cssi/SciSciGPT-SciSciNet huggingface dataset:
Disentangling the Relationship Between Race and Attitudes Toward the Police: Police Contact, Perceptions of Safety, and Procedural Justice:

Recent incidents involving police shootings of unarmed men of color have increased tensions between communities and police departments across the United States. In response, scholars have intensifi...
$S$-factor and scattering parameters from ${}^3$He + ${}^4$He $\rightarrow {}^7$Be + $\gamma$ data

We use the next-to-leading-order (NLO) amplitude in an effective field theory (EFT) for \({}^{3}\mathrm {He}+{}^{4}\mathrm {He}\rightarrow {}^{7}\mathrm {Be}+ \gamma \) to perform the extrapolation of higher-energy data to solar energies. At this order the EFT describes the capture process using an s-wave scattering length and effective range, the asymptotic behavior of \({}^{7}\mathrm {Be}\) and its excited state, and short-distance contributions to the E1 capture amplitude. We use a Bayesian analysis to infer the multi-dimensional posterior of these parameters from capture data below 2 MeV. The total S factor \(S(0)= 0.578^{+0.015}_{-0.016}\) keV b at 68% degree of belief. We also find significant constraints on \({}^{3}\mathrm {He}\)–\({}^{4}\mathrm {He}\) scattering parameters.
Using implementation science to initiate survivorship care plan practice change.

175Background: Failure to address coordination of cancer survivorship care can result in physical disability, emotional distress, and increased health care costs. The Institute of Medicine (IOM) re...
Approximation Algorithms for Minimizing Average Distortion

This paper considers embeddings f of arbitrary finite metrics into the line metric ℜ so that none of the distances is shrunk by the embedding f; the quantity of interest is the factor by which the average distance in the metric is stretched. We call this quantity the average distortion of the non-contracting map f. We prove that finding the best embedding of even a tree metric into a line metric to minimize the average distortion is NP-hard, and hence focus on approximating the average distortion of the best possible embedding for the given input metric. We give a constant-factor approximation for the problem of embedding general metrics into the line metric. For the case of n-point tree metrics, we provide a quasi-polynomial time approximation scheme which outputs an embedding with distortion at most (1 + e) times the optimum in time nO(log n/e^2). Finally, when the average distortion is measured only over the endpoints of the edges of an input tree metric, we show how to exploit the structure of tree metrics to give an exact solution in polynomial time.
Respiratory Selenite Reductase from Bacillus selenitireducens Strain MLS10

ABSTRACT The putative respiratory selenite [Se(IV)] reductase (Srr) from Bacillus selenitireducens MLS10 has been identified through a polyphasic approach involving genomics, proteomics, and enzymology. Nondenaturing gel assays were used to identify Srr in cell fractions, and the active band was shown to contain a single protein of 80 kDa. The protein was identified through liquid chromatography-tandem mass spectrometry (LC-MS/MS) as a homolog of the catalytic subunit of polysulfide reductase (PsrA). It was found to be encoded as part of an operon that contains six genes that we designated srrE, srrA, srrB, srrC, srrD, and srrF. SrrA is the catalytic subunit (80 kDa), with a twin-arginine translocation (TAT) leader sequence indicative of a periplasmic protein and one putative 4Fe-4S binding site. SrrB is a small subunit (17 kDa) with four putative 4Fe-4S binding sites, SrrC (43 kDa) is an anchoring subunit, and SrrD (24 kDa) is a chaperon protein. Both SrrE (38 kDa) and SrrF (45 kDa) were annotated as rhodanese domain-containing proteins. Phylogenetic analysis revealed that SrrA belonged to the PsrA/PhsA clade but that it did not define a distinct subgroup, based on the putative homologs that were subsequently identified from other known selenite-respiring bacteria (e.g., Desulfurispirillum indicum and Pyrobaculum aerophilum). The enzyme appeared to be specific for Se(IV), showing no activity with selenate, arsenate, or thiosulfate, with a Km of 145 ± 53 μM, a Vmax of 23 ± 2.5 μM min−1, and a kcat of 23 ± 2.68 s−1. These results further our understanding of the mechanisms of selenium biotransformation and its biogeochemical cycle. IMPORTANCE Selenium is an essential element for life, with Se(IV) reduction a key step in its biogeochemical cycle. This report identifies for the first time a dissimilatory Se(IV) reductase, Srr, from a known selenite-respiring bacterium, the haloalkalophilic Bacillus selenitireducens strain MLS10. The work extends the versatility of the complex iron-sulfur molybdoenzyme (CISM) superfamily in electron transfer involving chalcogen substrates with different redox potentials. Further, it underscores the importance of biochemical and enzymological approaches in establishing the functionality of these enzymes.
Feasibility of using a fully immersive virtual reality system for kinematic data collection.

Abstract Commercially-available Virtual Reality (VR) systems have the potential to be effective tools for simultaneous visual manipulation and kinematic data collection. Previously, these systems have been integrated with research-grade motion capture systems to provide both functionalities; however, they are yet to be used as stand-alone systems for kinematic data collection. The present study aimed to validate the HTC VIVE VR system for kinematic data collection by evaluating the accuracy of its position and orientation signals. The VIVE controller and tracker were each compared to a Polhemus Liberty magnetic tracking system sensor for angular and translational measurement error and signal drift. A sensor from each system was mounted to opposite ends of a rigid segment which was driven through fifty rotations and fifty translations. Mean angular errors for both the VIVE tracker and controller were below 0.4°. Mean translational error for both sensors was below 3 mm. Drift in the Liberty signal components was consistently lower than drift in VIVE components. However, all mean rotational drift measures were below 0.1° and all mean translational measures were below 0.35 mm. These data indicate that the HTC VIVE system has the potential to be a valid and reliable means of kinematic data collection. However, further investigation is necessary to determine the VIVE’s suitability for capturing extremely minute or high-volume movements.
Predicting the mechanical response of oligocrystals with deep learning

Abstract In this work we employ data-driven homogenization approaches to predict the particular mechanical evolution of polycrystalline aggregates with tens of individual crystals. In these oligocrystals the differences in stress response due to microstructural variation is pronounced. Shell-like structures produced by metal-based additive manufacturing and the like make the prediction of the behavior of oligocrystals technologically relevant. The predictions of traditional homogenization theories based on grain volumes are not sensitive to variations in local grain neighborhoods. Direct simulation of the local response with crystal plasticity finite element methods is more detailed, but the computations are expensive. To represent the stress-strain response of a polycrystalline sample given its initial grain texture and morphology we have designed a novel neural network that incorporates a convolution component to observe and reduce the information in the crystal texture field and a recursive component to represent the causal nature of the history information. This model exhibits accuracy on par with crystal plasticity simulations at minimal computational cost per prediction.
Immunological response between protozoa symbiotic to a roach and a termite.

L'analyse des responsabilites immunologiques apres immunisation d'animaux experimentaux avec les protozoaires symbiotiques du ‘roach’,Cryptocercus et du termiteZootermopsis indique une etroite affinite chimique entre les protozoas de ces hotes. Les resultats semblent confirmer indirectement la taxonomic morphologique courante des hotes.
Gradient Coding Using the Stochastic Block Model

Gradient descent and its many variants, including mini-batch stochastic gradient descent, form the algorithmic foundation of modern large-scale machine learning. Due to the size and scale of modern data, gradient computations are often distributed across multiple compute nodes. Unfortunately, such distributed implementations can face significant delays caused by straggler nodes, i. e., nodes that are much slower than average. Gradient coding is a new technique for mitigating the effect of stragglers via algorithmic redundancy. While effective, previously proposed gradient codes can be computationally expensive to construct, inaccurate, or susceptible to adversarial stragglers. In this work, we present the stochastic block code (SBC), a gradient code based on the stochastic block model. We show that SBCs are efficient, accurate, and that under certain settings, adversarial straggler selection becomes as hard as detecting a community structure in the multiple community, block stochastic graph model.
Brain Tumor Segmentation on MRI with Missing Modalities

Brain Tumor Segmentation from magnetic resonance imaging (MRI) is a critical technique for early diagnosis. However, rather than having complete four modalities as in BraTS dataset, it is common to have missing modalities in clinical scenarios. We design a brain tumor segmentation algorithm that is robust to the absence of any modality. Our network includes a channel-independent encoding path and a feature-fusion decoding path. We use self-supervised training through channel dropout and also propose a novel domain adaptation method on feature maps to recover the information from the missing channel. Our results demonstrate that the quality of the segmentation depends on which modality is missing. Furthermore, we also discuss and visualize the contribution of each modality to the segmentation results. Their contributions are along well with the expert screening routine.
Analysis of double-slit interference experiment at the atomic level

Abstract I argue that the marquis characteristics of the quantum-mechanical double-slit experiment (point detection, random distribution, Born rule) can be explained using Schroedinger's equation alone, if one takes into account that, for any atom in a detector, there is a small but nonzero gap between its excitation energy and the excitation energies of all other relevant atoms in the detector (isolated-levels assumption). To illustrate the point I introduce a toy model of a detector. The form of the model follows common practice in quantum optics and cavity QED. Each detector atom can be resonantly excited by the incoming particle, and then emit a detection signature (e.g., bright flash of light) or dissipate its energy thermally. Different atoms have slightly different resonant energies per the isolated-levels assumption, and the projectile preferentially excites the atom with the closest energy match. The toy model permits one easily to estimate the probability that any atom is resonantly excited, and also that a detection signature is produced before being overtaken by thermal dissipation. The end-to-end detection probability is the product of these two probabilities, and is proportional to the absolute-square of the incoming wavefunction at the atom in question, i.e. the Born rule. I consider how closely a published neutron interference experiment conforms to the picture developed here; I show how this paper's analysis steers clear of creating a scenario with local hidden variables; I show how the analysis steers clear of the irreversibility implicit in the projection postulate; and I discuss possible experimental tests of this paper's ideas. Hopefully, this is a significant step toward realizing the program of solving the measurement problem within unitary quantum mechanics envisioned by Landsman, among others.
On the suppression and distortion of non-equilibrium fluctuations by transpiration

A fluid in a nonequilibrium state exhibits long-ranged correlations of its hydrodynamic fluctuations. In this article, we examine the effect of a transpiration interface on these correlations—specifically, we consider a dilute gas in a domain bisected by the interface. The system is held in a nonequilibrium steady state by using isothermal walls to impose a temperature gradient. The gas is simulated using both direct simulation Monte Carlo (DSMC) and fluctuating hydrodynamics (FHD). For the FHD simulations, two models are developed for the interface based on master equation and Langevin approaches. For appropriate simulation parameters, good agreement is observed between DSMC and FHD results with the latter showing a significant advantage in computational speed. For each approach, we quantify the effects of transpiration on long-ranged correlations in the hydrodynamic variables. The principal effect of transpiration is a suppression of the correlations, an outcome largely explained by a reduction in the temperature gradient due to the interface. We also observe a distortion of the temperature correlations, specifically the appearance of a new peak located near the interface.A fluid in a nonequilibrium state exhibits long-ranged correlations of its hydrodynamic fluctuations. In this article, we examine the effect of a transpiration interface on these correlations—specifically, we consider a dilute gas in a domain bisected by the interface. The system is held in a nonequilibrium steady state by using isothermal walls to impose a temperature gradient. The gas is simulated using both direct simulation Monte Carlo (DSMC) and fluctuating hydrodynamics (FHD). For the FHD simulations, two models are developed for the interface based on master equation and Langevin approaches. For appropriate simulation parameters, good agreement is observed between DSMC and FHD results with the latter showing a significant advantage in computational speed. For each approach, we quantify the effects of transpiration on long-ranged correlations in the hydrodynamic variables. The principal effect of transpiration is a suppression of the correlations, an outcome largely explained by a reduction in the t...
The Exact Computational Complexity of Evolutionarily Stable Strategies

While the computational complexity of many game-theoretic solution concepts, notably Nash equilibrium, has now been settled, the question of determining the exact complexity of computing an evoluti...
Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening

Computational techniques such as structure-based virtual screening require carefully prepared 3D models of potential small-molecule ligands. Though powerful, existing commercial programs for virtual-library preparation have restrictive and/or expensive licenses. Freely available alternatives, though often effective, do not fully account for all possible ionization, tautomeric, and ring-conformational variants. We here present Gypsum-DL, a free, robust open-source program that addresses these challenges. As input, Gypsum-DL accepts virtual compound libraries in SMILES or flat SDF formats. For each molecule in the virtual library, it enumerates appropriate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms. As output, Gypsum-DL produces an SDF file containing each molecular form, with 3D coordinates assigned. To demonstrate its utility, we processed 1558 molecules taken from the NCI Diversity Set VI and 56,608 molecules taken from a Distributed Drug Discovery (D3) combinatorial virtual library. We also used 4463 high-quality protein–ligand complexes from the PDBBind database to show that Gypsum-DL processing can improve virtual-screening pose prediction. Gypsum-DL is available free of charge under the terms of the Apache License, Version 2.0.
Synthesis of triisopropyl α-(trimethylsilyloxy)propargyl stannanes

Abstract Acetyl(triisopropyl)stannane reacts with alkynyllithium reagents predominantly by way of carbonyl addition to give the title compounds after in situ trimethylsilylation.
Reactions of 2-methylthiazolines and N-methyl cyclic ketene-N,S-acetals with acid chlorides

Abstract Carbon–carbon bond formation occurs under mild conditions when 2-methylthiazolines react with acid chlorides to form N-acyl-β-keto cyclic ketene-N,S-acetals. N-Methyl cyclic ketene-N,S-acetals, generated from 2-methyl-thiazolines, can react further with acid chlorides to form N-methyl-β-keto cyclic ketene-N,S-acetals.
AGO4 is specifically required for heterochromatic siRNA accumulation at Pol V-dependent loci in Arabidopsis thaliana.

Summary In plants, 24 nucleotide long heterochromatic siRNAs (het-siRNAs) transcriptionally regulate gene expression by RNA-directed DNA methylation (RdDM). The biogenesis of most het-siRNAs depends on the plant-specific RNA polymerase IV (Pol IV), and ARGONAUTE4 (AGO4) is a major het-siRNA effector protein. Through genome-wide analysis of sRNA-seq data sets, we found that AGO4 is required for the accumulation of a small subset of het-siRNAs. The accumulation of AGO4-dependent het-siRNAs also requires several factors known to participate in the effector portion of the RdDM pathway, including RNA POLYMERASE V (POL V), DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and SAWADEE HOMEODOMAIN HOMOLOGUE 1 (SHH1). Like many AGO proteins, AGO4 is an endonuclease that can ‘slice’ RNAs. We found that a slicing-defective AGO4 was unable to fully recover AGO4-dependent het-siRNA accumulation from ago4 mutant plants. Collectively, our data suggest that AGO4-dependent siRNAs are secondary siRNAs dependent on the prior activity of the RdDM pathway at certain loci.
MANGANESE-PROMOTED, TITANOCENE-CATALYZED STEREOSELECTIVE PINACOL COUPLING OF ALDEHYDES

Abstract Aromatic and aliphatic aldehydes undergo pinacol coupling when treated with Mn/Me3SiCl in the presence of Cp2TiCl2 as catalyst. Good yields of bis-silyl pinacol ethers are obtained with varying degrees of diastereoselectivity. Enantioselective pinacolization has been achieved using an enantiomerically enriched catalyst
Isomerization of Allyl Ethers Initiated by Lithium Diisopropylamide

Lithium diisopropylamide (LDA) promotes virtually quantitative conversion of allylic ethers to (Z)-propenyl ethers. It was discovered that allylic ethers can be isomerized efficiently with very high stereoselectivity to (Z)-propenyl ethers by LDA in THF at room temperature. The reaction time for the conversion increases with more sterically hindered allylic ethers. Different amides were also compared with LDA for their ability to effect this isomerization.
Metal complexes of monocarbon carboranes bearing C-amine or -amino substituents

Abstract Icosahedral metal–monocarbollide complexes in which the carbon atom of the {nido-CB10} fragment carries an exo-polyhedral –NR3 or –NR2 group have an extensive chemistry. This is illustrated with complexes of ruthenium, osmium, rhodium, molybdenum, tungsten and rhenium. Many complexes with molecular structures new to the metallacarborane field have been discovered, and it has been shown that it is possible to introduce functional groups into the {nido-CB10} cage system in many different ways.
Iridium-Catalyzed Preparation of Silylboranes by Silane Borylation and Their Use in the Catalytic Borylation of Arenes

Silylboranes are versatile reagents for transition metal-catalyzed reactions of unsaturated organic molecules. These reagents are typically prepared by the addition of a silyl lithium species to a boron electrophile. However, the need to generate anionic silane reagents limits the scope of silylboranes that can be readily obtained. Here, we describe the synthesis of trialkylsilylboranes by the borylation of silanes catalyzed by iridium complexes. The reaction of trialkylhydrosilanes with B2pin2 catalyzed by the combination of [Ir(OMe)cod]2 and 4,4′-di-tert-butylbipyridine forms trialkylsilylboronic esters. In addition, we show that these trialkylsilylboranes serve as boron sources for the iridium-catalyzed borylation of aryl C−H bonds. In contrast to diboron reagents, the silylboranes react with methylarenes at both the aryl and methyl C−H bonds.
U3F12(H2O), a noncentrosymmetric uranium(IV) fluoride prepared via a convenient in situ route that creates U4+ under mild hydrothermal conditions.

A new noncentrosymmetric U4+-containing fluoride, U3F12(H2O), has been synthesized via a mild hydrothermal route and its crystal structure determined by single-crystal X-ray diffraction. The material exhibits a complex three-dimensional structure that is based on [U6F33(H2O)2)]9– hexanuclear building units consisting of corner- and edge-shared UF8, UF9, and UOF7 polyhedra. Powder second-harmonic generation (SHG) measurements revealed that the SHG efficiency for U3F12(H2O) is comparable to that of α-SiO2. Magnetic susceptibility measurements indicated that the U4+(f2)-containing material exhibits a singlet ground state at low temperature. IR and UV–vis reflectance spectra were obtained, and the thermal behavior was investigated by thermogravimetric analysis.
Wide bite angle diphosphine rhodium complexes: Synthesis, structure, and catalytic 1,4-addition of arylboronic acids to enones

A rhodium complex [ClRh(CO)( L1 )] featuring a wide bite angle diphosphine ligand ( L1 = 1,3-bis(2-diphenylphosphinomethylphenyl)benzene) has been synthesized and structurally characterized. L1 supports a bite angle (P–M–P angle, β ) of 171.4° in the trans -square planar complex. L1 was tested in Rh-catalyzed 1,4-addition reactions of arylboronic acids (six examples) to α,β-unsaturated ketones (five examples). In mixed aqueous/cyclohexane solution at 60 °C, addition reactions proceed in up to quantitative yield with a 1:1 arylboronic acid/enone ratio. Yields as high as 77% can be acquired even when one of the coupling partners is sterically encumbered 2,4,6-trimethylphenylboronic acid.
Total synthesis of a sialylated and sulfated oligosaccharide from O-linked glycoproteins

Abstract The total synthesis of a sialylated and sulfated oligosaccharide 1 representative of a structure occurring in respiratory mucins has been accomplished. Our strategy depends upon the employment of 2-naphthymethyl (NAP) protection for hydroxyl functions. Choice of the well-defined sialyl donor 15 was made because of its enhanced reactivity over the parent compound 14 for glycosylation.
Synthesis of m-terphenyl derivatives for potential use as tectons in crystal engineering

Abstract Treatment of 4,4-biphenyldiboronic acid with suitably substituted iodo-m-terphenyls provide easy access to the precursors for the synthesis of two rigid m-terphenyl derivatives bearing, H-bonding groups, for potential use as tectons in crystal engineering.
The Genome of the Human Pathogen Candida albicans Is Shaped by Mutation and Cryptic Sexual Recombination

The opportunistic fungal pathogen Candida albicans lacks a conventional sexual program and is thought to evolve, at least primarily, through the clonal acquisition of genetic changes. Here, we performed an analysis of heterozygous diploid genomes from 21 clinical isolates to determine the natural evolutionary processes acting on the C. albicans genome. Mutation and recombination shaped the genomic landscape among the C. albicans isolates. Strain-specific single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) clustered across the genome. Additionally, loss-of-heterozygosity (LOH) events contributed substantially to genotypic variation, with most long-tract LOH events extending to the ends of the chromosomes suggestive of repair via break-induced replication. Consistent with a model of inheritance by descent, most polymorphisms were shared between closely related strains. However, some isolates contained highly mosaic genomes consistent with strains having experienced interclade recombination during their evolutionary history. A detailed examination of mitochondrial genomes also revealed clear examples of interclade recombination among sequenced strains. These analyses therefore establish that both (para)sexual recombination and mitotic mutational processes drive evolution of this important pathogen. To further facilitate the study of C. albicans genomes, we also introduce an online platform, SNPMap, to examine SNP patterns in sequenced isolates.IMPORTANCE Mutations introduce variation into the genome upon which selection can act. Defining the nature of these changes is critical for determining species evolution, as well as for understanding the genetic changes driving important cellular processes. The heterozygous diploid fungus Candida albicans is both a frequent commensal organism and a prevalent opportunistic pathogen. A prevailing theory is that C. albicans evolves primarily through the gradual buildup of mitotic mutations, and a pressing issue is whether sexual or parasexual processes also operate within natural populations. Here, we establish that the C. albicans genome evolves by a combination of localized mutation and both short-tract and long-tract loss-of-heterozygosity (LOH) events within the sequenced isolates. Mutations are more prevalent within noncoding and heterozygous regions and LOH increases towards chromosome ends. Furthermore, we provide evidence for genetic exchange between isolates, establishing that sexual or parasexual processes have contributed to the diversity of both nuclear and mitochondrial genomes.
Studies on the synthesis of landomycin A. Synthesis of the originally assigned structure of the aglycone, landomycinone, and revision of structure.

The originally proposed structure (2) of landomycinone, the aglycone of landomycin A, has been synthesized and shown to be nonidentical to the naturally derived landomycin A aglycone. The synthesis of 2 features the Dotz benzannulation reaction of chromium carbene 5 and alkyne 6, and the intramolecular Michael-type cyclization reaction of the phenolic naphthoquinone 20. It is proposed that natural landomycinone possesses the alternative structure 3, but attempts to access this structure via the Michael-type cyclization of the isomeric phenolic naphthoquinone 38 have been unsuccessful.
Large-scale structure from quantum fluctuations in the early universe

A better understanding of the formation of largescale structure in the universe is arguably the most pressing question in cosmology. The most compelling and promising theoretical paradigm, inflatio...
Model-based analysis of the stiffness of the wrist joint in active and passive conditions.

The control of joint stiffness is a fundamental mechanism used to control human movements. While many studies have observed how stiffness is modulated for tasks involving shoulder and elbow motion, a limited amount of knowledge is available for wrist movements, though the wrist plays a crucial role in manipulation. We have developed a computational framework based on a realistic musculoskeletal model, which al to calculate the passive and active components of the wrist joint stiffness. We first used the framework to validate the musculoskeletal model against experimental measurements of the wrist joint stiffness, and then to study the contribution of different muscle groups to the passive joint stiffness. We finally used the framework to study the effect of muscle co-contraction on the active joint stiffness. The results show that thumb and finger muscles play a crucial role in determining the passive wrist joint stiff- ness: in the neutral posture, the direction of maximum stiffness aligns with the experimental measurements, and the magnitude increases by 113% when they are included. Moreover, the analysis of the controllability of joint stiffness showed that muscle co-contraction positively correlates with the stiffness magnitude and negatively correlates with the variability of the stiffness orientation (p < 0.01 in both cases). Finally, an exhaustive search showed that with appropriate selection of a muscle activation strategy, the joint stiffness orientation can be arbitrarily modulated. This observation suggests the absence of biomechanical constraints on the controllability of the orientation of the wrist joint stiffness.
Synthesis and novel reactivity of halomethyldimethylsulfonium salts

Iodomethyl-, chloromethyl-, and fluoromethyldimethylsulfonium salts, 4b−d, have been synthesized and are observed to be highly reactive molecules that exhibit extraordinary diversity with respect to the nature of their reactivity, undergoing facile direct substitution (SN2) reactions, but also being highly susceptible to electron-transfer reactions. Cyclic voltametry experiments indicated that the iodomethyldimethylsulfonium compound, 4b, is a potent electron acceptor, even surpassing the reactivity of perfluoro-n-alkyl iodides in that capacity. The iodo- and chloromethyldimethylsulfonium salts, 4b,c, as well as the analogous iodomethyltrimethylammonium salt, 3a, are shown to be reactive SET acceptors.
Automated visualization of rule-based models.

Frameworks such as BioNetGen, Kappa and Simmune use “reaction rules” to specify biochemical interactions compactly, where each rule specifies a mechanism such as binding or phosphorylation and its structural requirements. Current rule-based models of signaling pathways have tens to hundreds of rules, and these numbers are expected to increase as more molecule types and pathways are added. Visual representations are critical for conveying rule-based models, but current approaches to show rules and interactions between rules scale poorly with model size. Also, inferring design motifs that emerge from biochemical interactions is an open problem, so current approaches to visualize model architecture rely on manual interpretation of the model. Here, we present three new visualization tools that constitute an automated visualization framework for rule-based models: (i) a compact rule visualization that efficiently displays each rule, (ii) the atom-rule graph that conveys regulatory interactions in the model as a bipartite network, and (iii) a tunable compression pipeline that incorporates expert knowledge and produces compact diagrams of model architecture when applied to the atom-rule graph. The compressed graphs convey network motifs and architectural features useful for understanding both small and large rule-based models, as we show by application to specific examples. Our tools also produce more readable diagrams than current approaches, as we show by comparing visualizations of 27 published models using standard graph metrics. We provide an implementation in the open source and freely available BioNetGen framework, but the underlying methods are general and can be applied to rule-based models from the Kappa and Simmune frameworks also. We expect that these tools will promote communication and analysis of rule-based models and their eventual integration into comprehensive whole-cell models.
A Streamlined Route to Highly Conjugated, All-E Polyenes Characteristic of Oxo Polyene Macrolide Antibiotics

Conjugated polyenes of the all-E variety constitute key subsections of many natural, as well as unnatural, products. Among the more visible and timely members of the former group are the polyene macrolide antibiotics,1 which are clinically important antifungal agents, and selected retinoids,2 which have recently been found to be active against certain tumor lines. Capped polyacetylenes, especially valued as materials by virtue of their nonlinear optical (NLO) properties,3 are representative of the latter category. Routes to polyene functionality tend to rely mainly on traditional olefin elongations,4 although more recently alternative methods have started to accrue.5 Characteristic of most, however, is the requirement of many steps, oftentimes low overall yields, and not uncommon isomerizations or problematic separations of unwanted Z isomers. We now report a new approach to construction of all-E polyenes, in particular oxotetraand oxopentaenes, based on a readily prepared linchpin suitable for bidirectional elaboration. The key building block, stannylated dienyne 1, was envisioned as an all-E 1,6-dimetallohexatriene equivalent, taking advantage of the likely retention of olefin geometry in Pd(0)mediated vinyl-vinyl cross-couplings of stannanes6 and the anticipated regioand stereoselective addition of Schwartz’s reagent (Cp2Zr(H)Cl) to the desilylated alkyne terminus (Figure 1).7 Linchpin 1 is easily prepared as a pale yellow oil in multigram quantities in two operations (Scheme 1).8 Addition of our mixed stannylcuprate 29 to acetylenic acetal 3 according to Quintard10 affords enal 4 after hydrolysis. Wittig coupling with the ylide derived from the known salt 511 gives 1 in high
Side-Channel Analysis of MAC-Keccak Hardware Implementations.

As Keccak has been selected as the new SHA-3 standard, Message Authentication Code (MAC) (MAC-Keccak) using a secret key will be widely used for integrity checking and authenticity assurance. Recent works have shown the feasibility of side-channel attacks against software implementations of MAC-Keccak to retrieve the key, with the security assessment of hardware implementations remaining an open problem. In this paper, we present a comprehensive and practical side-channel analysis of a hardware implementation of MAC-Keccak on FPGA. Different from previous works, we propose a new attack method targeting the first round output of MAC-Keccak rather than the linear operation θ only. The results on sampled power traces show that the unprotected hardware implementation of MAC-Keccak is vulnerable to side-channel attacks, and attacking the nonlinear operation of MAC-Keccak is very effective. We further discuss countermeasures against side-channel analysis on hardware MAC-Keccak. Finally, we discuss the impact of the key length on side-channel analysis and compare the attack complexity between MAC-Keccak and other cryptographic algorithms.
A Versatile Synthetic Strategy for the Preparation and Discovery of New Iminocyclitols as Inhibitors of Glycosidases.

A series of iminocyclitols was prepared using a versatile synthetic strategy, and their inhibition of glycosidases was evaluated using capillary electrophoresis. The study has demonstrated that remarkable specificities in enzyme inhibition can be achieved with small modifications on the aglycon side chain and the ring nitrogen. Among the compounds synthesized, (2R,3R,4R,5R)-N-methyl-2-(acetamidomethyl)-3,4-dihydroxy-5-(hydroxymethyl)pyrrolidine was found to be very potent against β-N-acetylhexosaminidase P with the Ki value of 80 nM.
Asymmetric hydrocyanation of hydrazones catalyzed by lanthanide--PYBOX complexes.

The asymmetric addition of HCN to hydrazones is catalyzed in high yield and good-to-excellent enantioselectivity by the easily prepared (PhPYBOX)ErCl3 complex. This constitutes the first example of...
Incorporating Context into Language Encoding Models for fMRI

Language encoding models help explain language processing in the human brain by learning functions that predict brain responses from the language stimuli that elicited them. Current word embedding-based approaches treat each stimulus word independently and thus ignore the influence of context on language understanding. In this work we instead build encoding models using rich contextual representations derived from an LSTM language model. Our models show a significant improvement in encoding performance relative to state-of-the-art embeddings in nearly every brain area. By varying the amount of context used in the models and providing the models with distorted context, we show that this improvement is due to a combination of better word embeddings learned by the LSTM language model and contextual information. We are also able to use our models to map context sensitivity across the cortex. These results suggest that LSTM language models learn high-level representations that are related to representations in the human brain.
4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments

4C-Seq has proven to be a powerful technique to identify genome-wide interactions with a single locus of interest (or "bait") that can be important for gene regulation. However, analysis of 4C-Seq data is complicated by the many biases inherent to the technique. An important consideration when dealing with 4C-Seq data is the differences in resolution of signal across the genome that result from differences in 3D distance separation from the bait. This leads to the highest signal in the region immediately surrounding the bait and increasingly lower signals in far-cis and trans. Another important aspect of 4C-Seq experiments is the resolution, which is greatly influenced by the choice of restriction enzyme and the frequency at which it can cut the genome. Thus, it is important that a 4C-Seq analysis method is flexible enough to analyze data generated using different enzymes and to identify interactions across the entire genome. Current methods for 4C-Seq analysis only identify interactions in regions near the bait or in regions located in far-cis and trans, but no method comprehensively analyzes 4C signals of different length scales. In addition, some methods also fail in experiments where chromatin fragments are generated using frequent cutter restriction enzymes. Here, we describe 4C-ker, a Hidden-Markov Model based pipeline that identifies regions throughout the genome that interact with the 4C bait locus. In addition, we incorporate methods for the identification of differential interactions in multiple 4C-seq datasets collected from different genotypes or experimental conditions. Adaptive window sizes are used to correct for differences in signal coverage in near-bait regions, far-cis and trans chromosomes. Using several datasets, we demonstrate that 4C-ker outperforms all existing 4C-Seq pipelines in its ability to reproducibly identify interaction domains at all genomic ranges with different resolution enzymes.
Preparation of 8H‐Furo[3,4‐d]dibenz[b,f]azepine. A Novel Heterocyclic Ring system

The synthesis of 8H-furo[3,4-d]dibenz[b,f]azepine 8 from 5H-dibenz[b,f]azepine 1a is described. The preparation of 8 represents the synthesis of a new heterocyclic system.
Quantifying the unquantifiable: why Hymenoptera, not Coleoptera, is the most speciose animal order

We challenge the oft-repeated claim that the beetles (Coleoptera) are the most species-rich order of animals. Instead, we assert that another order of insects, the Hymenoptera, is more speciose, due in large part to the massively diverse but relatively poorly known parasitoid wasps. The idea that the beetles have more species than other orders is primarily based on their respective collection histories and the relative availability of taxonomic resources, which both disfavor parasitoid wasps. Though it is unreasonable to directly compare numbers of described species in each order, the ecology of parasitic wasps—specifically, their intimate interactions with their hosts—allows for estimation of relative richness. We present a simple logical model that shows how the specialization of many parasitic wasps on their hosts suggests few scenarios in which there would be more beetle species than parasitic wasp species. We couple this model with an accounting of what we call the “genus-specific parasitoid–host ratio” from four well-studied genera of insect hosts, a metric by which to generate extremely conservative estimates of the average number of parasitic wasp species attacking a given beetle or other insect host species. Synthesis of our model with data from real host systems suggests that the Hymenoptera may have 2.5–3.2× more species than the Coleoptera. While there are more described species of beetles than all other animals, the Hymenoptera are almost certainly the larger order.
Cycloaddition Reactions of Ketene Diethyl Acetal toward the Synthesis of Cyclobutene Monomers

Abstract The [2+2]-cycloaddition reactions of ketene diethyl acetal with methyl acrylate and acrylonitrile were optimized. Highly efficient ketal cleavage to either 2-cyano-1-cyclobutanone or 2-methoxycarbonyl-1-cyclobutanone was achieved using formic acid. Among the numerous reduction methods attempted, only sodium cyanoborohydride in acidic medium led successfully to the corresponding alcohols, but isolation of the desired products was not achievable. We show that the anomalous cyclobutanone chemistry is due to the acidic α-proton and the electron-withdrawing substituent in the α-position. Substitution of the α-proton by a methyl group results in a turnaround back to textbook chemistry.
The energetics of lanthanum tantalate materials

Abstract Lanthanum tantalates are important refractory materials with application in photocatalysis, solid oxide fuel cells, and phosphors. Soft-chemical synthesis utilizing the Lindqvist ion, [Ta6O19]8−, has yielded a new phase, La2Ta2O7(OH)2. Using the hydrated phase as a starting material, a new lanthanum orthotantalate polymorph was formed by heating to 850 °C, which converts to a previously reported LaTaO4 polymorph at 1200 °C. The stabilities of La2Ta2O7(OH)2 (LaTa−OH), the intermediate LaTaO4 polymorph (LaTa-850), and the high temperature phase (LaTa-1200) were investigated using high-temperature oxide melt solution calorimetry. The enthalpy of formation from the oxides were calculated from the enthalpies of drop solution to be −87.1±9.6, −94.9±8.8, and −93.1±8.7 kJ/mol for LaTa−OH, LaTa-850, and LaTa-1200, respectively. These results indicate that the intermediate phase, LaTa-850, is the most stable. This pattern of energetics may be related to cation–cation repulsion of the tantalate cations. We also investigated possible LnTaO4 and Ln2Ta2O7(OH)2 analogues of Ln=Pr, Nd to examine the relationship between cation size and the resulting phases.
Synthesis of 3‐alkyl‐8‐substituted‐ and 4‐hydroxy‐8‐substituted‐2,3,4,5‐tetrahydro‐1H‐2‐benzazepines

Based on the Schmidt reaction and an iodolactone ring expansion reaction, two different synthetic routes to substituted 2,3,4,5-tetrahydro-1H-2-benzazepines were developed. The Schmidt reaction on 2,3-dihydro-2H-1-naphthalenone (1) gave 3, the product resulting from the alkyl group migration, as the major product instead of the tetrazole 2. This prompted the investigation of the Schmidt reaction on aromatic ketones 8 and 12. The product 9 due to alkyl group migration was the major product of the Schmidt reaction on 2-methyl-3,4-dihydro-2H-1-naphthalenone (8). The β-keto diester 12 gave a mixture of decarb-oxylated lactams after the Schmidt reaction. In this case, the lactam 13 resulting from the migration of the aromatic ring dominated over the other lactam 14. When lactam 14 was subjected to nitration, a single regioisomer was produced and transformed to the bromo alcohol 19. The other approach was based on the single pot ring expansion of the iodolactone 22 to the lactam 23 in the presence of methanolic ammonia. The iodolactone 22 was readily prepared from 2-allylbenzoic acid.
Monocyte depletion attenuates the development of posttraumatic hydrocephalus and preserves white matter integrity after traumatic brain injury

Monocytes are amongst the first cells recruited into the brain after traumatic brain injury (TBI). We have shown monocyte depletion 24 hours prior to TBI reduces brain edema, decreases neutrophil infiltration and improves behavioral outcomes. Additionally, both lesion and ventricle size correlate with poor neurologic outcome after TBI. Therefore, we aimed to determine the association between monocyte infiltration, lesion size, and ventricle volume. We hypothesized that monocyte depletion would attenuate lesion size, decrease ventricle enlargement, and preserve white matter in mice after TBI. C57BL/6 mice underwent pan monocyte depletion via intravenous injection of liposome-encapsulated clodronate. Control mice were injected with liposome-encapsulated PBS. TBI was induced via an open-head, controlled cortical impact. Mice were imaged using magnetic resonance imaging (MRI) at 1, 7, and 14 days post-injury to evaluate progression of lesion and to detect morphological changes associated with injury (3D T1-weighted MRI) including regional alterations in white matter patterns (multi-direction diffusion MRI). Lesion size and ventricle volume were measured using semi-automatic segmentation and active contour methods with the software program ITK-SNAP. Data was analyzed with the statistical software program PRISM. No significant effect of monocyte depletion on lesion size was detected using MRI following TBI (p = 0.4). However, progressive ventricle enlargement following TBI was observed to be attenuated in the monocyte-depleted cohort (5.3 ± 0.9mm3) as compared to the sham-depleted cohort (13.2 ± 3.1mm3; p = 0.02). Global white matter integrity and regional patterns were evaluated and quantified for each mouse after extracting fractional anisotropy maps from the multi-direction diffusion-MRI data using Siemens Syngo DTI analysis package. Fractional anisotropy (FA) values were preserved in the monocyte-depleted cohort (123.0 ± 4.4mm3) as compared to sham-depleted mice (94.9 ± 4.6mm3; p = 0.025) by 14 days post-TBI. All TBI mice exhibited FA values lower than those from a representative naive control group with intact white matter tracts and FA~200 mm3). The MRI derived assessment of injury progression suggests that monocyte depletion at the time of injury may be a novel therapeutic strategy in the treatment of TBI. Furthermore, non-invasive longitudinal imaging allows for the evaluation of both TBI progression as well as therapeutic response over the course of injury.
Transcranial focused ultrasound neuromodulation of the human primary motor cortex

Transcranial focused ultrasound is an emerging form of non-invasive neuromodulation that uses acoustic energy to affect neuronal excitability. The effect of ultrasound on human motor cortical excitability and behavior is currently unknown. We apply ultrasound to the primary motor cortex in humans using a novel simultaneous transcranial ultrasound and magnetic stimulation paradigm that allows for concurrent and concentric ultrasound stimulation with transcranial magnetic stimulation (TMS). This allows for non-invasive inspection of the effect of ultrasound on motor neuronal excitability using the motor evoked potential (MEP). We test the effect of ultrasound on single pulse MEP recruitment curves and paired pulse protocols including short interval intracortical inhibition (SICI) and intracortical facilitation (ICF). In addition, we test the effect of ultrasound to motor cortex on a stimulus response reaction time task. Results show ultrasound inhibits the amplitude of single-pulse MEPs and attenuates intracortical facilitation but does not affect intracortical inhibition. Ultrasound also reduces reaction time on a simple stimulus response task. This is the first report of the effect of ultrasound on human motor cortical excitability and motor behavior and confirms previous results in the somatosensory cortex that ultrasound results in effective neuronal inhibition that confers a performance advantage.
Selective lithium ion binding involving inositol-based tris(spirotetrahydrofuranyl) ionophores: formation of a rodlike supramolecular ionic polymer from a homoditopic dimer.

The stereoselective replacement of all three hydroxyl groups in myo-inositol orthoformate by spirotetrahydrofuran rings in that manner which projects the C−O bonds in the molecular interior has been examined. The heterocyclic components were introduced sequentially, a protocol that demonstrated the utility of precomplexation to LiClO4 as a stereocontrol tactic. The capability of 3 to coordinate to alkali metal ions was quantified. The conformationally restricted nature of this ligand conveys high selectivity for binding to lithium ion. Beyond that, the ionophore prefers to form 2:1 complexes with Li+ and exhibits little tendency for 1:1 stoichiometry. These properties are shared by the “dimer” 36, in which two building blocks of type 3 have been conjoined by a 1,3-butadiyne tether positioned at the ortho ester terminus. This bifacial ligand reacts with one equivalent of LiClO4 or LiBF4 to form rodlike ionic polymers. Alternative recourse to lithium picrate results in production of the doubly capped homodi...