cssi/SciSciGPT-SciSciNet huggingface dataset:
Synthesis of an s‐butyldibenz[a,h]acridine. Alkyl migration in the bernthsen reaction

The Bernthsen reaction between N-1-naphthyl-2-naphthylamine and 2-methylbutanoic acid and its anhydride at 200-230 o for seven hours gives a low yield of 12- or 13-s-butyldibenz[a,h]acridine, instead of the expected 14-isomer. The parent molecule dibenz[a,h]acridine results from the same reaction conducted at 270 o for thirteen hours. It is suggested that alkyl migration may have occurred in some other cases where the Bernthsen reaction was reported to yield 14-alkyldibenz[a,h]acridines
Neural Illumination: Lighting Prediction for Indoor Environments

This paper addresses the task of estimating the light arriving from all directions to a 3D point observed at a selected pixel in an RGB image. This task is challenging because it requires predicting a mapping from a partial RGB observation by a camera to a complete illumination map for a different 3D point, which depends on the 3D location of the selected pixel, the distribution of unobserved light sources, the occlusions by scene geometry, etc. Previous methods attempt to learn this complex mapping directly using a single black-box neural network which often fails to estimate high-frequency lighting details for scenes with complicated 3D geometry. Instead, we propose "Neural Illumination," a new approach that decomposes illumination prediction into several simpler differentiable sub-tasks: 1) geometry estimation, 2) scene completion, and 3) LDR-to-HDR estimation. The advantage of this approach is that the sub-tasks are relatively easy to learn and can be trained with direct supervision, while the whole pipeline is fully differentiable and can be fine-tuned with end-to-end supervision. Experiments show that our approach performs significantly better quantitatively and qualitatively than prior work.
Analysis of deep learning methods for blind protein contact prediction in CASP12.

Here we present the results of protein contact prediction achieved in CASP12 by our RaptorX-Contact server, which is an early implementation of our deep learning method for contact prediction. On a set of 38 free-modeling target domains with a median family size of around 58 effective sequences, our server obtained an average top L/5 long- and medium-range contact accuracy of 47% and 44%, respectively (L = length). A complete implementation has an average accuracy of 59% and 57%, respectively. Our deep learning method formulates contact prediction as a pixel-level image labeling problem and simultaneously predicts all residue pairs of a protein using a combination of two deep residual neural networks, taking as input the residue conservation information, predicted secondary structure and solvent accessibility, contact potential, and coevolution information. Our approach differs from existing methods mainly in (1) formulating contact prediction as a pixel-level image labeling problem instead of an image-level classification problem; (2) simultaneously predicting all contacts of an individual protein to make effective use of contact occurrence patterns; and (3) integrating both one-dimensional and two-dimensional deep convolutional neural networks to effectively learn complex sequence-structure relationship including high-order residue correlation. This paper discusses the RaptorX-Contact pipeline, both contact prediction and contact-based folding results, and finally the strength and weakness of our method.
Fragmentation of the Fluorite Type in Fe8Al17.4Si7.6: Structural Complexity in Intermetallics Dictated by the 18 Electron Rule

This Article presents the synthesis, structure determination, and bonding analysis of Fe8Al17.4Si7.6. Fe8Al17.4Si7.6 crystallizes in a new monoclinic structure type based on columns of the fluorite (CaF2) structure type. As such, the compound can be seen as part of a structural series in which the fluorite structure—adopted by several transition metal disilicides (TMSi2)—is fragmented by the incorporation of Al. Electronic structure analysis using density functional theory (DFT) and DFT-calibrated Huckel calculations indicates that the fluorite-type TMSi2 phases (TM = Co, Ni) exhibit density of states (DOS) pseudogaps near their Fermi energies. An analogous pseudogap occurs for Fe8Al17.4Si7.6, revealing that its complex structure serves to preserve this stabilizing feature of the electronic structure. Pursuing the origins of these pseudogaps leads to a simple picture: the DOS minimum in the TMSi2 structures arises via a bonding scheme analogous to those of 18 electron transition metal complexes. Replaceme...
4-Azido-2-pyrimidinone Nucleosides and Related Chemistry.

As a part of azide prodrug approach, we synthesized a 4-azido analog of ara-C (4) as a prodrug for ara-C. The compound 4 was obtained from 1-(β-d-arabinofuranosyl)uracil (1) in three steps. At pH 7.0 and 11.0, a loss of UV absorption of the compound 4 was observed resulting from a transformation that was proved by identifying the transformed product 5 by 1-D, and 2-D NMR as well as tandem mass spectral studies. In NMR studies, changes in the chemical shifts were observed at positions 5, 6, 1‘, and 2‘ between the compounds 4 and 5. A molecular peak at m/z 270.1 (MH+) was observed in the mass spectra of compounds 4 and the transformed product 5. A fragment at 180.2 was identified to be the compound 6, containing the 6,2‘-anhydro linkage of compound 5. The X-ray analysis indicated that compound 4 exists as 1-(β-d-arabinofuranosyl)tetrazolo[4,5-c]pyrimidin-2-one, with the azide moiety cyclized. To understand if the chemical instability of the nucleoside 4 was due to the arabino configuration of 2‘-OH or due t...
Neuronal population mechanisms of lightness perception.

A core question in visual neuroscience is how the brain extracts stable representations of object properties from the retinal image. We searched for a neuronal mechanism of lightness perception by ...
Synthesis and characterization of the face-sharing bioctahedral [Mo2O6F3]3- anion.

The face-sharing bioctahedral molybdenum(VI) oxide fluoride anion [Mo 2 O 6 F 3 ] 3 - has been isolated in the new compound [Cu(3-apy) 4 ] 3 (Mo 2 O 6 F 3 ) 2 (3-apy = 3-aminopyridine) and has been characterized by experimental and computational techniques. Single-crystal X-ray diffraction studies show that the structure of the [Mo 2 O 6 F 3 ] 3 - anion resembles two distorted face-sharing octahedra, each with three short terminal metal-ligand bonds and three long metal-ligand-metal bridging interactions. Aspects of the electronic structure, as well as geometric comparisons of the bond lengths and angles in [Mo 2 O 6 F 3 ] 3 - with those in the similarly distorted [MoO 3 F 3 ] 3 - anion, suggest that the six terminal ligand positions of the confacial bioctahedra are occupied exclusively by oxide ligands and that the three bridging sites are occupied by fluorides. Crystal data for [Cu(3-apy) 4 ] 3 (Mo 2 O 6 F 3 ) 2 : trigonal space group R3 (No. 148) with hexagonal axes of a = 13.881(1) A and c = 31.783(3) A (Z = 3).
Conjugate addition of unactivated thiols to α,β-unsaturated ketones catalyzed by a bifunctional rhenium(V)–oxo complex

Abstract ReOCl3(OPPh3)(S(CH3)2) has been found to be an efficient bifunctional catalyst for the 1,4-addition of thiols to α,β-unsaturated ketones. The addition of thiophenol derivatives and alkyl thiols proceeds under mild reaction conditions without pre-activation of the thiol or exogenous base. Reactions of aryl, alkyl, and cyclic enones produce the corresponding β-sulfanyl ketones in good to excellent yield.
The synthesis of cis‐6,12‐Diaryl‐6H,12H‐dibenzo[b,f][1,5]dithiocin‐6,12‐imine and cis‐6,12‐Diphenyl‐6,12‐epoxy‐6H,12H‐dibenzo[b,f][1,5]dithiocin

When treated with concentrated hydrochloric acid or heated beyond its melting point, the versatile thioimine 2 2-mercaptobenzhydrylidenamine was unexpectedly converted to the title ring system. Also, this imine can be converted to 3-phenyl-1,2-benzisothiazoles by prolonged exposure to air.
2-[(Alkylsulfonyl)oxy]-6-substituted-1H-isoindole-1,3(2H)-dione mechanism-based inhibitors of human leukocyte elastase

Abstract Derivatives of 2-[(alkylsulfonyl)oxy]-1H-isoindole-1,3(2H)-diones (N-(sulfonyloxy)phthalimides) with ring substituents in the 6-position were found to exhibit enhanced inhibitory potency and selectivity for HLE. The most potent inhibitor of HLE in this series was 6-amino-2-[(methylsulfonyl)oxy]-1H-isoindole-1,3(2H)-dione10 with a k obs [I] of 110,000 M−1 s−1.
Phenomenology of Water Adsorption at Clay Surfaces

This chapter discusses phenomenology of water adsorption at clay surfaces. Clays are some of the most important minerals in many diverse uses. Indeed, clays and clay minerals are important in myths, art, medicine, agriculture, construction, engineering, process industries, and environmental applications. However, in basic, clays can be considered as part of a few great crystallographic families. Clays are lamellar aluminosilicates showing a wide variety of chemical effects, when put in contact with water; for instance dissolution, hydroxylation, fracture, delamination, and electrification. Many physicochemical phenomena limited to surfaces are also observed: adsorption, swelling (adsorption can be considered as a step in the swelling process), ionization, ionic exchange, and surface acidity. In surface thermodynamics, the extensive term is the surface area, and the intensive term is then the energy per unit of surface area. Unfortunately, the thermodynamic definitions are dependent on the volume of the spatial zone defined as the “surface” when analyzing the problem.
A Generalized Brezing-Weng Algorithm for Constructing Pairing-Friendly Ordinary Abelian Varieties.

We give an algorithm that produces families of Weil numbers for ordinary abelian varieties over finite fields with prescribed embedding degree. The algorithm uses the ideas of Freeman, Stevenhagen, and Streng to generalize the Brezing-Weng construction of pairing-friendly elliptic curves. We discuss how CM methods can be used to construct these varieties, and we use our algorithm to give examples of pairing-friendly ordinary abelian varieties of dimension 2 and 3 that are absolutely simple and have smaller ρ-values than any previous such example.
Curated compendium of human transcriptional biomarker data.

One important use of genome-wide transcriptional profiles is to identify relationships between transcription levels and patient outcomes. These translational insights can guide the development of biomarkers for clinical application. Data from thousands of translational-biomarker studies have been deposited in public repositories, enabling reuse. However, data-reuse efforts require considerable time and expertise because transcriptional data are generated using heterogeneous profiling technologies, preprocessed using diverse normalization procedures, and annotated in non-standard ways. To address this problem, we curated 45 publicly available, translational-biomarker datasets from a variety of human diseases. To increase the data's utility, we reprocessed the raw expression data using a uniform computational pipeline, addressed quality-control problems, mapped the clinical annotations to a controlled vocabulary, and prepared consistently structured, analysis-ready data files. These data, along with scripts we used to prepare the data, are available in a public repository. We believe these data will be particularly useful to researchers seeking to perform benchmarking studies—for example, to compare and optimize machine-learning algorithms' ability to predict biomedical outcomes. Machine-accessible metadata file describing the reported data (ISA-Tab format)
A Solid-State Metathesis Route to MgSiN2

Nitrides, such as magnesium silicon nitride, hold promise for applications requiring materials with high thermal conductivity. The synthesis of the ternary nitride MgSiN2 is accomplished using SiO2 and Mg3N2 as reactants in a solid-state metathesis (exchange) reaction. This self-propagating reaction is readily initiated when a flame with a temperature ≥1100 °C is brought into contact with a pressed SiO2/Mg3N2 pellet. By using Mg3N2 in ≥1 M excess, X-ray-pure MgSiN2 can be produced. With lower ratios, elemental silicon forms as an impurity. Increasing the flame initiation temperature to ≥2500 °C can also be used to eliminate silicon impurities with the benefit of increasing the crystallinity of the product. The use of other forms of silica as a silicon source provides an inexpensive alternative to produce MgSiN2. A variety of silica sources are examined, including fumed silica, sand, ground quartz, bottle glass, and rice hull ash. Since rice hull ash is an industrial waste product from rice processing, new...
Synthesis, structure, and NMR characterization of a novel [3.3] metacyclophane

The synthesis and crystal structure of metacyclophane 2 are reported. The nmr data relevant to conformational properties are also presented.
Rearrangement pathways of the tricyclo[4.1.0.01,3]heptyl skeleton

Abstract Syn - and anti -1-methyltricyclo[4.1.0.0 4,6 ]heptan-2-ol derivatives ( 4a and 4b ) have been prepared. Their buffered solvolyses in anhydrous 2,2,2-trifluoroethanol were studied. Anti dinitrobenzoate 4a solvolyzes to give mainly m -xylene and two trifluoroethyl ethers ( 5 and 6 ). Solvolysis of the syn mesylate 4b gives 6-methyl-1-(2,2,2-trifluoroethoxy)tricyclo[4.1.0.0 3,5 ]heptane ( 7 ), the product of a solvent trapped cyclopropyl cation.
HIV-1 Env gp41 Transmembrane Domain Dynamics Are Modulated by Lipid, Water, and Ion Interactions.

The gp41 transmembrane domain (TMD) of the envelope glycoprotein of the human immunodeficiency virus modulates the conformation of the viral envelope spike, the only druggable target on the surface of the virion. Targeting the envelope glycoprotein with small-molecule and antibody therapies requires an understanding of gp41 TMD dynamics, which is often challenging given the difficulties in describing native membrane properties. Here, atomistic molecular dynamics simulations of a trimeric, prefusion gp41 TMD in a model, asymmetric viral membrane that mimics the native viral envelope were performed. Water and chloride ions were observed to permeate the membrane and interact with the highly conserved arginine bundle, (R696)3, at the center of the membrane and influenced TMD stability by creating a network of hydrogen bonds and electrostatic interactions. We propose that this (R696)3 - water - anion network plays an important role in viral fusion with the host cell by modulating protein conformational changes within the membrane. Additionally, R683 and R707 at the exofacial and cytofacial membrane-water interfaces, respectively, are anchored in the lipid headgroup region and serve as a junction point for stabilization of the termini. The membrane thins as a result of the tilting of the gp41 trimer with nearby lipids increasing in volume, leading to an entropic driving force for TMD conformational change. These results provide additional detail and perspective on the influence of certain lipid types on TMD dynamics and a rationale for targeting key residues of the TMD for therapeutic design. These insights into the molecular details of TMD membrane anchoring will build toward a greater understanding of the dynamics that lead to viral fusion with the host cell.
An invariants-based method for efficient identification of hybrid species from large-scale genomic data.

Coalescent-based species tree inference has become widely used in the analysis of genome-scale multilocus and SNP datasets when the goal is inference of a species-level phylogeny. However, numerous evolutionary processes are known to violate the assumptions of a coalescence-only model and complicate inference of the species tree. One such process is hybrid speciation, in which a species shares its ancestry with two distinct species. Although many methods have been proposed to detect hybrid speciation, only a few have considered both hybridization and coalescence in a unified framework, and these are generally limited to the setting in which putative hybrid species must be identified in advance. Here we propose a method that can examine genome-scale data for a large number of taxa and detect those taxa that may have arisen via hybridization, as well as their potential “parental” taxa. The method is based on a model that considers both coalescence and hybridization together, and uses phylogenetic invariants to construct a test that scales well in terms of computational time for both the number of taxa and the amount of sequence data. We test the method using simulated data for up 20 taxa and 100,000bp, and find that the method accurately identifies both recent and ancient hybrid species in less than 30 s. We apply the method to two empirical datasets, one composed of Sistrurus rattlesnakes for which hybrid speciation is not supported by previous work, and one consisting of several species of Heliconius butterflies for which some evidence of hybrid speciation has been previously found. The proposed method is powerful for detecting hybridization for both recent and ancient hybridization events. The computations required can be carried out rapidly for a large number of sequences using genome-scale data, and the method is appropriate for both SNP and multilocus data.
Regioselective Barbier reactions of 2-bromomethylcyclohexenone

Abstract Although the addition of crotyl or prenyl organometallic reagents has certainly found application in organic synthesis, the use of other non-symmetric allylic organometallic reagents has not received much attention. In part this is due to potential problems in controlling the regioselectivity of the addition products. We have noted that the tin and zinc reagents derived from 2-bromomethylcyclohexenone afford the complementary α and γ addition products, respectively. These conditions work for the reaction with a range of aldehydes, affording the products in good to modest yield.
A novel approach for total synthesis of cryptophycins via asymmetric crotylboration protocol

Abstract Acyclic and a highly efficient stereoselective C C bond formation of aldehyde 3 with the crotylboron reagent 4 , derived from (−)-α-pinene, provided a homoallylic alcohol 6 in ≥99% enantio-(ee) and diastereomeric excess (de). The alcohol 6 was linearly converted into the desired Fragment A 10 of cryptophycins in seven steps. This enantiomerically pure Fragment A was conveniently and efficiently coupled with the other three fragments, namely B, C and D, and provided the desired cryptophycin A derivative ( LY404291 ). The terminal double bond in LY404291 was further elaborated to provide a terminal epoxide LY404292 , and cryptophycins 51 and 52 .
The Effect of Orbital Configuration on the Possible Climates and Habitability of Kepler-62f

Abstract As lower-mass stars often host multiple rocky planets, gravitational interactions among planets can have significant effects on climate and habitability over long timescales. Here we explore a specific case, Kepler-62f (Borucki et al., 2013), a potentially habitable planet in a five-planet system with a K2V host star. N-body integrations reveal the stable range of initial eccentricities for Kepler-62f is 0.00 ≤ e ≤ 0.32, absent the effect of additional, undetected planets. We simulate the tidal evolution of Kepler-62f in this range and find that, for certain assumptions, the planet can be locked in a synchronous rotation state. Simulations using the 3-D Laboratoire de Meteorologie Dynamique (LMD) Generic global climate model (GCM) indicate that the surface habitability of this planet is sensitive to orbital configuration. With 3 bar of CO2 in its atmosphere, we find that Kepler-62f would only be warm enough for surface liquid water at the upper limit of this eccentricity range, providing it has a...
Synthesis of monomeric and oligomeric naphtho- and biaryl-fused 1,8-diaza-14-crown-4 macrocycles

Abstract Efficient syntheses of naphtho- and biaryl-fused 1,8-diaza-14-crown-4 macrocycles 4a, 4b, 7a , and 7b and related oligomeric systems 11 and 15 are described. An X-ray structure determination for the N,N -dicyanomethyl substituted macrocycle 8 is reported.
Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding

RNA folding during transcription directs an order of folding that can determine RNA structure and function. However, the experimental study of cotranscriptional RNA folding has been limited by the lack of easily approachable methods that can interrogate nascent RNA structure at nucleotide resolution. To address this, we previously developed cotranscriptional selective 2΄-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) to simultaneously probe all intermediate RNA transcripts during transcription by stalling elongation complexes at catalytically dead EcoRIE111Q roadblocks. While effective, the distribution of elongation complexes using EcoRIE111Q requires laborious PCR using many different oligonucleotides for each sequence analyzed. Here, we improve the broad applicability of cotranscriptional SHAPE-Seq by developing a sequence-independent biotin-streptavidin (SAv) roadblocking strategy that simplifies the preparation of roadblocking DNA templates. We first determine the properties of biotin-SAv roadblocks. We then show that randomly distributed biotin-SAv roadblocks can be used in cotranscriptional SHAPE-Seq experiments to identify the same RNA structural transitions related to a riboswitch decision-making process that we previously identified using EcoRIE111Q. Lastly, we find that EcoRIE111Q maps nascent RNA structure to specific transcript lengths more precisely than biotin-SAv and propose guidelines to leverage the complementary strengths of each transcription roadblock in cotranscriptional SHAPE-Seq.
Stereocontrolled 1,3-dipolar cycloadditions using Oppolzer's camphor sultam as the chiral auxiliary for carbonyl stabilized azomethine ylides

Abstract Two complementary approaches to substituted pyrrolidines via stereocontrolled 1,3-dipolar cycloaddition reactions of chiral azomethine ylides are described. In one approach, chiral azomethine ylides were generated by thermolysis of aziridine carboxylate sultams and trapped with a variety of dipolarophiles to give good yields of the corresponding cycloadducts. In the second approach, chiral azomethine ylides were generated from glycyl sultams by ‘imine tautomerization’ and trapped with dipolarophiles to give good yields of the corresponding cycloadducts.
PerspectroScope: A Window to the World of Diverse Perspectives.

This work presents PerspectroScope, a web-based system which lets users query a discussion-worthy natural language claim, and extract and visualize various perspectives in support or against the claim, along with evidence supporting each perspective. The system thus lets users explore various perspectives that could touch upon aspects of the issue at hand.The system is built as a combination of retrieval engines and learned textual-entailment-like classifiers built using a few recent developments in natural language understanding. To make the system more adaptive, expand its coverage, and improve its decisions over time, our platform employs various mechanisms to get corrections from the users. PerspectroScope is available at github.com/CogComp/perspectroscope Web demo link: http://orwell.seas.upenn.edu:4002/ Link to demo video: https://www.youtube.com/watch?v=MXBTR1Sp3Bs
Synthesis of 2-phenyl-2-cycloalkenones via palladium-catalyzed tandem epoxide isomerization-intramolecular aldol condensation

We have extended the scope of our palladium-catalyzed tandem epoxide isomerization/aldol condensation reaction to encompass intramolecular condensations, which provide facile access to conjugated cycloalkenones from epoxy aldehydes or diepoxides. For example, reaction of 5,6-epoxy-6-phenylhexanal with Pd(OAc)2-PBu3 catalyst in the presence of NaHCO3 and 3A molecular sieves forms 2-phenyl-2-cyclopentenone (80%). Similarly, 1,2;5,6-diepoxy-1-phenylhexane affords 3-methyl-2-phenyl-2-cyclopentenone (72%). The observation of dicarbonyl intermediates (e.g., 1-phenyl-2,5-hexanedione in the latter case) demonstrates that the reaction proceeds via Pd-catalyzed isomerization of the diepoxide to the diketone, followed by base-catalyzed aldol condensation.
Transkernel: Bridging Monolithic Kernels to Peripheral Cores

Smart devices see a large number of ephemeral tasks driven by background activities. In order to execute such a task, the OS kernel wakes up the platform beforehand and puts it back to sleep afterwards. In doing so, the kernel operates various IO devices and orchestrates their power state transitions. Such kernel executions are inefficient as they mismatch typical CPU hardware. They are better off running on a low-power, microcontroller-like core, i.e., peripheral core, relieving CPU from the inefficiency. We therefore present a new OS structure, in which a lightweight virtual executor called transkernel offloads specific phases from a monolithic kernel. The transkernel translates stateful kernel execution through cross-ISA, dynamic binary translation (DBT); it emulates a small set of stateless kernel services behind a narrow, stable binary interface; it specializes for hot paths; it exploits ISA similarities for lowering DBT cost. Through an ARM-based prototype, we demonstrate transkernel's feasibility and benefit. We show that while cross-ISA DBT is typically used under the assumption of efficiency loss, it can enable efficiency gain, even on off-the-shelf hardware.
Estimating aqueous solvation and lipophilicity of small organic molecules: A comparative overview of atom/group contribution methods

Methods for the calculation of two properties of interest in drug design, namely free energy of aqueous solvation and lipophilicity (log P), using fragmental methods are reviewed here. Though aqueous solvation free energies are commonly estimated using `whole molecule' methods such as GB/SA and AMSOL, we have recently shown that fragmental approaches can offer high quality predictions as well (for molecules of the size of 20 atoms or less). In the case of log P predictions, the more commonly used ALOGP and CLOGP approaches represent the two extremes of the fragmental constant approach: ALOGP uses atom-sized fragments and no correction factors; CLOGP uses larger fragments and correction factors, which are typically obtained for each series of molecules separately. Anew approach (HLOGP) that uses both smaller (atom-sized) and larger fragments is shown to offer better performance than the other two widely used methods for the prediction of lipophilicity. In this approach, an automated `inventory' of fragments (bonded atom combinations) within a molecule, known as molecular hologram, is used as a composite descriptor and it is used in conjunction with partial least squares for the prediction of aqueous solvation or lipophilicity. It is emphasized that these different methods are useful in different types of drug design applications involving small organic molecules.
Synthesis and optical resolution of high affinity P2-ligands for HIV-1 protease inhibitors

Racemic bis-tetrahydrofuran ligand 6 was efficiently synthesized utilizing catalytic cobaloxime 10 mediated radical cyclization as the key step. Optical resolution of the racemic alcohol with immobilized-Amano lipase, afforded optically pure ligands.
Stereoselective synthesis of vancosamine and saccharosamine glycals via tungsten-catalyzed alkynol cycloisomerization.

A stereoselective synthesis of the C-3 branched amino glycals of vancosamine and saccharosamine is described that features a tungsten carbonyl catalyzed cycloisomerization of the corresponding alkynyl alcohol.
K2La6I12Os: A New Structure Type for Isolated Clusters That Is Generated by Cation Requirements

Reaction of KI, La, LaI{sub 3}, and Os in a welded niobium tube at 800 C yields black, air-sensitive crystals of K{sub 2}-La{sub 6}I{sub 12}Os. The phase was characterized by single-crystal X-ray diffraction. The structure contains tetragonally compressed La{sub 6}I{sub 12} clusters centered by Os and interbridged by I{sup a} atoms according to the general pattern of (R{sub 6}Z)I{sub 6}{sup i}I{sub 6/2}{sup i-a}I{sub 6/2}{sup a-i} for all examples with X:R ratios of 2:1. However, the detailed pattern of three-bonded I{sup i-a} and I{sup a-i} bridging is new owing to the need to accommodate a relatively large, distorted cluster and two potassium ions in a more open structure. One type of I{sup i-a} and I{sup a-i} bridging defines zigzag chains of clusters with strain evident in the interconnections. EHMO calculations show that the observed 0.49 {angstrom} tetragonal compression of the 16-electron cluster (relative to an optimal 18-e) splits the nominal t{sub 1u}{sup 4} HOMO into a two-below-one patterns and gives a closed-shell configuration. The compound accordingly exhibits only a small and typical temperature-independent paramagnetism, {approximately}6 {times} 10{sup {minus}4} emu/mol.
Stereoselective synthesis of conformationally constrained tropane analogues: 6-Chloro-2,5-diazatetracyclo[8.5.0.02,13.04,9]pentadeca-4,6,8-triene-11-one and 6-chloro-2,7-diazatetracyclo-[8.5.0.02,13.04,9]pentadeca-4,6,8-triene-11-one

Two conformationally constrained tropane derivatives were prepared as rigid nicotinic acetylcholine receptor ligands. A palladium catalyzed intramolecular α-arylation reaction was employed to generate the tricyclic compounds in good yields from N-(bromo-chloropyridylmethyl)-8-azabicyclo[3.2.1]octan-3-ones.
Copper-Catalyzed C–N Bond Formation with N-Heterocycles and Aryl Halides

The microwave-assisted, cuprous oxide catalyzed coupling of aryl bromides and iodides with imidazole, benzimidazole, pyrazole, or triazole was found to give a wide range of N-aryl heteroaromatic products in good to high yields. Aryl dibromides undergo selective monosubstitution even in the presence of large excess of N-heterocyclic nucleophiles which leaves the second aryl bromide functionality intact for further derivatization.
Linking neural and clinical measures of glaucoma with diffusion magnetic resonance imaging (dMRI)

PURPOSE To link optic nerve (ON) structural properties to clinical markers of glaucoma using advanced, semi-automated diffusion magnetic resonance imaging (dMRI) tractography in human glaucoma patients. METHODS We characterized optic neuropathy in patients with unilateral advanced-stage glaucoma (n = 6) using probabilistic dMRI tractography and compared their results to those in healthy controls (n = 6). RESULTS We successfully identified the ONs of glaucoma patients based on dMRI in all patients and confirmed that dMRI measures of the ONs correlated with clinical markers of glaucoma severity. Specifically, we found reduced fractional anisotropy (FA) in the ONs of eyes with advanced, as compared to mild, glaucoma (F(1,10) = 55.474, p < 0.0001, FDR < 0.0005). Furthermore, by comparing the ratios of ON FA in glaucoma patients to those of healthy controls (n = 6), we determined that this difference was beyond that expected from normal anatomical variation (F(1,9) = 20.276, p < 0. 005). Finally, we linked the dMRI measures of ON FA to standard clinical glaucoma measures. ON vertical cup-to-disc ratio (vCD) predicted ON FA (F(1,10) = 11.061, p < 0.01, R2 = 0.66), retinal nerve fiber layer thickness (RNFL) predicted ON FA (F(1,10) = 11.477, p < 0.01, R2 = 0.63) and ON FA predicted perceptual deficits (visual field index [VFI]) (F(1,10) = 15.308, p < 0.005, R2 = 0.52). CONCLUSION We describe semi-automated methods to detect glaucoma-related structural changes using dMRI and confirm that they correlate with clinical measures of glaucoma.
Signal integration and information transfer in an allosterically regulated network.

A biological reaction network may serve multiple purposes, processing more than one input and impacting downstream processes via more than one output. These networks operate in a dynamic cellular environment in which the levels of network components may change within cells and across cells. Recent evidence suggests that protein concentration variability could explain cell fate decisions. However, systems with multiple inputs, multiple outputs, and changing input concentrations have not been studied in detail due to their complexity. Here, we take a systems biochemistry approach, combining physiochemical modeling and information theory, to investigate how cyclooxygenase-2 (COX-2) processes simultaneous input signals within a complex interaction network. We find that changes in input levels affect the amount of information transmitted by the network, as does the correlation between those inputs. This, and the allosteric regulation of COX-2 by its substrates, allows it to act as a signal integrator that is most sensitive to changes in relative input levels. Cells respond to a constant stream of intra-and extra-cellular signals as they carry out their many functions. Multiple incoming signals are detected and processed through complex biochemical networks to yield outgoing responses that determine multiple aspects of cell behavior. Although this highly dynamic process is crucial to understanding how cells make decisions, it is poorly understood. Here we present a mechanistic analysis of signal flow in a model biochemical network with multiple incoming and outgoing signals. We find that the preferred path of signal flow between each input and output is dependent on both the levels of the inputs and the relationship between inputs. Our data suggests that the complexity of biochemical networks containing multiple inputs, outputs, and paths allows a cell to flexibly transmit multiple outgoing signals under a range of different incoming signals.
Investigation of Aerosol-Cloud Interactions under Different Absorptive Aerosol Regimes using ARM SGP Ground-Based Measurements

Abstract. The physicochemical properties of aerosols and their impacts on cloud microphysical properties are examined using data collected from the Department of Energy Atmospheric Radiation Measurement (ARM) facility over the Southern Great Plains region of the United States (ARM-SGP). A total of 16 low-level stratus cloud cases under daytime coupled boundary layer conditions are selected. The aerosol-cloud interaction index (ACIr) is used to quantify the aerosol impacts with respect to cloud-droplet effective radius. The mean value of ACIr calculated from all selected samples is 0.145 ± 0.05 and ranges from 0.09 to 0.24 at a range of cloud liquid water paths (LWP = 20–300 g m−2). The magnitude of ACIr decreases with increasing LWP which suggests a cloud microphysical response to diminished aerosol loading presumably due to enhanced collision-coalescence processes and enlarged particle size. In the presence of weak light-absorbing aerosols, the low-level clouds feature a higher number concentration of cloud condensation nuclei (NCCN) and smaller effective radii (re) while the opposite is true for strong light-absorbing aerosols. Furthermore, the mean activation ratio of aerosols to CCN (NCCN / Na) for weakly (strongly) absorbing aerosols is 0.54 (0.45), owing to the different hygroscopic abilities associated with the dominant aerosol species. In terms of the sensitivity of cloud droplet number concentration (Nd) to aerosol loading, the conversion ratio of Nd / NCCN for weakly (strongly) absorptive aerosols is 0.68 (0.54). Consequently, we expect larger shortwave radiative cooling effect from clouds influenced by weakly absorbing aerosols than strongly absorbing aerosols.
Error Correction in Fast Matrix Multiplication and Inverse

We present new algorithms to detect and correct errors in the product of two matrices, or the inverse of a matrix, over an arbitrary field. Our algorithms do not require any additional information or encoding other than the original inputs and the erroneous output. Their running time is softly linear in the number of nonzero entries in these matrices when the number of errors is sufficiently small, and they also incorporate fast matrix multiplication so that the cost scales well when the number of errors is large. These algorithms build on the recent result of Gasieniec et al (2017) on correcting matrix products, as well as existing work on verification algorithms, sparse low-rank linear algebra, and sparse polynomial interpolation.
A kicking basis for the two column Garsia-Haiman modules

In the early 1990s, Garsia and Haiman conjectured that the dimension of the Garsia-Haiman module $R_{\mu}$ is $n!$, and they showed that the resolution of this conjecture implies the Macdonald Positivity Conjecture. Haiman proved these conjectures in 2001 using algebraic geometry, but the question remains to find an explicit basis for $R_{\mu}$ which would give a simple proof of the dimension. Using the theory of Orbit Harmonics developed by Garsia and Haiman, we present a "kicking basis" for $R_{\mu}$ when $\mu$ has two columns.
Computing minimum cuts in hypergraphs

We study algorithmic and structural aspects of connectivity in hypergraphs. Given a hypergraph H = (V, E) with n = |V|, m = |E| and p = Σe∈E |e| the fastest known algorithm to compute a global minimum cut in H runs in O(np) time for the uncapacitated case, and in O(np + n2 log n) time for the capacitated case. We show the following new results.• Given an uncapacitated hypergraph H and an integer k we describe an algorithm that runs in O(p) time to find a subhypergraph H' with sum of degrees O(kn) that preserves all edge-connectivities up to k (a k-sparsifier). This generalizes the corresponding result of Nagamochi and Ibaraki from graphs to hypergraphs. Using this sparsification we obtain an O(p + λn2) time algorithm for computing a global minimum cut of H where λ is the minimum cut value.• We generalize Matula's argument for graphs to hypergraphs and obtain a (2 + e)-approximation to the global minimum cut in a capacitated hypergraph in O(1/e (p log n + n log2n)) time, and in in O(p/e) time for uncapacitated hypergraphs.• We show that a hypercactus representation of all the global minimum cuts of a capacitated hypergraph can be computed in O(np + n2 log n) time and O(p) space.Our results build upon properties of vertex orderings that were inspired by the maximum adjacency ordering for graphs due to Nagamochi and Ibaraki. Unlike graphs we observe that there are several different orderings for hypergraphs which yield different insights.
Generalized tight p-frames and spectral bounds for Laplace-like operators

We prove sharp upper bounds for sums of eigenvalues (and other spectral functionals) of Laplace-like operators, including bi-Laplacians and fractional Laplacians. We show that among linear images of a highly symmetric domain, our spectral functionals are maximal on the original domain. We exploit the symmetries of the domain, and the operator, avoiding the necessity of finding good test functions for variational problems. This is especially important for fractional Laplacians, since exact solutions are not even known on intervals, making it hard to find good test functions. To achieve our goals we generalize tight p-fusion frames, to extract the best possible geometric results for domains with isometry groups admitting tight p-frames. Any such group generates a tight p-fusion frame via conjugations of a fixed projection matrix. We show that generalized tight p-frames can also be obtained by conjugations of an arbitrary rectangular matrix, with the frame constant depending on the singular values of the matrix.
Representations of Rational Cherednik algebras with minimal support and torus knots

Abstract In this paper we obtain several results about representations of rational Cherednik algebras, and discuss their applications. Our first result is the Cohen–Macaulayness property (as modules over the polynomial ring) of Cherednik algebra modules with minimal support. Our second result is an explicit formula for the character of an irreducible minimal support module in type A n − 1 for c = m n , and an expression of its quasispherical part (i.e., the isotypic part of “hooks”) in terms of the HOMFLY polynomial of a torus knot colored by a Young diagram. We use this formula and the work of Calaque, Enriquez and Etingof to give explicit formulas for the characters of the irreducible equivariant D-modules on the nilpotent cone for SL m . Our third result is the construction of the Koszul–BGG complex for the rational Cherednik algebra, which generalizes the construction of the Koszul–BGG resolution from [3] and [21] , and the calculation of its homology in type A . We also show in type A that the differentials in the Koszul–BGG complex are uniquely determined by the condition that they are nonzero homomorphisms of modules over the Cherednik algebra. Finally, our fourth result is the symmetry theorem, which identifies the quasispherical components in the representations with minimal support over the rational Cherednik algebras H m n ( S n ) and H n m ( S m ) . In fact, we show that the simple quotients of the corresponding quasispherical subalgebras are isomorphic as filtered algebras. This symmetry was essentially established in [8] in the spherical case, and in [24] in the case GCD ( m , n ) = 1 , and it has a natural interpretation in terms of invariants of torus knots.
THE DISTRIBUTION OF SHORT CHARACTER SUMS

Letbe a non-real Dirichlet character modulo a prime q. In this paper we prove that the distribution of the short character sum S�,H(x) = P x<nx+H �(n), as x runs over the positive integers below q, converges to a two-dimensional Gaussian distribution on the complex plane, provided that logH = o(logq) and H → ∞ as q → ∞. Furthermore, we use a method of Selberg to give an upper bound on the rate of convergence.
Hermitian Yang–Mills metrics on reflexive sheaves over asymptotically cylindrical Kähler manifolds

We prove an analogue of the Donaldson–Uhlenbeck–Yau theorem for asymptotically cylindrical (ACyl) Kahler manifolds: If ℰ is a reflexive sheaf over an ACyl Kahler manifold, which is asymptotic to a ...
Green-Kubo relation for friction at liquid-solid interfaces

We have developed a Green-Kubo relation that enables accurate calculations of friction at solid-liquid interfaces directly from equilibrium molecular dynamics (MD) simulations and that provides a pathway to bypass the time-scale limitations of typical nonequilibrium MD simulations. The theory has been validated for a number of different interfaces and it is demonstrated that the liquid-solid slip is an intrinsic property of an interface. Because of the high numerical efficiency of our method, it can be used in the design of interfaces for applications in aqueous environments, such as nano- and microfluidics.
Local rigidity of higher rank homogeneous abelian actions: a complete solution via the geometric method

We show local and cocycle rigidity for most abelian higher-rank partially hyperbolic algebraic actions on homogeneous spaces obtained from semisimple Lie groups as well as their semidirect products. The method of proof uses a combination of geometric method and the theory of central extensions. The principal difference with previous work are the new aspects of the proof and treatment of abelian actions which are not restrictions of Weyl chamber flows. It is also the first time that partially hyperbolic twisted symmetric space examples have been treated in the literature.
On the Rate of Merging of Vorticity Level Sets for the 2D Euler Equations

We show that two distinct level sets of the vorticity of a solution to the 2D Euler equations on a disc can approach each other along a curve at an arbitrarily large exponential rate.
Two-Vertex Generators of Jacobians of Graphs

We give necessary and sufficient conditions under which the Jacobian of a graph is generated by a divisor that is the difference of two vertices. This answers a question posed by Becker and Glass and allows us to prove various other propositions about the order of divisors that are the difference of two vertices. We conclude with some conjectures about these divisors on random graphs and support them with empirical evidence.
Quenched large deviations for multiscale diffusion processes in random environments

We consider multiple time scales systems of stochastic differential equations with small noise in random environments. We prove a quenched large deviations principle with explicit characterization of the action functional. The random medium is assumed to be stationary and ergodic. In the course of the proof we also prove related quenched ergodic theorems for controlled diffusion processes in random environments that are of independent interest. The proof relies entirely on probabilistic arguments, allowing to obtain detailed information on how the rare event occurs. We derive a control, equivalently a change of measure, that leads to the large deviations lower bound. This information on the change of measure can motivate the design of asymptotically efficient Monte Carlo importance sampling schemes for multiscale systems in random environments
Finding syntax in human encephalography with beam search

Recurrent neural network grammars (RNNGs) are generative models of (tree , string ) pairs that rely on neural networks to evaluate derivational choices. Parsing with them using beam search yields a variety of incremental complexity metrics such as word surprisal and parser action count. When used as regressors against human electrophysiological responses to naturalistic text, they derive two amplitude effects: an early peak and a P600-like later peak. By contrast, a non-syntactic neural language model yields no reliable effects. Model comparisons attribute the early peak to syntactic composition within the RNNG. This pattern of results recommends the RNNG+beam search combination as a mechanistic model of the syntactic processing that occurs during normal human language comprehension.
On certain rings of differentiable type and finiteness properties of local cohomology

Abstract Let R be a commutative F-algebra, where F is a field of characteristic 0, satisfying the following conditions: R is equidimensional of dimension n, every residual field with respect to a maximal ideal is an algebraic extension of F, and Der F ( R ) is a finitely generated projective R-module of rank n such that R m ⊗ R Der F ( R ) = Der F ( R m ) . We show that the associated graded ring of the ring of differential operators, D ( R , F ) , is a commutative Noetherian regular with unity and pure graded dimension equal to 2 dim ( R ) . Moreover, we prove that D ( R , F ) has weak global dimension equal to dim ( R ) and that its Bernstein class is closed under localization at one element. Using these properties of D ( R , F ) , we show that the set of associated primes of every local cohomology module, H I i ( R ) , is finite. If ( S , m , K ) is a complete regular local ring of mixed characteristic p > 0 , we show that the localization of S at p, S p , is such a ring. As a consequence, the set of associated primes of H I i ( S ) that does not contain p is finite. Moreover, we prove this finiteness property for a larger class of functors.
Harnessing Correlations in Distributed Erasure-Coded Key-Value Stores

Motivated by applications of distributed storage systems to key-value stores, the multi-version coding problem has been formulated to efficiently store frequently updated data in asynchronous decentralized storage systems. Inspired by consistency requirements in distributed systems, the main goal in the multi-version coding problem is to ensure that the latest possible version of the data is decodable even if the data updates have not reached all the servers in the system. In this paper, we study the storage cost of ensuring consistency for the case where the data versions are correlated, in contrast to previous work where the data versions were treated as being independent. We provide multi-version code constructions that show that the storage cost can be significantly smaller than the previous constructions depending on the degree of correlation, despite the asynchrony and the decentralized nature. Our achievability results are based on Reed–Solomon codes and random binning. Through an information-theoretic converse, we show that our multi-version codes are asymptotically nearly optimal, within a factor of 2, in certain interesting regimes.