cssi/SciSciGPT-SciSciNet huggingface dataset:
The fiber of the persistence map for functions on the interval

In this paper we study functions on the interval that have the same persistent homology, which is what we mean by the fiber of the persistence map. By imposing an equivalence relation called graph-equivalence, the fiber of the persistence map becomes finite and a precise enumeration is given. Graph-equivalence classes are indexed by chiral merge trees, which are binary merge trees where a left-right ordering of the children of each vertex is given. Enumeration of merge trees and chiral merge trees with the same persistence makes essential use of the Elder Rule, which is given its first detailed proof in this paper.
Unintended impacts from forest certification: Evidence from indigenous Aka households in Congo

Abstract Does Forest Stewardship Council (FSC) certification of “responsible” commercial forestry change nutrition, health and wealth for indigenous peoples, like the Aka of the Congo Basin? Using hand-collected data from the boundary of a certified and an uncertified forest in the Republic of Congo five years after certification, I compare nutrition, health, and wealth using questions that are locally salient and survey timing designed to reach semi-nomadic hunter-gatherers. Though I only observe outcomes after certification, using a spatial regression discontinuity design I find suggestive evidence that activities to satisfy forest certification may cause increased food insecurity and illness frequency for Aka households. I find no evidence of increased material wealth; instead, the poorest 15th percentile is poorer for Aka households. Non-Aka households are unaffected. Activities to satisfy FSC include a road connection, likely requested by non-Aka households, which in combination with hunting restrictions may decrease food security for Aka hunter-gatherers.
Inhibiting hydrogen sulfide production in umbilical stem cells reduces their protective effects during experimental necrotizing enterocolitis.

Abstract Introduction Umbilical mesenchymal stem cells (USC) have been shown to reduce illness in animal models of necrotizing enterocolitis (NEC), possibly through the paracrine release of hydrogen sulfide (H2S). We hypothesized that animals treated with USCs with inhibited H2S synthesis would exhibit more severe disease. Methods NEC was induced in five-day-old mouse pups by formula feeding and hypoxic and hypothermic stress. Experimental groups received intraperitoneal injection of either saline vehicle or 80,000cells/gram of one of the following cell types: USC, USCs with negative-control siRNA, or USCs with targeted siRNA inhibition of the H2S-producing enzymes. Pups were monitored by clinical assessment and after euthanasia, intestine and lung histologic injury were scored. Tissue was homogenized, and concentrations of IL-6, IL-10, and VEGF were determined by ELISA. For statistical analysis, p Results Animals treated with negative-control siRNA USCs were significantly improved compared to vehicle. Clinical sickness scores as well as intestinal and lung histologic injury scores in the targeted siRNA groups were significantly worse when compared to the negative-control siRNA group. IL-6, IL-10, and VEGF had varying patterns of expression in the different groups. Conclusion Inhibition of H2S production in USCs reduces the beneficial effects of these cells during therapy in experimental NEC. Level of evidence Animal studies are typically described as “foundational evidence” without a true level assigned. Type of study Animal Study.
How the avidity of polymerase binding to the -35/-10 promoter sites affects gene expression.

Although the key promoter elements necessary to drive transcription in Escherichia coli have long been understood, we still cannot predict the behavior of arbitrary novel promoters, hampering our ability to characterize the myriad sequenced regulatory architectures as well as to design new synthetic circuits. This work builds upon a beautiful recent experiment by Urtecho et al. [G. Urtecho, et al., Biochemistry, 68, 1539–1551 (2019)] who measured the gene expression of over 10,000 promoters spanning all possible combinations of a small set of regulatory elements. Using these data, we demonstrate that a central claim in energy matrix models of gene expression—that each promoter element contributes independently and additively to gene expression—contradicts experimental measurements. We propose that a key missing ingredient from such models is the avidity between the –35 and –10 RNA polymerase binding sites and develop what we call a multivalent model that incorporates this effect and can successfully characterize the full suite of gene expression data. We explore several applications of this framework, namely, how multivalent binding at the –35 and –10 sites can buffer RNA polymerase (RNAP) kinetics against mutations and how promoters that bind overly tightly to RNA polymerase can inhibit gene expression. The success of our approach suggests that avidity represents a key physical principle governing the interaction of RNA polymerase to its promoter.
Solution Chemistry of Cyclotrigallazane: Supercritical Ammonia and Lewis Base Catalyzed Dehydrogenation To Produce Poly(imidogallane)

The polymeric hydrido gallium imide [HGaNH]n, or poly(imidogallane), was isolated as an intermediate in the conversion of cyclotrigallazane, [H2GaNH2]3, to gallium nitride in supercritical ammonia. Poly(imidogallane) can be converted to nanocrystalline GaN via solid-state pyrolysis or by extended thermolysis in supercritical ammonia. Characterization by IR spectroscopy, elemental analysis, and X-ray and electron diffraction suggests that the structure of poly(imidogallane) is a layered solid with a coherent length of approximately 15 nm. The interaction of [H2GaNH2]3 and various Lewis bases leads to the isolation of [HGaNH]n and gallane−Lewis base adducts, H3Ga·base, rather than the expected gallazane adducts, H2GaNH2·base. Experiments involving the use of ND3 resulted in the isolation of [H2GaND2]3 and suggest that the donor−acceptor complex H2Ga(NH2)(ND3) was present in solution. It was proposed that these gallazane−base adducts equilibrate via a ligand redistribution reaction and that the formation of ...
Synthetic Utility of Organometallic Reagents Derived from Group IV Metal Tetrachlorides and CH3Li. A Direct Synthesis of 2-(2-Keto-1-alkylidene)tetrahydropyrroles from 4-Alkynylamines and Acyl Cyanides

The non-Cp-bearing titanium alkyls (CH3)2TiCl2·L2 (1a) and (CH3)2Ti(OTFE)Cl·L2 (1b) and their Zr(IV) analogues have been shown to mediate efficient aminoalkyne cyclizations to provide azatitanium intermediates that undergo facial C-acylation in the presence of acyl cyanides.
Edge-Bridged Octahedral Tungsten−Oxygen−Chlorine Clusters: Synthesis and Characterization of Two D3d-Symmetric [W6O6Cl12]2- Isomers and [W6O7Cl11]3-

Initial access to the chemistry of hexanuclear tungsten oxohalide clusters is provided through the reduction of WOCl4 with bismuth metal at 360 °C. Reactions targeting W6O6Cl10 produce an amorphous black solid, which, upon treatment with concentrated aqueous HCl, releases the edge-bridged octahedral cluster [α-W6O6Cl12]2- into solution. The cluster exhibits a D3d-symmetry structure in which the six oxygen atoms bridge the edges between two opposing triangular faces of a trigonally compressed W6 octahedron. Reactions incorporating additional bismuth metal yield a mixture of soluble clusters, including a 5:7 ratio of [α-W6O6Cl12]2- and another D3d-symmetry isomer, [β-W6O6Cl12]2-. The latter species displays a different core structure, in which the six oxygen atoms are situated on the edges comprising two opposing triangular faces of a trigonally elongated W6 octahedron. Isolated as the BuN+ salts, the two isomers can be separated by a process relying on the differences in crystal morphology. Cyclic voltamme...
Phenotypic plasticity promotes recombination and gene clustering in periodic environments.

While theory offers clear predictions for when recombination will evolve in changing environments, it is unclear what natural scenarios can generate the necessary conditions. The Red Queen hypothesis provides one such scenario, but it requires antagonistic host–parasite interactions. Here we present a novel scenario for the evolution of recombination in finite populations: the genomic storage effect due to phenotypic plasticity. Using analytic approximations and Monte-Carlo simulations, we demonstrate that balanced polymorphism and recombination evolve between a target locus that codes for a seasonally selected trait and a plasticity modifier locus that modulates the effects of target-locus alleles. Furthermore, we show that selection suppresses recombination among multiple co-modulated target loci, in the absence of epistasis among them, which produces a cluster of linked selected loci. These results provide a novel biological scenario for the evolution of recombination and supergenes. Selection for recombination requires genetic diversity and negative linkage disequilibrium, which can be produced by coevolutionary arms races. Here the authors propose a qualitatively different scenario that can favour recombination in seasonal environments through the ‘genomic storage effect’.
4-ALKOXYCARBONYL, 4-ALKYLTHIOCARBONYL AND 5-ALKOXYCARBONYLOXY DERIVATIVES OF 1-SUBSTITUTED-3-METHYLPYRAZOL-5-ONES

The reaction of 1-substituted-3-methylpyrazol-5-ones 1 with alkyl chloroformates and calcium hydroxide in dioxane have been studied. With 1-phenyl-3-methylpyrazol-5-one, the isolated product was alkyl 3-methyl-5-oxo-1-phenylpyrazole-4-carboxylate 2 but with 1-alkyl-3-methylpyrazol-5-one formation of 1-alkyl-5-alkoxycarbonyloxy-3-methylpyrazole 3 was observed. Replacement of alkyl chloroformate by bis(alkoxythiocarbonyl) sulfide results in the formation of 4-alkoxythiocarbonyl derivatives 4 in low yield with both 1-substituted-3-methylpyrazol-5-ones.
First synthesis of enantiopure 1,6-difunctionalized dodecahydrobenz[f]indenes.

An enantiospecific route to the previously unreported 1,6-difunctionalized dodecahydrobenz[f]indene ring system is described. Optically pure Hajos−Parrish ketone is used as the building block for preparation of a 6-methyleneinden-5-ol. This allylic alcohol is then utilized in a Claisen rearrangement under Johnson's conditions to introduce a side chain that is further modified and cyclized to produce the benz[f]indene ring system.
Sperm should evolve to make female meiosis fair.

Genomic conflicts arise when an allele gains an evolutionary advantage at a cost to organismal fitness. Oogenesis is inherently susceptible to such conflicts because alleles compete for inclusion into the egg. Alleles that distort meiosis in their favor (i.e. meiotic drivers) often decrease organismal fitness, and therefore indirectly favor the evolution of mechanisms to suppress meiotic drive. In this light, many facets of oogenesis and gametogenesis have been interpreted as mechanisms of protection against genomic outlaws. That females of many animal species do not complete meiosis until after fertilization, appears to run counter to this interpretation, because this delay provides an opportunity for sperm-acting alleles to meddle with the outcome of female meiosis and help like alleles drive in heterozygous females. Contrary to this perceived danger, the population genetic theory presented herein suggests that, in fact, sperm nearly always evolve to increase the fairness of female meiosis in the face of genomic conflicts. These results are consistent with the apparent sperm dependence of the best characterized female meiotic drivers in animals. Rather than providing an opportunity for sperm collaboration in female meiotic drive, the ‘fertilization requirement’ indirectly protects females from meiotic drivers by providing sperm an opportunity to suppress drive.
Thermolysis of pentasubstituted 3‐hydroxy‐1,2‐dioxolanes

A series of pentasubstituted 3-hydroxy-1,2-dioxolanes, 1a-e, was synthesized by oxygen trapping of β-keto radicals formed during α-azo hydroperoxide decomposition. Thermolysis of the pentasubstituted 3-hydroxy-1,2-dioxolanes (hemiperketals) in benzene proceeded cleanly and yielded pairs of ketones and carboxylic acids. Two of the hemiperketals yielded only one pair of products while the others produced two sets of products. One of each pair of fragmentation products had undergone skeletal rearrangement. Only methyl migrations were observed when in cnmpetition with phenyl groups from the same position
Female Genetic Contributions to Sperm Competition in Drosophila melanogaster .

In many species, sperm can remain viable in the reproductive tract of a female well beyond the typical interval to remating. This creates an opportunity for sperm from different males to compete for oocyte fertilization inside the female’s reproductive tract. In Drosophila melanogaster, sperm characteristics and seminal fluid content affect male success in sperm competition. On the other hand, although genome-wide association studies (GWAS) have demonstrated that female genotype plays a role in sperm competition outcome as well, the biochemical, sensory, and physiological processes by which females detect and selectively use sperm from different males remain elusive. Here, we functionally tested 26 candidate genes implicated via a GWAS for their contribution to the female’s role in sperm competition, measured as changes in the relative success of the first male to mate (P1). Of these 26 candidates, we identified eight genes that affect P1 when knocked down in females, and showed that five of them do so when knocked down in the female nervous system. In particular, Rim knockdown in sensory pickpocket (ppk)+ neurons lowered P1, confirming previously published results, and a novel candidate, caup, lowered P1 when knocked down in octopaminergic Tdc2+ neurons. These results demonstrate that specific neurons in the female’s nervous system play a functional role in sperm competition and expand our understanding of the genetic, neuronal, and mechanistic basis of female responses to multiple matings. We propose that these neurons in females are used to sense, and integrate, signals from courtship or ejaculates, to modulate sperm competition outcome accordingly.
Synthesis of Pseudopterane Analogues by Intramolecular SE2' Cyclization.

Intramolecular Barbier-type additions of allylmetal intermediates derived from the allylic halides 13 and 14 and the allylic acetate 18 to aldehydes were examined as possible routes to pseudopterolide natural products. The halides cyclized upon treatment with SnCl2 or CrCl2 to afford a mixture of diastereomeric products 16a−d. In contrast, the acetate 18 afforded largely the 1,7-syn products 16a and 16b upon treatment with 5 mol % Pd(PPh3)4 and Et2Zn. When InI was employed in place of the Et2Zn, the syn,trans product 16a was formed exclusively. This intermediate was converted to the syn,cis- and syn,trans-butenolides 24 and 26. In the latter case, thermolysis of the tert-butyl ester at 210 °C followed by esterification with TMSCHN2 gave the methyl ester 35, an analogue of pseudopterolide.
Intramolecular hydroamination of conjugated enynes

An intramolecular hydroamination of conjugated enyne was developed using commercially available n-BuLi as a precatalyst. This hydroamination reaction led to products with allene and pyrrolidine functional groups. One of the enyne hydroamination products was successfully converted to natural products irniine and irnidine in three steps. The scope and mechanism of the enyne hydroamination are also discussed.
Microwave-assisted synthesis of mGluR1 ligands: carbon, nitrogen and oxygen linked derivatives of pyrido[3,4-d]pyrimidin-4-ylamines

The syntheses of 6-fluoropyrido[3,4-d]pyrimidin-4-ylamine derivatives is reported herein. Methods for generating C, N and O linked analogues under microwave irradiation are described.
Enantio- and diastereoselective addition of thioacetic acid to nitroalkenes via N-sulfinyl urea catalysis

The enantioselective addition of thioacetic acid to nitroalkenes was achieved using N-sulfinyl urea catalysis. In this report, the scope of the reaction was extended to the enantio- and diastereoselective thioacetic acid addition to cyclic α,β-disubstituted nitroalkenes. Additionally, the role of the sulfinyl group was investigated by replacing it with a variety of aryl and sulfonyl groups. Of 15 urea catalysts synthesized and tested, none displayed comparable selectivity to the sulfinyl catalysts, highlighting the importance of the sulfinyl group in attaining high enantioselectivity in the thioacetic acid addition.
Mesoporous silica supports for improved thermal stability in supported Au catalysts

In this work, we present a comprehensive review of our research on the role of mesoporous silica pore architecture, composition of the pore walls (addition of Co or Al), and silica surface chemistry (surface modification by TiO2) to improve the hydrothermal stability of Au particles. We have found that mesoporous silica architecture plays an important role in improving Au stability, with three dimensional mesoporous architectures being less effective than one dimensional (1-D) pores. The tortuous 1-D pores in aerosol silica were found to be most effective at controlling Au particle size. Since Au particles continue to grow larger than the pore diameter, we conclude that Ostwald ripening must be the dominant sintering pathway for these Au catalysts. These catalysts are active for CO oxidation even after the Au particles have grown large enough to block the pores, suggesting that the thin walls of mesoporous silica provide easy access to gas phase molecules. Further improvements in Au stability and reactivity were obtained by surface modification of the aerosol and MCM-41 silica with TiO2. After TiO2 modification of the silica, the Au particles remained smaller than the pore size (< 3 nm) even after three cycles of CO oxidation at temperatures up to 400 °C.
Dendrimeric molecular transporters: synthesis and evaluation of tunable polyguanidino dendrimers that facilitate cellular uptake.

Nine fluorescently labeled structurally varied polyguanidino dendrimers based on diamino acid monomeric units were individually synthesized in an efficient, scalable sequence using a trifluoroaceta...
The Value of Price Discrimination in Large Random Networks

We study the value of price discrimination in large random networks. Recent trends in industry suggest that increasingly firms are using information about social network to offer personalized prices to individuals based upon their positions in the social network. In the presence of positive network externalities, firms aim to increase their profits by offering discounts to influential individuals that can stimulate consumption by other individuals at a higher price. However, the lack of transparency in discriminative pricing can reduce consumer satisfaction and create mistrust. Recent research has focused on the computation of optimal prices in deterministic networks under positive externalities. We would like to answer the question: how valuable is such discriminative pricing? We find, surprisingly, that the value of such pricing policies (increase in profits due to price discrimination) in very large random networks are often not significant. We provide the exact rates at which this value grows in the size of the random networks for different ranges of network densities.
Synthesis and crystal structure of LiCaGaN2

Abstract The quaternary nitride LiCaGaN2 was synthesized from the elements and an excess of sodium and gallium at 900 ° C in a sealed niobium tube. LiCaGaN2 is colorless and crystallizes in the monoclinic space group P 2 1 / c ( Z = 4 ) with a = 5.790 ( 1 ) , b = 6.969 ( 1 ) , c = 5.895 ( 1 ) A; β = 90.037 ( 5 ) ° . The structure contains the nitridogallate species | ∞ 2 Ga2N2N4/2, which is formed by condensing edge-sharing GaN4 tetrahedral pairs.
Co-culture and biogeography of Prochlorococcus and SAR11.

Prochlorococcus and SAR11 are among the smallest and most abundant organisms on Earth. With a combined global population of about 2.7 × 1028 cells, they numerically dominate bacterioplankton communities in oligotrophic ocean gyres and yet they have never been grown together in vitro. Here we describe co-cultures of Prochlorococcus and SAR11 isolates representing both high- and low-light adapted clades. We examined: (1) the influence of Prochlorococcus on the growth of SAR11 and vice-versa, (2) whether Prochlorococcus can meet specific nutrient requirements of SAR11, and (3) how co-culture dynamics vary when Prochlorococcus is grown with SAR11 compared with sympatric copiotrophic bacteria. SAR11 grew 15–70% faster in co-culture with Prochlorococcus, while the growth of the latter was unaffected. When Prochlorococcus populations entered stationary phase, this commensal relationship rapidly became amensal, as SAR11 abundances decreased dramatically. In parallel experiments with copiotrophic bacteria; however, the heterotrophic partner increased in abundance as Prochlorococcus densities leveled off. The presence of Prochlorococcus was able to meet SAR11’s central requirement for organic carbon, but not reduced sulfur. Prochlorococcus strain MIT9313, but not MED4, could meet the unique glycine requirement of SAR11, which could be due to the production and release of glycine betaine by MIT9313, as supported by comparative genomic evidence. Our findings also suggest, but do not confirm, that Prochlorococcus MIT9313 may compete with SAR11 for the uptake of 3-dimethylsulfoniopropionate (DMSP). To give our results an ecological context, we assessed the relative contribution of Prochlorococcus and SAR11 genome equivalents to those of identifiable bacteria and archaea in over 800 marine metagenomes. At many locations, more than half of the identifiable genome equivalents in the euphotic zone belonged to Prochlorococcus and SAR11 – highlighting the biogeochemical potential of these two groups.
Further Definition of the D1 Dopamine Receptor Pharmacophore: Synthesis of trans-6,6a,7,8,9,13b-Hexahydro-5H-benzo[d]naphth[2,1-b]azepines as Rigid Analogues of β-Phenyldopamine

In an effort to define further the active geometry of the beta-phenyldopamine pharmacophore of certain dopamine D1 agonists, the title compounds have been synthesized as conformationally restricted homologues of the potent benzophenanthridine dopamine D1 agonist dihydrexidine 4a. The dihydroxy secondary amine 5b was evaluated as a potential agonist, whereas the N-methyl compounds 5a and 5c were hypothesized to be antagonists. Surprisingly, none of the three compounds had high affinity for dopamine D1 or D2 receptors. A comparison of the low-energy conformations of these molecules shows that the pendant phenyl ring of 5b is twisted about 28 degrees relative to that of the corresponding ring of 4a. Further, the additional methylene used to expand the C ring of 5b projects toward the alpha face of the molecule, perhaps suggesting that steric protrusion in this region of the molecule is not tolerated. Finally, the phenethylamine fragment incorporated into these molecules deviates about 30 degrees from the antiperiplanar conformation postulated to be necessary for agonist activity. On the other hand, the potential antagonist molecules 5a and 5c were compared with the dopamine D1 antagonist SCH 39166 2. The conformations of the former two structures differ quite dramatically from that of 2. The most notable differences lie in the relative orientations of the pendant phenyl rings in the two series, as well as the fact that the ethylamine fragment in 2 approximates a gauche conformation, while the comparable orientation in 5a and 5c more nearly approaches an antiperiplanar conformation. These findings will be used to refine further the model of the dopamine D1 agonist receptor that we have previously developed.
PROBING THE DENSITY DEPENDENCE OF SYMMETRY ENERGY AT SUBSATURATION DENSITY WITH HICs

The reaction mechanism of the central collisions and peripheral collisions for 112,124Sn + 112,124Sn at E/A = 50 MeV is investigated within the framework of the Improved Quantum Molecular Dynamics model. The results show that multifragmentation process is an important mechanism at this energy region, and the influence of the cluster emission on the double n/p ratios and the isospin transport ratio is important. Furthermore, three observables, double n/p ratios, isospin diffusion and the rapidity distribution of the ratio R7 for 112,124Sn+112,124Sn at E/A = 50 MeV are analyzed with the Improved Quantum Molecular Dynamics model. The results show that these three observables are sensitive to the density dependence of the symmetry energy. By comparing the calculation results to the data, the consistent constraint on the density dependence of the symmetry energy from these three observables is obtained.
Reductive amination using ammonia borane

Abstract A variety of primary, secondary, and tertiary amines were prepared in 84–95% yields using ammonia borane for the reductive amination of aldehydes and ketones in the presence of titanium isopropoxide.
Recent highlights in electrophilic fluorination with 1-chloromethyl-4-fluoro- 1,4-diazoniabicyclo[2.2.2]octane bis(tetrafluoroborate).

Synthetic and structural aspects of organofluorine compounds continue to be the focal points of vigorous research activities, as evidenced by the appearance of a large number of publications. Among the various useful methodologies for the introduction of fluorine into organic molecules, electrophilic fluorination is a promising and exciting area of research. While a variety of electrophilic fluorinating reagents are available, currently 1-chloromethyl-4-fluoro-1,4-diazoniabicyclo[2.2.2]octane bis(tetrafluoroborate) (Selectfluor) provides a remarkably straightforward and effective route. The breadth of applications realizable from this reagent in its role as a key electrophilic fluorinating reagent is highlighted here. This Account covers the literature for electrophilic fluorination reactions that employ Selectfluor during the period January 1999−January 2003.
Asymmetric addition of grignard reagents to chiral 1-acylpyridinium salts: A chiral auxiliary study

Abstract Various cyclohexyl-based chiral auxiliaries were studied for their effectiveness in the chiral 1-acylpyridinium salt/Grignard reaction.
Electrochemical Charge Transfer to Diamond and Other Materials

The oxygen redox couple in adsorbed water films acts as an “electrochemical ground” that tends to pin the Fermi level in solids at the electrochemical potential of the redox couple. We discuss this effect on the conductivity of diamond; the conductivity type of sp2-based carbons including single-walled, semiconducting carbon nanotubes and graphene; the photoluminescence of GaN and ZnO; and the contact charging of metals.
Synthesis and preliminary biological evaluation of 5-fluoro-5,8-dideazaisoaminopterin

The new folate antagonist, 5-fluoro-5,8-dideazaisoaminopterin was synthesized in four steps beginning with 2,4-diamino-5-fluoroquinazoline. It was found to be a potent inhibitor of human dihydrofolate reductase. Against L1210 leukemia in mice, 5-fluoro-5,8-dideazaisoaminopterin was equiactive with methotrexate at approximately one half of the total dose employed.
Regioselective Nucleophilic Addition to Pyridinium Salts: A New Route to Substituted Dihydropyridones

The regioselective addition of nucleophiles to pyridinium salts generates an intermediate enol-ether, which can be hydrolyzed in situ to provide a range of dihydropyridones. Certain Grignards have shown inherent differences in the regioselectivity of addition to these salts, and this difference can be tuned to give single regioisomeric addition products. The dihydropyridone products can be further manipulated in many ways using standard transformations.
Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates.

Motivation A key component in many RNA-Seq-based studies is contrasting multiple replicates from different experimental conditions. In this setup, replicates play a key role as they allow to capture underlying biological variability inherent to the compared conditions, as well as experimental variability. However, what constitutes a 'bad' replicate is not necessarily well defined. Consequently, researchers might discard valuable data or downstream analysis may be hampered by failed experiments. Results Here we develop a probability model to weigh a given RNA-Seq sample as a representative of an experimental condition when performing alternative splicing analysis. We demonstrate that this model detects outlier samples which are consistently and significantly different compared with other samples from the same condition. Moreover, we show that instead of discarding such samples the proposed weighting scheme can be used to downweight samples and specific splicing variations suspected as outliers, gaining statistical power. These weights can then be used for differential splicing (DS) analysis, where the resulting algorithm offers a generalization of the MAJIQ algorithm. Using both synthetic and real-life data, we perform an extensive evaluation of the improved MAJIQ algorithm in different scenarios involving perturbed samples, mislabeled samples, same condition groups, and different levels of coverage, showing it compares favorably to other tools. Overall, this work offers an outlier detection algorithm that can be combined with any splicing pipeline, a generalized and improved version of MAJIQ for DS detection, and evaluation metrics with matching code and data for DS algorithms. Availability and implementation Software and data are accessible via majiq.biociphers.org/norton_et_al_2017/. Contact yosephb@upenn.edu. Supplementary information Supplementary data are available at Bioinformatics online.
The metabolites NADP+ and NADPH are the targets of the circadian protein Nocturnin (Curled).

Nocturnin (NOCT) is a rhythmically expressed protein that regulates metabolism under the control of circadian clock. It has been proposed that NOCT deadenylates and regulates metabolic enzyme mRNAs. However, in contrast to other deadenylases, purified NOCT lacks the deadenylase activity. To identify the substrate of NOCT, we conducted a mass spectrometry screen and report that NOCT specifically and directly converts the dinucleotide NADP+ into NAD+ and NADPH into NADH. Further, we demonstrate that the Drosophila NOCT ortholog, Curled, has the same enzymatic activity. We obtained the 2.7 A crystal structure of the human NOCT•NADPH complex, which revealed that NOCT recognizes the chemically unique ribose-phosphate backbone of the metabolite, placing the 2′-terminal phosphate productively for removal. We provide evidence for NOCT targeting to mitochondria and propose that NADP(H) regulation, which takes place at least in part in mitochondria, establishes the molecular link between circadian clock and metabolism. Nocturnin is a rhythmically expressed protein that regulates metabolism under the control of circadian clock proposed to function through the deadenylation of metabolic enzyme mRNAs. Here the authors show that Nocturnin and its fly homolog Curled catalyze the removal of 2′-phosphate from NADP+ and NADPH, providing a direct link to metabolic regulation.
THE KNOEVENAGEL CONDENSATION OF O,S- AND S,S-DIETHYL MALONATES AND ETHYL PYRUVATE

Abstract The Knoevenagel condensation of O,O-, O,S- and S,S-diethyl malonates with ethyl pyruvate is described. The elimination sequence in 2 and 6 is suppressed by the presence of ZnCl2.
Polyoxoanion Occluded within Modified MCM-41: Spectroscopy and Structure

Polyoxoanions have enormous potential as drug delivery hosts, as catalysts, as agents for sequestering nuclear waste heavy metals, and as luminescent materials for laser and optical devices applications. We report the encapsulation of the polyoxoanion [Eu(H2O)3(α-1- P2W17O61)]7- within Mobil crystalline material (MCM)-41. For proper host−guest interaction, it was necessary to functionalize the surface walls of MCM-41 through use of a silylation reagent, specifically, (aminopropyl)triethoxysilane. A stable and integrated [Eu(H2O)3(α-1-P2W17O61)]7- polyoxoanion was shown to be formed inside the channels of modified MCM-41. X-ray diffraction, 29Si magic angle spinning (MAS) NMR, UV−vis absorption, emission and excitation spectra, and Raman scattering measurements have been used to structurally characterize the various products. Cross-polarization 29Si MAS NMR has been shown to better reveal the surface structural character of the modified MCM-41 than does regular 29Si MAS NMR. We find (when compared to bulk ...
Acid-Catalyzed Ring-Opening Isomerizations of Cyclopropenes

Acid-catalyzed cyclopropene cycloisomerizations are discussed as a means to generate ring systems. Herein, the recent results obtained in our group are contrasted with previous examples in the literature. Particular emphasis is placed on the mode of activation which, for our case, results in a different ring-opening mechanism than previously observed. The potential of the method as a tool for organic chemists is demonstrated by the synthesis of a host of benzo-fused heteroaromatic and heterobiaryl products.
Structure and properties of NaxM2SbO6·yH2O, M=Co(III), Ni(III) honeycomb oxyhydrates

Abstract The oxyhydrates Na 0.85 Co 2 SbO 6 ·1.7H 2 O and Na 0.95 Ni 2 SbO 6 ·1.5H 2 O were prepared by Br 2 oxidation of Na 3 Co 2 SbO 6 and Na 3 Ni 2 SbO 6 and exposure to ambient air. Their composition and structure are characterized by thermogravimetric analysis, elemental analysis and powder X-ray diffraction. Both form monolayer hydrates with metal cations (Co or Ni) near the 3+ oxidation state. In the parent materials, MO 6 octahedra surround SbO 6 units, forming a honeycomb geometry; Rietveld refinement of the hydrate phases indicate that this motif is retained. Magnetic susceptibility plots display paramagnetic behavior and Curie–Weiss fits support the 3+ oxidation state (low spin d 6 s =0 for Co and low spin d 7 s =1/2 for Ni). Close inspection of the Ni hydrate’s susceptibility reveals a feature at 6.2 K and a non-linear magnetization at 2 K with no saturation up to 9 T. Heat capacity measurements show a large amount of excess entropy in the Ni hydrate in the 2–20 K temperature range, while the heat capacity of the Co hydrate can be described by a simple lattice contribution. The Ni hydrate sample is easily dehydrated by heating above 100 °C and forms a new Na-deficient phase, Na 0.95 Ni 2 SbO 6 , which is stable at room temperature. Magnetic susceptibility of this phase is consistent with the Ni atom remaining in the 3+ oxidation state after dehydration.
Stereoselective synthesis of carbocyclic L-4'-fluoro-2',3'-dideoxyadenosine

l-(1‘S,3‘S)-9-[3-Fluoro-3-(hydroxymethyl)cyclopentan-1-yl]adenine 15 has been synthesized from ester 2, which can be conveniently prepared from 2,3-isopropylidene-d-glyceraldehyde 1 in six steps. The key ring closure has been accomplished through an intramolecular nucleophilic substitution reaction.
Zirconocene-Mediated Cyclization of 2-Bromo α,ω-Dienes

When it is first treated with n-butyllithium at −78 °C, zirconocene dichloride is an effective reagent for the cyclization of some 2-bromo α,ω-dienes at 25 °C. The products are carbo- and heterocyclic five-membered rings with adjacent methylene and methyl substituents. Reductive cyclization to form zirconacyclopentanes, followed by β-bromo elimination, is indicated as the order of steps in the reaction mechanism. Use of catalytic zirconocene dichloride with excess butylmagnesium chloride in diethyl ether at 25 °C is effective only for cyclization of 2-bromo-1,6-heptadiene.
Boundary behavior of solutions of elliptic operators in divergence form with a BMO anti-symmetric part

In this article, we investigate the boundary behavior of solutions of divergence-form operators with an elliptic symmetric part and a BMO antisymmetric part. Our results will hold in non-tangential...
A generative model of words and relationships from multiple sources

Neural language models are a powerful tool to embed words into semantic vector spaces. However, learning such models generally relies on the availability of abundant and diverse training examples. In highly specialised domains this requirement may not be met due to difficulties in obtaining a large corpus, or the limited range of expression in average use. Such domains may encode prior knowledge about entities in a knowledge base or ontology. We propose a generative model which integrates evidence from diverse data sources, enabling the sharing of semantic information. We achieve this by generalising the concept of co-occurrence from distributional semantics to include other relationships between entities or words, which we model as affine transformations on the embedding space. We demonstrate the effectiveness of this approach by outperforming recent models on a link prediction task and demonstrating its ability to profit from partially or fully unobserved data training labels. We further demonstrate the usefulness of learning from different data sources with overlapping vocabularies.
Gap Amplification for Small-Set Expansion via Random Walks.

In this work, we achieve gap amplification for the Small-Set Expansion problem. Specifically, we show that an instance of the Small-Set Expansion Problem with completeness epsilon and soundness 1/2 is at least as difficult as Small-Set Expansion with completeness epsilon and soundness f(epsilon), for any function f(epsilon) which grows faster than (epsilon)^(1/2). We achieve this amplification via random walks--the output graph corresponds to taking random walks on the original graph. An interesting feature of our reduction is that unlike gap amplification via parallel repetition, the size of the instances (number of vertices) produced by the reduction remains the same.
A lower bound for the nodal sets of Steklov eigenfunctions

We consider the lower bound of nodal sets of Steklov eigenfunctions on smooth Riemannian manifolds with boundary--the eigenfunctions of the Dirichlet-to-Neumann map. Let $N_\lambda$ be its nodal set. Assume that zero is a regular value of Steklov eigenfunctions. We show that $$H^{n-1}(N_\lambda)\geq C\lambda^{\frac{3-n}{2}}$$ for some positive constant $C$ depending only on the manifold.
Robust Actor-Critic Contextual Bandit for Mobile Health (mHealth) Interventions

We consider the actor-critic contextual bandit for the mobile health (mHealth) intervention. State-of-the-art decision-making algorithms generally ignore the outliers in the data-set. In this paper, we propose a novel robust contextual bandit method for the mHealth. It can achieve the conflicting goal of reducing the influence of outliers, while seeking for a similar solution compared with the state-of-the-art contextual bandit methods on the datasets without outliers. Such performance relies on two technologies: (1) the capped-L2 norm; (2) a reliable method to set the threshold hyper-parameter, which is inspired by one of the most fundamental techniques in the statistics. Although the model is non-convex and non-differentiable, we propose an effective reweighted algorithm and provide solid theoretical analyses. We prove that the proposed algorithm can sufficiently decrease the objective function value at each iteration and will converge after a finite number of iterations. Extensive experiment results on two datasets demonstrate that our method can achieve almost identical results compared with state-of-the-art contextual bandit methods on the dataset without outliers, and significantly outperform those state-of-the-art methods on the badly noised dataset with outliers in a variety of parameter settings.
Negative energy blowup results for the focusing Hartree hierarchy via identities of virial and localized virial type

AbstractWe establish virial and localized virial identities for solutions to the Hartree hierarchy, an infinite system of partial differential equations which arises in mathematical modeling of man...
Linear network coding capacity region of the smart repeater with broadcast erasure channels

This work considers the smart repeater network where a single source s wants to send two independent packet streams to destinations {d 1 , d 2 } with the help of relay r. The transmission from s or r is modeled by packet erasure channels: For each time slot, a packet transmitted by s may be received, with some probabilities, by a random subset of {d 1 , d 2 , r}; and those transmitted by r will be received by a random subset of {d 1 , d 2 }. Interference is avoided by allowing at most one of {s, r} to transmit in each time slot. One example of this model is any cellular network that supports two cell-edge users when a relay in the middle uses the same downlink resources for throughput/safety enhancement. In this setting, we study the capacity region of (R 1 , R 2 ) when allowing linear network coding (LNC). The proposed LNC inner bound introduces more advanced packing-mixing operations other than the previously well-known butterfly-style XOR operation on overheard packets of two co-existing flows. A new LNC outer bound is derived by exploring the inherent algebraic structure of the LNC problem. Numerical results show that, with more than 85% of the experiments, the relative sum-rate gap between the proposed outer and inner bounds is smaller than 0.08%, thus effectively bracketing the LNC capacity of the smart repeater problem.
Diagnosing Forward Operator Error Using Optimal Transport

We investigate overdetermined linear inverse problems for which the forward operator may not be given accurately. We introduce a new tool called the structure, based on the Wasserstein distance, and propose the use of this to diagnose and remedy forward operator error. Computing the structure turns out to use an easy calculation for a Euclidean homogeneous degree one distance, the Earth Mover’s Distance, based on recently developed algorithms. The structure is proven to distinguish between noise and signals in the residual and gives a plan to help recover the true direct operator in some interesting cases. We expect to use this technique not only to diagnose the error, but also to correct it, which we do in some simple cases presented below.
SMCQL: secure querying for federated databases

People and machines are collecting data at an unprecedented rate. Despite this newfound abundance of data, progress has been slow in sharing it for open science, business, and other data-intensive endeavors. Many such efforts are stymied by privacy concerns and regulatory compliance issues. For example, many hospitals are interested in pooling their medical records for research, but none may disclose arbitrary patient records to researchers or other healthcare providers. In this context we propose the Private Data Network (PDN), a federated database for querying over the collective data of mutually distrustful parties. In a PDN, each member database does not reveal its tuples to its peers nor to the query writer. Instead, the user submits a query to an honest broker that plans and coordinates its execution over multiple private databases using secure multiparty computation (SMC). Here, each database's query execution is oblivious, and its program counters and memory traces are agnostic to the inputs of others.We introduce a framework for executing PDN queries named smcql. This system translates SQL statements into SMC primitives to compute query results over the union of its source databases without revealing sensitive information about individual tuples to peer data providers or the honest broker. Only the honest broker and the querier receive the results of a PDN query. For fast, secure query evaluation, we explore a heuristics-driven optimizer that minimizes the PDN's use of secure computation and partitions its query evaluation into scalable slices.
Introspective perception: Learning to predict failures in vision systems

As robots aspire for long-term autonomous operations in complex dynamic environments, the ability to reliably take mission-critical decisions in ambiguous situations becomes critical. This motivates the need to build systems that have situational awareness to assess how quali ed they are at that moment to make a decision. We call this self-evaluating capability as introspection. In this paper, we take a small step in this direction and propose a generic framework for introspective behavior in perception systems. Our goal is to learn a model to reliably predict failures in a given system, with respect to a task, directly from input sensor data. We present this in the context of vision-based autonomous MAV flight in outdoor natural environments, and show that it effectively handles uncertain situations.
Light Field Blind Motion Deblurring

We study the problem of deblurring light fields of general 3D scenes captured under 3D camera motion and present both theoretical and practical contributions. By analyzing the motion-blurred light field in the primal and Fourier domains, we develop intuition into the effects of camera motion on the light field, show the advantages of capturing a 4D light field instead of a conventional 2D image for motion deblurring, and derive simple analytical methods of motion deblurring in certain cases. We then present an algorithm to blindly deblur light fields of general scenes without any estimation of scene geometry, and demonstrate that we can recover both the sharp light field and the 3D camera motion path of real and synthetically-blurred light fields.
Local kernels and the geometric structure of data

Abstract We introduce a theory of local kernels, which generalize the kernels used in the standard diffusion maps construction of nonparametric modeling. We prove that evaluating a local kernel on a data set gives a discrete representation of the generator of a continuous Markov process, which converges in the limit of large data. We explicitly connect the drift and diffusion coefficients of the process to the moments of the kernel. Moreover, when the kernel is symmetric, the generator is the Laplace–Beltrami operator with respect to a geometry which is influenced by the embedding geometry and the properties of the kernel. In particular, this allows us to generate any Riemannian geometry by an appropriate choice of local kernel. In this way, we continue a program of Belkin, Niyogi, Coifman and others to reinterpret the current diverse collection of kernel-based data analysis methods and place them in a geometric framework. We show how to use this framework to design local kernels invariant to various features of data. These data-driven local kernels can be used to construct conformally invariant embeddings and reconstruct global diffeomorphisms.
Twists over étale groupoids and twisted vector bundles

Inspired by recent papers on twisted $K$-theory, we consider in this article the question of when a twist $\mathcal{R}$ over a locally compact Hausdorff groupoid $\mathcal{G}$ (with unit space a CW-complex) admits a twisted vector bundle, and we relate this question to the Brauer group of $\mathcal{G}$. We show that the twists which admit twisted vector bundles give rise to a subgroup of the Brauer group of $\mathcal{G}$. When $\mathcal{G}$ is an etale groupoid, we establish conditions (involving the classifying space $B\mathcal{G}$ of $\mathcal{G}$) which imply that a torsion twist $\mathcal{R}$ over $\mathcal{G}$ admits a twisted vector bundle.
Communication Lower Bounds for Matricized Tensor Times Khatri-Rao Product

The matricized-tensor times Khatri-Rao product (MTTKRP) computation is the typical bottleneck in algorithms for computing a CP decomposition of a tensor. In order to develop high performance sequential and parallel algorithms, we establish communication lower bounds that identify how much data movement is required for this computation in the case of dense tensors. We also present sequential and parallel algorithms that attain the lower bounds and are therefore communication optimal. In particular, we show that the structure of the computation allows for less communication than the straightforward approach of casting the computation as a matrix multiplication operation.