cssi/SciSciGPT-SciSciNet huggingface dataset:
Learning polytrees

We consider the task of learning the maximum-likelihood polytree from data. Our first result is a performance guarantee establishing that the optimal branching (or Chow-Liu tree), which can be computed very easily, constitutes a good approximation to the best polytree. We then show that it is not possible to do very much better, since the learning problem is NP-hard even to approximately solve within some constant factor.
Chapter 16 – Alternative Exit and Restructuring Strategies: Divestitures, Spin-Offs, Carve-Outs, Split-Offs, and Tracking Stocks

Many corporations, particularly large, highly diversified organizations, are reviewing constantly ways in which they can enhance shareholder value by changing the composition of their assets, liabilities, equity, and operations. These activities generally are referred to as restructuring strategies. Restructuring may embody both growth and exit strategies. Growth strategies have been discussed elsewhere in this book. The focus in this chapter is on those strategic options allowing the firm to maximize shareholder value by redeploying assets through downsizing or refocusing the parent company. As such, this chapter discusses the myriad motives for existing businesses, the various restructuring strategies for doing so, and why firms select one strategy over other options. In this context, equity carve-outs, spin-offs, divestitures, and split-offs are discussed separately rather than as a specialized form of a carve-out. The chapter concludes with a discussion of what empirical studies say are the primary determinants of financial returns to shareholders resulting from undertaking the various restructuring strategies.
The Effect of Nitrogen Ion Damage on the Optical and Electrical Properties of MBE GaN Grown on MOCVD GaN/sapphire Templates

We have established a correlation between localized states responsible for mid-gap optical emission and film mobility of GaN grown under different nitrogen conditions. By imposing a deflector voltage at the tip of the plasma source, we varied the ion/neutral flux ratio to determine how N ions affect mid-gap luminescence and electrical mobility. Low energy electron-excited nanometer scale luminescence (LEEN) spectroscopy in ultrahigh vacuum (UHV) showed mid-gap emission intensities in the bulk that decreased in the ratio, 50: 1.3: 1 with increasing deflector voltage. Hall measurements indicated over a factor of two increase in mobility, and a factor of 8 decrease in residual charge density with increasing deflector voltage. The correlation of optical and electrical properties with a reduction in N ion flux suggests the primary role of native defects, such as N or Ga vacancies, in the mid-gap emissions.
Firearm injuries and children: Position statement of the American Pediatric Surgical Association.

Abstract Firearm injuries are the second most common cause of death in children who come to a trauma center, and pediatric surgeons provide crucial care for these patients. The American Pediatric Surgical Association (APSA) is committed to comprehensive pediatric trauma readiness, including firearm injury prevention. APSA supports a public health approach to firearm injury, and it supports availability of quality mental health services. APSA endorses policies for universal background checks, restrictions on assault weapons and high capacity magazines, strong child access protection laws, and a minimum purchase age of 21 years. APSA opposes efforts to keep physicians from counseling children and families about firearms. APSA promotes research to address this problem, including increased federal research support and research into the second victim phenomenon. APSA supports school safety and readiness, including bleeding control training. While it may be daunting to try to reduce firearm deaths in children, the U.S. has seen success in reducing motor vehicle deaths through a multidimensional approach – prevention, design, policy, behavior, trauma care. APSA believes that a similar public health approach can succeed to save children from death and injury from firearms. APSA is committed to building partnerships to accomplish this. Type of Study APSA Position Statement. Level of Evidence Level V, Expert Opinion.
Composite Quantization

This paper studies the compact coding approach to approximate nearest neighbor search. We introduce a composite quantization framework. It uses the composition of several ($M$M) elements, each of which is selected from a different dictionary, to accurately approximate a $D$D-dimensional vector, thus yielding accurate search, and represents the data vector by a short code composed of the indices of the selected elements in the corresponding dictionaries. Our key contribution lies in introducing a near-orthogonality constraint, which makes the search efficiency is guaranteed as the cost of the distance computation is reduced to $O(M)$O(M) from $O(D)$O(D) through a distance table lookup scheme. The resulting approach is called near-orthogonal composite quantization. We theoretically justify the equivalence between near-orthogonal composite quantization and minimizing an upper bound of a function formed by jointly considering the quantization error and the search cost according to a generalized triangle inequality. We empirically show the efficacy of the proposed approach over several benchmark datasets. In addition, we demonstrate the superior performances in other three applications: combination with inverted multi-index, inner-product similarity search, and query compression for mobile search.
Toll-managed lane pioneers: Lessons from five US states

Abstract Toll-managed lanes have become an increasingly popular technique among transportation policymakers for managing congestion on existing highways and, in some cases, financing the construction of new lanes in congested urban corridors. Although growing in popularity, the adoption of these facilities is concentrated in five states: Texas, California, Colorado, Minnesota, and Florida. This paper examines the adoption and utilization of toll-managed lanes in these pioneer states. Using archival, case-based research, our analysis suggests that the adoption of toll-managed lanes was driven by a combination of factors, including rapid population growth, near or above average growth in vehicle miles traveled (VMT), and insufficient gas tax funding for transportation investments. Implementation was also generally similar across states but some of the pioneers delegated the management of their toll-managed lane programs to special regional highway authorities while others used state highway agencies.
Kinetic studies on using photocatalytic coatings for removal of indoor volatile organic compounds

Titanium dioxide (TiO2) is a known photocatalyst with a capability of decomposing organic substances. However, the photocatalysis of the pure TiO2 is not effective for the indoor environment due to...
Development of a large-scale computer-controlled ozone inhalation exposure system for rodents.

Objective: Complete systems for laboratory-based inhalation toxicology studies are typically not commercially available; therefore, inhalation toxicologists utilize custom-made exposure systems. He...
Differential Canalograms Detect Outflow Changes from Trabecular Micro-Bypass Stents and Ab Interno Trabeculectomy

Recently introduced microincisional glaucoma surgeries that enhance conventional outflow offer a favorable risk profile over traditional surgeries, but can be unpredictable. Two paramount challenges are the lack of an adequate training model for angle surgeries and the absence of an intraoperative quantification of surgical success. To address both, we developed an ex vivo training system and a differential, quantitative canalography method that uses slope-adjusted fluorescence intensities of two different chromophores to avoid quenching. We assessed outflow enhancement by trabecular micro-bypass (TMB) implantation or by ab interno trabeculectomy (AIT). In this porcine model, TMB resulted in an insignificant (p > 0.05) outflow increase of 13 ± 5%, 14 ± 8%, 9 ± 3%, and 24 ± 9% in the inferonasal, superonasal, superotemporal, and inferotemporal quadrant, respectively. AIT caused a 100 ± 50% (p = 0.002), 75 ± 28% (p = 0.002), 19 ± 8%, and 40 ± 21% increase in those quadrants. The direct gonioscopy and tactile feedback provided a surgical experience that was very similar to that in human patients. Despite the more narrow and discontinuous circumferential drainage elements in the pig with potential for underperformance or partial stent obstruction, unequivocal patterns of focal outflow enhancement by TMB were seen in this training model. AIT achieved extensive access to outflow pathways beyond the surgical site itself.
Ab Initio Probing of the Aromatic Oxygen Cluster O42

The structure of the O 4 2 + dication has been studied theoretically using a few conventional theoretical methods. We found the O 4 2 + dication to be a metastable species with a perfect square structure. The molecular orbital analysis reveals that this dication is the first all-oxygen aromatic system with 6π electrons. Although the O 4 2 + dication is highly thermodynamically unstable, we believe that appropriate counteranions with very high electron detachment energy (superhalogens) can be found to form a solid-state compound containing O 4 2 + . Another way to probe the planar aromatic tetra oxygen dication could be a double-photoionization process of the (O 2 ) 2 dimer.
Microwave-enhanced palladium-catalyzed cross-coupling reactions of potassium vinyltrifluoroborates and allyl acetates: a new route to 1,4-pentadienes.

A novel and straightforward microwave synthesis of 1,4-pentadienes has been developed involving the cross-coupling of potassium vinyltrifluoroborates and allyl acetates in the presence of a palladium catalyst.
Hexagonal YFe1−xPdxO3−δ: Nonperovskite Host Compounds for Pd2+ and Their Catalytic Activity for CO Oxidation

Metastable YFeO3 with the hexagonal YAlO3 structure was obtained by a sol−gel process at 700 °C, using metal nitrate precursors with pH control and the appropriate citric acid to nitrate ratio. Under similar conditions, YFe1−xPdxO3−δ (0 < x ≤ 0.1) compositions were also prepared. The substitution of Fe by Pd stabilizes the YAlO3 structure at higher temperatures. The crystal structures of YFe1−xPdxO3−δ (0 ≤ x ≤ 0.1) were refined by Rietveld analysis of X-ray and neutron powder diffraction data. The parent hexagonal YFeO3 (x = 0) crystallizes in the space group P63/mmc with a = 3.5099(3) A and c = 11.759(2) A. The redox-driven mobility of Pd to integrate into the oxide host as ions and to dissociate from it as fcc-Pd nanoparticles was monitored by a combination of X-ray diffraction and X-ray photoelectron spectroscopy. Pd nanoparticles in the reduced samples were detected by scanning backscattered electron microscopy and transmission electron microscopy. The Pd2+-containing materials showed significant low-...
Allylic Phosphinates via Palladium-Catalyzed Allylation of H-Phosphinic Acids with Allylic Alcohols

A novel catalytic allylation of H-phosphinic acids is described. Using Pd/xantphos (2 mol %), H-phosphinic acids react directly with allylic alcohols to produce P-allylated disubstituted phosphinic acids.
Addition of bromine chloride and iodine monochloride to carbonyl-conjugated, acetylenic ketones: synthesis and mechanisms.

The reactions of 3-butyn-2-one (1), 3-hexyn-2-one (2), and 4-phenyl-3-butyn-2-one (3) with bromine chloride (BrCl) and iodine monochloride (ICl) in CH2Cl2, CH2Cl2/pyridine, and MeOH are described. The data show that the major products in CH2Cl2 are (Z)-AM (anti-Markovnikov) regioisomers. With the exception of 3 and ICl, the (E)-AM regioisomers predominate when pyridine was added as an acid scavenger. Minor amounts of the M regioisomers were formed with 1 and 2 and BrCl. The percentage of M regioisomer increased significantly with 1 and BrCl in MeOH, but MeOH had little affect on the other reactions. Isolation and stability of the products are discussed. Detailed evidence for the structures of the products, involving a combination of MS, 1H and 13C NMR, and IR, is presented; HRMS analyses are provided as proofs for all of the products. The acid-catalyzed mechanism and the halonium ion mechanism are considered as possible pathways in the formation of the products.
Rh(I)-Catalyzed Transformation of Propargyl Vinyl Ethers into (E,Z)-Dienals: Stereoelectronic Role of trans Effect in a Metal-Mediated Pericyclic Process and a Shift from Homogeneous to Heterogeneous Catalysis During a One-Pot Reaction

The combination of experiments and computations reveals unusual features of stereoselective Rh(I)-catalyzed transformation of propargyl vinyl ethers into (E,Z)-dienals. The first step, the conversion of propargyl vinyl ethers into allene aldehydes, proceeds under homogeneous conditions via a “cyclization-mediated” mechanism initiated by Rh(I) coordination at the alkyne. This path agrees well with the small experimental effects of substituents on the carbinol carbon. The key feature revealed by the computational study is the stereoelectronic effect of the ligand arrangement at the catalytic center. The rearrangement barriers significantly decrease due to the greater transfer of electron density from the catalytic metal center to the CO ligand oriented trans to the alkyne. This effect increases electrophilicity of the metal and lowers the calculated barriers by 9.0 kcal/mol. Subsequent evolution of the catalyst leads to the in situ formation of Rh(I) nanoclusters that catalyze stereoselective tautomerizatio...
An Intramolecular Allenic [2 + 2 + 1] Cycloaddition

A new stereo- and regioselective method for the preparation of α-methylene and 4-alkylidene cyclopentenones is described. These substructures were achieved by an intramolecular [2 + 2 + 1] cycloaddition of an allene, alkyne, and carbon monoxide moieties to afford the target compounds stereoselectively and in good yields. In some cases, the target compounds were obtained as mixtures, but it is demonstrated that the formation of either the α-methylene or 4-alkylidene cyclopentenone can be controlled by the allene structure or reaction conditions. Monosubstituted allenes afford α-methylene cyclopentenones as the only cycloadduct. Disubstitution on the allene alters the course of the allenic [2 + 2 + 1] reaction. 3,3-Disubstituted allenes undergo cycloaddition with the least substituted π-bond of the allene. This affords the bicyclo[4.3.0]nonane ring system. Cycloaddition of 1,3-disubstituted allenes afford mixtures of several possible cycloadducts. However, it has been shown that good control over the produc...
Transiting topological sectors with the overlap

Abstract The overlap operator provides an elegant definition for the winding number of lattice gauge field configurations. Only for a set of configurations of measure zero is this procedure undefined. Without restrictions on the lattice fields, however, the space of gauge fields is simply connected. I present a simple low dimensional illustration of how the eigenvalues of a truncated overlap operator flow as one travels between different topological sectors.
A Novel Class of CC-1065 and Duocarmycin Analogues Subject to Mitomycin-Related Reductive Activation.

A new class of DNA alkylating agents is described that incorporate the quinone of the mitomycins, which is thought to impart tumor cell selectivity as a result of preferential reduction and activation in hypoxic tumors, into the AT-selective binding framework of the duocarmycins capable of mitomycin-like reductive activation and duocarmycin-like spirocyclization and subsequent DNA alkylation. Consistent with this design, the quinone prodrugs fail to alkylate DNA unless reductively activated and then do so with an adenine N3 alkylation sequence selectivity identical to that of the duocarmycins. Additionally, the agents exhibit a selectivity toward DT-Diaphorase (NQO1)-containing versus DT-Diaphorase-deficient (resistant) tumor cell lines, and they were shown to be effective substrates for reduction by recombinant human DT-Diaphorase. As such, the agents constitute effective duocarmycin and CC-1065 analogues subject to reductive activation. In addition, the solvolysis pH rate dependence of a series of react...
Selective formation of six-membered cyclic sulfones and sulfonates by C-H insertion.

Carbethoxy diazosulfones and sulfonates, easily available from corresponding sulfones and sulfonates, undergo C−H insertion with preferential formation of six membered cyclic sulfones and sulfonates.
Genome-Wide Association Analysis With a 50K Transcribed Gene SNP-Chip Identifies QTL Affecting Muscle Yield in Rainbow Trout

Detection of coding/functional SNPs that change the biological function of a gene may lead to identification of putative causative alleles within QTL regions and discovery of genetic markers with large effects on phenotypes. Two bioinformatics pipelines, GATK and SAMtools, were used to identify ~21K transcribed SNPs with allelic imbalances associated with important aquaculture production traits including body weight, muscle yield, muscle fat content, shear force, and whiteness in addition to resistance/susceptibility to bacterial cold-water disease (BCWD). SNPs were identified from pooled RNA-Seq data collected from ~620 fish, representing 98 families from growth- and 54 families from BCWD-selected lines with divergent phenotypes. In addition, ~29K transcribed SNPs without allelic-imbalances were strategically added to build a 50K Affymetrix SNP-chip. SNPs selected included two SNPs per gene from 14K genes and ~5K non-synonymous SNPs. The SNP-chip was used to genotype 1728 fish. The average SNP calling-rate for samples passing quality control (QC; 1,641 fish) was ≥ 98.5%. Genome-wide association (GWA) study on 878 fish (representing 197 families from 2 consecutive generations) with muscle yield phenotypes and genotyped for 35K polymorphic markers (passing QC) identified several QTL regions explaining together up to 28.40% of the additive genetic variance for muscle yield in this rainbow trout population. The most significant QTLs were on chromosomes 14 and 16 with 12.71% and 10.49% of the genetic variance, respectively. Many of the annotated genes in the QTL regions were previously reported as important regulators of muscle development and cell signaling. No major QTLs were identified in a previous GWA study using a 57K genomic SNP chip on the same fish population. These results indicate improved detection power of the transcribed gene SNP-chip in the target trait and population, allowing identification of large-effect QTLs for important traits in rainbow trout.
Can transcranial electric stimulation with multiple electrodes reach deep targets

To reach a deep target in the brain with transcranial electric stimulation (TES), currents have to pass also through the cortical surface. Thus, it is generally thought that TES cannot achieve focal deep brain stimulation. Recent efforts with interfering waveforms and pulsed stimulation have argued that one can achieve deeper or more intense stimulation in the brain. Here we argue that conventional transcranial stimulation with multiple current sources is just as effective as these new approaches. The conventional multi-electrode approach can be numerically optimized to maximize intensity or focality at a desired target location. Using such optimal electrode configurations we find in a detailed and realistic head model that deep targets may in fact be strongly stimulated, with cerebro-spinal fluid guiding currents deep into the brain.
A0.3ZrNF1.3 Phases (A = Na, K) with Layered ZrNCl-Type Structures Prepared by Anion Metathesis

β-ZrNCl reacts with excess NaF in the solid state (350−400 °C) via anion exchange to give metastable NaxZrNF1+x (x ≈ 0.3), the first fluoride structural analogue of the MNX system (M = Zr, Hf; X = Cl, Br, I). The sodium-stabilized phase (P63/mmc; a = 3.654(1) A, c = 18.266(8) A) was characterized by powder X-ray and neutron diffraction studies and was shown to contain successive FZr2N2F layers that are shifted from the original ZrNCl parent structure, giving a two-layer unit cell. Partially occupied Na and F sites create a stabilizing cluster effect between these layers. Heating the reaction mixture above 500 °C leads to the formation of the ZrNxF4-3x phase reported by Jung and Juza. Further heating results in decomposition to several known sodium fluorozirconate phases.
Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster

High-resolution transcription start site (TSS) mapping in D. melanogaster embryos and cell lines has revealed a rich and detailed landscape of both cis- and trans-regulatory elements and factors. However, TSS profiling has not been investigated in an orthogonal in vivo setting. Here, we present a comprehensive dataset that links TSS dynamics with nucleosome occupancy and gene expression in the wandering third instar larva, a developmental stage characterized by large-scale shifts in transcriptional programs in preparation for metamorphosis. The data recapitulate major regulatory classes of TSSs, based on peak width, promoter-proximal polymerase pausing, and cis-regulatory element density. We confirm the paucity of divergent transcription units in D. melanogaster, but also identify notable exceptions. Furthermore, we identify thousands of novel initiation events occurring at unannotated TSSs that can be classified into functional categories by their local density of histone modifications. Interestingly, a sub-class of these unannotated TSSs overlaps with functionally validated enhancer elements, consistent with a regulatory role for “enhancer RNAs” (eRNAs) in defining developmental transcription programs. High-depth TSS mapping is a powerful strategy for identifying and characterizing low-abundance and/or low-stability RNAs. Global analysis of transcription initiation patterns in a developing organism reveals a vast number of novel initiation events that identify potential eRNAs as well as other non-coding transcripts critical for animal development.
Regioselective Synthesis of Sucrose Monoesters as Surfactants

ABSTRACT A highly regioselective conversion of sucrose into 6-O-acyl derivatives is reported. First sucrose was transformed into the dibutyltin acetal, thus enhancing the nucleophilicity at the C-6 oxygen and restricting the subsequent acylation reaction. The surface activity properties of the sucrose monoesters obtained were determined and compared with those of commercially available ionic and non-ionic surfactants.
Total Synthesis of Calyculin C

The study of phosphatases continues to flourish given their prominence in signal transduction pathways and the regulation of cell function. Our research efforts in this area focus on the potent inhibition of serine/threonine phosphatases, PP1 and PP2A, by a structurally diverse class of natural products. We herein report the completed total synthesis of the serine/threonine phosphatase inhibitor calyculin C (1) as part of an ongoing effort to elucidate key structural requirements for phosphatase inhibition by the aforementioned diverse class of natural products. Synthetic issues addressed include (1) the remote protecting group effect on Brown crotylboration diastereoselectivity during the introduction of the C10−C11 stereocenters and (2) the formation of the C25−C26 double bond using a fully deprotected C26−C37 phosphonium salt (3). In addition, the concurrent synthesis of 34R-calyculin C (29) clarified our previous C34-stereochemical assignment of C26−C37 phosphonium salts (3 and 27) (Ogawa, A. K.; DeMa...
A Practical Preparation of Thiol Carboxylic Esters of 2-(Isoxazolyl) Acetic Acids

Abstract High yields of several thiolesters of 2-[3-(4-cyanophenyl)-4,5-dihydro-5-isoxazolyl]acetic acid are easily prepared from the corresponding oxoester by the reaction with trimethyl silylated mercaptan and aluminum chloride. The selection of mercaptans expands the previous scope of this synthetic method.
Optimization of DNA extraction from human urinary samples for mycobiome community profiling.

Author(s): Ackerman, A Lenore; Anger, Jennifer Tash; Khalique, Muhammad Umair; Ackerman, James E; Tang, Jie; Kim, Jayoung; Underhill, David M; Freeman, Michael R; NIH Multidisciplinary Approach to the Study of Chronic Pelvic Pain (MAPP) | Abstract: IntroductionRecent data suggest the urinary tract hosts a microbial community of varying composition, even in the absence of infection. Culture-independent methodologies, such as next-generation sequencing of conserved ribosomal DNA sequences, provide an expansive look at these communities, identifying both common commensals and fastidious organisms. A fundamental challenge has been the isolation of DNA representative of the entire resident microbial community, including fungi.Materials and methodsWe evaluated multiple modifications of commonly-used DNA extraction procedures using standardized male and female urine samples, comparing resulting overall, fungal and bacterial DNA yields by quantitative PCR. After identifying protocol modifications that increased DNA yields (lyticase/lysozyme digestion, bead beating, boil/freeze cycles, proteinase K treatment, and carrier DNA use), all modifications were combined for systematic confirmation of optimal protocol conditions. This optimized protocol was tested against commercially available methodologies to compare overall and microbial DNA yields, community representation and diversity by next-generation sequencing (NGS).ResultsOverall and fungal-specific DNA yields from standardized urine samples demonstrated that microbial abundances differed significantly among the eight methods used. Methodologies that included multiple disruption steps, including enzymatic, mechanical, and thermal disruption and proteinase digestion, particularly in combination with small volume processing and pooling steps, provided more comprehensive representation of the range of bacterial and fungal species. Concentration of larger volume urine specimens at low speed centrifugation proved highly effective, increasing resulting DNA levels and providing greater microbial representation and diversity.ConclusionsAlterations in the methodology of urine storage, preparation, and DNA processing improve microbial community profiling using culture-independent sequencing methods. Our optimized protocol for DNA extraction from urine samples provided improved fungal community representation. Use of this technique resulted in equivalent representation of the bacterial populations as well, making this a useful technique for the concurrent evaluation of bacterial and fungal populations by NGS.
Enantioselective catalytic epoxidation of cinnamate esters

Abstract A broad study of the (salen)Mn(III)-catalyzed asymmetric epoxidation of cis-cinnamate esters reveals that the steric properties of the ester group have a profound influence on enantioselectivity in the epoxidation reaction, with bulkier esters affording highest ee's. The sensitivity of the reaction selectivity to the steric properties of the cis-alkene are consistent with a “skewed” side-on approach of olefin to the metal-oxo. The electronic properties of the substrate arene ring substituents do not correlate with epoxidation ee, but instead with the cis/trans partitioning of product formation. Evidence is provided for a non-polar intermediate in a stepwise oxygen-atom-transfer mechanism. The presence of pyridine N-oxide derivatives has a significant effect on catalysts rates and total turnovers, but negligible influence on the stereoselectivity of epoxidation. A mechanistic basis for the role of these additives is proposed. The synthetic applicability of the cinnamate epoxidation methodology is illustrated in the highly enantioselective synthesis of diltiazem.
An Improved Synthesis of O-Benzoyl Protected Hydroxamates.

Several primary amines (R-NH2) were converted to their corresponding O-benzoyl protected hydroxamates under biphasic conditions. The intermediate (benzoyloxy)amines (R-NHOCOPh) were generated using benzoyl peroxide dissolved in CH2Cl2 and an aqueous carbonate buffer (pH 10.5) at room temperature. Subsequent acylation with R‘COCl gave the protected hydroxamates (R‘CONROCOPh) in good overall yields (56−89%).
Lewis acid-promoted electron transfer deoxygenation of epoxides, sulfoxides, and amine N-oxides: the role of low-valent niobium complexes from NbCl5 and Zn

Abstract A mild and operationally simple deoxygenation of epoxides, sulfoxides, and amine N -oxides is described using a sub-stoichiometric amount of low-valent niobium complexes generated in situ from commercially available NbCl 5 and zinc dust. The deoxygenation proceeds by a reductive cleavage of polarized O–C/O–N/O–S bonds through a single electron transfer from zinc metal to the niobium–substrate complex due to the high oxophilic nature of the niobium species. The presence of adjacent radical-stabilizing groups is beneficial to epoxide substrates; however the similar prerequisite does not apply to sulfoxides and amine N -oxides, where a broad range of substrates are efficiently deoxygenated in excellent yields.
Sex differences in aggression: Differential roles of 5-HT2, neuropeptide F and tachykinin

Despite the conserved function of aggression across taxa in obtaining critical resources such as food and mates, serotonin’s (5-HT) modulatory role on aggressive behavior appears to be largely inhibitory for vertebrates but stimulatory for invertebrates. However, critical gaps exist in our knowledge of invertebrates that need to be addressed before definitively stating opposing roles for 5-HT and aggression. Specifically, the role of 5-HT receptor subtypes are largely unknown, as is the potential interactive role of 5-HT with other neurochemical systems known to play a critical role in aggression. Similarly, the influence of these systems in driving sex differences in aggressive behavior of invertebrates is not well understood. Here, we investigated these questions by employing complementary approaches in a novel invertebrate model of aggression, the stalk-eyed fly. A combination of altered social conditions, pharmacological manipulation and 5-HT2 receptor knockdown by siRNA revealed an inhibitory role of this receptor subtype on aggression. Additionally, we provide evidence for 5-HT2’s involvement in regulating neuropeptide F activity, a suspected inhibitor of aggression. However, this function appears to be stage-specific, altering only the initiation stage of aggressive conflicts. Alternatively, pharmacologically increasing systemic concentrations of 5-HT significantly elevated the expression of the neuropeptide tachykinin, which did not affect contest initiation but instead promoted escalation via production of high intensity aggressive behaviors. Notably, these effects were limited solely to males, with female aggression and neuropeptide expression remaining unaltered by any manipulation that affected 5-HT. Together, these results demonstrate a more nuanced role for 5-HT in modulating aggression in invertebrates, revealing an important interactive role with neuropeptides that is more reminiscent of vertebrates. The sex-differences described here also provide valuable insight into the evolutionary contexts of this complex behavior.
Crystal growth of novel osmium-containing triple perovskites.

Single crystals of two new osmium-containing triple perovskites, Ba 3 LiOs 2 O 9 and Ba 3 NaOs 2 O 9 , were grown from reactive molten hydroxide fluxes in sealed silver tubes. They crystallize in the space group P6 3 /mmc with lattice parameters of a = 5.8025(1) A, c = 14.1468(4) A for Ba 3 LiOs 2 O 9 and a = 5.8858(1) A, c = 14.3451-(5) A for Ba 3 NaOs 2 O 9 . The magnetic susceptibility of these osmates indicates significant Os-Os coupling within the octahedra pair.
Synthesis of (±)-palasonin

Abstract (±)-Palasonin (1) was prepared in nine steps from α-methoxycarbonylmaleic anhydride (3).
Regioselective synthesis of derivatives of l-idopyranuronic acid: A key constituent of glycosaminoglycans

Abstract Synthesis of new and potentially universal l -idopyranuronic glycosyl-donor and/or -acceptor 13 was performed starting from d -glucofuranurono-6,3-lactone 1 . After simple C-5-epimerization, C-1thioacetalization and regioselective p -methoxybenzylidenation to the hydroxylactone 6, the lactone ring was opened. The resulting diolamide stereoselectively protected, providing compound 7. Regioselective reductive cleavage of the 1,3-dioxane ring and subsequent deprotection afforded the target molecule 13 .
No Cost of Complexity in Bacteriophages Adapting to a Complex Environment.

A long-standing prediction in evolutionary biology is that organisms experience a so-called “cost of complexity” manifested as a decreasing rate of adaptation in populations as organisms or selective environments become increasingly complex. This theory assumes the ubiquity of antagonistic pleiotropy, or trade-offs in fitness, for mutations affecting multiple traits or phenotypes. A particular manifestation of antagonism thought to be at play in adaptive dynamics involves the relationship between viral growth rate and capsid stability, an interaction that may impede the adaptation of viral pathogens to novel hosts and environments. Here, we present a comparison of the genetics of adaptation for populations of bacteriophages undergoing complete adaptive walks under both simple and complex selective conditions, with complexity being determined by the number of traits under directional selection. We found no evidence for a long-term cost of complexity in viruses experiencing complex selection, with on average at least as great a rate of adaptation under more complex conditions, and rampant evidence for synergistic, rather than antagonistic, pleiotropy. The lack of evident trade-offs between multiple phenotypes implies that emerging pathogens may be able to improve their growth in many different hosts or environments simultaneously, and to do so at a faster rate than previously anticipated.
AptaBlocks: Accelerating the Design of RNA-based Drug Delivery Systems

Synthetic RNA molecules are increasingly used to alter cellular functions. These successful applications indicate that RNA-based therapeutics might be able to target currently undruggable genes. However, to achieve this promise, an effective method for delivering therapeutic RNAs into specific cells is required. Recently, RNA aptamers emerged as promising delivery agents due to their ability of binding specific cell receptors. Crucially, these aptamers can frequently be internalized into the cells expressing these receptors on their surfaces. This property is leveraged in aptamer based drug delivery systems by combining such receptor-specific aptamers with a therapeutic "cargo" such that the aptamer facilitates the internalization of the cargo into the cell. The advancement of this technology however is contingent on an efficient method to produce stable molecular complexes that include specific aptamers and cargoes. A recently proposed experimental procedure for obtaining such complexes relies on conjugating the aptamer and the cargo with complementary RNA strands so that when such modified molecules are incubated together, the complementary RNA strands hybridize to form a double-stranded "sticky bridge" connecting the aptamer with its cargo. However, designing appropriate sticky bridge sequences guaranteeing the formation and stability of the complex while simultaneously not interfering with the aptamer or the cargo as well as not causing spurious aggregation of the molecules during incubation has proven highly challenging. To fill this gap, we developed AptaBlocks, a computational method to design sticky bridges to connect RNA-based molecules (blocks). AptaBlocks relies on a biophysically inspired theoretical model capturing the complex objectives of the design and yet is simple enough to allow for efficient parameter estimation. Given this model, the sticky bridge sequence is optimized using a Monte Carlo algorithm based on heat-bath transitions. The effectiveness of the algorithm has been verified computationally and experimentally. AptaBlocks can be used in variety of experimental settings and its preliminary version has already been leveraged to design an aptamer based delivery system for a cytotoxic drug targeting Pancreatic ductal adenocarcinoma cells. It is thus expected that AptaBlocks will play a substantial role in accelerating RNA-based drug delivery design. AptaBlocks is available at https://github.com/wyjhxq/AptaBlocks.
Aldol reactions of α-(N,N-dibenzylamino) ethyl ketones

Abstract Aldol reactions of the sodium enolates of α-(N,N-dibenzylamino) ethyl ketones proceed in a highly diastereoselective fashion and result in the formation of the all syn adduct. The observed stereoselectivities are most easily understood in the context of an open transition state.
Unusual sensitivity to the concentration of ethanol in the boron trifluoride/ethanol‐catalyzed synthesis of 5,10,15,20‐tetrakis‐(4‐cyano‐2,6‐dimethylphenyl)porphyrin by the lindsey method

The boron trifluoride/ethanol-catalyzed condensation of 4-cyano-2,6-dtmethylbenzaldehyde 1b with pyrrole by the Lindsey method to give the new, ortho-disubstituted 5,10,15,20-tetrakis(4-cyano-2,6-dimethylphenyl)porphyrin 2 was found to be highly sensitive to the concentration of ethanol. In the absence of ethanol the yield of porphyrin is only 1%. Yields can be increased to 20–25% with ethanol concentrations of 0.05–0.1% (v/v) but they decrease rapidly at higher concentrations of ethanol. Optimized procedures for the preparation of both 1b and 2 are described and the newly synthesized molecules are characterized by nmr (1H and 13C), mass spectra and elemental analysis.
Gallium Nitride Photodetector Measurements of UV Emission from a Gaseous CH4/O2 Hybrid Rocket Igniter Plume

Owing to its wide (3.4 eV) and direct-tunable band gap, gallium nitride (GaN) is an excellent material platform to make UV photo detectors. GaN is also stable in radiation-rich and high-temperature environments, which makes photo detectors fabricated using this material useful for in-situ flame detection and combustion monitoring. In this paper, we use a GaN photo detector to measure ultraviolet (UV) emissions from a hybrid rocket motor igniter plume. The GaN photo detector, built at the Stanford Nanofabrication Facility, has 5 μm wide regions of AlGaN/GaN two-dimensional electron gas (2DEG)electrodes spaced by intrinsic GaN channels. In most applications, the ideal photodetector would exhibit a high responsivity to maximize the signal, in addition to a low dark current to minimize quiescent power. A performance metric which simultaneously captures these two values is the normalized photocurrent-to-dark current ratio (NPDR), defined as the ratio of responsivity to dark current, with units of W−1. The NPDR of our device is record-high with a value of 6 × 1014 W−1 and the UV-to-visible rejection ratio is 4 × 106. The high rejection ratio is essential as it eliminates cross-sensitivity of the detector to visible light. The spectral response can be modeled as a rectangular window with a peak responsivity of 7,800 AW−1 at 362 nm and a bandwidth of 16 nm. The photo detector shows operation at high temperatures (up to 250°C). The NPDR still remains above 109 W−1 at the higher temperatures, and the peak wavelength shifts from 362 nm to 375 nm at 250°C. The photo detector was placed at three radial distances ( $3^{\prime\prime},5.5^{\prime\prime}$ , and $7^{\prime\prime}$ ) from the base of the igniter plume and the oxidizer-to-fuel ratio (O 2 /CH 4 ) was varied to alter the size and strength of the plume. The current measured from the device was proportional to the intensity of the emission from the plume. The data demonstrates a clear trend of increasing current with increasing fuel concentration. Further, the current decreases with larger separation between the photo detector and the plume. A calibration curve constructed from the responsivity measurements taken over four orders of magnitude was used to convert the current into incident optical power. By treating the plume as a black body, and calculating a radiative configuration factor corresponding to the geometry of the plume and the detector, we calculated average plume temperatures at each of the three oxidizer-to-fuel ratios. The estimated plume temperatures were between 850 and 950 K for all three combustion conditions. The temperature is roughly invariant for a fixed fuel concentration for the three tested distances. These data demonstrate the functionality of GaN as a material platform for use in harsh environment flame monitoring.
Magnetic superstructures of cupric oxide CuO as ordered arrangements of one-dimensional antiferromagnetic chains.

In cupric oxide CuO, each Cu2+ ion has 12 nearest-neighbor Cu2+ ions grouped into six pairs related by inversion symmetry. The relative strengths of the Cu−O−Cu superexchange interactions in cupric oxide CuO were estimated by spin dimer analysis to confirm that the strongest superexchange interactions form one-dimensional antiferromagnetic chains along the [101] direction, and the remaining interactions are weak. We analyzed ordered arrangements of these one-dimensional antiferromagnetic chains to examine why the antiferromagnetic phase transition of CuO below 212.5 K adopts a (2a, b, 2c) superstructure. The local spin arrangement around each Cu2+ ion is more balanced in the ordered spin structures leading to a (2a, b, 2c) supercell than in any other ordered spin structures.
HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.

Summary Genome-wide proximity ligation based assays like Hi-C have opened a window to the 3D organization of the genome. In so doing, they present data structures that are different from conventional 1D signal tracks. To exploit the 2D nature of Hi-C contact maps, matrix techniques like spectral analysis are particularly useful. Here, we present HiC-spector, a collection of matrix-related functions for analyzing Hi-C contact maps. In particular, we introduce a novel reproducibility metric for quantifying the similarity between contact maps based on spectral decomposition. The metric successfully separates contact maps mapped from Hi-C data coming from biological replicates, pseudo-replicates and different cell types. Availability and implementation Source code in Julia and Python, and detailed documentation is available at https://github.com/gersteinlab/HiC-spector . Contact koonkiu.yan@gmail.com or mark@gersteinlab.org. Supplementary information Supplementary data are available at Bioinformatics online.
Transcriptional analysis shows a robust host response to Toxoplasma gondii during early and late chronic infection in both male and female mice

ABSTRACT The long-term host effects caused by the protozoan parasite Toxoplasma gondii are poorly understood. High-throughput RNA sequencing analysis previously determined that the host response in the brain was greater and more complex at 28 days than at 10 days postinfection. Here, we analyzed the host transcriptional profile of age- and sex-matched mice during very early (21 days), early (28 days), mid (3 months), and late (6 months) chronic infection. We found that a majority of the host genes which increase in abundance at day 21 postinfection are still increased at 6 months postinfection for both male and female mice. While most of the differentially expressed genes were similar between sexes, females had far fewer genes that were significantly less abundant, which may have led to the slightly increased cyst burden in males. Transcripts for C-X-C motif chemokine ligand 13 and a C-C motif chemokine receptor 2 (CCR2) were significantly higher in females than in males during infection. As T. gondii chronic infection and profilin (PRF) confer resistance to Listeria monocytogenes infection in a CCR2-dependent manner, the differences in CCR2 expression led us to retest the protection of PRF in both sexes. Male mice were nearly as effective as female mice at reducing the bacterial burden either with a chronic infection or when treated with PRF. These data show that most of the host genes differentially expressed in response to T. gondii infection are similar between males and females. While differences in transcript abundance exist between the sexes, the infection phenotypes tested here did not show significant differences.
JM-PHOS Ligands: Second-Generation Phosphine Oxazolines for Asymmetric Catalysis

A small library of phosphine oxazoline ligands 2 was prepared and tested in palladium-mediated allylation processes (reactions 1 and 2). They were found to be superior to the first-generation ligands 1 and as effective as the well-known phosphine oxazolines 3.
Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles

Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1 × 109 reads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily and annual variation. We identified 12,042 diurnally-cyclic transcripts, 9299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 circannual transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light intensity at diurnal scales and photoperiod at annual scales, with approximately half of transcripts reaching maximum expression +/− 2 h from sunrise and sunset, and +/− 20 days from winter and summer solstices. Comparisons with published studies from other conifers shows congruent behavior in clock genes with Japanese cedar (Cryptomeria), and a significant preservation of gene expression patterns for 2278 putative orthologs from Douglas-fir during the summer growing season, and 760 putative orthologs from spruce (Picea) during the transition from fall to winter. Our study highlight the extensive diurnal and circannual transcriptome variability demonstrated in conifer needles. At these temporal scales, 29% of expressed transcripts show a significant diurnal cycle, and 58.7% show a significant circannual cycle. Remarkably, thousands of genes reach their annual peak activity during winter dormancy. Our study establishes the fine-scale timing of daily and annual maximum gene expression for diverse needle genes in Douglas-fir, and it highlights the potential for using this information for evaluating hypotheses concerning the daily or seasonal timing of gene activity in temperate-zone conifers, and for identifying cyclic transcriptome components in other conifer species.