cssi/SciSciGPT-SciSciNet huggingface dataset:
Genome-wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication

Background and objectives The diversity of eutherian reproductive strategies has led to variation in many traits, such as number of offspring, age of reproductive maturity and gestation length. While reproductive trait variation has been extensively investigated and is well established in mammals, the genetic loci contributing to this variation remain largely unknown. The domestic dog, Canis lupus familiaris is a powerful model for studies of the genetics of inherited disease due to its unique history of domestication. To gain insight into the genetic basis of reproductive traits across domestic dog breeds, we collected phenotypic data for four traits, cesarean section rate, litter size, stillbirth rate and gestation length, from primary literature and breeders' handbooks. Methodology By matching our phenotypic data to genomic data from the Cornell Veterinary Biobank, we performed genome-wide association analyses for these four reproductive traits, using body mass and kinship among breeds as covariates. Results We identified 12 genome-wide significant associations between these traits and genetic loci, including variants near CACNA2D3 with gestation length, MSRB3 and MSANTD1 with litter size, SMOC2 with cesarean section rate and UFM1 with stillbirth rate. A few of these loci, such as CACNA2D3 and MSRB3, have been previously implicated in human reproductive pathologies, whereas others have been associated with domestication-related traits, including brachycephaly (SMOC2) and coat curl (KRT71). Conclusions and implications We hypothesize that the artificial selection that gave rise to dog breeds also influenced the observed variation in their reproductive traits. Overall, our work establishes the domestic dog as a system for studying the genetics of reproductive biology and disease. Lay summary The genetic contributors to variation in mammalian reproductive traits remain largely unknown. We took advantage of the domestic dog, a powerful model system, to test for associations between genome-wide variants and four reproductive traits (cesarean section rate, litter size, stillbirth rate and gestation length) that vary extensively across breeds. We identified associations at a dozen loci, including ones previously associated with domestication-related traits, suggesting that selection on dog breeds also influenced their reproductive traits.
Convenient enol equivalents for catalytic aldol-transfer reactions

Solid crystalline and stable 1,1-diphenyl-1-hydroxy-3-butanone was shown to serve as an excellent precursor of the Al-enolate of acetone generated in situ for Al-BINOL catalyzed aldol-transfer reactions of aldehydes. The best yields were obtained with electron rich aromatic aldehydes and 2-pyridine carbaldehyde of which the latter gave 1-hydroxy-1-(2-pyridyl)-3-butanone in 79% yield.
Dianions of 3-oxodithioic acids: preparation and conversion to 3H-1,2-dithiole-3-thiones

Abstract Reaction of ketones with CS2 and 2 equivalents of KH in THF–N,N′-dimethylpropyleneurea solution produces the dianions of 3-oxodithioic acids. These dianions are converted in good yield to 3H-1,2-dithiole-3-thiones by the sequential action of hexamethyldisilathiane and an oxidizing agent such as hexachloroethane.
Crystallization of Sodium−Birnessite and Accompanied Phase Transformation

X-ray diffraction (XRD), infrared (IR), and scanning electron microscopy (SEM) techniques have been used to monitor the crystallization of birnessite (Na4Mn14O27·9H2O, JCPDS card 32-1128) by aging MnOx, which was produced from the oxidation of Mn(OH)2 by KMnO4 in an NaOH solution in the presence of Mg2+. The crystallization process of birnessite can be divided into three stages: an induction period, a fast crystallization period, and a steady-state period. The crystallization of birnessite was accompanied by the crystallization and phase transformation of feitknechtite (β-MnOOH, JCPDS card 18-0804). Increasing the temperature will reduce the induction period and accelerate the crystallization and phase transformation. Increasing the basicity has almost the same effect as increasing the aging temperature. The crystallization process is also influenced by varying the molar ratio of MnO4-/Mn2+. A diagram of produced phases at room temperature at different basicities and ratios of MnO4-/Mn2+ is obtained. The...
Expanding the scope of the asymmetric anti-aldol addition of chiral N-amino cyclic carbamate hydrazones

An asymmetric anti-aldol addition process of ketone-derived donors that is not limited by the structure of the ketone is described. This is achieved by merging the enantioselective α,α-bisalkylation of N-amino cyclic carbamate (ACC) hydrazones with the asymmetric anti-aldol addition of ACC hydrazones. The products of this process are obtained with essentially perfect stereoselectivity. Using this procedure it is possible to gain access to ketone-based anti-aldol addition products that are inaccessible in a controlled sense via direct aldol methods.
Synthesis of benzocyclic ketones via palladium-catalyzed cyclization of ω-(2-iodoaryl)alkanenitriles

Abstract An efficient procedure for the synthesis of 2,2-disubstituted benzocyclic ketones by intramolecular carbopalladation of nitriles has been developed. The cyclization of substituted 3-(2-iodoaryl)propanenitriles affords indanones in high yields. The reaction is compatible with a wide variety of functional groups. This chemistry has been extended to the synthesis of tetralones, a 9-fluorenone and a cyclopentenone.
Observing with a space-borne gamma-ray telescope: selected results from INTEGRAL

The International Gamma-Ray Astrophysics Laboratory, i.e. the INTEGRAL satellite of ESA, in orbit since about 3 years, performs gamma-ray observations of the sky in the 15 keV to 8 MeV energy range. Thanks to its imager IBIS, and in particular the ISGRI detection plane based on 16384 CdTe pixels, it achieves an excellent angular resolution (12 arcmin) for point source studies with good continuum spectrum sensitivity. Thanks to its spectrometer SPI, based on 19 germanium detectors maintained at 85 K by a cryogenic system, located inside an active BGO veto shield, it achieves excellent spectral resolution of about 2 keV for 1 MeV photons, which permits astrophysical gamma-ray line studies with good narrow-line sensitivity. In this paper we review some goals of gamma-ray astronomy from space and present the INTEGRAL satellite, in particular its instruments ISGRI and SPI. Ground and in-flight calibration results from SPI are presented, before presenting some selected astrophysical results from INTEGRAL. In particular results on point source searches are presented, followed by results on nuclear astrophysics, exemplified by the study of the 1809 keV gamma-ray line from radioactive 26Al nuclei produced by the ongoing stellar nucleosynthesis in the Galaxy. Finally a review on the study of the positron-electron annihilation in the Galactic center region, producing 511 keV gamma-rays, is presented.
A genomic view of the peopling of the Americas

Whole-genome studies have documented that most Native American ancestry stems from a single population that diversified within the continent more than twelve thousand years ago. However, this shared ancestry hides a more complex history whereby at least four distinct streams of Eurasian migration have contributed to present-day and prehistoric Native American populations. Whole genome studies enhanced by technological breakthroughs in ancient DNA now provide evidence of a sequence of events involving initial migrations from a structured Northeast Asian source population with differential relatedness to present-day Australasian populations, followed by a divergence into northern and southern Native American lineages. During the Holocene, new migrations from Asia introduced the Saqqaq/Dorset Paleoeskimo population to the North American Arctic ∼4500 years ago, ancestry that is potentially connected with ancestry found in Athabaskan-speakers today. This was then followed by a major new population turnover in the high Arctic involving Thule-related peoples who are the ancestors of present-day Inuit. We highlight several open questions that could be addressed through future genomic research.
Improved and new syntheses of potential molecular electronics devices

New syntheses of ethyl and nitro substituted oligo(phenylene ethynylene)s (OPEs) have been developed. To further explore whether the presence of nitro functionality in OPEs leads to switching and memory capabilities, new nitro substituted OPEs have been designed and synthesized. An isatogen-based system, a structure that is isomeric to the nitro OPE, has been synthesized. Additionally, pyridine-based and chromium-based compounds have been synthesized. We surmise that redox reactions of these candidates may impart switching capabilities and electrochemical studies are shown. U-shaped OPEs were synthesized to inhibit leakage of metals deposited during formation of top contacts on self-assembled monolayers (SAMs). The OPEs contain either thiol-based moieties or isonitrile groups to enable formation of SAMs on metal substrates.
An Infant Mouse Model of Influenza Virus Transmission Demonstrates the Role of Virus-Specific Shedding, Humoral Immunity, and Sialidase Expression by Colonizing Streptococcus pneumoniae

The pandemic potential of influenza A viruses (IAV) depends on the infectivity of the host, transmissibility of the virus, and susceptibility of the recipient. While virus traits supporting IAV transmission have been studied in detail using ferret and guinea pig models, there is limited understanding of host traits determining transmissibility and susceptibility because current animal models of transmission are not sufficiently tractable. Although mice remain the primary model to study IAV immunity and pathogenesis, the efficiency of IAV transmission in adult mice has been inconsistent. Here we describe an infant mouse model that supports efficient transmission of IAV. We demonstrate that transmission in this model requires young age, close contact, shedding of virus particles from the upper respiratory tract (URT) of infected pups, the use of a transmissible virus strain, and a susceptible recipient. We characterize shedding as a marker of infectiousness that predicts the efficiency of transmission among different influenza virus strains. We also demonstrate that transmissibility and susceptibility to IAV can be inhibited by humoral immunity via maternal-infant transfer of IAV-specific immunoglobulins and modifications to the URT milieu, via sialidase activity of colonizing Streptococcus pneumoniae Due to its simplicity and efficiency, this model can be used to dissect the host's contribution to IAV transmission and explore new methods to limit contagion.IMPORTANCE This study provides insight into the role of the virus strain, age, immunity, and URT flora on IAV shedding and transmission efficiency. Using the infant mouse model, we found that (i) differences in viral shedding of various IAV strains are dependent on specific hemagglutinin (HA) and/or neuraminidase (NA) proteins, (ii) host age plays a key role in the efficiency of IAV transmission, (iii) levels of IAV-specific immunoglobulins are necessary to limit infectiousness, transmission, and susceptibility to IAV, and (iv) expression of sialidases by colonizing S. pneumoniae antagonizes transmission by limiting the acquisition of IAV in recipient hosts. Our findings highlight the need for strategies that limit IAV shedding and the importance of understanding the function of the URT bacterial composition in IAV transmission. This work reinforces the significance of a tractable animal model to study both viral and host traits affecting IAV contagion and its potential for optimizing vaccines and therapeutics that target disease spread.
Acetic acid activates distinct taste pathways in Drosophila to elicit opposing, state-dependent feeding responses

Taste circuits are genetically determined to elicit an innate appetitive or aversive response, ensuring that animals consume nutritious foods and avoid the ingestion of toxins. We have examined the response of Drosophila melanogaster to acetic acid, a tastant that can be a metabolic resource but can also be toxic to the fly. Our data reveal that flies accommodate these conflicting attributes of acetic acid by virtue of a hunger-dependent switch in their behavioral response to this stimulus. Fed flies show taste aversion to acetic acid, whereas starved flies show a robust appetitive response. These opposing responses are mediated by two different classes of taste neurons, the sugar- and bitter-sensing neurons. Hunger shifts the behavioral response from aversion to attraction by enhancing the appetitive sugar pathway as well as suppressing the aversive bitter pathway. Thus a single tastant can drive opposing behaviors by activating distinct taste pathways modulated by internal state.
Remarkable catalytic activity of silica nanoparticle in the bis-Michael addition of active methylene compounds to conjugated alkenes

We have demonstrated the remarkable catalytic activity of silica nanoparticles (NPs) in the unusual bis-Michael addition of active methylene compounds to conjugated alkenes at room temperature. The catalyst silica NPs were reused up to seven runs without appreciable loss of catalytic activity.
REDUCTION OF IMINES VIA TITANIUM-CATALYZED HYDROMAGNESATION

Abstract We have recently discovered that imines can be reduced to amines via a titanium catalyzed hydromagnesation reaction. These reactions employ n -BuMgCl (1.2 eq) as the stoichiometric reducing agent and Cp 2 TiCl 2 (3–5 mol%) as a catalyst. Reactions are run under nitrogen at ambient temperature and pressure. For most aldimine and cyclic ketimine substrates amine products are obtained in yields ranging from 69–94%. The reaction is not tolerant of bulky nitrogen substituents or primary enolizable protons on the imine substrate. © 1997 Elsevier Science Ltd.
The relationship between species richness and ecosystem variability is shaped by the mechanism of coexistence

Theory relating species richness to ecosystem variability typically ignores the potential for environmental variability to promote species coexistence. Failure to account for fluctuation-dependent coexistence may explain deviations from the expected negative diversity–ecosystem variability relationship, and limits our ability to predict the consequences of increases in environmental variability. We use a consumer-resource model to explore how coexistence via the temporal storage effect and relative nonlinearity affects ecosystem variability. We show that a positive, rather than negative, diversity–ecosystem variability relationship is possible when ecosystem function is sampled across a natural gradient in environmental variability and diversity. We also show how fluctuation-dependent coexistence can buffer ecosystem functioning against increasing environmental variability by promoting species richness and portfolio effects. Our work provides a general explanation for variation in observed diversity–ecosystem variability relationships and highlights the importance of conserving regional species pools to help buffer ecosystems against predicted increases in environmental variability.
A Proteolytic Complex Targets Multiple Cell Wall Hydrolases in Pseudomonas aeruginosa.

ABSTRACT Carboxy-terminal processing proteases (CTPs) occur in all three domains of life. In bacteria, some of them have been associated with virulence. However, the precise roles of bacterial CTPs are poorly understood, and few direct proteolytic substrates have been identified. One bacterial CTP is the CtpA protease of Pseudomonas aeruginosa, which is required for type III secretion system (T3SS) function and for virulence in a mouse model of acute pneumonia. Here, we have investigated the function of CtpA in P. aeruginosa and identified some of the proteins it cleaves. We discovered that CtpA forms a complex with a previously uncharacterized protein, which we have named LbcA (lipoprotein binding partner of CtpA). LbcA is required for CtpA activity in vivo and promotes its activity in vitro . We have also identified four proteolytic substrates of CtpA, all of which are uncharacterized proteins predicted to cleave the peptide cross-links within peptidoglycan. Consistent with this, a ctpA null mutant was found to have fewer peptidoglycan cross-links than the wild type and grew slowly in salt-free medium. Intriguingly, the accumulation of just one of the CtpA substrates was required for some Δ ctpA mutant phenotypes, including the defective T3SS. We propose that LbcA-CtpA is a proteolytic complex in the P. aeruginosa cell envelope, which controls the activity of several peptidoglycan cross-link hydrolases by degrading them. Furthermore, based on these and other findings, we suggest that many bacterial CTPs might be similarly controlled by partner proteins as part of a widespread mechanism to control peptidoglycan hydrolase activity. IMPORTANCE Bacterial carboxy-terminal processing proteases (CTPs) are widely conserved and have been associated with the virulence of several species. However, their roles are poorly understood, and few direct substrates have been identified in any species. Pseudomonas aeruginosa is an important human pathogen in which one CTP, known as CtpA, is required for type III secretion system function and for virulence. This work provides an important advance by showing that CtpA works with a previously uncharacterized binding partner to degrade four substrates. These substrates are all predicted to hydrolyze peptidoglycan cross-links, suggesting that the CtpA complex is an important control mechanism for peptidoglycan hydrolysis. This is likely to emerge as a widespread mechanism used by diverse bacteria to control some of their peptidoglycan hydrolases. This is significant, given the links between CTPs and virulence in several pathogens and the importance of peptidoglycan remodeling to almost all bacterial cells.
Crystal structure and magnetic properties of ZnV2O4

Abstract We present structural and magnetic data on ZnV 2 O 4 single crystals. Single crystal X-ray diffraction shows the measured crystals to be of very high quality, especially with respect to atomic order. The measured magnetic susceptibility resembles to that of a spin glass system, surprising for a translational invariant structure. The results are discussed in the framework of disorder in a magnetically frustrated lattice.
Studies toward gymnodimine: development of a single-pot Hua reaction for the synthesis of highly hindered cyclic imines.

In studies directed toward gymnodimine and related marine toxins, a single-pot variation of the Hua cyclic imine synthesis has been developed. The reaction involves generation of N-trimethylsilyl lactams in situ followed by alkyllithium addition leading directly to cyclic imines. Importantly, this reaction proceeds efficiently with highly hindered α,α-dialkyl lactams, provided 1,2-dimethoxyethane (DME) is used as solvent, leading to stable cyclic imines. Overall, this transformation allows a one-pot coupling of an alkyliodide and a lactam to give a cyclic imine.
A Metastable Contact and Structural Disorder in the Estrogen Receptor Transactivation Domain

Summary The N-terminal transactivation domain (NTD) of estrogen receptor alpha, a well-known member of the family of intrinsically disordered proteins, mediates the receptor's transactivation function. However, an accurate molecular dissection of NTD's structure-function relationships remains elusive. Here, we show that the NTD adopts a mostly disordered, unexpectedly compact conformation that undergoes structural expansion on chemical denaturation. By combining small-angle X-ray scattering, hydroxyl radical protein footprinting, and computational modeling, we derive the ensemble-structures of the NTD and determine its ensemble-contact map revealing metastable long-range contacts, e.g., between residues I33 and S118. We show that mutation at S118, a known phosphorylation site, promotes conformational changes and increases coactivator binding. We further demonstrate via fluorine-19 (19F) nuclear magnetic resonance that mutations near I33 alter 19F chemical shifts at S118, confirming the proposed I33-S118 contact in the ensemble of structural disorder. These findings extend our understanding of how specific contact metastability mediates critical functions of disordered proteins.
Internal Diels−Alder Cycloaddition with a Z-Dienophile: Synthesis of (±)-α-Oplopenone

The preparation of the Z-triene 3 is described. Internal Diels−Alder cycloaddition of 3 proceeds smoothly in the presence of BF3·OEt2 to give 2. Ketone 2 is converted by epimerization, carbonyl extrusion, and homologation to the sesquiterpene (±)-α-oplopenone (1).
[2,3]-Wittig rearrangement of allylic glycolate esters via boron and tin enolates

Abstract Wittig rearrangement of allylic glycolate esters via boron and tin enolates gave diastereoselectivities as high as 99.5 : 0.5. Tin enolates were more stereoselective than boron enolates.
Total synthesis of (±)-allosamizoline from a symmetric trisubstituted cyclopentene

Abstract A convergent synthesis of the aminocyclitol allosamizoline 1 , which is found in a class of pseudotrisaccharide chitinase inhibitors known as the allosamidins, is reported.
Atom-Economical C2 + N1 Aziridination: Progress towards Catalytic Intermolecular Reactions Using Alkenes and Aryl Azides

The direct synthesis of aziridines from alkenes and a nitrene source with the correct functionality on the nitrogen atom has remained an elusive goal in synthetic chemistry. Ruthenium, cobalt, and iron porphyrin complexes have been demonstrated to catalyze the formation of aziridines from electron-withdrawing aryl azides and a limited selection of conjugated alkenes. Our group is expanding the scope of catalytic aziridination to include electron-donating aryl azides and aliphatic alkenes through the use of a novel tetracarbene iron catalyst.
Design, Synthesis, SAR, and Biological Evaluation of Highly Potent Benzimidazole-Spaced Phosphono-α-Amino Acid Competitive NMDA Antagonists of the AP-6 Type

A series of 2-amino-(phosphonoalkyl)-1H-benzimidazole-2-alkanoic acids was synthesized and evaluated for NMDA receptor affinity using a [3H]CPP binding assay. Functional antagonism of the NMDA receptor complex was evaluated in vitro using a stimulated [3H]TCP binding assay and in vivo by employing an NMDA-induced seizure model. Several compounds of the AP-6 type demonstrated potent and selective NMDA antagonistic activity both in vitro and in vivo. In particular, [R(-)]-2-amino-3-(5-chloro-1-phosphonomethyl-1H-benzoimidazol-2-yl)-propionic acid (1) displayed an IC(50) value of 7.1 nM in the [3H]CPP binding assay and an ED(50) value of 0.13 mg/kg (ip) in the NMDA lethality model. Compound 1, when administered intravenously as a single bolus dose of 3 mg/kg following permanent occlusion of the middle cerebral artery in the rat, reduced the volume of infarcted brain tissue by 45%. These results support a promising therapeutic potential for compound 1 as a neuroprotective agent.
A Convenient Synthesis of 2,2,4-Trimethylcyclohexane-1,3-Dione: A Useful Precursor for The Taxoid a Ring

Abstract: A simple and inexpensive route to the title compound is described which should be readily amenable to large scale synthesis. Thus, reaction of 3-pentanone with methyl acrylate in the presence of sodium methoxide provided 2,4-dimethylcyclohexane- 1,3-dione. Methylation with iodomethane gave the title compound in 63% overall yield.
PRACTICAL SYNTHESIS OF METHYL Z-2-(N-ACETYLAMINO) BUT-2-ENOATE. AN INTERMEDIATE TO D- AND L-2-AMINOBUTYRIC ACID

Abstract Treatment of inexpensive L- or DL-threonine methyl ester with acetic anhydride and either pyridine or anhydrous sodium acetate at reflux results in dehydration yielding the N,N-diacetamide of the title compound in >80% yield. Monodeacetylation of the diacetamide with 0.1 equiv of triethylamine in methanol affords the title monoacetamido derivative 1 in nearly quantitative yield.
Emerging methods in amide- and peptide-bond formation

Amide bonds are the key chemical connections in proteins and peptides and have a long-established presence in small-molecule therapeutics. Despite their recognized importance, amide bond synthesis relies almost solely on variants of a single reaction: the dehydrative coupling of carboxylic acids and amines. While phenomenally successful in many applications, this process requires superstoichiometric quantities of expensive reagents and precludes chemoselective ligation reactions. This review summarizes emerging chemical alternatives to amide-bond formation with particular emphasis on the development of ligation reactions that permit the coupling of unprotected peptide fragments.
The synthesis of a porphyrin with a hydrocarbon encapsulated face

Abstract The uniquely hydrocarbon-like capped porphyrin (C70H68N4), 1i, has been successfully prepared by a high dilution reaction of pyrrole with tetrakis-1,2,4,5-[pentyl-5′-(2″-formylphenyl)]-benzene 1h in the presence of boron trifluoride etherate. The aldehyde 1h was prepared by four simultaneous Wittig condensations of a phosphonium salt, 1e, with 1,2,4,5-tetraformylbenzene, followed by reduction of the double bonds with Raney nickel and deprotection with perchloric acid.
Magnetism and Structural Chemistry of the n = 1 Ruddlesden−Popper Phases La4LiMnO8 and La3SrLiMnO8

Polycrystalline samples of La4LiMnO8 and La3SrLiMnO8 have been studied by a combination of X-ray diffraction (XRD), neutron diffraction (ND), 6Li MAS NMR, electron microscopy (EM), and magnetometry. Room-temperature XRD and ND measurements suggest that both compounds have the K2NiF4 structure, with a disordered arrangement of Li and Mn over the six-coordinate sites. However, MAS NMR and EM demonstrate the presence of local 1:1 Li:Mn order on these sites, and EM shows that although cation order is well-developed in each xy sheet of corner-sharing octahedra, the sheets are stacked randomly along z. The structures are best described as paracrystalline, and many of the concepts of conventional crystallography are inapplicable. Magnetometry and low-temperature ND experiments show that, despite their paracrystallinity, the two compounds are ordered antiferromagnetically with susceptibility maxima at 26 and 18 K, respectively, and with ordered magnetic moments of 3.61(6) and 2.3(1) μB per Mn cation at 2 K. Aniso...
A rapid flux-assisted synthetic approach towards the bandgap engineering of layered perovskites

The metal-halide-exchanged (CuCl)LaM2O7 and (CuCl)Ca2M3O10 (M = Nb, Ta) are obtained in high purity from the parent layered perovskite hosts using a rapid synthetic approach in molten alkali-nitrate or alkali-bisulfate fluxes at 300−400 °C in only 1 −2 h. The insertion of CuCl layers also introduces new higher-energy valence bands into the electronic structure of the perovskite hosts and lowers their band gap sizes by 1.0−1.4 eV into the visible region, shown in TOC Figure. Thus, the CuCl layers are shown to modify both the atomic and electronic structures and suggest their potential use in visible-light sensitization of photocatalysts.
Alkylation and Reductive Decyanation of 4-Cyano-2,2-dimethyl-1,3-dioxanes (Cyanohydrin Acetonides)

Cyanohydrin acetonide couplings are a very effective methodology for the synthesis of polyol chains. We report a detailed investigation of the alkylation and reductive decyanation of 4-cyano-2,2-di...
Transcriptome profile of Carrizo citrange roots in response to Phytophthora parasitica infection

Phytophthora parasitica is one of the most widespread Phytophthora species, which is known to cause root rot, foot rot/gummosis and brown rot of fruits in citrus. In this study, we have analyzed th...
Genome Characterization, Prevalence, and Transmission Mode of a Novel Picornavirus Associated with the Threespine Stickleback Fish (Gasterosteus aculeatus)

The complete genome sequence of an RNA virus was assembled from RNA sequencing of virus particles purified from threespine stickleback intestine tissue samples. This new virus is most closely related to the Eel picornavirus and can be assigned to the genus Potamipivirus in the family Picornaviridae Its unique genetic properties are enough to establish a new species, dubbed the Threespine Stickleback picornavirus (TSPV). Due to their broad geographic distribution throughout the Northern Hemisphere and parallel adaptation to freshwater, threespine sticklebacks have become a model in evolutionary ecology. Further analysis using diagnostic PCRs revealed that TSPV is highly prevalent in both anadromous and freshwater populations of threespine sticklebacks, infects almost all fish tissues, and is transmitted vertically to offspring obtained from in vitro fertilization in laboratory settings. Finally, TSPV was found in Sequence Reads Archives of transcriptome of Gasterosteus aculeatus, further demonstrating its wide distribution and unsought prevalence in samples. It is thus necessary to test the impact of TSPV on the biology of threespine sticklebacks, as this widespread virus could interfere with the behavioral, physiological, or immunological studies that employ this fish as a model system.IMPORTANCE The threespine stickleback species complex is an important model system in ecological and evolutionary studies because of the large number of isolated divergent populations that are experimentally tractable. For similar reasons, its coevolution with the cestode parasite Schistocephalus solidus, its interaction with gut microbes, and the evolution of its immune system are of growing interest. Herein we describe the discovery of an RNA virus that infects both freshwater and anadromous populations of sticklebacks. We show that the virus is transmitted vertically in laboratory settings and found it in Sequence Reads Archives, suggesting that experiments using sticklebacks were conducted in the presence of the virus. This discovery can serve as a reminder that the presence of viruses in wild-caught animals is possible, even when animals appear healthy. Regarding threespine sticklebacks, the impact of Threespine Stickleback picornavirus (TSPV) on the fish biology should be investigated further to ensure that it does not interfere with experimental results.
An acid-free Pictet–Spengler reaction using deep eutectic solvents (DES)

Abstract Deep eutectic solvents (such as the combination of either urea or glycerol with choline chloride) are effective solvents/organocatalysts for Pictet–Spengler condensations to form carbolines. The reaction conditions are quite mild and do not require additional Bronsted or Lewis acid catalyst. Given the inexpensive, non-toxic, and recyclable nature of the DES, these reaction conditions are simple and highly environmentally friendly.
Modified Pearson correlation coefficient for two-color imaging in spherocylindrical cells

The revolution in fluorescence microscopy enables sub-diffraction-limit (“superresolution”) localization of hundreds or thousands of copies of two differently labeled proteins in the same live cell. In typical experiments, fluorescence from the entire three-dimensional (3D) cell body is projected along the z-axis of the microscope to form a 2D image at the camera plane. For imaging of two different species, here denoted “red” and “green”, a significant biological question is the extent to which the red and green spatial distributions are positively correlated, anti-correlated, or uncorrelated. A commonly used statistic for assessing the degree of linear correlation between two image matrices R and G is the Pearson Correlation Coefficient (PCC). PCC should vary from − 1 (perfect anti-correlation) to 0 (no linear correlation) to + 1 (perfect positive correlation). However, in the special case of spherocylindrical bacterial cells such as E. coli or B. subtilis, we show that the PCC fails both qualitatively and quantitatively. PCC returns the same + 1 value for 2D projections of distributions that are either perfectly correlated in 3D or completely uncorrelated in 3D. The PCC also systematically underestimates the degree of anti-correlation between the projections of two perfectly anti-correlated 3D distributions. The problem is that the projection of a random spatial distribution within the 3D spherocylinder is non-random in 2D, whereas PCC compares every matrix element of R or G with the constant mean value $$ \overline{R} $$ or $$ \overline{G} $$ . We propose a modified Pearson Correlation Coefficient (MPCC) that corrects this problem for spherocylindrical cell geometry by using the proper reference matrix for comparison with R and G. Correct behavior of MPCC is confirmed for a variety of numerical simulations and on experimental distributions of HU and RNA polymerase in live E. coli cells. The MPCC concept should be generalizable to other cell shapes.
Pd/C-mediated coupling of aryl halides with terminal alkynes in water

Abstract 2-Aminoethanol facilitated the alkynylation of aryl halides (Sonogashira reaction) under palladium/charcoal–copper catalysis in water affording a mild and practical method for the synthesis of arylalkynes. A variety of terminal alkynes were coupled with aryl iodides and bromides possessing no hydrophilic functional groups to give the coupled products in good to excellent yields.
Prioritized memory access explains planning and hippocampal replay

To make decisions, animals must evaluate candidate choices by accessing memories of relevant experiences. Yet little is known about which experiences are considered or ignored during deliberation, which ultimately governs choice. We propose a normative theory predicting which memories should be accessed at each moment to optimize future decisions. Using nonlocal 'replay' of spatial locations in hippocampus as a window into memory access, we simulate a spatial navigation task in which an agent accesses memories of locations sequentially, ordered by utility: how much extra reward would be earned due to better choices. This prioritization balances two desiderata: the need to evaluate imminent choices versus the gain from propagating newly encountered information to preceding locations. Our theory offers a simple explanation for numerous findings about place cells; unifies seemingly disparate proposed functions of replay including planning, learning, and consolidation; and posits a mechanism whose dysfunction may underlie pathologies like rumination and craving.
Genomic Relatedness Strengthens Genetic Connectedness Across Management Units

Genetic connectedness refers to a measure of genetic relatedness across management units ( e.g. , herds and flocks). With the presence of high genetic connectedness in management units, best linear unbiased prediction (BLUP) is known to provide reliable comparisons between estimated genetic values. Genetic connectedness has been studied for pedigree-based BLUP; however, relatively little attention has been paid to using genomic information to measure connectedness. In this study, we assessed genome-based connectedness across management units by applying prediction error variance of difference (PEVD), coefficient of determination (CD), and prediction error correlation r to a combination of computer simulation and real data (mice and cattle). We found that genomic information ( G ) increased the estimate of connectedness among individuals from different management units compared to that based on pedigree ( A ). A disconnected design benefited the most. In both datasets, PEVD and CD statistics inferred increased connectedness across units when using G - rather than A -based relatedness, suggesting stronger connectedness. With r once using allele frequencies equal to one-half or scaling G to values between 0 and 2, which is intrinsic to A , connectedness also increased with genomic information. However, PEVD occasionally increased, and r decreased when obtained using the alternative form of G , instead suggesting less connectedness. Such inconsistencies were not found with CD. We contend that genomic relatedness strengthens measures of genetic connectedness across units and has the potential to aid genomic evaluation of livestock species.
Biological Impact of a Large-Scale Genomic Inversion That Grossly Disrupts the Relative Positions of the Origin and Terminus Loci of the Streptococcus pyogenes Chromosome.

ABSTRACT A large-scale genomic inversion encompassing 0.79 Mb of the 1.816-Mb-long Streptococcus pyogenes serotype M49 strain NZ131 chromosome spontaneously occurs in a minor subpopulation of cells, and in this report genetic selection was used to obtain a stable lineage with this chromosomal rearrangement. This inversion, which drastically displaces the ori site relative to the terminus, changes the relative length of the replication arms so that one replichore is approximately 0.41 Mb while the other is about 1.40 Mb in length. Genomic reversion to the original chromosome constellation is not observed in PCR-monitored analyses after 180 generations of growth in rich medium. Compared to the parental strain, the inversion surprisingly demonstrates a nearly identical growth pattern in the first phase of the exponential phase, but differences do occur when resources in the medium become limited. When cultured separately in rich medium during prolonged stationary phase or in an experimental acute infection animal model (Galleria mellonella), the parental strain and the invertant have equivalent survival rates. However, when they are coincubated together, both in vitro and in vivo, the survival of the invertant declines relative to the level for the parental strain. The accompanying aspect of the study suggests that inversions taking place near oriC always happen to secure the linkage of oriC to DNA sequences responsible for chromosome partition. The biological relevance of large-scale inversions is also discussed. IMPORTANCE Based on our previous work, we created to our knowledge the largest asymmetric inversion, covering 43.5% of the S. pyogenes genome. In spite of a drastic replacement of origin of replication and the unbalanced size of replichores (1.4 Mb versus 0.41 Mb), the invertant, when not challenged with its progenitor, showed impressive vitality for growth in vitro and in pathogenesis assays. The mutant supports the existing idea that slightly deleterious mutations can provide the setting for secondary adaptive changes. Furthermore, comparative analysis of the mutant with previously published data strongly indicates that even large genomic rearrangements survive provided that the integrity of the oriC and the chromosome partition cluster is preserved.
Addition of a sulfur-stabilized radical to electron-deficient alkenes via phenyl selenide transfer

Abstract Photolysis of 2-phenylseleno-1,3-dithiane in the presence of electron-deficient alkenes led to formation of addition products. These reactions illustrate the second reported case of radical atom transfer addition arising from a heteroatom-stabilized radical.
Synthesis and Characterization of Cs5Sb8S18(HCO3): A New Layered Phase Containing Interstitial Cations and Anions

A new pseudoternary phase, Cs5Sb8S18(HCO3), was prepared from supercritical ammonia at 160 °C over 4 days using stoichiometric quantities of Cs2CO3, Sb2S3, and S8. Red parallelepipeds of the title phase crystallize in the centrosymmetric monoclinic space group C2/c, with a = 27.064(3) A, b = 11.634(4) A, c = 12.642(3) A, β = 97.45(2)°, and Z = 4. The compound has a layered structure, with the layers formed from ribbons of condensed ψ-SbS4 trigonal bipyramids linked via S32- chains, and both Cs+ and HCO3- ions between the layers, giving rise to the formula Cs5Sb8S12(S3)2(HCO3). Each layer is approximately 10 A thick, with two layers per unit cell. The condensation of the group 15/16 building blocks into ribbons is the result of a combination of edge- and vertex-shared antimony(III) sulfide pseudo trigonal bipyramids. In this phase, the S3 chains always link adjacent ribbons via apical coordination sites on the antimony atoms. The open cavities created by the linking trisulfide dianions between neighboring ...
Novel α-substituted β-amino diesters from acylnitroso-derived hetero-Diels–Alder cycloadducts

Abstract α-Methyl β-amino diesters were synthesized in a simple three-step procedure starting from acylnitroso-derived Diels–Alder adducts of cyclopentadiene. Treatment of the cycloadducts with copper catalyst-modified methylmagnesium bromide gave anti -1,2-cyclopentenyl hydroxamic acids. Reduction of the hydroxamate N O bond with titanium(III) chloride followed by ozonolytic cleavage of the cyclopentenyl olefin provided the desired α-methyl β-amino diesters.
Two New Noncentrosymmetric Polar Oxides: Synthesis, Characterization, Second-Harmonic Generating, and Pyroelectric Measurements on TlSeVO5 and TlTeVO5

Two new noncentrosymmetric (NCS) polar quaternary oxides, TlMVO5 (M = Se4+ or Te4+), have been synthesized by hydrothermal techniques using Tl2CO3, SeO2 (TeO2), and V2O5 as reagents. The structures were determined by single-crystal X-ray diffraction (TlSeVO5, orthorhombic, space group Pna21 (No. 33) with a = 7.1639(15) A, b = 8.6630(19) A, c = 7.8946(17) A, V = 489.95(18) A3, and Z = 4; TlTeVO5, orthorhombic, space group Pna21 (No. 33) with a = 7.319(3) A, b = 8.749(4) A, c = 7.868(3) A, V = 503.8(4) A3, Z = 4). The materials exhibit NCS and polar three-dimensional structures consisting of chains of corner shared VO6 octahedra connected by SeO3 (TeO4) and TlO8 polyhedra. The V5+, Se4+ (Te4+), and Tl+ cations are in asymmetric coordination environments attributable to second-order Jahn−Teller (SOJT) effects. The V5+ cations undergo intra-octahedral distortions toward an edge (local C2 direction), whereas the Se4+ (Te4+) and Tl+ cations are in distorted coordination environments attributable to their lone-p...
A convenient procedure for the esterification of benzoic acids with phenols: a new application for the Mitsunobu reaction

The Mitsunobu reaction was found to be a convenient and effective method for the esterification of various benzoic acids with differentially functionalized phenols producing the corresponding phenyl esters in good to excellent yields.
Synthesis of l-Sugars from 4-Deoxypentenosides

4-Deoxypentenosides, which are readily derived from d-sugars, resemble glycals in structure and reactivity and can undergo stereoselective epoxidation and SN2 nucleophilic addition to produce l-sugars in pyranosidic form.
Orthogonal Dietary Niche Enables Reversible Engraftment of a Gut Bacterial Commensal.

Summary Interest in manipulating the gut microbiota to treat disease has led to a need for understanding how organisms can establish themselves when introduced into a host with an intact microbial community. Here, we employ the concept of orthogonal niche engineering: a resource typically absent from the diet, seaweed, creates a customized niche for an introduced organism. In the short term, co-introduction of this resource at 1% in the diet along with an organism with exclusive access to this resource, Bacteroides plebeius DSM 17135, enables it to colonize at a median abundance of 1% and frequently up to 10 or more percent, both on pulsed and constant seaweed diets. In a two-month follow-up after the initial treatment period, B. plebeius stops responding to seaweed in mice initially on the constant seaweed diet, suggesting treatment regime will affect controllability. These results offer potential for diet-based intervention to introduce and control target organisms.
Roles for Stress Response and Cell Wall Biosynthesis Pathways in Caspofungin Tolerance in Cryptococcus neoformans.

Limited antifungal diversity and availability are growing problems for the treatment of fungal infections in the face of increasing drug resistance. The echinocandins, one of the newest classes of antifungal drugs, inhibit production of a crucial cell wall component. However, these compounds do not effectively inhibit the growth of the opportunistic fungal pathogen Cryptococcus neoformans, despite potent inhibition of the target enzyme in vitro. Therefore, we performed a forward genetic screen to identify cellular processes that mediate the relative tolerance of this organism to the echinocandin drug caspofungin. Through these studies, we identified 14 genetic mutants that enhance caspofungin antifungal activity. Rather than directly affecting caspofungin antifungal activity, these mutations seem to prevent the activation of various stress-induced compensatory cellular processes. For example, the pfa4Δ mutant has defects in the palmitoylation and localization of many of its target proteins, including the Ras1 GTPase and the Chs3 chitin synthase, which are both required for caspofungin tolerance. Similarly, we have confirmed the link between caspofungin treatment and calcineurin signaling in this organism, but we suggest a deeper mechanism in which caspofungin tolerance is mediated by multiple pathways downstream of calcineurin function. In summary, we describe here several pathways in C. neoformans that contribute to the complex caspofungin tolerance phenotype in this organism.
Managing adoption under network effects

The consumption of several modern products is marked by strong network effects, i.e., the utility to a consumer improves with the overall adoption in the market. Examples include mobile platforms that significantly rely on user-generated content, social media platforms, massively multiplayer games, cryptocurrencies, etc. For a firm that intends to launch a new product in this space, the biggest initial challenge is to stimulate sufficient adoption through appropriately designed incentives - a problem that is exacerbated by the presence of strategic consumers who anticipate the informational benefits of delaying their adoption decisions.
A unifying representation for a class of dependent random measures

We present a general construction for dependent random measures based on thinning Poisson processes on an augmented space. The framework is not restricted to dependent versions of a specific nonparametric model, but can be applied to all models that can be represented using completely random measures. Several existing dependent random measures can be seen as specific cases of this framework. Interesting properties of the resulting measures are derived and the efficacy of the framework is demonstrated by constructing a covariate-dependent latent feature model and topic model that obtain superior predictive performance.
An Undergraduate Primer on Quality-Differentiated Demand

This article presents a student exercise on the logic underlying demand for quality-differentiated products. The argument builds and extends on basic constructs from undergraduate microeconomics, d...
Nebula around R Corona Borealis

The star R Corona Borealis (R CrB) shows forbidden lines of [O II], [N II], and [S II] during the deep minimum when the star is fainter by about 8 to 9 magnitudes from normal brightness, suggesting the presence of nebular material around it. We present low and high spectral resolution observations of these lines during the ongoing deep minimum of R CrB, which started in July 2007. These emission lines show double peaks with a separation of about 170 km/s. The line ratios of [S II] and [O II] suggest an electron density of about 100 cm$^{-3}$. We discuss the physical conditions and possible origins of this low density gas. These forbidden lines have also been seen in other R Coronae Borealis stars during their deep light minima and this is a general characteristic of these stars, which might have some relevance to their origins.