bluuebunny/crossref_metadata_2025 huggingface dataset:
Reporting in studies of protein biomarkers of prognosis in colorectal cancer in relation to the REMARK guidelines
Authors: Jankova Lucy , Dent Owen F. , Molloy Mark P. , Chan Charles , Chapuis Pierre H. , Howell Viive M. , Clarke Stephen J.
Published: March 2015

Purpose

The REMARK guidelines give authors comprehensive and specific advice on the complete and transparent reporting of studies of prognostic tumor markers. The aim of this study was to use the REMARK guidelines to evaluate the quality of reporting in a sample of studies assessing tissue‐based protein markers for survival after resection of colorectal cancer.

Experimental design

Eighty pertinent articles were scored according to their conformity to 26 items derived from the REMARK criteria.

Results

Overall, on a scale of adequacy of reporting that potentially ranged from 26 to 78, the median for these studies was 60 (interquartile range 54–64) and several criteria were adequately covered in a large proportion of studies. However, others were either not dealt with or inadequately covered, including description of the study design (35%), definition of survival endpoints (48%), adjuvant therapy (54%), follow‐up procedures and time (59%), neoadjuvant therapy (63%), inclusion/exclusion criteria (73%), multivariable modeling methods and results (74%), and discussion of study limitations (85%).

Conclusions and clinical relevance

Inadequacies in presentation militate against comparability among protein marker studies and undermine the generalizability of their findings. The quality of reporting could be improved if journal editors were to require authors to ensure that their work satisfied the REMARK criteria.
Urinary extracellular vesicles as reservoirs of altered proteins during the pathogenesis of polycystic kidney disease
Authors: Pocsfalvi Gabriella , Raj Delfin A. A. , Fiume Immacolata , Vilasi Annalisa , Trepiccione Francesco , Capasso Giovambattista
Published: March 2015

Purpose

Recent findings indicate that urinary extracellular vesicles (EVs) might reflect the pathophysiological state of urinary system; and that EVs‐induced ciliary signaling is a possible mechanism of intercellular communication within the tract. Here, we aimed to analyze the protein expression of urinary EVs during autosomal dominant polycystic kidney disease (ADPKD).

Experimental design

EVs were isolated from pooled urine samples of healthy control and ADPKD patients at two different stages of the disease and under tolvaptan treatment using the double‐cushion ultracentrifugation method. Proteins were identified and quantified by iTRAQ and multidimensional protein identification technology (MudPIT)‐based quantitative proteomics.

Results

Quantitative analyses identified 83 differentially expressed EV proteins. Many of these have apical membrane origin and are involved in signal transduction pathways of primary cilia, Ca2+‐activated signaling, cell‐cycle regulation, and cell differentiation.

Conclusions and clinical relevance

The reduced AQP‐2 and the increased APO‐A1 levels observed in all ADPKD‐affected groups may reflects the impaired renal concentrating capability of these patients and correlated with estimated glomerular filtration rate decline. The levels of some upregulated proteins involved in Ca2+‐activated signaling declined upon tolvaptan treatment. The results obtained suggest that the quantitative proteomics of urinary EVs might be useful to monitor proteins difficult to access noninvasively, and thus advance our understanding of urinary tract physiology and pathology.
Charge‐neutralization effect of the tail regions on the histone H2A/H2B dimer structure
Authors: Saikusa Kazumi , Shimoyama Singo , Asano Yuuki , Nagadoi Aritaka , Sato Mamoru , Kurumizaka Hitoshi , Nishimura Yoshifumi , Akashi Satoko
Published: March 2015

It is well known that various modifications of histone tails play important roles in the regulation of transcription initiation. In this study, some lysine (Lys) and arginine (Arg) residues were acetylated and deiminated, respectively, in the histone H2A/H2B dimer, and charge‐neutralization effects on the dimer structure were studied by native mass spectrometry. Given that both acetylation and deimination neutralize the positive charges of basic amino acid residues, it had been expected that these modifications would correspondingly affect the gas‐phase behavior of the histone H2A/H2B dimer. Contrary to this expectation, it was found that Arg deimination led to greater difficulty of dissociation of the dimer by gas‐phase collision, whereas acetylation of Lys residues did not cause such a drastic change in the dimer stability. In contrast, ion mobility‐mass spectrometry (IM‐MS) experiments showed that arrival times in the mobility cell both of acetylated and of deiminated dimer ions changed little from those of the unmodified dimer ions, indicating that the sizes of the dimer ions did not change by modification. Charge neutralization of Arg, basicity of which is higher than Lys, might have triggered some alteration of the dimer structure that cannot be found in IM‐MS but can be detected by collision in the gas phase.
Drug driving law changes: what it means for patients
Authors: Chaplin Steve
Published: March 2015

A new drug driving law comes into force on 2 March 2015. Here we look at the implications for both prescribers and patients.
A stochastic convective backscatter scheme for use in ensemble prediction systems
Authors: Shutts Glenn
Published: March 2015

Stochastic kinetic energy backscatter schemes are amongst several different types of stochastic parametrization used in operational ensemble weather prediction to account for model uncertainty. They aim to introduce structured wind perturbations randomly into the forecast model, targeting regions of high numerical dissipation, mountain‐wave drag and deep convection. Substantially different implementations of the backscatter scheme in different weather centres confirm the weak scientific underpinning of such stochastic parametrizations and the lack of knowledge of where the true model uncertainty lies.

The stochastic scheme presented here makes the reasonable assumption that random model error lies primarily with the parametrization of deep convection and, in particular, with its interaction with model dynamics close to the grid scale. This scheme introduces well‐defined, circularly symmetric patterns of wind forcing centred on grid columns containing parametrized convective mass transfer. Tests of the scheme in ensemble mode are carried out in the European Centre for Medium‐Range Weather Forecasts (ECMWF) forecast model, the spectral basis of which enables a clean implementation in terms of spatially filtered vorticity and divergence forcing fields. Its effectiveness as a model error representation is assessed relative to ECMWF's operational backscatter and perturbed parametrization tendency schemes. Bearing in mind the simplicity of the scheme, it is surprisingly effective in increasing spread, reducing the error of the ensemble mean and increasing probability skill scores, particularly in the Tropics. It is proposed that this representation of backscatter addresses model uncertainty more realistically than current operational stochastic backscatter schemes and may remove the need for a perturbed parametrization tendency approach.
A generalised stochastic backscatter model: large‐eddy simulation of the neutral surface layer
Authors: O'Neill J. J. , Cai X.‐M. , Kinnersley R.
Published: March 2015

The Smagorinsky subgrid model remains popular in large‐eddy simulation (LES) modelling despite its failure to reproduce mean velocity shear within the atmospheric surface layer. Overpredictions as large as 100% are not uncommon, leading to local simulation degradation, and potentially infecting scales further from the surface. Mason and Thomson achieved significant reduction in excessive velocity shear by adding stochastic accelerations on top of the Smagorinsky model to account for backscattered energy from the subgrid scales. However, neither this model nor its later implementation by Weinbrecht and Mason are able to ensure a physically appropriate spatial structure for the backscatter acceleration fields throughout the domain: with the Mason and Thomson model, the backscatter length‐scale and anisotropy depend on the local grid spacing and aspect ratio; with the Weinbrecht and Mason model, the backscatter is unavoidably isotropic with uniform length‐scale. We propose a new method for the generation of stochastic backscatter acceleration fields which utilises a grid‐adaptive filter (GAF) capable of controlling spatial variations in the backscatter length‐scale and anisotropy, independently of the model grid. When applied to the atmospheric surface layer, this allows for the backscatter length‐scale to be reduced towards surfaces in an appropriate manner, and the backscatter anisotropy to be varied in accordance with the physical anisotropy of the subgrid scales. The GAF model also has wider applicability: it may be used when the LES filter width, and hence the backscatter length‐scale, varies spatially with local three‐dimensional grid refinement. The GAF model is initially tested for the case of LES of the neutral atmospheric boundary layer, for grid aspect ratios ranging from α = Δx/Δz = 1 − 10, and found to give a reduction in maximum excessive mean velocity shear (from that obtained without backscatter) of around 80%, that is largely independent of α.
Gain‐scheduled leader‐follower tracking control for interconnected parameter varying systems
Authors: Cheng Yi , Ugrinovskii V.
Published: March 2015

This paper considers the gain‐scheduled leader‐follower tracking control problem for a parameter varying complex interconnected system with directed communication topology and uncertain norm‐bounded coupling between the agents. A gain‐scheduled consensus‐type control protocol is proposed and a sufficient condition is obtained, which guarantees a suboptimal bound on the system tracking performance under this protocol. An interpolation technique is used to obtain a protocol schedule, which is continuous in the scheduling parameter. The effectiveness of the proposed method is demonstrated using a simulation example. Copyright © 2015 John Wiley & Sons, Ltd.
Analysis of repeated low‐dose challenge studies
Authors: Nolen Tracy L. , Hudgens Michael G. , Senb Pranab K. , Koch Gary G.
Published: March 2015

Preclinical evaluation of candidate human immunodeficiency virus (HIV) vaccines entails challenge studies whereby non‐human primates such as macaques are vaccinated with either an active or control vaccine and then challenged (exposed) with a simian‐version of HIV. Repeated low‐dose challenge (RLC) studies in which each macaque is challenged multiple times (either until infection or some maximum number of challenges is reached) are becoming more common in an effort to mimic natural exposure to HIV in humans. Statistical methods typically employed for the testing for a vaccine effect in RLC studies include a modified version of Fisher's exact test as well as large sample approaches such as the usual log‐rank test. Unfortunately, these methods are not guaranteed to provide a valid test for the effect of vaccination. On the other hand, valid tests for vaccine effect such as the exact log‐rank test may not be easy to implement using software available to many researchers. This paper details which statistical approaches are appropriate for the analysis of RLC studies, and how to implement these methods easily in SAS or R. Copyright © 2015 John Wiley & Sons, Ltd.
Signals and mechanics shaping compartment boundaries in Drosophila
Authors: Umetsu Daiki , Dahmann Christian
Published: March 2015

During animal development groups of cells with similar fates and functions often stay together and separate from cells with different fates. An example for this cellular behavior is the formation of compartments, groups of cells with similar fates that are separated by sharp boundaries from neighboring groups of cells. Compartments play important roles during patterning by serving as units of growth and gene expression. Boundaries between compartments are associated with organizers that secrete signaling molecules instructing growth and differentiation throughout the tissue. The straight shape of the boundary between compartments is important for maintaining the position and shape of the organizer and thus for precise patterning. The straight shape of compartment boundaries, however, is challenged by cell divisions and cell intercalations that take place in many developing tissues. Early work established a role for selector genes and signaling pathways in setting up and keeping boundaries straight. Recent work in Drosophila has now begun to further unravel the physical and cellular mechanisms that maintain compartment boundaries. Key to the separation of compartments is a local increase of actomyosin‐dependent mechanical tension at cell junctions along the boundary. Increased mechanical tension acts as a barrier to cell mixing during cell division and influences cell rearrangements during cell intercalations along the compartment boundary in a way that the straight shape of the boundary is maintained. An important question for the future is how the signaling pathways that maintain the straight shape of compartment boundaries control mechanical tension along these boundaries. WIREs Dev Biol 2015, 4:407–417. doi: 10.1002/wdev.178

This article is categorized under:

Establishment of Spatial and Temporal Patterns > Cell Sorting and Boundary Formation
Cylindrical vortex wake model: skewed cylinder, application to yawed or tilted rotors
Authors: Branlard E. , Gaunaa M.
Published: March 2015

A vortex system consisting of a bound vortex disk, a root vortex and a vortex cylinder is presented and applied for skewed wake situations. Both the longitudinal and tangential components of vorticity of the cylinder are considered. A subset of this system leads to a model, which is commonly used in Blade Element Momentum method codes for yawed conditions. Here, all the components of the full vortex system are analyzed in view of extending Blade Element Momentum models. The main assumptions of the current study are a constant uniform circulation, an infinite number of blades, an un‐expanding wake shape and a finite tip‐speed ratio. The investigation remains within the context of inviscid potential flow theory. The model is derived for horizontal‐axis rotors in general, but results are presented for wind‐turbine applications. For each vortex element, the velocity components in all directions are computed analytically or semi‐analytically for the entire domain. Simplified engineering models are provided to ease the evaluation of velocities in the rotor plane. The predominant velocity components are assessed. Copyright © 2015 John Wiley & Sons, Ltd.
Postprandial Lipid Responses do not Differ Following Consumption of Butter or Vegetable Oil when Consumed with Omega‐3 Polyunsaturated Fatty Acids
Authors: Dias Cintia B. , Phang Melinda , Wood Lisa G. , Garg Manohar L.
Published: March 2015

Dietary saturated fat (SFA) intake has been associated with elevated blood lipid levels and increased risk for the development of chronic diseases. However, some animal studies have demonstrated that dietary SFA may not raise blood lipid levels when the diet is sufficient in omega‐3 polyunsaturated fatty acids (n‐3PUFA). Therefore, in a randomised cross‐over design, we investigated the postprandial effects of feeding meals rich in either SFA (butter) or vegetable oil rich in omega‐6 polyunsaturated fatty acids (n‐6PUFA), in conjunction with n‐3PUFA, on blood lipid profiles [total cholesterol, low density lipoprotein cholesterol (LDL‐C), high density lipoprotein cholesterol (HDL‐C) and triacylglycerol (TAG)] and n‐3PUFA incorporation into plasma lipids over a 6‐h period. The incremental area under the curve for plasma cholesterol, LDL‐C, HDL‐C, TAG and n‐3PUFA levels over 6 h was similar in the n‐6PUFA compared to SFA group. The postprandial lipemic response to saturated fat is comparable to that of n‐6PUFA when consumed with n‐3PUFA; however, sex‐differences in response to dietary fat type are worthy of further attention.
Decomposing the Effect of Crime on Population Changes
Authors: Foote Andrew
Published: March 2015

This article estimates the effect of crime on migration rates for counties in U.S. metropolitan areas and makes three contributions to the literature. First, I use administrative data on migration flows between counties, which gives me more precise estimates of population changes than data used in previous studies. Second, I am able to decompose net population changes into gross migration flows in order to identify how individuals respond to crime rate changes. Finally, I include county-level trends so that my identification comes from shocks away from the trend. I find effects that are one-fiftieth the size of the most prominent estimate in the literature; and although the long-run effects are somewhat larger, they are still only approximately one-twentieth as large. I also find that responses to crime rates differ by subgroups, and that increases in crime cause white households to leave the county, with effects almost 10 times as large as for black households.
A generalised enzyme kinetic model for predicting the behaviour of complex biochemical systems
Authors: Wong Martin Kin Lok , Krycer James Robert , Burchfield James Geoffrey , James David Ernest , Kuncic Zdenka
Published: March 2015

Quasi steady‐state enzyme kinetic models are increasingly used in systems modelling. The Michaelis Menten model is popular due to its reduced parameter dimensionality, but its low‐enzyme and irreversibility assumption may not always be valid in thein vivo context. Whilst the total quasi‐steady state assumption (tQSSA) model eliminates the reactant stationary assumptions, its mathematical complexity is increased. Here, we propose the differential quasi‐steady state approximation (dQSSA) kinetic model, which expresses the differential equations as a linear algebraic equation. It eliminates the reactant stationary assumptions of the Michaelis Menten model without increasing model dimensionality. The dQSSA was found to be easily adaptable for reversible enzyme kinetic systems with complex topologies and to predict behaviour consistent with mass action kineticsin silico. Additionally, the dQSSA was able to predict coenzyme inhibition in the reversible lactate dehydrogenase enzyme, which the Michaelis Menten model failed to do. Whilst the dQSSA does not account for the physical and thermodynamic interactions of all intermediate enzyme‐substrate complex states, it is proposed to be suitable for modelling complex enzyme mediated biochemical systems. This is due to its simpler application, reduced parameter dimensionality and improved accuracy.
Southern Sudanese Narratives of Displacement, and the Ambiguity of “Voice”
Authors: Kindersley Nicki
Published: March 2015

Refugee life stories have developed as a popular medium for attempting to portray southern Sudanese wartime experience. These narratives of war and exile have been told, edited and published in what has become an explanatory industry in refugee work worldwide. The development of this economy of life stories from the early 1980s, however, has encouraged the propagation of standardized displaced “life stories” as a discrete narrative genre. This article traces the formulation of this distinctive style of historical explanation and argues that this genre, while claiming emancipatory agency and “voice” for marginalized people, has instead become a narrative trap.
The wall-pressure spectrum of high-Reynolds-number turbulent boundary-layer flows over rough surfaces
Authors: Meyers Timothy , Forest Jonathan B. , Devenport William J.
Published: March 2015

Experiments have been performed on a series of high-Reynolds-number flat-plate turbulent boundary layers formed over rough and smooth walls. The boundary layers were fully rough, yet the elements remained a very small fraction$({<}1.4\,\%)$of the boundary-layer thickness, ensuring conditions free of transitional effects. The wall-pressure spectrum and its scaling were studied in detail. One of the major findings is that the rough-wall turbulent pressure spectrum at vehicle relevant conditions is comprised of three scaling regions. These include a newly discovered high-frequency region where the pressure spectrum has a viscous scaling controlled by the friction velocity, adjusted to exclude the pressure drag on the roughness elements.
Pumiliobelus, a new dwarf coleoid genus (Belemnoidea: Dimitobelidae) from the Cenomanian of Western Australia
Authors: Williamson Toni , Henderson Robert A.
Published: March 2015

A rare diminutive belemnite, Pumiliobelus n. gen., is described based on the new species P. haigi and P. tumidus from the upper Gearle Siltstone (Cenomanian) of the Carnarvon Basin, Western Australia. No smaller belemnites than these species are known. That they are based on adult specimens rather than juveniles is supported by a large sample, some 80 specimens, of P. haigi which collectively show a proportional range in size typical of belemnite species in general, a group in which juveniles are conspicuously lacking in the fossil record. Rostral morphology places Pumiliobelus in the Dimitobelidae, a distinctively Austral family of Aptian–Maastrichtian age, which became progressively restricted to high latitudes through the late Cretaceous. Each species of Pumiliobelus is known from a single locality where it co-occurs with the long-ranging (Albian–Cenomanian) Dimitobelus diptychus Whitehouse of widespread distribution at mid to high latitudes in the Southern Hemisphere. Dwarfism in the Dimitobelidae, as expressed by Pumiliobelus, is considered to reflect adaptive evolution to engage opportunistic life strategies that favored small body size and rapid population turnover. The rare occurrence of dwarf Dimitobelidae indicates that such strategies were limited in both geographic range and duration. Dwarfism expressed by Pumiliobelus may relate to paedomorphosis induced by rising seawater temperatures in the mid Cretaceous.
New long-stemmed eocrinoid from the Furongian Point Peak Shale Member of the Wilberns Formation, central Texas
Authors: Zamora Samuel , Sumrall Colin D. , Sprinkle James
Published: March 2015

Llanocystis wilbernsensisn. gen. n. sp. (Eocrinoidea, Echinodermata) is described based on three specimens from the Furongian Point Peak Shale Member of the Wilberns Formation in central Texas. It displays a unique morphology including a very long stem constructed with holomeric columnals, few feeding appendages, and a polyplated theca. The specimens occur in an intraformational conglomerate deposited in a proximal carbonate platform environment and represent an example of the poorly documented “pelmatozoan” radiation that occurred in proximal facies by the end of the Cambrian.
Generic concepts in the Actinocrinitidae Austin and Austin, 1842 (class Crinoidea) and evaluation of generic assignments of species
Authors: Rhenberg Elizabeth C. , Ausich William I. , Kammer Thomas W.
Published: March 2015

The family Actinocrinitidae was a significant contributor to the global biodiversity peak of crinoids that occurred during the Mississippian and is referred to as the “Age of Crinoids.” Although the actinocrinitids are a major component of that high diversity, they are also a source of much taxonomic confusion. Previously, generic concepts were not applied equally between Europe and North America creating disparity in the definition of genera. In this contribution, all genera are defined objectively by discrete characters, and the generic assignments of all species are reevaluated. Twenty genera are described. A total of 206 species were evaluated of which 56 species and one taxon in open nomenclature are reassigned to different genera, 21 species are designated asnomina dubia, and three species and one genus are nowincertae sedis.

A phylogenetic hypothesis is presented for the relationships of the genera of Actinocrinitidae genera based on a parsimony-based analysis and plotted against stratigraphic ranges. Although groupings were revealed in this analysis, the Actinocrinitidae cannot be readily subdivided into subfamilies. Rapid diversification occurred during the Tournaisian following the Hangenberg Extinction of probable fish predators. The late Devonian (Famennian) occurrence of the highly derived generaAbactinocrinusandPhysetocrinussuggests there is a more extensive, but undocumented, evolutionary history for the Actinocrinitidae during the Devonian.
A new middle Cambrian bradoriid arthropod from Greenland and western Canada
Authors: Peel John S. , Streng Michael
Published: March 2015

Circum-Laurentian middle Cambrian (Cambrian Series 3) deposits in Greenland and British Columbia yield a new hipponicharionid bradoriid arthropod,Flumenoglaciesn. gen., characterized by a comarginal, ramp-like structure which is crested by a continuous lobe. The narrow lobe is the result of the medial fusion of anterior and posterior lobes, seemingly a recurrent theme in hipponicharionid evolution. The type species,F.groenlandican. sp., is described from the Ekspedition Brae Formation (Drumian Stage) of Peary Land but the description of two unnamed species from slightly older middle Cambrian strata of the Stephen Formation of British Columbia provides additional evidence for the wide distribution of Small Shelly Faunas during the Cambrian.
Providing more protected space for tigers Panthera tigris: a landscape conservation approach in the Western Ghats, southern India
Authors: Gubbi Sanjay , Mukherjee Kaushik , Swaminath M.H. , Poornesha H.C.
Published: March 2015

Conservation of large carnivores is challenging as they face various threats, including habitat loss and fragmentation. One of the current challenges to tiger Panthera tigris conservation in India is the conversion of habitat to uses that are incompatible with conservation of the species. Bringing more tiger habitat within a protected area system and in the process creating a network of connected protected areas will deliver dual benefits of wildlife conservation and protection of watersheds. Focusing on the southern Indian state of Karnataka, which holds one of the largest contiguous tiger populations, we attempted to address this challenge using a conservation planning technique that considers ecological, social and political factors. This approach yielded several conservation successes, including an expansion of the protected area network by 2,385 km2, connection of 23 protected areas, and the creation of three complexes of protected areas, increasing the protected area network in Karnataka from 3.8 to 5.2% of the state's land area. This represents the largest expansion of protected areas in India since the 1970s. Such productive partnerships between government officials and conservationists highlight the importance of complementary roles in conservation planning and implementation.
A usage-based approach to early-discourse pragmatic functions of the Japanese subject markerswaandga*
Authors: UNO MARIKO
Published: March 2015

This study investigates the emergence and development of the discourse-pragmatic functions of the Japanese subject markerswaandgafrom a usage-based perspective (Tomasello, 2000). The use of each marker in longitudinal speech data for four Japanese children from 1;0 to 3;1 and their parents available in the CHILDES database (MacWhinney, 2000) was coded and analyzed. Findings showed that the four children initially usedwaas awh-question marker. They then gradually shifted its use to convey the proposition of given information. In contrast, the use ofgavaried among the children. One child usedgawith dynamic verbs in the past tense to report events he witnessed/experienced, while the other three children used it with a particular stative predicate in the present tense, expressing their subjective feeling toward referents. Findings were explained by the frequency of input to which the children had been exposed.
Solid solubility and superconductivity of FeyTe1−xXx (X = Se, S)
Authors: Guo Z. N. , Han B. L. , Li P. , Zhang H. H. , Yuan W. X.
Published: March 2015

In this work, we present a systematic study on the solid solution, lattice parameters and superconductivity on the FeyTe1−xXx (X = Se, S) system. It has been found that the limit of the Te-site doping with Se and S is around 0.5 and 0.15, respectively. The solid solution with the Fe content changing is also measured in this work, and the single-phase region for preparing pure sample is presented. Based on the magnetic susceptibility measurements, we presented a three-dimensional graph for showing the variation of superconducting critical temperature as a function of both the chalcogen and Fe content in FeyTe1−xXx.
Trust in a Masculine Space and a Community within a Community: Pre-1950 Auction Mart Culture in Lower Wharfedale, Yorkshire
Authors: ROWLING JANE E.
Published: March 2015

In an area characterised by livestock farming, the auction mart had a pivotal role, both economically and culturally, and was crucial to the continued success of the community and the businesses of the area. Although made up from the surrounding farming community, the community of the auction mart was separate and different, if only on a temporary basis, with its own physical and social boundaries, cultural norms, and traditions, which had a significant effect on the personal identities of those who counted themselves as members. This article explores the auction mart community, its links to a wider farming network, and its influence on rural ideas about masculine identity, through an oral history study of the Lower Wharfedale area. This offers a window onto a community and a culture which has received very little academic attention due to its closed nature. The article concludes that the auction mart regulars constituted a community within the farming community, in which the theme of trust ran through every interaction, linking the everyday activity of the mart space to wider debates about the meaning of masculinity, transitions and ritual, social networks, and the nature of community.
‘I think myself honestly decked’: Attitudes to the Clothing of the Rural Poor in Seventeenth-Century England
Authors: TANKARD DANAE
Published: March 2015

This article explores attitudes to the clothing of the rural poor in seventeenth-century England. It begins with an analysis of the representation of rural clothing in country themed ballads, showing how ‘homely’ country clothing was used to construct an image of a contented and industrious rural population. It then considers how such popular literary representations influenced the way that diarists Samuel Pepys and John Evelyn recorded their encounters with the rural poor. The final part of the article looks at attitudes of the rural poor to their own clothing, drawing on evidence from a range of documentary sources as well as the autobiographical writings of Edward Barlow. In contrast to the stereotypical depiction of the rural poor recorded by ballad writers and elite observers, the article will show that for the actual poor clothing could serve both as an expression of the ‘self’ and as a potent marker of social differences and moral and material inferiority.
PW1/Peg3 expression regulates key properties that determine mesoangioblast stem cell competence
Authors: Bonfanti Chiara , Rossi Giuliana , Tedesco Francesco Saverio , Giannotta Monica , Benedetti Sara , Tonlorenzi Rossana , Antonini Stefania , Marazzi Giovanna , Dejana Elisabetta , Sassoon David , Cossu Giulio , Messina Graziella
Published: March 2015

Mesoangioblasts are vessel-associated progenitor cells that show therapeutic promise for the treatment of muscular dystrophy. Mesoangioblasts have the ability to undergo skeletal muscle differentiation and cross the blood vessel wall regardless of the developmental stage at which they are isolated. Here we show that PW1/Peg3 is expressed at high levels in mesoangioblasts obtained from mouse, dog and human tissues and its level of expression correlates with their myogenic competence. Silencing PW1/Peg3 markedly inhibits myogenic potential of mesoangioblasts in vitro through MyoD degradation. Moreover, lack of PW1/Peg3 abrogates mesoangioblast ability to cross the vessel wall and to engraft into damaged myofibres through the modulation of the junctional adhesion molecule-A. We conclude that PW1/Peg3 function is essential for conferring proper mesoangioblast competence and that the determination of PW1/Peg3 levels in human mesoangioblasts may serve as a biomarker to identify the best donor populations for therapeutic application in muscular dystrophies.
Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data
Authors: Ginn Helen M. , Messerschmidt Marc , Ji Xiaoyun , Zhang Hanwen , Axford Danny , Gildea Richard J. , Winter Graeme , Brewster Aaron S. , Hattne Johan , Wagner Armin , Grimes Jonathan M. , Evans Gwyndaf , Sauter Nicholas K. , Sutton Geoff , Stuart David I.
Published: March 2015

The X-ray free-electron laser (XFEL) allows the analysis of small weakly diffracting protein crystals, but has required very many crystals to obtain good data. Here we use an XFEL to determine the room temperature atomic structure for the smallest cytoplasmic polyhedrosis virus polyhedra yet characterized, which we failed to solve at a synchrotron. These protein microcrystals, roughly a micron across, accrue within infected cells. We use a new physical model for XFEL diffraction, which better estimates the experimental signal, delivering a high-resolution XFEL structure (1.75 Å), using fewer crystals than previously required for this resolution. The crystal lattice and protein core are conserved compared with a polyhedrin with less than 10% sequence identity. We explain how the conserved biological phenotype, the crystal lattice, is maintained in the face of extreme environmental challenge and massive evolutionary divergence. Our improved methods should open up more challenging biological samples to XFEL analysis.
Incipient charge order observed by NMR in the normal state of YBa2Cu3Oy
Authors: Wu Tao , Mayaffre Hadrien , Krämer Steffen , Horvatić Mladen , Berthier Claude , Hardy W.N. , Liang Ruixing , Bonn D.A. , Julien Marc-Henri
Published: March 2015

The pseudogap regime of high-temperature cuprates harbours diverse manifestations of electronic ordering whose exact nature and universality remain debated. Here, we show that the short-ranged charge order recently reported in the normal state of YBa2Cu3Oy corresponds to a truly static modulation of the charge density. We also show that this modulation impacts on most electronic properties, that it appears jointly with intra-unit-cell nematic, but not magnetic, order, and that it exhibits differences with the charge density wave observed at lower temperatures in high magnetic fields. These observations prove mostly universal, they place new constraints on the origin of the charge density wave and they reveal that the charge modulation is pinned by native defects. Similarities with results in layered metals such as NbSe2, in which defects nucleate halos of incipient charge density wave at temperatures above the ordering transition, raise the possibility that order–parameter fluctuations, but no static order, would be observed in the normal state of most cuprates if disorder were absent.
Triggering HIV polyprotein processing by light using rapid photodegradation of a tight-binding protease inhibitor
Authors: Schimer Jiří , Pávová Marcela , Anders Maria , Pachl Petr , Šácha Pavel , Cígler Petr , Weber Jan , Majer Pavel , Řezáčová Pavlína , Kräusslich Hans-Georg , Müller Barbara , Konvalinka Jan
Published: March 2015

HIV protease (PR) is required for proteolytic maturation in the late phase of HIV replication and represents a prime therapeutic target. The regulation and kinetics of viral polyprotein processing and maturation are currently not understood in detail. Here we design, synthesize, validate and apply a potent, photodegradable HIV PR inhibitor to achieve synchronized induction of proteolysis. The compound exhibits subnanomolar inhibition in vitro. Its photolabile moiety is released on light irradiation, reducing the inhibitory potential by 4 orders of magnitude. We determine the structure of the PR-inhibitor complex, analyze its photolytic products, and show that the enzymatic activity of inhibited PR can be fully restored on inhibitor photolysis. We also demonstrate that proteolysis of immature HIV particles produced in the presence of the inhibitor can be rapidly triggered by light enabling thus to analyze the timing, regulation and spatial requirements of viral processing in real time.
TLR9 signalling in microglia attenuates seizure-induced aberrant neurogenesis in the adult hippocampus
Authors: Matsuda Taito , Murao Naoya , Katano Yuki , Juliandi Berry , Kohyama Jun , Akira Shizuo , Kawai Taro , Nakashima Kinichi
Published: March 2015

Pathological conditions such as epilepsy cause misregulation of adult neural stem/progenitor populations in the adult hippocampus in mice, and the resulting abnormal neurogenesis leads to impairment in learning and memory. However, how animals cope with abnormal neurogenesis remains unknown. Here we show that microglia in the mouse hippocampus attenuate convulsive seizure-mediated aberrant neurogenesis through the activation of Toll-like receptor 9 (TLR9), an innate immune sensor known to recognize microbial DNA and trigger inflammatory responses. We found that microglia sense self-DNA from degenerating neurons following seizure, and secrete tumour necrosis factor-α, resulting in attenuation of aberrant neurogenesis. Furthermore, TLR9 deficiency exacerbated seizure-induced cognitive decline and recurrent seizure severity. Our findings thus suggest the existence of bidirectional communication between the innate immune and nervous systems for the maintenance of adult brain integrity.
Demonstration of asymmetric electron conduction in pseudosymmetrical photosynthetic reaction centre proteins in an electrical circuit
Authors: Kamran Muhammad , Friebe Vincent M. , Delgado Juan D. , Aartsma Thijs J. , Frese Raoul N. , Jones Michael R.
Published: March 2015

Photosynthetic reaction centres show promise for biomolecular electronics as nanoscale solar-powered batteries and molecular diodes that are amenable to atomic-level re-engineering. In this work the mechanism of electron conduction across the highly tractable Rhodobacter sphaeroides reaction centre is characterized by conductive atomic force microscopy. We find, using engineered proteins of known structure, that only one of the two cofactor wires connecting the positive and negative termini of this reaction centre is capable of conducting unidirectional current under a suitably oriented bias, irrespective of the magnitude of the bias or the applied force at the tunnelling junction. This behaviour, strong functional asymmetry in a largely symmetrical protein–cofactor matrix, recapitulates the strong functional asymmetry characteristic of natural photochemical charge separation, but it is surprising given that the stimulus for electron flow is simply an externally applied bias. Reasons for the electrical resistance displayed by the so-called B-wire of cofactors are explored.
Direction-Controlled Chemical Doping for Reversible G-Phonon Mixing in ABC Trilayer Graphene
Authors: Park Kwanghee , Ryu Sunmin
Published: March 2015

Not only the apparent atomic arrangement but the charge distribution also defines the crystalline symmetry that dictates the electronic and vibrational structures. In this work, we report reversible and direction-controlled chemical doping that modifies the inversion symmetry of AB-bilayer and ABC-trilayer graphene. For the “top-down” and “bottom-up” hole injection into graphene sheets, we employed molecular adsorption of electronegative I2 and annealing-induced interfacial hole doping, respectively. The chemical breakdown of the inversion symmetry led to the mixing of the G phonons, Raman active Eg and Raman-inactive Eu modes, which was manifested as the two split G peaks, G− and G+. The broken inversion symmetry could be recovered by removing the hole dopants by simple rinsing or interfacial molecular replacement. Alternatively, the symmetry could be regained by double-side charge injection, which eliminated G− and formed an additional peak, Go, originating from the barely doped interior layer. Chemical modification of crystalline symmetry as demonstrated in the current study can be applied to other low dimensional crystals in tuning their various material properties.
Active control of electromagnetic radiation through an enhanced thermo-optic effect
Authors: Sheng Chong , Liu Hui , Zhu Shining , Genov Dentcho A.
Published: March 2015

The control of electromagnetic radiation in transformation optical metamaterials brings the development of vast variety of optical devices. Of a particular importance is the possibility to control the propagation of light with light. In this work, we use a structured planar cavity to enhance the thermo-optic effect in a transformation optical waveguide. In the process, a control laser produces apparent inhomogeneous refractive index change inside the waveguides. The trajectory of a second probe laser beam is then continuously tuned in the experiment. The experimental results agree well with the developed theory. The reported method can provide a new approach toward development of transformation optical devices where active all-optical control of the impinging light can be achieved.
Pattern segmentation with activity dependent natural frequency shift and sub-threshold resonance
Authors: Shtrahman E. , Zochowski M.
Published: March 2015

Understanding the mechanisms underlying distributed pattern formation in brain networks and its content driven dynamical segmentation is an area of intense study. We investigate a theoretical mechanism for selective activation of diverse neural populations that is based on dynamically shifting cellular resonances in functionally or structurally coupled networks. We specifically show that sub-threshold neuronal depolarization from synaptic coupling or external input can shift neurons into and out of resonance with specific bands of existing extracellular oscillations and this can act as a dynamic readout mechanism during information storage and retrieval. We find that this mechanism is robust and suggest it as a general coding strategy that can be applied to any network with oscillatory nodes.
(Pro)renin receptor is crucial for Wnt/β-catenin-dependent genesis of pancreatic ductal adenocarcinoma
Authors: Shibayama Yuki , Fujimori Takayuki , Nguyen Genevieve , Hirose Takuo , Totsune Kazuhito , Ichihara Atsuhiro , Kitada Kento , Nakano Daisuke , Kobori Hiroyuki , Kohno Masakazu , Masaki Tsutomu , Suzuki Yasuyuki , Yachida Shinichi , Nishiyama Akira
Published: March 2015

Although Wnt/β-catenin signaling is known to be aberrantly activated in PDAC, mutations of CTNNB1, APC or other pathway components are rare in this tumor type, suggesting alternative mechanisms for Wnt/β-catenin activation. Recent studies have implicated the (pro)renin receptor ((P)RR) is related to the Wnt/β-catenin signaling pathway. We therefore investigated the possible role of (P)RR in pancreatic carcinogenesis. Plasma s(P)RR levels were significantly (P < 0.0001) higher in patients with PDAC than in healthy matched controls. We also identified aberrant expression of (P)RR in premalignant PanIN and PDAC lesions and all the PDAC cell lines examined. Inhibiting (P)RR with an siRNA attenuated activation of Wnt/β-catenin signaling pathway and reduced the proliferative ability of PDAC cells in vitro and the growth of engrafted tumors in vivo. Loss of (P)RR induced apoptosis of human PDAC cells. This is the first demonstration that (P)RR may be profoundly involved in ductal tumorigenesis in the pancreas.
ZnO-dotted porous ZnS cluster microspheres for high efficient, Pt-free photocatalytic hydrogen evolution
Authors: Wu Aiping , Jing Liqiang , Wang Jianqiang , Qu Yang , Xie Ying , Jiang Baojiang , Tian Chungui , Fu Honggang
Published: March 2015

The Pt-free photocatalytic hydrogen evolution (PHE) has been the focus in the photocatalysis field. Here, the ZnO-dotted porous ZnS cluster microsphere (PCMS) is designed for high efficient, Pt-free PHE. The PCMS is designed through an easy “controlling competitive reaction” strategy by selecting the thiourea as S2− source and Zn(Ac)2·2H2O as Zn source in ethylene glycol medium. Under suitable conditions, one of the PCMS, named PCMS-1, with high SBET specific area of 194 m2g−1, microsphere size of 100 nm and grain size of 3 nm can be obtained. The formation of PCMS is verified by TEM, XAES, XPS, Raman and IR methods. Importantly, a series of the experiments and theoretical calculation demonstrate that the dotting of ZnO not only makes the photo-generated electrons/hole separate efficiently, but also results in the formation of the active catalytic sites for PHE. As a result, the PCMS-1 shows the promising activity up to 367 μmol h−1 under Pt-free condition. The PHE activity has no obvious change after addition 1 wt.% Pt, implying the presence of active catalytic sites for hydrogen evolution in the PCMS-1. The easy synthesis process, low preparation cost of the PCMS makes their large potential for Pt-free PHE.
Novel inhibitor discovery and the conformational analysis of inhibitors of listeriolysin O via protein-ligand modeling
Authors: Wang Jianfeng , Zhou Xuan , Liu Shui , Li Gen , Zhang Bing , Deng Xuming , Niu Xiaodi
Published: March 2015

Increasing bacterial resistance to available antibiotics makes the discovery of novel efficacious antibacterial agents a priority. A previous report showed that listeriolysin O (LLO) is a critical virulence factor and suggested that it is a target for developing anti-virulence drugs against Listeria monocytogenes infections. In this study, we report the discovery of LLO natural compound inhibitors with differential activity by using hemolysis assay. The mechanism of action of the inhibitors was consistent with that of fisetin, a natural flavonoid without antimicrobial activity, which we showed in our previous report via molecular simulation. Furthermore, a substantial increase in anti-hemolytic activity was observed when the single bond (C1-C2) was replaced by a double bond (C1-C2) in the inhibitor molecule. This change was based on the decomposition of the ligand-residue interaction, which indicated that the double bond (C1-C2) in the inhibitors was required for their inhibition of LLO. The current MD simulation work provides insights into the mechanism by which the compounds inhibit LLO at the atomic level and will be useful for the development of new, selective LLO inhibitors.
Interfacial dominated ferromagnetism in nanograined ZnO: a μSR and DFT study
Authors: Tietze Thomas , Audehm Patrick , Chen Yu–Chun , Schütz Gisela , Straumal Boris B. , Protasova Svetlana G. , Mazilkin Andrey A. , Straumal Petr B. , Prokscha Thomas , Luetkens Hubertus , Salman Zaher , Suter Andreas , Baretzky Brigitte , Fink Karin , Wenzel Wolfgang , Danilov Denis , Goering Eberhard
Published: March 2015

Diamagnetic oxides can, under certain conditions, become ferromagnetic at room temperature and therefore are promising candidates for future material in spintronic devices. Contrary to early predictions, doping ZnO with uniformly distributed magnetic ions is not essential to obtain ferromagnetic samples. Instead, the nanostructure seems to play the key role, as room temperature ferromagnetism was also found in nanograined, undoped ZnO. However, the origin of room temperature ferromagnetism in primarily non–magnetic oxides like ZnO is still unexplained and a controversial subject within the scientific community. Using low energy muon spin relaxation in combination with SQUID and TEM techniques, we demonstrate that the magnetic volume fraction is strongly related to the sample volume fraction occupied by grain boundaries. With molecular dynamics and density functional theory we find ferromagnetic coupled electron states in ZnO grain boundaries. Our results provide evidence and a microscopic model for room temperature ferromagnetism in oxides.