cssi/SciSciGPT-SciSciNet huggingface dataset:
Finding de novo methylated DNA motifs

Motivation Increasing evidence has shown that nucleotide modifications such as methylation and hydroxymethylation on cytosine would greatly impact the binding of transcription factors (TFs). However, there is a lack of motif finding algorithms with the function to search for motifs with modified bases. In this study, we expand on our previous motif finding pipeline Epigram to provide systematic de novo motif discovery and performance evaluation on methylated DNA motifs. Results mEpigram outperforms both MEME and DREME on finding modified motifs in simulated data that mimics various motif enrichment scenarios. Furthermore we were able to identify methylated motifs in Arabidopsis DNA affinity purification sequencing (DAP-seq) data that were previously demonstrated to contain such motifs. When applied to TF ChIP-seq and DNA methylome data in H1 and GM12878, our method successfully identified novel methylated motifs that can be recognized by the TFs or their co-factors. We also observed spacing constraint between the canonical motif of the TF and the newly discovered methylated motifs, which suggests operative recognition of these cis-elements by collaborative proteins. Availability and implementation The mEpigram program is available at http://wanglab.ucsd.edu/star/mEpigram. Supplementary information Supplementary data are available at Bioinformatics online.
Generalization via superposition: combined effects of mixed reference frame representations for explicit and implicit learning in a visuomotor adaptation task

Generalization following learning in visuomotor adaptation tasks can reflect how the brain represents what it learns. In this study, we isolated explicit and implicit forms of learning and showed t...
A new and efficient method for the synthesis of trifluoromethylthio- and selenoethers.

A new atom-economic procedure for preparation of trifluoromethyl thio- and selenoethers is reported, wherein both halves of aryl and alkyl disulfides and diselenides are able to be utilized with high efficiency.
Distinct cellular states determine calcium signaling response.

The heterogeneity in mammalian cells signaling response is largely a result of pre-existing cell-to-cell variability. It is unknown whether cell-to-cell variability rises from biochemical stochastic fluctuations or distinct cellular states. Here, we utilize calcium response to adenosine trisphosphate as a model for investigating the structure of heterogeneity within a population of cells and analyze whether distinct cellular response states coexist. We use a functional definition of cellular state that is based on a mechanistic dynamical systems model of calcium signaling. Using Bayesian parameter inference, we obtain high confidence parameter value distributions for several hundred cells, each fitted individually. Clustering the inferred parameter distributions revealed three major distinct cellular states within the population. The existence of distinct cellular states raises the possibility that the observed variability in response is a result of structured heterogeneity between cells. The inferred parameter distribution predicts, and experiments confirm that variability in IP3R response explains the majority of calcium heterogeneity. Our work shows how mechanistic models and single-cell parameter fitting can uncover hidden population structure and demonstrate the need for parameter inference at the single-cell level.
Facile Synthesis of dl-4,4-Difluoroornithine, dl-4,4-Difluoroglutamine, and γ-dl-4,4-Difluoroglutamyl-Containing Peptides: Regiospecific Addition of Nucleophiles to N-Cbz-di-tert-butyl-dl-4,4-difluoroglutamate

The reaction of several nucleophiles with N-Cbz-protected di-tert-butyl-dl-4,4-difluoroglutamate was investigated as an approach to the synthesis of various fluorinated amino acids and peptides. The γ-carboxyl group is highly activated by the two adjacent fluorine atoms, and nucleophilic reactions occurred exclusively at that carbonyl carbon. Further transformations of the reaction products resulted in the synthesis of dl-4,4-difluoroornithine, dl-4,4-difluoroglutamine, and γ-dl-4,4-difluoroglutamyl-containing dipeptides.
Translation of upstream open reading frames in a model of neuronal differentiation

Upstream open reading frames (uORFs) initiate translation within mRNA 5′ leaders, and have the potential to alter main coding sequence (CDS) translation on transcripts in which they reside. Ribosome profiling (RP) studies suggest that translating ribosomes are pervasive within 5′ leaders across model systems. However, the significance of this observation remains unclear. To explore a role for uORF usage in a model of neuronal differentiation, we performed RP on undifferentiated and differentiated human neuroblastoma cells. Using a spectral coherence algorithm (SPECtre), we identify 4954 consistently translated uORFs across 31% of all neuroblastoma transcripts. These uORFs predominantly utilize non-AUG initiation codons and exhibit translational efficiencies (TE) comparable to annotated coding regions. On a population basis, the global impact of both AUG and non-AUG initiated uORFs on basal CDS translation were small, even when analysis is limited to conserved and consistently translated uORFs. However, uORFs did alter the translation of a subset of genes, including the Diamond-Blackfan Anemia associated ribosomal gene RPS24. With retinoic acid induced differentiation, we observed an overall positive correlation in translational shifts between uORF/CDS pairs. However, CDSs downstream of uORFs show smaller shifts in TE with differentiation relative to CDSs without a predicted uORF, suggesting that uORF translation buffers cell state dependent fluctuations in CDS translation. This work provides insights into the dynamic relationships and potential regulatory functions of uORF/CDS pairs in a model of neuronal differentiation.
Infectious Disease Dynamics Inferred from Genetic Data via Sequential Monte Carlo

Genetic sequences from pathogens can provide information about infectious disease dynamics that may supplement or replace information from other epidemiological observations. Most currently available methods first estimate phylogenetic trees from sequence data, then estimate a transmission model conditional on these phylogenies. Outside limited classes of models, existing methods are unable to enforce logical consistency between the model of transmission and that underlying the phylogenetic reconstruction. Such conflicts in assumptions can lead to bias in the resulting inferences. Here, we develop a general, statistically efficient, plug-and-play method to jointly estimate both disease transmission and phylogeny using genetic data and, if desired, other epidemiological observations. This method explicitly connects the model of transmission and the model of phylogeny so as to avoid the aforementioned inconsistency. We demonstrate the feasibility of our approach through simulation and apply it to estimate stage-specific infectiousness in a subepidemic of human immunodeficiency virus in Detroit, Michigan. In a supplement, we prove that our approach is a valid sequential Monte Carlo algorithm. While we focus on how these methods may be applied to population-level models of infectious disease, their scope is more general. These methods may be applied in other biological systems where one seeks to infer population dynamics from genetic sequences, and they may also find application for evolutionary models with phenotypic rather than genotypic data.
Synthesis of C-aryl-Δ2,3-glycopyranosides via uncatalyzed addition of triarylindium reagents to glycals

Abstract 2,3-Unsaturated- C -aryl glycopyranosides are important intermediates in the synthesis of medicinally important C -aryl glycosides. Treatment of glycal acetates with triarylindiums in ether at room temperature gives good yields of C -aryl-Δ 2,3 -glycosides of predominantly α-configuration. The mechanism of this reaction likely involves the formation of an oxocarbenium ion intermediate via indium(III) Lewis acid-assisted ionization of the glycal C.3 acetate. Coupling of trivinyl- and tris(alkynyl)indiums with glycals similarly led to C -vinyl- and C -alkynyl-Δ 2,3 -glycosides in good yield.
DNA topology in chromatin is defined by nucleosome spacing.

In eukaryotic nucleosomes, DNA makes ~1.7 superhelical turns around histone octamer. However, there is a long-standing discrepancy between the nucleosome core structure determined by x-ray crystallography and measurements of DNA topology in circular minichromosomes, indicating that there is only ~1.0 superhelical turn per nucleosome. Although several theoretical assumptions were put forward to explain this paradox by conformational variability of the nucleosome linker, none was tested experimentally. We analyzed topological properties of DNA in circular nucleosome arrays with precisely positioned nucleosomes. Using topological electrophoretic assays and electron microscopy, we demonstrate that the DNA linking number per nucleosome strongly depends on the nucleosome spacing and varies from −1.4 to −0.9. For the predominant {10n + 5} class of nucleosome repeats found in native chromatin, our results are consistent with the DNA topology observed earlier. Thus, we reconcile the topological properties of nucleosome arrays with nucleosome core structure and provide a simple explanation for the DNA topology in native chromatin with variable DNA linker length. Topological polymorphism of the chromatin fibers described here may reflect a more general tendency of chromosomal domains containing active or repressed genes to acquire different nucleosome spacing to retain topologically distinct higher-order structures.
An unprecedented Favorski-like ring contraction of the 1,3,4-oxadiazinone ring to a bimane

Abstract The reaction of oxadiazinone 5 with sodium hydride in THF leads to an unprecedented Favorski-like ring contraction to the diazacyclopentadienone 1 which then dimerizes with loss of one molecule of nitrogen to give the observed bimane 3.
Highly Unsaturated Hydrogenated Silicon Clusters, SinHx (n = 3−10, x = 0−3), in Flash Pyrolysis of Silane and Disilane

Bare and partially hydrogenated neutral silicon clusters, SinHx (n = 3−10, x = 0−3), were produced upon flash pyrolysis of dilute (1%) mixtures of disilane, Si2H6, in Ar and of silane, SiH4, in He at temperatures above ∼1000 K. Immediately following the flash pyrolysis of the precursors (on an ∼20 μs time scale), the clusters were isolated in a supersonic molecular beam and detected by single vacuum ultraviolet (VUV) photon (λ = 118.2 or 121.6 nm) ionization time-of-flight mass spectrometry (TOFMS). The clusters produced were similar for both precursors with SinHx (n = 4, 6, 7, 10) being significantly populated and Si6Hx being the most abundant, consistent with the known “magic numbers” of Si clusters. Hydrogen contents in these SinHx clusters were small with typical hydrogen mole fractions near 10%. The most stable structures of the Si6H and Si6H2 clusters were identified using ab initio quantum mechanical methods. Initial thermal decomposition intermediates and reaction products, such as SiH2, Si2H4, Si...
Studies on ristocetin A. A synthesis of protected ristomycinic acid using organomanganese chemistry

Abstract Aryl ether formation by reaction of phenoxide nucleophiles with chloroarene-Mn(CO)3 cationic complexes, followed by reaction of the aryloxyarene-Mn(CO)3 complex with chiral glycine enolate equivalents, provides methodology for the synthesis of protected ristomycinic acid derivatives in a state of high optical purity.
Facile synthesis of 6,12b-diaza-dibenzo[a,h]azulen-7-ones and benzo[f]pyrrolo[1,2-a][1,4]diazepin-4-ones via CuI/l-proline catalyzed intramolecular N-arylation

Abstract Facile intramolecular N-arylation catalyzed by CuI/ l -proline has been developed to prepare 6,12b-diaza-dibenzo[a,h]azulen-7-ones and benzo[f]pyrrolo[1,2-a][1,4]diazepin-4-ones in good to excellent yields.
Catalytic Asymmetric Allylation Reactions Using BITIP Catalysis and 2-Substituted Allylstannanes as Surrogates for β-Keto Ester Dianions

Catalytic asymmetric allylation (CAA) reactions using the indicated allylstannane and the BITIP catalysts previously described by us give high yields and enantioselectivities in additions to aldehydes. The products are convertible to β-keto esters by oxidative cleavage of the olefin. These reactions thus provide a useful catalytic enantioselective method for chain extension with introduction of a versatile four-carbon unit.
Synthesis of 4-(2-chloroethyl)-2,3-dihydro[1,4]oxazino[2,3- b ]quinoline and 4-(2-chloroethyl)2,3-dihydropyrido[2,3- b ][1,4]oxazine

The title compounds were synthesized from 3-[bis(2-hydroxyethyl)- amino]quinolin-2(1H)-one (11a) and 3-[bis(2-hydroxyethyl)amino]- pyridin-2(1H)-one (18) respectively. The preparation involved a tandem chlorination/cyclization reaction
Direct Extraction of Ag+ and Hg2+ from Cyanide Complexes and Mode of Binding by the Layered K2MgSn2S6 (KMS-2)

K1.38Mg0.69Sn1.31S4 is prepared by solid state reaction of Sn, Mg, K2S, and S (silica tube, 800 °C, 6 h, 80% yield) as well as hydrothermally from aqueous mixtures of Sn, K2CO3, Mg, and S (autoclave, 220 °C, 4 h, 76% yield).
Rh(I)/diene-catalyzed addition reactions of aryl/alkenylboronic acids with aldehydes

Abstract [Rh(COD)Cl] 2 -catalyzed addition reactions of arylboronic acids with aldehydes, with low Rh(I) catalyst loading, are described. We also found that the reaction of arylboronic acids with α,β-unsaturated aldehydes greatly depends on the solvent and the steric hindrance of the reagents/substrates.
Conversion of α,β-epoxyketones to diosphenols using 6-methyl-2-pyridone anion as an hydroxide equivalent

Abstract Treatment of α,β-epoxyketones with 6-methyl-2-pyridone anion gives diosphenol (6-methyl-2-pyridyl) ethers that can be cleaved to diosphenols under mild basic conditions.
What ignites optical jets

The properties of radio galaxies and quasars with and without optical or X-ray jets are compared. The majority of jets from which high-frequency emission has been detected so far (13 with optical emission, 11 with X-rays, 13 with both) are associated with the most powerful radio sources at any given redshift. It is found that optical/X-ray jet sources are more strongly beamed than the average population of extragalactic radio sources. This suggests that the detection or non-detection of optical emission from jets has so far been dominated by surface brightness selection effects, not by jet physics. It implies that optical jets are much more common than is currently appreciated.
Possible spontaneous breaking of Lorentz and CPT symmetry

One possible ramification of unified theories of nature such as string theory that may underlie the conventional standard model is the possible spontaneous breakdown of Lorentz and CPT symmetry. In this talk, the formalism for inclusion of such effects into a low-energy effective field theory is presented. An extension of the standard model that includes Lorentz-and CPT-breaking terms is developed. The restriction of the standard model extension to the QED sector is then discussed.
Copper-catalyzed allylic amination of olefins with nitrosoarenes

Abstract The transition metal catalyzed allylic amination of olefins are studied. A screening of catalysts known for the intermediacy of PhNO in the amination of alkene with phenylhydroxylamine reveals that the hydrated copper salt in conjugation with copper powder as reductant has the best catalytic properties using nitrosobenzene as nitrogen-fragment donor. The catalytic system has been studied for a variety of alkenes. Unsymmetrical alkenes react with high regioselectivity with N -functionalization at the less substituted vinylic carbon.
Enantioselective Scandium-Catalyzed Vinylsilane Additions: A New Approach to the Synthesis of Enantiopure β,γ-Unsaturated α-Hydroxy Acid Derivatives

The development of the Lewis acid-catalyzed alkenylation using trimethylvinylsilanes is described. Both aliphatic and aromatic vinylsilanes were effective nucleophiles at room temperature affording chiral allylic alcohol products in excellent enantioselectivities (97 → 99% ee) and in moderate to good yields (45−99%). Complete retention of vinysilane geometry was observed where applicable.
Case Study of a γ-Butyrolactone Alkylation with 1,3-Dimethyl-2-imidazolidinone as a Promoter

1,3-Dimethyl 2-imidazolidinone (DMI) is of lower toxicological risk than 1,3-dimethyl-3,4,5,6-tetrahydro-2(1H)-pyrimidinone (DMPU), hexamethyl-phosphorus triamide (HMPT), and hexamethylphosphoramid...
First representatives of porphyrinylnucleosides

Abstract 5′-0-(5-p-Phenylene-10,15,20-tri-p-tolylporphyrin)uridine and similarly substituted(2′,3′-0-isopropylidene)adenosine were obtained as first representatives of nucleosides containing covalently bonded porphyrin.
Electronic Nature of α-Methoxy, Amino, Cyano, and Mercapto Nitrones

The electronic nature of various C-substituted nitrones was investigated by IR spectroscopy and 13 C NMR as well as MNDO calculations. These include α-methoxy nitrones (imidate N-oxides) RC(OMe)=N(O)t-Bu with R = p -MeOC 6 H 4 ( Ia ), C 6 H 5 ( Ib ), p -NO 2 C 6 H 4 ( Ic ), and H ( Id ) and nitrones YCH=N(O)t-Bu with Y = CN ( IIIa ), n-BuS ( IIIb ), C 6 H 5 CH 2 NH ( IIIc ). Upfield 13 C shifts of C(α), the iminyl (C=N) carbon, of imidate N-oxides I versus the corresponding imidates are less than the usual upfield shifts of imine N-oxides versus imines, suggesting less buildup of electron density on C(α) in the case of alcoxy nitrones. Charge density and π bond order values from MNDO calculations for C-methoxy-C-phenyl nitrones versus model systems confirm this result and indicate a more localized C=N π bond in nitrones bearing an α-methoxy group. For N-tert-butyl nitrones with an α heteroatom (nitrogen or sulfur), phenyl, or cyano group, C(α) shifts move downfield for π-donating groups and upfield for π-accepting groups. This "reverse substituent effect" as well as C=N stretching frequencies can also be readily explained by C=N π bond containment by lone pair groups. The reported enhanced cycloaddition reactivity of α-alkoxy nitrones and their electrochemical behavior are discussed in terms of HOMO energy levels.
Deprotection of a primary Boc group under basic conditions

Treatment of a primary t-butyl carbamate (Boc) group with excess sodium t-butoxide in slightly wet tetrahydrofuran or 2-methyltetrahydrofuran provides the corresponding primary amine in excellent yield. We believe the reaction proceeds through an isocyanate intermediate.
Leveraging Quality Prediction Models for Automatic Writing Feedback.

User-generated, multi-paragraph writing is pervasive and important in many social media platforms (i.e. Amazon reviews, AirBnB host profiles, etc). Ensuring high-quality content is important. Unfortunately, content submitted by users is often not of high quality. Moreover, the characteristics that constitute high quality may even vary between domains in ways that users are unaware of. Automated writing feedback has the potential to immediately point out and suggest improvements during the writing process. Most approaches, however, focus on syntax/phrasing, which is only one characteristic of high-quality content. Existing research develops accurate quality prediction models. We propose combining these models with model explanation techniques to identify writing features that, if changed, will most improve the text quality. To this end, we develop a perturbation-based explanation method for a popular class of models called tree-ensembles. Furthermore, we use a weak-supervision technique to adapt this method to generate feedback for specific text segments in addition to feedback for the entire document. Our user study finds that the perturbation-based approach, when combined with segment-specific feedback, can help improve writing quality on Amazon (review helpfulness) and Airbnb (host profile trustworthiness) by > 14% (3X improvement over recent automated feedback techniques).
Phosphoryl Transfer Enzymes and Hypervalent Phosphorus Chemistry: A Keynote Lecture of the 7th International Conference on Heteroatom Chemistry

The coordination tendencies of phosphorus to form a hexacoordinated state from a pentacoordinated state which might assist in describing mechanistic action of phosphoryl transfer enzymes are delineated. The factors discussed include substrate and transition or intermediate state anionicity; hydrogen bonding; packing effects, i.e., van der Waals forces; the ease of formation of hexacoordinate phosphorus from lower coordinate states; and the pseudorotation problem common to nonrigid pentacoordinate phosphorus. In view of the work reported in this account and recent work on enzyme promiscuity and moonlighting activities, it is suggested that donor action should play a role in determining active-site interactions in phosphoryl transfer enzyme mechanisms.
Polymeric DABCO–bromine complex: a mild oxidant for the preparation of ketones and aldehydes

Abstract A stable, shelf-ready polymeric oxidant was prepared from the addition of Br2 to DABCO in CCl4. This material was used to convert simple primary and secondary alcohols to the corresponding aldehydes and ketones in biphasic CH2Cl2/H2O.
Synthesis and structure of a new family of 3d–4f heterometallic compounds Rb7LnFe6O2(PO4)8 (Ln=Sm, Eu, Gd, Dy): Magnetic properties of the Sm-, Gd-, Dy-derivatives

Abstract A new family of mixed lanthanide(III) and iron(III) oxo-phosphate phases, Rb7LnFe6O2(PO4)8 (Ln=Sm 1, Eu 2, Gd 3, Dy 4), was isolated by using a high-temperature, solid-state method in molten-salt media. The X-ray single-crystal structure analysis shows that these isomorphic derivatives crystallize in a triclinic space group P–1 (no. 2); Z=1. The 3-D framework of these 3d–4f oxo-phosphates are comprised of LnO6 octahedral, FeO5 trigonal bipyramidal (tbp), and μ3-oxo [Fe4O18] tetrameric units interconnected through PO4 tetrahedra. The preliminary results of the temperature-dependent magnetic susceptibility measurements for selected compounds (1, 3, 4) reveal antiferromagnetic-like behavior. 1 shows a weak antiferromagnetric ordering at TN=∼7 K while others show little evidence of long-range magnetic order down to 2 K. All three compounds have measured magnetic moments significantly smaller than the expected values.
Optically Active Cyclobutanone Chemistry: Synthesis of (−)-Cyclobut-A and (±)-3‘-Epi-Cyclobut-A

The carbocyclic nucleoside analogues (−)-cyclobut-A and (±)-3‘-epi-cyclobut-A were synthesized utilizing photolysis of the (benzyloxymethyl)(methoxy) chromium carbene complex 4 with optically active ene-carbamate 5 to produce the corresponding optically active α,α-disubstituted cyclobutanone 6. Stereoselective removal of the α-ethoxy group with inversion gave cyclobutanone 7, which was converted by existing methodology to the title compounds.
Synthesis of the Glycosphingolipid β-Galactosyl Ceramide and Analogues via Olefin Cross Metathesis

The preparation of the glycosphingolipid galactosyl ceramide from an orthogonally protected five-carbon building block is described. The main chain of the lipid is installed via a highly stereoselective olefin cross metathesis reaction. The methodology permits the facile preparation of glycolipids which vary in the length of the main carbon chain.
Anonymous Signatures Revisited.

We revisit the notion of the anonymous signature, first formalized by Yang, Wong, Deng and Wang [12], and then further developed by Fischlin [6] and Zhang and Imai [13]. We present a new formalism of anonymous signature, where instead of the message, a part of the signature is withheld to maintain anonymity. We introduce the notion unpretendability to guarantee infeasibility for someone other than the correct signer to pretend authorship of the message and signature. Our definition retains applicability for all previous applications of the anonymous signature, provides stronger security, and is conceptually simpler. We give a generic construction from any ordinary signature scheme, and also show that the short signature scheme by Boneh and Boyen [4] can be naturally regarded as such a secure anonymous signature scheme according to our formalism.
Hydrothermal synthesis and crystal structures of two novel acentric mixed alkaline earth metal berylloborates Sr3Be2B5O12(OH) and Ba3Be2B5O12(OH).

The synthesis and structure of the isostructural acentric compounds Sr(3)Be(2)B(5)O(12)(OH) (1) and Ba(3)Be(2)B(5)O(12)(OH) (2) are reported for the first time. These compounds crystallize in the space group R3m, and the unit cell parameters are a = 10.277(15) A and c = 8.484(17) A for 1 and a = 10.5615(15) A and c = 8.8574(18) A for 2. The structures consist of a network of [Be(2)B(4)O(12)(OH)] units interwoven with a network consisting of MO(9) polyhedra (M = Sr, Ba) and BO(3) triangles and exemplify how acentric building blocks such as [BO(3)](3-), [BO(4)](5-), and [BeO(4)](6-) can be especially suitable to build noncentrosymmetric long-range structures. Both networks are centered on the 3-fold rotation axis and present themselves in alternating fashion along [001]. Acentricity is imparted by the alignment of the polarities of BO(3) and BeO(4) environments. Infrared spectroscopy has been used to confirm the local geometries of B and Be, as well as the presence of hydroxide in the crystal structure. Another interesting feature of these compounds is the presence of disorder involving Be and B at the tetrahedral Be site. The degree of the disorder has been confirmed by observing a noticeable shortening of average Be-O bond distances.
Carbometalations of Simple Alkenes with Allyldibromoborane

The allylboration of alkenes with allyldibromoborane is described. Utilizing an improved methodology for the synthesis of allyldibromoborane, 1,3-dienes, styrene, and even isolated alkenes could be...
One pot direct synthesis of oxazolines, benzoxazoles, and oxadiazoles from carboxylic acids using the Deoxo-Fluor reagent

A one-pot, high yield direct synthesis of various 2-substituted oxazolines, benzoxazoles, and 2-oxadiazoles from carboxylic acids using Deoxo-Fluor reagent is described.
Increased ring closing metathesis activity of ruthenium-based olefin metathesis catalysts coordinated with imidazolin-2-ylidene ligands

Abstract The novel air and water tolerant, imidazolinylidene-substituted ruthenium-based complex 3, has been prepared starting from RuCl2(CHPh)(PCy3)2 2 and shown to exhibit increased ring-closing metathesis activity at elevated temperature compared to that of the parent complex 2. Di-, tri-, and even tetra-substituted cycloolefins were successfully prepared from corresponding diene precursors using catalytic amounts of 3 in moderate to excellent yields.
Exploratory synthesis with molten aluminum as a solvent and routes to multinary aluminum silicides. Sm2Ni(NixSi1-x)Al4Si6 (x = 0.18-0.27) : A new silicide with a ferromagnetic transition at 17.5 K

A new quaternary silicide, Sm2Ni(NixSi1-x)Al4Si6 (x = 0.18−0.27), has been synthesized from Sm2O3, NiO, and Si or Sm, Ni, and Si in Al metal flux at 800 °C. The structure, determined by single-crystal X-ray diffraction, is tetragonal, space group P4/nmm (No. 129) with Z = 2, and lattice parameters a = b = 5.8060(3) A, c = 14.845(1) A. Refinement based upon F2 [I > 2σ(I)] yielded R1 = 0.0252 and wR2 = 0.0634. The compound exhibits a new structure type containing two different alternating layers which are linked together through Si/Ni−Si bonds to form a three-dimensional framework. One layer is formed by edge-shared (the edges parallel to c) NiAl8 cubes. The other layer is a Si-based net which consists of six-member, five-member, and square planar rings. The structure of this compound cannot be rationalized on the basis of the Zintl−Klemm concept. Extended Huckel, tight binding calculations were carried out for different hypothetical stoichiometries, besides the observed one, of the compound Sm2Ni(NixSi1-x)...
Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data.

The accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence of contaminants—DNA sequences not truly present in the sample. Contaminants come from various sources, including reagents. Appropriate laboratory practices can reduce contamination, but do not eliminate it. Here we introduce decontam ( https://github.com/benjjneb/decontam ), an open-source R package that implements a statistical classification procedure that identifies contaminants in MGS data based on two widely reproduced patterns: contaminants appear at higher frequencies in low-concentration samples and are often found in negative controls. Decontam classified amplicon sequence variants (ASVs) in a human oral dataset consistently with prior microscopic observations of the microbial taxa inhabiting that environment and previous reports of contaminant taxa. In metagenomics and marker-gene measurements of a dilution series, decontam substantially reduced technical variation arising from different sequencing protocols. The application of decontam to two recently published datasets corroborated and extended their conclusions that little evidence existed for an indigenous placenta microbiome and that some low-frequency taxa seemingly associated with preterm birth were contaminants. Decontam improves the quality of metagenomic and marker-gene sequencing by identifying and removing contaminant DNA sequences. Decontam integrates easily with existing MGS workflows and allows researchers to generate more accurate profiles of microbial communities at little to no additional cost.
Sequential Nucleophilic Acyl Substitution/Alkenyl Transfer Reactions Mediated by Samarium(II) Iodide

Samarium(II) iodide (SmI2) has been employed in a one-pot, three-step, nucleophilic acyl substitution/ketyl−olefin coupling/β-elimination reaction sequence. This novel protocol combines two recently developed SmI2-mediated processes to permit the net delivery of an alkenyl moiety to a ketone carbonyl generated as an intermediate along the sequential reaction pathway. A remarkable measure of stereocontrol over three to five contiguous stereocenters is established in the process as a result of the excellent facial selectivity conveyed in the ketyl−olefin coupling reaction. Unique to the SmI2-mediated process, the relative asymmetric induction engendered in these addition reactions is complementary to more traditional nucleophilic addition reactions in that the alkenyl group is delivered to the carbonyl center by an attached tether. Moreover, the protocol avoids the basic reaction conditions characteristic of alkenylmagnesium halides and alkenyllithium reagents.
Concern noted: A descriptive study of editorial expressions of concern in PubMed and PubMed Central.

An editorial expression of concern (EEoC) is issued by editors or publishers to draw attention to potential problems in a publication, without itself constituting a retraction or correction. We searched PubMed, PubMed Central (PMC), and Google Scholar to identify EEoCs issued for publications in PubMed and PMC up to 22 August 2016. We also searched the archives of the Retraction Watch blog, some journal and publisher websites, and studies of EEoCs. In addition, we searched for retractions of EEoCs and affected articles in PubMed up to 8 December 2016. We analyzed overall historical trends, as well as reported reasons and subsequent editorial actions related to EEoCs issued between August 2014 and August 2016. After screening 5076 records, we identified 230 EEoCs that affect 300 publications indexed in PubMed, the earliest issued in 1985. Half of the primary EEoCs were issued between 2014 and 2016 (52%). We found evidence of some EEoCs that had been removed by the publisher without leaving a record, and some were not submitted for PubMed or PMC indexing. A minority of publications affected by EEoCs had been retracted by early December 2016 (25%). For the subset of 92 EEoCs issued between August 2014 and August 2016, affecting 99 publications, the rate of retraction was similar (29%). The majority of EEoCs were issued because of concerns with validity of data, methods, or interpretation of the publication (68%), and 31% of cases remained open. Issues with images were raised in 40% of affected publications. Ongoing monitoring after the study identified another 17 EEoCs to year’s end in 2016, increasing the number of EEoCs to 247 and publications in PubMed known to be affected by EEoCs to 320 at the end of 2016. EEoCs have been rare publishing events in the biomedical literature, but their use has been increasing. Most have not led to retractions, and many remain unresolved. Lack of prominence and inconsistencies in management of EEoCs reduce the ability of these notices to alert the scientific community to potentially serious problems in publications. EEoCs will be made identifiable in PubMed in 2017.
Determination of the Enthalpies of Formation of DyI2 and DyI3 and estimation of the Dy3+/Dy2+ standard aqueous electrode potential

DyI2 and Dy3I were synthesized by literature techniques. Their enthalpies of solution were determined and their enthalpies of formation calculated to be ΔfH°(DyI2, s, 298 K) = −(394 ± 16) kJ· mol−1 and ΔfH°(DyI3, s, 298 K) = −(616 ± 10) kJ· mol−1. With appropriate literature and estimated enthalpies of solution and standard entropies, the E°(Dy3+/Dy2+, aq) was calculated to be −(2.6 ± 0.2) V. A comparison is made of the enthalpies of reduction of DyI3 to DyI2 and of DyCl3 to DyCl2. Bestimmung der Bildungsenthalpien von DyI2 und DyI3 sowie Abschatzung des Dy3+/Dy2+-Standardelektrodenpotentials in wasrigem Medium DyI2 and DyI3 wurden nach Literaturmethoden hergestellt. Ihre Losungsenthalpien wurden bestimmt und die Bildungsenthalpien zu ΔfH°(DyI3, s, 298 K) = −(394 ± 16) kJ · mol−1 und ΔfH°(DyI2, s, 298 K) = -(616 ± 10) kJ· mol−1 berechnet. Entsprechenden Literaturangaben sowie geschatzten Losungsenthalpien und Standardentropien wurde E°(Dy3+/Dy2+, aq.) zu −(2.6 ± 0.2) V berechnet. Ein Vergleich der Enthalpien fur die Reduktion von DyI3 zu DyI2 bzw. DyI zu DyI2 wird vorgenommen.
Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function

Non-coding gene regulatory enhancers are essential to transcription in mammalian cells. As a result, a large variety of experimental and computational strategies have been developed to identify cis-regulatory enhancer sequences. Given the differences in the biological signals assayed, some variation in the enhancers identified by different methods is expected; however, the concordance of enhancers identified by different methods has not been comprehensively evaluated. This is critically needed, since in practice, most studies consider enhancers identified by only a single method. Here, we compare enhancer sets from eleven representative strategies in four biological contexts. All sets we evaluated overlap significantly more than expected by chance; however, there is significant dissimilarity in their genomic, evolutionary, and functional characteristics, both at the element and base-pair level, within each context. The disagreement is sufficient to influence interpretation of candidate SNPs from GWAS studies, and to lead to disparate conclusions about enhancer and disease mechanisms. Most regions identified as enhancers are supported by only one method, and we find limited evidence that regions identified by multiple methods are better candidates than those identified by a single method. As a result, we cannot recommend the use of any single enhancer identification strategy in all settings. Our results highlight the inherent complexity of enhancer biology and identify an important challenge to mapping the genetic architecture of complex disease. Greater appreciation of how the diverse enhancer identification strategies in use today relate to the dynamic activity of gene regulatory regions is needed to enable robust and reproducible results.
Gd13Fe10C13: indications of Fe-Fe multiple bonding emerging from chemical frustration.

We report the synthesis and crystal structure of the carbide Gd13Fe10C13. This compound adopts a new structure type that is remarkable for its 'H'-shaped C2FeFeC2 units, which have some of the shortest Fe-Fe contacts known. A bonding analysis using DFT-calibrated Hueckel calculations hints that Fe-Fe multiple bonding underlies these short distances. Gd13Fe10C13 undergoes ferromagnetic ordering at ~55 K.
Thermodynamic studies on the cyclodextrin complexation of aromatic and aliphatic guests in water and water-urea mixtures. Experimental evidence for the interaction of urea with arene surfaces

The thermodynamic functions that describe the complexation of a series of four carboxylic acid guests and two related quaternary ammonium derivatives with β-cyclodextrin were measured using flow calorimetry at 298 K in aqueous media in the presence and in the absence of large concentrations of urea. The relative differences of the thermodynamic parameters of complexation revealed the existence of specific interactions between urea and the aromatic surfaces of some of the nonpolar guests. As expected, the relative changes in the complex stability constants upon addition of urea have been found to depend on the balance of opposing enthalpic and entropic contributions. The interpretation as well as the magnitude of the interaction between urea and aromatic surfaces are in line with previous experimental and computational studies. The experimental evidence presented in this work provides insight into the mechanism by which large amounts of urea denature globular proteins in aqueous media.
A New Reaction for Organoselenium Compounds: Alkyl Transfer from Diorganoselenium(IV) Dibromides to Alkenoic Acids To Give γ- and δ-Lactones

Various 1-[[bis(1-methylethyl)amino]carbonyl]-2-(dibromo-n-alkylseleno)ferrocene derivatives reacted with 2 equiv of 4-pentenoic acid or 5-hexenoic acid to give the corresponding γ- or δ-lactones, respectively, from transfer of the alkyl group bound to selenium to the terminal alkene carbon. In the lactone cyclization, 1-[[bis(1-methylethyl)amino]carbonyl]-2-(bromoselenenyl)ferrocene (25) is formed and reacts with a second equivalent of the alkenoic acid to give either 5-[1-[[bis(1-methylethyl)amino]carbonyl]ferrocene-2-selenenylmethyl]tetrahydro-2-furanone (23) or 6-[1-[[bis(1-methylethyl)amino]carbonyl]ferrocene-2-selenenylmethyl]tetrahydro-2H-pyran-2-one (26) as a mixture of diastereomers in yields comparable to the corresponding γ- or δ-lactone. The addition of 1-[[bis(1-methylethyl)amino]carbonyl]-2-(dibromo-n-butylseleno)ferrocene to 3-butenoic acid gave alkyl transfer to the internal alkene carbon and formation of the γ-lactone. Density functional theory (DFT) geometry optimizations were performed ...
EFFICIENT HYDROGENATION OF STERICALLY HINDERED OLEFINS WITH BORANE-METHYL SULFIDE COMPLEX

Sterically hindered olefins are efficiently reduced to the corresponding alkanes by the borane−methyl sulfide (BMS) complex at room temperature (or below) in dichloromethane containing a mild one-electron oxidant (such as an aromatic cation radical) or by the passage of an anodic current. In an alternative procedure, the hydrogenation of the same (electron-rich) olefins with the BMS complex (in the absence of a one-electron oxidant) is also carried out in the presence of a strong Bronsted acid (such as HBF4). In the oxidative activation, olefin cation radicals are the first observable intermediates, and separate experiments (including transient electrochemistry) confirm the facile reduction of the olefin cation radical by borane to produce the corresponding alkane. The direct protonation of olefins produces carbocationic intermediates which are also efficiently reduced by borane to the corresponding alkanes. The intermediacy of both olefin cation radicals and carbocations in the hydrogenation procedure wi...
The number of minimum k-cuts: improving the Karger-Stein bound

Given an edge-weighted graph, how many minimum k-cuts can it have? This is a fundamental question in the intersection of algorithms, extremal combinatorics, and graph theory. It is particularly interesting in that the best known bounds are algorithmic: they stem from algorithms that compute the minimum k-cut. In 1994, Karger and Stein obtained a randomized contraction algorithm that finds a minimum k-cut in O(n(2−o(1))k) time. It can also enumerate all such k-cuts in the same running time, establishing a corresponding extremal bound of O(n(2−o(1))k). Since then, the algorithmic side of the minimum k-cut problem has seen much progress, leading to a deterministic algorithm based on a tree packing result of Thorup, which enumerates all minimum k-cuts in the same asymptotic running time, and gives an alternate proof of the O(n(2−o(1))k) bound. However, beating the Karger–Stein bound, even for computing a single minimum k-cut, has remained out of reach. In this paper, we give an algorithm to enumerate all minimum k-cuts in O(n(1.981+o(1))k) time, breaking the algorithmic and extremal barriers for enumerating minimum k-cuts. To obtain our result, we combine ideas from both the Karger–Stein and Thorup results, and draw a novel connection between minimum k-cut and extremal set theory. In particular, we give and use tighter bounds on the size of set systems with bounded dual VC-dimension, which may be of independent interest.
A Study on Graph-Structured Recurrent Neural Networks and Sparsification with Application to Epidemic Forecasting

We study epidemic forecasting on real-world health data by a graph-structured recurrent neural network (GSRNN). We achieve state-of-the-art forecasting accuracy on the benchmark CDC dataset. To improve model efficiency, we sparsify the network weights via a transformed-\(\ell _1\) penalty without losing prediction accuracy in numerical experiments.
An efficient synthesis of vinylogous carbamates from alkyl azides

Abstract An efficient one-pot synthesis of vinylogous carbamates is reported starting from alkyl azides by using NH 4 Cl/Zn dust.
Assessing the Chemistry and Bioavailability of Dissolved Organic Matter From Glaciers and Rock Glaciers

As glaciers in the western United States thaw in response to warming, they release dissolved organic matter (DOM) to alpine lakes and streams. Biological availability of DOM from small mountain glaciers is unknown. Differences in DOM bioavailability between glacier types like rock and ice glaciers remains undefined, yet rock glaciers outnumber ice glacier approximately ten to one at low latitudes. To assess which components of aquatic DOM are most reactive and the potential for glacial DOM from low latitude glaciers to subsidize heterotrophy in alpine headwaters we evaluated reactivity and molecular composition of DOM from ice glaciers and rock glaciers from four paired catchments (each with a glacier and rock glacier at their headwaters). Biological reactivity was linked to molecular composition by evaluating the chemical characteristics of each DOM pool pre- and post-incubation using common microbial community laboratory assays paired with untargeted mass spectrometry-based metabolomics. Glacier and rock glacier DOM was similar in concentration and chemodiversity, but differed in composition. When incubated with a common microbial community, DOM from ice glacier meltwaters contained a higher proportion of bioavailable DOM (BDOM), and resulted in greater bacterial growth efficiency. Differences in DOM reactivity between glacier types was determined by differences in the relative abundance of only a few dozen compounds. Though BDOM was lower in rock glaciers, because rock glaciers are more abundant and are expected to have greater longevity, we propose that both glacial types will be important sources of bioavailable DOM to alpine headwaters over the coming years to decades.
On the Round-Trip Efficiency of an HVAC-Based Virtual Battery

Flexible loads, especially heating, ventilation, and air-conditioning (HVAC) systems can be used to provide a battery-like service to the power grid by varying their demand up and down over a baseline. Recent work has reported that providing virtual energy storage with HVAC systems leads to a net loss of energy, akin to a low round-trip efficiency (RTE) of a battery. In this paper, we rigorously analyze the RTE of a virtual battery through a simplified physics-based model. We show that the low RTEs reported in recent experimental and simulation work are an artifact of the experimental/simulation setup. When the HVAC system is repeatedly used as a virtual battery, the asymptotic RTE is 1. Robustness of the result to assumptions made in the analysis is illustrated through a simulation case study.
Negative results in computer vision: A perspective

Abstract A negative result is when the outcome of an experiment or a model is not what is expected or when a hypothesis does not hold. Despite being often overlooked in the scientific community, negative results are results and they carry value. While this topic has been extensively discussed in other fields such as social sciences and biosciences, less attention has been paid to it in the computer vision community. The unique characteristics of computer vision, particularly its experimental aspect, call for a special treatment of this matter. In this manuscript, I will address what makes negative results important, how they should be disseminated and incentivized, and what lessons can be learned from cognitive vision research in this regard. Further, I will discuss matters such as experimental design, statistical hypothesis testing, explanatory versus predictive modeling, performance evaluation, model comparison, reproducibility of findings, the confluence of computer vision and human vision, as well as computer vision research culture.
Regularizing Deep Networks by Modeling and Predicting Label Structure

We construct custom regularization functions for use in supervised training of deep neural networks. Our technique is applicable when the ground-truth labels themselves exhibit internal structure; we derive a regularizer by learning an autoencoder over the set of annotations. Training thereby becomes a two-phase procedure. The first phase models labels with an autoencoder. The second phase trains the actual network of interest by attaching an auxiliary branch that must predict output via a hidden layer of the autoencoder. After training, we discard this auxiliary branch. We experiment in the context of semantic segmentation, demonstrating this regularization strategy leads to consistent accuracy boosts over baselines, both when training from scratch, or in combination with ImageNet pretraining. Gains are also consistent over different choices of convolutional network architecture. As our regularizer is discarded after training, our method has zero cost at test time; the performance improvements are essentially free. We are simply able to learn better network weights by building an abstract model of the label space, and then training the network to understand this abstraction alongside the original task.