cssi/SciSciGPT-SciSciNet huggingface dataset:
Facile preparation of trans-2,3-bis(-tert-butylaminomethyl) norbornene

(2002). FACILE PREPARATION OF trans-2,3-bis(-tert-BUTYLAMINOMETHYL) NORBORNENE. Organic Preparations and Procedures International: Vol. 34, No. 6, pp. 655-657.
A Simple Method for Automated Equilibration Detection in Molecular Simulations

Molecular simulations intended to compute equilibrium properties are often initiated from configurations that are highly atypical of equilibrium samples, a practice which can generate a distinct initial transient in mechanical observables computed from the simulation trajectory. Traditional practice in simulation data analysis recommends this initial portion be discarded to equilibration, but no simple, general, and automated procedure for this process exists. Here, we suggest a conceptually simple automated procedure that does not make strict assumptions about the distribution of the observable of interest in which the equilibration time is chosen to maximize the number of effectively uncorrelated samples in the production timespan used to compute equilibrium averages. We present a simple Python reference implementation of this procedure and demonstrate its utility on typical molecular simulation data.
One-Step Bulk Synthesis of Stable, Near Unit-Cell Sized Oxide Nanoparticles and Nanoparticle Blends Using KO2

Presented here is a novel one-step synthesis of oxide or hydroxide nanoparticles using, for the first time, potassium superoxide (KO2). This work demonstrates that the reaction of KO2 with different salt solutions produces grams of stable, near unit-cell sized nanoparticles. This new synthetic technique is applied to representative elements from across the periodic table to rapidly produce nanometer sized oxides or hydroxides of Mg, Al, Y, Ti, Mn, Fe, Co, Ni, Cu, Zn, Sn, Tl, Pb, and Ce. This technique is also used to produce blends of nanoparticles, demonstrating the ability to prepare complex materials such as nanoparticulate blends of a lithium cathode material (LiCoO2), the multiferroic compound (BiMnO3+δ), and the superconducting YBa2Cu3O7–γ.
A method for the catalytic enantioselective synthesis of 6-silylated 2-cyclohexenones

6-Silylated-2-cyclohexenones can be synthesized enantioselectively by hydrosilylation of the corresponding diazo-2-cyclohexenone in the presence of a chiral Rh(II) catalyst.
A closer look at cross-validation for assessing the accuracy of gene regulatory networks and models

Cross-validation (CV) is a technique to assess the generalizability of a model to unseen data. This technique relies on assumptions that may not be satisfied when studying genomics datasets. For example, random CV (RCV) assumes that a randomly selected set of samples, the test set, well represents unseen data. This assumption doesn't hold true where samples are obtained from different experimental conditions, and the goal is to learn regulatory relationships among the genes that generalize beyond the observed conditions. In this study, we investigated how the CV procedure affects the assessment of supervised learning methods used to learn gene regulatory networks (or in other applications). We compared the performance of a regression-based method for gene expression prediction estimated using RCV with that estimated using a clustering-based CV (CCV) procedure. Our analysis illustrates that RCV can produce over-optimistic estimates of the model's generalizability compared to CCV. Next, we defined the 'distinctness' of test set from training set and showed that this measure is predictive of performance of the regression method. Finally, we introduced a simulated annealing method to construct partitions with gradually increasing distinctness and showed that performance of different gene expression prediction methods can be better evaluated using this method.
New Perspectives on Direct Heterogeneous Olefin Epoxidation

Important commercial direct oxidation processes include the epoxidation of ethylene to ethylene oxide and the newer epoxidation of butadiene to epoxybutene (EpB), both carried out with silver catalysts. However, detailed reaction mechanisms for these processes are still matters of debate. The guiding hypothesis of our research is that surface oxametallacycles are key intermediates in selective olefin epoxidation. By a combination of surface science experiments and density functional theory (DFT) calculations, we have synthesized the first stable surface oxametallacycles and have verified their identities and structures. In the case of EpB chemistry, we have been able to demonstrate direct connections between surface oxametallacycles and epoxide products. The EpB ring opens with an activation energy of 8.4 kcal/mol on Ag(110) to form a stable surface oxametallacycle. Spectroscopic results for this species are in excellent agreement with DFT calculations for an oxametallacycle bound to three silver atoms of a seven-atom cluster. This oxametallacycle undergoes 1,2 and 1,4 ring-closure reactions during temperature programmed desorption to form EpB and 2,5-dihydrofuran, respectively. This reaction represents the first demonstration of surface oxametallacycle ring closure to form an epoxide, and we suggest that surface oxametallacycles are of general importance in silver-catalyzed olefin epoxidation.
A facile transformation of 2-aminochromone to 4-chlorocoumarin and its reaction with ethylenediamine:

2-Aminochromones 1a–c and 8a–c are converted into 4-chlorocoumarins 2a–c and 9a–c. On treatment with ethylenediamine, 2a–c produce 2,3,4,5-tetrahydro-7-(2′-hydroxyphenyl)-1,4-diazepin-5-one 3a,b an...
[Li−Si−O]-MFI: A New Microporous Lithosilicate with the MFI Topology

We report the synthesis and structure solution of [Li-Si-O]-MFI (a = 19.793(4) A, b = 19.766(4) A, c = 13.266(3) A, space group P2 12 12 1), a framework zeolite related to ZSM-5 (silicalite) with a Li/Si ratio of 4:92. Single-crystal synchrotron X-ray diffraction data, 29Si NMR, and infrared spectroscopy indicate that the Li is randomly distributed over the framework sites. In addition, Li occupies ordered positions on extraframework sites that are occluded in voids outlined by the double five- or six-membered rings. The strong interaction between the extraframework Li cations and the negatively charged framework may be responsible for the distortion of the lattice from Pnma, the usual symmetry associated with as-synthesized members of the MFI-family, to its subgroup symmetry P2 12 12 1. Variable-temperature 7Li and 1H MAS NMR experiments show that the extraframework Li cations are not directly accessible to gas molecules, but that the protons formed on calcination are accessible.
Modeling Improvement for Underrepresented Minorities in Online STEM Education

Previous research has shown that students from underrepresented minority groups tend to receive lower grades in online classes than their peers, especially in science-focused courses. We propose that there may also be benefits to online courses for these students (e.g., opportunities for peer discussions where minority status is less salient), though little is currently known about these potential benefits. We present a new perspective on learning outcomes by measuring improvement, rather than grades alone. In learning management system data from seven semesters of an online introductory science course, we found that students from underrepresented minority racial groups were indeed less likely to receive high grades, and scored lower on exams; however, their exam scores improved throughout the semester a similar amount compared to their peers. We also compared improvement to students' behaviors, including exam submission times and forum usage, finding that these behaviors were related to improvement. Finally, we also briefly discuss implications of these findings for reducing inequalities in education, and the possibilities for underrepresented minority students in online STEM education in particular.
Draft Genome Sequence of Candida auris Strain LOM, a Human Clinical Isolate from Greater Metropolitan Houston, Texas

ABSTRACT Candida auris is an emerging pathogen of considerable public health importance. We present the draft genome sequence of a strain recently cultured from the urine of a patient hospitalized in the greater Houston metropolitan region. Two combined Oxford Nanopore sequencing runs provided sufficient data to rapidly generate a draft genome.
Zinc Doping in Cosubstituted In2-2xSnxZnxO3-δ

The cosubstituted solid solution In2-2xSnxZnxO3-δ was acceptor-doped with Zn2+ to form In2-x-ySnxZnyO3-δ (y > x). A 4% Zn2+ “excess” can be introduced in In1.6Sn0.2Zn0.2O3-δ while maintaining the bixbyite structure. The n-type conductivity of the doped material decreases with zinc substitution. Zn-doped In1.6Sn0.2Zn0.2O3-δ was annealed under high oxygen pressure (∼170 atm) to eliminate anion vacancies, VO••. Owing to a decrease in carrier concentration by up to 2 orders of magnitude from 1020 to 1018 carriers/cm3, the conductivity of the annealed material decreases. Hall measurements show that the carriers remain as n-type. The results imply the existence of neutral Zn−VO•• complexes that prevent the donation of holes by Zn2+.
Internal Tensile Force and A2 Domain Unfolding of von Willebrand Factor Multimers in Shear Flow.

Abstract Using Brownian molecular dynamics simulations, we examine the internal dynamics and biomechanical response of von Willebrand factor (vWF) multimers subject to shear flow. The coarse grain multimer description employed here is based on a monomer model in which the A2 domain of vWF is explicitly represented by a nonlinear elastic spring whose mechanical response was fit to experimental force/extension data from vWF monomers. This permits examination of the dynamic behavior of hydrodynamic forces acting on A2 domains as a function of shear rate and multimer length, as well as position of an A2 domain along the multimer contour. Force/position data reveal that collapsed multimers exhibit a force distribution with two peaks, one near each end of the chain; unraveled multimers, however, show a single peak in A2 domain force near the center of multimers. Guided further by experimental data, significant excursions of force acting on a domain are associated with an increasing probability for A2 domain unfolding. Our results suggest that the threshold shear rate required to induce A2 domain unfolding is inversely proportional to multimer length. By examining data for the duration and location of significant force excursions, convincing evidence is advanced that unfolding of A2 domains, and therefore scission of vWF multimers by the size-regulating blood enzyme ADAMTS13, happen preferentially near the center of unraveled multimers.
Microwave accelerated, Ni/C-catalyzed cross-couplings of in situ-derived zirconocenes

Both vinyl and alkyl zirconocenes undergo rapid couplings with aryl halides under heterogeneous conditions in a microwave reactor using Ni/C as catalyst. Ligand variations both in type and stoichiometry play major roles in the extent of conversion.
Three-dimensional organization of transzonal projections and other cytoplasmic extensions in the mouse ovarian follicle

Each mammalian oocyte is nurtured by its own multi-cellular structure, the ovarian follicle. We used new methods for serial section electron microscopy to examine entire cumulus and mural granulosa cells and their projections in mouse antral ovarian follicles. Transzonal projections (TZPs) are thin cytoplasmic projections that connect cumulus cells to the oocyte and are crucial for normal oocyte development. We studied these projections in detail and found that most TZPs do not reach the oocyte, and that they often branch and make gap junctions with each other. Furthermore, the TZPs that connect to the oocyte are usually contacted on their shaft by oocyte microvilli. Mural granulosa cells were found to possess randomly oriented cytoplasmic projections that are strikingly similar to the free-ended TZPs. We propose that granulosa cells use cytoplasmic projections to search for the oocyte, and cumulus cell differentiation results from a contact-mediated paracrine interaction with the oocyte.
Structure and stability of small boron and boron oxide clusters.

To rationally design and explore a potential energy source based on the highly exothermic oxidation of boron, density functional theory (DFT) was used to characterize small boron clusters with 0−3 oxygen atoms and a total of up to ten atoms. The structures, vibrational frequencies, and stabilities were calculated for each of these clusters. A quantum molecular dynamics procedure was used to locate the global minimum for each species, which proved to be crucial given the unintuitive structure of many of the most stable isomers. Additionally, due to the plane-wave, periodic DFT code used in this study a straightforward comparison of these clusters to the bulk boron and B2O3 structures was possible despite the great structural and energetic differences between the two forms. Through evaluation of previous computational and experimental work, the relevant low-energy structures of all but one of the pure boron clusters can be assigned with great certainty. Nearly all of the boron oxide clusters are described h...
Novel routes to 1-aryl-1,4-dihydro-3(2H)-isoquinolinones and 2-substituted or 2,3-disubstituted benzofurans by intramolecular cyclizations

N-(α-Benzotriazolylalkyl)arylacetamides, readily available from an arylacetamide, an aldehyde and benzotriazole, undergo intramolecular cyclization under acidic conditions to give 1-aryl-1,4-dihydro-3(2H)-isoquinolinones in good to excellent yields. Similarly, 2-(benzotriazol-1-yl)-2-(o-hydroxyphenyl)ethanols, obtained by lithiation of 2-(benzotriazol-1-ylmethyl)phenols followed by quenching with aldehydes or ketones, eliminate a molecule of water and a molecule of benzotriazole yielding 2-substituted and 2,3-disubstituted benzofurans.
Ring closing metathesis reactions on a phosphonate template

The first examples of ring-closing metathesis reactions on a phosphonate template catalyzed by the ruthenium alkylidene 3 are described. The yield, rate, and mode of cyclization in these reactions are sensitive to simple olefin substitution. The highlight of this method is the efficient syntheses of 2-alkyloxy-3,6-dihydro-[1,2]oxaphosphinine 2-oxide heterocycles (2).
Synthesis and reactions of halogenated thiazole isocyanates

A synthesis of 2-chloro-4-(trifluoromethyl)-5-isocyanatothiazole and 2,5-dichloro-5-isocyanatothiazole is described via the “Curtius Rearrangement” performed under anhydrous conditions. The synthetic procedure described allows for the isolation, storage, and manipulation of these highly reactive isocyanates. A number of derivatives of the above isocyanates were prepared. These include: carbamates, thiocarbamates, ureas, amines, amidines, and amides.
Ancestral Chromatin Configuration Constrains Chromatin Evolution on Differentiating Sex Chromosomes in Drosophila

Sex chromosomes evolve distinctive types of chromatin from a pair of ancestral autosomes that are usually euchromatic. In Drosophila, the dosage-compensated X becomes enriched for hyperactive chromatin in males (mediated by H4K16ac), while the Y chromosome acquires silencing heterochromatin (enriched for H3K9me2/3). Drosophila autosomes are typically mostly euchromatic but the small dot chromosome has evolved a heterochromatin-like milieu (enriched for H3K9me2/3) that permits the normal expression of dot-linked genes, but which is different from typical pericentric heterochromatin. In Drosophila busckii, the dot chromosomes have fused to the ancestral sex chromosomes, creating a pair of ‘neo-sex’ chromosomes. Here we collect genomic, transcriptomic and epigenomic data from D. busckii, to investigate the evolutionary trajectory of sex chromosomes from a largely heterochromatic ancestor. We show that the neo-sex chromosomes formed <1 million years ago, but nearly 60% of neo-Y linked genes have already become non-functional. Expression levels are generally lower for the neo-Y alleles relative to their neo-X homologs, and the silencing heterochromatin mark H3K9me2, but not H3K9me3, is significantly enriched on silenced neo-Y genes. Despite rampant neo-Y degeneration, we find that the neo-X is deficient for the canonical histone modification mark of dosage compensation (H4K16ac), relative to autosomes or the compensated ancestral X chromosome, possibly reflecting constraints imposed on evolving hyperactive chromatin in an originally heterochromatic environment. Yet, neo-X genes are transcriptionally more active in males, relative to females, suggesting the evolution of incipient dosage compensation on the neo-X. Our data show that Y degeneration proceeds quickly after sex chromosomes become established through genomic and epigenetic changes, and are consistent with the idea that the evolution of sex-linked chromatin is influenced by its ancestral configuration.
Concise synthesis of the bicyclic core of the chromoprotein antibiotics kedarcidin and neocarzinostatin by transannular reductive cyclization of a tetrayne precursor

Abstract The oxygenated [7.3.0]-bicyclododecadienediyne 8 is synthesized in 9 steps from l -dimethyl tartrate. In the key transformation, transannular reductive cyclization of the potassium salt of the tetrayne alcohol 7 with NaAIH(OCH 2 CH 2 (NCH 3 ) 2 ) 3 affords the bicyclic product 8 in 50–54% yield. This sequence provides a rapid entry into the strained bicyclic core structures of kedarcidin and neocarzinostatin chromophores ( 1 and 2 , respectively).
Dissociable medial temporal pathways for encoding emotional item and context information

Abstract Emotional experiences are typically remembered with a greater sense of recollection than neutral experiences, but memory benefits for emotional items do not typically extend to their source contexts. Item and source memory have been attributed to different subregions of the medial temporal lobes (MTL), but it is unclear how emotional item recollection fits into existing models of MTL function and, in particular, what is the role of the hippocampus. To address these issues, we used high-resolution functional magnetic resonance imaging (fMRI) to examine MTL contributions to successful emotional item and context encoding. The results showed that emotional items were recollected more often than neutral items. Whereas amygdala and perirhinal cortex (PRC) activity supported the recollection advantage for emotional items, hippocampal and parahippocampal cortex activity predicted subsequent source memory for both types of items, reflecting a double dissociation between anterior and posterior MTL regions. In addition, amygdala activity during encoding modulated the relationships of PRC activity and hippocampal activity to subsequent item recollection and source memory, respectively. Specifically, whereas PRC activity best predicted subsequent item recollection when amygdala activity was relatively low, hippocampal activity best predicted source memory when amygdala activity was relatively high. We interpret these findings in terms of complementary compared to synergistic amygdala-MTL interactions. The results suggest that emotion-related enhancements in item recollection are supported by an amygdala-PRC pathway, which is separable from the hippocampal pathway that binds items to their source context.
A Class of C2 and Pseudo C2 Symmetric Ketone Catalysts for Asymmetric Epoxidation. Conformational Effect on Catalysis

A class of C2 and pseudo C2 symmetric ketones with one fused ring at each side of the carbonyl group have been prepared from quinic acid and found to be effective catalysts for the asymmetric epoxidation of a variety of olefins. Electron deficient olefins such as enones can be efficiently epoxidized. Encouragingly good enantioselectivity is also obtained for the epoxidation of styrenes. The studies show that the ketone conformation plays an important role in the reactivity and selectivity of the catalyst.
Genes Relocated Between Drosophila Chromosome Arms Evolve Under Relaxed Selective Constraints Relative to Non-Relocated Genes.

Gene duplication creates a second copy of a gene either in tandem to the ancestral locus or dispersed to another chromosomal location. When the ancestral copy of a dispersed duplicate is lost from the genome, it creates the appearance that the gene was “relocated” from the ancestral locus to the derived location. Gene relocations may be as common as canonical dispersed duplications in which both the ancestral and derived copies are retained. Relocated genes appear to be under more selective constraints than the derived copies of canonical duplications, and they are possibly as conserved as single-copy non-relocated genes. To test this hypothesis, we combined comparative genomics, population genetics, gene expression, and functional analyses to assess the selection pressures acting on relocated, duplicated, and non-relocated single-copy genes in Drosophila genomes. We find that relocated genes evolve faster than single-copy non-relocated genes, and there is no evidence that this faster evolution is driven by positive selection. In addition, relocated genes are less essential for viability and male fertility than single-copy non-relocated genes, suggesting that relocated genes evolve fast because of relaxed selective constraints. However, relocated genes evolve slower than the derived copies of canonical dispersed duplicated genes. We therefore conclude that relocated genes are under more selective constraints than canonical duplicates, but are not as conserved as single-copy non-relocated genes.
Explaining unexpected data via competitive equilibria and processes in radical reactions with reversible deactivation.

ConspectusIn the game rock–paper–scissors, each of the three options, or pathways, has an equal chance of dominating, that is, rock beats scissors, scissors beats paper, and paper beats rock. In the classical form of the game, there is no one dominant pathway to follow, but they are all balanced in likelihood. However, in chemical reactions with several competing reagents, the question must be asked, are all competing reactions and pathways accessible? A related question is, if there are two, or more reversible processes that compete for the same reagent, will both processes equilibrate simultaneously, or will one process dominate system? Can these competing processes shed light on otherwise puzzling data?Several unexpected and counterintuitive experiments have been reported in radical reactions with reversible deactivation. These unexpected observations can be illustrated by the near absence of the products of conventional bimolecular radical coupling in the radical transformation of methylcobaltamine to...
Asymmetric allylation with chiral formamide catalysts

Abstract The successful example of chiral formamides that function as asymmetric catalysts is described. (S,S)-N,N-Bis(α-methylbenzyl)formamide mediates the enantioselective addition of allyl- and crotyltrichlorosilanes to aliphatic aldehydes with the assistance of hexamethylphosphoramide (HMPA) to afford the corresponding homoallylic alcohols in up to 98% enantiomeric excess.
QuASAR-MPRA: accurate allele-specific analysis for massively parallel reporter assays.

Motivation The majority of the human genome is composed of non-coding regions containing regulatory elements such as enhancers, which are crucial for controlling gene expression. Many variants associated with complex traits are in these regions, and may disrupt gene regulatory sequences. Consequently, it is important to not only identify true enhancers but also to test if a variant within an enhancer affects gene regulation. Recently, allele-specific analysis in high-throughput reporter assays, such as massively parallel reporter assays (MPRAs), have been used to functionally validate non-coding variants. However, we are still missing high-quality and robust data analysis tools for these datasets. Results We have further developed our method for allele-specific analysis QuASAR (quantitative allele-specific analysis of reads) to analyze allele-specific signals in barcoded read counts data from MPRA. Using this approach, we can take into account the uncertainty on the original plasmid proportions, over-dispersion, and sequencing errors. The provided allelic skew estimate and its standard error also simplifies meta-analysis of replicate experiments. Additionally, we show that a beta-binomial distribution better models the variability present in the allelic imbalance of these synthetic reporters and results in a test that is statistically well calibrated under the null. Applying this approach to the MPRA data, we found 602 SNPs with significant (false discovery rate 10%) allele-specific regulatory function in LCLs. We also show that we can combine MPRA with QuASAR estimates to validate existing experimental and computational annotations of regulatory variants. Our study shows that with appropriate data analysis tools, we can improve the power to detect allelic effects in high-throughput reporter assays. Availability and implementation http://github.com/piquelab/QuASAR/tree/master/mpra. Contact fluca@wayne.edu or rpique@wayne.edu. Supplementary information Supplementary data are available online at Bioinformatics.
Mathematical Approach to Differentiate Spontaneous and Induced Evolution to Drug Resistance During Cancer Treatment.

PurposeDrug resistance is a major impediment to the success of cancer treatment. Resistance is typically thought to arise from random genetic mutations, after which mutated cells expand via Darwini...
NEUTRINO PHYSICS (THEORY)

Nonzero neutrino masses are the first definitive need to extend the standard model. After reviewing the basic framework, I describe the status of some of the major issues, including tests of the basic framework of neutrino masses and mixings; the question of Majorana vs. Dirac; the spectrum, mixings, and number of neutrinos; models, with special emphasis on constraints from typical superstring constructions (which are not consistent with popular bottom-up assumptions); and other implications.
CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity

Motivation The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cpf1 system has been successfully applied in genome editing. However, target efficiency of the CRISPR-Cpf1 system varies among different guide RNA (gRNA) sequences. Results In this study, we reanalyzed the published CRISPR-Cpf1 gRNAs data and found many sequence and structural features related to their target efficiency. With the aid of Random Forest in feature selection, a support vector machine model was created to predict target efficiency for any given gRNAs. We have developed the first CRISPR-Cpf1 web service application, CRISPR-DT (CRISPR DNA Targeting), to help users design optimal gRNAs for the CRISPR-Cpf1 system by considering both target efficiency and specificity. CRISPR-DT will empower researchers in genome editing. Availability and implementation CRISPR-DT, mainly implemented in Perl, PHP and JavaScript, is freely available at http://bioinfolab.miamioh.edu/CRISPR-DT. Supplementary information Supplementary data are available at Bioinformatics online.
Cu(I)-catalyzed substitution reactions of activated vinyl triflates with functionalized organozinc reagents

Abstract Treatment of a mixed, functionalized dialkylzinc species with catalytic amounts of CuCN·2LiCl produces a reagent which readily displaces an activated vinyl triflate in high yields.
Corruption, Regulatory Burden and Firm Productivity

Using firm-level data from more than 39,000 firms in 111 economies, this paper tests the hypothesis that corruption impedes productivity more at higher levels of regulation. The analysis finds that there is a significant negative relationship between corruption and firm productivity when regulation is high and an insignificant relationship when it is low. These findings are robust to different controls and specifications.
The p-adic analysis of Stirling numbers via higher order Bernoulli numbers

In this paper, we use our previous study of the higher order Bernoulli numbers Bn(l) to investigate p-adic properties of Stirling numbers of the second kind S(n,k). For example we give a new greatl...
Elliptic Carmichael numbers and elliptic Korselt criteria

Let E/Q be an elliptic curve, let L(E,s)=\sum a_n/n^s be the L-series of E/Q, and let P be a point in E(Q). An integer n > 2 having at least two distinct prime factors will be be called an elliptic pseudoprime for (E,P) if E has good reduction at all primes dividing n and (n+1-a_n)P = 0 (mod n). Then n is an elliptic Carmichael number for E if n is an elliptic pseudoprime for every P in E(Z/nZ). In this note we describe two elliptic analogues of Korselt's criterion for Carmichael numbers, and we analyze elliptic Carmichael numbers of the form pq.
Restart-based fault-tolerance: System design and schedulability analysis

Embedded systems in safety-critical environments are continuously required to deliver more performance and functionality, while expected to provide verified safety guarantees. Nonetheless, platform-wide software verification (required for safety) is often expensive. Therefore, design methods that enable utilization of components such as real-time operating systems (RTOS), without requiring their correctness to guarantee safety, is necessary. In this paper, we propose a design approach to deploy safe-by-design embedded systems. To attain this goal, we rely on a small core of verified software to handle faults in applications and RTOS and recover from them while ensuring that timing constraints of safety-critical tasks are always satisfied. Faults are detected by monitoring the application timing and fault-recovery is achieved via full platform restart and software reload, enabled by the short restart time of embedded systems. Schedulability analysis is used to ensure that the timing constraints of critical plant control tasks are always satisfied in spite of faults and consequent restarts. We derive schedulability results for four restart-tolerant task models. We use a simulator to evaluate and compare the performance of the considered scheduling models.
New and Old about Renormalons: in Memoriam Kolya Uraltsev

I summarize what we know of renormalons from the 1970s and 80s: their uses and theoretical status. It is emphasized that renormalons in QCD are closely related to the Wilsonean operator product expansion (OPE) — a setup ideally suited for dealing with the factorially divergent series reflecting infrared dynamics. I discuss a breakthrough proposal due to Uraltsev et al. to use renormalons to evaluate nonperturbative (power) corrections in the processes without OPE. Some fresh ideas which were put forward recently are briefly discussed too, with emphasis on a possible relationship between resurgence via trans-series and OPE. This article is devoted to the memory of my friend Kolya Uraltsev. I should emphasize that these are my personal recollections. Other people who closely knew Kolya may or may not agree with my opinions.
Vision-Aided Absolute Trajectory Estimation Using an Unsupervised Deep Network with Online Error Correction

Adstract- We present an unsupervised deep neural network approach to the fusion of RGB-D imagery with inertial measurements for absolute trajectory estimation. Our network, dubbed the Visual-Inertial-Odometry Learner (VIOLearner), learns to perform visual-inertial odometry (VIO) without inertial measurement unit (IMU) intrinsic parameters (corresponding to gyroscope and accelerometer bias or white noise) or the extrinsic calibration between an IMU and camera. The network learns to integrate IMU measurements and generate hypothesis trajectories which are then corrected online according to the Jacobians of scaled image projection errors with respect to a spatial grid of pixel coordinates. We evaluate our network against state-of-the-art (SOA) visual-inertial odometry, visual odometry, and visual simultaneous localization and mapping (VSLAM) approaches on the KITTI Odometry dataset [1] and demonstrate competitive odometry performance.
Decentralized Task Allocation in Multi-Robot Systems via Bipartite Graph Matching Augmented With Fuzzy Clustering

Robotic systems, working together as a team, are becoming valuable players in different real-world applications, from disaster response to warehouse fulfillment services. Centralized solutions for coordinating multi-robot teams often suffer from poor scalability and vulnerability to communication disruptions. This paper develops a decentralized multi-agent task allocation (Dec-MATA) algorithm for multi-robot applications. The task planning problem is posed as a maximum-weighted matching of a bipartite graph, the solution of which using the blossom algorithm allows each robot to autonomously identify the optimal sequence of tasks it should undertake. The graph weights are determined based on a soft clustering process, which also plays a problem decomposition role seeking to reduce the complexity of the individual-agents' task assignment problems. To evaluate the new Dec-MATA algorithm, a series of case studies (of varying complexity) are performed, with tasks being distributed randomly over an observable 2D environment. A centralized approach, based on a state-of-the-art MILP formulation of the multi-Traveling Salesman problem is used for comparative analysis. While getting within 7-28% of the optimal cost obtained by the centralized algorithm, the Dec-MATA algorithm is found to be 1-3 orders of magnitude faster and minimally sensitive to task-to-robot ratios, unlike the centralized algorithm.
A transversality theorem for some classical varieties

In 2009, de Fernex and Hacon [10] proposed a generalization of the notion of the singularities to normal varieties that are not Q-Gorenstein. Based on their work, we generalize Kleiman�s transversality theorem to subvarieties with log terminal or log canonical singularities. We also show that some classical varieties, such as generic determinantal varieties, Wr d for general smooth curves, and certain Schubert varieties in G(k, n) are log terminal in de Fernex and Hacon�s notion, and canonical with some suitable boundary in the classical sense.
Reward Learning from Narrated Demonstrations

Humans effortlessly "program" one another by communicating goals and desires in natural language. In contrast, humans program robotic behaviours by indicating desired object locations and poses to be achieved [5], by providing RGB images of goal configurations [19], or supplying a demonstration to be imitated [17]. None of these methods generalize across environment variations, and they convey the goal in awkward technical terms. This work proposes joint learning of natural language grounding and instructable behavioural policies reinforced by perceptual detectors of natural language expressions, grounded to the sensory inputs of the robotic agent. Our supervision is narrated visual demonstrations (NVD), which are visual demonstrations paired with verbal narration (as opposed to being silent). We introduce a dataset of NVD where teachers perform activities while describing them in detail. We map the teachers' descriptions to perceptual reward detectors, and use them to train corresponding behavioural policies in simulation. We empirically show that our instructable agents (i) learn visual reward detectors using a small number of examples by exploiting hard negative mined configurations from demonstration dynamics, (ii) develop pick-and-place policies using learned visual reward detectors, (iii) benefit from object-factorized state representations that mimic the syntactic structure of natural language goal expressions, and (iv) can execute behaviours that involve novel objects in novel locations at test time, instructed by natural language.
Formation of ordered and disordered interfacial films in immiscible metal alloys

Abstract Atomistic simulations are used to study segregation-induced intergranular film formation in Cu Zr and Cu Nb alloys. While Cu Zr forms structurally disordered or amorphous films, ordered films comprised of a second phase usually precipitate in Cu Nb, with a critical nucleation size of ~ 1 nm below which the ordered phase cannot form. While the ordered film is retained at high temperature for a low energy Ʃ11 (113) boundary, a disordering transition is observed for a high energy Σ5 (310) boundary at low dopant concentrations. Finally, the effect of free surfaces on dopant segregation and intergranular film formation is investigated for both alloys.
Adaptive Policies for Scheduling With Reconfiguration Delay: An End-to-End Solution for All-Optical Data Centers

All-optical switching networks have been considered a promising candidate for the next generation data center networks thanks to its scalability in data bandwidth and power efficiency. However, the bufferless nature and the nonzero reconfiguration delay of optical switches remain great challenges in deploying all-optical networks. This paper considers the end-to-end scheduling for all-optical data center networks with no in-network buffer and nonzero reconfiguration delay. A framework is proposed to deal with the nonzero reconfiguration delay. The proposed approach constructs an adaptive variant of any given scheduling policy. It is shown that if a scheduling policy guarantees its schedules to have schedule weights close to the MaxWeight schedule (and thus is throughput optimal in the zero reconfiguration regime), then the throughput optimality is inherited by its adaptive variant (in any nonzero reconfiguration delay regime). As a corollary, a class of adaptive variants of the well-known MaxWeight policy is shown to achieve throughput optimality without prior knowledge of the traffic load. Furthermore, through numerical simulations, the simplest such policy, namely, the Adaptive MaxWeight, is shown to exhibit better delay performance than all prior work.
Generic elements of a Zariski-dense subgroup form an open subset

Let G be a semi-simple algebraic group over a finitely generated field K of characteristic zero, and let \Gamma < G(K) be a finitely generated Zariski-dense subgroup. In this note we prove that the set of K-generic elements of \Gamma (whose existence was established earlier in [9]) is open in the profinite topology of \Gamma. We then extend this result to the fields of positive characteristic, and also prove the existence of generic elements in this case.
Generalizations of generating functions for higher continuous hypergeometric orthogonal polynomials in the Askey scheme

Abstract We use connection relations and series rearrangement to generalize generating functions for several higher continuous orthogonal polynomials in the Askey scheme, namely the Wilson, continuous dual Hahn, continuous Hahn, and Meixner–Pollaczek polynomials. We also determine corresponding definite integrals using the orthogonality relations for these polynomials.
A proof of Tomescu's graph coloring conjecture

Abstract In 1971, Tomescu conjectured that every connected graph G on n vertices with chromatic number k ≥ 4 has at most k ! ( k − 1 ) n − k proper k-colorings. Recently, Knox and Mohar proved Tomescu's conjecture for k = 4 and k = 5 . In this paper, we complete the proof of Tomescu's conjecture for all k ≥ 4 , and show that equality occurs if and only if G is a k-clique with trees attached to each vertex.
Variance-Aware Optimal Power Flow

The incorporation of stochastic loads and generation into the operation of power grids gives rise to an exposure to stochastic risk. This risk has been addressed in prior work through a variety of mechanisms, such as scenario generation or chance constraints, that can be incorporated into OPF computations. Nevertheless, numerical experiments reveal that the resulting operational decisions can produce power flows with very high variance. In this paper we introduce a variety of convex variants of OPF that explicitly address the interplay of (power flow) variance with cost minimization, and present numerical experiments that highlight our contributions.
Collaborative Human-AI (CHAI): Evidence-Based Interpretable Melanoma Classification in Dermoscopic Images

Automated dermoscopic image analysis has witnessed rapid growth in diagnostic performance. Yet adoption faces resistance, in part, because no evidence is provided to support decisions. In this work, an approach for evidence-based classification is presented. A feature embedding is learned with CNNs, triplet-loss, and global average pooling, and used to classify via kNN search. Evidence is provided as both the discovered neighbors, as well as localized image regions most relevant to measuring distance between query and neighbors. To ensure that results are relevant in terms of both label accuracy and human visual similarity for any skill level, a novel hierarchical triplet logic is implemented to jointly learn an embedding according to disease labels and non-expert similarity. Results are improved over baselines trained on disease labels alone, as well as standard multiclass loss. Quantitative relevance of results, according to non-expert similarity, as well as localized image regions, are also significantly improved.
Fuzzy Adaptive Resonance Theory, Diffusion Maps and their applications to Clustering and Biclustering

In this paper, we describe an algorithm FARDiff (Fuzzy Adaptive Resonance Diffusion) which combines Diffusion Maps and Fuzzy Adaptive Resonance Theory to do clustering on high dimensional data. We describe some applications of this method and some problems for future research. Dedicated to our friend and colleague Prof. Alexander Gorban
Contrastive structured anomaly detection for gaussian graphical models

Gaussian graphical models (GGMs) are probabilistic tools of choice for analyzing conditional dependencies between variables in complex networked systems such as social networks, sensor networks, financial markets, etc. Finding changepoints in the structural evolution of a GGM is therefore essential to detecting anomalies in the underlying system modeled by the GGM. In order to detect structural anomalies in a GGM, we consider the problem of estimating changes in the precision matrix of the corresponding multivariate Gaussian distribution. We take a two-step approach to solving this problem:- (i) estimating a background precision matrix using system observations from the past without any anomalies, and (ii) estimating a foreground precision matrix using a sliding temporal window during anomaly monitoring. Our primary contribution is in estimating the foreground precision using a novel contrastive inverse covariance estimation procedure. In order to accurately learn only the structural changes to the GGM, we maximize a penalized log-likelihood where the penalty is the l 1 norm of difference between the foreground precision being estimated and the already learned background precision. We suitably modify the alternating direction method of multipliers (ADMM) algorithm for sparse inverse covariance estimation to perform contrastive estimation of the foreground precision matrix. Our results on simulated GGM data show significant improvement in precision and recall for detecting structural changes to the GGM, compared to a non-contrastive sliding window baseline.
Why (and How) Networks Should Run Themselves

The proliferation of networked devices, systems, and applications that we depend on every day makes managing networks more important than ever. The increasing security, availability, and performance demands of these applications suggest that these increasingly difficult network management problems be solved in real time, across a complex web of interacting protocols and systems. Alas, just as the importance of network management has increased, the network has grown so complex that it is seemingly unmanageable. In this new era, network management requires a fundamentally new approach. Instead of optimizations based on closed-form analysis of individual protocols, network operators need data-driven, machine-learning-based models of end-to-end and application performance based on high-level policy goals and a holistic view of the underlying components. Instead of anomaly detection algorithms that operate on offline analysis of network traces, operators need classification and detection algorithms that can make realtime, closed-loop decisions. Networks should learn to drive themselves. This paper explores this concept, discussing how we might attain this ambitious goal by more closely coupling measurement with realtime control and by relying on learning for inference and prediction about a networked application or system, as opposed to closed-form analysis of individual protocols.
On the quasi-hereditary property for staggered sheaves

Let G be an algebraic group over an algebraically closed field, acting on a variety X with finitely many orbits. Staggered sheaves are certain complexes of G-equivariant coherent sheaves on X that seem to possess many remarkable properties. In this paper, we construct "standard" and "costandard" objects in the category of staggered sheaves, and we prove that that category has enough projectives and injectives.
Spherical Panoramas for Astrophysical Data Visualization

Data immersion has advantages in astrophysical visualization. Complex multi-dimensional data and phase spaces can be explored in a seamless and interactive viewing environment. Putting the user in the data is a first step toward immersive data analysis. We present a technique for creating 360 degree spherical panoramas with astrophysical data. The three-dimensional software package Blender and the Google Spatial Media module are used together to immerse users in data exploration. Several examples employing these methods exhibit how the technique works using different types of astronomical data.
Bayesian latent structure discovery from multi-neuron recordings

Neural circuits contain heterogeneous groups of neurons that differ in type, location, connectivity, and basic response properties. However, traditional methods for dimensionality reduction and clustering are ill-suited to recovering the structure underlying the organization of neural circuits. In particular, they do not take advantage of the rich temporal dependencies in multi-neuron recordings and fail to account for the noise in neural spike trains. Here we describe new tools for inferring latent structure from simultaneously recorded spike train data using a hierarchical extension of a multi-neuron point process model commonly known as the generalized linear model (GLM). Our approach combines the GLM with flexible graph-theoretic priors governing the relationship between latent features and neural connectivity patterns. Fully Bayesian inference via Polya-gamma augmentation of the resulting model allows us to classify neurons and infer latent dimensions of circuit organization from correlated spike trains. We demonstrate the effectiveness of our method with applications to synthetic data and multi-neuron recordings in primate retina, revealing latent patterns of neural types and locations from spike trains alone.