bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leveraging ancestry to improve causal variant identification in exome sequencing for monogenic disorders
Authors: Brown Robert , Lee Hane , Eskin Ascia , Kichaev Gleb , Lohmueller Kirk E. , Reversade Bruno , Nelson Stanley F. , Pasaniuc Bogdan 
Published: October 2014

AbstractRecent breakthroughs in exome sequencing technology have made possible the identification of many causal variants of monogenic disorders. Although extremely powerful when closely related individuals (e.g. child and parents) are simultaneously sequenced, exome sequencing of individual only cases is often unsuccessful due to the large number of variants that need to be followed-up for functional validation. Many approaches remove from consideration common variants above a given frequency threshold (e.g. 1%), and then prioritize the remaining variants according to their allele frequency, functional, structural and conservation properties. In this work, we present methods that leverage the genetic structure of different populations while accounting for the finite sample size of the reference panels to improve the variant filtering step. Using simulations and real exome data from individuals with monogenic disorders, we show that our methods significantly reduce the number of variants to be followed-up (e.g. a 36% reduction from an average 418 variants per exome when ancestry is ignored to 267 when ancestry is taken into account for case-only sequenced individuals). Most importantly our proposed approaches are well calibrated with respect to the probability of filtering out a true causal variant (i.e. false negative rate, FNR), whereas existing approaches are susceptible to high FNR when reference panel sizes are limited.
Density‐dependent habitat selection of spawning Chinook salmon: broad‐scale evidence and implications
Authors: Falcy Matthew R. 
Published: October 2014

Summary

An extensive body of theory suggests that density‐dependent habitat selection drives many fundamental ecological processes. The ideal free distribution and the ideal despotic distribution make contrasting predictions about the effect of total population size on relative abundances among habitats. Empirical assessment of these habitat selection models is uncommon because data must be collected over large temporal and spatial scales.

I ask whether fluctuation in Chinook salmon (Oncorhynchus tshawytscha) spawner population size through time leads to different relative densities over space.

Twenty‐six years of monitoring data on spawning Chinook salmon across the entire coast of Oregon, USA, were used to evaluate models that make contrasting statements about the interactions of a latent population abundance parameter with physical habitat characteristics.

There is strong information‐theoretic support for models that include terms that allow the spatial variation in density to change as population size changes through time. Analysis of the best model reveals nonlinear isodars, which suggests a ‘despotic’ or ‘preemptive’ distribution of individuals across habitats, indicating that dominant or early‐arriving individuals exclude others from breeding sites.

This finding has implications for genetic dynamics, population dynamics and conservation metrics of these highly valued fish. The novel application of modelling techniques used here to assess mechanisms of habitat selection from observational data can be used in the emerging field of eco‐evolutionary dynamics.
Assembly patterns of mixed‐species avian flocks in the Andes
Authors: Colorado Gabriel J. , Rodewald Amanda D. 
Published: October 2014

Summary

The relative contribution of deterministic and stochastic processes in the assembly of biotic communities is a central issue of controversy in community ecology. However, several studies have shown patterns of species segregation that are consistent with the hypothesis that deterministic factors such as competition and niche‐partitioning structure species assemblages in animal communities.

Community assembly provides a theoretical framework for understanding these processes, but it has been seldom applied to social aggregations within communities.

In this research, we assessed patterns of non‐randomness in Andean mixed‐species flocks using three assembly models: (i) co‐occurrence patterns; (ii) guild proportionality; and (iii) constant body‐size ratios using data from 221 species of resident and Neotropical migrant birds participating in 311 mixed‐species flocks at 13 regions distributed in Venezuela, Colombia, Ecuador and Peru.

Significant assembly patterns for mixed‐species flocks based on co‐occurrence models and guild proportionality models suggest that competitive interactions play an important role in structuring this social system in the Andes. Distribution of species among foraging guilds (i.e. insectivore, frugivore, omnivore, nectivore) was generally similar among flocks, though with some regional variation.

In contrast, we found little evidence that structuring of mixed‐species flocks in the Andes was mediated by body size. Rather, we found greater than expected variance of body‐size ratios within flocks, indicating that birds did not segregate morphologically.

Overall, our findings suggest that deterministic factors associated to competitive interactions are important contributors to mixed‐species flock assemblages across the Andes.
Complete mesocolic excision in colorectal cancer: a systematic review
Authors: Kontovounisios C. , Kinross J. , Tan E. , Brown G. , Rasheed S. , Tekkis P. 
Published: October 2014

AbstractAimSeveral studies have suggested an increased lymph node yield, reduced locoregional recurrence and increased disease‐free survival after complete mesocolic excision (CME) for colorectal cancer. This review was undertaken to assess the use of CME for colon cancer by evaluating the technique and its clinical outcome.MethodA literature search of publications was performed using PubMed and Medline. Only studies published in English were included. Studies assessed for quality and data were extracted by two independent reviewers. End‐points included number of lymph nodes per patient, quality of the plane of mesocolic excision, postoperative mortality and morbidity, 5‐year locoregional recurrence and 5‐year cancer‐specific survival.ResultsThere were 34 articles comprising 12 retrospective studies, nine prospective studies and 13 original articles including case series, observational studies and editorials. Of the prospective studies, four reported an increased lymph node harvest and a survival benefit. The others reported an improvement in the quality of the specimen as assessed by histopathological examination. Laparoscopic CME has the same oncological outcome as open surgery but completeness of excision during laparoscopy may be compromised for tumours in the transverse colon.ConclusionStudies demonstrate that CME removes significantly more tissue around the tumour including maximal lymph node clearance. There is little information on serious adverse events after CME and a long‐term survival benefit has not been proved.
Fixierung cyclischer Peptide: Mimetika von Proteinstrukturmotiven
Authors: Hill Timothy A. , Shepherd Nicholas E. , Diness Frederik , Fairlie David P. 
Published: October 2014

AbstractViele Proteine entfalten ihre biologische Aktivität über kleine exponierte Oberflächenregionen aus gefalteten Peptiden mit wohldefinierten dreidimensionalen Strukturen, Epitope genannt. Kurze synthetische Peptidsequenzen, die diesen bioaktiven Proteinoberflächen entsprechen, bilden in Wasser keine thermodynamisch stabilen proteinähnlichen Strukturen. Die Bildung proteinähnlicher biologisch aktiver Konformationen (Stränge, Helices, Kehren) kann jedoch durch Cyclisierung in Verbindung mit anderen molekularen Verstrebungen induziert werden. Letztere helfen bei der Feinabstimmung der dreidimensionalen Struktur. Solche fixierten cyclischen Peptide können ähnliche biologische Aktivitäten und Wirkungen wie das als Vorbild dienende Protein haben, sodass sie als biologische Sonden und Leitstrukturen für Therapeutika, Diagnostika und Impfstoffe dienen können. Dieser Aufsatz beleuchtet Beispiele für cyclische Peptide, die dreidimensionale Strukturen von Strang‐, Kehren‐ oder Helixabschnitten von Peptiden und Proteinen nachahmen und beschreibt einige weitere Elemente, die in cyclisch peptidischen Naturstoffen und synthetischen makrocyclischen Peptidomimetika vorkommen, dort die Peptidstruktur verfeinern und ihr biologische Aktivitäten verleihen.
Enantioselective Iron‐Catalyzed Intramolecular Cyclopropanation Reactions
Authors: Shen Jun‐Jie , Zhu Shou‐Fei , Cai Yan , Xu Huan , Xie Xiu‐Lan , Zhou Qi‐Lin 
Published: October 2014

AbstractAn iron‐catalyzed asymmetric intramolecular cyclopropanation was realized in high yields and excellent enantioselectivity (up to 97 % ee) by using the iron complexes of chiral spiro‐bisoxazoline ligands as catalysts. The superiority of iron catalysts exhibited in this reaction demonstrated the potential abilities of this sustainable metal in asymmetric carbenoid transformation reactions.
Isolation of an Imino‐N‐heterocyclic Carbene/Germanium(0) Adduct: A Mesoionic Germylene Equivalent
Authors: Su Bochao , Ganguly Rakesh , Li Yongxin , Kinjo Rei 
Published: October 2014

AbstractAn autoionization of germanium dichloride/dioxane complex with an imino‐N‐heterocyclic carbene ligand (L) afforded a novel germyliumylidene ion, [(L)GeCl]+[GeCl3]−, which was fully characterized. Reduction of the germyliumylidene ion with potassium graphite produced a cyclic species [(L)Ge], which can be viewed as both a Ge0 species and a mesoionic germylene. X‐ray diffraction analysis and computational studies revealed one of the lone pairs on the Ge atom is involved in the π system on the GeC2N2 five‐membered ring. It was also confirmed that the nucleophilic behavior of [(L)Ge] as a two lone‐pair donor.
B(C6F5)3‐Catalyzed Hydrogenation of Oxime Ethers without Cleavage of the NO Bond
Authors: Mohr Jens , Oestreich Martin 
Published: October 2014

AbstractThe hydrogenation of oximes and oxime ethers is usually hampered by NO bond cleavage, hence affording amines rather than hydroxylamines. The boron Lewis acid B(C6F5)3 is found to catalyze the chemoselective hydrogenation of oxime ethers at elevated or even room temperature under 100 bar dihydrogen pressure. The use of the triisopropylsilyl group as a protecting group allows for facile liberation of the free hydroxylamines.
Zeolites with Continuously Tuneable Porosity
Authors: Wheatley Paul S. , Chlubná‐Eliášová Pavla , Greer Heather , Zhou Wuzong , Seymour Valerie R. , Dawson Daniel M. , Ashbrook Sharon E. , Pinar Ana B. , McCusker Lynne B. , Opanasenko Maksym , Čejka Jiří , Morris Russell E. 
Published: October 2014

AbstractZeolites are important materials whose utility in industry depends on the nature of their porous structure. Control over microporosity is therefore a vitally important target. Unfortunately, traditional methods for controlling porosity, in particular the use of organic structure‐directing agents, are relatively coarse and provide almost no opportunity to tune the porosity as required. Here we show how zeolites with a continuously tuneable surface area and micropore volume over a wide range can be prepared. This means that a particular surface area or micropore volume can be precisely tuned. The range of porosity we can target covers the whole range of useful zeolite porosity: from small pores consisting of 8‐rings all the way to extra‐large pores consisting of 14‐rings.
Total Synthesis of (−)‐Haouamine B Pentaacetate and Structural Revision of Haouamine B
Authors: Momoi Yuichi , Okuyama Kei‐ichiro , Toya Hiroki , Sugimoto Kenji , Okano Kentaro , Tokuyama Hidetoshi 
Published: October 2014

AbstractThe enantiocontrolled total synthesis of (−)‐haouamine B pentaacetate was accomplished via an optically active indane‐fused β‐lactam, which was prepared by a newly developed Friedel–Crafts reaction. Subsequent cleavage of the β‐lactam and an intramolecular McMurry coupling reaction provided the core indane‐fused tetrahydropyridine, which led to the elucidation of the structure, as proposed by Trauner and Zubía.
Palladium‐Catalyzed Cross‐Coupling of Styrenes with Aryl Methyl Ketones in Ionic Liquids: Direct Access to Cyclopropanes
Authors: Cotugno Pietro , Monopoli Antonio , Ciminale Francesco , Milella Antonella , Nacci Angelo 
Published: October 2014

AbstractThe combined use of Pd(OAc)2, Cu(OAc)2, and dioxygen in molten tetrabutylammonium acetate (TBAA) promotes an unusual cyclopropanation reaction between aryl methyl ketones and styrenes. The process is a dehydrogenative cyclizing coupling that involves a twofold CH activation at the α‐position of the ketone. The substrate scope highlights the flexibility of the catalyst; a reaction mechanism is also proposed.
Composite Aromatic Boxes for Enzymatic Transformations of Quaternary Ammonium Substrates
Authors: Nagy Gergely N. , Marton Lívia , Contet Alicia , Ozohanics Olivér , Ardelean Laura‐Mihaela , Révész Ágnes , Vékey Károly , Irimie Florin Dan , Vial Henri , Cerdan Rachel , Vértessy Beáta G. 
Published: October 2014

AbstractCation–π interactions to cognate ligands in enzymes have key roles in ligand binding and enzymatic catalysis. We have deciphered the key functional role of both charged and aromatic residues within the choline binding subsite of CTP:phosphocholine cytidylyltransferase and choline kinase from Plasmodium falciparum. Comparison of quaternary ammonium binding site structures revealed a general composite aromatic box pattern of enzyme recognition sites, well distinguished from the aromatic box recognition site of receptors.
Direct Mass Spectrometry Analysis of Biofluid Samples Using Slug‐Flow Microextraction Nano‐Electrospray Ionization
Authors: Ren Yue , McLuckey Morgan N. , Liu Jiangjiang , Ouyang Zheng 
Published: October 2014

AbstractDirect mass spectrometry (MS) analysis of biofluids with simple procedures represents a key step in the translation of MS techniques to clinical and point‐of‐care applications. The current study reports the development of a single‐step method using slug‐flow microextraction and nano‐electrospray ionization for MS analysis of organic compounds in blood and urine. High sensitivity and quantitation precision have been achieved in the analysis of therapeutic and illicit drugs in 5 μL samples. Real‐time chemical derivatization has been incorporated for analyzing anabolic steroids. The monitoring of enzymatic functions has also been demonstrated with cholinesterase in wet blood. The reported study encourages the future development of disposable cartridges, which function with simple operation to replace the traditional complex laboratory procedures for MS analysis of biological samples.
β‐Functionalization of Carboxylic Anhydrides with β‐Alkyl Substituents through Carbene Organocatalysis
Authors: Jin Zhichao , Chen Shaojin , Wang Yuhuang , Zheng Pengcheng , Yang Song , Chi Yonggui Robin 
Published: October 2014

AbstractThe first NHC‐catalyzed functionalization of carboxylic anhydrides is described. In this reaction, the β carbon behaves as a nucleophilic carbon and undergoes asymmetric reactions with electrophiles. Anhydrides with challenging β‐alkyl substituents work effectively.
Control of Regioselectivity over Gold Nanocrystals of Different Surfaces for the Synthesis of 1,4‐Disubstituted Triazole through the Click Reaction
Authors: Rej Sourav , Chanda Kaushik , Chiu Chun‐Ya , Huang Michael H. 
Published: October 2014

AbstractGold nanocubes, octahedra, and rhombic dodecahedra were examined for facet‐dependent catalytic activity in the formation of triazoles. Rhombic dodecahedra gave 100 % regioselective 1,4‐triazoles. The product yield was increased by decreasing the particle size. However, a mixture of 1,4‐ and 1,5‐triazoles was obtained in lower yields when cubes and octahedra of similar sizes were used. The lowest Au‐atom density on the {110} surface and largest unsaturated coordination number of surface Au atoms may explain their best catalytic efficiency and product regioselectivity. Various spectroscopic techniques were employed to verify the formation of the Au–acetylide intermediate and establish the reaction mechanism, in which phenylacetylene binds to the Au {110} surface through the terminal‐binding mode to result in the exclusive formation of 1,4‐triazoles. The smallest rhombic dodecahedra can give diverse 1,4‐disubstituted triazoles in good yields by coupling a wide variety of alkynes and organic halides.
Chemical Preparation of Graphene Materials Results in Extensive Unintentional Doping with Heteroatoms and Metals
Authors: Chua Chun Kiang , Ambrosi Adriano , Sofer Zdeněk , Macková Anna , Havránek Vladimír , Tomandl Ivo , Pumera Martin 
Published: October 2014

AbstractChemical synthesis of graphene relies on the usage of various chemical reagents. The initial synthesis step, in which graphite is oxidized to graphite oxide, is achieved by a combination of chemical oxidants and acids. A subsequent chemical reduction step eliminates/reduces most oxygen functionalities to yield graphene. We demonstrate here that these chemical treatments significantly contaminate graphene with heteroatoms/metals, depending on the procedures followed. Contaminations with heteroatoms (N, B, Cl, S) or metals (Mn, Al) were present at relatively high concentrations (up to 3 at %), with their chemical states dependent on the procedures. Such unintentional contaminations (unwanted doping) during chemical synthesis are rarely anticipated and reported, although the heteroatoms/metals may alter the electronic and catalytic properties of graphene. In fact, the levels of unintentionally introduced contaminants on graphene are often higher than typical levels found on intentionally doped graphene. Our findings are important for scientists applying chemical methods to prepare graphene.
Chemical Modification and Energetically Favorable Atomic Disorder of a Layered Thermoelectric Material TmCuTe2 Leading to High Performance
Authors: Lin Hua , Chen Hong , Shen Jin‐Ni , Chen Ling , Wu Li‐Ming 
Published: October 2014

AbstractThermoelectric (TE) materials have continuously attracted interest worldwide owing to their capability of converting heat into electricity. However, discovery and design of new TE material system remains one of the greatest difficulties. A TE material, TmCuTe2, has been designed by a substructure approach and successfully synthesized. The structure mainly features CuTe4‐based layers stacking along the c axis that are separated by Tm3+ cations. Such an intrinsic Cu site vacancy structure undergoes a first‐order phase transition at around 606 K driven by the energetically favorable uniform Cu atom re‐distribution on the covalent CuTe4‐based layer substructure, as shown by crystal structure simulations and variable‐temperature XRD data. Featured with very low thermal conductivity (ca. 0.6 W m−1 K−1), large Seebeck coefficient (+185 μV K−1), and moderate electrical conductivity (220 S cm−1), TmCuTe2 has a maximum ZT of 0.81 at 745 K, which is nine times higher than the value of 0.09 for binary Cu2Te, thus making it a promising candidate for mid‐temperature TE applications. Theoretical studies uncover the electronic structure modifications from the metallic Cu2Te to the narrow gap semiconductor TmCuTe2 that lead to such a remarkable performance enhancement.
Functionalized Membranes for Photocatalytic Hydrogen Production
Authors: Troppmann Stefan , König Burkhard 
Published: October 2014

AbstractFunctionalized vesicles for photocatalytic hydrogen production in water have been prepared by co‐embedding of amphiphilic photosensitizers and a hydrogen‐evolving catalyst in phospholipid membranes. The self‐assembly allows a simple two‐dimensional arrangement of the multicomponent system with close spatial proximity, which gave turnover numbers up to 165 for the incorporated amphiphilic cobaloxime water reduction catalyst 3 b under optimized conditions in purely aqueous solution. Superior photocatalytic activity in fluid membranes indicates that mobility and dynamic reorganization of catalytic subunits in the membrane promote the visible‐light‐driven hydrogen production. The functionalized membranes represent nanostructured assemblies for hydrogen production in aqueous solution mimicking natural photosynthesis.
Phosphinothiolates as Ligands for Polyhydrido Copper Nanoclusters
Authors: Huertos Miguel A. , Cano Israel , Bandeira Nuno A. G. , Benet‐Buchholz Jordi , Bo Carles , van Leeuwen Piet W. N. M. 
Published: October 2014

AbstractThe reaction of [CuI(HSC6H4PPh2)]2 with NaBH4 in CH2Cl2/EtOH led to air‐ and moisture‐stable copper hydride nanoparticles (CuNPs) containing phosphinothiolates as new ligands, one of which was isolated by crystallization. The X‐ray crystal structure of [Cu18H7L10I] (L=−S(C6H4)PPh2) shows unprecedented features in its 28‐atom framework (18 Cu and 10 S atoms). Seven hydrogen atoms, in hydride form, are needed for charge balance and were located by density functional theory methods. H2 was released from the copper hydride nanoparticles by thermolysis and visible light irradiation.
Iridium(I)‐Catalyzed Regioselective CH Activation and Hydrogen‐Isotope Exchange of Non‐aromatic Unsaturated Functionality
Authors: Kerr William J. , Mudd Richard J. , Paterson Laura C. , Brown Jack A. 
Published: October 2014

AbstractIsotopic labelling is a key technology of increasing importance for the investigation of new CH activation and functionalization techniques, as well as in the construction of labelled molecules for use within both organic synthesis and drug discovery. Herein, we report for the first time selective iridium‐catalyzed CH activation and hydrogen‐isotope exchange at the β‐position of unsaturated organic compounds. The use of our highly active [Ir(cod)(IMes)(PPh3)][PF6] (cod=1,5‐cyclooctadiene) catalyst, under mild reaction conditions, allows the regioselective β‐activation and labelling of a range of α,β‐unsaturated compounds with differing steric and electronic properties. This new process delivers high levels of isotope incorporation over short reaction times by using low levels of catalyst loading.
Direct Catalytic Addition of Alkylnitriles to Aldehydes by Transition‐Metal/NHC Complexes
Authors: Sureshkumar Devarajulu , Ganesh Venkataraman , Kumagai Naoya , Shibasaki Masakatsu 
Published: October 2014

AbstractInvited for the cover of this issue is the group of Masakatsu Shibasaki at the Institute of Microbial Chemistry (BIKAKEN), Tokyo. The image depicts an arsenal of alkylnitriles as highly useful and readily available nucleophiles. Read the full text of the article at 10.1002/chem.201404808.
Water Confined in the Local Field of Ions
Authors: Kojić Dušan , Tsenkova Roumiana , Tomobe Katsufumi , Yasuoka Kenji , Yasui Masato 
Published: October 2014

AbstractInterionic distances are shorter in concentrated ionic solutions, thus instigating the interaction and overlap of hydration shells, as ions become separated by only one or two layers of water molecules. The simultaneous interaction of water with two oppositely charged ions has, so far, only been investigated by computer simulation studies, because the isolated vibrational spectroscopic signature of these molecules remains undetected. Our combined near‐infrared spectroscopic and molecular dynamics simulation studies of alkali halide solutions present a distinct spectral feature, which is highly responsive to depletion of bulk water and merging of hydration shells. The analysis of this spectral feature demonstrates that absorption trends are in good agreement with the law of matching affinities, thus providing the first successful vibrational spectroscopic treatment of this topic. Combined with commonly observed near‐infrared bands, this feature provides a spectral pattern that describes some relevant aspects of ionic hydration.