cssi/SciSciGPT-SciSciNet huggingface dataset:
Homologues of anti-HIV active isodideoxynucleosides

Abstract The synthesis of a homologous series of compounds related to the anti-HIV active class of compounds known as (S,S)-isodideoxynucleosides has been completed by a convergent route using a modified carbohydrate intermediate. This precursor, synthesized from d -glucose, was coupled with a variety of natural purine and pyrimidine bases to regiospecifically and stereospecifically afford the desired new class of compounds.
Mechanism and control of molecular energy flow: a modeling perspective

Vibrational energy flow in organic molecules occurs by a multiple-time-scale mechanism that can be modeled by a single exponential only in its initial stages. The mechanism is a consequence of the hierarchical structure of the vibrational Hamiltonian, which leads to diffusion of vibrational wavepackets on a manifold with far fewer than the 3N−6 dimensions of the full vibrational state space. The dynamics are controlled by a local density of states, which does not keep increasing with molecular size. In addition, the number of vibrational coordinates severely perturbed during chemical reaction is small, leading to preservation of the hierarchical structure at chemically interesting energies. This regularity opens up the possibility of controlling chemical reactions by controlling the vibrational energy flow. Computationally, laser control of intramolecular vibrational energy redistribution can be modeled by quantum-classical, or by purely quantum-mechanical models of the molecule and control field.
Persistent coding of outcome-predictive cue features in the rat nucleus accumbens

The nucleus accumbens (NAc) is important for learning from feedback, and for biasing and invigorating behaviour in response to cues that predict motivationally relevant outcomes. NAc encodes outcome-related cue features such as the magnitude and identity of reward. However, little is known about how features of cues themselves are encoded. We designed a decision making task where rats learned multiple sets of outcome-predictive cues, and recorded single-unit activity in the NAc during performance. We found that coding of cue identity and location occurred alongside coding of expected outcome. Furthermore, this coding persisted both during a delay period, after the rat made a decision and was waiting for an outcome, and after the outcome was revealed. Encoding of cue features in the NAc may enable contextual modulation of on-going behaviour, and provide an eligibility trace of outcome-predictive stimuli for updating stimulus-outcome associations to inform future behaviour.
Nickel-Catalyzed Cyclizations of Enoate Equivalents: Application to the Synthesis of Angular Triquinanes

Unsaturated acyloxazolidinones and α‘-silyloxy enones were found to be effective substrates in nickel-catalyzed organozinc-promoted cyclizations. Both groups served as convenient enoate equivalents, whereas methyl enoates themselves were inefficient substrates. A five-step procedure for the conversion of dimethylcyclopentenone into a highly functionalized angular triquinane was developed utilizing this observation. The key step of the procedure involves a nickel-catalyzed reductive cyclization/Dieckmann condensation sequence involving a cyclic enone tethered to an unsaturated acyloxazolidinone or α‘-silyloxy enone. The method was applied in a formal synthesis of pentalenene, pentalenic acid, and deoxypentalenic acid.
Regiospecific Control of Additions of 4-Substituted 3,5-Dimethylisoxazoles to α,β Unsaturated Carbonyls

Transmetalation of C-5-lithiomethylisoxazoles with the lower-order cuprate reagent lithium thienylcyanocuprate (Li[ThCuCN]) in THF results in exclusive conjugate addition to α,β-unsaturated carbonyls. In contrast, transmetalation with samarium tris(hexamethyldisilazide) (Sm[HMDS]3) in diethyl ether directs 1,2-carbonyl addition. In both cases, optimum results were realized with a 4,5-dihydro-4,4-dimethyl-Δ2-oxazoline substituent at the C-4 position of the isoxazole.
G2 AB INITIO CALCULATIONS OF ENTHALPIES OF HYDROGENATION, ISOMERIZATION, AND FORMATION OF C3 CYCLIC AND ACYCLIC KETONES AND ALCOHOLS

We report the ab initio G2 enthalpies of hydrogenation and isomerization (ΔhydH and ΔisomH) in the gaseous state, at 298 K, of 8 C3 cyclic and acyclic ketones and alcohols, including cyclopropenone, cyclopropenol, and allyl alcohol. ΔhydH298 and ΔisomH298 are found from the differences in total energy (E0) of the participants in the hydrogenation and isomerization reactions. Combination of calculated ΔhydH298 and ΔisomH298 with one experimental enthalpy of formation (ΔfH298) in the set yields ΔfH298 of all the rest. Results lead to an estimate of 20.5 kcal mol-1 for the resonance energy of cyclopropenone.
A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality.

There does not currently exist a standardized indicator of how well cryo-EM-derived models represent the density from which they were generated. We present a straightforward methodology that utilizes freely available tools to generate a suite of independent models and to evaluate their convergence in an EM density. These analyses provide both a quantitative and qualitative assessment of the precision of the models and their representation of the density, respectively, while concurrently providing a platform for assessing both global and local EM map quality. We further use standardized datasets to provide an expected deviation within a suite of models refined against EM maps reported to be at 5 A resolution or better. Associating multiple atomic models with a deposited EM map provides a rapid and accessible reporter of convergence, a strong indicator of highly resolved molecular detail, and is an important step toward an FSC-independent assessment of map and model quality.
Kinetic study and determination of the enthalpies of activation of the dehydrogenation of titanium- and zirconium-doped NaAlH4 and Na3AlH6

The rates of the dehydrogenation of the sodium alanates NaAlH4 and Na3AlH6 doped with 2 mol % Ti or Zr have been measured over the temperature range 363−423 K. NaAlH4 and Na3AlH6 undergo dehydrogenation at equal rates upon direct doping with titanium. However, Na3AlH6 arising from the dehydrogenation of Ti-doped NaAlH4 undergoes dehydrogenation at much slower rates. Rate constants were determined from the slopes of the dehydrogenation profiles. On the basis of Eyring theory, the enthalpies of activation, ΔH⧧, for the dehydrogenation reactions were determined to be ∼100 kJ·mol-1 for both Ti-doped NaAlH4 and Na3AlH6 and ∼135 kJ·mol-1 for both Zr-doped NaAlH4 and Na3AlH6. These results suggest that the dehydrogenation reaction pathways are highly sensitive to the nature and distribution of the dopant but not to differences in the Al−H bonding interactions in [AlH4]- and [AlH6]3- complex anions. Furthermore, we conclude that the kinetics are probably influenced by processes such as nucleation and growth and/o...
Synthesis and Characterization of Uranium(IV)-Bearing Members of the [NZP] Structural Family

The sodium dizirconium tris(phosphate) structural family ([NZP]) includes compounds that may be represented by the general formula M‘M‘ ‘1-3A2(PO4)3. The ability of KZr2(PO4)3, a member of the [NZP] structural family, to accommodate U(IV) on the octahedrally coordinated A site has been demonstrated for compounds in the series KZr2-xUx(PO4)3 (0 ≤ x ≤ 0.20). KU2(PO4)3, the end member of the series, was found to adopt a monoclinic structure with 9-fold coordination of U(IV) that does not belong to the [NZP] family. The compounds were prepared from sol−gel derived precursors in an argon environment. X-ray microanalyses indicated that the precursor powders had reacted fully to produce compounds of the expected stoichiometries. Rietveld refined X-ray powder diffraction data of KZr2-xUx(PO4)3 (0 ≤ x ≤ 0.20) confirmed a rhombohedral (R3c) structure and suggested random occupation of the A site by U/Zr. The presence of U(IV) was established by comparison of the UV/vis spectra of KZr2-xUx(PO4)3 (0 ≤ x ≤ 0.20) with...
Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: a whole genome comparison of two spacecraft assembly facility isolates

Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spores resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. pumilus SAFR-032, and the draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. pumilus ATCC7061T. Additional comparisons were made to 61 draft genomes that have been mostly identified as strains of B. pumilus or B. safensis. The FO-36b gene order is essentially the same as that in SAFR-032 and other B. pumilus strains. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by MERTA and ATCC7061T. The FO-36b genome has ten unique open reading frames and two phage-like regions, homologous to the Bacillus bacteriophage SPP1 and Brevibacillus phage Jimmer1. Differing remnants of the Jimmer1 phage are found in essentially all B. safensis / B. pumilus strains. Seven unique genes are part of these phage elements. Whole Genome Phylogenetic Analysis of the B. pumilus, B. safensis and other Firmicutes genomes, separate them into three distinct clusters. Two clusters are subgroups of B. pumilus while one houses all the B. safensis strains. The Genome-genome distance analysis and a phylogenetic analysis of gyrA sequences corroborated these results. It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism’s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. Multiple genome comparison indicates that many strains named as B. pumilus likely belong to the B. safensis group.
The job rating game: Revolving doors and analyst incentives

Abstract Investment banks frequently hire analysts from rating agencies. While many argue that this “revolving door” creates captured analysts, it can also create incentives to improve accuracy. To study this issue, I construct an original data set, linking analysts to their career paths and the securitized finance ratings they issue. First, I show that accurate analysts are more frequently hired by underwriting investment banks. Second, I exploit two distinct sources of variation in the likelihood of being hired by a bank. Both indicate that, as this likelihood rises, analyst accuracy improves. The findings suggest policymakers should consider incentive effects alongside capture concerns.
Lithium N-trityl-N-(R)-1-phenethylamide, a readily available and useful base for the enantioselective formation of chiral enolates from achiral ketones

Abstract Lithium N-trityl-N-(R)-1-phenylethylamide (6) is a readily available and useful reagent for the enantioselective (20:1) conversion of 4-t-butylcyclohexanone to the corresponding (S)-enolate. This reaction provides access to numerous useful chiral compounds.
DNCON2: improved protein contact prediction using two-level deep convolutional neural networks.

Motivation Significant improvements in the prediction of protein residue-residue contacts are observed in the recent years. These contacts, predicted using a variety of coevolution-based and machine learning methods, are the key contributors to the recent progress in ab initio protein structure prediction, as demonstrated in the recent CASP experiments. Continuing the development of new methods to reliably predict contact maps is essential to further improve ab initio structure prediction. Results In this paper we discuss DNCON2, an improved protein contact map predictor based on two-level deep convolutional neural networks. It consists of six convolutional neural networks-the first five predict contacts at 6, 7.5, 8, 8.5 and 10 A distance thresholds, and the last one uses these five predictions as additional features to predict final contact maps. On the free-modeling datasets in CASP10, 11 and 12 experiments, DNCON2 achieves mean precisions of 35, 50 and 53.4%, respectively, higher than 30.6% by MetaPSICOV on CASP10 dataset, 34% by MetaPSICOV on CASP11 dataset and 46.3% by Raptor-X on CASP12 dataset, when top L/5 long-range contacts are evaluated. We attribute the improved performance of DNCON2 to the inclusion of short- and medium-range contacts into training, two-level approach to prediction, use of the state-of-the-art optimization and activation functions, and a novel deep learning architecture that allows each filter in a convolutional layer to access all the input features of a protein of arbitrary length. Availability and implementation The web server of DNCON2 is at http://sysbio.rnet.missouri.edu/dncon2/ where training and testing datasets as well as the predictions for CASP10, 11 and 12 free-modeling datasets can also be downloaded. Its source code is available at https://github.com/multicom-toolbox/DNCON2/. Contact chengji@missouri.edu. Supplementary information Supplementary data are available at Bioinformatics online.
5,7,12,14-Tetramethyldimethoxybenzo[b,i][1,4,8,11]tetraazacyclodecine, a new tumoricidal pseudo-porphyrin

The title compound, a mixture of two isomers differing in the position of a methoxy substituent in one benzene ring, was obtained in a Ni-templated synthesis directly as a water soluble dihydrochloride of the free base. The cyclic voltametry study indicated that in a neutral solution the reduction and oxidation are irreversible one electron processes, the latter leading to cation radical undergoing polymerization, a process followed by deposition of a film on the electrode. In 1,2-dichloroethane the cation radical is oxidized to a dication, both species being much less stable than those originating from meso-tetraphenylporphyrin. The title compoud at 2.5 × 10−5 M in Tris buffer showed a 50% inhibition of the growth of malignant melanoma cells as compared to a 44% inhibition shown by a water soluble meso-monomethoxy-tris(N-methylpyridinium)porphyrin. The exposure to light for 30 minutes at 2.5 times smaller concentration increased the inhibition caused by the pseudo-porphyrin from 9% to 49%.
Organoyttrium-catalyzed sequential Cyclization/Silylation reactions of nitrogen-heteroaromatic dienes demonstrating "Aryl-Directed" regioselectivity

The reaction of 1-allyl-2-vinyl-1H-pyrroles and 1-allyl-2-vinyl-1H-indoles with arylsilanes in the presence of catalytic [CpTMS2Y(μ-Me)]2 leads to highly selective cyclization/silylation events. In this process the active catalyst for the reaction, “CpTMS2YH”, undergoes initial olefin insertion at the vinyl group. Even isopropenyl substituents on the heteroaromatics react in preference to less sterically encumbered allyl groups. Furthermore, the observed regioselectivity reflects an “aryl-directed” process, whereby the more highly substituted secondary or tertiary organometallic is initially generated. This intermediate undergoes cyclization onto the remaining alkene and subsequent silylation by a σ-bond metathesis reaction, affording the observed products.
Germanium Nanowire Growth via Simple Vapor Transport

Germanium nanowires are synthesized in bulk quantities and high purity using a simple vapor transport process. X-ray diffraction, scanning electron microscopy and transmission electron microscopy studies show that these wires are single crystalline with [111] growth direction; they have diameters ranging from 5 to 300 nm, and lengths up to hundreds micrometer. With brief vacuum thermal treatment, the average diameters of the wires can be further reduced to 16 nm.
Investigation of the Binding of Fluorolumazines to the 1-MDa Capsid of Lumazine Synthase by 15N{19F} REDOR NMR

The 15N{19F} REDOR NMR spectra of two fluorolumazines complexed to the 1-MDa β60 capsid of lumazine synthase have been obtained at 20.3 and 50.7 MHz. Distances from CF3 groups of the ligands to six...
Signals of Variation in Human Mutation Rate at Multiple Levels of Sequence Context

Our understanding of the human mutation rate helps us build evolutionary models and interpret patterns of genetic variation observed in human populations. Recent work indicates that the frequencies of specific polymorphism types have been elevated in Europe, and that many more, subtler signatures of global polymorphism variation may yet remain unidentified. Here, we present an analysis of the 1000 Genomes Project supported by analysis in the Simons Genome Diversity Panel, suggesting additional putative signatures of mutation rate variation across populations and the extent to which they are shaped by local sequence context. First, we compiled a list of the most significantly variable polymorphism types in a cross-continental statistical test. Clustering polymorphisms together, we observe three sets that showed distinct shared patterns of relative enrichment among ancestral populations, and we characterize each one of these putative "signatures" of polymorphism variation. For three of these signatures, we found that a single flanking base pair of sequence context was sufficient to determine the majority of enrichment or depletion of a polymorphism type. However, local genetic context up to 2-3 bp away contributes additional variability and may help to interpret a previously noted enrichment of certain polymorphism types in some East Asian groups. Moreover, considering broader local genetic context highlights patterns of polymorphism variation, which were not captured by previous approaches. Building our understanding of mutation rate in this way can help us to construct more accurate evolutionary models and better understand the mechanisms that underlie genetic change.
Dissection of MAPK signaling specificity through protein engineering in a developmental context

Mitogen-activated protein kinases (MAPK) signaling affects many processes, some of which have different outcomes in the same cell. In Arabidopsis, activation of a MAPK cascade consisting of YODA, MKK4/5 and MPK3/6 inhibits early stages of stomatal developmental, but the ability to halt stomatal progression is lost at the later stage when guard mother cells (GMCs) transition to guard cells (GCs). Rather than downregulating cascade components, stomatal precursors must have a mechanism to prevent late stage inhibition because the same MKKs and MPKs mediate other physiological responses. We artificially activated the MAPK cascade using MKK7, another MKK that can modulate stomatal development, and found that inhibition of stomatal development is still possible in GMCs. This suggests that MKK4/5, but not MKK7, are specifically prevented from inhibiting stomatal development. To identify regions of MKKs responsible for cell-type specific regulation, we used a domain swap approach with MKK7 and a battery of in vitro and in vivo kinase assays. We found that N-terminal regions of MKK5 and MKK7 establish specific signal-to-output connections like they do in other organisms, but they do so in combination with previously undescribed modules in the C-terminus. One of these modules encoding the GMC-specific regulation of MKK5, when swapped with sequences from the equivalent region of MKK7, allows MKK5 to mediate robust inhibition of late stomatal development. Because MKK structure is conserved across species, the identification of new MKK specificity modules and signaling rules furthers our understanding of how eukaryotes create specificity in complex biological systems.
Seeding with Costly Network Information

Seeding the most influential individuals based on the contact structure can substantially enhance the extent of a spread over the social network. Most of the influence maximization literature assumes the knowledge of the entire network graph. However, in practice, obtaining full knowledge of the network structure is very costly. We propose polynomial-time algorithms that provide almost tight approximation guarantees using a bounded number of queries to the graph structure. We also provide impossibility results to lower bound the query complexity and show tightness of our guarantees.
Intrinsic checkpoint deficiency during cell cycle re-entry from quiescence

To maintain tissue homeostasis, cells transition between cell cycle quiescence and proliferation. An essential G1 process is minichromosome maintenance complex (MCM) loading at DNA replication origins to prepare for S phase, known as origin licensing. A p53-dependent origin licensing checkpoint normally ensures sufficient MCM loading before S phase entry. We used quantitative flow cytometry and live cell imaging to compare MCM loading during the long first G1 upon cell cycle entry and the shorter G1 phases in the second and subsequent cycles. We discovered that despite the longer G1 phase, the first G1 after cell cycle re-entry is significantly underlicensed. Consequently, the first S phase cells are hypersensitive to replication stress. This underlicensing results from a combination of slow MCM loading with a severely compromised origin licensing checkpoint. The hypersensitivity to replication stress increases over repeated rounds of quiescence. Thus, underlicensing after cell cycle re-entry from quiescence distinguishes a higher-risk first cell cycle that likely promotes genome instability.
In Situ Studies of Nitridation of Zirconia (ZrO2)

The nitridation of an amorphous ZrO2 ·H2O precursor with gaseous ammonia has been studied by in situ X-ray powder diffraction (temperature range 25−1100 °C), electron diffraction (temperature range...
FORMAL SYNTHESIS OF HAPALINDOLE O AND SYNTHETIC EFFORTS TOWARDS HAPALINDOLE K AND AMBIGUINE A

The formal synthesis of D,L-hapalindole O has been accomplished intercepting Natsume's total synthesis route. The intercepted substrate was synthesized in an overall 36% yield over ten-synthetic steps compared to Natsume's overall 1% yield over eighteen-synthetic steps. In addition, advanced substrates for the continuing progress towards hapalindole K and ambiguine A has been synthesized. All routes described herein employ a novel silyl ether-based strategy accessing the 6:5:6:6 ring system, that has previously been used in our laboratory to access the total synthesis of D,L-hapalindoles J and U.
Lipid Bilayers, NMR Relaxation, and Computer Simulations

Brownian and molecular dynamics simulations of a lipid bilayer are described, and the calculated frequency-dependent (13)C NMR T(1) relaxation times are compared with experiment. A consistent model emerges. Through fast internal motions, individual lipids average themselves into relatively cylindrical shapes on the 100 ps time scale and "wobble" in a cone-like potential on the nanosecond time scale. These motions take place in a highly fluid environment, much like a liquid alkane. Lateral diffusion of the lipids is on a significantly longer time scale because of restrictions at the bilayer/water interface, not because the interior of the bilayer is highly viscous.
Podocarpaside, a triterpenoid possessing a new backbone from Actaea podocarpa.

Podocarpaside (1), a novel arabinoside possessing a unique triterpene skeleton was isolated from Actaea podocarpa, a closely related species to black cohosh (dietary supplement used for menopausal disorders). Podocarpaside belongs to a new class of triterpenoids, for which the name “ranunculane” is proposed. Compound 1 possesses anticomplement activity.
Supermassive black holes in the early universe

The emergence of the first black holes during the first billion years of cosmic history marks a key event in cosmology. Their formation is part of the overall process of ending the cosmic d...
Reaction of the hydroxy groups of zeolites with phosphorylating agents

Hydroxy groups on the surface of zeolite Y can be converted to phosphate groups by reaction with alkyl phosphoric acids as well as with metaphosphates when generated in the presence of the solid. Phosphonic and phosphinic acids also reacted readily with the OH groups. The products were characterized by 31P, 29Si, and 27Al NMR spectroscopy. © 1998 John Wiley & Sons, Inc. Heteroatom Chem 9: 691–698, 1998
Studies on the total synthesis of formamicin: synthesis of the C(1)-C(11) fragment.

An efficient and highly concise synthesis of 6, corresponding to the C(1)−C(11) fragment of formamicin (1), has been accomplished by a route utilizing a diastereoselective lactate aldol reaction to set the C(6) tertiary ether and the TES−OTf mediated transketalization of the C(6) tertiary methoxymethyl ether and the C(25) PMB ether to set the seven-membered methylene acetal unit (see 37 → 38).
Stereoselective synthesis of tetrahydrofurans: reactions of protected β-hydroxy ketones with benzyl diazoacetate

Abstract The stereoselective synthesis of 2,3,3,4-tetrasubstituted tetrahydrofurans from the Lewis acid catalyzed reaction of protected β-hydroxy ketones with benzyl diazoacetate is described. The reaction can be used to set three contiguous stereocenters including one that is a tertiary alcohol.
Fast animal pose estimation using deep neural networks.

The need for automated and efficient systems for tracking full animal pose has increased with the complexity of behavioral data and analyses. Here we introduce LEAP (LEAP estimates animal pose), a deep-learning-based method for predicting the positions of animal body parts. This framework consists of a graphical interface for labeling of body parts and training the network. LEAP offers fast prediction on new data, and training with as few as 100 frames results in 95% of peak performance. We validated LEAP using videos of freely behaving fruit flies and tracked 32 distinct points to describe the pose of the head, body, wings and legs, with an error rate of <3% of body length. We recapitulated reported findings on insect gait dynamics and demonstrated LEAP’s applicability for unsupervised behavioral classification. Finally, we extended the method to more challenging imaging situations and videos of freely moving mice. LEAP is a deep-learning-based approach for the analysis of animal pose. LEAP’s graphical user interface facilitates training of the deep network. The authors illustrate the method by analyzing Drosophila and mouse behavior.
Self-propelled particle in a nonconvex external potential: Persistent limit in one dimension.

Equilibrium mapping techniques for nonaligning self-propelled particles have made it possible to predict the density profile of an active ideal gas in a wide variety of external potentials. However, they fail when the self-propulsion is very persistent and the potential is nonconvex, which is precisely when the most uniquely active phenomena occur. Here, we show how to predict the density profile of a 1D active Ornstein-Uhlenbeck particle in an arbitrary external potential in the persistent limit and discuss the consequences of the potential’s nonconvexity on the structure of the solution, including the central role of the potential’s inflection points and the nonlocal dependence of the density profile on the potential.
Chemodivergent transformations of alkynyl imines

The investigation of cycloisomerization cascades of alkynyl imines towards pyrroles unexpectedly led to the development of chemodivergent routes towards quinolines and fused pyrrolines. It was found that, depending on the nature of the nitrogen substituent and choice of reagents, up to three different heterocyclic cores can be accessed from a common structural precursor.
SYNTHESIS OF SOME SUBSTITUTED DIBENZODIAZEPINONES AND PYRIDOBENZODIAZEPINONES

Some fluoro- and iodo-derivative of 5-[[4-[(4-diisobutylamino)butyl]-1-phenyl]acetyl]-10,11-dihydro-5H-dibenzo[b,e][1,4]diazepin-1l-one and 11-[[4-[(dialkylamino)butyl]-1-phenyl]acetyl]-5,11-dihydro-6H-pyrido[2,3-b][1,4]benzodiazepin-6-ones 6 (Scheme 1) and their analogues were synthesized. The synthesis of dibenzodiazepinones 1 (Scheme 1) is based on the reaction between 1,4-phenylenediamine and substituted benzoic acids. The intermediate pyridobenzodiazepinones 3 (Scheme 1) were prepared by condensation of 2-chloro-3-aminopyridine with methyl anthranilate and its chlorine derivative. The condensation of 4-[(halo)alkyl]phenylacetyl chloride with dibenzodiazepinones and pyridobenzodiazepinones followed by the reaction of mono- or dialkyl- or dialkenylamine provides 6 (Scheme 1).
AKT: ancestry and kinship toolkit.

Motivation: Ancestry and Kinship Toolkit (AKT) is a statistical genetics tool for analysing large cohorts of whole-genome sequenced samples. It can rapidly detect related samples, characterize sample ancestry, calculate correlation between variants, check Mendel consistency and perform data clustering. AKT brings together the functionality of many state-of-the-art methods, with a focus on speed and a unified interface. We believe it will be an invaluable tool for the curation of large WGS datasets. Availability and Implementation: The source code is available at https://illumina.github.io/akt. Contacts: joconnell@illumina.com or rudy.d.arthur@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
Incompressibility and Hardness of Solid Solution Transition Metal Diborides: Os1−xRuxB2

Interest in new ultraincompressible hard materials has prompted studies of transition metal diboride solid solutions. We have synthesized pure RuB2 and solid solutions of Os1−xRuxB2. The mechanical properties of these materials are investigated using in situ high-pressure X-ray diffraction and Vickers hardness testing techniques. Both bulk moduli and hardness vary linearly with composition in accordance with Vegard’s law, whereas the differing behavior among end-members can be explained by relativistic effects, core electron density, and differences in the cohesive energy of the parent metals. The results provide a refinement of the rules previously reported for the design of new superhard materials.
Recent Developments in the Syntheses of the Epothilones and Related Analogues

The macrocyclic class of antitumor compounds known as the epothilones has generated considerable interest since its discovery in 1993. Numerous total syntheses of this class of molecules have been published and countless structural analogues have been developed and tested for their abilities to promote tubulin polymerization. Several of these compounds are presently in clinical trials.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Elaboration of 1,8-naphthyridine-2,7-dicarboxaldehyde into novel 2,7-dimethylimine derivatives

The known 1,8-naphthyridine-2,7-dicarboxaldehyde was prepared by SeO2 oxidation of 2,7-dimethyl-1,8-naphthyridine. The dimethylated naphthyridine molecule was assembled from an adaptation of the Skraup synthesis using 2-amino-6-methylpyridine and crotonaldehyde to afford a reproducible 37% yield, and constitute a significant advance over the literature of this reaction. The condensation of 1,8-naph-thyridine-2,7-dicarboxaldehyde with various primary amines (R = -C6H11, -CH2C6H5, -C(CH3)3, -C10H15, and CH2CH2SCH2CH3) in alcohol affords diimines 1(a-e). The inherent crystallinity of 1(a-e) affords pure compounds in reasonable to excellent yields (ca. 70%) after evaporation of solvent and recrystallization. The anticipated spectroscopic features of (N=C-H) 1H nmr shift and v(C=N) in the ir spectrum appear around 8.50 δ and 1640 cm−1, respectively, for the series 1(a-e). These novel naph-thyridines typically display the signature 1H nmr doublets at ca. 8.15-8.30 δ ascribed to the 3 and 4 naphthyridine protons, consistent with a mirror plane (through the quaternary carbons) perpendicular to the naphthyridine plane, and syn, syn relationships of the naphthyridine moiety with each imine nitrogen lone pair. Complexation studies of 1(a-e) with transition metals of biological relevance such as copper(I) and copper(II) will be reported elsewhere.
Deposit insurance, remittances, and dollarization: Survey‐based evidence from a top remittance‐receiving country

The paper uses a unique survey of remittance-receiving individuals from Tajikistan to study the impact of policy awareness on consumer behavior. The results show that knowledge of deposit insurance encourages the use of formal channels for transmitting remittances and reduces dollarization. Given the size and importance of remittances in Tajikistan, improving financial literacy and better publicizing details of the social safety net may encourage a more frequent use of formal channels for transferring remittances and reduce reliance on foreign exchange for transaction purposes. This is likely to improve bank profitability, enhance financial stability, and improve access to finance.
Evaluating the role of fish as surrogates for amphibians in pesticide ecological risk assessment.

Abstract Ecological risk of chemicals to aquatic-phase amphibians has historically been evaluated by comparing estimated environmental concentrations in surface water to surrogate toxicity data from fish species. Despite their obvious similarities, there are biological disparities among fish and amphibians that could affect their exposure and response to chemicals. Given the alarming decline in amphibians, in which anthropogenic pollutants play at least some role, investigating the risk of chemicals to amphibians is becoming increasingly important. Here, we evaluate relative sensitivity of fish and larval aquatic-phase amphibians to 45 different pesticides using existing data from three standardized toxicity test designs: (1) amphibian metamorphosis assay (AMA) with the African clawed frog (Xenopus laevis); (2) fish short-term reproduction assay (FSTRA) with the fathead minnow (Pimephales promelas); (3) fish early life stage test (ELS) with fathead minnows or rainbow trout (Oncorhynchus mykiss). The advantage of this dataset over previous work is that the underlying studies are consistent in exposure method, study duration, test species, endpoints measured, and number of concentrations tested. We found very strong positive relationships between fish and frog lowest adverse effect concentrations (LOAEC) for survival [Spearman's rank correlation (rs) = 0.88], body weight (rs = 0.86), and length (rs = 0.89) with only one out of 45 chemicals (propiconazole) exhibiting 100-folder greater sensitivity in frogs relative to fish. While our results suggest comparable toxicity for pesticides between fish and aquatic-phase amphibians under these test conditions, further research with a greater diversity of amphibians and exposure scenarios will help determine the relevance of these results across species and life stages.
Kei modules and unoriented link invariants

We define invariants of unoriented knots and links by enhancing the integral kei counting invariant Phi_X^Z (K) for a finite kei X using representations of the kei algebra, Z_K[X], a quotient of the quandle algebra Z[X] defined by Andruskiewitsch and Grana. We give an example that demonstrates that the enhanced invariant is stronger than the unenhanced kei counting invariant. As an application, we use a quandle module over the Takasaki kei on Z_3 which is not a Z_K[X]-module to detect the non-invertibility of a virtual knot.
Stability of Relative Equilibria in the Planar $n$-Vortex Problem

We study the linear and nonlinear stability of relative equilibria in the planar $n$-vortex problem, adapting the approach of Moeckel from the corresponding problem in celestial mechanics. After establishing some general theory, a topological approach is taken to show that for the case of positive circulations, a relative equilibrium is linearly stable if and only if it is a nondegenerate minimum of the Hamiltonian restricted to a level surface of the angular impulse (moment of inertia). Using a criterion of Dirichlet's, this implies that any linearly stable relative equilibrium with positive vorticities is also nonlinearly stable. Two symmetric families, the rhombus and the isosceles trapezoid, are analyzed in detail, with stable solutions found in each case.
Optimal data attacks on power grids: Leveraging detection & measurement jamming

Meter measurements in the power grid are susceptible to manipulation by adversaries that can lead to errors in state estimation. This paper presents a general framework to study attacks on state estimation by adversaries capable of injecting bad-data into measurements and further, of jamming their reception. Through these two techniques, a novel ‘detectable jamming’ attack is designed that changes the state estimation despite failing bad-data detection checks. Compared to commonly studied ‘hidden’ data attacks, these attacks have lower costs and a wider feasible operating region. It is shown that the entire domain of jamming costs can be divided into two regions, with distinct graph-cut based formulations for the design of the optimal attack. The most significant insight arising from this result is that the adversarial capability to jam measurements changes the optimal ‘detectable jamming’ attack design only if the jamming cost is less than half the cost of bad-data injection. A polynomial time approximate algorithm for attack vector construction is developed and its efficacy in attack design is demonstrated through simulations on IEEE test systems.
Sequential experimentation to efficiently test automated vehicles

Automated vehicles have been under heavy developments in major auto and tech companies and are expected to release into market in the foreseeable future. However, the road safety of these vehicles remains a concern. One approach to evaluate their safety is via on-track experimentation, but this requires gigantic costs and time investments. This paper discusses a sequential learning approach based on kriging models to reduce the experimental runs and economize on-track experimentation. The approach relies on a heuristic simulation-based gradient descent procedure to search for the best next test scenario. We demonstrate our approach with some numerical test cases.
How deep is the feature analysis underlying rapid visual categorization

Rapid categorization paradigms have a long history in experimental psychology: Characterized by short presentation times and speeded behavioral responses, these tasks highlight the efficiency with which our visual system processes natural object categories. Previous studies have shown that feed-forward hierarchical models of the visual cortex provide a good fit to human visual decisions. At the same time, recent work in computer vision has demonstrated significant gains in object recognition accuracy with increasingly deep hierarchical architectures. But it is unclear how well these models account for human visual decisions and what they may reveal about the underlying brain processes. We have conducted a large-scale psychophysics study to assess the correlation between computational models and human behavioral responses on a rapid animal vs. non-animal categorization task. We considered visual representations of varying complexity by analyzing the output of different stages of processing in three state-of-the-art deep networks. We found that recognition accuracy increases with higher stages of visual processing (higher level stages indeed outperforming human participants on the same task) but that human decisions agree best with predictions from intermediate stages. Overall, these results suggest that human participants may rely on visual features of intermediate complexity and that the complexity of visual representations afforded by modern deep network models may exceed the complexity of those used by human participants during rapid categorization.
Integrating Human-Provided Information into Belief State Representation Using Dynamic Factorization

In partially observed environments, it can be useful for a human to provide the robot with declarative information that represents probabilistic relational constraints on properties of objects in the world, augmenting the robot's sensory observations. For instance, a robot tasked with a search-and-rescue mission may be informed by the human that two victims are probably in the same room. An important question arises: how should we represent the robot's internal knowledge so that this information is correctly processed and combined with raw sensory information? In this paper, we provide an efficient belief state representation that dynamically selects an appropriate factoring, combining aspects of the belief when they are correlated through information and separating them when they are not. This strategy works in open domains, in which the set of possible objects is not known in advance, and provides significant improvements in inference time over a static factoring, leading to more efficient planning for complex partially observed tasks. We validate our approach experimentally in two open-domain planning problems: a 2D discrete gridworld task and a 3D continuous cooking task. A supplementary video can be found at http://tinyurl.com/chitnis-iros-18.
Im2Pano3D: Extrapolating 360° Structure and Semantics Beyond the Field of View

We present Im2Pano3D, a convolutional neural network that generates a dense prediction of 3D structure and a probability distribution of semantic labels for a full 360° panoramic view of an indoor scene when given only a partial observation (= 50%) in the form of an RGB-D image. To make this possible, Im2Pano3D leverages strong contextual priors learned from large-scale synthetic and real-world indoor scenes. To ease the prediction of 3D structure, we propose to parameterize 3D surfaces with their plane equations and train the model to predict these parameters directly. To provide meaningful training supervision, we use multiple loss functions that consider both pixel level accuracy and global context consistency. Experiments demonstrate that Im2Pano3D is able to predict the semantics and 3D structure of the unobserved scene with more than 56% pixel accuracy and less than 0.52m average distance error, which is significantly better than alternative approaches.
Exact MAP Inference by Avoiding Fractional Vertices

Given a graphical model, one essential problem is MAP inference, that is, finding the most likely configuration of states according to the model. Although this problem is NP-hard, large instances can be solved in practice. A major open question is to explain why this is true. We give a natural condition under which we can provably perform MAP inference in polynomial time. We require that the number of fractional vertices in the LP relaxation exceeding the optimal solution is bounded by a polynomial in the problem size. This resolves an open question by Dimakis, Gohari, and Wainwright. In contrast, for general LP relaxations of integer programs, known techniques can only handle a constant number of fractional vertices whose value exceeds the optimal solution. We experimentally verify this condition and demonstrate how efficient various integer programming methods are at removing fractional solutions.
An Optimal Control Approach for the Data Harvesting Problem

We propose a new method for trajectory planning to solve the data harvesting problem. In a two-dimensional mission space, N mobile agents are tasked with the collection of data generated at M stationary sources and delivery to a base aiming at minimizing expected delays. An optimal control formulation of this problem provides some initial insights regarding its solution, but it is computationally intractable, especially in the case where the data generating processes are stochastic. We propose an agent trajectory parameterization in terms of general function families which can be subsequently optimized on line through the use of Infinitesimal Perturbation Analysis (IPA). Explicit results are provided for the case of elliptical and Fourier series trajectories and some properties of the solution are identified, including robustness with respect to the data generation processes and scalability in the size of an event set characterizing the underlying hybrid dynamic system.
TeV gamma rays from Galactic Center pulsars

Abstract Measurements of the nearby pulsars Geminga and B0656+14 by the HAWC and Milagro telescopes have revealed the presence of bright TeV-emitting halos surrounding these objects. If young and middle-aged pulsars near the Galactic Center transfer a similar fraction of their energy into TeV photons, then these sources could plausibly dominate the emission that is observed by HESS and other ground-based telescopes from the innermost ∼ 1 0 2 pc of the Milky Way. In particular, both the spectral shape and the angular extent of this emission is consistent with TeV halos produced by a population of pulsars, although the reported correlation of this emission with the distribution of molecular gas suggests that diffuse hadronic processes also must contribute. The overall flux of this emission requires a birth rate of ∼ 100–1000 neutron stars per Myr near the Galactic Center, in good agreement with recent estimates.
Interlacement and activities in delta-matroids

Abstract We generalize theories of graph, matroid, and ribbon-graph activities to delta-matroids. As a result, we obtain an activity based feasible-set expansion for a transition polynomial of delta-matroids defined by Brijder and Hoogeboom. This result yields feasible-set expansions for the two-variable Bollobas–Riordan and interlace polynomials of a delta-matroid. In the former case, the expansion obtained directly generalizes the activities expansions of the Tutte polynomial of graphs and matroids.
WEAKLY NULL SEQUENCES WITH UPPER ESTIMATES

We prove that if (vi) is a normalized basic sequence and X is a Banach space such that every normalized weakly null sequence in X has a subsequence that is dominated by (vi), then there exists a uniform constant C � 1 such that every normalized weakly null sequence in X has a subsequence that is C-dominated by (vi). This extends a result of Knaust and Odell, who proved this for the cases in which (vi) is the standard basis for lp or c0.
Convexity of Decentralized Controller Synthesis

In decentralized control problems, a standard approach is to specify the set of allowable decentralized controllers as a closed subspace of linear operators. This then induces a corresponding set of Youla–Kucera parameters. Previous work has shown that quadratic invariance of the controller set implies that the set of Youla–Kucera parameters is convex. In this technical note, we prove the converse. We thereby show that the only decentralized control problems for which the set of Youla–Kucera parameters is convex are those which are quadratically invariant. We further show that under additional assumptions, quadratic invariance is necessary and sufficient for the set of achievable closed-loop maps to be convex. We give two versions of our results. The first applies to bounded linear operators on a Banach space and the second applies to (possibly unstable) causal LTI systems in discrete or continuous time.
On computing distributions of products of random variables via Gaussian multiresolution analysis

Abstract We introduce a new approximate multiresolution analysis (MRA) using a single Gaussian as the scaling function, which we call Gaussian MRA (GMRA). As an initial application, we employ this new tool to accurately and efficiently compute the probability density function (PDF) of the product of independent random variables. In contrast with Monte-Carlo (MC) type methods (the only other universal approach known to address this problem), our method not only achieves accuracies beyond the reach of MC but also produces a PDF expressed as a Gaussian mixture, thus allowing for further efficient computations. We also show that an exact MRA corresponding to our GMRA can be constructed for a matching user-selected accuracy.