bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tire choices in Roman chariot racing
Authors: Sandor Bela I. 
Published: October 2016

Formal chariot racing was a sophisticated and popular sport for over 1800 years, from Etruria in the 6th c. B.C. down to the fall of Constantinople, and the races held in a large number of circuses and hippodromes imply that huge numbers of racing chariots were made over the course of those centuries. It may therefore be thought surprising that no racing machine has been found, but the dearth of such hardware is plausible given the perishable wood and leather components of the lightweight vehicles and the desirability of recycling the metal parts. In this situation a particular artifact must be accorded special significance. It is a hand-sized bronze model of a Roman racing biga, known as the Tiber model because found in the river. Dated to the 1st-2nd c. A.D., it is now on display in the British Museum (GR 1894.10-30.1, Bronze 2694). With this model as our guide, all the major dimensions of Roman racing chariots have been reasonably well determined; further, several technical aspects (some obvious, others quite subtle) of actual racing chariots can be established from it. Among the subtle details of the model, one feature is especially intriguing in view of the remarkably realistic work of its maker, who was clearly knowledgeable in matters large and small of vehicular racing. As first mentioned to me by J. Swaddling of the British Museum during our latest study of the model (November 2014), an unusual tire configuration is apparently represented on this all-bronze model: the right wheel has a slightly raised rim, as if to indicate a thin iron tire, but the left wheel lacks this feature (fig. 1). This asymmetrical arrangement is not only curious, it also implies extra work and expense. What, then, could be the reason for it?One possibility for having apparently only one tire on the Tiber model — which was probably a toy for a rich individual; the emperor Nero, an avid racer, was said to play with toy chariots — is that two different castings were used in the toy's production, and either one could have been used in the assembly, in random selection from a box.
A value-based assessment of alternative US state pension plans
Authors: LEKNIŪTĖ ZINA , BEETSMA ROEL , PONDS EDUARD 
Published: October 2016

AbstractWe explore how the contract values of the various stakeholders of a typical US state civil servants pension fund are affected under the continuation of current policies and under alternative policies, such as changes in contribution, indexation and investment allocation policies. We find that all participant cohorts derive a substantial net benefit from the current pension contract, while all tax-paying cohorts make substantial contributions. The shift in value from tax payers to participants can be reduced substantially by having the latter make larger contributions or making indexation less generous. Under our baseline calibration, and continuation of existing policies, the chances are high that the fund's assets get depleted in the coming decades.
‘CHASING’ THE DIAGRAM—THE USE OF VISUALIZATIONS IN ALGEBRAIC REASONING
Authors: DE TOFFOLI SILVIA 
Published: October 2016

AbstractThe aim of this article is to investigate the roles of commutative diagrams (CDs) in a specific mathematical domain, and to unveil the reasons underlying their effectiveness as a mathematical notation; this will be done through a case study. It will be shown that CDs do not depict spatial relations, but represent mathematical structures. CDs will be interpreted as a hybrid notation that goes beyond the traditional bipartition of mathematical representations into diagrammatic and linguistic. It will be argued that one of the reasons why CDs form a good notation is that they are highly mathematically tractable: experts can obtain valid results by ‘calculating’ with CDs. These calculations, take the form of ‘diagram chases’. In order to draw inferences, experts move algebraic elements around the diagrams. It will be argued that these diagrams are dynamic. It is thanks to their dynamicity that CDs can externalize the relevant reasoning and allow experts to draw conclusions directly by manipulating them. Lastly, it will be shown that CDs play essential roles in the context of proof as well as in other phases of the mathematical enterprise, such as discovery and conjecture formation.
Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex
Authors: Vijay Nagarjun , Bossu Christen M. , Poelstra Jelmer W. , Weissensteiner Matthias H. , Suh Alexander , Kryukov Alexey P. , Wolf Jochen B. W. 
Published: October 2016

AbstractUncovering the genetic basis of species diversification is a central goal in evolutionary biology. Yet, the link between the accumulation of genomic changes during population divergence and the evolutionary forces promoting reproductive isolation is poorly understood. Here, we analysed 124 genomes of crow populations with various degrees of genome-wide differentiation, with parallelism of a sexually selected plumage phenotype, and ongoing hybridization. Overall, heterogeneity in genetic differentiation along the genome was best explained by linked selection exposed on a shared genome architecture. Superimposed on this common background, we identified genomic regions with signatures of selection specific to independent phenotypic contact zones. Candidate pigmentation genes with evidence for divergent selection were only partly shared, suggesting context-dependent selection on a multigenic trait architecture and parallelism by pathway rather than by repeated single-gene effects. This study provides insight into how various forms of selection shape genome-wide patterns of genomic differentiation as populations diverge.
KAT2A/KAT2B-targeted acetylome reveals a role for PLK4 acetylation in preventing centrosome amplification
Authors: Fournier Marjorie , Orpinell Meritxell , Grauffel Cédric , Scheer Elisabeth , Garnier Jean-Marie , Ye Tao , Chavant Virginie , Joint Mathilde , Esashi Fumiko , Dejaegere Annick , Gönczy Pierre , Tora László 
Published: October 2016

AbstractLysine acetylation is a widespread post-translational modification regulating various biological processes. To characterize cellular functions of the human lysine acetyltransferases KAT2A (GCN5) and KAT2B (PCAF), we determined their acetylome by shotgun proteomics. One of the newly identified KAT2A/2B substrate is polo-like kinase 4 (PLK4), a key regulator of centrosome duplication. We demonstrate that KAT2A/2B acetylate the PLK4 kinase domain on residues K45 and K46. Molecular dynamics modelling suggests that K45/K46 acetylation impairs kinase activity by shifting the kinase to an inactive conformation. Accordingly, PLK4 activity is reduced uponin vitroacetylation of its kinase domain. Moreover, the overexpression of the PLK4 K45R/K46R mutant in cells does not lead to centrosome overamplification, as observed with wild-type PLK4. We also find that impairing KAT2A/2B-acetyltransferase activity results in diminished phosphorylation of PLK4 and in excess centrosome numbers in cells. Overall, our study identifies the global human KAT2A/2B acetylome and uncovers that KAT2A/2B acetylation of PLK4 prevents centrosome amplification.
Structure of the bacterial plant-ferredoxin receptor FusA
Authors: Grinter Rhys , Josts Inokentijs , Mosbahi Khedidja , Roszak Aleksander W. , Cogdell Richard J. , Bonvin Alexandre M. J. J. , Milner Joel J. , Kelly Sharon M. , Byron Olwyn , Smith Brian O. , Walker Daniel 
Published: October 2016

AbstractIron is a limiting nutrient in bacterial infection putting it at the centre of an evolutionary arms race between host and pathogen. Gram-negative bacteria utilize TonB-dependent outer membrane receptors to obtain iron during infection. These receptors acquire iron either in concert with soluble iron-scavenging siderophores or through direct interaction and extraction from host proteins. Characterization of these receptors provides invaluable insight into pathogenesis. However, only a subset of virulence-related TonB-dependent receptors have been currently described. Here we report the discovery of FusA, a new class of TonB-dependent receptor, which is utilized by phytopathogenic Pectobacterium spp. to obtain iron from plant ferredoxin. Through the crystal structure of FusA we show that binding of ferredoxin occurs through specialized extracellular loops that form extensive interactions with ferredoxin. The function of FusA and the presence of homologues in clinically important pathogens suggests that small iron-containing proteins represent an iron source for bacterial pathogens.
How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome
Authors: Noel Jeffrey K. , Whitford Paul C. 
Published: October 2016

AbstractIt has long been recognized that the thermodynamics of mRNA–tRNA base pairing is insufficient to explain the high fidelity and efficiency of aminoacyl-tRNA (aa-tRNA) selection by the ribosome. To rationalize this apparent inconsistency, Hopfield proposed that the ribosome may improve accuracy by utilizing a multi-step kinetic proofreading mechanism. While biochemical, structural and single-molecule studies have provided a detailed characterization of aa-tRNA selection, there is a limited understanding of how the physical–chemical properties of the ribosome enable proofreading. To this end, we probe the role of EF-Tu during aa-tRNA accommodation (the proofreading step) through the use of energy landscape principles, molecular dynamics simulations and kinetic models. We find that the steric composition of EF-Tu can reduce the free-energy barrier associated with the first step of accommodation: elbow accommodation. We interpret this effect within an extended kinetic model of accommodation and show how EF-Tu can contribute to efficient and accurate proofreading.
Ubc13 haploinsufficiency protects against age-related insulin resistance and high-fat diet-induced obesity
Authors: Joo Erina , Fukushima Toru , Harada Norio , Reed John C. , Matsuzawa Shu-ichi , Inagaki Nobuya 
Published: October 2016

AbstractObesity is associated with low-grade inflammation that leads to insulin resistance and type 2 diabetes via Toll-like Receptor (TLR) and TNF-family cytokine receptor (TNFR) signaling pathways. Ubc13 is an ubiquitin-conjugating enzyme responsible for non-canonical K63-linked polyubiquitination of TNF receptor-associated factor (TRAF)-family adapter proteins involved in TLR and TNFR pathways. However, the relationship between Ubc13 and metabolic disease remains unclear. In this study, we investigated the role of Ubc13 in insulin resistance and high-fat diet (HFD)-induced obesity. We compared wild-type (WT) and Ubc13 haploinsufficient (ubc13+/−) mice under normal diet (ND) and HFD, since homozygous knockout mice (ubc13−/−) are embryonic lethal. Male and female ubc13+/− mice were protected against age-related insulin resistance under ND and HFD compared to WT mice. Interestingly, only female ubc13+/− mice were protected against HFD-induced obesity and hepatic steatosis. Moreover, only female HFD-fed ubc13+/− mice showed lower expression of inflammatory cytokines that was secondary to reduction in weight gain not present in the other groups. In summary, our results indicate that suppression of Ubc13 activity may play a metabolic role independent of its inflammatory function. Thus, Ubc13 could represent a therapeutic target for insulin resistance, diet-induced obesity, and associated metabolic dysfunctions.
Three-dimensional ultrastructural analyses of anterior pituitary gland expose spatial relationships between endocrine cell secretory granule localization and capillary distribution
Authors: Yoshitomi Munetake , Ohta Keisuke , Kanazawa Tomonoshin , Togo Akinobu , Hirashima Shingo , Uemura Kei-ichiro , Okayama Satoko , Morioka Motohiro , Nakamura Kei-ichiro 
Published: October 2016

AbstractEndocrine and endothelial cells of the anterior pituitary gland frequently make close appositions or contacts, and the secretory granules of each endocrine cell tend to accumulate at the perivascular regions, which is generally considered to facilitate secretory functions of these cells. However, three-dimensional relationships between the localization pattern of secretory granules and blood vessels are not fully understood. To define and characterize these spatial relationships, we used scanning electron microscopy (SEM) three-dimensional reconstruction method based on focused ion-beam slicing and scanning electron microscopy (FIB/SEM). Full three-dimensional cellular architectures of the anterior pituitary tissue at ultrastructural resolution revealed that about 70% of endocrine cells were in apposition to the endothelial cells, while almost 30% of endocrine cells were entirely isolated from perivascular space in the tissue. Our three-dimensional analyses also visualized the distribution pattern of secretory granules in individual endocrine cells, showing an accumulation of secretory granules in regions in close apposition to the blood vessels in many cases. However, secretory granules in cells isolated from the perivascular region tended to distribute uniformly in the cytoplasm of these cells. These data suggest that the cellular interactions between the endocrine and endothelial cells promote an uneven cytoplasmic distribution of the secretory granules.
Thermophysical properties and oxygen transport in (Thx,Pu1−x)O2
Authors: Galvin C. O. T. , Cooper M. W. D. , Rushton M. J. D. , Grimes R. W. 
Published: October 2016

AbstractUsing Molecular Dynamics, this paper investigates the thermophysical properties and oxygen transport of (Thx,Pu1−x)O2 (0 ≤ x ≤ 1) between 300–3500 K. In particular, the superionic transition is investigated and viewed via the thermal dependence of lattice parameter, linear thermal expansion coefficient, enthalpy and specific heat at constant pressure. Oxygen diffusivity and activation enthalpy are also investigated. Below the superionic temperature an increase of oxygen diffusivity for certain compositions of (Thx,Pu1−x)O2 compared to the pure end members is predicted. Oxygen defect formation enthalpies are also examined, as they underpin the superionic transition temperature and the increase in oxygen diffusivity. The increase in oxygen diffusivity for (Thx,Pu1−x)O2 is explained in terms of lower oxygen defect formation enthalpies for (Thx,Pu1−x)O2 than PuO2 and ThO2, while links are drawn between the superionic transition temperature and oxygen Frenkel disorder.
microRNAs Involved in the Control of Innate Immunity in Candida Infected Caenorhabditis elegans
Authors: Sun Lingmei , Zhi Lingtong , Shakoor Shumaila , Liao Kai , Wang Dayong 
Published: October 2016

AbstractThe role of microRNAs (miRNAs) in regulating innate immune response to Candida albicans infection in Caenorhabditis elegans is still largely unclear. Using small RNA SOLiD deep sequencing technique, we profiled the miRNAs that were dysregulated by C. albicans infection. We identified 16 miRNAs that were up-regulated and 4 miRNAs that were down-regulated in nematodes infected with C. albicans. Bioinformatics analysis implied that these dysregulated miRNAs may be involved in the control of many important biological processes. Using available mutants, we observed that mir-251 and mir-252 loss-of-function mutants were resistant to C. albicans infection, whereas mir-360 mutants were hypersensitive to C. albicans infection. The expression pattern of antimicrobial genes suggested that mir-251, mir-252, and mir-360 played crucial roles in regulating the innate immune response to C. albicans infection. Fungal burden might be closely associated with altered lifespan and innate immune response in mir-251, mir-252, and mir-360 mutants. Moreover, mir-251 and mir-252 might function downstream of p38 mitogen activated protein kinase (MAPK) or IGF-1/insulin-like pathway to regulate the innate immune response to C. albicans infection. Our results provide an important molecular basis for further elucidating how miRNA-mRNA networks may control the innate immune response to C. albicans infection.
Evolutionary study of Yersinia genomes deciphers emergence of human pathogenic species
Authors: Tan Shi Yang , Tan Irene Kit Ping , Tan Mui Fern , Dutta Avirup , Choo Siew Woh 
Published: October 2016

AbstractOn record, there are 17 species in the Yersinia genus, of which three are known to be pathogenic to human. While the chromosomal and pYV (or pCD1) plasmid-borne virulence genes as well as pathogenesis of these three species are well studied, their genomic evolution is poorly understood. Our study aims to predict the key evolutionary events that led to the emergence of pathogenic Yersinia species by analyzing gene gain-and-loss, virulence genes, and “Clustered regularly-interspaced short palindromic repeats”. Our results suggest that the most recent ancestor shared by the human pathogenic Yersinia was most probably an environmental species that had adapted to the human body. This might have led to ecological specialization that diverged Yersinia into ecotypes and distinct lineages based on differential gene gain-and-loss in different niches. Our data also suggest that Y. pseudotuberculosis group might be the donor of the ail virulence gene to Y. enterocolitica. Hence, we postulate that evolution of human pathogenic Yersinia might not be totally in parallel, but instead, there were lateral gene transfer events. Furthermore, the presence of virulence genes seems to be important for the positive selection of virulence plasmid. Our studies provide better insights into the evolutionary biology of these bacteria.
Smooth deuterated cellulose films for the visualisation of adsorbed bio-macromolecules
Authors: Su Jielong , Raghuwanshi Vikram S. , Raverty Warwick , Garvey Christopher J. , Holden Peter J. , Gillon Marie , Holt Stephen A. , Tabor Rico , Batchelor Warren , Garnier Gil 
Published: October 2016

AbstractNovel thin and smooth deuterated cellulose films were synthesised to visualize adsorbed bio-macromolecules using contrast variation neutron reflectivity (NR) measurements. Incorporation of varying degrees of deuteration into cellulose was achieved by growing Gluconacetobacter xylinus in deuterated glycerol as carbon source dissolved in growth media containing D2O. The derivative of deuterated cellulose was prepared by trimethylsilylation(TMS) in ionic liquid(1-butyl-3-methylimidazolium chloride). The TMS derivative was dissolved in toluene for thin film preparation by spin-coating. The resulting film was regenerated into deuterated cellulose by exposure to acidic vapour. A common enzyme, horseradish peroxidase (HRP), was adsorbed from solution onto the deuterated cellulose films and visualized by NR. The scattering length density contrast of the deuterated cellulose enabled accurate visualization and quantification of the adsorbed HRP, which would have been impossible to achieve with non-deuterated cellulose. The procedure described enables preparing deuterated cellulose films that allows differentiation of cellulose and non-deuterated bio-macromolecules using NR.
Opportunistic brood theft in the context of colony relocation in an Indian queenless ant
Authors: Paul Bishwarup , Paul Manabi , Annagiri Sumana 
Published: October 2016

AbstractBrood is a very valuable part of an ant colony and behaviours increasing its number with minimum investment is expected to be favoured by natural selection. Brood theft has been well documented in ants belonging to the subfamilies Myrmicinae and Formicinae. In this study we report opportunistic brood theft in the context of nest relocation in Diacamma indicum, belonging to the primitively eusocial subfamily Ponerinae. Pupae was the preferred stolen item both in laboratory conditions and in natural habitat and a small percentage of the members of a colony acting as thieves stole about 12% of the brood of the victim colony. Stolen brood were not consumed but became slaves. We propose a new dimension to the risks of relocation in the form of brood theft by conspecific neighbours and speculate that examination of this phenomenon in other primitively eusocial species will help understand the origin of brood theft in ants.
Phenotype-genotype correlation in multiple primary lung cancer patients in China
Authors: Yang Yang , Yin Wei , He Wenxin , Jiang Chao , Zhou Xiao , Song Xiao , Zhu Junjie , Fei Ke , Cao Weijun , Jiang Gening 
Published: October 2016

AbstractDue to recent advances in high-resolution detection technology, multiple primary lung cancer (MPLC) is becoming an increasingly common diagnosis. However, the genotype-phenotype correlations in MPLC patients have not yet been assessed. In this study, we analyzed the clinical and pathological data for 129 consecutive MPLC patients who received curative surgery at the Tongji University Shanghai Pulmonary Hospital, China. We have screened 129 patients in the present study and found mutations in EGFR, BRAF, ROS1 and KRAS genes, as well as the rearrangement of the EML4-ALK gene in 113 patients. The mean patient age was 59.9 (25–78) years old and 41 patients were males (31.8%). Among the total patients, 123 (95.4%) had two primary lesions, 5 (3.9%) had three primary lesions, and 1 (0.8%) had four primary lesions. In 38.8% of the patients, all lesions were located on only one side of the body. Most of the detected mutations (98 patients) were in the EGFR gene. The patients exhibited significant differences in the EGFR mutation, age at diagnosis, and foci location.
Calculation of exchange integrals and Curie temperature for La-substituted barium hexaferrites
Authors: Wu Chuanjian , Yu Zhong , Sun Ke , Nie Jinlan , Guo Rongdi , Liu Hai , Jiang Xiaona , Lan Zhongwen 
Published: October 2016

AbstractAs the macro behavior of the strength of exchange interaction, state of the art of Curie temperature Tc, which is directly proportional to the exchange integrals, makes sense to the high-frequency and high-reliability microwave devices. Challenge remains as finding a quantitative way to reveal the relationship between the Curie temperature and the exchange integrals for doped barium hexaferrites. Here in this report, for La-substituted barium hexaferrites, the electronic structure has been determined by the density functional theory (DFT) and generalized gradient approximation (GGA). By means of the comparison between the ground and relative state, thirteen exchange integrals have been calculated as a function of the effective value Ueff. Furthermore, based on the Heisenberg model, the molecular field approximation (MFA) and random phase approximation (RPA), which provide an upper and lower bound of the Curie temperature Tc, have been adopted to deduce the Curie temperature Tc. In addition, the Curie temperature Tc derived from the MFA are coincided well with the experimental data. Finally, the strength of superexchange interaction mainly depends on 2b-4f1, 4f2-12k, 2a-4f1, and 4f1-12k interactions.