bluuebunny/crossref_metadata_2025_split huggingface dataset:
Y‐chromosome evidence supports asymmetric dog introgression into eastern coyotes
Authors: Wheeldon Tyler J. , Rutledge Linda Y. , Patterson Brent R. , White Bradley N. , Wilson Paul J. 
Published: July 2013

AbstractHybridization has played an important role in the evolutionary history of Canis species in eastern North America. Genetic evidence of coyote–dog hybridization based on mitochondrial DNA (mtDNA) is lacking compared to that based on autosomal markers. This discordance suggests dog introgression into coyotes has potentially been male biased, but this hypothesis has not been formally tested. Therefore, we investigated biparentally, maternally, and paternally inherited genetic markers in a sample of coyotes and dogs from southeastern Ontario to assess potential asymmetric dog introgression into coyotes. Analysis of autosomal microsatellite genotypes revealed minimal historical and contemporary admixture between coyotes and dogs. We observed only mutually exclusive mtDNA haplotypes in coyotes and dogs, but we observed Y‐chromosome haplotypes (Y‐haplotypes) in both historical and contemporary coyotes that were also common in dogs. Species‐specific Zfy intron sequences of Y‐haplotypes shared between coyotes and dogs confirmed their homology and indicated a putative origin from dogs. We compared Y‐haplotypes observed in coyotes, wolves, and dogs profiled in multiple studies, and observed that the Y‐haplotypes shared between coyotes and dogs were either absent or rare in North American wolves, present in eastern coyotes, but absent in western coyotes. We suggest the eastern coyote has experienced asymmetric genetic introgression from dogs, resulting from predominantly historical hybridization with male dogs and subsequent backcrossing of hybrid offspring with coyotes. We discuss the temporal and spatial dynamics of coyote–dog hybridization and the conditions that may have facilitated the introgression of dog Y‐chromosomes into coyotes. Our findings clarify the evolutionary history of the eastern coyote.
Implications of a temperature increase for host plant range: predictions for a butterfly
Authors: Audusseau Hélène , Nylin Sören , Janz Niklas 
Published: July 2013

AbstractAlthough changes in phenology and species associations are relatively well‐documented responses to global warming, the potential interactions between these phenomena are less well understood. In this study, we investigate the interactions between temperature, phenology (in terms of seasonal timing of larval growth) and host plant use in the polyphagous butterfly Polygonia c‐album. We found that the hierarchy of larval performance on three natural host plants was not modified by a temperature increase as such. However, larval performance on each host plant and temperature treatment was affected by rearing season. Even though larvae performed better at the higher temperature regardless of the time of the rearing, relative differences between host plants changed with the season. For larvae reared late in the season, performance was always better on the herbaceous plant than on the woody plants. In this species, it is likely that a prolonged warming will lead to a shift from univoltinism to bivoltinism. The demonstrated interaction between host plant suitability and season means that such a shift is likely to lead to a shift in selective regime, favoring specialization on the herbaceous host. Based on our result, we suggest that host range evolution in response to temperature increase would in this species be highly contingent on whether the population undergoes a predicted shift from one to two generations. We discuss the effect of global warming on species associations and the outcome of asynchrony in rates of phenological change.
(π‐Allyl)Pd Complexes Containing N‐Heterocyclic Carbene and Pseudohalogen Ligands – Synthesis, Reactivity toward Organic Isothiocyanates and Isocyanides, and Their Catalytic Activity in Suzuki–Miyaura Cross‐Couplings
Authors: Kim Hyun‐Kyung , Lee Jung‐Hyun , Kim Yong‐Joo , Nu Zheng Zhen , Lee Soon W. 
Published: July 2013

AbstractDinuclear (π‐allyl)palladium chlorides, [(π‐allyl)Pd(μ‐Cl)]2, were cleaved by N‐heterocyclic carbenes (NHCs) to give mononuclear (π‐allyl)palladium–NHC chlorides, [(π‐allyl)Pd(Cl)(NHC)] (1–6) [NHC = 1,3‐bis(2,6‐diisopropylphenyl)imidazol‐2‐ylidene (IPR), 1,3‐bis(2,6‐diisopropylphenyl)‐4,5‐dihydroimidazol‐2‐ylidine (SIPR), 1,3‐bis(2,4,6‐trimethylphenyl)imidazol‐2‐ylidene (IMes)]. Complexes 1–6 were subsequently treated with aqueous NaN3, KSCN, KOCN, and CF3COOAg to produce the corresponding mononuclear (π‐allyl)palladium–NHC pseudohalogen complexes, [(π‐allyl)Pd(X)(NHC)] (X = N3, NCS, SCN, NCO, CF3COO) (7–30). These products could also be obtained by treating dinuclear pseudohalogen‐bridged Pd complexes, [(π‐allyl)Pd(μ‐X)]2, which were prepared by replacing the μ‐Cl ligand in [(π‐allyl)Pd(μ‐Cl)]2, with aqueous NaN3, KSCN, KOCN, or CF3COOAg, followed by cleavage with the NHCs. Reactions of [(π‐allyl)Pd(N3)(NHC)] with organic isothiocyanates (R–NCS) or CH3O(CO)C≡CO(CO)CH3 resulted in selective 1,3‐dipolar cycloaddition into the Pd–azido bond to give heterocyclic compounds. By contrast, analogous reactions of [(η3‐allyl)Pd(N3)(IPr)] with an organic isocyanide (R–NC: R = tert‐butyl, benzyl) gave the adduct [(η3‐allyl)Pd(N3)(IPr)]·(R–NC) as the only product or a mixture of the adduct and a dipolar cycloaddition product, [(η3‐allyl)Pd{CN4(R)}(IPr)], depending on the isocyanides used. Finally, a series of (π‐allyl)Pd–NHC pseudohalogen complexes, [(π‐allyl)Pd(X)(NHC)], exhibited high catalytic activity in Suzuki–Miyaura cross‐coupling reactions of aryl chlorides with arylboronic acids.
Copper‐Catalyzed Aerobic Dehydrogenation of C–C to C=C Bonds in the Synthesis of Pyridazinones
Authors: Liang Lei , Yang Guanyu , Xu Fengrong , Niu Yan , Sun Qi , Xu Ping 
Published: July 2013

AbstractA simple and efficient procedure for the synthesis of pyridazin‐3(2H)‐ones through copper‐catalyzed dehydrogenation of a single C–C bond of 4,5‐dihydropyridazin‐3(2H)‐ones to a C=C bond with oxygen as the terminal oxidant is described. Functional groups including hydroxy, carboxylic, bromo, chloro, cyano, nitro and alkoxy were all tolerated under the reaction conditions. Moreover, this methodology was applied to the preparation of a series of structurally similar N‐substituted 6‐phenylpyridazinone compounds containing fluorine. The dehydrogenation reactions exhibit good yields and selectivity.
Ruthenium‐Catalyzed Enantioselective Synthesis of β‐Amino Alcohols from 1,2‐Diols by “Borrowing Hydrogen”
Authors: Eka Putra Anggi , Oe Yohei , Ohta Tetsuo 
Published: July 2013

AbstractEnantioselective synthesis of β‐amino alcohols from 1,2‐diols by the use of [RuCl2(p‐cymene)]2/(S,R)‐JOSIPHOS catalysis was developed. Several 1,2‐diols were treated with secondary amines to afford the corresponding optically active β‐amino alcohols in up to 99 % yield with 77 % ee.
Initiation of the West Antarctic Ice Sheet and estimates of total Antarctic ice volume in the earliest Oligocene
Authors: Wilson Douglas S. , Pollard David , DeConto Robert M. , Jamieson Stewart S.R. , Luyendyk Bruce P. 
Published: July 2013

AbstractReconstructions of Antarctic paleotopography for the late Eocene suggest that glacial erosion and thermal subsidence have lowered West Antarctic elevations considerably since then, with Antarctic land area having decreased ~20%. A new climate‐ice sheet model based on these reconstructions shows that the West Antarctic Ice Sheet first formed at the Eocene‐Oligocene transition (33.8–33.5 Ma, E‐O) in concert with the continental‐scale expansion of the East Antarctica Ice Sheet and that the total volume of East and West Antarctic ice (33.4–35.9 × 106 km3) was >1.4 times greater than previously assumed. This larger modeled ice volume is consistent with a modest cooling of 1–2°C in the deep ocean during the E‐O transition, lower than other estimates of ~3°C cooling, and suggests the possibility of substantial ice in the Antarctic interior before the Eocene‐Oligocene boundary.
A possible mechanism for the North Pacific regime shift in winter of 1998/1999
Authors: Jo Hyun‐Su , Yeh Sang‐Wook , Kim Cheol‐Ho 
Published: July 2013

AbstractThis study examines a possible mechanism for the North Pacific regime shift in the winter of 1998/1999. Since the 1976/1977 climate regime shift, the sea surface temperature (SST) in the North Pacific has exhibited a long‐term warming trend in the western and central regions, which is mainly due to the two regime shifts that occurred in the winter of 1988/1989 and 1998/1999, respectively. In particular, the 1998/1999 regime shift is characterized by a dipole‐like structure along 40°N where a significant warming is prominent in the southwestern and central North Pacific. The slow dynamic adjustments of SST and zonal wind to the meridional heat exchange through thermal advection may be responsible for the 1998/1999 regime shift. We also assert that an intrinsic multidecadal SST oscillation in the North Pacific contributes to the 1998/1999 regime shift. Furthermore, another possibility, which is associated with the oceanic teleconnection from the tropics to the midlatitude, is also briefly discussed.
ALONE TOGETHER
Authors: Hoare Michael Rand 
Published: July 2013

POEMS OF SCIENCE: Edited by John Heath‐Stubbs and Phillips Salman Penguin BooksPERMUTATIONS: Readings in Science and Literature Edited by Joan Digby and Bob Brier William Morrow and CompanySONGS FROM UNSUNG WORLDS: Science in Poetry Edited by Bonnie Bilyeu Gordon Birkhaüser;
PHYSICS FOR MYSTICS
Authors: Crease Robert P. , Mann Charles C. 
Published: July 2013

BEYOND THE QUANTUM by Michael TalbotQUANTUM PHYSICS: ILLUSION OR REALITY? by Alastair I. M. RaeTHE SHAKY GAME Einstein, Realism, and the Quantum Theory by Arthur FineTHE SOCIAL RELATIONS OF PHYSICS, MYSTICISM, AND MATHEMATICS Studies in Social Structure, Interests, and Ideas by Sal Restivo
THE SEAMY SIDE OF SCIENCE
Authors: Kanigel Robert , Cowley Geoffrey 
Published: July 2013

BONES OF CONTENTION Controversies in the Search for Human Origins by Roger LewinEXPLORERS OF THE BLACK BOX The Search for the Cellular Basis of Memory by Susan AllportINVISIBLE FRONTIERS The Race to Synthesize a Human Gene by Stephen S. HallNOBEL DREAMS Power, Deceit, and the Ultimate Experiment by Gary Taubes
SHAPING NATURE
Authors: Volk Tyler 
Published: July 2013

WONDERFUL LIFE The Burgess Shale and the Nature of History by Stephen Jay GouldLIFE'S DEVICES The Physical World of Animals and Plants by Steven VogelINVENTION AND EVOLUTION Design in Nature and Engineering by M. J. FrenchDYNAMICS OF DINOSAURS AND OTHER EXTINCT GIANTS by R. McNeill Alexander
Reversing LRP
5-Dependent Osteoporosis and SOST Deficiency–Induced Sclerosing Bone Disorders by Altering WNT Signaling Activity
Authors: Chang Ming-Kang , Kramer Ina , Keller Hansjoerg , Gooi Jonathan H , Collett Corinne , Jenkins David , Ettenberg Seth A , Cong Feng , Halleux Christine , Kneissel Michaela 
Published: July 2013

ABSTRACT

The bone formation inhibitor sclerostin encoded by SOST binds in vitro to low-density lipoprotein receptor-related protein (LRP) 5/6 Wnt co-receptors, thereby inhibiting Wnt/β-catenin signaling, a central pathway of skeletal homeostasis. Lrp5/LRP5 deficiency results in osteoporosis-pseudoglioma (OPPG), whereas Sost/SOST deficiency induces lifelong bone gain in mice and humans. Here, we analyzed the bone phenotype of mice lacking Sost (Sost−/−), Lrp5 (Lrp5−/−), or both (Sost−/−;Lrp5−/−) to elucidate the mechanism of action of Sost in vivo. Sost deficiency–induced bone gain was significantly blunted in Sost−/−;Lrp5−/− mice. Yet the Lrp5 OPPG phenotype was fully rescued in Sost−/−;Lrp5−/− mice and most bone parameters were elevated relative to wild-type. To test whether the remaining bone increases in Sost−/−;Lrp5−/− animals depend on Lrp6, we treated wild-type, Sost−/−, and Sost−/−;Lrp5−/− mice with distinct Lrp6 function blocking antibodies. Selective blockage of Wnt1 class–mediated Lrp6 signaling reduced cancellous bone mass and density in wild-type mice. Surprisingly, it reversed the abnormal bone gain in Sost−/− and Sost−/−;Lrp5−/− mice to wild-type levels irrespective of enhancement or blockage of Wnt3a class-mediated Lrp6 activity. Thus, whereas Sost deficiency–induced bone anabolism partially requires Lrp5, it fully depends on Wnt1 class–induced Lrp6 activity. These findings indicate: first, that OPPG syndrome patients suffering from LRP5 loss-of-function should benefit from principles antagonizing SOST/sclerostin action; and second, that therapeutic WNT signaling inhibitors may stop the debilitating bone overgrowth in sclerosing disorders related to SOST deficiency, such as sclerosteosis, van Buchem disease, and autosomal dominant craniodiaphyseal dysplasia, which are rare disorders without viable treatment options. © 2014 American Society for Bone and Mineral Research.
Chemical characteristics and mineral composition of quinoa by near‐infrared spectroscopy
Authors: González Martín M Inmaculada , Wells Moncada Guillermo , Fischer Susana , Escuredo Olga 
Published: July 2013

AbstractBACKGROUNDQuinoa (Chenopodium quinoa Willd.) has been traditionally used as a foodstuff in the Andes and it has gained increasing interest in recent years owing to its high nutritional value. The potential of near‐infrared spectroscopy (NIRS) for estimating chemical compounds in quinoa was studied because of the possibility of conducting direct measurement without prior sample treatment.RESULTSThe use of NIRS technology with a remote reflectance fiber‐optic probe for the analysis of major compounds and mineral composition of 48 quinoa samples was studied. The calibration of the NIRS instrument was conducted using modified partial least squares (MPLS) analysis. This allowed the determination of protein (16.0–20.2 g 100g−1), crude fiber (1.8–3.1 g 100g−1), fat (4.4–7.5 g 100g−1), calcium (298.8–1164.5 mg kg−1), iron (0–948.5 mg kg−1) and phosphorus (2735.0–4543.3 mg kg−1). The correlation coefficients (RSQ) were 0.83 for protein, 0.73 for crude fiber, 0.93 for fat; 0.60 for calcium; 0.76 for iron and 0.75 for phosphorus. The robustness of the equations obtained was verified by external validation on unknown quinoa samples.CONCLUSIONSNIRS with fiber‐optic probe provides an alternative for the determination of chemical compounds of quinoa, faster and at lower cost, with results comparable with chemical methods. © 2013 Society of Chemical Industry
Influence of acidification, pasteurization, centrifugation and storage time and temperature on watermelon juice quality
Authors: Tarazona‐Díaz Martha Patricia , Aguayo Encarna 
Published: July 2013

ABSTRACTBACKGROUNDWatermelon juice has gained increasing popularity among consumers as a rich natural source of functional compounds such as lycopene and citrulline. However, the final quality of the juice depends significantly on its acidification, pasteurization, centrifugation and storage time and temperature. In this study, these characteristics were assessed in watermelon juice pasteurized at 87.7 °C for 20 s and stored for up to 30 days at 4 or 8 °C.RESULTSThe acidifier citric acid provided an adequate sensory quality, similar to natural watermelon juice. Centrifugation and pasteurization significantly reduced the red color, bioactive compounds (lycopene, antioxidant capacity and total polyphenols) and sensory quality of the juice, particularly when the storage time was extended and a temperature of 8 °C was used (P ≤ 0.05). All treated juices were microbiologically safe for up to 30 days when stored at 4 or 8 °C. In terms of sensory acceptability, only non‐centrifuged juices stored for up to 20 days at 4 °C remained above the commercial limit.CONCLUSIONThe present results suggest that using a non‐centrifugation process and a storage temperature of 4 °C yields a watermelon juice that better retains its sensory and functional qualities. © 2013 Society of Chemical Industry
Application of the numerical manifold method for stress wave propagation across rock masses
Authors: Zhao G. F. , Zhao X. B. , Zhu J. B. 
Published: July 2013

SUMMARYIn this paper, the numerical manifold method (NMM) is extended to study wave propagation across rock masses. First, improvements to the system equations, contact treatment, and boundary conditions of the NMM are performed, where new system equations are derived based on the Newmark assumption of the space–time relationship, the edge‐to‐edge contact treatment is further developed for the NMM to handle stress wave propagation across discontinuities, and the viscous non‐reflection boundary condition is derived based on the energy minimisation principle. After the modification, numerical comparisons between the original and improved NMM are presented. The results show that the original system equations result in artificial numerical damping, which can be overcome by the Newmark system equations. Meanwhile, the original contact scheme suffers some calculation problems when modelling stress wave propagation across a discontinuity, which can be solved by the proposed edge‐to‐edge contact scheme. Subsequently, the influence of the mesh size and time step on the improved NMM for stress wave propagation is studied. Finally, 2D wave propagation is modelled, and the model's results are in good agreement with the analytical solution. Copyright © 2013 John Wiley & Sons, Ltd.
Nonuniform chain collapse during early stages of staphylococcal nuclease folding detected by fluorescence resonance energy transfer and ultrarapid mixing methods
Authors: Mizukami Takuya , Xu Ming , Cheng Hong , Roder Heinrich , Maki Kosuke 
Published: July 2013

AbstractThe development of tertiary structure during folding of staphylococcal nuclease (SNase) was studied by time‐resolved fluorescence resonance energy transfer measured using continuous‐ and stopped‐flow techniques. Variants of this two‐domain protein containing intradomain and interdomain fluorescence donor/acceptor pairs (Trp and Cys‐linked fluorophore or quencher) were prepared to probe the intradomain and interdomain structural evolution accompanying SNase folding. The intra‐domain donor/acceptor pairs are within the β‐barrel domain (Trp27/Cys64 and Trp27/Cys97) and the interdomain pair is between the α‐helical domain and the β‐barrel domain (Trp140/Cys64). Time‐resolved energy transfer efficiency accompanying folding and unfolding at different urea concentrations was measured over a time range from 30 μs to ∼10 s. Information on average donor/acceptor distances at different stages of the folding process was obtained by using a quantitative kinetic modeling approach. The average distance for the donor/acceptor pairs in the β‐barrel domain decreases to nearly native values whereas that of the interdomain donor/acceptor pairs remains unchanged in the earliest intermediate (<500 μs of refolding). This indicates a rapid nonuniform collapse resulting in an ensemble of heterogeneous conformations in which the central region of the β‐barrel domain is well developed while the C‐terminal α‐helical domain remains disordered. The distance between Trp140 and Cys64 decreases to native values on the 100‐ms time scale, indicating that the α‐helical domain docks onto the preformed β‐barrel at a late stage of the folding. In addition, the unfolded state is found to be more compact under native conditions, suggesting that changes in solvent conditions may induce a nonspecific hydrophobic collapse.
β‐Bulges: Extensive structural analyses of β‐sheets irregularities
Authors: Craveur Pierrick , Joseph Agnel Praveen , Rebehmed Joseph , de Brevern Alexandre G. 
Published: July 2013

Abstractβ‐Sheets are quite frequent in protein structures and are stabilized by regular main‐chain hydrogen bond patterns. Irregularities in β‐sheets, named β‐bulges, are distorted regions between two consecutive hydrogen bonds. They disrupt the classical alternation of side chain direction and can alter the directionality of β‐strands. They are implicated in protein‐protein interactions and are introduced to avoid β‐strand aggregation. Five different types of β‐bulges are defined. Previous studies on β‐bulges were performed on a limited number of protein structures or one specific family. These studies evoked a potential conservation during evolution. In this work, we analyze the β‐bulge distribution and conservation in terms of local backbone conformations and amino acid composition. Our dataset consists of 66 times more β‐bulges than the last systematic study (Chan et al. Protein Science 1993, 2:1574–1590). Novel amino acid preferences are underlined and local structure conformations are highlighted by the use of a structural alphabet. We observed that β‐bulges are preferably localized at the N‐ and C‐termini of β‐strands, but contrary to the earlier studies, no significant conservation of β‐bulges was observed among structural homologues. Displacement of β‐bulges along the sequence was also investigated by Molecular Dynamics simulations.
Evaluation of predictions in the CASP10 model refinement category
Authors: Nugent Timothy , Cozzetto Domenico , Jones David T. 
Published: July 2013

ABSTRACTHere we report on the assessment results of the third experiment to evaluate the state of the art in protein model refinement, where participants were invited to improve the accuracy of initial protein models for 27 targets. Using an array of complementary evaluation measures, we find that five groups performed better than the naïve (null) method—a marked improvement over CASP9, although only three were significantly better. The leading groups also demonstrated the ability to consistently improve both backbone and side chain positioning, while other groups reliably enhanced other aspects of protein physicality. The top‐ranked group succeeded in improving the backbone conformation in almost 90% of targets, suggesting a strategy that for the first time in CASP refinement is successful in a clear majority of cases. A number of issues remain unsolved: the majority of groups still fail to improve the quality of the starting models; even successful groups are only able to make modest improvements; and no prediction is more similar to the native structure than to the starting model. Successful refinement attempts also often go unrecognized, as suggested by the relatively larger improvements when predictions not submitted as model 1 are also considered. Proteins 2014; 82(Suppl 2):98–111. © 2013 Wiley Periodicals, Inc.