinolide K is reported.
On the Construction of Knots and Links from Thompson’s Groups

We review recent developments in the theory of Thompson group representations related to knot theory.
ASYMPTOTIC SHAPES FOR ERGODIC FAMILIES OF METRICS ON NILPOTENT GROUPS

Let be a finitely generated nilpotent group. We consider thr ee closely related prob- lems: (i) the asymptotic cone for an equivariant ergodic family of inner metrics on , generalizing Pansu's theorem; (ii) the limit shapes for First Passage Percolation for general (not necessarily independent) ergodic process on edges of a Cayley graph of ; (iii) a sub-additive ergodic theorem over a general ergodic -action. The limiting objects are gi ven in terms of a Carnot-Caratheodory metric on the graded nilpotent group associated to the Mal'cev completion of . 1. Introduction and statement of the main results Let be a finitely generated nilpotent group. The topic of thi s paper may be viewed from three slightly different perspectives: (i) As a generalization of the result of Pansu (12) showing that the asymptotic cone of an inner right-invariant metric d on is the graded nilpotent Lie group G∞ (associated with the Mal'cev completion G of ) equipped with a certain Carnot-Caratheodory metric d∞. Here we show that if one replaces a single invariant metric d by an equivariant ergodic family {dx | x ∈ X} of inner metrics on , then a.e. ( ,dx,e) has the same asymptotic cone which is the graded nilpotent Lie group G∞ equipped with a fixed Carnot-Caratheodory metric associated to certain averages of the family {dx | x ∈ X}. (ii) As a result about asymptotic shape for First Passage Percolation model over driven by a general ergodic process y (X,m). (The case of independent times was recently studied by Benjamini and Tessera (2)). (iii) As a Subadditive Ergodic Theorem over a general ergodic probability measure preserving (hereafter p.m.p.) action y (X,m). Given a measurable function c : × X → R, satisfying
A new stable peer-to-peer protocol with non-persistent peers

Recent studies have suggested that the stability of peer-to-peer networks may rely on persistent peers, who dwell on the network after they obtain the entire file. In the absence of such peers, one piece becomes extremely rare in the network, which leads to instability. Technological developments, however, are poised to reduce the incidence of persistent peers, giving rise to a need for a protocol that guarantees stability with nonpersistent peers. We propose a novel peer-to-peer protocol, the group suppression protocol, to ensure the stability of peer-to-peer networks under the scenario that all the peers adopt non-persistent behavior. Using a suitable Lyapunov potential function, the group suppression protocol is proven to be stable when the file is broken into two pieces, and detailed experiments demonstrate the stability of the protocol for arbitrary number of pieces. Straightforward incorporation of the group suppression protocol into BitTorrent while retaining most of BitTorrent's core mechanisms is also presented. Subsequent simulations show that under certain assumptions, BitTorrent with the official protocol cannot escape from the missing piece syndrome, but BitTorrent with group suppression does.
Numerical Modeling of Pulse Wave Propagation in a Stenosed Artery using Two-Way Coupled Fluid Structure Interaction (FSI)

As the heart beats, it creates fluctuation in blood pressure leading to a pulse wave that propagates by displacing the arterial wall. These waves travel through the arterial tree and carry information about the medium that they propagate through as well as information of the geometry of the arterial tree. Pulse wave velocity (PWV) can be used as a non-invasive diagnostic tool to study the functioning of cardiovascular system. A stenosis in an artery can dampen the pulse wave leading to changes in the propagating pulse. Hence, PWV analysis can be performed to detect a stenosed region in arteries. This paper presents a numerical study of pulse wave propagation in a stenosed artery by means of two-way coupled fluid structure interaction (FSI). The computational model was validated by the comparison of the simulated PWV results with theoretical values for a healthy artery. Propagation of the pulse waves in the stenosed artery was compared with healthy case using spatiotemporal maps of wall displacements. The analysis for PWV showed significance differences between the healthy and stenosed arteries including damping of propagating waves and generation of high wall displacements downstream the stenosis caused by flow instabilities. This approach can be used to develop patient-specific models that are capable of predicting PWV signatures associated with stenosis changes. The knowledge gained from these models may increase utility of this approach for managing patients at risk of stenosis occurrence.
Nonlinear large deviations

Abstract We present a general technique for computing large deviations of nonlinear functions of independent Bernoulli random variables. The method is applied to compute the large deviation rate functions for subgraph counts in sparse random graphs. Previous technology, based on Szemeredi's regularity lemma, works only for dense graphs. Applications are also made to exponential random graphs and three-term arithmetic progressions in random sets of integers.
Syzygies of the apolar ideals of the determinant and permanent

We investigate the space of syzygies of the apolar ideals $${\text {det}}_n^\perp $$ and $${\mathrm{perm}}_n^\perp $$ of the determinant $${\text {det}}_n$$ and permanent $${\mathrm{perm}}_n$$ polynomials. Shafiei had proved that these ideals are generated by quadrics and provided a minimal generating set. Extending on her work, in characteristic distinct from two, we prove that the space of relations of $${\text {det}}_n^{\perp }$$ is generated by linear relations and we describe a minimal generating set. The linear relations of $${\mathrm{perm}}_n^{\perp }$$ do not generate all relations, but we provide a minimal generating set of linear and quadratic relations. For both $${\text {det}}_n^\perp $$ and $${\mathrm{perm}}_n^\perp $$, we give formulas for the Betti numbers $$\beta _{1,j}$$, $$\beta _{2,j}$$ and $$\beta _{3,4}$$ for all j as well as conjectural descriptions of other Betti numbers. Finally, we provide representation-theoretic descriptions of certain spaces of linear syzygies.
Active Covariance Estimation by Random Sub-Sampling of Variables

We study covariance matrix estimation for the case of partially observed random vectors, where different samples contain different subsets of vector coordinates. Each observation is the product of the variable of interest with a 0 − 1 Bernoulli random variable. We analyze an unbiased covariance estimator under this model, and derive an error bound that reveals relations between the sub-sampling probabilities and the entries of the covariance matrix. We apply our analysis in an active learning framework, where the expected number of observed variables is small compared to the dimension of the vector of interest, and propose a design of optimal sub-sampling probabilities and an active covariance matrix estimation algorithm.
Dark galactic halos without dark matter

Using standard Einstein theory, baryonic mass cannot account for observed galactic rotation velocities and gravitational lensing, attributed to galactic dark-matter halos. In contrast, theory constrained by Weyl conformal scaling symmetry explains observed galactic rotation in the halo region without invoking dark matter. An explanation of dark halos, gravitational lensing, and structural stabilization, without dark matter and consistent with conformal theory, is proposed here. Condensation of uniform primordial matter into a material cloud or galaxy vacates a large surrounding spherical halo. Within such an extended vacancy in the original cosmic background mass-energy density, conformal theory predicts centripetal acceleration of the observed magnitude.
Galois coverings of pointed coalgebras

We introduce the concept of a Galois covering of a pointed coalgebra. The theory developed shows that Galois coverings of pointed coalgebras can be concretely expressed by smash coproducts using the coaction of the automorphism group of the covering. Thus the theory of Galois coverings is seen to be equivalent to group gradings of coalgebras. An advantageous feature of the coalgebra theory is that neither the grading group nor the quiver is assumed finite in order to obtain a smash product coalgebra.
Deep embedding kernel

Abstract In this paper, we propose a novel supervised learning method that is called Deep Embedding Kernel (DEK). DEK combines the advantages of deep learning and kernel methods in a unified framework. More specifically, DEK is a learnable kernel represented by a newly designed deep architecture. Compared with predefined kernels, this kernel can be explicitly trained to map data to an optimized high-level feature space where data may have favorable features toward the application. Compared with typical deep learning using SoftMax or logistic regression as the top layer, DEK is expected to be more generalizable to new data. Experimental results show that DEK has superior performance than typical machine learning methods in identity detection and classification, and transfer learning, on different types of data including images, sequences, and regularly structured data.
A Linear Dynamical System Model for Text

Low dimensional representations of words allow accurate NLP models to be trained on limited annotated data. While most representations ignore words' local context, a natural way to induce context-dependent representations is to perform inference in a probabilistic latent-variable sequence model. Given the recent success of continuous vector space word representations, we provide such an inference procedure for continuous states, where words' representations are given by the posterior mean of a linear dynamical system. Here, efficient inference can be performed using Kalman filtering. Our learning algorithm is extremely scalable, operating on simple cooccurrence counts for both parameter initialization using the method of moments and subsequent iterations of EM. In our experiments, we employ our inferred word embeddings as features in standard tagging tasks, obtaining significant accuracy improvements. Finally, the Kalman filter updates can be seen as a linear recurrent neural network. We demonstrate that using the parameters of our model to initialize a non-linear recurrent neural network language model reduces its training time by a day and yields lower perplexity.
Real classes of finite special unitary groups

We classify all real and strongly real classes of the finite special unitary group SUn(q). Unless q ≡ 3(mod 4) and n|4, the classification of real classes is similar to that of the finite special linear group SLn(q). We relate strong reality in SUn(q) to strong reality in the finite special orthogonal groups SO± n (q), and we classify real and strongly real classes in the last case for the group SO± n (q), when q is odd and n ≡ 2(mod 4). 2010 Mathematics Subject Classification: 20G40, 20E45
Metallicity of Ca2Cu6P5 with single and double copper-pnictide layers

Abstract We report thermodynamic and transport properties, and also theoretical calculations, for Cu-based compound Ca 2 Cu 6 P 5 and compare with CaCu 2-δ P 2 . Both materials have layers of edge-sharing copper pnictide tetrahedral CuP 4 , similar to Fe–As and Fe–Se layers (with FeAs 4 , FeSe 4 ) in the iron-based superconductors. Despite the presence of this similar transition-metal pnictide layer, we find that both Ca 2 Cu 6 P 5 and CaCu 2-δ P 2 have temperature-independent magnetic susceptibility and show metallic behavior with no evidence of either magnetic ordering or superconductivity down to 1.8 K CaCu 2-δ P 2 is slightly off-stoichiometric, with δ = 0.14. Theoretical calculations suggest that unlike Fe 3 d -based magnetic materials with a large density of states (DOS) at the Fermi surface, Cu have comparatively low DOS, with the majority of the 3 d spectral weight located well below Fermi level. The room-temperature resistivity value of Ca 2 Cu 6 P 5 is only 9 μΩ-cm, due to a substantial plasma frequency and an inferred electron-phonon coupling λ of 0.073 (significantly smaller than that of metallic Cu). Also, microscopy result shows that Cu–Cu distance along the c -axis within the double layers can be very short (2.5 A), even shorter than metallic elemental copper bond (2.56 A). The value of dρ/dT for CaCu 2-δ P 2 at 300 K is approximately three times larger than in Ca 2 Cu 6 P 5 , which suggests the likelihood of stronger electron-phonon coupling. This study shows that the details of Cu–P layers and bonding are important for their transport characteristics. In addition, it emphasizes the remarkable character of the DOS of ‘122’ iron-based materials, despite much structural similarities.
Asymptotic behavior of Allen–Cahn-type energies and Neumann eigenvalues via inner variations

We use the notion of first and second inner variations as a bridge allowing one to pass to the limit of first and second Gateaux variations for the Allen–Cahn, Cahn–Hilliard and Ohta–Kawasaki energies. Under suitable assumptions, this allows us to show that stability passes to the sharp interface limit, including boundary terms, by considering noncompactly supported velocity and acceleration fields in our variations. This complements the results of Tonegawa, and Tonegawa and Wickramasekera, where interior stability is shown to pass to the limit. As a further application, we prove an asymptotic upper bound on the $$k\mathrm{th}$$ Neumann eigenvalue of the linearization of the Allen–Cahn operator, relating it to the $$k\mathrm{th}$$ Robin eigenvalue of the Jacobi operator, taken with respect to the minimal surface arising as the asymptotic location of the zero set of the Allen–Cahn critical points. We also prove analogous results for eigenvalues of the linearized operators arising in the Cahn–Hilliard and Ohta–Kawasaki settings. These complement the earlier result of the first author where such an asymptotic upper bound is achieved for Dirichlet eigenvalues for the linearized Allen–Cahn operator. Our asymptotic upper bound on Allen–Cahn Neumann eigenvalues extends, in one direction, the asymptotic equivalence of these eigenvalues established in the work of Kowalczyk in the two-dimensional case where the minimal surface is a line segment and specific Allen–Cahn critical points are suitably constructed.
Making Space to Sensemake: Epistemic Distancing in Small Group Physics Discussions

Students in inquiry science classrooms face an essential tension between sharing new ideas and critically evaluating those ideas. This tension poses affective risks that can discourage further disc...
High-temperature scaling limit for directed polymers on a hierarchical lattice with bond disorder

Diamond “lattices” are sequences of recursively-defined graphs that provide a network of directed pathways between two fixed root nodes, A and B. The construction recipe for diamond graphs depends on a branching number $$b\in {\mathbb {N}}$$ and a segmenting number $$s\in {\mathbb {N}}$$ , for which a larger value of the ratio s / b intuitively corresponds to more opportunities for intersections between two randomly chosen paths. By attaching i.i.d. random variables to the bonds of the graphs, we construct a random Gibbs measure on the set of directed paths by assigning each path an “energy” through summing the random variables along the path. For the case $$b=s$$ , we propose a scaling regime in which the temperature grows along with the number of hierarchical layers of the graphs, and the partition function (the normalization factor of the Gibbs measure) appears to converge in law. We prove that all of the positive integer moments of the partition function converge in this limiting regime. The motivation of this work is to prove a functional limit theorem that is analogous to a previous result obtained in the $$b<s$$ case.
Quasilocal angular momentum and center of mass in general relativity

For a spacelike 2-surface in spacetime, we propose a new definition of quasi-local angular momentum and quasi-local center of mass, as an element in the dual space of the Lie algebra of the Lorentz group. Together with previous defined quasi-local energy-momentum, this completes the definition of conserved quantities in general relativity at the quasi-local level. We justify this definition by showing the consistency with the theory of special relativity and expectations on an axially symmetric spacetime. The limits at spatial infinity provide new definitions for total conserved quantities of an isolated system, which do not depend on any asymptotically flat coordinate system or asymptotic Killing field. The new proposal is free of ambiguities found in existing definitions and presents the first definition that precisely describes the dynamics of the Einstein equation.
Analysis of weighted Laplacian and applications to Ricci solitons

We study both function theoretic and spectral properties of the weighted Laplacian ∆f on complete smooth metric measure space (M, g, e dv) with its Bakry-Emery curvature Ricf bounded from below by a constant. In particular, we establish a gradient estimate for positive f−harmonic functions and a sharp upper bound of the bottom spectrum of ∆f in terms of the lower bound of Ricf and the linear growth rate of f. We also address the rigidity issue when the bottom spectrum achieves its optimal upper bound under a slightly stronger assumption that the gradient of f is bounded. Applications to the study of the geometry and topology of gradient Ricci solitons are also considered. Among other things, it is shown that the volume of a noncompact shrinking Ricci soliton must be of at least linear growth. It is also shown that a nontrivial expanding Ricci soliton must be connected at infinity provided its scalar curvature satisfies a suitable lower bound.