cssi/SciSciGPT-SciSciNet huggingface dataset:
On selection of semiparametric spatial regression models

In this paper, we focus on the variable selection techniques for a class of semiparametric spatial regression models which allow one to study the effects of explanatory variables in the presence of the spatial information. The spatial smoothing problem in the nonparametric part is tackled by means of bivariate splines over triangulation, which is able to deal efficiently with data distributed over irregularly shaped regions. In addition, we develop a unified procedure for variable selection to identify significant covariates under a double penalization framework, and we show that the penalized estimators enjoy the "oracle" property. The proposed method can simultaneously identify non-zero spatially distributed covariates and solve the problem of "leakage" across complex domains of the functional spatial component. To estimate the standard deviations of the proposed estimators for the coefficients, a sandwich formula is developed as well. In the end, Monte Carlo simulation examples and a real data example are provided to illustrate the proposed methodology. All technical proofs are given in the supplementary materials.
Using Green-Kubo modal analysis (GKMA) and interface conductance modal analysis (ICMA) to study phonon transport with molecular dynamics

While current descriptions of thermal transport exist for well-ordered solids, i.e., crystal lattices, new methods are needed to describe thermal transport in systems with lack of symmetry such as structurally/compositionally disordered solids and interfaces. In this tutorial, we discuss the formalism, implementation, and application of two recently developed methods, Green-Kubo modal analysis and interface conductance modal analysis, to predict the thermal conductivity and thermal interface conductance, respectively. Specifically, these methods enable the prediction of phonon contributions to transport in crystalline materials with any level of defects, up through fully amorphous solids, dilute to fully random alloys, molecules, nanostructures, and across interfaces involving any of these material classes—all within a single and unified perspective. This tutorial article not only describes the methods, but also provides example codes that can be used for their direct implementation. The design and functionality of the codes is also discussed in order to reduce the barrier to more extensive utilization of these approaches by others.
Does Partisanship Affect Compliance with Government Recommendations

This article studies the role of partisanship in American's willingness to follow government recommendations. I combine survey and behavioral data to examine partisans' vaccination rates during the Bush and Obama administrations. I find that presidential co-partisans are more likely to believe that vaccines are safe and more likely to vaccinate themselves and their children than presidential out-partisans. Depending on the vaccine, presidential co-partisans are 4-10 percentage points more likely to vaccinate than presidential out-partisans. Using causal mediation analysis, I find that this effect is the result of partisans' differing levels of trust in government. This finding sheds light on the far-reaching role of partisanship in Americans' interactions with the federal government.
Global Mission – “Glocal” Internationalization: United Nations Academic Impact (UNAI) and Lehigh University

This study explores the relevance between the missions of the UNAI and the strategic planning of internationalization of Lehigh University. Lehigh University is purposefully selected due to its unique partnership with the UNAI and its role as a “Global Citizenship Hub” in 2011. Though Lehigh University actively implements internationalization plans at home and abroad, which align with the missions of the UNAI, the relevant activities strongly illustrate the hegemony of the West in terms of language, power, and discourse.
Effect of nanoparticle size on the mechanical properties of nanoparticle assemblies.

Nanoparticle assemblies (NPAs) have attracted tremendous interests of various research communities. The particle-size-effect on mechanical properties of NPAs is systematically studied. With decreasing the particle size d from 300 nm to 10 nm, the SiO2 NPAs become drastically harder (∼39×), stiffer (∼15×), and tougher (>3.5×). The results are consistent with the data scattered in the literature for various nanoparticle (NP) systems, indicating a fundamentally universal d-effect for all NPAs. A model is developed to correlate the hardness and the NP junction (NPJ) strength f. Here, f is mainly due to van der Waals and capillary interactions, roughly a constant (140 nN) for d = 100–300 nm, and then f decreases with decreasing d from ∼100 nm. The deformation mechanism of NPAs (for indentation depth ≫d) is shear plasticity involving shear breaking of NPJs. The fundamental mechanism for the d-effect is that, with decreasing d, the NPJ's planar density increases much faster than the decrease of f. Moreover, three deformation mechanisms of NPAs, (1) nanoparticle dislodging, (2) shear-band formation, and (3) cracking are naturally d-dependent. These new findings can provide important insights into the fundamental understanding of the inter-NP interaction, the mechanical behavior of the NPAs, and the design of robust NP-based devices.
Shaping the Values of a Milk Cooperative: Theoretical and Practical Considerations

Dairy cooperatives bestow upon farmers the virtues of controlling a large supply quantity of a relatively scarce product, i.e., milk (e.g., higher bargaining power, fixed cost sharing, etc.). However, the cooperative structure also encourages individual farmers to free-ride (i.e., provide low-quality milk in the hope that other farmers provide good-quality milk). The question arises: How can the bene ts of a cooperative be retained, while eliminating free-riding, especially when individual inspection costs are high? We examine this question from the perspective of a social planner, who wishes to achieve the simultaneous goals of quantity efficiency, quality efficiency, and minimal testing. The basic challenge in this quest is that of countering an endogenous value function associated with a coalition of farmers. This value function emerges from the joint interaction of three forces: (1) an individual farmer's payment-maximizing behavior, (2) the testing policies employed by the cooperative, and (3) the manner in which the revenue earned by a coalition is shared among the farmers (allocation rule). A novel allocation rule - that exploits individual incentives to guide the collective behavior of the farmers and thereby the value-function endogeneity - is proposed that achieves the planner's goals in the presence of these forces. A modification to this allocation rule is made to address the goals of practicality, e.g., the presence of low-income farmers and unintended variation in the quality of a farmer's output. We examine our interventions in the light of sample data from actual dairy cooperatives to demonstrate the viability of our proposals.
A Deep Learning Approach for Automated Detection of Geographic Atrophy from Color Fundus Photographs.

Purpose To assess the utility of deep learning in the detection of geographic atrophy (GA) from color fundus photographs and to explore potential utility in detecting central GA (CGA). Design A deep learning model was developed to detect the presence of GA in color fundus photographs, and 2 additional models were developed to detect CGA in different scenarios. Participants A total of 59 812 color fundus photographs from longitudinal follow-up of 4582 participants in the Age-Related Eye Disease Study (AREDS) dataset. Gold standard labels were from human expert reading center graders using a standardized protocol. Methods A deep learning model was trained to use color fundus photographs to predict GA presence from a population of eyes with no AMD to advanced AMD. A second model was trained to predict CGA presence from the same population. A third model was trained to predict CGA presence from the subset of eyes with GA. For training and testing, 5-fold cross-validation was used. For comparison with human clinician performance, model performance was compared with that of 88 retinal specialists. Main Outcome Measures Area under the curve (AUC), accuracy, sensitivity, specificity, and precision. Results The deep learning models (GA detection, CGA detection from all eyes, and centrality detection from GA eyes) had AUCs of 0.933–0.976, 0.939–0.976, and 0.827–0.888, respectively. The GA detection model had accuracy, sensitivity, specificity, and precision of 0.965 (95% confidence interval [CI], 0.959–0.971), 0.692 (0.560–0.825), 0.978 (0.970–0.985), and 0.584 (0.491–0.676), respectively, compared with 0.975 (0.971–0.980), 0.588 (0.468–0.707), 0.982 (0.978–0.985), and 0.368 (0.230–0.505) for the retinal specialists. The CGA detection model had values of 0.966 (0.957–0.975), 0.763 (0.641–0.885), 0.971 (0.960–0.982), and 0.394 (0.341–0.448). The centrality detection model had values of 0.762 (0.725-0.799), 0.782 (0.618–0.945), 0.729 (0.543–0.916), and 0.799 (0.710–0.888). Conclusions A deep learning model demonstrated high accuracy for the automated detection of GA. The AUC was noninferior to that of human retinal specialists. Deep learning approaches may also be applied to the identification of CGA. The code and pretrained models are publicly available at https://github.com/ncbi-nlp/DeepSeeNet .
Study of the Kulinkovich Synthesis of 1-Methylcyclopropanol and Its Conversion into 1-Methylcyclopropyl 4-Nitrophenyl Carbonate

A detailed investigation of the preparation of 1-methylcyclopropanol via the Kulinkovich reaction is presented. Reaction and workup parameters were optimized to provide a reproducible procedure for the synthesis of multigram quantities of 1-methylcyclopropanol. Key improvements were the use of titanium tetra(2-ethyl)hexyloxide as catalyst, reduction in the volume of reaction solvent, addition of the methyl acetate starting material in portions, and azeotropic distillation to remove by-products. The preparation of the 4-nitrophenyl carbonate ester was likewise studied and optimized.
Examining the Bromination of Benzobicyclooctadiene by ab Initio Methods.

The bromination of 5.8-diacetoxy-1,4-dihydro-1,4-ethanonaphthalene was reported several years ago to yield a single stereospecificly formed dibromide. Given related cases from the literature, the result was interpreted as indicating a significant interaction between the aryl and olefin π-electron systems. This paper reports an ab initio study of the mechanism of the bromination of benzobicyclooctadiene. It is proposed that the stereochemistry is best accommodated by an asynchronous concerted electrophilic addition of bromine across carbons 1 and 3, and that it proceeds via an ion pair transition structure in which the Wagner−Meerwein portion of the reaction has already occurred. All final results were calculated at the Becke3LYP/6-31G* level.
A general route to 5-aminotetrazoles

Various di- and trisubstituted (benzotriazolyl)carboximidamides were used for the preparation of N,N-di- and 1,N,N-trisubstituted 5-aminotetrazoles 3a-e and 6a-d under mild conditions in good to excellent yields.
A synthesis of (−)-indolactam V

(−)-Indolactam V (1) was synthesized in 14 steps from 2,6-dinitrotoluene in 15% overall yield via enantiospecific SN2 displacement of a chiral triflate with the 4-amino group of a 4-aminoindole and coupling of 3-bromomethyl indole with Schollkopf's asymmetric bislactim ether.
Repeat-specific functions for the C-terminal domain of RNA polymerase II in budding yeast

The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (RNAPII) is required to regulate transcription and to integrate it with other essential cellular processes. In the budding yeast Saccharomyces cerevisiae, the CTD of Rpb1p consists of 26 conserved heptad repeats that are post-translationally modified to orchestrate protein factor binding at different stages of the transcription cycle. A long-standing question in the study of the CTD is if there are any functional differences between the 26 repeats. In this study, we present evidence that repeats of identical sequence have different functions based on their position within the CTD. We assembled plasmids expressing Rpb1p with serine to alanine substitutions in three defined regions of the CTD and measured a range of phenotypes for yeast expressing these constructs. Mutations in the beginning and middle regions of the CTD had drastic, and region-specific effects, while mutating the distal region had no observable phenotype. Further mutational analysis determined that Ser5 within the first region of repeats was solely responsible for the observed growth differences and sequencing fast-growing suppressors allowed us to further define the functional regions of the CTD. This mutational analysis is consistent with current structural models for how the RNAPII holoenzyme and the CTD specifically would reside in complex with Mediator and establishes a foundation for studying regioselective binding along the repetitive RNAPII CTD.
An Efficient Strategy for the Synthesis of α,α′-cis and trans-Disubstituted Medium Ring Ethers

An asymmetric alkylation-ring-closing metathesis strat- egy was developed for the construction of a,a'-disubstituted medi- um ring ethers. The approach features an asymmetric alkylation of highly functionalized a-alkoxy acyl oxazolidinones followed by ring closure effected by Grubbs ' ruthenium catalyst. The relation- ship between diene conformation and the rate of ring-closure was examined.
Intramolecular Cyclization of Radicals Generated from α-Halomethylsulfonamides

A series of homologous α-sulfonamidyl radicals has been generated by reaction of α-halomethyl precursors with tri-n-butyltin hydride under AIBN catalysis. The intramolecular cyclization capability of these highly reactive intermediates has been evaluated. Where possible, five-membered sultams are formed by 5-exo transition states. The longer C−SO2 and SO2−NR2 bonds have little demonstrable effect on this pathway. In larger systems, however, the 7-endo option predominates over the 6-exo alternative. A preparatively useful route to sultams has emerged from this investigation.
PHOTOCHEMISTRY OF CHLORINE DIOXIDE IN POLYCRYSTALLINE ICE (T = 140-185 K) : PRODUCTION OF CHLORYL CHLORIDE, CL-(OCLO)

The photochemistry of chlorine dioxide, OClO, in polycrystalline ice has been investigated at T = 140−185 K using FTIR and UV−vis spectroscopy. Photolysis with ultraviolet light at 360 nm produced ...
Single Cancer Cell Detection by Near Infrared Microspectroscopy, Infrared Chemical Imaging and Fluorescence Microspectroscopy

Novel techniques are currently being developed and established for the accurate chemical analysis and detection of single cancer cells, single embryos and single seeds by Fourier Transform Near Infrared (FT-NIR) Microspectroscopy, Fourier Transform Infrared (FT-IR), Fluorescence and High-Resolution NMR (HR-NMR). The first FT-NIR chemical images of biological systems approaching 1micron resolution are here reported. 400 and 500 MHz, H-1 NMR analyses were carried out that allowed the selection of mutagenized embryos. Detailed chemical analyses are being demonstrated to be also possible by FT-NIR Chemical Imaging/ Microspectroscopy of single cancer cells. FT-NIR Microspectroscopy and Chemical Imaging are also shown to be potentially important in Functional Genomics and Proteomics research through the rapid and accurate detection of high-content microarrays (HCMA). Multi-photon (MP), pulsed femtosecond laser NIR Fluorescence Excitation techniques were shown to be capable of Single Molecule Detection (SMD. Thus, MP NIR excitation for Fluorescence Correlation Spectroscopy (FCS) allowed not only single molecule detection, but also molecular dynamics observations and high resolution, submicron imaging of sub-femtoliter volumes inside living cells with 0.25 micron spatial resolution, in both normal and cancer cells, as well as neoplastic tissues. These novel, ultra-sensitive and rapid FT-NIR/FCS analyses have, therefore, substantial potential for numerous applications in important research areas, such as: medicine, medical/cancer research, pharmacology, agricultural biotechnology, food safety, as well as clinical diagnosis of viral diseases and cancers.
Nickel-Catalyzed Allylation of α-Amido Sulfones To Form Protected Homoallylic Amines

The allylation of stable, protected imine precursors, α-amido sulfones, with allylic acetates to form homoallylic amines is catalyzed by nickel under mild reducing conditions. Aliphatic and aryl imines are tolerated, as are substituted allylic acetates. In the case of substituted allylic acetates, high diastereoselectivity and regioselectivity is observed in some cases and the branched product is obtained almost exclusively.
Permanent neuroglial remodeling of the retina following infiltration of CSF1R inhibition-resistant peripheral monocytes

Previous studies have demonstrated that ocular injury can lead to prompt infiltration of bone-marrow–derived peripheral monocytes into the retina. However, the ability of these cells to integrate into the tissue and become microglia has not been investigated. Here we show that such peripheral monocytes that infiltrate into the retina after ocular injury engraft permanently, migrate to the three distinct microglia strata, and adopt a microglia-like morphology. In the absence of ocular injury, peripheral monocytes that repopulate the retina after depletion with colony-stimulating factor 1 receptor (CSF1R) inhibitor remain sensitive to CSF1R inhibition and can be redepleted. Strikingly, consequent to ocular injury, the engrafted peripheral monocytes are resistant to depletion by CSF1R inhibitor and likely express low CSF1R. Moreover, these engrafted monocytes remain proinflammatory, expressing high levels of MHC-II, IL-1β, and TNF-α over the long term. The observed permanent neuroglia remodeling after injury constitutes a major immunological change that may contribute to progressive retinal degeneration. These findings may also be relevant to other degenerative conditions of the retina and the central nervous system.
Substituent effects in pericyclic reactions of radical cations: the ring opening of 3-substituted cyclobutene radical cations

The substituent effects on the ring-opening reaction of cyclobutene radical cations have been studied at the Becke3LYP/6-31G* level of theory. The effect on the reaction energies and activation energies of the concerted and stepwise pathways of electron-donating substituents such as methyl and methoxy as well as electron-withdrawing substituents such as nitrile and carboxaldehyde in the 3-position of the cyclobutene is discussed. The exothermicity of the reaction correlates well with the ability of the substituent to stabilize the 1,3-butadiene radical cation by electron donation or conjugation. The relative stability of the (E) and (Z) isomers of the resulting 1,3-butadiene radical cations depends largely on steric effects. Similarly, steric effects are responsible for the relative energies of the different diastereomeric transition structures. The cyclopropyl carbinyl intermediate of the stepwise pathway resembles the nonclassical carbocation and is stabilized by electron-donating substituents. In the c...
Pyridoxal 5‘-Phosphate-Dependent α,β-Elimination Reactions: Mechanism of O-Acetylserine Sulfhydrylase

O-Acetylserine sulfhydrylase catalyzes the replacement of the β-acetoxy group of O-acetyl-l-serine with sulfide to generate l-cysteine. The reaction represents the final step in the biosynthesis of l-cysteine in enteric bacteria and plants. A quinonoid intermediate has not been detected using a variety of kinetic and spectroscopic probes for the wild-type or mutant enzymes, ruling out an E1 mechanism. The structure of the external Schiff base intermediate indicates an anti elimination. O-Acetylserine sulfhydrylase is the only known pyridoxal 5‘-phosphate-dependent enzyme that catalyzes a β-elimination reaction to have an anti E2 mechanism.
Enantio- and diastereoselective synthesis of syn-β-hydroxy-α-alkenyl carboxamides via reductive aldol reactions of morpholine 4-methyl-2,3-pentadienoic carboxamide with diisopinocampheylborane

A highly enantio- and diastereoselective synthesis of morpholine syn-β-hydroxy-α-alkenyl carboxamides 11 via the reductive aldol reaction of allenyl carboxamide 8 with diisopinocampheylborane is described.
Alignment-free approaches for predicting novel Nuclear Mitochondrial Segments (NUMTs) in the human genome.

Abstract The nuclear human genome harbors sequences of mitochondrial origin, indicating an ancestral transfer of DNA from the mitogenome. Several Nuclear Mitochondrial Segments (NUMTs) have been detected by alignment-based sequence similarity search, as implemented in the Basic Local Alignment Search Tool (BLAST). Identifying NUMTs is important for the comprehensive annotation and understanding of the human genome. Here we explore the possibility of detecting NUMTs in the human genome by alignment-free sequence similarity search, such as k-mers (k-tuples, k-grams, oligos of length k) distributions. We find that when k=6 or larger, the k-mer approach and BLAST search produce almost identical results, e.g., detect the same set of NUMTs longer than 3 kb. However, when k=5 or k=4, certain signals are only detected by the alignment-free approach, and these may indicate yet unrecognized, and potentially more ancestral NUMTs. We introduce a “Manhattan plot” style representation of NUMT predictions across the genome, which are calculated based on the reciprocal of the Jensen-Shannon divergence between the nuclear and mitochondrial k-mer frequencies. The further inspection of the k-mer-based NUMT predictions however shows that most of them contain long-terminal-repeat (LTR) annotations, whereas BLAST-based NUMT predictions do not. Thus, similarity of the mitogenome to LTR sequences is recognized, which we validate by finding the mitochondrial k-mer distribution closer to those for transposable sequences and specifically, close to some types of LTR.
Identification of co-evolving temporal networks

Biological networks describes the mechanisms which govern cellular functions. Temporal networks show how these networks evolve over time. Studying the temporal progression of network topologies is of utmost importance since it uncovers how a network evolves and how it resists to external stimuli and internal variations. Two temporal networks have co-evolving subnetworks if the evolving topologies of these subnetworks remain similar to each other as the network topology evolves over a period of time. In this paper, we consider the problem of identifying co-evolving subnetworks given a pair of temporal networks, which aim to capture the evolution of molecules and their interactions over time. Although this problem shares some characteristics of the well-known network alignment problems, it differs from existing network alignment formulations as it seeks a mapping of the two network topologies that is invariant to temporal evolution of the given networks. This is a computationally challenging problem as it requires capturing not only similar topologies between two networks but also their similar evolution patterns. We present an efficient algorithm, Tempo, for solving identifying co-evolving subnetworks with two given temporal networks. We formally prove the correctness of our method. We experimentally demonstrate that Tempo scales efficiently with the size of network as well as the number of time points, and generates statistically significant alignments—even when evolution rates of given networks are high. Our results on a human aging dataset demonstrate that Tempo identifies novel genes contributing to the progression of Alzheimer’s, Huntington’s and Type II diabetes, while existing methods fail to do so. Studying temporal networks in general and human aging specifically using Tempo enables us to identify age related genes from non age related genes successfully. More importantly, Tempo takes the network alignment problem one huge step forward by moving beyond the classical static network models.
Intramolecular Imino Diels−Alder Reaction of a 3-Vinyl Indole: Application to a Total Synthesis of (±)-Eburnamonine

The intramolecular [4 + 2] cycloaddition of imine 1 has been examined under a variety of conditions including thermal; catalysis by acid, lithium cation, and Florisil; and the use of 5.0 M lithium ...
Generalized Rayleigh-Plesset Theory for Cell Size Maintenance in Viruses and Bacteria

The envelopes covering bacterial cytoplasm possess remarkable elastic properties. They are rigid enough to resist large pressures while being flexible enough to adapt to growth under environmental constraints. Similarly, the virus shells play an important role in their functions. However, the effects of mechanical properties of the outer shell in controlling and maintaining the sizes of bacteria or viruses are unknown. Here, we present a hydrodynamic "bubbles with shell" model, motivated by the study of bubble stability in fluids, to demonstrate that shell rigidity and turgor pressure control the sizes of bacteria and viruses. A dimensionless compliance parameter, expressed in terms of the elastic modulus of the shell, its thickness and the turgor pressure, determines membrane response to deformation and the size of the organisms. By analyzing the experiment data, we show that bacterial and viral sizes correlate with shell elasticity, which plays a critical role in regulating size.
Stereocontrol in hydride addition to ketone-derived chiral N-acylhydrazones

Abstract Chiral N -acylhydrazones derived from various aldehydes and N -amino-4-benzyl-2-oxazolidinone have previously been shown to be effective for acyclic stereocontrol of intermolecular radical and allylsilane additions. Treatment of the propionaldehyde hydrazone with tributyltin hydride in the presence of boron trifluoride etherate led to rapid chemoselective reduction of the imine bond in high yield. Preparation of similar hydrazones from ketones led to E / Z isomer mixtures, usually in ratios of 4:1 or greater. Geometry of the CN bond was assigned by steric compression shifts in 13 C NMR spectra. Reduction with tributyltin hydride and boron trifluoride etherate afforded diastereomer mixtures in ratios very similar to the original E / Z isomer ratios. The chiral auxiliary blocked the opposite face of the CN bond relative to a related process using a chelated Lewis acid. A stereocontrol model involving monodentate interaction of the N -acylhydrazone and boron trifluoride is consistent with the observed stereochemical outcome.
Potent cyclic urea HIV protease inhibitors with benzofused heterocycles as P2/P2′ groups

Abstract A series of benzofused heterocycles was examined to replace the metabolically unstable benzyl alcohol P2/P2′ groups of DMP 323 (1). Extremely potent inhibitors of HIV protease (Ki
Reduced frontal gamma power at 24 months is associated with better expressive language in toddlers at risk for autism.

Frontal gamma power has been associated with early language development in typically developing toddlers, and gamma band abnormalities have been observed in individuals with autism spectrum disorder (ASD), as well as high-risk infant siblings (those having an older sibling with ASD), as early as 6 months of age. The current study investigated differences in baseline frontal gamma power and its association with language development in toddlers at high versus low familial risk for autism. Electroencephalography recordings as well as cognitive and behavioral assessments were acquired at 24 months as part of prospective, longitudinal study of infant siblings of children with and without autism. Diagnosis of autism was determined at 24-36 months, and data were analyzed across three outcome groups-low-risk without ASD (n = 43), high-risk without ASD (n = 42), and high-risk with ASD (n = 16). High-risk toddlers without ASD had reduced baseline frontal gamma power (30-50 Hz) compared to low-risk toddlers. Among high-risk toddlers increased frontal gamma was only marginally associated with ASD diagnosis (P = 0.06), but significantly associated with reduced expressive language ability (P = 0.007). No association between gamma power and language was present in the low-risk group. These findings suggest that differences in gamma oscillations in high-risk toddlers may represent compensatory mechanisms associated with improved developmental outcomes. Autism Res 2019, 12: 1211-1224. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: This study looked at differences in neural activity in the gamma range and its association with language in toddlers with and without increased risk for ASD. At 2 years of age, gamma power was lower in high-risk toddlers without ASD compared to a low-risk comparison group. Among high-risk toddlers both with and without later ASD, reduced gamma power was also associated with better language outcomes, suggesting that gamma power may be a marker of language development in high-risk children.
Microwave-assisted cross-coupling of 3-chloro-2-pyrazolines and 3-chloro-1-phenyl-1,4,5,6-tetrahydropyridazine with aryl boronic acids

3-Chloro-1-phenyl-2-pyrazoline and 3-chloro-1-phenyl-1,4,5,6-tetrahydropyridazine were coupled with aryl boronic acids in good yields under microwave heating conditions (140 °C, 5 min).
Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima

Understanding the genetic basis of phenotypic adaptation to changing environments is an essential goal of population and quantitative genetics. While technological advances now allow interrogation of genome-wide genotyping data in large panels, our understanding of the process of polygenic adaptation is still limited. To address this limitation, we use extensive forward-time simulation to explore the impacts of variation in demography, trait genetics, and selection on the rate and mode of adaptation and the resulting genetic architecture. We simulate a population adapting to an optimum shift, modeling sequence variation for 20 QTL for each of 12 different demographies for 100 different traits varying in the effect size distribution of new mutations, the strength of stabilizing selection, and the contribution of the genomic background. We then use random forest regression approaches to learn the relative importance of input parameters in determining a number of aspects of the process of adaptation, including the speed of adaptation, the relative frequency of hard sweeps and sweeps from standing variation, or the final genetic architecture of the trait. We find that selective sweeps occur even for traits under relatively weak selection and where the genetic background explains most of the variation. Though most sweeps occur from variation segregating in the ancestral population, new mutations can be important for traits under strong stabilizing selection that undergo a large optimum shift. We also show that population bottlenecks and expansion impact overall genetic variation as well as the relative importance of sweeps from standing variation and the speed with which adaptation can occur. We then compare our results to two traits under selection during maize domestication, showing that our simulations qualitatively recapitulate differences between them. Overall, our results underscore the complex population genetics of individual loci in even relatively simple quantitative trait models, but provide a glimpse into the factors that drive this complexity and the potential of these approaches for understanding polygenic adaptation.
Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids.

Summary Mutations in the gene encoding the type II transmembrane protease 3 ( TMPRSS3 ) cause human hearing loss, although the underlying mechanisms that result in TMPRSS3 -related hearing loss are still unclear. We combined the use of stem cell-derived inner ear organoids with single-cell RNA sequencing to investigate the role of TMPRSS3. Defective Tmprss3 leads to hair cell apoptosis without altering the development of hair cells and the formation of the mechanotransduction apparatus. Prior to degeneration, Tmprss3 -KO hair cells demonstrate reduced numbers of BK channels and lower expressions of genes encoding calcium ion-binding proteins, suggesting a disruption in intracellular homeostasis. A proteolytically active TMPRSS3 was detected on cell membranes in addition to ER of cells in inner ear organoids. Our in vitro model recapitulated salient features of genetically associated inner ear abnormalities and will serve as a powerful tool for studying inner ear disorders.
Synthesis of 4-O-acetyl-l-rhodinopyranose via a tandem sharpless asymmetric dihydroxylation/lipase-catalyzed transesterification

Abstract An enantioselective synthesis of the trideoxy sugar 4-O- acetyl- l -rhodinopyranose ( 7 ) is described. A key feature of the synthetic strategy is a Sharpless asymmetric dihydroxylation followed by a lipase-mediated mono-esterification of the resultant diol ( 3→4→6 ).
Homogeneous Catalysis. Metallocene Catalysts for [3+2] Nitrone−Olefin Cycloaddition Reactions

The complex [Cp2Ti(OTf)2] is a catalyst for the [3+2] cycloaddition of nitrones with electron-rich olefins. In the presence of small amounts of water, catalyst hydrolysis leads to the production of triflic acid, which is a powerful catalyst for these cycloaddition reactions. Acid catalysis can be suppressed by the use of Proton-Sponge. Metal catalysis appears to proceed via the bis(nitrone) adduct [Cp2Ti(nitrone)2]2+. A crystal structure of one of these adducts is reported.
Neutron powder diffraction study of the orthorhombic to monoclinic transition in Sc2W3O12 on compression

Abstract Time-of-flight powder neutron diffraction combined with Rietveld analysis was used to study Sc2W3O12 at pressures of up to 0.6 GPa in a large volume helium gas cell. Orthorhombic (Pnca) Sc2W3O12, bulk modulus 32(3) GPa, transforms to a softer monoclinic (P21/a) structure, 11.8(8) GPa, on compression at between 0.25 and 0.30 GPa. This transition shows significant hysteresis and involves a volume reduction of ∼1.5%. The volume reduction during compression of the orthorhombic phase is much less anisotropic than that induced by heating this negative thermal expansion phase at ambient pressure. While the volume reduction on heating orthorhombic Sc2W3O12 is associated with pronounced changes in Sc O W angles, there are no major changes in these angles on compression to similar densities. The structural changes seen at the pressure induced orthorhombic to monoclinic transition in Sc2W3O12 are similar, although not identical, to those seen for the equivalent thermally induced transition in Sc2Mo3O12.
Na8Au9.8(4)Ga7.2 and Na17Au5.87(2)Ga46.63: The diversity of pseudo 5-fold symmetries in the Na–Au–Ga system

Abstract The Na-rich part (~30% Na) of the Na–Au–Ga system between NaAu2, NaGa4, and Na22Ga39 has been found to contain the ternary phases Na8Au9.8(4)Ga7.2 (I) and Na17Au5.87(2)Ga46.63 (II), according to the results of single crystal X-ray diffraction measurements. I is orthorhombic, Cmcm, a=5.3040(1), b=24.519(5), c=14.573(3) A, and contains a network of clusters with local 5-fold symmetry along the a-axis. Such clusters are frequent building units in decagonal quasicrystals and their approximants. II is rhombohedral, R 3 ¯ m , a=16.325(2), c=35.242(7) A, and contains building blocks that are structurally identical to the Bergman-type clusters as well as fused icosahedral units known with active metals, triels and late transition elements. II also contains a polycationic network with elements of the clathrate V type structure. Tight-binding electronic structure calculations using linear muffin–tin-orbital (LMTO) methods on idealized models of I and II indicate that both compounds are metallic with evident pseudogaps at the corresponding Fermi levels. The overall Hamilton bond populations are generally dominated by Au–Ga and Au–Au bonds in I and by Ga–Ga bonds in II; moreover, the Na–Au and Na–Ga contributions in I are unexpectedly large, ~20% of the total. A similar involvement of sodium in covalent bonding has also been found in the electron-richer i-Na13Au12Ga15 quasicrystal approximant.
Structural Characterization of Pb6Sb6Se17

The ternary selenide Pb6Sb6Se17 was synthesized hydrothermally from the binaries (PbSe and Sb2Se3) and crystallizes in the orthorhombic space group Pbam (a = 15.835(3), b = 24.043(5), c = 4.134(2)A, Z = 2). The main building blocks of the crystal structure are ribbons made of square pyramidal [(Pb,Sb)Se5] groups running along [010].
A Novel Catalytic role of Molecular Iodine in the Oxidation of Benzylic Alcohols: Microwave-Assisted Reaction:

Molecular iodine was used to catalyse the oxidation of several benzylic alcohols to the corresponding ketones under the microwave-irradiated method, and the role of iodine was explored.
The characterization and absolute stereochemistry of barbaline, a diterpenoid alkaloid from Delphinium barbeyi

The structure and absolute stereochemistry of a new diterpenoid alkaloid, barbaline, was determined by NMR spectroscopy techniques and single-crystal X-ray diffraction analysis.
Petrophysical rock typing in unconventional shale plays: The Niobrara Formation case study

AbstractProduction from organic-rich shale petroleum systems is extremely challenging due to the complex rock and flow characteristics. An accurate characterization of shale reservoir rock properti...
One- and two-electron oxidations and reductions of organoselenium and organotellurium compounds

Publisher Summary Oxidation and reduction reactions of organotellurium and organoselenium compounds have provided much varied and interesting chemistry with respect not only to physical organic studies, but also to synthetic transformations. One electron oxidation to selenium- and tellurium-centered radical cations has allowed the comparison of substituent effects in various organoselenides and tellurides to the corresponding sulfides and oxygen-containing molecules. Two-electron oxidations of organotellurium and organoselenium compounds to the corresponding chalcogen compounds have been examined kinetically and, through the process of microscopic reversibility, have provided insight into the two-electron, reductive elimination process from chalcogen to chalcogen. Organochalcogen compounds have been used as synthetic reagents for the dehalogenation of vicinal-dihalides and for the reduction of α-halo ketones. Organochalcogen compounds have been utilized as halogenating agents and as mild oxidants for a variety of transformations. One-electron oxidation of organoselenium and organotellurium compounds results in initial formation of a radical cation. The eventual fate of the radical cation depends on several variables, but is typically a Se or Te compound. The chapter describes one-electron oxidation of selenides and tellurides that are not contained in a heteroaromatic compound, and ones in which the Se and Te are bonded to two carbons, rather than to other heteroatoms.
Photoredox Catalysts: Synthesis of the Bipyrazine Ligand

The bipyrazine ligand is often employed in photoredox catalysts in order to increase the excited state oxidation potential of the catalyst. However, literature syntheses of the ligand are cumbersome and typically lead to low yields. This hampers use of the desired catalysts. We report here an efficient copper based synthesis of the bipyrazine ligand that affords the product in 65–76% yield on a multigram scale.
Room temperature preparation of trifluoroethenylzinc reagent by metalation of the readily available halocarbon HFC-134a and an efficient, economically viable synthesis of 1,2,2-trifluorostyrenes.

Trifluoroethenylzinc reagent [CF2CFZnX] was generated from the readily available halocarbon HFC-134a by an in situ metalation−transmetalation procedure at temperatures near to room temperature (15−20 °C). By systematic standardization of the metalation experiments by manipulation of solvent, cosolvent, temperature, zinc salt, and the base, the trifluoroethenylzinc reagent was produced in 73% yield at 20 °C in THF medium. The palladium-catalyzed cross-coupling reaction of the trifluoroethenylzinc reagent with various aryl iodides was carried out under mild reaction conditions to produce 1,2,2-trifluorostyrenes in 59−86% isolated yields. The stability of the intermediate trifluoroethenyllithium reagent was compared at different temperatures and solvent systems. Experimental evidence for the mono-anion from HFC-134a (CF3CHF-) was obtained by the trapping of the mono-anion with zinc halide in THF/TMEDA medium. The structure and complexation of both the mono- and bis-trifluoroethenylzinc reagents with TMEDA an...
DIASTEREOSELECTIVE 6-EXO RADICAL CYCLIZATIONS OF OXIME ETHERS : TOTAL SYNTHESIS OF 7-DEOXYPANCRATISTATIN

The development of an approach leading to the total synthesis of 7-deoxypancratistatin is described. The key features of the approach include a 6-exo radical cyclization reaction between a benzylic radical and an O-benzyloxime ether to establish the C4a−C10b bond. The stereochemistry of this reaction was examined in both acyclic radical precursors and ones in which the aryl moiety was tethered to the C1 oxygen substituent. It was found that the use of such a tether was essential to obtain the stereochemical result required for the synthesis. The correct absolute and relative configurations at the hydroxylated carbons C1−C4 were obtained using d-gulonolactone as the source of C10b−C4a.
Eu4Bi3: Crystal Structure, Magnetic and Electronic Properties

The EuBi system contains the phases Eu5Bi3, Eu4Bi3 and Eu11Bi10. The structure types of these phases have been determined by powder X-ray diffraction. Crystals of Eu4Bi3 (cubic, space group I43d; a = 9.920 A, Z = 4, T = 130 K, R1/wR2 = 4.86/10.84%) were obtained in low yield by reaction of Eu, Mn, and Bi in the ratio 14:1:11 in a closed niobium tube (heating rate 30°C/h; reaction at 1050°C for 300 h, cooling rate 100°C/h). The crystal structure consists of distorted octahedra made up of six Bi coordinated to a central Eu atom. Eu is also coordinated to a three other Eu atoms and forms a three-dimensional network composed of interconnected rings. The Bi atoms are coordinated to eight Eu atoms. High yields of Eu4Bi3 can be prepared by reacting stoichiometric amount of the elements in a sealed tantalum tube at 1100°C for 24 h. Temperature dependent magnetic susceptibility is consistent with antiferromagnetic behavior with an ordering temperature of 18 K. The data could be fit with the Curie-Weiss law and a moment of 7.38 μB/Eu is obtained, consistent with all Eu atoms being Eu11. Temperature dependent resistivity indicates that Eu4Bi3 is a metal with a room temperature resistance of 1.3 Ωcm. Eu4Bi3: Kristallstruktur, magnetische und elektronische Eigenschaften Das System EuBi enthalt die Phasen Eu5Bi3, Eu4Bi3 und Eu11Bi10. Die Strukturen dieser Phasen wurden durch Pulver-Rontgenbeugungsuntersuchungen bestimmt. Kristalle von Eu4Bi3 (kubisch, Raumgruppe I43d; a = 9,920 A, Z = 4, T = 130 K, R1/wR2 = 4,86/10,84%) wurden in geringer Ausbeute durch Reaktion von Eu, Mn und Bi im molaren Verhaltnis 14:1:11 in einer verschlossenen Niobampulle erhalten (Aufheizrate: 30°C/h; Reaktion bei 1050°C, 300 h; Abkuhlrate: 100°C/h). Die Kristallstruktur besteht aus [EuBi6]-Oktaedern, wobei Eu zu drei weiteren Eu-Atomen koordiniert ist und ein dreidimensionales Netzwerk aus miteinander verknupften Ringen bildet. Die Bi-Atome haben 8 Eu-Atome als nachste Nachbarn. Eu4Bi3 kann in hoher Ausbeute durch Umsetzung von stochiometrischen Mengen der Elemente in einer verschlossenen Tantalampulle bei 1100°C (24 h) erhalten werden. Messungen der magnetischen Suszeptibilitat in Abhangigkeit von der Temperatur zeigen antiferromagnetisches Verhalten mit einer Ordnungstemperatur von 18 K. Die Werte gehorchen dem Curie-Weiss-Gesetz mit einem magnetischen Moment von 7,38 μB/Eu, was fur zweiwertiges Europium spricht. Widerstandsmessungen in Abhangigkeit von der Temperatur zeigen, das Eu4Bi3 metallisch ist mit einem Widerstand von 1,3 Ωcm bei Raumtemperatur.
Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome

Entomopathogenic nematodes from the genus Steinernema are lethal insect parasites that quickly kill their insect hosts with the help of their symbiotic bacteria. Steinernema carpocapsae is one of the most studied entomopathogens due to its broad lethality to diverse insect species and its effective commercial use as a biological control agent for insect pests, as well as a genetic model for studying parasitism, pathogenesis, and symbiosis. In this study, we used long-reads from the Pacific Biosciences platform and BioNano Genomics Irys system to assemble the most complete genome of the S. carpocapsae ALL strain to date, comprising 84.5 Mb in 16 scaffolds, with an N50 of 7.36 Mb. The largest scaffold, with 20.9 Mb, was identified as chromosome X based on sex-specific genome sequencing. The high level of contiguity allowed us to characterize gene density, repeat content, and GC content. RNA-seq data from 17 developmental stages, spanning from embryo to adult, were used to predict 30,957 gene models. Using this improved genome, we performed a macrosyntenic analysis to Caenorhabditis elegans and Pristionchus pacificus and found S. carpocapsae's chromosome X to be primarily orthologous to C. elegans' and P. pacificus' chromosome II and IV. We also investigated the expansion of protein families and gene expression differences between adult male and female stage nematodes. This new genome and more accurate set of annotations provide a foundation for additional comparative genomic and gene expression studies within the Steinernema clade and across the Nematoda phylum.
Synthesis of atovaquone

Abstract A short synthesis of atovaquone 1 is achieved via the radical coupling of the trans-1,4-substituted cyclohexyl mono-oxalate 2 and 2-chloronapthoquinone under phase transfer conditions.
Searching for Sympatric Speciation in the Genomic Era.

Sympatric speciation illustrates how natural and sexual selection may create new species in isolation without geographic barriers. However, recent genomic reanalyses of classic examples of sympatric speciation reveal complex histories of secondary gene flow from outgroups into the radiation. In contrast, the rich theoretical literature on this process distinguishes among a diverse range of models based on simple genetic histories and different types of reproductive isolating barriers. Thus, there is a need to revisit how to connect theoretical models of sympatric speciation and their predictions to empirical case studies in the face of widespread gene flow. Here, theoretical differences among different types of sympatric speciation and speciation-with-gene-flow models are reviewed and summarized, and genomic analyses are proposed for distinguishing which models apply to case studies based on the timing and function of adaptive introgression. Investigating whether secondary gene flow contributed to reproductive isolation is necessary to test whether predictions of theory are ultimately borne out in nature.
Convolutional Neural Network of Atomic Surface Structures To Predict Binding Energies for High-Throughput Screening of Catalysts

High-throughput screening of catalysts can be performed using density functional theory calculations to predict catalytic properties, often correlated with adsorbate binding energies. However, more...