cssi/SciSciGPT-SciSciNet huggingface dataset:
Geometric classification of brain network dynamics via conic derivative discriminants.

Abstract Background Over the past decade, pattern decoding techniques have granted neuroscientists improved anatomical specificity in mapping neural representations associated with function and cognition. Dynamical patterns are of particular interest, as evidenced by the proliferation and success of frequency domain methods that reveal structured spatiotemporal rhythmic brain activity. One drawback of such approaches, however, is the need to estimate spectral power, which limits the temporal resolution of classification. New method We propose an alternative method that enables classification of dynamical patterns with high temporal fidelity. The key feature of the method is a conversion of time-series data into temporal derivatives. By doing so, dynamically-coded information may be revealed in terms of geometric patterns in the phase space of the derivative signal. Results We derive a geometric classifier for this problem which simplifies into a straightforward calculation in terms of covariances. We demonstrate the relative advantages and disadvantages of the technique with simulated data and benchmark its performance with an EEG dataset of covert spatial attention. We reveal the timecourse of covert spatial attention and, by mapping the classifier weights anatomically, its retinotopic organization. Comparison with existing method We especially highlight the ability of the method to provide strong group-level classification performance compared to existing benchmarks, while providing information that is complementary with classical spectral-based techniques. The robustness and sensitivity of the method to noise is also examined relative to spectral-based techniques. Conclusion The proposed classification technique enables decoding of dynamic patterns with high temporal resolution, performs favorably to benchmark methods, and facilitates anatomical inference.
Facile Synthesis of Fluorinated Phosphonates via Photochemical and Thermal Reactions

Under UV irradiation (254 nm) at ambient temperature, a degassed mixture of (EtO)2POP(OEt)2 and RfI {Rf = CF3, C2F5, C4F9, C6F13, (CF3)2CF, CF2CFCF2, ClCF2CF2, BrCF2CF2, C6F5, ClCF2CFClCF2CF2, I(CF2)3, I(CF2)4, FO2S(CF2)4, FO2S(CF2)2O(CF2)2} affords the fluorinated phosphonite, [RfP(OEt)2]. Oxidation of the phosphonites, [RfP(OEt)2], with Me3COOH gave the corresponding fluorinated phosphonates, (EtO)2P(O)Rf (1−14), in 35−80% isolated yields. CF3CCl2I reacts with (EtO)2POP(OEt)2 at room tempearture in the absence of UV irradiation to afford [CF3CCl2P(OEt)2] which upon oxidation gave a 52% yield of CF3CCl2P(O)(OEt)2 (15). The reaction of (EtO)2POP(OEt)2 and RfI (Rf = ClCF2CF2, BrCF2CF2, C2F5) at 125 °C in the presence of Me3COOCMe3 and subsequent oxidation of the resultant phosphonites afforded phosphonates (2, 7, and 8) albeit in lower yields (49−62%) compared to those of the photochemical reaction (58−80%). (RO)2P(O)CF2CF2I (R = Et, i-Pr) (16 and 17) was obtained (42−48%) when a degassed mixture of (RO)3P...
Synthesis of a Model Bicyclic CDE Ring System of Ristocetin A and Observation of a Facile Inversion of Configuration in a 16-Membered DE Ring Model

Areneruthenium chemistry was used to effect intramolecular SNAr reactions between phenoxide nucleophiles and chlorophenylalanine residues that are connected by a peptide chain, resulting in the construction of a bicyclic peptido aryl ether system that corresponds to the BCDF system of the glycopeptide antibiotics ristocetin A and teicoplanin. A facile and selective base-catalyzed complete inversion of configuration at the D ring arylglycine residue was observed when this unit is the carboxylate terminus on a 16-membered ring system corresponding to the DEF rings of the target molecules. The inversion appears to result from an overwhelming thermodynamic preference for the inverted system and is supported by molecular mechanics and semiempirical calculations on the minimized conformations of the epimeric molecules.
What about BOB? A synthetically useful protecting group

Abstract Benzyloxybutyryl (BOB) esters of alcohols can be prepared from commercially available 4-benzyloxybutyric acid by standard acylation techniques, by the Mitsunobu reaction (with inversion of configuration), or by the Jacobsen asymmetric nucleophilic ring opening of epoxides. BOB esters can be removed selectively in the presence of other esters under conditions that are compatible with a variety of sensitive functional groups.
Divergent Diels–Alder methodology from methyl coumalate toward functionalized aromatics

Abstract An inverse electron-demand Diels–Alder reaction between methyl coumalate and electron-rich dienophiles produces substituted benzoates. A high-yielding, single-pot procedure transforms readily accessible vinyl ether, ketal, or orthoester dienophiles into functionalized aromatic systems in a versatile route.
The total synthesis of (±)-arisugacin A

Abstract A 20-step total synthesis of (±)-arisugacin A with an overall yield of 2.1% is described here in detail. This synthesis features a formal [3+3] cycloaddition reaction of α,β-unsaturated iminium salts with 6-aryl-4-hydroxy-2-pyrones through a highly stereoselective 6π-electron electrocyclic ring-closure of 1-oxatriene. A strategic dihydroxylation–deoxygenation protocol leading to the desired angular C12a–OH was developed to serve as a critical step in leading to the final total syntheses of arisugacin A. This synthetic endeavor also led to an interesting and unexpected retro-aldol–aldol sequence in the AB-ring.
Convergence of a Family of Series

In this article we will construct a family of expressions e (n). This article gives also applications.
Selenium oxoanion compounds of palladium(II).

Three new palladium compounds, PdSeO3, PdSe2O5, and Na2Pd(SeO4)2, containing selenium oxoanions of both Se(IV) and Se(VI) have been prepared under mild hydrothermal conditions. PdSe2O5 and Na2Pd(SeO4)2 both possess one-dimensional structures. Within the structure of PdSe2O5, [PdO4] square planar building blocks are joined together through diselenite, Se2O52-, anions, and form a zigzag chain along the c axis. In Na2Pd(SeO4)2, [PdO4] units are connected by two selenate, SeO42-, anions, and extend along the a axis to form a [Pd(SeO4)2]2- chain. Na+ cations reside in the space between the [Pd(SeO4)2]2- chains and act as counter cations. Unlike above two compounds, PdSeO3 exhibits a layered structure. In the structure of PdSeO3, [PdO4] units are connected to each other by corner-sharing and form a zigzag chain along the b axis. The chains are further joined together by tridentate selenite, SeO32-, anions to form layers in the [ab] plane that stack along the c axis. Crystallographic data: (193 K; Mo Kα, λ = 0....
Heterologous Protection against Asian Zika Virus Challenge in Rhesus Macaques.

Background Zika virus (ZIKV; Flaviviridae, Flavivirus) was declared a public health emergency of international concern by the World Health Organization (WHO) in February 2016, because of the evidence linking infection with ZIKV to neurological complications, such as Guillain-Barre Syndrome in adults and congenital birth defects including microcephaly in the developing fetus. Because development of a ZIKV vaccine is a top research priority and because the genetic and antigenic variability of many RNA viruses limits the effectiveness of vaccines, assessing whether immunity elicited against one ZIKV strain is sufficient to confer broad protection against all ZIKV strains is critical. Recently, in vitro studies demonstrated that ZIKV likely circulates as a single serotype. Here, we demonstrate that immunity elicited by African lineage ZIKV protects rhesus macaques against subsequent infection with Asian lineage ZIKV. Methodology/Principal Findings Using our recently developed rhesus macaque model of ZIKV infection, we report that the prototypical ZIKV strain MR766 productively infects macaques, and that immunity elicited by MR766 protects macaques against heterologous Asian ZIKV. Furthermore, using next generation deep sequencing, we found in vivo restoration of a putative N-linked glycosylation site upon replication in macaques that is absent in numerous MR766 strains that are widely being used by the research community. This reversion highlights the importance of carefully examining the sequence composition of all viral stocks as well as understanding how passage history may alter a virus from its original form. Conclusions/Significance An effective ZIKV vaccine is needed to prevent infection-associated fetal abnormalities. Macaques whose immune responses were primed by infection with East African ZIKV were completely protected from detectable viremia when subsequently rechallenged with heterologous Asian ZIKV. Therefore, these data suggest that immunogen selection is unlikely to adversely affect the breadth of vaccine protection, i.e., any Asian ZIKV immunogen that protects against homologous challenge will likely confer protection against all other Asian ZIKV strains.
CHASMplus Reveals the Scope of Somatic Missense Mutations Driving Human Cancers.

Summary Large-scale cancer sequencing studies of patient cohorts have statistically implicated many genes driving cancer growth and progression, and their identification has yielded substantial translational impact. However, a remaining challenge is to increase the resolution of driver prediction from the level of genes to mutations because mutation-level predictions are more closely aligned with the goal of precision cancer medicine. Here, we present CHASMplus, a computational method that is uniquely capable of identifying driver missense mutations, including those specific to a cancer type, as evidenced by significantly superior performance on diverse benchmarks. Applied to 8,657 tumor samples across 32 cancer types in The Cancer Genome Atlas (TCGA), CHASMplus identifies over 4,000 unique driver missense mutations in 240 genes, supporting a prominent role for rare driver mutations. We show which TCGA cancer types are likely to yield discovery of new driver missense mutations by additional sequencing, which has important implications for public policy.
Evaluating the Information Content of Shallow Shotgun Metagenomics

ABSTRACT Although microbial communities are associated with human, environmental, plant, and animal health, there exists no cost-effective method for precisely characterizing species and genes in such communities. While deep whole-metagenome shotgun (WMS) sequencing provides high taxonomic and functional resolution, it is often prohibitively expensive for large-scale studies. The prevailing alternative, 16S rRNA gene amplicon (16S) sequencing, often does not resolve taxonomy past the genus level and provides only moderately accurate predictions of the functional profile; thus, there is currently no widely accepted approach to affordable, high-resolution, taxonomic, and functional microbiome analysis. To address this technology gap, we evaluated the information content of shallow shotgun sequencing with as low as 0.5 million sequences per sample as an alternative to 16S sequencing for large human microbiome studies. We describe a library preparation protocol enabling shallow shotgun sequencing at approximately the same per-sample cost as 16S sequencing. We analyzed multiple real and simulated biological data sets, including two novel human stool samples with ultradeep sequencing of 2.5 billion sequences per sample, and found that shallow shotgun sequencing recovers more-accurate species-level taxonomic and functional profiles of the human microbiome than 16S sequencing. We discuss the inherent limitations of shallow shotgun sequencing and note that 16S sequencing remains a valuable and important method for taxonomic profiling of novel environments. Although deep WMS sequencing remains the gold standard for high-resolution microbiome analysis, we recommend that researchers consider shallow shotgun sequencing as a useful alternative to 16S sequencing for large-scale human microbiome research studies where WMS sequencing may be cost-prohibitive. IMPORTANCE A common refrain in recent microbiome-related academic meetings is that the field needs to move away from broad taxonomic surveys using 16S sequencing and toward more powerful longitudinal studies using shotgun sequencing. However, performing deep shotgun sequencing in large longitudinal studies remains prohibitively expensive for all but the most well-funded research labs and consortia, which leads many researchers to choose 16S sequencing for large studies, followed by deep shotgun sequencing on a subset of targeted samples. Here, we show that shallow- or moderate-depth shotgun sequencing may be used by researchers to obtain species-level taxonomic and functional data at approximately the same cost as amplicon sequencing. While shallow shotgun sequencing is not intended to replace deep shotgun sequencing for strain-level characterization, we recommend that microbiome scientists consider using shallow shotgun sequencing instead of 16S sequencing for large-scale human microbiome studies.
Structural relationship between the putative hair cell mechanotransduction channel TMC1 and TMEM16 proteins

The hair cell mechanotransduction (MET) channel complex is essential for hearing, yet it's molecular identity and structure remain elusive. The transmembrane channel-like 1 (TMC1) protein localizes to the site of the MET channel, interacts with the tip-link responsible for mechanical gating, and genetic alterations in TMC1 alter MET channel properties and cause deafness, supporting the hypothesis that TMC1 forms the MET channel. We generated a model of TMC1 based on X-ray and cryo-EM structures of TMEM16 proteins, revealing the presence of a large cavity near the protein-lipid interface that also harbors the Beethoven mutation, suggesting that it could function as a permeation pathway. We also find that hair cells are permeable to 3 kDa dextrans, and that dextran permeation requires TMC1/2 proteins and functional MET channels, supporting the presence of a large permeation pathway and the hypothesis that TMC1 is a pore forming subunit of the MET channel complex.
Exploring the impact of inoculum dose on host immunity and morbidity to inform model-based vaccine design

Vaccination is an effective method to protect against infectious diseases. An important consideration in any vaccine formulation is the inoculum dose, i.e., amount of antigen or live attenuated pathogen that is used. Higher levels generally lead to better stimulation of the immune response but might cause more severe side effects and allow for less population coverage in the presence of vaccine shortages. Determining the optimal amount of inoculum dose is an important component of rational vaccine design. A combination of mathematical models with experimental data can help determine the impact of the inoculum dose. We illustrate the concept of using data and models to inform inoculum dose determination for vaccines, wby fitting a mathematical model to data from influenza A virus (IAV) infection of mice and human parainfluenza virus (HPIV) infection of cotton rats at different inoculum doses. We use the model to map inoculum dose to the level of immune protection and morbidity and to explore how such a framework might be used to determine an optimal inoculum dose. We show how a framework that combines mathematical models with experimental data can be used to study the impact of inoculum dose on important outcomes such as immune protection and morbidity. Our findings illustrate that the impact of inoculum dose on immune protection and morbidity can depend on the specific pathogen and that both protection and morbidity do not necessarily increase monotonically with increasing inoculum dose. Once vaccine design goals are specified with required levels of protection and acceptable levels of morbidity, our proposed framework can help in the rational design of vaccines and determination of the optimal amount of inoculum.
Enantiomerically pure dihydropyrimidinones as reagents and auxiliaries for asymmetric synthesis

We report herein full experimental details of the synthesis, structure, and reactivity of (R)- and (S)-2-tert-butyl-1-carbomethoxy-2,3-dihydropyrimidin-4(1H)-one (1). The synthesis employs asparagine as the starting material and provides 1 in 55% yield without the need for chromatographic purification. The structure of 1, as determined by X-ray crystallographic analysis, demonstrates significant pyramidalization at the C4 (carbonyl) and N1 centers, with little evidence of conjugation of N1 with the α,β-unsaturated (vinylogous urea) system
Integrating Discovery-driven Proteomics and Selected Reaction Monitoring To Develop a Noninvasive Assay for Geoduck Reproductive Maturation

Geoduck clams (Panopea generosa) are an increasingly important fishery and aquaculture product along the eastern Pacific coast from Baja California, Mexico, to Alaska. These long-lived clams are highly fecund, although sustainable hatchery production of genetically diverse larvae is hindered by the lack of sexual dimorphism, resulting in asynchronous spawning of broodstock, unequal sex ratios, and low numbers of breeders. The development of assays of gonad physiology could indicate sex and maturation stage as well as be used to assess the status of natural populations. Proteomic profiles were determined for three reproductive maturation stages in both male and female clams using data-dependent acquisition (DDA) of gonad proteins. Gonad proteomes became increasingly divergent between males and females as maturation progressed. The DDA data were used to develop targets analyzed with selected reaction monitoring (SRM) in gonad tissue as well as hemolymph. The SRM assay yielded a suite of indicator peptides t...
SpliceV: analysis and publication quality printing of linear and circular RNA splicing, expression and regulation.

In eukaryotes, most genes code for multiple transcript isoforms that are generated through the complex and tightly regulated process of RNA splicing. Despite arising from identical precursor transcripts, alternatively spliced RNAs can have dramatically different functions. Transcriptome complexity is elevated further by the production of circular RNAs (circRNAs), another class of mature RNA that results from the splicing of a downstream splice donor to an upstream splice acceptor. While there has been a rapid expansion of circRNA catalogs in the last few years through the utilization of next generation sequencing approaches, our understanding of the mechanisms and regulation of circular RNA biogenesis, the impact that circRNA generation has on parental transcript processing, and the functions carried out by circular RNAs remains limited. Here, we present a visualization and analysis tool, SpliceV, that rapidly plots all relevant forward- and back-splice data, with exon and single nucleotide level coverage information from RNA-seq experiments in a publication quality format. SpliceV also integrates analysis features that assist investigations into splicing regulation and transcript functions through the display of predicted RNA binding protein sites and the configuration of repetitive elements along the primary transcript. SpliceV is an easy-to-use splicing visualization tool, compatible with both Python 2.7 and 3+, and distributed under the GNU Public License. The source code is freely available for download at https://github.com/flemingtonlab/SpliceV and can be installed from PyPI using pip.
CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis.

We present CoPhosK to predict kinase-substrate associations for phosphopeptide substrates detected by mass spectrometry (MS). The tool utilizes a Naive Bayes framework with priors of known kinase-substrate associations (KSAs) to generate its predictions. Through the mining of MS data for the collective dynamic signatures of the kinases' substrates revealed by correlation analysis of phosphopeptide intensity data, the tool infers KSAs in the data for the considerable body of substrates lacking such annotations. We benchmarked the tool against existing approaches for predicting KSAs that rely on static information (e.g. sequences, structures and interactions) using publically available MS data, including breast, colon, and ovarian cancer models. The benchmarking reveals that co-phosphorylation analysis can significantly improve prediction performance when static information is available (about 35% of sites) while providing reliable predictions for the remainder, thus tripling the KSAs available from the experimental MS data providing to a comprehensive and reliable characterization of the landscape of kinase-substrate interactions well beyond current limitations.
BioMake: a GNU make-compatible utility for declarative workflow management

Motivation The Unix 'make' program is widely used in bioinformatics pipelines, but suffers from problems that limit its application to large analysis datasets. These include reliance on file modification times to determine whether a target is stale, lack of support for parallel execution on clusters, and restricted flexibility to extend the underlying logic program. Results We present BioMake, a make-like utility that is compatible with most features of GNU Make and adds support for popular cluster-based job-queue engines, MD5 signatures as an alternative to timestamps, and logic programming extensions in Prolog. Availability and implementation BioMake is available for MacOSX and Linux systems from https://github.com/evoldoers/biomake under the BSD3 license. The only dependency is SWI-Prolog (version 7), available from http://www.swi-prolog.org/. Contact ihholmes + biomake@gmail.com or cmungall + biomake@gmail.com. Supplementary information Feature table comparing BioMake to similar tools. Supplementary data are available at Bioinformatics online.
A Synthesis of (±)-Stemodinone: An Application of Organoiron Chemistry to the Construction of Sterically Congested Quaternary Carbon Centers

A synthesis of racemic stemodinone is described, using tricarbonyl(1−5-η-4-methoxy-1,3-dimethylcyclohexadienyl)iron(I) hexafluorophosphate (9) as an electrophile that is the A-ring precursor. Reaction of 9 with the tin enolate from 4,4-(ethylenedioxy)cyclohexanecarbaldehyde proceeded with excellent regioselectivity and high yield to generate an intermediate representing the A and C rings of the target molecule. The B ring was constructed by introducing a two-carbon electrophilic group onto the A ring, followed by ring closure using an intramolecular enolate alkylation. Installation of the D ring and manipulation to give the final product followed transformations precedented with this series of compounds.
New CuM2/3Sb1/3O2 and AgM2/3Sb1/3O2 compounds with the delafossite structure

Abstract Several new compounds have been prepared with the delafossite structure: CuMn 2/3 Sb 1/3 O 2 , CuCo 2/3 Sb 1/3 O 2 , CuNi 2/3 Sb 1/3 O 2 , CuZn 2/3 Sb 1/3 O 2 , CuMg 2/3 Sb 1/3 O 2 , AgNi 2/3 Sb 1/3 O 2 , and AgZn 2/3 Sb 1/3 O 2 . The structures of the CuM 2/3 Sb 1/3 O 2 compounds are generally based on 2H stacking along the c axis, and the M 2+ and Sb 5+ cations can be ordered or disordered. The structures of the AgM 2/3 Sb 1/3 O 2 compounds are based on 3R stacking along c with the M 2+ and Sb 5+ cations disordered. The structures of CuMn 2/3 Sb 1/3 O 2 (disordered) and CuMg 2/3 Sb 1/3 O 2 (ordered) were refined from single crystal X-ray diffraction data. Pellets and transparent thin films of CuNi 2/3 Sb 1/3 O 2 with 10% Sn doping for Sb showed p-type electronic conduction.
Synthesis and Properties of (O-Acyl imidato)carbene Complexes of Chromium, Molybdenum, and Tungsten

Preparation d'une serie de complexes ylidenes d'imides O-acylees du chrome, du molybdene et du tungstene
MECHANISM OF HYDROXYLATION OF ALKANES BY DIMETHYLDIOXIRANE. A RADICAL-CLOCK STUDY

Abstract The oxidation of 2-cyclopropylpropane by dimethyldioxirane (DMD) to 2-cyclopropyl-propan-2-ol is not a free -radical chain reaction. It is suggested the free -radical chain observed by Minisci et al. 8 when alkane / DMD reactions were carried out in the presence of CCl 3 Br involves H-atom abstraction from the alkane by Cl 3 ,COO· (in air) and by Me 2 C(O·)OCCl 3 , as well as by the Cl 3 C· radical.
Synthetic Studies on Quassinoids: Total Synthesis and Biological Evaluation of (+)-Des-D-chaparrinone.

A total synthesis of des-d-chaparrinone (2), which lacks the ring D δ-lactone of (−)-chaparrinone (1) has been developed. The synthesis commences with the known, readily available tricyclic ketone 3 (R = Me). Elaboration of the configuration at C(5) followed by resolution of 6 employing 2(R),3(R)-2,3-butanediol gave rise to 9. Installation of the ring C functionality provided 15 which was transformed into tricyclic diketone 25. Introduction of the ring A functional groups afforded 29, which upon exposure to aluminum trichloride and sodium iodide gave rise directly to (+)-des-d-chaparrinone (2). Biological studies revealed that (+)-2 was devoid of any solid tumor activity.
An efficient approach to bridged-bicyclic rings via intramolecular diazo ketone insertion

A regioselective intramolecular diazo ketone insertion reaction of chiral cyclohexenones is described. The methodology shows potential utility in the syntheses of bicyclo[4.2.1]nonan-9-one, bicyclo[4.3.1]decan-10-one and cyclooctanoid rings.
Initiator tRNA genes template the 3' CCA end at high frequencies in bacteria.

While the CCA sequence at the mature 3′ end of tRNAs is conserved and critical for translational function, a genetic template for this sequence is not always contained in tRNA genes. In eukaryotes and Archaea, the CCA ends of tRNAs are synthesized post-transcriptionally by CCA-adding enzymes. In Bacteria, tRNA genes template CCA sporadically. In order to understand the variation in how prokaryotic tRNA genes template CCA, we re-annotated tRNA genes in tRNAdb-CE database version 0.8. Among 132,129 prokaryotic tRNA genes, initiator tRNA genes template CCA at the highest average frequency (74.1%) over all functional classes except selenocysteine and pyrrolysine tRNA genes (88.1% and 100% respectively). Across bacterial phyla and a wide range of genome sizes, many lineages exist in which predominantly initiator tRNA genes template CCA. Convergent and parallel retention of CCA templating in initiator tRNA genes evolved in independent histories of reductive genome evolution in Bacteria. Also, in a majority of cyanobacterial and actinobacterial genera, predominantly initiator tRNA genes template CCA. We also found that a surprising fraction of archaeal tRNA genes template CCA. We suggest that cotranscriptional synthesis of initiator tRNA CCA 3′ ends can complement inefficient processing of initiator tRNA precursors, “bootstrap” rapid initiation of protein synthesis from a non-growing state, or contribute to an increase in cellular growth rates by reducing overheads of mass and energy to maintain nonfunctional tRNA precursor pools. More generally, CCA templating in structurally non-conforming tRNA genes can afford cells robustness and greater plasticity to respond rapidly to environmental changes and stimuli.
Development of a highly α-selective galactopyranosyl donor based on a rational design

Abstract A galactosyl donor was rationally designed based on protecting group-stereoselectivity study. This donor was prepared and tested in a series of glycosylation reaction. Excellent α-selectivity was observed in the test reactions.
Synthesis of C-5 substituted nucleosides via palladium-catalyzed coupling of dienes and amines

Abstract The palladium-catalyzed coupling of C-5 iodopyrimidine nucleosides; 1,2-, 1,3-, or 1,ω-dienes; and amines provides a novel and efficient method for the preparation of a wide variety of C-5 aminoalkyl-substituted nucleosides. Adding certain Lewis acids, particularly zinc salts, improves the yields significantly. Secondary amines are the most effective amines for this process. Acyclic and cyclic dienes have been successfully employed. Protection of the 3′- and 5′-hydroxyl groups of iodouridine is required in order to obtain good yields when the coupling process is carried out on 1,3-dienes or long chain or branched non-conjugated dienes.
Efficient synthesis of 4,4-dimethyl-1,9,10(1H)-anthracenetrione

A concise route to the title compound was achieved via annulation of 4,4-dimethylcyclohexenone with 3-cyanophthalide, followed by oxidation with DDQ.
Ribofuranosides N-substituted with meso-porphyrin as nucleoside-like compounds

Abstract Meso-tri(4-pyridyl)porphyrin-p-phenylene-1′-amino-D-ribose and the respective D-2-deoxyribose derivative were synthesized as first representatives of porphyrinyl-N-glycosides.
Functionalized carbocyclic rings via intramolecular Diels-Alder reactions of in situ-generated, γ substituted, heteroatom-stabilized allyl cations in acidic polar media

Abstract The synthesis of highly structured carbocyclic ring systems possessing quaternary carbon atoms has been realized via intramolecular Diels-Alder reactions of in situ-generated, γ substituted, heteroatom-stabilized allyl cations in acidic polar media.
Nanocrystalline Zeolites: Synthesis, Characterization, and Applications with Emphasis on Zeolite L Nanoclusters

Publisher Summary Zeolites are crystalline aluminosilicates possessing a regular microporous channel network. Unique properties of zeolites such as the presence of framework cations, acid sites, and their well-defined porous structure∼ with pore sizes similar to those of small moleculesmaccount for their traditional utilization in ion exchange, catalysis, and separations. In addition, zeolites are being investigated for novel emerging applications in a diversity of areas including optoelectronic devices and reactive membranes because they provide for discrimination, recognition, and organization of molecules with great precision. Zeolites synthesized in nanocrystalline form include sodalite and zeolites A, Y, ZSM-2, ZSM-5, and L. A wide variety of techniques have been employed to characterize these nanocrystalline systems. Due to their short-channel lengths zeolite nanocrystals provide for fast diffusion times and increased activity. Small zeolite particles also provide high external to internal surface ratios resulting in increased resistance to deactivation and catalysis with molecules that are unable to enter the zeolite pores. The price to pay for catalysis from external surfaces is the loss of shape selectivity. A possible direction toward increasing selectivity lies in the control of interzeolitic porosity.
Identification of Genes With Enriched Expression in Early Developing Mouse Cone Photoreceptors.

Purpose The early transcriptional events that occur in newly generated cone photoreceptors are not well described. Knowledge of these events is critical to provide benchmarks for in vitro-derived cone photoreceptors and to understand the process of cone and rod photoreceptor diversification. We sought to identify genes with differential gene expression in embryonic mouse cone photoreceptors. Methods The specificity of expression of the LHX4 transcription factor in developing cone photoreceptors was examined using immunofluorescence visualization in both mouse and chicken retinas. A LHX4 transgenic reporter line with high specificity for developing mouse cone photoreceptors was identified and used to purify early-stage cone photoreceptors for profiling by single-cell RNA sequencing. Comparisons were made to previous datasets targeting photoreceptors. Results The LHX4 transcription factor and a transgenic reporter were determined to be highly specific to early developing cone photoreceptors in the mouse. Single-cell transcriptional profiling identified new genes with enriched expression in cone photoreceptors relative to concurrent cell populations. Comparison to previous profiling datasets allowed for further characterization of these genes across developmental time, species, photoreceptor type, and gene regulatory network. Conclusions The LHX4 gene is highly enriched in developing cone photoreceptors as are several new genes identified through transcriptional profiling, some of which are expressed in subclusters of cones. Many of these cone-enriched genes do not show obvious de-repression in profiling of retinas mutant for the rod-specific transcription factor NRL, highlighting differences between endogenous cones and those induced in NRL mutants.
The impact of credit ratings on corporate behavior: Evidence from Moody's adjustments

Abstract Moody's adjusts a firm's reported leverage across several dimensions to determine credit ratings. I find that changes to this adjustment methodology affect firm capital structure and investment decisions. In particular, in 2006, Moody's made several changes to its adjustment methodologies, which are arguably exogenous to changes in firm fundamentals. I show these changes significantly affect adjustments for firms in this year. I then show that these changes to adjustments in 2006 affect capital structure and investment decisions in 2007, especially for those firms with greatest exposure to the methodology changes. These results show that rating agencies have the power to affect corporate decisions.
Beyond normality: Learning sparse probabilistic graphical models in the non-Gaussian setting

We present an algorithm to identify sparse dependence structure in continuous and non-Gaussian probability distributions, given a corresponding set of data. The conditional independence structure of an arbitrary distribution can be represented as an undirected graph (or Markov random field), but most algorithms for learning this structure are restricted to the discrete or Gaussian cases. Our new approach allows for more realistic and accurate descriptions of the distribution in question, and in turn better estimates of its sparse Markov structure. Sparsity in the graph is of interest as it can accelerate inference, improve sampling methods, and reveal important dependencies between variables. The algorithm relies on exploiting the connection between the sparsity of the graph and the sparsity of transport maps, which deterministically couple one probability measure to another.
Automatic Compositor Attribution in the First Folio of Shakespeare.

Compositor attribution, the clustering of pages in a historical printed document by the individual who set the type, is a bibliographic task that relies on analysis of orthographic variation and inspection of visual details of the printed page. In this paper, we introduce a novel unsupervised model that jointly describes the textual and visual features needed to distinguish compositors. Applied to images of Shakespeare’s First Folio, our model predicts attributions that agree with the manual judgements of bibliographers with an accuracy of 87%, even on text that is the output of OCR.
ELECTROMAGNETICALLY INDUCED DISTORTION OF A FIBRIN MATRIX WITH EMBEDDED MICROPARTICLES

Blood clots occur in the human body when they are required to prevent bleeding. In pathological states such as diabetes and sickle cell disease, blood clots can also form undesirably due to hypercoagulable plasma conditions. With the continued effort in developing fibrin therapies for potential life-saving solutions, more mechanical modeling is needed to understand the properties of fibrin structures with inclusions. In this study, a fibrin matrix embedded with magnetic micro particles (MMPs) was subjected to a magnetic field to determine the magnitude of the required force to create plastic deformation within the fibrin clot. Using finite element (FE) analysis, we estimated the magnetic force from an electromagnet at a sample space located approximately 3cm away from the coil center. This electromagnetic force coupled with gravity was applied on a fibrin mechanical system with MMPs to calculate the stresses and displacements. Using appropriate coil parameters, it was determined that application of a magn...
An Analysis of the t-SNE Algorithm for Data Visualization

A first line of attack in exploratory data analysis is data visualization, i.e., generating a 2-dimensional representation of data that makes clusters of similar points visually identifiable. Standard Johnson-Lindenstrauss dimensionality reduction does not produce data visualizations. The t-SNE heuristic of van der Maaten and Hinton, which is based on non-convex optimization, has become the de facto standard for visualization in a wide range of applications. This work gives a formal framework for the problem of data visualization - finding a 2-dimensional embedding of clusterable data that correctly separates individual clusters to make them visually identifiable. We then give a rigorous analysis of the performance of t-SNE under a natural, deterministic condition on the "ground-truth" clusters (similar to conditions assumed in earlier analyses of clustering) in the underlying data. These are the first provable guarantees on t-SNE for constructing good data visualizations. We show that our deterministic condition is satisfied by considerably general probabilistic generative models for clusterable data such as mixtures of well-separated log-concave distributions. Finally, we give theoretical evidence that t-SNE provably succeeds in partially recovering cluster structure even when the above deterministic condition is not met.
Rainbow arithmetic progressions in finite abelian groups

For positive integers $n$ and $k$, the \emph{anti-van der Waerden number} of $\mathbb{Z}_n$, denoted by $aw(\mathbb{Z}_n,k)$, is the minimum number of colors needed to color the elements of the cyclic group of order $n$ and guarantee there is a rainbow arithmetic progression of length $k$. Butler et al. showed a reduction formula for $aw(\mathbb{Z}_{n},3) = 3$ in terms of the prime divisors of $n$. In this paper, we analagously define the anti-van der Waerden number of a finite abelian group $G$ and show $aw(G,3)$ is determined by the order of $G$ and the number of groups with even order in a direct sum isomorphic to $G$. The \emph{unitary anti-van der Waerden number} of a group is also defined and determined.
{SLEUTH}: Real-time Attack Scenario Reconstruction from {COTS} Audit Data

We present an approach and system for real-time reconstruction of attack scenarios on an enterprise host. To meet the scalability and real-time needs of the problem, we develop a platform-neutral, main-memory based, dependency graph abstraction of audit-log data. We then present efficient, tag-based techniques for attack detection and reconstruction, including source identification and impact analysis. We also develop methods to reveal the big picture of attacks by construction of compact, visual graphs of attack steps. Our system participated in a red team evaluation organized by DARPA and was able to successfully detect and reconstruct the details of the red team's attacks on hosts running Windows, FreeBSD and Linux.
Pseudo-deterministic Proofs

We introduce pseudo-deterministic interactive proofs (psdIP): interactive proof systems for search problems where the verifier is guaranteed with high probability to output the same output on different executions. As in the case with classical interactive proofs, the verifier is a probabilistic polynomial time algorithm interacting with an untrusted powerful prover. We view pseudo-deterministic interactive proofs as an extension of the study of pseudo-deterministic randomized polynomial time algorithms: the goal of the latter is to find canonical solutions to search problems whereas the goal of the former is to prove that a solution to a search problem is canonical to a probabilistic polynomial time verifier. Alternatively, one may think of the powerful prover as aiding the probabilistic polynomial time verifier to find canonical solutions to search problems, with high probability over the randomness of the verifier. The challenge is that pseudo-determinism should hold not only with respect to the randomness, but also with respect to the prover: a malicious prover should not be able to cause the verifier to output a solution other than the unique canonical one. The IP=PSPACE characterization implies that psdIP = IP. The challenge is to find constant round pseudo-deterministic interactive proofs for hard search problems. We show a constant round pseudo-deterministic interactive proof for the graph isomorphism problem: on any input pair of isomorphic graphs (G_0,G_1), there exist a unique isomorphism phi from G_0 to G_1 (although many isomorphism many exist) which will be output by the verifier with high probability, regardless of any dishonest prover strategy. In contrast, we show that it is unlikely that psdIP proofs with constant rounds exist for NP-complete problems by showing that if any NP-complete problem has a constant round psdIP protocol, then the polynomial hierarchy collapses.
Nonparametric Preference Completion.

We consider the task of collaborative preference completion: given a pool of items, a pool of users and a partially observed item-user rating matrix, the goal is to recover the \emph{personalized ranking} of each user over all of the items. Our approach is nonparametric: we assume that each item $i$ and each user $u$ have unobserved features $x_i$ and $y_u$, and that the associated rating is given by $g_u(f(x_i,y_u))$ where $f$ is Lipschitz and $g_u$ is a monotonic transformation that depends on the user. We propose a $k$-nearest neighbors-like algorithm and prove that it is consistent. To the best of our knowledge, this is the first consistency result for the collaborative preference completion problem in a nonparametric setting. Finally, we demonstrate the performance of our algorithm with experiments on the Netflix and Movielens datasets.
Deep Probabilistic Programming

We propose Edward, a Turing-complete probabilistic programming language. Edward defines two compositional representations---random variables and inference. By treating inference as a first class citizen, on a par with modeling, we show that probabilistic programming can be as flexible and computationally efficient as traditional deep learning. For flexibility, Edward makes it easy to fit the same model using a variety of composable inference methods, ranging from point estimation to variational inference to MCMC. In addition, Edward can reuse the modeling representation as part of inference, facilitating the design of rich variational models and generative adversarial networks. For efficiency, Edward is integrated into TensorFlow, providing significant speedups over existing probabilistic systems. For example, we show on a benchmark logistic regression task that Edward is at least 35x faster than Stan and 6x faster than PyMC3. Further, Edward incurs no runtime overhead: it is as fast as handwritten TensorFlow.
Minority carrier diffusion lengths and mobilities in low-doped n-InGaAs for focal plane array applications

The hole diffusion length in n-InGaAs is extracted for two samples of different doping concentrations using a set of long and thin diffused junction diodes separated by various distances on the order of the diffusion length. The methodology is described, including the ensuing analysis which yields diffusion lengths between 70 - 85 μm at room temperature for doping concentrations in the range of 5 − 9 × 1015 cm−3 . The analysis also provides insight into the minority carrier mobility which is a parameter not commonly reported in the literature. Hole mobilities on the order of 500 − 750 cm2/V·s are reported for the aforementioned doping range, which are comparable albeit longer than the majority hole mobility for the same doping magnitude in p-InGaAs. A radiative recombination coefficient of (0.5±0.2)×10−10 cm−3 s −1 is also extracted from the ensuing analysis for an InGaAs thickness of 2.7 μm. Preliminary evidence is also given for both heavy and light hole diffusion. The dark current of InP/InGaAs p-i-n photodetectors with 25 and 15 μm pitches are then calibrated to device simulations and correlated to the extracted diffusion lengths and doping concentrations. An effective Shockley-Read-Hall lifetime of between 90-200 μs provides the best fit to the dark current of these structures.
Semi-Online Bipartite Matching

In this paper we introduce the semi-online model that generalizes the classical online computational model. The semi-online model postulates that the unknown future has a predictable part and an adversarial part; these parts can be arbitrarily interleaved. An algorithm in this model operates as in the standard online model, i.e., makes an irrevocable decision at each step. We consider bipartite matching in the semi-online model. Our main contributions are competitive algorithms for this problem and a near-matching hardness bound. The competitive ratio of the algorithms nicely interpolates between the truly offline setting (i.e., no adversarial part) and the truly online setting (i.e., no predictable part).
Tau neutrinos in IceCube, KM3NeT and the Pierre Auger Observatory

In 2018, the IceCube collaboration reported evidence for the identification of a blazar as an astrophysical neutrino source. That evidence is briefly summarised here before focusing on the prospects of tau neutrino physics in IceCube, both at high energies (astrophysical neutrinos) and at lower energies (atmospheric neutrino oscillations). In addition, future neutrino detectors such as KM3NeT and the IceCube Upgrade and their tau neutrino physics potential are discussed. Finally, the detection mechanism for high-energy (tau) neutrinos in the Pierre Auger Observatory and the resulting flux upper limits are presented.
Robust topology identification and control of LTI networks

This paper reports a robust scheme for topology identification and control of networks running on linear dynamics. In the proposed method, the unknown network is enforced to asymptotically follow a reference dynamics using the combination of Lyapunov based adaptive feedback input and sliding mode control. The adaptive part controls the dynamics by learning the network structure, while the sliding mode part rejects the input uncertainty. Simulation studies are presented in several scenarios (detection of link failure, tracking time varying topology, achieving dynamic synchronization) to give support to theoretical findings.
Components of Affine Springer Fibers

Let $\mathbf{G}$ be a connected split reductive group over a field of characteristic zero or sufficiently large characteristic, $\gamma_0\in(\operatorname{Lie}\mathbf{G})((t))$ be any topologically nilpotent regular semisimple element, and $\gamma=t\gamma_0$. Using methods from $p$-adic orbital integrals, we show that the number of components of the Iwahori affine Springer fiber over $\gamma$ modulo $Z_{\mathbf{G}((t))}(\gamma)$ is equal to the order of the Weyl group.
Rating Effects on Social News Posts and Comments

At a time when information seekers first turn to digital sources for news and opinion, it is critical that we understand the role that social media plays in human behavior. This is especially true when information consumers also act as information producers and editors through their online activity. In order to better understand the effects that editorial ratings have on online human behavior, we report the results of a two large-scale in vivo experiments in social media. We find that small, random rating manipulations on social media posts and comments created significant changes in downstream ratings, resulting in significantly different final outcomes. We found positive herding effects for positive treatments on posts, increasing the final rating by 11.02% on average, but not for positive treatments on comments. Contrary to the results of related work, we found negative herding effects for negative treatments on posts and comments, decreasing the final ratings, on average, of posts by 5.15% and of comments by 37.4%. Compared to the control group, the probability of reaching a high rating ( g 2,000) for posts is increased by 24.6% when posts receive the positive treatment and for comments it is decreased by 46.6% when comments receive the negative treatment.
k-Isomorphism classes of local field extensions

Abstract Let K be a local field of characteristic p with perfect residue field k. In this paper we find a set of representatives for the k-isomorphism classes of totally ramified separable extensions L / K of degree p. This extends work of Klopsch, who found representatives for the k-isomorphism classes of totally ramified Galois extensions L / K of degree p.