cssi/SciSciGPT-SciSciNet huggingface dataset:
Esterification Delivers a Functional Enzyme into a Human Cell

A major hurdle in chemical biology is the delivery of native proteins into the cytosol of mammalian cells. Herein, we report that esterification of the carboxyl groups of an enzyme with a diazo compound enables not only its passage into the cytosol but also the retention of its catalytic activity there. This scenario is demonstrated with human ribonuclease 1, which manifests ribonucleolytic activity that can be cytotoxic. After internalization, the nascent esters are hydrolyzed in situ by endogenous esterases, making the process traceless. This strategy provides unprecedented opportunities for the delivery of functional enzymes into human cells.
Blockchain Transaction Processing.

A blockchain is an append-only linked-list of blocks, which is maintained at each participating node. Each block records a set of transactions and their associated metadata. Blockchain transactions act on the identical ledger data stored at each node. Blockchain was first perceived by Satoshi Nakamoto as a peer-to-peer digital-commodity (also known as crypto-currency) exchange system. Blockchains received traction due to their inherent property of immutability-once a block is accepted, it cannot be reverted.
Minimizing Classification Energy of Binarized Neural Network Inference for Wearable Devices

In this paper, we propose a low-power hardware for efficient deployment of binarized neural networks (BNNs) that have been trained for physiological datasets. BNNs constrain weights and feature-map to 1 bit, can pack in as many 1-bit weights as the width of a memory entry provides, and can execute multiple multiply-accumulate (MAC) operations with one fused bit-wise xnor and population-count instruction over aligned packed entries. Our proposed hardware is scalable with the number of processing engines (PEs) and the memory width, both of which adjustable for the most energy efficient configuration given an application. We implement two real case studies including Physical Activity Monitoring and Stress Detection on our platform, and for each case study on the target platform, we seek the optimal PE and memory configurations. Our implementation results indicate that a configuration with a good choice of memory width and number of PEs can be optimized up to 4x and 2.5 x in energy consumption respectively on Artix-7 FPGA and on 65nm CMOS ASIC implementation. We also show that, generally, wider memories make more efficient BNN processing hardware. To further reduce the energy, we introduce Pool-Skipping technique that can skip at least 50% of the operations that are accompanied by a Max-Pool layer in BNNs, leading to 37% operation reduction in the Stress Detection case study. Compared to the related works using the same case studies on the same target platform and with the same classification accuracy, our hardware is respectively 4.5x and 250x more energy efficient for the Stress Detection on FPGA and Physical Activity Monitoring on ASIC, respectively.
General De Finetti Type Theorems in Noncommutative Probability

We prove general de Finetti type theorems for classical and free independence. The de Finetti type theorems work for all non-easy quantum groups, which generalize a recent work of Banica, Curran and Speicher. We determine maximal distributional symmetries which means the corresponding de Finetti type theorem fails if a sequence of random variables satisfy more symmetry relations other than the maximal one. In addition, we define Boolean quantum semigroups in analogous to the easy quantum groups, by universal conditions on matrix coordinate generators and an orthogonal projection. Then, we show a general de Finetti type theorem for Boolean independence.
Electrical suppression of all nonradiative recombination pathways in monolayer semiconductors

Defects in conventional semiconductors substantially lower the photoluminescence (PL) quantum yield (QY), a key metric of optoelectronic performance that directly dictates the maximum device efficiency. Two-dimensional transition-metal dichalcogenides (TMDCs), such as monolayer MoS2, often exhibit low PL QY for as-processed samples, which has typically been attributed to a large native defect density. We show that the PL QY of as-processed MoS2 and WS2 monolayers reaches near-unity when they are made intrinsic through electrostatic doping, without any chemical passivation. Surprisingly, neutral exciton recombination is entirely radiative even in the presence of a high native defect density. This finding enables TMDC monolayers for optoelectronic device applications as the stringent requirement of low defect density is eased.
The Integrated Islet Distribution Program Answers the Call for Improved Human Islet Phenotyping and Reporting of Human Islet Characteristics in Research Articles.

In recent years, the need for enhanced rigor, reproducibility, and transparency in biomedical research has been the topic of much discussion. The National Institutes of Health (NIH) led the way in this conversation with issuance of the NIH guidelines for rigor and reproducibility, which have been mandated for all grant applications since 2016 (1,2). In support of this initiative, a recent review article by Hart and Powers, published in Diabetologia (3), with an accompanying editorial copublished in Diabetes and Diabetologia by Poitout et al. (4,5) highlighted the need for improved standardization of human islet data and its reporting in scientific publications. Diabetologia and Diabetes have initiated a checklist that is now required at the time of manuscript submission. At a minimum, the source and isolation center, a unique identifier number for each human islet preparation, and key demographic/clinical data must be included. Although not mandatory, the editorial encourages the inclusion of additional data, such as the cause of donor death, measurements of islet purity and viability, functional measures, ischemia duration, and culture time. Since 2004, the Integrated Islet Distribution Program (IIDP) has served as the main source of human islets for research in the U.S. (6–8). Directed by Joyce C. Niland at the City of Hope in Duarte, CA, the IIDP is funded by the National Institutes of Diabetes and Digestive and Kidney Diseases (NIDDK) and the JDRF. To date, the IIDP has distributed over 250 million islets, serving more than 400 islet studies across nine different countries, with the resulting research yielding more than 700 publications. Thus, the IIDP is a …
Bikesharing in Philadelphia: Do lower-income areas generate trips?

Abstract Many bikeshare programs seek to equitably serve residents from different income strata. Experience from other cities in the US and elsewhere in the developed world suggest that bikeshare systems are used mostly by more affluent populations. In order to encourage more bikeshare usage among low-income populations, the City of Philadelphia sited docking stations in low-income neighborhoods, allowed cash payments, and provided discounts to those receiving food-stamps. We examined one-year of data for Philadelphia’s Indego bikeshare system between April 2017 and March 2018. Travel patterns were examined and suggested that bikeshare trips taken from docking stations in lower-income areas are for work commute trips. Multivariate regression models confirmed that lower-income areas generate fewer trips while controlling for other factors such as transit access and whether the station is proximate to a bicycle lane. Our results suggest that despite Indego’s efforts, more work is needed to generate bikeshare trips in lower income neighborhoods.
Competitive Statistical Estimation With Strategic Data Sources

In recent years, data have played an increasingly important role in the economy as a good in its own right. In many settings, data aggregators cannot directly verify the quality of the data they purchase, nor the effort exerted by data sources when creating the data. Recent work has explored mechanisms to ensure that the data sources share high-quality data with a single data aggregator, addressing the issue of moral hazard. Oftentimes, there is a unique, socially efficient solution. In this paper, we consider data markets where there is more than one data aggregator. Since data can be cheaply reproduced and transmitted once created, data sources may share the same data with more than one aggregator, leading to free-riding between data aggregators. This coupling can lead to nonuniqueness of equilibria and social inefficiency. We examine a particular class of mechanisms that have received study recently in the literature, and we characterize all the generalized Nash (GN) equilibria of the resulting data market. We show that, in contrast to the single-aggregator case, there is either infinitely many GN equilibria or none. We also provide necessary and sufficient conditions for all equilibria to be socially inefficient. In our analysis, we identify the components of these mechanisms that give rise to these undesirable outcomes, showing the need for research into mechanisms for competitive settings with multiple data purchasers and sellers.
Remarkable stereoselectivity in the alkylation of a hydroazulenone: progress towards the total synthesis of guanacastepene

Abstract exo-Methylene ketone 6 serves as a vehicle for elaboration of the C8 quaternary center en route to guanacastepene via a conjugate addition–alkylation sequence. Methylation of the cycloheptadienolate derived from 7 is highly selective for the desired relative stereochemistry, as determined by NMR and crystallographic analysis.
Olefin metathesis on nanostructures

Alkene metathesis processes on nanostructures can proceed via radial or lateral pathways. Radial metathesis installs new functionalities on the surface of a nanostructure through outward growth from its core. Lateral metathesis involves successive crosslinking of neighboring alkenes on the nanostructure and creates a polymer shell around the particle.
β-Nitrostyrenes as electrophiles in Parham cyclization chemistry: reaction with o-lithiobenzonitrile

Abstract β-Nitrostyrenes react with o-lithiobenzonitrile, generated from the requisite aryl bromide at −100 °C by bromine–lithium exchange with n-butyllithium in THF, to afford 2-nitro-3-phenyl-3H-inden-1-ylamines resulting from 1,4-addition to the β-nitrostyrene followed by intramolecular capture of the resultant nitronate anion by the ortho-cyano functional group.
(Ph4P)4[Pd7As10S22]: A Sulfosalt with a Large Cluster Anion Whose Structure Resembles a Gondola

The [Pd7As10S22]4- molecule assembles under hydrothermal conditions from Pd2+ and [AsS3]3- to adopt the unusual shape of a gondola. Key to its formation appears to be the creation of direct Pd−As bonds.
Synthetic and Mechanistic Studies on the Azabicyclo[7.3.1]enediyne Core and Naphtho[2,3-h]quinoline Portions of Dynemicin A

The synthesis of the 13-keto-10-azabicyclo[7.3.1]enediyne core structure of dynemicin A has been achieved by two routes, Schemes 4 and 6. The chemistry of the 13-keto core structure is dominated by the unusually facile bridgehead enolization. Comparison of the rates of cycloaromatization of a variety of enediynes revealed that substantial rate differences occurred even though the distance between the bonding acetylenes was virtually identical. A non-radical cycloaromatization pathway, initiated by thiol addition to the enediyne system, was discovered, and the simple core amine 26 exhibits modest in vitro and in vivo antitumor activity. Finally, two methods for the synthesis of the naphtho[2,3-h]quinoline portion of dynemicin A are described, and both these compounds also exhibit antitumor activity.
Novel Extended Solids Composed of Transition Metal Oxide Clusters

Abstract Transition metal oxide clusters and their derivatives offer an unmatched variety of structural motifs that are potential building blocks for the design and development of extended solids. In view of the proven applications of these clusters in catalysis, molecular recognition, environmental decontamination, clinical and analytical processes, materials science, nanotechnology, and medicine, their usage as building blocks promises the development of new materials whose properties could be rationalized in terms of their constituents. Although the technique of assembling appropriate transition metal oxide clusters to generate new solids is still underdeveloped, recent progress made in this direction is promising. During our ongoing research program focused on this aspect, we have been able to prepare and characterize a series of novel framework materials, composed of well defined vanadium oxide clusters {V 18 O 42 ( X O 4 )} ( X =V, S, Cl). We have also prepared three-dimensional composite solids by incorporating organic ligands into the transition metal oxide framework. Some of the results of this work are reviewed with reference to the synthesis, structure, and physicochemical properties of the newly prepared extended solids.
Identification of different putative outer membrane electron conduits necessary for Fe(III) citrate, Fe(III) oxide, Mn(IV) oxide, or electrode reduction by geobacter sulfurreducens

At least five gene clusters in the Geobacter sulfurreducens genome encode putative "electron conduits" implicated in electron transfer across the outer membrane, each containing a periplasmic multiheme c-type cytochrome, integral outer membrane anchor, and outer membrane redox lipoprotein(s). Markerless single-gene-cluster deletions and all possible multiple-deletion combinations were constructed and grown with soluble Fe(III) citrate, Fe(III) and Mn(IV) oxides, and graphite electrodes poised at +0.24 V and -0.1 V versus the standard hydrogen electrode (SHE). Different gene clusters were necessary for reduction of each electron acceptor. During metal oxide reduction, deletion of the previously described omcBC cluster caused defects, but deletion of additional components in an ΔomcBC background, such as extEFG, were needed to produce defects greater than 50% compared to findings with the wild type. Deletion of all five gene clusters abolished all metal reduction. During electrode reduction, only the ΔextABCD mutant had a severe growth defect at both redox potentials, while this mutation did not affect Fe(III) oxide, Mn(IV) oxide, or Fe(III) citrate reduction. Some mutants containing only one cluster were able to reduce particular terminal electron acceptors better than the wild type, suggesting routes for improvement by targeting specific electron transfer pathways. Transcriptomic comparisons between fumarate and electrode-based growth conditions showed all of these ext clusters to be constitutive, and transcriptional analysis of the triple-deletion strain containing only extABCD detected no significant changes in expression of genes encoding known redox proteins or pilus components. These genetic experiments reveal new outer membrane conduit complexes necessary for growth of G. sulfurreducens, depending on the available extracellular electron acceptor.IMPORTANCE Gram-negative metal-reducing bacteria utilize electron conduits, chains of redox proteins spanning the outer membrane, to transfer electrons to the extracellular surface. Only one pathway for electron transfer across the outer membrane of Geobacter sulfurreducens has been linked to Fe(III) reduction. However, G. sulfurreducens is able to respire a wide array of extracellular substrates. Here we present the first combinatorial genetic analysis of five different electron conduits via creation of new markerless deletion strains and complementation vectors. Multiple conduit gene clusters appear to have overlapping roles, including two that have never been linked to metal reduction. Another recently described cluster (ExtABCD) was the only electron conduit essential during electrode reduction, a substrate of special importance to biotechnological applications of this organism.
Efficient isomer-pure synthesis of a benzo[b]thiophene analogue of pentacene.

Isomer-pure thieno[3,2-f:4,5-f ‘]bis[1]benzothiophene (2, n = 2) has been synthesized in an efficient four step approach without column chromatography.
Conformational changes in Arp2/3 complex induced by ATP, WASp-VCA, and actin filaments.

We used fluorescence spectroscopy and EM to determine how binding of ATP, nucleation-promoting factors, actin monomers, and actin filaments changes the conformation of Arp2/3 complex during the process that nucleates an actin filament branch. We mutated subunits of Schizosaccharomyces pombe Arp2/3 complex for labeling with fluorescent dyes at either the C termini of Arp2 and Arp3 or ArpC1 and ArpC3. We measured Forster resonance energy transfer (FRET) efficiency (ETeff) between the dyes in the presence of the various ligands. We also computed class averages from electron micrographs of negatively stained specimens. ATP binding made small conformational changes of the nucleotide-binding cleft of the Arp2 subunit. WASp-VCA, WASp-CA, and WASp-actin-VCA changed the ETeff between the dyes on the Arp2 and Arp3 subunits much more than between dyes on ArpC1 and ArpC3. Ensemble FRET detected an additional structural change that brought ArpC1 and ArpC3 closer together when Arp2/3 complex bound actin filaments. VCA binding to Arp2/3 complex causes a conformational change that favors binding to the side of an actin filament, which allows further changes required to nucleate a daughter filament.
FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET.

Single-molecule Forster Resonance Energy Transfer (smFRET) allows probing intermolecular interactions and conformational changes in biomacromolecules, and represents an invaluable tool for studying cellular processes at the molecular scale. smFRET experiments can detect the distance between two fluorescent labels (donor and acceptor) in the 3-10 nm range. In the commonly employed confocal geometry, molecules are free to diffuse in solution. When a molecule traverses the excitation volume, it emits a burst of photons, which can be detected by single-photon avalanche diode (SPAD) detectors. The intensities of donor and acceptor fluorescence can then be related to the distance between the two fluorophores. While recent years have seen a growing number of contributions proposing improvements or new techniques in smFRET data analysis, rarely have those publications been accompanied by software implementation. In particular, despite the widespread application of smFRET, no complete software package for smFRET burst analysis is freely available to date. In this paper, we introduce FRETBursts, an open source software for analysis of freely-diffusing smFRET data. FRETBursts allows executing all the fundamental steps of smFRET bursts analysis using state-of-the-art as well as novel techniques, while providing an open, robust and well-documented implementation. Therefore, FRETBursts represents an ideal platform for comparison and development of new methods in burst analysis. We employ modern software engineering principles in order to minimize bugs and facilitate long-term maintainability. Furthermore, we place a strong focus on reproducibility by relying on Jupyter notebooks for FRETBursts execution. Notebooks are executable documents capturing all the steps of the analysis (including data files, input parameters, and results) and can be easily shared to replicate complete smFRET analyzes. Notebooks allow beginners to execute complex workflows and advanced users to customize the analysis for their own needs. By bundling analysis description, code and results in a single document, FRETBursts allows to seamless share analysis workflows and results, encourages reproducibility and facilitates collaboration among researchers in the single-molecule community.
Bridged to fused ring interchange. The total synthesis of (±)-ledol

Abstract The type two intramolecular Diels-Alder reaction, when coupled with bridged to fused ring interchange, provides an efficient stereoselective route to fused 5,7- and 5,8-ring systems. This methodology has been utilized in the total synthesis of (±)-ledol, an aromadendrane sesquiterpene.
Chemical synthesis of peptides.

The chemical synthesis of peptides has developed into a rapid, reliable, automated procedure available to an increasingly broad spectrum of investigators. The term polypeptide was proposed in 1906 by Emil Fischer to describe structures consisting of variable numbers of amino acids linked together by amide bonds. The structural information of a peptide is principally provided by the sequence of its amino acids. The method for simultaneous removal of amino acid side-chain protecting groups and cleavage of the bound peptide from its solid support is treatment with anhydrous liquid HF at low temperature in the presence of scavengers. Peptide hormones and neurotransmitters are recognized by specific cell surface receptors from the information residing in their individual amino acid sequences. The messages contained within the amino acid sequences of a peptide are not always, or even usually, separated neatly into domains for receptor binding and for the triggering of various biological actions.
Aminocyclopropenium Ions: Synthesis, Properties, and Applications

This review covers the preparation, physical properties, and applications of cyclopropenium ions bearing one, two, or three amino substituents. It provides a description of the most reliable methods to access these unique structures as well as a discussion of the reactivity profiles of the common subtypes. 1 Introduction 2 Preparation 3 Properties 3.1 Stability 3.2 Redox Behavior 3.3 Ion Pair Strain 4 Reactions 5 Applications 5.1 Ionic Liquids 5.2 Metal Complexes 5.2.1 TDAC π-Complexes 5.2.2 BDAC σ-Complexes 5.2.3 Cyclopropenimine Ligands 5.2.4 BDAC–Phosphorus Ligands 5.3 Bronsted Bases 6 Conclusion
One-pot conversion of olefins to carbonyl compounds by hydroboration / NMO-TPAP oxidation

Abstract An efficient method to oxidize an olefin to the less substituted carbonyl compound is described. This new methodology utilizes borane dimethyl sulfide followed by tetrapropylammonium perruthenate N-methylmorpholine N-oxide to oxidize the resulting alkylborane.
Some allylic substituent effects in ring-closing metathesis reactions: allylic alcohol activation.

Dienes 2a−e were used to study allylic substituent effects in the ring-closing metathesis reaction (RCM). Both the steric and electronic character of the allylic substituents were found to influenc...
Building Alkali-Metal-Halide Layers within a Perovskite Host by Sequential Intercalation: (A2Cl)LaNb2O7 (A = Rb, Cs)

Alkali-metal-halide layers were constructed within Dion−Jacobson (DJ) layered perovskites by a two-step sequential intercalation method. Reductive intercalation with an alkali metal, followed by oxidative intercalation with chlorine gas, leads to the formation of the compounds, (A2Cl)LaNb2O7 (A = Rb, Cs). Rietveld refinement of X-ray powder diffraction data shows that an alkali-metal-halide layer is formed between the perovskite blocks. The alkali-metal cation is eight-coordinate with four oxygens from the perovskite layer and four chlorides from the new halide layer; this environment is similar to cesium in the CsCl structure (B2). Thermal analysis indicates that these are low-temperature phases where decomposition begins by 400 °C. Details on the synthesis and characterization of this set of compounds are presented, and the general utility of this approach discussed.
Bringing Diffuse X-ray Scattering Into Focus

X-ray crystallography is experiencing a renaissance as a method for probing the protein conformational ensemble. The inherent limitations of Bragg analysis, however, which only reveals the mean structure, have given way to a surge in interest in diffuse scattering, which is caused by structure variations. Diffuse scattering is present in all macromolecular crystallography experiments. Recent studies are shedding light on the origins of diffuse scattering in protein crystallography, and provide clues for leveraging diffuse scattering to model protein motions with atomic detail.
One-Step Synthesis of Complex Nitrogen Heterocycles from Imines and Alkyl-Substituted Maleic Anhydrides

Substituted maleic anhydrides react with imines to form polycyclic lactam products. Diastereoselectivity can be controlled by altering the reaction conditions in some cases, and regiochemistry is dictated by the structure of the allylic substituents on the anhydride. Cyclic imines, including dihydro-β-carbolines and dihydroisoquinolines, exhibit the highest level of reactivity in these new annulation reactions.
The dodecahedryl anion

Abstract The feasibility of generating the anion of dodecahedrane by direct metalation, by reductive lithiation with aromatic radical anions, and by transmetalation with alkyllithiums has been examined.
Organic catalysis over zeolites: A perspective on reaction paths within micropores

Abstract Since the early 1960s, the field of organic catalysis over zeolites and related microporous materials has shown enormous international expansion. Not only has a multiplicity of new reactions been explored over a continually increasing assemblage of zeolite structures, but also the depth of understanding of the catalytic chemistry and structure—reactivity relationships has shown dramatic growth. Further, the utilization of ZSM-5 and related medium-pore zeolites has truly enabled a revolution in shape-selective control of reaction selectivity. In the present review, we first conduct a broad classification and survey of organic chemistry over zeolites. This reflects, for the most part, a mechanistic rather than a process or applications frame of reference. We then examine selected examples of underlying physicochemical phenomena and structure—reactivity patterns that are peculiar to heterogeneous catalytic reactions within zeolite micropores. These include diffusion/adsorption effects, shape-selective principles, mechanistic disguises, catalyst deactivation pathways and related considerations.
Synthesis and absolute configuration of (−)-serantrypinone

Abstract A synthesis of (−)-serantrypinone (3) has been achieved from l -tryptophan. A key reaction involves the transformation of a selenoxide to an acetate via trapping of a presumed intermediate in a seleno-Pummerer reaction.
Asymmetric domino Michael–Henry reaction of 1,2-diones with nitroolefins catalyzed by a chiral bisoxazolidine–Ni(acac)2 complex

Abstract The asymmetric domino Michael–Henry reaction of 1,2-cyclohexadione with nitroolefins catalyzed by chiral ligand bisoxazolidine 1 and Ni(acac)2 has been developed. This process provided highly functionalized chiral bicycle[3,2,1] octane derivatives with the generation of four new stereogenic centers in high yields (76–99%), and with excellent enantioselectivities (up to 99%) and good diastereoselectivities (up to 9:1) under mild reaction conditions. The procedure presented is simple and makes this method suitable for practical use.
Increasing the Time Resolution of Single-Molecule Experiments with Bayesian Inference.

Abstract Many time-resolved single-molecule biophysics experiments seek to characterize the kinetics of biomolecular systems exhibiting dynamics that challenge the time resolution of the given technique. Here, we present a general, computational approach to this problem that employs Bayesian inference to learn the underlying dynamics of such systems, even when they are much faster than the time resolution of the experimental technique being used. By accurately and precisely inferring rate constants, our Bayesian inference for the analysis of subtemporal resolution dynamics approach effectively enables the experimenter to super-resolve the poorly resolved dynamics that are present in their data.
Reflections on routes to enantioselective solid catalysts

The intellectual and practical challenges of preparing enantioselective solids are discussed and two routes to the possible assembly of chiral inorganic structures highlighted. These synthesis methods are the imprinting of amorphous structures and the crystallization of chiral, crystalline, and microporous materials. For both types of solids, there is the potential to create chirality within the structure that may allow for long-term, robust use in catalytic reactions without significant loss of enantioselectivity.
Stable transgenesis in Astyanax mexicanus using the Tol2 transposase system

Background Astyanax mexicanus is a well-established fish model system for evolutionary and developmental biology research. These fish exist as surface forms that inhabit rivers and 30 different populations of cavefish. Despite important progress in the deployment of new technologies, deep mechanistic insights into the genetic basis of evolution, development, and behavior have been limited by a lack of transgenic lines commonly used in genetic model systems. Results Here, we expand the toolkit of transgenesis by characterizing two novel stable transgenic lines that were generated using the highly efficient Tol2 system, commonly used to generate transgenic zebrafish. A stable transgenic line consisting of the zebrafish ubiquitin promoter expresses enhanced green fluorescent protein ubiquitously throughout development in a surface population of Astyanax. To define specific cell-types, a Cntnap2-mCherry construct labels lateral line mechanosensory neurons in zebrafish. Strikingly, both constructs appear to label the predicted cell types, suggesting many genetic tools and defined promoter regions in zebrafish are directly transferrable to cavefish. Conclusion The lines provide proof-of-principle for the application of Tol2 transgenic technology in A. mexicanus. Expansion on these initial transgenic lines will provide a platform to address broadly important problems in the quest to bridge the genotype-phenotype gap.
Automated assembly of a reference taxonomy for phylogenetic data synthesis

Taxonomy and nomenclature data are critical for any project that synthesizes biodiversity data, as most biodiversity data sets use taxonomic names to identify taxa. Open Tree of Life is one such project, synthesizing sets of published phylogenetic trees into comprehensive supertrees. No single published taxonomy met the taxonomic and nomenclatural needs of the project. Here we describe a system for reproducibly combining several source taxonomies into a synthetic taxonomy, and we discuss the challenges of taxonomic and nomenclatural synthesis for downstream biodiversity projects.
Asymmetric Synthesis of (−)-Anatoxin-a via an Asymmetric Cyclization Using a New Ligand for Pd-Catalyzed Alkylations

Palladium-catalyzed asymmetric allylic alkylations have been explored in the context of medium-sized ring substrates, intramolecular vs intermolecular processes involving attack on a formally meso π-allyl intermediate in the desymmetrization, and the presence of electron-withdrawing groups on the cationic π-allylpalladium intermediate. The synthesis of anatoxin-a, also known as the “very fast death factor”, raises all of these questions. Ligands derived from trans-1,2-diaminocyclohexane and 2-diphenylphosphinobenzoic acid effect asymmetric alkylations with an allyl substrate bearing an electron-withdrawing group. On the other hand, a new type of ligand wherein the diamine is derivatized with both 2-diphenylphosphinobenzoic acid and 2-picolinic acid was required to effect asymmetric cyclization to form the 9-azabicyclo[4.2.1]non-2-ene system. A total synthesis of anatoxin-a from 5-hydroxy-1,8-nonadiene employing a metathesis reaction to form the cycloheptene and a palladium-catalyzed asymmetric cyclization...
Synthesis of β-lactams and β-aminoesters via high intensity ultrasound-promoted Reformatsky reactions

Reformatsky reactions of an imine, an α-bromoester, zinc dust and a catalytic amount of iodine in dioxane under high intensity ultrasound (HIU) irradiation from an ultrasonic probe are explored. A series of 16 aldimines with varying electronic demands is evaluated as potential electrophiles for reactions with three α-bromoesters of differing steric demands. This HIU method is successful for both enolizable and non-enolizable imines affording in short reaction times high yields of a β-lactam, the corresponding β-aminoester or a mixture of the two products depending on the identity of the imine and α-bromoester.
On locally conformally flat manifolds with finite total Q-curvature

In this paper, we study the ends of a locally conformally flat complete manifold with finite total Q-curvature. We prove that for such a manifold, the integral of the Q-curvature equals an integral multiple of a dimensional constant $$c_n$$ , where $$c_n$$ is the integral of the Q-curvature on the unit n-sphere. It provides further evidence that the Q-curvature on a locally conformally flat manifold controls geometry as the Gaussian curvature does in two dimension.
Reservoir Computing Based Neural Image Filters

Clean images are an important requirement for machine vision systems to recognize visual features correctly. However, the environment, optics, electronics of the physical imaging systems can introduce extreme distortions and noise in the acquired images. In this work, we explore the use of reservoir computing, a dynamical neural network model inspired from biological systems, in creating dynamic image filtering systems that extracts signal from noise using inverse modeling. We discuss the possibility of implementing these networks in hardware close to the sensors.
Nonparametric operator-regularized covariance function estimation for functional data

Abstract In functional data analysis (FDA), the covariance function is fundamental not only as a critical quantity for understanding elementary aspects of functional data but also as an indispensable ingredient for many advanced FDA methods. A new class of nonparametric covariance function estimators in terms of various spectral regularizations of an operator associated with a reproducing kernel Hilbert space is developed. Despite their nonparametric nature, the covariance estimators are automatically positive semi-definite, which is an essential property of covariance functions, via a one-step procedure. An unconventional representer theorem is established to provide a finite dimensional representation for this class of covariance estimators based on data, although the solutions are searched over infinite dimensional functional spaces. To further achieve a low-rank representation, another desirable property, e.g., for dimension reduction and easy interpretation, the trace-norm regularization is particularly studied, under which an efficient algorithm is developed based on the accelerated proximal gradient method. The outstanding practical performance of the trace-norm-regularized covariance estimator is demonstrated by a simulation study and the analysis of a traffic dataset. Under both fixed and random designs, an excellent rate of convergence is established for a broad class of operator-regularized covariance function estimators, which generalizes both the trace-norm-regularized covariance estimator and other popular alternatives.
Learning quadrotor dynamics using neural network for flight control

Traditional learning approaches proposed for controlling quadrotors or helicopters have focused on improving performance for specific trajectories by iteratively improving upon a nominal controller, for example learning from demonstrations, iterative learning, and reinforcement learning. In these schemes, however, it is not clear how the information gathered from the training trajectories can be used to synthesize controllers for more general trajectories. Recently, the efficacy of deep learning in inferring helicopter dynamics has been shown. Motivated by the generalization capability of deep learning, this paper investigates whether a neural network based dynamics model can be employed to synthesize control for trajectories different than those used for training. To test this, we learn a quadrotor dynamics model using only translational and only rotational training trajectories, each of which can be controlled independently, and then use it to simultaneously control the yaw and position of a quadrotor, which is non-trivial because of nonlinear couplings between the two motions. We validate our approach in experiments on a quadrotor testbed.
Energy-Efficient Mobile Network I&#x002F;O

By year 2020, the number of smartphone users globally will reach 3 Billion and the mobile data traffic (cellular &#x002B; WiFi) will exceed PC Internet traffic the first time. As the number of smartphone users and the amount of data transferred per smartphone grow exponentially, limited battery power is becoming an increasingly critical problem for mobile devices which heavily depend on network I&#x002F;O. Despite the growing body of research in power management techniques for mobile devices at the hardware and networking layers, there has been little work focusing on saving energy at the application layer for mobile network I&#x002F;O. In this paper, we show that significant energy savings can be achieved with application-layer solutions at the mobile systems during data transfer with no performance penalty. In many cases, performance increase and energy savings can be achieved simultaneously.
Two results on ill-posed problems

Let A = A∗ be a linear operator in a Hilbert space H. Assume that equation Au = f (1) is solvable, not necessarily uniquely, and y is its minimal-norm solution. Assume that problem (1) is ill-posed. Let fδ, ||f − fδ|| ≤ δ, be noisy data, which are given, while f is not known. Variational regularization of problem (1) leads to an equation A∗Au+αu = Afδ. Operation count for solving this equation is much higher, than for solving the equation (A + ia)u = fδ (2). The first result is the theorem which says that if a = a(δ), limδ→0 a(δ) = 0 and limδ→0 δ a(δ) = 0, then the unique solution uδ to equation (2), with a = a(δ), has the property limδ→0 ||uδ − y|| = 0. The second result is an iterative method for stable calculation of the values of unbounded operator on elements given with an error.
Fast graph construction using auction algorithm

In practical machine learning systems, graph based data representation has been widely used in various learning paradigms, ranging from unsupervised clustering to supervised classification. Besides those applications with natural graph or network structure data, such as social network analysis and relational learning, many other applications often involve a critical step in converting data vectors to an adjacency graph. In particular, a sparse subgraph extracted from the original graph is often required due to both theoretic and practical needs. Previous study clearly shows that the performance of different learning algorithms, e.g., clustering and classification, benefits from such sparse subgraphs with balanced node connectivity. However, the existing graph construction methods are either computationally expensive or with unsatisfactory performance. In this paper, we utilize a scalable method called auction algorithm and its parallel extension to recover a sparse yet nearly balanced subgraph with significantly reduced computational cost. Empirical study and comparison with the state-of-art approaches clearly demonstrate the superiority of the proposed method in both efficiency and accuracy.
Initial complex associated to a jet scheme of a determinantal variety

Abstract We show in this paper that the principal component of the first-order jet scheme over the classical determinantal variety of m × n matrices of rank at most 1 is arithmetically Cohen–Macaulay, by showing that an associated Stanley–Reisner simplicial complex is shellable.
Inverse Sampling for Nonasymptotic Sequential Estimation of Bounded Variable Means

Abstract In this article, we consider the nonasymptotic sequential estimation of means of random variables bounded in between zero and one. We have rigorously demonstrated that, in order to guarantee a prescribed relative precision and confidence level, it suffices to continue sampling until the sample sum is no less than a certain bound and then take the sample mean as an estimate for the mean of the bounded random variable. We have developed an explicit formula and a bisection search method for the determination of such bound of sample sum, without any knowledge of the bounded variable. Moreover, we have derived bounds for the distribution of sample size. In the special case of Bernoulli random variables, we have established analytical and numerical methods to further reduce the bound of sample sum and thus improve the efficiency of sampling.
Multiscale analysis of collective motion and decision-making in swarms: An advection-diffusion equation with memory approach

Abstract We propose a (time) multiscale method for the coarse-grained analysis of collective motion and decision-making in self-propelled particle models of swarms comprising a mixture of ‘naive’ and ‘informed’ individuals. The method is based on projecting the particle configuration onto a single ‘meta-particle’ that consists of the elongation of the flock together with the mean group velocity and position. We find that the collective states can be associated with the transient and asymptotic transport properties of the random walk followed by the meta-particle, which we assume follows a continuous time random walk (CTRW). These properties can be accurately predicted at the macroscopic level by an advection–diffusion equation with memory (ADEM) whose parameters are obtained from a mean group velocity time series obtained from a single simulation run of the individual-based model.
MIMO First and Second Order Discrete Sliding Mode Controls of Uncertain Linear Systems Under Implementation Imprecisions

The performance of a conventional model-based controller significantly depends on the accuracy of the modeled dynamics. The model of a plant's dynamics is subjected to errors in estimating the numerical values of the physical parameters, and variations over operating environment conditions and time. These errors and variations in the parameters of a model are the major sources of uncertainty within the controller structure. Digital implementation of controller software on an actual electronic control unit (ECU) introduces another layer of uncertainty at the controller inputs/outputs. The implementation uncertainties are mostly due to data sampling and quantization via the analog-to-digital conversion (ADC) unit. The failure to address the model and ADC uncertainties during the early stages of a controller design cycle results in a costly and time consuming verification and validation (V&V) process. In this paper, new formulations of the first and second order discrete sliding mode controllers (DSMC) are presented for a general class of uncertain linear systems. The knowledge of the ADC imprecisions is incorporated into the proposed DSMCs via an online ADC uncertainty prediction mechanism to improve the controller robustness characteristics. Moreover, the DSMCs are equipped with adaptation laws to remove two different types of modeling uncertainties (multiplicative and additive) from the parameters of the linear system model. The proposed adaptive DSMCs are evaluated on a DC motor speed control problem in real-time using a processor-in-the-loop (PIL) setup with an actual ECU. The results show that the proposed SISO and MIMO second order DSMCs improve the conventional SISO first order DSMC tracking performance by 69% and 84%, respectively. Moreover, the proposed adaptation mechanism is able to remove the uncertainties in the model by up to 90%.
Constant-time predictive distributions for Gaussian processes

One of the most compelling features of Gaussian process (GP) regression is its ability to provide well-calibrated posterior distributions. Recent advances in inducing point methods have sped up GP marginal likelihood and posterior mean computations, leaving posterior covariance estimation and sampling as the remaining computational bottlenecks. In this paper we address these shortcomings by using the Lanczos algorithm to rapidly approximate the predictive covariance matrix. Our approach, which we refer to as LOVE (LanczOs Variance Estimates), substantially improves time and space complexity. In our experiments, LOVE computes covariances up to 2,000 times faster and draws samples 18,000 times faster than existing methods, all without sacrificing accuracy.
Tail Positive Words and Generalized Coinvariant Algebras

Let $n,k,$ and $r$ be nonnegative integers and let $S_n$ be the symmetric group. We introduce a quotient $R_{n,k,r}$ of the polynomial ring $\mathbb{Q}[x_1, \dots, x_n]$ in $n$ variables which carries the structure of a graded $S_n$-module. When $r \ge n$ or $k = 0$ the quotient $R_{n,k,r}$ reduces to the classical coinvariant algebra $R_n$ attached to the symmetric group. Just as algebraic properties of $R_n$ are controlled by combinatorial properties of permutations in $S_n$, the algebra of $R_{n,k,r}$ is controlled by the combinatorics of objects called tail positive words . We calculate the standard monomial basis of $R_{n,k,r}$ and its graded $S_n$-isomorphism type. We also view $R_{n,k,r}$ as a module over the 0-Hecke algebra $H_n(0)$, prove that $R_{n,k,r}$ is a projective 0-Hecke module, and calculate its quasisymmetric and nonsymmetric 0-Hecke characteristics. We conjecture a relationship between our quotient $R_{n,k,r}$ and the delta operators of the theory of Macdonald polynomials.
Stochastic stability analysis of discrete-time system using Lyapunov measure

In this paper, we study the stability problem of a stochastic, nonlinear, discrete-time system. We introduce a linear transfer operator-based Lyapunov measure as a new tool for stability verification of stochastic systems. Weaker set-theoretic notion of almost everywhere stochastic stability is introduced and verified, using Lyapunov measure-based stochastic stability theorems. Furthermore, connection between Lyapunov functions, a popular tool for stochastic stability verification, and Lyapunov measures is established. Using the duality property between the linear transfer Perron-Frobenius and Koopman operators, we show the Lyapunov measure and Lyapunov function used for the verification of stochastic stability are dual to each other. The results in this paper extend our earlier work on the use of Lyapunov measures for almost everywhere stability verification of deterministic dynamical systems [1].
A law of large numbers for weighted plurality

Consider an election between \(k\) candidates in which each voter votes randomly (but not necessarily independently) for a single candidate, and suppose that there is a single candidate that every voter prefers (in the sense that each voter is more likely to vote for this special candidate than any other candidate). Suppose we have a voting rule that takes all of the votes and produces a single outcome and suppose that each individual voter has little effect on the outcome of the voting rule. If the voting rule is a weighted plurality, then we show that with high probability, the preferred candidate will win the election. Conversely, we show that this statement fails for all other reasonable voting rules. This result is an extension of one by Haggstrom, Kalai and Mossel, who proved the above in the case \(k=2\).