cssi/SciSciGPT-SciSciNet huggingface dataset:
Cis-regulatory basis of sister cell type divergence in the vertebrate retina.

Humans see the world through a light-sensitive tissue at the back of the eye called the retina, which is made up of three layers that each contain specific cell types. The layers form a circuit, with light-sensing photoreceptor cells in the outermost layer connected to bipolar cells in the middle layer, which connect to the brain via specialized cells in the innermost layer. Photoreceptors and bipolar cells share similar characteristics and are thought to be ‘sister cells’ which evolved from a common ancestral cell type. However, it is not well understood how these two cells types diverged during evolution. Every cell type has a specific role, which is largely determined by the set of genes that it switches on or off. Specialized regions of DNA, called enhancers, determine whether a gene is turned on or off in a particular cell type. In each cell, DNA strands are bundled together with proteins into a coiled structure known as chromatin. In some cells, a particular enhancer may be ‘shut down’ and rendered inactive on account of being tightly packed within chromatin. Whilst in other cells, the same enhancer may be ‘open’ and ready for action. For a given cell type, which genes are turned on is determined, in part, by which enhancers are open. One way to distinguish between cells is by examining how their chromatin is packaged to see which enhancers are open. Researchers have previously characterized the chromatin structure of photoreceptor cells, but the structure of chromatin in bipolar cells, and how it compares to that of photoreceptors, remained unknown. Now, Murphy et al. have examined the chromatin profile of bipolar cells from the mouse retina in order to gain a better understanding of how these two cell types may be evolutionarily related. The analysis revealed that although bipolar and photoreceptor cells switch on different sets of genes, the enhancers open in each cell type are very similar. Despite this similarity, Murphy et al. were able to detect subtle differences in short sequences of DNA, known as motifs, present in bipolar and photoreceptor enhancers. Further experiments showed that one of these motifs may be responsible for turning photoreceptor genes off in bipolar cells. This motif therefore appears to play a critical role in distinguishing photoreceptors from bipolar cells. This comparison of photoreceptor and bipolar cells has provided a possible mechanism whereby photoreceptor and bipolar cells diverged in evolution from a single common ancestral cell type. This insight may help explain how complex organisms with many cell types may have evolved from a single-cell ancestor long ago.
Chance-Constrained Unit Commitment With N-1 Security and Wind Uncertainty

As renewable wind energy penetration rates continue to increase, one of the major challenges facing grid operators is the question of how to control transmission grids in a reliable and a cost-efficient manner. The stochastic nature of wind forces an alteration of traditional methods for solving day-ahead and look-ahead unit commitment and dispatch. In particular, the variability of wind generation increases the risk of unexpected overloads and cascading events. To address these questions, we present an N-1 security and chance-constrained unit commitment (SCCUC) that includes models of generation reserves that respond to wind fluctuations and component outages. We formulate the SCCUC as a mixed-integer, second-order cone problem that limits the probability of failure. We develop a modified Benders decomposition algorithm to solve the problem to optimality and present detailed case studies on the IEEE RTS-96 three area and the IEEE 300 NESTA test systems. The case studies assess the economic impacts of contingencies and various degrees of wind power penetration and demonstrate the effectiveness and scalability of the algorithm.
Transient Hyperfine Magnetic Fields

Fast ions traversing magnetized materials experience very large transient hyperfine magnetic fields. The processes responsible for these interactions are related to the interchange of electrons between the moving ion and the polarized medium. The dependence of the transient hyperfine fields on the atomic number and the velocity of the ion, and on the magnetization of the host has been mapped for a wide range of nuclei and magnetic hosts. The experimental evidence supporting specific models will be presented and applications to the measurement of magnetic moments of short-lived excited states will be described.
Structural consequences of electron hyperdeficiency. Synthesis and crystal structure of an iron-cobalt metallocarborane having two closed polyhedra fused along an edge

Abstract : A metallocarborane of novel structure, (CH3)4C4B8H8FeCo(Eta to the 5th power -C5H5), has been synthesized and structurally characterized from FTNMR, mass spectroscopic, infrared, and single crystal X-ray diffraction data. The dark green crystals are monoclinic, space group P2 sub 1, with two molecules per unit cell and a = 7.203(4) A, b = 14.77(2) A, c = 8.830(2) A, and beta = 99.7(1) degrees. (rho calcd = 1.38 g/cc, rho obsd = 1.38 g/cc). The structure was solved by the heavy-atom method and refined by full-matrix least-squares procedures to a final R value of 0.069 and R sub W = 0.081 for the 1657 reflectionions. The molecule contains a direct iron-cobalt bond and consists of two pentagonal bipyramidal units fused at a common iron atom with an additional BH group capping triangular faces on both polyhedra simultaneously. The structure is explained in terms of a shortage of two electrons in the cage framework, relative to the normal requirement for polyhedral clusters, which causes one BH group to adopt a capping location. These results are discussed in relation to the known structures of two osmium carbonyls and a diiron metallocarborane.
Catalytic Enantioselective Nozaki−Hiyama Allylation Reaction with Tethered Bis(8-quinolinolato) (TBOx) Chromium Complex

The utility of the new class of chiral ligand, tethered bis(8-quinolinol) (TBOxH), is further explored. Its chromium complex, TBOxCr(III)Cl, effectively catalyzes the Nozaki−Hiyama allylation reactions of various aldehydes at room temperature with high yield (up to 95%) and high enantioselectivity (up to 99% ee). The scope of the present method is shown to be wide, and this method represents an efficient access to chiral homoallylic alcohols.
Genome sequence analysis of 91 Salmonella Enteritidis isolates from mice caught on poultry farms in the mid 1990s

Abstract A total of 91 draft genome sequences were used to analyze isolates of Salmonella enterica serovar Enteritidis obtained from feral mice caught on poultry farms in Pennsylvania. One objective was to find mutations disrupting open reading frames (ORFs) and another was to determine if ORF-disruptive mutations were present in isolates obtained from other sources. A total of 83 mice were obtained between 1995–1998. Isolates separated into two genomic clades and 12 subgroups due to 742 mutations. Nineteen ORF-disruptive mutations were found, and in addition, bigA had exceptional heterogeneity requiring additional evaluation. The TRAMS algorithm detected only 6 ORF disruptions. The sefD mutation was the most frequently encountered mutation and it was prevalent in human, poultry, environmental and mouse isolates. These results confirm previous assessments of the mouse as a rich source of Salmonella enterica serovar Enteritidis that varies in genotype and phenotype.
Synthesis of the tricyclic triamine core of martinelline and martinellic acid

Abstract The tricyclic triamine core27 of martinellic acid (2) has been prepared stereospecifically in eight steps from 2-hydroxymethylaniline in 11% overall yield. The key steps are the addition of 2-hydroxymethylaniline to vinylcyclopropane14 to prepare cycloaddition precursor19 in only two steps and an intramolecular [3+2] azomethine ylide cycloaddition reaction to produce tetracycle20 with>9:1 diastereoselectivity. Download : Download full-size image
Bohmian mechanics and consistent histories

Abstract The interpretations of a particular quantum gedanken experiment provided by Bohmian mechanics and consistent histories are shown to contradict each other, both in the absence and in the presence of a measuring device. The consistent histories result seems closer to standard quantum mechanics, and shows no evidence of the mysterious nonlocal influences present in the Bohmian description.
Exploring new reactive species for cyclopropanation

Abstract An organozinc species RXZnCH 2 I generated by reacting Zn(CH 2 I) 2 with RXH was found to be an efficient reagent for the cyclopropanation of olefins at room temperature. A 50.7% ee was obtained for the cyclopropanation of trans -β-methylstyrene when a chiral alcohol was used.
Pressure stabilized Se–Se dimer formation in PbSe2

Abstract The preparation of PbSe2 through the reaction of PbSe with excess Se at 4.5 GPa and 650 °C is reported. The crystal structure, determined from X-ray powder diffraction data (CuAl2 structure type, I4/mcm (#140), a = 6.42695(11) A, c = 7.70254(13) A, Z = 4), consists of layers of [Se2]2- dimers with Pb2+ in square antiprismatic coordination with Se. This is a rare crystal structure for divalent metal chalcogenides, previously only identified for SrS2 and BaTe2. Undoped PbSe2 as well as Bi3+- and Ag+-doped samples (10% Pb substitution) show semi-metallic resistivity down to 0.4 K. Magnetic susceptibility measurement of PbSe2 shows no magnetic ordering above 1.8 K. The Seebeck coefficients show nearly linear behavior from 35 to 400 K and the largest numerical values are found in the case of undoped PbSe2, + 99 μVK−1, and Bi3+-doped PbSe2, - 146 μVK−1, at the highest temperature measured, 400 K.
Restoring universality to the pinch-off of a bubble

The pinch-off of a bubble is an example of the formation of a singularity, exhibiting a characteristic separation of length and time scales. Because of this scale separation, one expects universal dynamics that collapse into self-similar behavior determined by the relative importance of viscous, inertial, and capillary forces. Surprisingly, however, the pinch-off of a bubble in a large tank of viscous liquid is known to be nonuniversal. Here, we show that the pinch-off dynamics of a bubble confined in a capillary tube undergo a sequence of two distinct self-similar regimes, even though the entire evolution is controlled by a balance between viscous and capillary forces. We demonstrate that the early-time self-similar regime restores universality to bubble pinch-off by erasing the system's memory of the initial conditions. Our findings have important implications for bubble/drop generation in microfluidic devices, with applications in inkjet printing, medical imaging, and synthesis of particulate materials.
An efficient synthesis of 4-substituted coumarin derivatives via a palladium-catalyzed Suzuki cross-coupling reaction

An efficient Pd-catalyzed Suzuki cross-coupling reaction of sterically crowded 4-chlorocoumarin derivatives with air- and moisture-stable potassium organotrifluoroborates is developed. This methodology has been used to generate a series of novel alkyl, aryl, and vinyl substituted coumarin derivatives in good to excellent yields. The twisted conformation of the vinyl groups in the X-ray crystal structures of (2-oxo-4-vinyl-2H-chromen-3-yl)methyl acetate (2) and (2-oxo-4-vinyl-2H-chromen-3-yl)methyl 2,2,2-trichloroacetimidate (3), along with the atropisomerism of 3-(hydroxymethyl)-4-(2-methoxyphenyl)-2H-chromen-2-one (1d), are evidence of the steric crowding in these adducts.
Insulin Receptor deletion in S100a4-lineage cells accelerates age-related bone loss.

Abstract Type I and Type II Diabetes dramatically impair skeletal health. Altered Insulin Receptor (IR) signaling is a common feature of both diseases, and insulin has potent bone anabolic functions. Several previous studies have demonstrated that loss of IR in bone cells results in disrupted bone homeostasis during early post-natal growth. Here we have deleted IR in S100a4-lineage cells (IRcKOS100a4) and assessed the effects on bone homeostasis in both young (15 weeks) and older adult (48 weeks) mice. S100a4-Cre has previously been shown to target the perichondrium during bone development, and here we show that S100a4 is expressed by adult trabecular and cortical bone cells, and that S100a4-Cre effectively targets adult bone, resulting in efficient deletion of IRβ. Deletion of IRβ in S100a4-lineage cells does not affect initial bone acquisition or homeostasis with no changes in cortical, trabecular or mechanical properties at 15-weeks of age, relative to wild type (WT) littermates. However, by 48-weeks of age, IRcKOS100a4 mice display substantial declines in trabecular bone volume, bone volume fraction and torsional rigidity, relative to age-matched WT controls. This work establishes the utility of using S100a4-cre to target bone and demonstrates that IRβ in S100a4-lineage cells is required for maintenance of bone homeostasis in adult mice.
Model studies on total synthesis of the chartellines, spirocyclic β-lactam alkaloids from a marine bryozoan

Abstract A chartelline alkaloid model system containing a spirocyclic β-lactam moiety and α,β-unsaturated imine has been constructed from isatin using a Staudinger imine–ketene cycloaddition and an addition to an N-activated γ-lactam as key steps.
An unusual selectivity in Pd catalyzed cross-coupling of terminal alkynes with “Unactivated” alkynes

Abstract The previous premise that a conjugating electron withdrawing group is required for the title reaction has been challenged and found to be incorrect.
Biochemical characterization of the methylmercaptopropionate: Cob(I)alamin Methyltransferase from Methanosarcina acetivorans

ABSTRACT Methanogenesis from methylated substrates is initiated by substrate-specific methyltransferases that generate the central metabolic intermediate methyl-coenzyme M. This reaction involves a methyl-corrinoid protein intermediate and one or two cognate methyltransferases. Based on genetic data, the Methanosarcina acetivorans MtpC (corrinoid protein) and MtpA (methyltransferase) proteins were suggested to catalyze the methylmercaptopropionate (MMPA):coenzyme M (CoM) methyl transfer reaction without a second methyltransferase. To test this, MtpA was purified after overexpression in its native host and characterized biochemically. MtpA catalyzes a robust methyl transfer reaction using free methylcob(III)alamin as the donor and mercaptopropionate (MPA) as the acceptor, with kcat of 0.315 s−1 and apparent Km for MPA of 12 μM. CoM did not serve as a methyl acceptor; thus, a second unidentified methyltransferase is required to catalyze the full MMPA:CoM methyl transfer reaction. The physiologically relevant methylation of cob(I)alamin with MMPA, which is thermodynamically unfavorable, was also demonstrated, but only at high substrate concentrations. Methylation of cob(I)alamin with methanol, dimethylsulfide, dimethylamine, and methyl-CoM was not observed, even at high substrate concentrations. Although the corrinoid protein MtpC was poorly expressed alone, a stable MtpA/MtpC complex was obtained when both proteins were coexpressed. Biochemical characterization of this complex was not feasible, because the corrinoid cofactor of this complex was in the inactive Co(II) state and was not reactivated by incubation with strong reductants. The MtsF protein, composed of both corrinoid and methyltransferase domains, copurifies with the MtpA/MtpC, suggesting that it may be involved in MMPA metabolism. IMPORTANCE Methylmercaptopropionate (MMPA) is an environmentally significant molecule produced by degradation of the abundant marine metabolite dimethylsulfoniopropionate, which plays a significant role in the biogeochemical cycles of both carbon and sulfur, with ramifications for ecosystem productivity and climate homeostasis. Detailed knowledge of the mechanisms for MMPA production and consumption is key to understanding steady-state levels of this compound in the biosphere. Unfortunately, the biochemistry required for MMPA catabolism under anoxic conditions is poorly characterized. The data reported here validate the suggestion that the MtpA protein catalyzes the first step in the methanogenic catabolism of MMPA. However, the enzyme does not catalyze a proposed second step required to produce the key intermediate, methyl coenzyme M. Therefore, the additional enzymes required for methanogenic MMPA catabolism await discovery.
Fine-Grained Spoiler Detection from Large-Scale Review Corpora

This paper presents computational approaches for automatically detecting critical plot twists in reviews of media products. First, we created a large-scale book review dataset that includes fine-grained spoiler annotations at the sentence-level, as well as book and (anonymized) user information. Second, we carefully analyzed this dataset, and found that: spoiler language tends to be book-specific; spoiler distributions vary greatly across books and review authors; and spoiler sentences tend to jointly appear in the latter part of reviews. Third, inspired by these findings, we developed an end-to-end neural network architecture to detect spoiler sentences in review corpora. Quantitative and qualitative results demonstrate that the proposed method substantially outperforms existing baselines.
How “Stable” Is Cyclobutyne? The Activation Energy for the Unimolecular Rearrangement to Butatriene

The barrier height for the disappearance of the singlet ground state of cyclobutyne has been investigated using ab initio molecular quantum mechanical methods. Stationary-point geometries were determined using the two-configuration self-consistent-field (TCSCF) method in conjunction with double zeta plus polarization (DZP) basis sets. The transition state exhibits strong biradical behavior. At the DZ+P TCSCF level, the classical barrier for unimolecular rearrangement to butatriene is 55 kcal/mol. With configuration interaction including all single and double excitations with respect to both TCSCF reference configurations, the classical barrier is reduced to 51 kcal/mol. Significant further lowerings in the cyclobutyne barrier occur when coupled cluster (CC) methods are applied
Synthesis, in vitro anti-breast cancer activity, and intracellular decomposition of amino acid methyl ester and alkyl amide phosphoramidate monoesters of 3'-azido-3'-deoxythymidine (AZT).

We report the synthesis and anticancer activity of a series of AZT phosphoramidate monoesters containing amino acid methyl ester (3a−11a) and N-alkyl amide (3b−11b, 9c−9f) moieties. The aromatic amino acid methyl esters were found to be more cytotoxic than the aliphatic analogues toward MCF-7 cells (human pleural effusion breast adenocarcinoma cell line). A marked stereochemical preference for the l-amino acid stereochemistry was also observed in MCF-7 cells. There was no consistent enhancement of cytotoxicity of the methyl amides over the corresponding methyl esters. AZT and the two AZT aromatic amino acid methyl ester phosphoramidates 8a and 9a were found to be more cytotoxic toward MCF-7 cells than to CEM cells (human T-cell lymphoblastic leukemia). The selective cytotoxicity toward MCF-7 cells may be associated with greater intracellular levels of phosphoramidate monoester and/or phosphorylated AZT.
TASI: A software tool for spatial-temporal quantification of tumor spheroid dynamics

Spheroid cultures derived from explanted cancer specimens are an increasingly utilized resource for studying complex biological processes like tumor cell invasion and metastasis, representing an important bridge between the simplicity and practicality of 2-dimensional monolayer cultures and the complexity and realism of in vivo animal models. Temporal imaging of spheroids can capture the dynamics of cell behaviors and microenvironments, and when combined with quantitative image analysis methods, enables deep interrogation of biological mechanisms. This paper presents a comprehensive open-source software framework for Temporal Analysis of Spheroid Imaging (TASI) that allows investigators to objectively characterize spheroid growth and invasion dynamics. TASI performs spatiotemporal segmentation of spheroid cultures, extraction of features describing spheroid morpho-phenotypes, mathematical modeling of spheroid dynamics, and statistical comparisons of experimental conditions. We demonstrate the utility of this tool in an analysis of non-small cell lung cancer spheroids that exhibit variability in metastatic and proliferative behaviors.
Recent Developments in the Synthesis of Bioactive 2,4,6-Trisubstituted 1,3,5-Triazines

1,3,5-Triazine derivatives have widespread applications in the pharmaceutical, material, and agrochemical industries. In the biological arena, small-molecule libraries of 2,4,6-trisubstituted 1,3,5-triazines have yielded selective and potent chemical probes for diverse protein families. The structural symmetry and ease of functionalization of the 1,3,5-triazine core renders it a powerful scaffold for the rapid generation of diverse molecular libraries. Numerous synthetic routes, both solid-phase and solution-phase, have been developed to arrive at alkyl/aryl amino- and oxy-substituted triazine libraries. Here, we feature a subset of the recent synthetic advances towards generating 2,4,6-trisubstituted 1,3,5-triazines and highlight biologically active compounds that have resulted from these endeavors.
An asymmetric synthesis of (+)-apogossypol hexamethyl ether

Abstract The first asymmetric synthesis of the gossypol backbone via a stereocontrolled oxazoline mediated 2,2′ Ullmann coupling has been achieved.
Novel anti-β-functionalized γ,δ-unsaturated amino acids via a thio–Claisen rearrangement

Abstract A significantly improved thio–Claisen rearrangement method was developed for preparing anti-β-functionalized γ,δ-unsaturated amino acids, which are extremely useful nonproteinogenic amino acids used in chemistry and biology research. The mild reaction condition successfully introduced base labile functional groups into the amino acids with excellent anti/syn selectivities.
Synthesis of Cribrostatin 6

The synthesis of cribrostatin 6 (1) is described. A regioselective bromination, a biaryl coupling, and an intramolecular cyclization are the key steps in the synthesis.
Isotropic Covariance Matrix Functions on Compact Two-Point Homogeneous Spaces

The covariance matrix function is characterized in this paper for a Gaussian or elliptically contoured vector random field that is stationary, isotropic, and mean square continuous on the compact two-point homogeneous space. Necessary and sufficient conditions are derived for a symmetric and continuous matrix function to be an isotropic covariance matrix function on all compact two-point homogeneous spaces. It is also shown that, for a symmetric and continuous matrix function with compact support, if it makes an isotropic covariance matrix function in the Euclidean space, then it makes an isotropic covariance matrix function on the sphere or the real projective space.
Gd7I12Zn: a group 12 atom in the octahedral Gd6 Cluster.

The title compound was synthesized from Gd, Gdl 3 and Zn under Ar atmosphere at 850 °C. It crystallizes in the space group R3 (No. 148) with lattice constants a = 15.686(1) A and c = 10.4882(8) A. The structure features isolated Zn-centered Gd 6 octahedra with all edges and corners capped by I atoms. The disorder of the Gd atoms is rationalized via electron microscopic techniques. A computational analysis using the extended Huckel method has been carried out in order to understand the bonding of this compound. The structure of isotypic La 7 l 12 Co is also remarked (a = 16.040(1) A and c = 10.905(2) A).
Transient activation of the UPRER is an essential step in the acquisition of pluripotency during reprogramming.

Somatic cells can be reprogrammed into pluripotent stem cells using the Yamanaka transcription factors. Reprogramming requires both epigenetic landscape reshaping and global remodeling of cell identity, structure, basic metabolic processes, and organelle form and function. We hypothesize that variable regulation of the proteostasis network and its influence upon the protein-folding environment within cells and their organelles is responsible for the low efficiency and stochasticity of reprogramming. We find that the unfolded protein response of the endoplasmic reticulum (UPRER), the mitochondrial UPR, and the heat shock response, which ensure proteome quality during stress, are activated during reprogramming. The UPRER is particularly crucial, and its ectopic, transient activation, genetically or pharmacologically, enhances reprogramming. Last, stochastic activation of the UPRER predicts reprogramming efficiency in naive cells. Thus, the low efficiency and stochasticity of cellular reprogramming are due partly to the inability to properly initiate the UPRER to remodel the ER and its proteome.
A6U3Sb2P8S32 (A = Rb, Cs): Quinary Uranium(IV) Thiophosphates Containing the [Sb(PS4)3]6– Anion

The reaction of A2S3/U/P2S5/S at 500 °C affords the quinary U(IV) thiophosphates A6U3Sb2P8S32 (A = Rb, Cs). These compounds contain {U3(PS4)2[Sb(PS4)3]2}6– layers separated by alkali metal cations. The layers are composed of trimeric uranium units connected to each other by the thiophosphato-antimonite anion, [Sb(PS4)3]6–. This unit contains a central Sb(III) cation bound by three [PS4]3– anions, creating a trigonal pyramidal environment around Sb(III). Each uranium cation is surrounded by eight sulfides in a distorted square antiprism that shares two edges with two other US8 units to form a trimeric [U3S18]24– cluster. Magnetic susceptibility measurements indicate that the close proximity of the U(IV) within these clusters leads to antiferromagnetic ordering at 53 K. Reflectance spectroscopy indicates that these compounds are semiconductors with a band gap of 1.48 eV.
Synthesis of (2-chlorophenyl)(phenyl)methanones and 2-(2-chlorophenyl)-1-phenylethanones by Friedel―Crafts acylation of 2-chlorobenzoic acids and 2-(2-chlorophenyl)acetic acids using microwave heating

Abstract Several 2-(2-chlorophenyl)-1-phenylethanones and (2-chlorophenyl)(phenyl)methanones were prepared by the Friedel–Crafts acylation reaction of 2-(2-chlorophenyl) acetic acids and 2-chlorocarboxylic acids, respectively, in the presence of cyanuric chloride, pyridine, and AlCl3 or FeCl3 using microwave heating. The yields of the ketones were significantly higher than those obtained using conventional heating. In addition, similar reactions carried out with the less inexpensive and less toxic FeCl3 gave titled ketones in comparable yields. Interestingly, the FeCl3 catalyzed reactions gave pure ketones (no chromatographic purification required), whereas the AlCl3 catalyzed reaction gave impure product that required chromatographic purification.
Bulk synthesis of iron-based superconductors

Abstract Exploratory synthesis efforts for iron-based superconductors (FeSCs) have been driven by hopes of improving superconducting critical temperatures ( T C s), providing high-quality samples for in-depth studies of intrinsic properties, and exploring potential superconductivity in similar families of materials. This manuscript summarizes the synthesis routes that are used for producing FeSC and their undoped parents, in single crystal and polycrystalline forms. A few of the materials challenges are summarized.
OMCD: OncomiR Cancer Database.

microRNAs (miRNAs) are crucially important in the development of cancer. Their dysregulation, commonly observed in various types of cancer, is largely cancer-dependent. Thus, to understand the tumor biology and to develop accurate and sensitive biomarkers, we need to understand pan-cancer miRNA expression. At the University of Minnesota, we developed the OncomiR Cancer Database (OMCD), hosted on a web server, which allows easy and systematic comparative genomic analyses of miRNA sequencing data derived from more than 9500 cancer patients tissue samples available in the Cancer Genome Atlas (TCGA). OMCD includes associated clinical information and is searchable by organ-specific terms common to the TCGA. Freely available to all users ( www.oncomir.umn.edu/omcd/ ), OMCD enables (1) simple visualization of TCGA miRNA sequencing data, (2) statistical analysis of differentially expressed miRNAs for each cancer type, and (3) exploration of miRNA clusters across cancer types. www.oncomir.umn.edu/omcd
A practical, efficient, and rapid method for the oxidation of electron deficient pyridines using trifluoroacetic anhydride and hydrogen peroxide–urea complex

Abstract A general method for the oxidation of electron-poor pyridines to their N-oxides using UHP and TFAA in either CH2Cl2 or CH3CN was developed. The methodology proved to tolerate a number of functional groups and substitution patterns and proceeded on notoriously difficult to oxidize substrates.
Environmentally benign process for the synthesis of 2,3-disubstituted benzo[b]thiophenes using electrophilic cyclization

Abstract We have developed a greener process for the synthesis of 2,3-disubstituted benzo[ b ]thiophenes using electrophilic cyclization as a key step. Our method not only employs an environmentally friendly solvent ethanol, but also utilizes safe and inexpensive inorganic reagents to furnish the desired products in high yields under mild reaction conditions. In addition to iodo- and bromocyclization, chlorocylization was also successfully accomplished.
Self-Condensation of N-tert-Butanesulfinyl Aldimines: Application to the Rapid Asymmetric Synthesis of Biologically Important Amine-Containing Compounds

Highly diastereoselective intra- and intermolecular self-condensation reactions of N-tert-butanesulfinyl aldimines have been developed and applied to the rapid, asymmetric synthesis of trans-2-amin...
Spontaneous compositional nanopatterning in Li-containing perovskite oxides.

A structure designed to show functionality on the nanometer length scale ideally would spontaneously form periodic nanometer-scale patterns comprising regions with contrasting properties. Here we report the synthesis of three new oxides that spontaneously form a variety of nanostructures with a periodic arrangement of phases with compositional and functional contrast. This is achieved through the partial substitution of Ti by Al, Cr, and Mn in periodically phase-separated (Nd2/3-xLi3x)TiO3 nanochessboard structures. The generality of this spontaneous compositional nanopatterning is promising for an array of exotic bulk and nanostructural properties.
Direct Binding to Replication Protein A (RPA)-coated Single-stranded DNA Allows Recruitment of the ATR Activator TopBP1 to Sites of DNA Damage

A critical event for the ability of cells to tolerate DNA damage and replication stress is activation of the ATR kinase. ATR activation is dependent on the BRCT (BRCA1 C terminus) repeat-containing protein TopBP1. Previous work has shown that recruitment of TopBP1 to sites of DNA damage and stalled replication forks is necessary for downstream events in ATR activation; however, the mechanism for this recruitment was not known. Here, we use protein binding assays and functional studies in Xenopus egg extracts to show that TopBP1 makes a direct interaction, via its BRCT2 domain, with RPA-coated single-stranded DNA. We identify a point mutant that abrogates this interaction and show that this mutant fails to accumulate at sites of DNA damage and that the mutant cannot activate ATR. These data thus supply a mechanism for how the critical ATR activator, TopBP1, senses DNA damage and stalled replication forks to initiate assembly of checkpoint signaling complexes.
Temporal data exchange

Abstract Data exchange is the problem of transforming data that is structured under a source schema into data structured under another schema, called the target schema, so that both the source and target data satisfy the relationship between the schemas. Many applications such as planning, scheduling, medical and fraud detection systems, require data exchange in the context of temporal data. Even though the formal framework of data exchange for relational database systems is well-established, it does not immediately carry over to the settings of temporal data, which necessitates reasoning over unbounded periods of time. In this work, we study data exchange for temporal data. We first motivate the need for two views of temporal data: the concrete view, which depicts how temporal data is compactly represented and on which the implementations are based, and the abstract view, which defines the semantics of temporal data as a sequence of snapshots. We first extend the chase procedure for the abstract view to have a conceptual basis for the data exchange for temporal databases. Considering non-temporal source-to-target tuple generating dependencies and equality generating dependencies, the chase algorithm can be applied on each snapshot independently. Then we define a chase procedure (called c-chase) on concrete instances and show the result of c-chase on a concrete instance is semantically aligned with the result of chase on the corresponding abstract instance. In order to interpret intervals as constants while checking if a dependency or a query is satisfied by a concrete database, we will normalize the instance with respect to the dependency or the query. To obtain the semantic alignment, the nulls (which are introduced by data exchange and model incompleteness) in the concrete view are annotated with temporal information. Furthermore, we show that the result of the concrete chase provides a foundation for query answering. We define naive evaluation on the result of the c-chase and show it produces certain answers.
Superradiance on the millihertz linewidth strontium clock transition.

Laser frequency noise contributes a significant limitation to today’s best atomic clocks. A proposed solution to this problem is to create a superradiant laser using an optical clock transition as its gain medium. This laser would act as an active atomic clock and would be highly immune to the fluctuations in reference cavity length that limit today’s best lasers. We demonstrate and characterize superradiant emission from the millihertz linewidth clock transition in an ensemble of laser-cooled 87Sr atoms trapped within a high-finesse optical cavity. We measure a collective enhancement of the emission rate into the cavity mode by a factor of more than 10,000 compared to independently radiating atoms. We also demonstrate a method for seeding superradiant emission and observe interference between two independent transitions lasing simultaneously. We use this interference to characterize the relative spectral properties of the two lasing subensembles.
A Capacity-Price Game for Uncertain Renewables Resources

Renewable resources are starting to constitute a growing portion of the total generation mix of the power system. A key difference between renewables and traditional generators is that many renewable resources are managed by individuals, especially in the distribution system. In this paper, we study the capacity investment and pricing problem, where multiple renewable producers compete in a decentralized market. It is known that most deterministic capacity games tend to result in very inefficient equilibria, even when there are a large number of similar players. In contrast, we show that due to the inherent randomness of renewable resources, the equilibria in our capacity game becomes efficient as the number of players grows and coincides with the centralized decision from the social planner's problem. This result provides a new perspective on how to look at the positive influence of randomness in a game framework as well as its contribution to resource planning, scheduling, and bidding. We validate our results by simulation studies using real world data.
To observe or not to observe: Queuing game framework for urban parking

We model parking in urban centers as a set of parallel queues and overlay a game theoretic structure. We model arriving drivers as utility maximizers and consider two games: one in which it is free to observe the queue length and one in which it is not. Not only do we compare the Nash induced welfare to the socially optimal welfare, confirming the usual result that Nash is worse for society, we also show that by other performance metrics more commonly used in transportation— such as occupancy and time spent circling—the Nash solution is suboptimal. We find that gains to welfare do not require everyone to observe. Through simulation, we explore a more complex scenario where drivers decide based the queueing game whether or not to enter a collection of queues over a network. Our simulated models use parameters informed by real-world data collected by the Seattle Department of Transportation.
Time-Agnostic Prediction: Predicting Predictable Video Frames.

Prediction is arguably one of the most basic functions of an intelligent system. In general, the problem of predicting events in the future or between two waypoints is exceedingly difficult. However, most phenomena naturally pass through relatively predictable bottlenecks---while we cannot predict the precise trajectory of a robot arm between being at rest and holding an object up, we can be certain that it must have picked the object up. To exploit this, we decouple visual prediction from a rigid notion of time. While conventional approaches predict frames at regularly spaced temporal intervals, our time-agnostic predictors (TAP) are not tied to specific times so that they may instead discover predictable "bottleneck" frames no matter when they occur. We evaluate our approach for future and intermediate frame prediction across three robotic manipulation tasks. Our predictions are not only of higher visual quality, but also correspond to coherent semantic subgoals in temporally extended tasks.
Effect of Neuromodulation of Short-term Plasticity on Information Processing in Hippocampal Interneuron Synapses

Neurons in a micro-circuit connected by chemical synapses can have their connectivity affected by the prior activity of the cells. The number of synapses available for releasing neurotransmitter can be decreased by repetitive activation through depletion of readily releasable neurotransmitter (NT), or increased through facilitation, where the probability of release of NT is increased by prior activation. These competing effects can create a complicated and subtle range of time-dependent connectivity. Here we investigate the probabilistic properties of facilitation and depression (FD) for a presynaptic neuron that is receiving a Poisson spike train of input. We use a model of FD that is parameterized with experimental data from a hippocampal basket cell and pyramidal cell connection, for fixed frequency input spikes at frequencies in the range of theta (3–8 Hz) and gamma (20–100 Hz) oscillations. Hence our results will apply to micro-circuits in the hippocampus that are responsible for the interaction of theta and gamma rhythms associated with learning and memory. A control situation is compared with one in which a pharmaceutical neuromodulator (muscarine) is employed. We apply standard information-theoretic measures such as entropy and mutual information, and find a closed form approximate expression for the probability distribution of release probability. We also use techniques that measure the dependence of the response on the exact history of stimulation the synapse has received, which uncovers some unexpected differences between control and muscarine-added cases.
Online First-Order Framework for Robust Convex Optimization

Robust optimization (RO) is a technique to tractably model uncertain parameters in optimization problems. More recently, it has attracted interest in applications from machine learning and statisti...
Forecasting the Presence and Intensity of Hostility on Instagram Using Linguistic and Social Features.

Online antisocial behavior, such as cyberbullying, harassment, and trolling, is a widespread problem that threatens free discussion and has negative physical and mental health consequences for victims and communities. While prior work has proposed automated methods to identify hostile comments in online discussions, these methods work retrospectively on comments that have already been posted, making it difficult to intervene before an interaction escalates. In this paper we instead consider the problem of forecasting future hostilities in online discussions, which we decompose into two tasks: (1) given an initial sequence of non-hostile comments in a discussion, predict whether some future comment will contain hostility; and (2) given the first hostile comment in a discussion, predict whether this will lead to an escalation of hostility in subsequent comments. Thus, we aim to forecast both the presence and intensity of hostile comments based on linguistic and social features from earlier comments. To evaluate our approach, we introduce a corpus of over 30K annotated Instagram comments from over 1,100 posts. Our approach is able to predict the appearance of a hostile comment on an Instagram post ten or more hours in the future with an AUC of .82 (task 1), and can furthermore distinguish between high and low levels of future hostility with an AUC of .91 (task 2).
Causal inference by surrogate experiments: z-identifiability

We address the problem of estimating the effect of intervening on a set of variables X from experiments on a different set, Z, that is more accessible to manipulation. This problem, which we call z-identifiability, reduces to ordinary identifiability when Z = O and, like the latter, can be given syntactic characterization using the do-calculus [Pearl, 1995; 2000]. We provide a graphical necessary and sufficient condition for z-identifiability for arbitrary sets X, Z, and Y (the outcomes). We further develop a complete algorithm for computing the causal effect of X on Y using information provided by experiments on Z. Finally, we use our results to prove completeness of do-calculus relative to z-identifiability, a result that does not follow from completeness relative to ordinary identifiability.
The Chevalley–Shephard–Todd theorem for finite linearly reductive group schemes

We generalize the classical Chevalley–Shephard–Todd theorem to the case of finite linearly reductive group schemes. As an application, we prove that every scheme X which is etale-locally the quotient of a smooth scheme by a finite linearly reductive group scheme is the coarse space of a smooth tame Artin stack (as defined by Abramovich, Olsson, and Vistoli), whose stacky structure is supported on the singular locus of X.
Acyclic and Star Colorings of Cographs

Abstract An acyclic coloring of a graph is a proper vertex coloring such that the union of any two color classes induces a disjoint collection of trees. The more restricted notion of star coloring requires that the union of any two color classes induces a disjoint collection of stars. We prove that every acyclic coloring of a cograph is also a star coloring and give a linear-time algorithm for finding an optimal acyclic and star coloring of a cograph. If the graph is given in the form of a cotree, the algorithm runs in O ( n ) time. We also show that the acyclic chromatic number, the star chromatic number, the treewidth plus 1, and the pathwidth plus 1 are all equal for cographs.
Normalization propagation: a parametric technique for removing internal covariate shift in deep networks

While the authors of Batch Normalization (BN) identify and address an important problem involved in training deep networks- Internal Covariate Shift- the current solution has certain drawbacks. For instance, BN depends on batch statistics for layerwise input normalization during training which makes the estimates of mean and standard deviation of input (distribution) to hidden layers inaccurate due to shifting parameter values (especially during initial training epochs). Another fundamental problem with BN is that it cannot be used with batch-size 1 during training. We address these drawbacks of BN by proposing a non-adaptive normalization technique for removing covariate shift, that we call Normalization Propagation. Our approach does not depend on batch statistics, but rather uses a data-independent parametric estimate of mean and standard-deviation in every layer thus being computationally faster compared with BN. We exploit the observation that the pre-activation before Rectified Linear Units follow Gaussian distribution in deep networks, and that once the first and second order statistics of any given dataset are normalized, we can forward propagate this normalization without the need for recalculating the approximate statistics for hidden layers.
Randomized longest-queue-first scheduling for large-scale buffered systems

We develop diffusion approximations for parallel-queueing systems with the randomized longest-queue-first scheduling (LQF) algorithm by establishing new mean-field limit theorems as the number of buffers n → ∞. We achieve this by allowing the number of sampled buffers d = d(n) to depend on the number of buffers n, which yields an asymptotic 'decoupling' of the queue length processes. We show through simulation experiments that the resulting approximation is accurate even for moderate values of n and d(n). To the best of the authors' knowledge, this is the first derivation of diffusion approximations for a queueing system in the large-buffer mean-field regime. Another noteworthy feature of our scaling idea is that the randomized LQF algorithm emulates the LQF algorithm, yet is computationally more attractive. The analysis of the system performance as a function of d(n) is facilitated by the multi-scale nature in our limit theorems: the various processes we study have different space scalings. This allows us to show the trade-off between performance and complexity of the randomized LQF scheduling algorithm.
Inverse Satake Transforms

Let H be a split reductive group over a local non-Archimedean field, and let \(\check {H}\) denote its Langlands dual group. We present an explicit formula for the generating function of an unramified L-function associated to a highest weight representation of the dual group, considered as a series of elements in the Hecke algebra of H. This offers an alternative approach to a solution of the same problem by Wen-Wei Li. Moreover, we generalize the notion of “Satake transform” and perform the analogous calculation for a large class of spherical varieties.
Two-temperature logistic regression based on the Tsallis divergence

We develop a variant of multiclass logistic regression that is significantly more robust to noise. The algorithm has one weight vector per class and the surrogate loss is a function of the linear activations (one per class). The surrogate loss of an example with linear activation vector $\mathbf{a}$ and class $c$ has the form $-\log_{t_1} \exp_{t_2} (a_c - G_{t_2}(\mathbf{a}))$ where the two temperatures $t_1$ and $t_2$ ``temper'' the $\log$ and $\exp$, respectively, and $G_{t_2}(\mathbf{a})$ is a scalar value that generalizes the log-partition function. We motivate this loss using the Tsallis divergence. Our method allows transitioning between non-convex and convex losses by the choice of the temperature parameters. As the temperature $t_1$ of the logarithm becomes smaller than the temperature $t_2$ of the exponential, the surrogate loss becomes ``quasi convex''. Various tunings of the temperatures recover previous methods and tuning the degree of non-convexity is crucial in the experiments. In particular, quasi-convexity and boundedness of the loss provide significant robustness to the outliers. We explain this by showing that $t_1 1$ makes the predictive distribution have a heavy tail. We show that the surrogate loss is Bayes-consistent, even in the non-convex case. Additionally, we provide efficient iterative algorithms for calculating the log-partition value only in a few number of iterations. Our compelling experimental results on large real-world datasets show the advantage of using the two-temperature variant in the noisy as well as the noise free case.
Maximal amenability and disjointness for the radial masa

Abstract We prove that the radial masa C in the free group factor is disjoint from other maximal amenable subalgebras in the following sense: any distinct maximal amenable subalgebra cannot have diffuse intersection with C.