cssi/SciSciGPT-SciSciNet huggingface dataset:
Validation of RT-qPCR Approaches to Monitor Pseudomonas syringae Gene Expression During Infection and Exposure to Pattern-Triggered Immunity

Pseudomonas syringae pv. tomato DC3000 is an important model plant pathogen, with a fully annotated genome and multiple compatible plant hosts. Very few studies have examined the regulation of DC3000 gene expression in vivo. We developed a quantitative reverse transcription-polymerase chain reaction assay to monitor transcriptional changes in DC3000 inoculated into Arabidopsis thaliana leaves during disease and exposure to pattern-triggered immunity (PTI). In our approach, bacterial RNA concentrations in total tissue RNA are standardized using P. syringae-specific 16S ribosomal RNA primers. We validated multiple stable reference genes for normalization in calculating the relative expression of genes of interest. We used empirically derived rates of amplification efficiency to calculate relative expression of key marker genes for virulence-associated regulation. We demonstrated that exposure to PTI alters DC3000 expression of type III secretion system, coronatine synthesis genes, and flagellar marker genes.
Rhodium-catalyzed formylation of organomercurials: application to efficient polyol synthesis.

The rhodium-catalyzed formylation of organomercurialsa new transformation of organomercurialsis reported. The addition of 0.50 equiv of 1,4-diazabicyclo[2.2.2]octane (DABCO) was found to promote the reaction, and it is postulated that the DABCO acts as a ligand for mercury. Several examples are presented to document the scope of the reaction. This reaction was developed in the context of a larger program focused on the development of efficient strategies for the synthesis of polyol-derived natural products, and an efficient (8 steps) synthesis of Tolypothrix pentaether that employs this methodology is reported.
Cell lineage and communication network inference via optimization for single-cell transcriptomics

The use of single-cell transcriptomics has become a major approach to delineate cell subpopulations and the transitions between them. While various computational tools using different mathematical methods have been developed to infer clusters, marker genes, and cell lineage, none yet integrate these within a mathematical framework to perform multiple tasks coherently. Such coherence is critical for the inference of cell-cell communication, a major remaining challenge. Here, we present similarity matrix-based optimization for single-cell data analysis (SoptSC), in which unsupervised clustering, pseudotemporal ordering, lineage inference, and marker gene identification are inferred via a structured cell-to-cell similarity matrix. SoptSC then predicts cell-cell communication networks, enabling reconstruction of complex cell lineages that include feedback or feedforward interactions. Application of SoptSC to early embryonic development, epidermal regeneration, and hematopoiesis demonstrates robust identification of subpopulations, lineage relationships, and pseudotime, and prediction of pathway-specific cell communication patterns regulating processes of development and differentiation.
Palladium-catalyzed trans-selective alkynylation-alkylation tandem process for the synthesis of (E)-3-alkyl-1-trialkylsilyl-3-alken-1-ynes

Abstract The Pd-catalyzed trans-selective monoalkynylation of 1,1-dihalo-1-alkenes with XZnC CSiMe3, where X is Br or Cl, can proceed generally in excellent yields in the presence of Pd(DPEphos)Cl2 or Pd(dppf)Cl2, and subsequent alkylation with methyl- and ethylzincs can proceed in excellent yields with ≥98% retention of configuration in the presence of Pd(tBu3P)2 as a catalyst.
Speed control and force-vectoring of bluebottle flies in a magnetically levitated flight mill.

ABSTRACT Flies fly at a broad range of speeds and produce sophisticated aerial maneuvers with precisely controlled wing movements. Remarkably, only subtle changes in wing motion are used by flies to produce aerial maneuvers, resulting in little directional tilt of the aerodynamic force vector relative to the body. Therefore, it is often considered that flies fly according to a helicopter model and control speed mainly via force vectoring by body pitch change. Here, we examined the speed control of bluebottle flies using a magnetically levitated (MAGLEV) flight mill, as they fly at different body pitch angles and with different augmented aerodynamic damping. We identified wing kinematic contributors to the changes of estimated aerodynamic force through testing and comparing two force-vectoring models – a constant force-vectoring model and a variable force-vectoring model – while using Akaike9s information criterion for selection of the best-approximating model. The results show that the best-approximating variable force-vectoring model, which includes the effects of wing kinematic changes, yields a considerably more accurate prediction of flight speed, particularly in higher velocity range, as compared with those of the constant force-vectoring model. Examination of the variable force-vectoring model reveals that, in the flight mill tethered flight, flies use a collection of wing kinematic variables to control primarily the force magnitude, while the force direction is also modulated, albeit to a smaller extent compared with those due to the changes in body pitch. The roles of these wing kinematic variables are analogous to those of throttle, and collective and cyclic pitch of helicopters.
SWI/SNF remains localized to chromatin in the presence of SCHLAP1

SCHLAP1 is a long noncoding RNA that is reported to function by depleting the SWI/SNF complex from the genome. We investigated the hypothesis that SCHLAP1 affects only specific compositions of SWI/SNF. Using several assays, we found that SWI/SNF is not depleted from the genome by SCHLAP1 and that SWI/SNF is associated with many coding and noncoding RNAs, suggesting that SCHLAP1 may function in a SWI/SNF-independent manner.
Enantioselective H-atom transfer reaction: a strategy to synthesize formaldehyde aldol products.

Enantioselective radical alkylation of Baylis−Hillman adducts furnished aldol products in good yield and selectivity. The results illustrate that the selectivity in the hydrogen atom transfer is dependent on the size of the ester substituent, with smaller substituents providing better enantioselectivity.
Olefin epoxidation with bis(trimethylsilyl) peroxide catalyzed by inorganic oxorhenium derivatives. Controlled release of hydrogen peroxide.

The replacement of organometallic rhenium species (e.g., CH3ReO3) by less expensive and more readily available inorganic rhenium oxides (e.g., Re2O7, ReO3(OH), and ReO3) can be accomplished using bis(trimethylsilyl) peroxide (BTSP) as oxidant in place of aqueous H2O2. Using a catalytic amount of a proton source, controlled release of hydrogen peroxide helps preserve sensitive peroxorhenium species and enables catalytic turnover to take place. Systematic investigation of the oxorhenium catalyst precursors, substrate scope, and effects of various additives on olefin epoxidation with BTSP are reported in this contribution.
A nonlocal transport equation describing roots of polynomials under differentiation

Let $p_n$ be a polynomial of degree $n$ having all its roots on the real line distributed according to a smooth function $u(0,x)$. One could wonder how the distribution of roots behaves under iterated differentation of the function, i.e. how the density of roots of $p_n^{(k)}$ evolves. We derive a nonlinear transport equation with nonlocal flux $$ u_t + \frac{1}{\pi}\left( \arctan{ \left( \frac{Hu}{ u}\right)} \right)_x = 0,$$ where $H$ is the Hilbert transform. This equation has three very different compactly supported solutions: (1) the arcsine distribution $u(t,x) = (1-x^2)^{-1/2} \chi_{(-1,1)}$, (2) the family of semicircle distributions $$ u(t,x) = \frac{2}{\pi} \sqrt{(T-t) - x^2}$$ and (3) a family of solutions contained in the Marchenko-Pastur law.
Ordering and magnetostriction in Fe alloy single crystals

Abstract Short-range and long-range ordering in α-Fe terminal solid solution phase (A2 phase with bcc structure) influences its physical, mechanical, magnetic and magnetostrictive behavior. Single crystal sample forms are ideal for examining order in these alloys using X-ray and neutron scattering techniques. Limited structural information available suggests that the lattice of A2 phase at room temperature contains a mixture of regions with local atomic environments similar to those expected in the long-range ordered structures in stable/metastable equilibrium with the A2 phase. The nature and extent of these regions are sensitive to alloy composition and the thermal history. The lattice strain modulations result from the nature of solute atom distribution (short-range ordering) in each region and impact the physical, mechanical, corrosion and magnetic behaviors. A need for a fundamental understanding of ordering in Fe and other alloys through structural evaluations of local atomic environments in alloy single crystals is suggested in this review.
Mechanism of Alkaline Hydrolysis of Cyclic and Acyclic Sulfates: An ab Initio Study with Solvation Correction

The large difference in the activation barriers for the alkaline hydrolysis of cyclic and acyclic sulfate esters (the activation barrier of the cyclic sulfate is 10.3 kcal/mol lower than that for the acyclic sulfate, leading to 106−107-fold rate acceleration) is investigated. Ab initio studies of the reaction paths for the basic hydrolysis of ethylene sulfate (ES) and dimethyl sulfate (DMS) have been performed in vacuum and in solution. The calculations focus on the attack of the hydroxyl ion on sulfur, the rate-determining step for these reactions. In analogy with the calculated results for the isoelectronic phosphate esters (EP and DMP), differential solvation is the dominant factor that leads to the faster rate of hydrolysis of the cyclic ester. In both systems, the preferential solvation of the cyclic ester transition states is due primarily to the greater exposure and resulting stabilization of the attacking hydroxide ion. Although the differential solvation effects are the same, the overall effect o...
The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives.

Over the past decade, there has been both great interest and confusion about whether recent demographic events — notably the Out-of-Africa-bottleneck and recent population growth — have led to differences in mutation load among human populations. The confusion can be traced to the use of different summary statistics to measure load, which lead to apparently conflicting results. We argue, however, that when statistics more directly related to load are used, the results of different studies and data sets consistently reveal little or no difference in the load of non-synonymous mutations among human populations. Theory helps to understand why no such differences are seen, as well as to predict in what settings they are to be expected. In particular, as predicted by modeling, there is evidence for changes in the load of recessive loss of function mutations in founder and inbred human populations. Also as predicted, eastern subspecies of gorilla, Neanderthals and Denisovans, who are thought to have undergone reductions in population sizes that exceed the human Out-of-Africa bottleneck in duration and severity, show evidence for increased load of non-synonymous mutations (relative to western subspecies of gorillas and modern humans, respectively). A coherent picture is thus starting to emerge about the effects of demographic history on the mutation load in populations of humans and close evolutionary relatives.
P(i-BuNCH2CH2)3N: an efficient promoter for the microwave synthesis of diaryl ethers

With the title proazaphosphatrane as a promoter, the coupling of aryl fluorides with aryl TBDMS ethers under microwave conditions gave moderate to high yields of the desired products at low catalyst loadings and in short times. In this methodology, electron deficient aryl fluorides possessing substituents, such as nitro, cyano, and ester, were coupled with sterically demanding aryl TBDMS ethers as well as with aryl TBDMS ethers bearing a variety of functionalities such as methoxy, halo, and cyano groups.
S-(2-Pyridinyl)-1,1,3,3-Tetramethylthiouronium Hexafluorophosphate. A New Reagent for the Synthesis of 2-Pyridinethiol Esters

A new thiouronium-based reagent for the synthesis of 2-pyridinethiol esters under non-nucleophilic conditions from the corresponding carboxylic acids was developed. The resulting procedure enables the preparation of previously unavailable α,β-unsaturated 2-pyridinethiol esters as well as their aliphatic and aromatic counterparts.
Variability and stability of large-scale cortical oscillation patterns

Individual differences in brain organization exist at many spatiotemporal scales and underlie the diversity of human thought and behavior. Oscillatory neural activity is crucial for these processes...
Measurement of select radical processes in hydrocarbon pyrolysis

Abstract Methods for the measurement of absolute and relative rates of reactions of organic free radicals related to hydrocarbon pyrolysis in the condensed phase are illustrated. Examples are provided of methods for the determination of absolute rate expressions. The absolute rate expressions are employed in competition kinetic experiments that measure the ratio of an unknown rate constant to the known basis rate constant, yielding the desired competing reaction rate. Examples of use of the absolute and competition kinetic methods to measure rates of select free radical reactions of interest to hydrocarbon pyrolysis are illustrated. Methods for the measurement of absolute rate expressions for reactions of organic free radicals that will be covered include kinetic laserflash optical spectroscopy (KLS), kinetic electron spin resonance spectroscopy (KESR), and kinetic laserflash time resolved infrared spectroscopy (TRIR).
The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago

A primary goal of biogeography is to understand how large-scale environmental processes, like climate change, affect diversification. One often-invoked but seldom tested process is the "species-pump" model, in which repeated bouts of cospeciation are driven by oscillating climate-induced habitat connectivity cycles. For example, over the past three million years, the landscape of the Philippine Islands has repeatedly coalesced and fragmented due to sea-level changes associated with glacial cycles. This repeated climate-driven vicariance has been proposed as a model of speciation across evolutionary lineages codistributed throughout the islands. This model predicts speciation times that are temporally clustered around the times when interglacial rises in sea level fragmented the islands. To test this prediction, we collected comparative genomic data from 16 pairs of insular gecko populations. We analyze these data in a full-likelihood, Bayesian model-choice framework to test for shared divergence times among the pairs. Our results provide support against the species-pump model prediction in favor of an alternative interpretation, namely that each pair of gecko populations diverged independently. These results suggest the repeated bouts of climate-driven landscape fragmentation have not been an important mechanism of speciation for gekkonid lizards across the Philippine Archipelago.
anti-Selective enolboration–aldolization of propanoic acid

Abstract A systematic examination of enolboration–aldolization of propanoic acid has led to an efficient synthesis of anti -β-hydroxy-α-methyl carboxylic acids in consistently high yields and diastereoselectivities by using B -bromodicyclohexylborane as the enolization reagent and triethylamine as the base.
Coordination chemistry of polychalcogen anions and transition metal carbonyls

Abstract This article focuses on the chemistry of heavy polychalcogenides as ligands to transition metal centers. After reviewing some of the general synthetic strategies leading to metal polyselenides and polytellurides, work from the author's labs is discussed, which involves the coordination of polychalcogenide anions to metal carbonyls. It has been found that coordination of polychalcogenide anions to metal carbonyls often results in oxidation of the metal center, with loss of some or all of the carbonyl ligands. This oxidative decarbonylation reaction provides a convenient entry to a wide variety of new and existing metal chalcogenide complexes. The scope and potential of this unusual reaction is discussed.
Menthyldichlorophosphate: A chiral derivatizing agent for symmetrical diols

Abstract Menthyldichlorophosphate reacts readily with a variety of C2-chiral and meso diols to yield phosphate esters that exhibit useful diastereomeric differences in the 31P NMR spectra. Meso and d,l diols are easily differentiated with this reagent.
A regio- and stereocontrolled method for preparing 3,3-diarylacrylamides

Palladium-catalyzed hydroarylation of acetylenes provides regio- and stereodefined olefins. This methodology has been extended to arylpropiolamides where 3,3-diarylacrylamides are prepared stereospecifically. In an independent fashion, both the E- and Z-isomers were prepared by judicious choice of arylpropiolamide preparation and the palladium catalyzed hydroarylation reaction.
Preventing S. aureus biofilm formation on titanium surfaces by the release of antimicrobial β-peptides from polyelectrolyte multilayers

Abstract Staphylococcus aureus infections represent the major cause of titanium based-orthopaedic implant failure. Current treatments for S. aureus infections involve the systemic delivery of antibiotics and additional surgeries, increasing health-care costs and affecting patient’s quality of life. As a step toward the development of new strategies that can prevent these infections, we build upon previous work demonstrating that the colonization of catheters by the fungal pathogen Candida albicans can be prevented by coating them with thin polymer multilayers composed of chitosan (CH) and hyaluronic acid (HA) designed to release a β-amino acid-based peptidomimetic of antimicrobial peptides (AMPs). We demonstrate here that this β-peptide is also potent against S. aureus (MBPC = 4 μg/mL) and characterize its selectivity toward S. aureus biofilms. We demonstrate further that β-peptide-containing CH/HA thin-films can be fabricated on the surfaces of rough planar titanium substrates in ways that allow mammalian cell attachment and permit the long-term release of β-peptide. β-Peptide loading on CH/HA thin-films was then adjusted to achieve release of β-peptide quantities that selectively prevent S. aureus biofilms on titanium substrates in vitro for up to 24 days and remained antimicrobial after being challenged sequentially five times with S. aureus inocula, while causing no significant MC3T3-E1 preosteoblast cytotoxicity compared to uncoated and film-coated controls lacking β-peptide. We conclude that these β-peptide-containing films offer a novel and promising localized delivery approach for preventing orthopaedic implant infections. The facile fabrication and loading of β-peptide-containing films reported here provides opportunities for coating other medical devices prone to biofilm-associated infections. Statement of Significance Titanium (Ti) and its alloys are used widely in orthopaedic devices due to their mechanical strength and long-term biocompatibility. However, these devices are susceptible to bacterial colonization and the subsequent formation of biofilms. Here we report a chitosan and hyaluronic acid polyelectrolyte multilayer-based approach for the localized delivery of helical, cationic, globally amphiphilic β-peptide mimetics of antimicrobial peptides to inhibit S. aureus colonization and biofilm formation. Our results reveal that controlled release of this β-peptide can selectively kill S. aureus cells without exhibiting toxicity toward MC3T3-E1 preosteoblast cells. Further development of this polymer-based coating could result in new strategies for preventing orthopaedic implant-related infections, improving outcomes of these titanium implants.
Circuit directionality for motivation: Lateral accumbens-pallidum, but not pallidum-accumbens, connections regulate motivational attraction to reward cues.

Abstract Sign-tracking behavior, in which animals interact with a cue that predicts reward, provides an example of how incentive salience can be attributed to cues and elicit motivation. The nucleus accumbens (NAc) and ventral pallidum (VP) are two regions involved in cue-driven motivation. The VP, and NAc subregions including the medial shell and core, are critical for sign-tracking. Further, connections between the medial shell and VP are known to participate in sign-tracking and other motivated behaviors. The NAc lateral shell (NAcLSh) is a distinct and understudied subdivision of the NAc, and its contribution to the process by which reward cues acquire value remains unclear. The NAcLSh has been implicated in reward-directed behavior, and has reciprocal connections with the VP, suggesting that NAcLSh and VP interactions could be important mechanisms for incentive salience. Here, we use DREADDs (Designer Receptors Exclusively Activated by Designer Drugs) and an intersectional viral delivery strategy to produce a biased inhibition of NAcLSh neurons projecting to the VP, and vice versa. We find that disruption of connections from NAcLSh to VP reduces sign-tracking behavior while not affecting consumption of food rewards. In contrast, VP to NAcLSh disruption affected neither sign-tracking nor reward consumption, but did produce a greater shift in animals’ behavior more towards the reward source when it was available. These findings indicate that the NAcLSh → VP pathway plays an important role in guiding animals towards reward cues, while VP → NAcLSh back-projections may not and may instead bias motivated behavior towards rewards.
Realization of Complete Regiochemical Control during the Conversion of Squarate Esters into Complex Linear and Angular Polyquinanes. The Consequences of Incorporating a Leaving Group into One of the Alkenyllithium Reactants

A useful method is presented for controlling whether linear or angular triquinanes are formed during a reaction cascade initiated by the 2-fold addition of alkenyl anions to diisopropyl squarate. The key feature of the process involves the incorporation of a leaving group into one of the original nucleophilic reagents. Placement of the nucleofuge within a cyclic anion leads ultimately to formation of a linear product. Extracyclic and intracyclic options are possible, with preference given to the better leaving group when a competitive situation exists. When the leaving group is incorporated into an acyclic component, angular triquinanes result instead. Several other aspects of this impressive scaffolding scheme are detailed.
Photodissociation of methylacetylene at 193 nm

The photolysis of methylacetylene (MA) at 193 nm was studied using Fourier transform infrared spectroscopy for product analysis. Main primary processes are CH 3 C 2 H+hv→CH 3 C 2 +H and CH 3 C 2 H+hv→CH 2 +C 2 H 2 with a quantum yield of 0.7±0.1 and 0.11±0.01, respectively. Cl 2 was used as H atom scavenger. The CD 3 C 2 H photolysis was used to confirm that acetylene-d 1 formed is a primary product and is independent of reactant pressures
5-Heteroaryl-2-thiophenecarboxylic acids: Oxazoles and oxadiazoles

The synthesis of novel thiophene-2-carboxylic acids bearing alkyl and aryl-substituted oxazole and oxadiazole rings is reported. Sequential functionalization of the key precursor, 5-formyl-2- thiophenecarboxylic acid furnished the intermediate carboxylic acid esters which were converted into desired acids by basic cleavage
Three-dimensional mobility and muscle attachments in the pectoral limb of the Triassic cynodont Massetognathus pascuali (Romer, 1967).

The musculoskeletal configuration of the mammalian pectoral limb has been heralded as a key anatomical feature leading to the adaptive radiation of mammals, but limb function in the non-mammaliaform cynodont outgroup remains unresolved. Conflicting reconstructions of abducted and adducted posture are based on mutually incompatible interpretations of ambiguous osteology. We reconstruct the pectoral limb of the Triassic non-mammaliaform cynodont Massetognathus pascuali in three dimensions, by combining skeletal morphology from micro-computed tomography with muscle anatomy from an extended extant phylogenetic bracket. Conservative tests of maximum range of motion suggest a degree of girdle mobility, as well as substantial freedom at the shoulder and the elbow joints. The glenoid fossa supports a neutral pose in which the distal end of the humerus points 45° posterolaterally from the body wall, intermediate between classically 'sprawling' and 'parasagittal' limb postures. Massetognathus pascuali is reconstructed as having a near-mammalian complement of shoulder muscles, including an incipient rotator cuff (m. subscapularis, m. infraspinatus, m. supraspinatus, and m. teres minor). Based on close inspection of the morphology of the glenoid fossa, we hypothesize a posture-driven scenario for the evolution of the therian ball-and-socket shoulder joint. The musculoskeletal reconstruction presented here provides the anatomical scaffolding for more detailed examination of locomotor evolution in the precursors to mammals.
Prey Range and Genome Evolution of Halobacteriovorax marinus Predatory Bacteria from an Estuary

ABSTRACT Halobacteriovorax strains are saltwater-adapted predatory bacteria that attack Gram-negative bacteria and may play an important role in shaping microbial communities. To understand how Halobacteriovorax strains impact ecosystems and develop them as biocontrol agents, it is important to characterize variation in predation phenotypes and investigate Halobacteriovorax genome evolution. We isolated Halobacteriovorax marinus BE01 from an estuary in Rhode Island using Vibrio from the same site as prey. Small, fast-moving, attack-phase BE01 cells attach to and invade prey cells, consistent with the intraperiplasmic predation strategy of the H. marinus type strain, SJ. BE01 is a prey generalist, forming plaques on Vibrio strains from the estuary, Pseudomonas from soil, and Escherichia coli. Genome analysis revealed extremely high conservation of gene order and amino acid sequences between BE01 and SJ, suggesting strong selective pressure to maintain the genome in this H. marinus lineage. Despite this, we identified two regions of gene content difference that likely resulted from horizontal gene transfer. Analysis of modal codon usage frequencies supports the hypothesis that these regions were acquired from bacteria with different codon usage biases than H. marinus. In one of these regions, BE01 and SJ carry different genes associated with mobile genetic elements. Acquired functions in BE01 include the dnd operon, which encodes a pathway for DNA modification, and a suite of genes involved in membrane synthesis and regulation of gene expression that was likely acquired from another Halobacteriovorax lineage. This analysis provides further evidence that horizontal gene transfer plays an important role in genome evolution in predatory bacteria. IMPORTANCE Predatory bacteria attack and digest other bacteria and therefore may play a role in shaping microbial communities. To investigate phenotypic and genotypic variation in saltwater-adapted predatory bacteria, we isolated Halobacteriovorax marinus BE01 from an estuary in Rhode Island, assayed whether it could attack different prey bacteria, and sequenced and analyzed its genome. We found that BE01 is a prey generalist, attacking bacteria from different phylogenetic groups and environments. Gene order and amino acid sequences are highly conserved between BE01 and the H. marinus type strain, SJ. By comparative genomics, we detected two regions of gene content difference that likely occurred via horizontal gene transfer events. Acquired genes encode functions such as modification of DNA, membrane synthesis and regulation of gene expression. Understanding genome evolution and variation in predation phenotypes among predatory bacteria will inform their development as biocontrol agents and clarify how they impact microbial communities.
CORANNULENE SYNTHESIS VIA THE PYROLYSIS OF SILYL VINYL ETHERS

Abstract The bis(trimethylsilyl enol ether) derived from 7,10-diacetylfluoranthene undergoes pyrolysis to afford corannulene. This is important in cases where the usual precursor, the bis(chlorovinyl) derivative, is not accessible from the diketone.
Survival and development of potato psyllid (Hemiptera: Triozidae) on Convolvulaceae: effects of a plant-fungus symbiosis (Periglandula)

Plant species in the family Solanaceae are the usual hosts of potato psyllid, Bactericera cockerelli (Sulc) (Hemiptera: Psylloidea: Triozidae). However, the psyllid has also been shown to develop on some species of Convolvulaceae (bindweeds and morning glories). Developmental success on Convolvulaceae is surprising given the rarity of psyllid species worldwide associated with this plant family. We assayed 14 species of Convolvulaceae across four genera (Convolvulus, Calystegia, Ipomoea, Turbina) to identify species that allow development of potato psyllid. Two populations of psyllids were assayed (Texas, Washington). The Texas population overlaps extensively with native Convolvulaceae, whereas Washington State is noticeably lacking in Convolvulaceae. Results of assays were overlain on a phylogenetic analysis of plant species to examine whether Convolvulaceae distantly related to the typical host (potato) were less likely to allow development than species of Convolvulaceae more closely related. Survival was independent of psyllid population and location of the plant species on our phylogenetic tree. We then examined whether presence of a fungal symbiont of Convolvulaceae (Periglandula spp.) affected psyllid survival. These fungi associate with Convolvulaceae and produce a class of mycotoxins (ergot alkaloids) that may confer protection against plant-feeding arthropods. Periglandula was found in 11 of our 14 species, including in two genera (Convolvulus, Calystegia) not previously known to host the symbiont. Of these 11 species, leaf tissues from five contained large quantities of two classes of ergot alkaloids (clavines, amides of lysergic acid) when evaluated by LC-MS/MS. All five species also harbored Periglandula. No ergot alkaloids were detected in species free of the fungal symbiont. Potato psyllid rapidly died on the five species that harbored Periglandula and contained ergot alkaloids, but survived to adulthood on seven of the nine species in which ergot alkaloids were not detected. These results support the hypothesis that a plant-fungus symbiotic relationship affects the suitability of certain Convolvulaceae to potato psyllid.
A tandem oximation–cyclization route to Δ2-isoxazolines

Abstract 3,5-Disubstituted Δ 2 -isoxazolines can be prepared from the corresponding β,γ-unsaturated ketones by treatment with hydroxylamine hydrochloride and sodium hydroxide. Evidence indicates that the mechanism of this reaction involves the formation of three intermediates; oximation of the ketone, rearrangement of the alkene, and intramolecular Michael addition of the resulting α,β-unsaturated oxime.
Further studies on the chemistry of piperazic acids: New building blocks for β-hydroxy-α-aminoacids through the aza-achmatowicz reaction

Abstract The abnormal reluctance of piperazic acids to undergo N-2 acylation seems to be due to an electronic effect, not a steric / conformational problem. A system suitable for probing these issues was assembled by methods that have produced a versatile building block for β-hydroxy-α-aminoacids of either relative stereochemistry and of either (L) or (D) configuration.
Nonlinear optical phenomena in conjugated organic chromophores. Theoretical investigations via a π-electron formalism

This contribution explores the use of perturbation theory and the chemically oriented, computationally efficient PPP π-eletron model Hamiltonian to describe the first three molecular hyperpolarizabilitied and their interrelationships. Relationships between various nonlinear phenomena are treated as degeneracy factors, and a more general definition emerges from this analysis. Derivations of formulas describing second- to fourth-order susceptibilities are given for the monoexcited CI (MECI) and doubly excited CI (DECI) perturbation approaches, and numerical results are in good to excellent agreement with experimental value where available for a variety a second
Enantioselective reactions of radicals at the α position of γ-lactams

Abstract γ-Lactams derived from 2-aminopyridines undergo free radical reactions with allyltrimethylsilane in the presence of Lewis acids and chiral bisoxazolines. Products have been obtained with enantiomeric excesses as high as 99%.
Synthesis of the (Z) and (E) isomers of 1,2-diaryl-3-methyl-4,5-dioxo-3-pyrrolidinecarboxylic acid esters. Structural assignment by nmr and mass spectroscopy

Reaction of N-benzylideneaniline, 1a, with 3-methyl-2-oxobutanedioic acid diethyl ester, 2a, produced isomeric 3-methyl-4,5-dioxo-1,2-diphenyl-3-pyrrolidinecarboxylic acid ethyl esters, 3a and 3b. The higher melting isomer, 3a, was shown to have the (Z) configuration by nmr spectroscopy. The (Z) and (E) isomers of 3-methyl-4,5-dioxo-1,2-diphenyl-3-pyrrolidinecarboxylic acid methyl esters, 3c and 3d, were prepared from 1a and 3-methyl-2-oxobutanedioic acid dimethyl ester, 2b. The higher melting isomer, 3c, was shown to have the (Z) configuration. Similarly, N-benzylidene-p-toluidine, 1b, reacted with 2a to form (Z) and (E) isomers of 3-methyl-4,5-dioxo-1-(4-methylphenyl)-2-phenyl-3-pyrrolidinecarboxlic acid ethyl esters, 3e and 3f. Assignment of the 13C carbonyl carbon nmr chemical shift was made by preparing 2-methyl-3-oxobutanedioic-1-13C acid diethyl ester, 4, and from it the corresponding (Z) and (E) isomers of 3-methyl-4,5-dioxo-1,2-diphenyl-3-pyrrolidinecarboxylic 13C acid ester, 5a and 5b. The mass spectra of the (Z) isomers exhibit prominent ions corresponding to the masses of the Schiff bases used to make them, and ions corresponding to the loss of ArNCOCO from the parent ion. The (E) isomers 3b, 3d and 5b exhibit a prominent ion of mass 264; 3f gives mass 278, corresponding to the loss of the carboalkoxy group.
The HCN channel voltage sensor undergoes a large downward motion during hyperpolarization.

Voltage-gated ion channels (VGICs) contain positively charged residues within the S4 helix of the voltage-sensing domain (VSD) that are displaced in response to changes in transmembrane voltage, promoting conformational changes that open the pore. Pacemaker hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are unique among VGICs because their open probability is increased by membrane hyperpolarization rather than depolarization. Here we measured the precise movement of the S4 helix of a sea urchin HCN channel using transition metal ion fluorescence resonance energy transfer (tmFRET). We show that the S4 undergoes a substantial (~10 A) downward movement in response to membrane hyperpolarization. Furthermore, by applying distance constraints determined from tmFRET experiments to Rosetta modeling, we reveal that the carboxy-terminal part of the S4 helix exhibits an unexpected tilting motion during hyperpolarization activation. These data provide a long-sought glimpse of the hyperpolarized state of a functioning VSD and also a framework for understanding the dynamics of reverse gating in HCN channels. Transition metal FRET and Rosetta modeling reveal that the S4 helix in the voltage-sensing domain of the HCN channel moves downward and its carboxy-terminal portion tilts during hyperpolarization activation.
Relay-Aided Channel Estimation for mmWave Systems with Imperfect Antenna Arrays

Compressed Sensing (CS) based channel estimation techniques have recently emerged as an effective way to acquire the channel of millimeter-wave (mmWave) systems with a small number of measurements. These techniques, however, are based on prior knowledge of transmit and receive array manifolds, and assume perfect antenna arrays at both the transmitter and the receiver. In the presence of antenna imperfections, the geometry and response of the arrays are modified. This distorts the CS measurement matrix and results in channel estimation errors. This paper studies the effects of both transmit and receive antenna imperfections on the mmWave channel estimate. A relay-aided solution which corrects for errors caused by faulty transmit arrays is then proposed. Simulation results demonstrate the effectiveness of the proposed solution and show that comparable channel estimates can be obtained when compared to systems with perfect antennas without the need for additional training overhead.
Shapes and Context: In-The-Wild Image Synthesis & Manipulation

We introduce a data-driven model for interactively synthesizing in-the-wild images from semantic label input masks. Our approach is dramatically different from recent work in this space, in that we make use of no learning. Instead, our approach uses simple but classic tools for matching scene context, shapes, and parts to a stored library of exemplars. Though simple, this approach has several notable advantages over recent work: (1) because nothing is learned, it is not limited to specific training data distributions (such as cityscapes, facades, or faces); (2) it can synthesize arbitrarily high-resolution images, limited only by the resolution of the exemplar library; (3) by appropriately composing shapes and parts, it can generate an exponentially large set of viable candidate output images (that can say, be interactively searched by a user). We present results on the diverse COCO dataset, significantly outperforming learning-based approaches on standard image synthesis metrics. Finally, we explore user-interaction and user-controllability, demonstrating that our system can be used as a platform for user-driven content creation.
Real-time robust finger gaits planning under object shape and dynamics uncertainties

Dexterous manipulation has broad applications in assembly lines, warehouses and agriculture. To perform large-scale manipulation tasks for various objects, a multi-fingered robotic hand sometimes has to sequentially adjust its grasping gestures, i.e. the finger gaits, to address the workspace limits and guarantee the object stability. However, realizing finger gaits planning in dexterous manipulation is challenging due to the complicated grasp quality metrics, uncertainties on object shapes and dynamics (mass and moment of inertia), and unexpected slippage under uncertain contact dynamics. In this paper, a dual-stage optimization based planner is proposed to handle these challenges. In the first stage, a velocity-level finger gaits planner is introduced by combining object grasp quality with hand manipulability. The proposed finger gaits planner is computationally efficient and realizes finger gaiting without 3D model of the object. In the second stage, a robust manipulation controller using robust control and force optimization is proposed to address object dynamics uncertainties and external disturbances. The dual-stage planner is able to guarantee stability under unexpected slippage caused by uncertain contact dynamics. Moreover, it does not require velocity measurement or expensive 3D/6D tactile sensors. The proposed dual-stage optimization based planner is verified by simulations on Mujoco. The simulation video is available at [1].
Stochastic Unrelatedness, Couplings, and Contextuality

Abstract R. Duncan Luce once mentioned in a conversation that he did not consider Kolmogorov’s probability theory well-constructed because it treats stochastic independence as a “numerical accident”, while it should be treated as a fundamental relation, more basic than the assignment of numerical probabilities. I argue here that stochastic independence is indeed a “numerical accident”, a special form of stochastic dependence between random variables (most broadly defined). The idea that it is fundamental may owe its attractiveness to the confusion of stochastic independence with stochastic unrelatedness, the situation when two or more random variables have no joint distribution, “have nothing to do with each other”. Kolmogorov’s probability theory cannot be consistently constructed without allowing for stochastic unrelatedness, in fact making it a default situation: any two random variables recorded under mutually incompatible conditions are stochastically unrelated. However, stochastically unrelated random variables can always be probabilistically coupled, i.e., imposed a joint distribution upon, and this generally can be done in an infinity of ways, independent coupling being merely one of them. The notions of stochastic unrelatedness and all possible couplings play a central role in the foundation of probability theory and, especially, in the theory of probabilistic contextuality.
On Galois action in rigid DAHA modules

Given an elliptic curve over a field $K$ of algebraic numbers, we associate with it an action of the absolute Galois group $G_K$ in the type $A_1$ rigid DAHA-modules at roots of unity $q$ and over the rings $Z[q^{1/4}]/(p^m)$ for sufficiently general prime $p$. We describe rigid modules in characteristic zero and for such rings. The main examples of rigid modules are generalized nonsymmetric Verlinde algebras; their deformations for arbitrary $q$ are constructed in this paper, which is of independent interest on its own. The Galois action preserves the images of the elliptic braid group in the groups of automorphisms of rigid modules over $Z[q^{1/4}]/(p^m)$. If they are finite in characteristic zero, then $G_K$ acts there and no reduction modulo $(p^m)$ is needed; we find all such cases. In the case of $3$-dimensional DAHA-modules, these images are quotients of equilateral triangle groups directly related to the Livn\'e groups. Also, this paper can be viewed as an extension of the DAHA theory of refined Jones polynomials of torus knots (for $A_1$) to $G_K$.
Small Representations of Big Kidney Exchange Graphs.

Kidney exchanges are organized markets where patients swap willing but incompatible donors. In the last decade, kidney exchanges grew from small and regional to large and national---and soon, international. This growth results in more lives saved, but exacerbates the empirical hardness of the $\mathcal{NP}$-complete problem of optimally matching patients to donors. State-of-the-art matching engines use integer programming techniques to clear fielded kidney exchanges, but these methods must be tailored to specific models and objective functions, and may fail to scale to larger exchanges. In this paper, we observe that if the kidney exchange compatibility graph can be encoded by a constant number of patient and donor attributes, the clearing problem is solvable in polynomial time. We give necessary and sufficient conditions for losslessly shrinking the representation of an arbitrary compatibility graph. Then, using real compatibility graphs from the UNOS nationwide kidney exchange, we show how many attributes are needed to encode real compatibility graphs. The experiments show that, indeed, small numbers of attributes suffice.
Clustrophile 2: Guided Visual Clustering Analysis

Data clustering is a common unsupervised learning method frequently used in exploratory data analysis. However, identifying relevant structures in unlabeled, high-dimensional data is nontrivial, requiring iterative experimentation with clustering parameters as well as data features and instances. The number of possible clusterings for a typical dataset is vast, and navigating in this vast space is also challenging. The absence of ground-truth labels makes it impossible to define an optimal solution, thus requiring user judgment to establish what can be considered a satisfiable clustering result. Data scientists need adequate interactive tools to effectively explore and navigate the large clustering space so as to improve the effectiveness of exploratory clustering analysis. We introduce Clustrophile 2 , a new interactive tool for guided clustering analysis. Clustrophile 2 guides users in clustering-based exploratory analysis, adapts user feedback to improve user guidance, facilitates the interpretation of clusters, and helps quickly reason about differences between clusterings. To this end, Clustrophile 2 contributes a novel feature, the Clustering Tour, to help users choose clustering parameters and assess the quality of different clustering results in relation to current analysis goals and user expectations. We evaluate Clustrophile 2 through a user study with 12 data scientists, who used our tool to explore and interpret sub-cohorts in a dataset of Parkinson's disease patients. Results suggest that Clustrophile 2 improves the speed and effectiveness of exploratory clustering analysis for both experts and non-experts.
Crystal analysis of type $C$ Stanley symmetric functions

Combining results of T.K. Lam and J. Stembridge, the type $C$ Stanley symmetric function $F_w^C(\mathbf{x})$, indexed by an element $w$ in the type $C$ Coxeter group, has a nonnegative integer expansion in terms of Schur functions. We provide a crystal theoretic explanation of this fact and give an explicit combinatorial description of the coefficients in the Schur expansion in terms of highest weight crystal elements.
The diffusion of networking technologies

There has been significant interest in the networking community on the impact of cascade effects on the diffusion of networking technology upgrades in the Internet. Thinking of the global Internet as a graph, where each node represents an economically-motivated Internet Service Provider (ISP), a key problem is to determine the smallest set of nodes that can trigger a cascade that causes every other node in the graph to adopt the protocol. We design the first approximation algorithm with a provable performance guarantee for this problem, in a model that captures the following key issue: a node's decision to up-grade should be influenced by the decisions of the remote nodes it wishes to communicate with.Given an internetwork G(V, E) and threshold function θ, we assume that node u activates (upgrades to the new technology) when it is adjacent to a connected component of active nodes in G of size exceeding node u's threshold θ(u). Our objective is to choose the smallest set of nodes that can cause the rest of the graph to activate. Our main contribution is an approximation algorithm based on linear programming, which we complement with computational hardness results and a near-optimum integrality gap. Our algorithm, which does not rely on submodular optimization techniques, also highlights the substantial algorithmic difference between our problem and similar questions studied in the context of social networks.
Quasi-isometric rigidity of a class of right-angled Coxeter groups

We establish quasi-isometric rigidity for a class of right-angled Coxeter groups. Let $\Gamma_1,\Gamma_2$ be joins of finite generalized thick $m$-gons with $m\geq 3$. We show that the corresponding right-angled Coxeter groups are quasi-isometric if and only if $\Gamma_1,\Gamma_2$ are isomorphic. We also give a construction of commensurable right-angled Coxeter groups.
A generalized spin statistics theorem

In this article we generalize the spin statistics theorem and show that a state obeys Fermi-Dirac statistics if and only if the state is invariant under the action of SL(n, C). We also briefly discuss the experimental evidence and how the theorem relates to spin entanglement.
Calculations of the invariant measure for Hurwitz Continued Fractions

We study the density of the invariant measure of the Hurwitz complex continued fraction from a computational perspective. It is known that this density is piece-wise real-analytic and so we provide...