cssi/SciSciGPT-SciSciNet huggingface dataset:
Today’s economic history and tomorrow’s scholars

While first highlighted by Romer (J Econ Educ 25:49–66, 1994), economic history has only continued to become more integrated into the broader discipline. This paper utilizes a sample of recent articles in top Economics journals to help assess what characteristics economic history papers share and a sample of recent graduate syllabi to examine the role that a required economic history class can play more broadly in the training of economists. The samples confirm that economic history research utilizing a wide range of topics and tools is being published in top economics journals and taught in economic history classes. The findings suggest that economic history is a complement to the research of other fields and that a required economic history class offers an early applied course that could help students regardless of what field they go on to pursue.
How We Transmit Memories to Other Brains: Constructing Shared Neural Representations Via Communication

Humans are able to mentally construct an episode when listening to another person's recollection, even though they themselves did not experience the events. However, it is unknown how strongly the neural patterns elicited by mental construction resemble those found in the brain of the individual who experienced the original events. Using fMRI and a verbal communication task, we traced how neural patterns associated with viewing specific scenes in a movie are encoded, recalled, and then transferred to a group of naive listeners. By comparing neural patterns across the 3 conditions, we report, for the first time, that event-specific neural patterns observed in the default mode network are shared across the encoding, recall, and construction of the same real-life episode. This study uncovers the intimate correspondences between memory encoding and event construction, and highlights the essential role our common language plays in the process of transmitting one's memories to other brains.
A Novel (2,2‐Diarylvinyl)phosphine/Palladium Catalyst for Effective Aromatic Amination

A new series of diarylvinylphosphine ligands was designed and synthesized. A catalyst system, consisting of the ligands and palladium species, effectively catalyzed the coupling reaction of aryl bromides and chlorides with amines to afford the corresponding products in good to excellent yields. The efficiency is likely derived from an interaction between the palladium center and the cis-aryl moiety on the diarylvinylphosphine ligand stabilizing a catalytic intermediate during the coupling reaction.
Biocatalytic synthesis of a nanostructured and crystalline bimetallic perovskite-like barium oxofluorotitanate at low temperature.

Silicatein, an enzymatic biocatalyst from the marine sponge Tethya aurantia, is demonstrated to catalyze and template the hydrolysis/condensation of the molecular precursor BaTiF6 at low temperature to form nanocrystalline BaTiOF4, an orthorhombic oxofluorotitanate. The kinetics of hydrolysis and growth were studied in-situ via pH profiling and quartz crystal microbalance (QCM) techniques. The composition and structure of the resulting BaTiOF4 microstructures on the silicatein surface were characterized using FT-IR spectroscopy, X-ray photoelectron spectroscopy, energy-dispersive X-ray spectroscopy, scanning electron microscopy, transmission electron microscopy, and selected area electron diffraction. The silicatein- mediated hydrolysis/condensation of BaTiF6 generates nanocrystalline BaTiOF4 (a high-temperature intermediate to BaTiO3 )a t 16°C without any added acid or base, and the growth is templated along the protein filaments into floret microstructures. The unique combination of silicatein and the single-source molecular precursor has allowed a multimetallic perovskite-like material to be biocatalytically synthesized, in vitro, for the first time.
Molecular Dynamics Study of [2]Rotaxanes: Influence of Solvation and Cation on Co-conformation

The conformational preference of a [2]rotaxane system has been examined by molecular dynamics simulations. The rotaxane wheel consists of two bridged binding components: a cis-dibenzo-18-crown-6 ether and a 1,3-phenyldicarboxamide, and the penetrating axle consists of a central isophthaloyl unit with phenyltrityl capping groups. The influence of solvation on the co-conformation of the [2]rotaxane was evaluated by comparing the conformational flexibility in two solvents: chloroform and dimethyl sulfoxide. Attention was also paid to the effect of cation binding on the dynamical properties of the [2]rotaxane. The conformational stability of the [2]rotaxane was calculated using a MM/PB-SA strategy, and the occurrence of specific motions was examined by essential dynamics analysis. The changes in the co-conformational properties in the two solvents and upon cation binding are discussed in light of the available NMR data. The results indicate that in chloroform solution the [2]rotaxane system exists as a mixture of co-conformational states including some that have hydrogen bonds between axle C=O and wheel NH groups. Analysis of the simulations allow us to hypothesize that the [2]rotaxane's circumrotation motion can occur as the result of a dynamic process that combines a preliminary axle sliding step that breaks these hydrogen bonds and a conformational change in the ester group more distant from the wheel. In contrast, no hydrogen-bonded co-conformation was found in dimethyl sulfoxide, which appears to be due to the preferential formation of hydrogen bonds between the wheel NH groups with solvent molecules. Moreover, the axle experiences notable changes in anisotropic shielding, which would explain why the NMR signals are broadened in this solvent. Insertion of a sodium cation into the crown ether reduces co-conformational flexibility due to an interaction of the axle with the cation. Overall, the results reveal how both solvent and ionic atmosphere can influence the co-conformational preferences of rotaxanes.
Cobalt Phosphate Based Zeolite Structures with the Edingtonite Framework Topology

Hydrothermal syntheses and crystal structures of five zeolite edingtonite analogues are presented. For the first time, the edingtonite framework topology is assembled using an amine-assisted synthesis approach with either 1,2-diaminopropane or 1,2-diamino-2-methylpropane. These materials are created in the cobalt phosphate system with a small concentration of trivalent cations (Al3+ and Ga3+) incorporated into the framework for the host−guest charge matching. ACP-EDI1 and GCP-EDI1 are monoclinic, whereas ACP-EDI2, ACP-EDI3, and GCP-EDI2 are tetragonal (ACP = aluminum cobalt phosphate; GCP = gallium cobalt phosphate). The difference in lattice symmetries between ACP-EDI1 and ACP-EDI2 (or GCP-EDI1 and GCP-EDI2) is related to the synthesis conditions. All five structures have three-dimensional 8-ring channels along the crystallographic [001], [110], and [110] directions, regardless of the difference in symmetry. Amine molecules are more ordered in the monoclinic phases than in the tetragonal phases, and the...
A β-Lactone Route to Chiral γ-Substituted α-Amino Acids: Application to the Concise Synthesis of (S)-α-Azidobutyro Lactone and a Natural Amino Acid

β-Lactones are useful synthetic intermediates allowing access to a number of functional arrays. In this report, enantiomerically pure 4-trichloromethyl-2-oxetanone is shown to be a versatile amino acid synthon leading to a variety of γ-substituted α-amino acid precursors. The utility of this methodology was demonstrated by the concise synthesis of a protected homoserine equivalent, α-azidobutyro lactone, and a naturally occurring α-amino acid from the seeds of Blighia unijugata.
The synthesis, single-crystal structure, optical absorption, and resistivity of Th2GeSe5

Abstract The compound Th2GeSe5 has been synthesized by the reaction of the elements at 1273 K. From a single-crystal study Th2GeSe5 crystallizes in the Ba5Si3 structure type with four formula units in the space group D84h−P4/ncc of the tetragonal system in a cell with dimensions a=7.4968(4) A and c=13.6302(9) A at 100(2) K. From optical absorption measurements Th2GeSe5 is found to have an optical band gap of 1.92 eV (indirect) or 1.98 eV (direct), consistent with its red color. Th2GeSe5 is a wide gap semiconductor, as indicated by its electrical resistivity at 298 K of 4.37(2)×109 Ω cm measured on a single crystal.
Enantioselective addition of terminal alkynes to isolated isoquinoline iminiums.

The asymmetric, catalytic addition of terminal alkynes to discrete alkyliminium species in the presence of copper bromide, QUINAP ligand, and triethylamine is reported. The reaction proceeds in high yield and high enantiomeric excess with a variety of substrates in solution and is also amenable to solid-phase synthesis.
Reactions of 2-alkylimidazoles and 2-methylbenzimidazoles with 1,3-diacid chlorides. Synthesis of highly functionalized hetero-cycles under mild conditions

Abstract Highly functionalized heterocycles were synthesized in one-pot reactions of 2-alkylimidazoles or 2-methylbenzimidazoles with 1,3-diacid chlorides. Some of the cyclizations proceed through cyclic-N,N′-ketene acetal intermediates.
Formation of crystalline nanoclusters of Fe2P, RuP, Co2P, Rh2P, Ni2P, Pd5P2, or PtP2 in a silica xerogel matrix from single-source molecular precursors

Metal complexes containing bifunctional phosphine ligands that possess alkoxysilyl functional groups have been prepared for seven metals of the first, second, or third transition metal series. Incorporation of these single-source precursors into silica xerogel matrixes using sol−gel chemistry affords molecularly doped xerogels. Subsequent thermal treatment of these doped xerogels under solely reducing conditions selectively affords nanoclusters of Fe2P, RuP, Co2P, Rh2P, Ni2P, Pd5P2, or PtP2 which are highly dispersed throughout the bulk of the xerogel matrix. Characterization of these nanocomposite materials by transmission electron microscopy, energy-dispersive spectrometry, X-ray diffraction, and electron diffraction indicates that the metal phosphide nanoclusters are highly crystalline with some exhibiting nonspherical morphology.
Synthesis, Structure, and Spectroscopy of Two Ternary Uranium(IV) Thiophosphates: UP2S9 and UP2S7 Containing P2S92– and P2S72– Ligands

The two ternary uranium thiophosphate compounds were isolated from polychalcogenide flux reactions. UP2S9 crystallizes in the tetragonal space group P42/mcm with two formula units per unit cell, where a = 7.762(1) and c = 9.691(3) A. UP2S7 crystallizes in the orthorhombic space group Fddd with 16 formula units per unit cell, here a = 8.919(3), b = 15.198(4), and c = 30.104(9) A. Both compounds were characterized through single crystal X-ray, UV–vis–NIR, and Raman spectroscopy. The structures of the two compounds are formed from [US6]8– chains connected to each other by either the tridentate-chelating P2S94– in UP2S9 or the P2S74– in UP2S7 resulting in 3D frameworks. These two ligands have different geometries, but they exhibit similar coordination modes, comparable to the ethane-like P2S64–. The uranium cations in both compounds can be assigned an unambiguous oxidation state of +4. The two compounds are semiconductors with nearly identical band-gaps of 1.41 eV.
Synthesis and properties of gem-(difluorocyclopropyl)amine derivatives of bicyclo[n.1.0]alkanes.

Generation of difluorocarbene(carbenoid) in the presence of enamines derived from cyclic ketones results in overall insertion of CF2 to produce bicyclic difluorocyclopropylamines. These adducts are very weakly basic, and their thermal stabilities vary markedly with their structures.
HIGH ENERGY PHOTON–PHOTON COLLISIONS AT A LINEAR COLLIDER

High intensity back-scattered laser beams will allow the efficient conversion of a substantial fraction of the incident lepton energy into high energy photons, thus significantly extending the physics capabilities of an e-e± linear collider. The annihilation of two photons produces C = + final states in virtually all angular momentum states. An important physics measurement is the measurement of the Higgs coupling to two photons. The annihilation of polarized photons into the Higgs boson determines its fundamental H0γγ coupling as well as determining its parity. Other novel two-photon processes include the two-photon production of charged pairs τ+τ-, W+W-, $t{\bar t}$, and supersymmetric squark and slepton pairs. The one-loop box diagram leads to the production of pairs of neutral particles such as γγ → Z0Z0, γZ0, and γγ. At the next order one can study Higgstrahlung processes, such as γγ → W+W-W-H. Since each photon can be resolved into a W+W- pair, high energy photon-photon collisions can also provide a...
Enantioselective synthesis of butadien-2-ylcarbinols via (silylmethyl)allenic alcohols from chromium-catalyzed additions to aldehydes utilizing chiral carbazole ligands

Abstract The synthesis of chiral, nonracemic butadienylcarbinols by employing intermediate (trimethylsilyl)methylallenic alcohols is described. Allenic alcohols are obtained by treatment of aldehydes with (4-bromobut-2-ynyl)trimethylsilane in the presence of a catalytic amount of CrCl3 or CrCl2. Several new tridentate bis(oxazolinyl)carbazole ligands were synthesized and evaluated as the source of chirality. The synthesis of chiral allenic alcohols can be achieved in good yields (58–88%) and enantioselectivities (55–78% ee). Allenic alcohols may be treated with TBAF or 2 M HCl to provide the desired dienes in 43–86% yields. Alternatively, the (trimethylsilyl)methyl allenic alcohols afford iodobutadienyl carbinols when treated with N-iodosuccinimide.
Synthesis of 8-(S)-methoxy-11-desmethyl laulimalide: a novel laulimalide analogue

A strategy is outlined which enables preparation of novel laulimalide analogues at C.8 and C.11. A representative analogue, 8-(S)-methoxy-11-desmethyl laulimalide, was synthesized via this route.
Octanol-water partition: Searching for predictive models

The log n-octanol/water partition coefficient (log Po/w) still represents one of the most informative physicochemical parameters available to medicinal chemists. In the present work, principles, methodologies, and parameters are briefly reviewed for a variety of models developed to predict this parameter based on molecular structure. To include the developments of recent years, a total of more than 40 different approaches are mentioned with relevant bibliography within four major categories: group contribution methods, atomic contribution methods, molecular methods, and other physicochemical methods. To underscore once more the utility of this partition coefficient, a comprehensive and reevaluated correlation between log Po/w and in vivo permeability data of rat brain capillaries is included. Most deviants that fell below the trendline are those that have been recently found to be substrates for P-glycoprotein, a multidrug transporter that actively removes them from the brain. Accurate predictions of log Po/w may necessitate many parameters, but there is mounting evidence that molecular size and hydrogen bonding ability can account for a major part of the variance. Our recently developed, molecular size-based approach is reviewed, and it is argued that introduction of three-dimensionality allows the elimination of many empirically derived fragment constants without a significant deterioration of the predictive accuracy. A comparison of predictive power for six different methods on 145 molecules of interest for medicinal chemists is also included.
Commentary: BRAIN NETWORKS. Correlated Gene Expression Supports Synchronous Activity in Brain Networks. Science 348, 1241–4

A recent report claims that functional brain networks defined with resting-state functional magnetic resonance imaging (fMRI) can be recapitulated with correlated gene expression (i.e. high within-network tissue-tissue “strength fraction”, SF) (1). However, the authors do not adequately control for spatial proximity. We replicated their main analysis, performed a more effective adjustment for spatial proximity, and tested whether “null networks” (i.e. clusters with center coordinates randomly placed throughout cortex) also exhibit high SF. Removing proximal tissue-tissue correlations by Euclidean distance, as opposed to removing correlations within arbitrary tissue labels as in (1), reduces within-network SF to no greater than null. Moreover, randomly placed clusters also have significantly high SF, indicating that high within-network SF is entirely attributable to proximity and is unrelated to functional brain networks defined by resting-state fMRI. We discuss why additional validations in the original article are invalid and/or misleading and suggest future directions.
Synthetic evolutions in the nucleophilic addition to alkynes

Abstract This short account describes our efforts to transform the simple nucleophilic addition of alkynes into a more efficient, selective and environmentally benign synthetic tool. We have circumvented the lack of regioselectivity in the gold-catalyzed triple bond addition of water through neighboring group participation and in the process we developed a ‘functionalized hydration’ (multiple bond formation and hydration in a one-pot process) using fluorine-engendered cationic gold catalysis. In addition, we have conducted the synthesis of O-heterocycles through a gold-catalyzed tandem addition/cycloisomerization sequence, the synthesis of N-heterocycles through a copper-catalyzed cyclization-triggered addition of alkynes, and a green synthesis of thioethers ‘on water’ without catalyst or initiator. These nucleophilic synthetic evolutions, catapulted by a simple addition to an alkyne, will surely contribute to provide a wider synthetic access to sophisticated biological targets.
COUPLING OF GLYCAL DERIVED THIOETHYL GLYCOSYL DONORS WITH GLYCAL ACCEPTORS. AN ADVANCE IN THE SCOPE OF THE GLYCAL ASSEMBLY

Glycals were converted into thioethyl glycosyl donors through 1,2-anhydrosugar intermediates. Various participating groups in the C-2 position were examined for formation of β-glucosyl, β-galactosyl, and α-mannosyl linkages. A number of disaccharides was prepared employing a novel coupling protocol involving thioethyl 2-pivaloyl glycosyl donors and glycal acceptors. Using this methodology, a linear tetrasaccharide containing exclusively β-glucosyl-(1→4) linkages was prepared in high yields. Ready application to α-mannosylation and C2 branching are other hallmarks of the method.
Divergent enantioselective pathways in the catalytic asymmetric addition of diethylzinc to aldehydes in the presence and absence of titanium tetraisopropoxide

Abstract The stereochemical outcome of the asymmetric addition of diethylzinc to aldehydes catalyzed by ( R , R )-hydrobenzoin can be influenced by the absence or presence of Ti(O- i Pr) 4 . The enantiomeric ratios obtained in the absence of Ti(O- i Pr) 4 favor the ( S )-enantiomer, whereas the ratios obtained from the use of Ti(O- i Pr) 4 favor the formation of the ( R )-enantiomer. The formation of the opposite enantiomers is attributed to the different transition states mediated by either zinc or titanium.
Asymmetric Synthesis of Highly Substituted β-Nitro Alcohols and Enantiomerically Enriched 4,4,5-Trisubstituted Oxazolidinones

It is demonstrated that alpha,alpha-disubstituted-alpha-nitroketones are reduced to the corresponding trisubstituted nitro alcohols in good to excellent yield and enantiomeric excess by borane-dimethyl sulfide in the presence of a chiral oxazaborolidine catalyst. Reduction of the nitro alcohols to the corresponding amino alcohols and their subsequent conversion to enantiomerically enriched 4,4,5-trisubstituted oxazoldinones is also reported.
Preparation and anticonvulsant activity of a series of functionalized .alpha.-heteroatom-substituted amino acids

Potent anticonvulsant activity has been reported for (R,S)-2-acetamido-N-benzyl-2-methylacetamide (2a). Select alpha-heteroatom substituted derivatives of 2a have been prepared (26 examples) in which the alpha-methyl group has been replaced by nitrogen (3a-q), oxygen (3r-u), and sulfur (3v-z) containing moieties. The functionalized amino acid derivatives were evaluated in the maximal electroshock seizure (MES) and horizontal screen (tox) tests in mice. The most active compounds were (R,S)-2-acetamido-N-benzyl-2-(methoxyamino)acetamide (31), and (R,S)-2-acetamido-N-benzyl-2-(methoxymethylamino)acetamide (3n). After ip administration, the MES ED50 values for 31 (6.2 mg/kg) and 3n (6.7 mg/kg) compared favorably with phenytoin (9.50 mg/kg).
Microwave-assisted Cu2O-catalyzed one-pot synthesis of symmetrical diaryl selenides from elemental selenium

Abstract A novel and simple microwave-assisted one-pot protocol to prepare symmetrical diaryl selenides has been developed. A cross-coupling reaction between aryl iodide and elemental selenium takes place in the presence of KOH and a catalytic amount of Cu 2 O/NH 2 CH 2 CH 2 NH 2 , leading to C–Se bond formation. The reactions are highly efficient with a reaction time of 1 h under microwave irradiation and yields from 50% to 90%.
Protein Mismatches Caused by Reassortment Influence Functions of the Reovirus Capsid.

Following attachment to host receptors via σ1, reovirus particles are endocytosed and disassembled to generate infectious subvirion particles (ISVPs). ISVPs undergo conformational changes to form ISVP*, releasing σ1 and membrane-targeting peptides from the viral μ1 protein. ISVP* formation is required for delivery of the viral core into the cytoplasm for replication. We characterized the properties of T3DF/T3DCS1, an S1 gene monoreassortant between two laboratory isolates of prototype reovirus strain T3D: T3DF and T3DC. T3DF/T3DCS1 is poorly infectious. This deficiency is a consequence of inefficient encapsidation of S1-encoded σ1 on T3DF/T3DCS1 virions. Additionally, compared to T3DF, T3DF/T3DCS1 undergoes ISVP-to-ISVP* conversion more readily, revealing an unexpected role for σ1 in regulating ISVP* formation. The σ1 protein is held within turrets formed by the λ2 protein. To test if the altered properties of T3DF/T3DCS1 are due to a mismatch between σ1 and λ2 proteins from T3DF and T3DC, properties of T3DF/T3DCL2 and T3DF/T3DCS1L2, which express a T3DC-derived λ2, were compared. The presence of T3DC λ2 allowed more efficient σ1 incorporation, producing particles that exhibit T3DF-like infectivity. Compared to T3DF, T3DF/T3DCL2 prematurely converts to ISVP*, uncovering a role for λ2 in regulating ISVP* formation. Importantly, a virus with matching σ1 and λ2 displayed a more regulated conversion to ISVP* than either T3DF/T3DCS1 or T3DF/T3DCL2. In addition to identifying new regulators of ISVP* formation, our results highlight that protein mismatches produced by reassortment can alter virus assembly and thereby influence subsequent functions of the virus capsid. IMPORTANCE Cells coinfected with viruses that possess a multipartite or segmented genome reassort to produce progeny viruses that contain a combination of gene segments from each parent. Reassortment places new pairs of genes together, generating viruses in which mismatched proteins must function together. To test if such forced pairing of proteins that form the virus shell or capsid alters the function of the particle, we investigated properties of reovirus variants in which the σ1 attachment protein and the λ2 protein that anchors σ1 on the particle are mismatched. Our studies demonstrate that a σ1-λ2 mismatch produces particles with lower levels of encapsidated σ1, consequently decreasing virus attachment and infectivity. The mismatch between σ1 and λ2 also altered the capacity of the viral capsid to undergo conformational changes required for cell entry. These studies reveal new functions of reovirus capsid proteins and illuminate both predictable and novel implications of reassortment.
Preparation of Protected syn-α,β-Dialkyl β-Amino Acids That Contain Polar Side Chain Functionality†

We report the synthesis of syn-α,β-dialkyl β-amino acid derivatives suitably protected for solid-phase synthesis that give rise to residues containing positively charged lysine-like side chains. These amino acids, as well as syn-α,β-dialkyl β-amino acids that contain diverse hydrophobic side chains, are prepared in good de and ee. The key step in this route involves Davies's protocol for the conjugate addition of a chiral lithium amide to α,β-unsaturated tert-butyl esters (Davies, S. G.; Ichihara, O.; Walters, I. A. S. J. Chem. Soc., Perkin Trans. 1 1994, 9, 1141). syn-α,β-Dialkyl β-amino acids are interesting building blocks because of their sheet-forming propensity and because of their presence in bioactive compounds.
Synthetic studies of antitumor macrolide laulimalide: a stereoselective synthesis of the C17-C28 segment.

A stereoselective synthesis of the C17–C28 segment of the potent antitumor macrolide, laulimalide has been accomplished. The key steps are a ring-closing olefin metathesis to construct the dihydropyran unit, nucleophilic addition of an alkynyl anion to the Weinreb amide, stereoselective reduction of the resulting ketone to set the C20-hydroxyl stereochemistry, and elaboration of the C21–C22 trans-olefin geometry.
Dynamic interaction network inference from longitudinal microbiome data.

Several studies have focused on the microbiota living in environmental niches including human body sites. In many of these studies, researchers collect longitudinal data with the goal of understanding not only just the composition of the microbiome but also the interactions between the different taxa. However, analysis of such data is challenging and very few methods have been developed to reconstruct dynamic models from time series microbiome data. Here, we present a computational pipeline that enables the integration of data across individuals for the reconstruction of such models. Our pipeline starts by aligning the data collected for all individuals. The aligned profiles are then used to learn a dynamic Bayesian network which represents causal relationships between taxa and clinical variables. Testing our methods on three longitudinal microbiome data sets we show that our pipeline improve upon prior methods developed for this task. We also discuss the biological insights provided by the models which include several known and novel interactions. The extended CGBayesNets package is freely available under the MIT Open Source license agreement. The source code and documentation can be downloaded from https://github.com/jlugomar/longitudinal_microbiome_analysis_public . We propose a computational pipeline for analyzing longitudinal microbiome data. Our results provide evidence that microbiome alignments coupled with dynamic Bayesian networks improve predictive performance over previous methods and enhance our ability to infer biological relationships within the microbiome and between taxa and clinical factors.
The bio-organometallic chemistry of active site iron in hydrogenases

Abstract The recent X-ray crystal structure determinations of several hydrogenase enzymes have engaged the organometallic community owing to the presence of CN − and CO ligands bound to iron in the active sites. This review focuses primarily on the structural features of these metalloproteins and discusses synthetic efforts to develop small molecule models of the active sites. Specific attention is given to the use of infrared spectroscopy as an additional tool to probe different enzyme states. In addition, structurally dissimilar complexes which show some ability to facilitate either dihydrogen uptake or production, are reviewed as possible functional models. Insights from earlier work with metal hydride chemistry and recent theoretical studies are discussed in terms of functional mechanistic proposals.
Lost Dollars Threaten Research in Public Academic Health Centers

The decrease of federal and state support threatens long-term sustainability of research in publicly supported academic health centers. In weathering these financial threats, research at the University of California, San Francisco (UCSF), has undergone 3 substantial changes: institutional salary support goes preferentially to senior faculty, whereas the young increasingly depend on grants; private and government support for research grows apace in clinical departments but declines in basic science departments; and research is judged more on its quantity (numbers of investigators and federal and private dollars) than on its goals, achievements, or scientific quality. We propose specific measures to alleviate these problems. Other large public academic health centers probably confront similar issues, but—except for UCSF—such centers have not been subjected to detailed public analysis.—Bourne, H. R., Vermillion, E. B. Lost dollars threaten research in public academic health centers.
Mechanochemical Coupling and Junctional Forces during Collective Cell Migration.

Abstract Cell migration, a fundamental physiological process in which cells sense and move through their surrounding physical environment, plays a critical role in development and tissue formation, as well as pathological processes, such as cancer metastasis and wound healing. During cell migration, dynamics are governed by the bidirectional interplay between cell-generated mechanical forces and the activity of Rho GTPases, a family of small GTP-binding proteins that regulate actin cytoskeleton assembly and cellular contractility. These interactions are inherently more complex during the collective migration of mechanically coupled cells because of the additional regulation of cell-cell junctional forces. In this study, we adapted a recent minimal modeling framework to simulate the interactions between mechanochemical signaling in individual cells and interactions with cell-cell junctional forces during collective cell migration. We find that migration of individual cells depends on the feedback between mechanical tension and Rho GTPase activity in a biphasic manner. During collective cell migration, waves of Rho GTPase activity mediate mechanical contraction/extension and thus synchronization throughout the tissue. Further, cell-cell junctional forces exhibit distinct spatial patterns during collective cell migration, with larger forces near the leading edge. Larger junctional force magnitudes are associated with faster collective cell migration and larger tissue size. Simulations of heterogeneous tissue migration exhibit a complex dependence on the properties of both leading and trailing cells. Computational predictions demonstrate that collective cell migration depends on both the emergent dynamics and interactions between cellular-level Rho GTPase activity and contractility and multicellular-level junctional forces.
Li2PbGeS4 and Li2EuGeS4: Polar chalcopyrites with a severe tetragonal compression

Li2PbGeS4 and Li2EuGeS4 form by dissolving Pb/Eu and Ge in molten Li2S9 at 600−650 °C. They crystallize in the tetragonal, noncentrosymmetric space group I-42m with a = 6.5224(5) A, c = 7.7603(8) A, Z = 2, R1 = 0.0253, and wR2 = 0.0646 for Li2PbGeS4 and a = 6.5447(4) A, c = 7.6960(6) A, Z = 2, R1 = 0.0224, and wR2 = 0.0551 for Li2EuGeS4. These polar compounds possess a compressed chalcopyrite-like structure. The compression occurs along the c axis and results in an expanded coordination sphere for Pb and Eu that can be described as a distorted dodecahedron. The Pb/EuS8 dodecahedra share edges and corners with the GeS4 tetrahedra in such a way as to create small tunnels down the c axis in which the lithium cations reside. The Li+ cations are surrounded by four S2- anions that create a highly distorted tetrahedral pocket. Both compounds are semiconductors with indirect band gaps of 2.41 and 2.54 eV, respectively. We also discuss the results of an LAPW band structure calculation for Li2PbGeS4 and report infr...
A novel imidazol-2-ylidene as a ligand for palladium-catalyzed synthesis of oxyindoles from o-haloanilides

Abstract Oxyindoles were formed in good yields from 2-bromo- or chloroanilide in the presence of a base and a novel palladium imidazol-2-ylidene complex, through a process of metal-catalyzed intramolecular arylation of amide enolates. A wide range of substrates, including electron rich aryl chlorides, were found active under the catalysis of this non-phosphinic, easily prepared ligand–metal system.
tHapMix: simulating tumour samples through haplotype mixtures.

Motivation Large-scale rearrangements and copy number changes combined with different modes of clonal evolution create extensive somatic genome diversity, making it difficult to develop versatile and scalable variant calling tools and create well-calibrated benchmarks. Results We developed a new simulation framework tHapMix that enables the creation of tumour samples with different ploidy, purity and polyclonality features. It easily scales to simulation of hundreds of somatic genomes, while re-use of real read data preserves noise and biases present in sequencing platforms. We further demonstrate tHapMix utility by creating a simulated set of 140 somatic genomes and showing how it can be used in training and testing of somatic copy number variant calling tools. Availability and implementation tHapMix is distributed under an open source license and can be downloaded from https://github.com/Illumina/tHapMix CONTACT: sivakhno@illumina.comSupplementary information: Supplementary data are available at Bioinformatics online.
Theory for Nonlinear Spectroscopy of Vibrational Polaritons

Molecular polaritons have gained considerable attention due to their potential to control nanoscale molecular processes by harnessing electromagnetic coherence. Although recent experiments with liquid-phase vibrational polaritons have shown great promise for exploiting these effects, significant challenges remain in interpreting their spectroscopic signatures. We develop a quantum-mechanical theory of pump-probe spectroscopy for this class of polaritons based on the quantum Langevin equation and the input-output theory. Comparison with recent experimental data shows good agreement upon consideration of the various vibrational anharmonicities that modulate the signals. Finally, a simple and intuitive interpretation of the data based on an effective mode-coupling theory is provided. Our work provides a solid theoretical framework to elucidate nonlinear optical properties of molecular polaritons as well as to analyze further multidimensional spectroscopy experiments on these systems.
How do restatements affect outside directors and boards? A review of the literature

Abstract This paper reviews academic literature related to the consequences that outside directors and boards may face in the wake of earnings restatements and suggests directions for future research. We examine loss of board seats; recruitment of new directors; proxy recommendations and shareholder support; pre-emptive director departures; director wealth effects; director reputation, litigation, and sanction risks; international evidence; and legal proposals for reform. The overall picture that emerges from the literature is that directors’ primary risk in the wake of earnings restatements is loss of board seats, in part through adverse proxy advisor recommendations and reduced shareholder support. Directors typically face little risk of legal liability or SEC sanctions, and some directors pre-emptively leave a problem company’s board and reduce their loss of interlocked board seats. Some legal scholars have called for director liability to be increased so as to promote more vigilant board oversight. Companies often focus on increasing the independence of the board in the wake of a restatement in an effort to repair organizational reputation. While researchers have revealed a host of important findings to date, much more can be learned about the effects of restatements on outside directors and boards.
Scaling Active Search using Linear Similarity Functions

Active Search has become an increasingly useful tool in information retrieval problems where the goal is to discover as many target elements as possible using only limited label queries. With the advent of big data, there is a growing emphasis on the scalability of such techniques to handle very large and very complex datasets. In this paper, we consider the problem of Active Search where we are given a similarity function between data points. We look at an algorithm introduced by Wang et al. [2013] for Active Search over graphs and propose crucial modifications which allow it to scale significantly. Their approach selects points by minimizing an energy function over the graph induced by the similarity function on the data. Our modifications require the similarity function to be a dot-product between feature vectors of data points, equivalent to having a linear kernel for the adjacency matrix. With this, we are able to scale tremendously: for $n$ data points, the original algorithm runs in $O(n^2)$ time per iteration while ours runs in only $O(nr + r^2)$ given $r$-dimensional features. We also describe a simple alternate approach using a weighted-neighbor predictor which also scales well. In our experiments, we show that our method is competitive with existing semi-supervised approaches. We also briefly discuss conditions under which our algorithm performs well.
Random Perturbation of Low Rank Matrices: Improving Classical Bounds

Abstract Matrix perturbation inequalities, such as Weyl's theorem (concerning the singular values) and the Davis–Kahan theorem (concerning the singular vectors), play essential roles in quantitative science; in particular, these bounds have found application in data analysis as well as related areas of engineering and computer science. In many situations, the perturbation is assumed to be random, and the original matrix has certain structural properties (such as having low rank). We show that, in this scenario, classical perturbation results, such as Weyl and Davis–Kahan, can be improved significantly. We believe many of our new bounds are close to optimal and also discuss some applications.
Tensor Regression Meets Gaussian Processes

Low-rank tensor regression, a new model class that learns high-order correlation from data, has recently received considerable attention. At the same time, Gaussian processes (GP) are well-studied machine learning models for structure learning. In this paper, we demonstrate interesting connections between the two, especially for multi-way data analysis. We show that low-rank tensor regression is essentially learning a multi-linear kernel in Gaussian processes, and the low-rank assumption translates to the constrained Bayesian inference problem. We prove the oracle inequality and derive the average case learning curve for the equivalent GP model. Our finding implies that low-rank tensor regression, though empirically successful, is highly dependent on the eigenvalues of covariance functions as well as variable correlations.
Gravitational wave astronomy and cosmology

a b s t r a c t The first direct observation of gravitational waves’ action upon matter has recently been reported by the BICEP2 experiment. Advanced ground-based gravitational-wave detectors are being installed. They will soon be commissioned, and then begin searches for high-frequency gravitational waves at a sensitivity level that is widely expected to reach events involving compact objects like stellar mass black holes and neutron stars. Pulsar timing arrays continue to improve the bounds on gravitational waves at nanohertz frequencies, and may detect a signal on roughly the same timescale as ground-based detectors. The science case for space-based interferometers targeting millihertz sources is very strong. The decade of gravitational-wave discovery is poised to begin. In this writeup of a talk given at the 2013 TAUP conference, we will briefly review the physics of gravitational waves and gravitational-wave detectors, and then discuss the promise of these measurements for making cosmological measurements in the near future. © 2014 The Author. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).
Machine-Learning-Augmented Predictive Modeling of Turbulent Separated Flows over Airfoils

A modeling paradigm is developed to augment predictive models of turbulence by effectively using limited data generated from physical experiments. The key components of the current approach involve...
Study of the fracturing behavior of thermoset polymer nanocomposites via cohesive zone modeling

Abstract This work proposes an investigation of the fracturing behavior of polymer nanocomposites . Towards this end, the study leverages the analysis of a large bulk of fracture tests from the literature with the goal of critically investigating the effects of the nonlinear Fracture Process Zone (FPZ). It is shown that for most of the fracture tests the effects of the nonlinear FPZ are not negligible, leading to significant deviations from Linear Elastic Fracture Mechanics (LEFM) sometimes exceeding 150% depending on the specimen size and nanofiller content. To get a deeper understanding of the characteristics of the FPZ, fracture tests on geometrically-scaled Single Edge Notch Bending (SENB) specimens are analyzed leveraging a cohesive zone model . It is found that the FPZ cannot be neglected and a bi-linear cohesive crack law generally provides the best match of the experimental data.
Behavioral Cloning from Observation

Humans often learn how to perform tasks via imitation: they observe others perform a task, and then very quickly infer the appropriate actions to take based on their observations. While extending this paradigm to autonomous agents is a well-studied problem in general, there are two particular aspects that have largely been overlooked: (1) that the learning is done from observation only (i.e., without explicit action information), and (2) that the learning is typically done very quickly. In this work, we propose a two-phase, autonomous imitation learning technique called behavioral cloning from observation (BCO), that aims to provide improved performance with respect to both of these aspects. First, we allow the agent to acquire experience in a self-supervised fashion. This experience is used to develop a model which is then utilized to learn a particular task by observing an expert perform that task without the knowledge of the specific actions taken. We experimentally compare BCO to imitation learning methods, including the state-of-the-art, generative adversarial imitation learning (GAIL) technique, and we show comparable task performance in several different simulation domains while exhibiting increased learning speed after expert trajectories become available.
A mean-variance control framework for platoon control problems: Weak convergence results and applications on reduction of complexity

This paper introduces a new approach of treating platoon systems using meanvariance control formulation. The underlying system is a controlled switching diffusion in which the random switching process is a continuous-time Markov chain. This switching process is used to represent random environment and other random factors that cannot be given by stochastic differential equations driven by a Brownian motion. The state space of the Markov chain is large in our setup, which renders practically infeasible a straightforward implementation of the mean-variance control strategy obtained in the literature. By partitioning the states of the Markov chain into sub-groups (or clusters) and then aggregating the states of each cluster as a super state, we are able to obtain a limit system of much reduced complexity. The justification of the limit system is rigorously supported by establishing certain weak convergence results.
Localization and the link floer homology of doubly-periodic knots

A knot \widetilde{K} \subset S^3 is q-periodic if there is a \mathbb Z_q-action preserving \widetilde{K} whose fixed set is an unknot U. The quotient of \widetilde{K} under the action is a second knot K. We construct equivariant Heegaard diagrams for q-periodic knots, and show that Murasugi's classical condition on the Alexander polynomials of periodic knots is a quick consequence of these diagrams. For \widetilde{K} a two-periodic knot, we show there is a spectral sequence whose E^1 page is \hat{\mathit{HFL}}(S^3,\widetilde{K}\cup U)\otimes V^{\otimes (2n-1)})\otimes \mathbb Z_2((\theta)) and whose E^{\infty} pages is isomorphic to (\hat{\mathit{HFL}}(S^3,K\cup U)\otimes V^{\otimes (n-1)})\otimes \mathbb Z_2((\theta)), as \mathbb Z_2((\theta))-modules, and a related spectral sequence whose E^1 page is (\hat{\mathit{HFK}}(S^3,\widetilde{K})\otimes V^{\otimes (2n-1)}\otimes W)\otimes \mathbb Z_2((\theta)) and whose E^{\infty} page is isomorphic to (\hat{\mathit{HFK}}(S^3,K)\otimes V^{\otimes (n-1)} \otimes W)\otimes \mathbb Z_2((\theta)). As a consequence, we use these spectral sequences to recover a classical lower bound of Edmonds on the genus of \widetilde{K}, along with a weak version of a classical fibredness result of Edmonds and Livingston.
High-order accurate FDTD schemes for dispersive Maxwell’s equations in second-order form using recursive convolutions

Abstract We propose a novel finite-difference time-domain (FDTD) scheme for the solution of Maxwell’s equations in which linear dispersive effects are present. The method uses high-order accurate approximations in space and time for the dispersive Maxwell’s equations written as a second-order vector wave equation with a time-history convolution term. The modified equation approach is combined with the recursive convolution (RC) method to develop high-order approximations accurate to any desired order in space and time. High-order-accurate centered approximations of the physical Maxwell interface conditions are derived for the dispersive setting in order to fully restore accuracy at discontinuous material interfaces. Second- and fourth-order accurate versions of the scheme are presented and implemented in two spatial dimensions for the case of the Drude linear dispersion model. The stability of these schemes is analyzed. Finally, our approach is also amenable to curvilinear numerical grids if used with an appropriate generalized Laplace operator.
A Tale of Two DRAGGNs: A Hybrid Approach for Interpreting Action-Oriented and Goal-Oriented Instructions

Robots operating alongside humans in diverse, stochastic environments must be able to accurately interpret natural language commands. These instructions often fall into one of two categories: those that specify a goal condition or target state, and those that specify explicit actions, or how to perform a given task. Recent approaches have used reward functions as a semantic representation of goal-based commands, which allows for the use of a state-of-the-art planner to find a policy for the given task. However, these reward functions cannot be directly used to represent action-oriented commands. We introduce a new hybrid approach, the Deep Recurrent Action-Goal Grounding Network (DRAGGN), for task grounding and execution that handles natural language from either category as input, and generalizes to unseen environments. Our robot-simulation results demonstrate that a system successfully interpreting both goal-oriented and action-oriented task specifications brings us closer to robust natural language understanding for human-robot interaction.
KoSzul duality for dioperads

We introduce the notion of a dioperad to describe certain operations with multiple inputs and multiple outputs. The framework of Koszul duality for operads is generalized to dioperads. We show that the Lie bialgebra dioperad is Koszul.
A Gross-Kohnen-Zagier formula for Heegner-Drinfeld cycles

Abstract Let F be the field of rational functions on a smooth projective curve over a finite field, and let π be an unramified cuspidal automorphic representation for PGL 2 over F. We prove a variant of the formula of Yun and Zhang relating derivatives of the L-function of π to the self-intersections of Heegner-Drinfeld cycles on moduli spaces of shtukas. In our variant, instead of a self-intersection, we compute the intersection pairing of Heegner-Drinfeld cycles coming from two different quadratic extensions of F, and relate the intersection to the r-th derivative of a product of two toric period integrals.