bluuebunny/crossref_metadata_2025 huggingface dataset:
The importance of sponges and mangroves in supporting fish communities on degraded coral reefs in Caribbean Panama
Authors: Seemann Janina , Yingst Alexandra , Stuart-Smith Rick D. , Edgar Graham J. , Altieri Andrew H.
Published: March 2018

Fish communities associated with coral reefs worldwide are threatened by habitat degradation and overexploitation. We assessed coral reefs, mangrove fringes, and seagrass meadows on the Caribbean coast of Panama to explore the influences of their proximity to one another, habitat cover, and environmental characteristics in sustaining biomass, species richness and trophic structure of fish communities in a degraded tropical ecosystem. We found 94% of all fish across all habitat types were of small body size (≤10 cm), with communities dominated by fishes that usually live in habitats of low complexity, such as Pomacentridae (damselfishes) and Gobiidae (gobies). Total fish biomass was very low, with the trend of small fishes from low trophic levels over-represented, and top predators under-represented, relative to coral reefs elsewhere in the Caribbean. For example, herbivorous fishes comprised 27% of total fish biomass in Panama relative to 10% in the wider Caribbean, and the small parrotfishScarus isericomprised 72% of the parrotfish biomass. We found evidence that non-coral biogenic habitats support reef-associated fish communities. In particular, the abundance of sponges on a given reef and proximity of mangroves were found to be important positive correlates of reef fish species richness, biomass, abundance and trophic structure. Our study indicates that a diverse fish community can persist on degraded coral reefs, and that the availability and arrangement within the seascape of other habitat-forming organisms, including sponges and mangroves, is critical to the maintenance of functional processes in such ecosystems.
Simulated Disperser Analysis: determining the number of loci required to genetically identify dispersers
Authors: Cardilini Adam P.A. , Sherman Craig D.H. , Sherwin William B. , Rollins Lee A.
Published: March 2018

Empirical genetic datasets used for estimating contemporary dispersal in wild populations and to correctly identify dispersers are rarely tested to determine if they are capable of providing accurate results. Here we test whether a genetic dataset provides sufficient information to accurately identify first-generation dispersers. Using microsatellite data from three wild populations of common starlings (Sturnus vulgaris), we artificially simulated dispersal of a subset of individuals; we term this ‘Simulated Disperser Analysis’. We then ran analyses for diminishing numbers of loci, to assess at which point simulated dispersers could no longer be correctly identified. Not surprisingly, the correct identification of dispersers varied significantly depending on the individual chosen to ‘disperse’, the number of loci used, whether loci had high or low Polymorphic Information Content and the location to which the dispersers were moved. A review of the literature revealed that studies that have implemented first-generation migrant detection to date have used on average 10 microsatellite loci. Our results suggest at least 27 loci are required to accurately identify dispersers in the study system evaluated here. We suggest that future studies use the approach we describe to determine the appropriate number of markers needed to accurately identify dispersers in their study system; the unique nature of natural systems means that the number of markers required for each study system will vary. Future studies can use Simulated Disperser Analysis on pilot data to test marker panels for robustness to contemporary dispersal identification, providing a powerful tool in the efficient and accurate design of studies using genetic data to estimate dispersal.
Pilot study of EEG in neonates born to mothers with gestational diabetes mellitus
Authors: Léveillé‐ Pauline , Hamel Mathieu , Ardilouze Jean‐Luc , Pasquier Jean‐Charles , Deacon Charles , Whittingstall Kevin , Plourde Mélanie
Published: March 2018

Background

The goal was to evaluate whether there was neurodevelopmental deficits in newborns born to mothers with gestational diabetes mellitus (GDM) compared to control newborns born to healthy mothers.

Methods

Forty‐six pregnant women (21 controls and 25 GDM) were recruited. Electroencephalogram (EEG) was recorded in the newborns within 48 h after birth. The EEG signal was quantitatively analyzed using power spectral density (PSD); coherence between hemispheres was calculated in paired channels of frontal, temporal, central and occipital regions.

Results

The left centro‐occipital PSD in control newborns was 12% higher than in GDM newborns (p = 0.036) but was not significant after adjustment for gestational age. While coherence was higher in the frontal regions compared to the occipital regions (p < 0.001), there was no difference between the groups for the fronto‐temporal, frontal‐central, centro‐occipital and tempo‐occipital regions.

Conclusion

Our results support that EEG differences between groups were mainly modified by gestational age and less by GDM status of the mothers. However, there is a need to confirm this result with a higher number of mother‐newborns. Quantitative EEG in GDM newborns within 48 h after birth is feasible. This study emphasizes the importance of controlling blood glucose during GDM to protect infant brain development.
Richard II and the Wider Gaelic World: A Reassessment
Authors: Egan Simon
Published: March 2018

Although Richard II's Irish expedition of 1394–95 has attracted considerable scholarly attention, the focus has largely been on Richard's relations with the colonial administration in Ireland, pointing mainly to the colonial government's plea for greater royal investment in the colony as the main factor underpinning Richard's decision to intervene in Ireland. Little attention, by comparison, has been devoted to exploring the king's relations with both the Gaelic Irish and Gaelic Scottish nobility. Using Richard's relations with the expanding Gaelic world as the main case study, this article reconsiders how developments in the Gaelic west influenced the king's decision to intervene in Ireland. Set against the backdrop of Anglo-Scottish relations and the Hundred Years’ War, the article draws on a broad range of Gaelic sources from Ireland and Scotland, English and Scottish governmental records, and material from the Avignon papacy. It uncovers and traces the development of the main Gaelic Irish and Gaelic Scottish dynasties during the late fourteenth century, their relationships with one another, and their unfolding connections with the English and Scottish crowns. By locating Richard's expeditions within the broader archipelagic context, this article argues that the wider Gaelic world, though on the geographic periphery of Ireland and Scotland, was capable of exerting a far greater degree of influence on the course of “British” politics than has previously been acknowledged.
The Use of Force to Prevent War? The Bryce Group's “Proposals for the Avoidance of War,” 1914–15
Authors: Kaiga Sakiko
Published: March 2018

This article reappraises the debate about war prevention in the Bryce Group, the first study circle in Britain to devise a plan for the League of Nations. While scholars have tended to associate pro–league of nations activists with idealism, more focused accounts of the group have mostly depicted its postwar plan as a product of realistic thinking. Drawing on the underused manuscripts of the intellectual founders of the League of Nations, this study first reveals that their early thinking defies simple categorization. Not only was their war prevention plan realistic about the role of armed force but it also depended critically on idealistic expectations about the moral force of public opinion. This article shows that realistic and idealistic views could rarely be separated, and both developed the group's plan for peace, which incorporated the collective use of force as a crucial element of the postwar order. A mixture of the two views, however, hardly ensured consistencies and a balance between them. The paradox of collective security discussed by the group in 1914–15—that peace at least in part rested on the threat of force—was unresolved by the foundation of the League, and remains intact to this day.
End-of-Life-Care auf der Intensivstation
Authors: Cyrol Katharina , Fröhlich Martin R. , Piatti Francesca , Imhof Lorenz
Published: March 2018

Zusammenfassung. Hintergrund: Familienangehörige von Sterbenden auf der Intensivstation (IPS) sind vielen Belastungen ausgesetzt und erleben kaum Einbezug in Situationen am Lebensende. Sie kritisieren eine geringe Beteiligung an der Pflege, mangelnde Information sowie fehlende Privatsphäre. Auch Pflegende sehen sich mit Hürden in der Pflege am Lebensende auf der Intensivstation konfrontiert. Ziel: Diese Studie untersuchte, welche Strategien Intensivpflegende in der Deutschschweiz haben, um Familienangehörige in Situationen am Lebensende einzubeziehen. Methode: Mit dem Ansatz von Grounded Theory wurde mit zwölf halbstrukturierten Interviews ein Modell entwickelt, das pflegerische Strategien zum Einbezug von Familienangehörigen in End-of-Life-Situationen (EoL) auf der Intensivstation zeigt. Ergebnisse: Pflegende schaffen persönlichen Raum und Ruhe für Familienangehörige und ermöglichen ein Dasein zu jeder Zeit. Sie sind den Familienangehörigen ein Halt und ermöglichen, sich bewusst vom sterbenden Menschen zu verabschieden. Schlussfolgerungen: Künftige Arbeiten sollten die Wirksamkeit der beschriebenen Strategien besonders im Hinblick auf Belastungsreaktionen Familienangehöriger nach EoL-Situationen untersuchen. In der Praxis müssen Räumlichkeiten geschaffen werden, die Privatsphäre ermöglichen. Die Orientierung des Betreuungsteams an gemeinsamen Werten und Zielen ist indiziert. Ein intradisziplinärer Austausch und Mentoring müssen unterstützt werden. Um Pflegende zukünftig für EoL-Situationen auf der Intensivstation zu befähigen, ist es unumgänglich, ihre Edukationsleistung anzuerkennen und zu fördern.
Measurement Invariance of Three Brief Emotion Regulation	Questionnaires in People With and Without a History of Non-Suicidal	Self-Injury
Authors: Kiekens Glenn , Hasking Penelope , Boyes Mark
Published: March 2018

Abstract. In this study, we investigated the factor structure and measurement invariance of three brief emotion regulation questionnaires in samples of young adults (17–30 years) with and without a history of non-suicidal self-injury (NSSI; n = 705–836). Results revealed configural, full metric, and full scalar invariance for the Difficulties in Emotion Regulation Scale – Short Form (DERS-SF) and the Cognitive Emotion Regulation Questionnaire – Short (CERQ-S). In addition, the CERQ-S also showed full residual error invariance. In contrast, the proposed factor structure of the Emotion Regulation Questionnaire (ERQ) was not confirmed in either sample. Further, we observed that some items function differently for people who self-injure and people who do not, which could result in artificial differences being reported in use of cognitive reappraisal. While the current findings offer confidence that observed differences using the DERS-SF and CERQ-S reflect reliable discrepancies in emotion regulation processes between people who self-injure and do not, the validity of statistical inferences using the ERQ could not be ensured and need further psychometric evaluation.
Ruminating in English, Ruminating in Spanish
Authors: Bravo Adrian J. , Pearson Matthew R. , Pilatti Angelina , Mezquita Laura , Ibáñez Manuel I. , Ortet Generós
Published: March 2018

Abstract. The present study aimed to adapt and validate a Spanish version of the Ruminative Thought Style Questionnaire (RTSQ) and test for measurement invariance of the RTSQ across college students in the US, Spain, and Argentina ( n = 1,632). Additionally, we examined/compared across these countries, criterion-related (i.e., concurrent) validity of RTSQ factors (i.e., problem-focused thoughts, counterfactual thinking, repetitive thoughts, and anticipatory thoughts) on constructs theoretically-associated with rumination. Consistent with previous findings, we found that a 15-item 4-factor RTSQ provided a more adequate model compared to single-factor CFA models (15- and 20-item versions) in every country. The reliability and validity of the subscales for the Spanish version were satisfactory-to-good in Spain and Argentina. Using multigroup confirmatory factor analyses, we found the 15-item 4-factor version of the RTSQ to be invariant across countries and sex. Bivariate correlations provided evidence for the criterion-related validity of the 4-factor RTSQ across the countries. Our findings suggest that self-report items of the RTSQ convey the same meaning, and that responses to those items load onto the same set of factors, across languages and cultures of administration. Taken together, our findings serve as a foundation for future cross-cultural work testing models in which rumination is a central facet.
The Big Picture in Geospace
Authors: Goldstein Jerry
Published: March 2018

A NASA stereo-imaging mission called TWINS continues to push the boundaries of what we know about the region of space close to Earth.
The Upside to a “Bad” Ozone Precursor
Authors: Witman Sarah
Published: March 2018

In Sweden’s wet heathland, scientists see how a sensitive ecosystem adapts to rising global temperatures.
iMETHYL: an integrative database of human DNA methylation, gene expression, and genomic variation
Authors: Komaki Shohei , Shiwa Yuh , Furukawa Ryohei , Hachiya Tsuyoshi , Ohmomo Hideki , Otomo Ryo , Satoh Mamoru , Hitomi Jiro , Sobue Kenji , Sasaki Makoto , Shimizu Atsushi
Published: March 2018

We launched an integrative multi-omics database, iMETHYL (http://imethyl.iwate-megabank.org). iMETHYL provides whole-DNA methylation (~24 million autosomal CpG sites), whole-genome (~9 million single-nucleotide variants), and whole-transcriptome (>14 000 genes) data for CD4+ T-lymphocytes, monocytes, and neutrophils collected from approximately 100 subjects. These data were obtained from whole-genome bisulfite sequencing, whole-genome sequencing, and whole-transcriptome sequencing, making iMETHYL a comprehensive database.
Structural rearrangements of the histone octamer translocate DNA
Authors: Bilokapic Silvija , Strauss Mike , Halic Mario
Published: March 2018

Nucleosomes, the basic unit of chromatin, package and regulate expression of eukaryotic genomes. Nucleosomes are highly dynamic and are remodeled with the help of ATP-dependent remodeling factors. Yet, the mechanism of DNA translocation around the histone octamer is poorly understood. In this study, we present several nucleosome structures showing histone proteins and DNA in different organizational states. We observe that the histone octamer undergoes conformational changes that distort the overall nucleosome structure. As such, rearrangements in the histone core α-helices and DNA induce strain that distorts and moves DNA at SHL 2. Distortion of the nucleosome structure detaches histone α-helices from the DNA, leading to their rearrangement and DNA translocation. Biochemical assays show that cross-linked histone octamers are immobilized on DNA, indicating that structural changes in the octamer move DNA. This intrinsic plasticity of the nucleosome is exploited by chromatin remodelers and might be used by other chromatin machineries.
Longer and more frequent marine heatwaves over the past century
Authors: Oliver Eric C. J. , Donat Markus G. , Burrows Michael T. , Moore Pippa J. , Smale Dan A. , Alexander Lisa V. , Benthuysen Jessica A. , Feng Ming , Sen Gupta Alex , Hobday Alistair J. , Holbrook Neil J. , Perkins-Kirkpatrick Sarah E. , Scannell Hillary A. , Straub Sandra C. , Wernberg Thomas
Published: March 2018

Heatwaves are important climatic extremes in atmospheric and oceanic systems that can have devastating and long-term impacts on ecosystems, with subsequent socioeconomic consequences. Recent prominent marine heatwaves have attracted considerable scientific and public interest. Despite this, a comprehensive assessment of how these ocean temperature extremes have been changing globally is missing. Using a range of ocean temperature data including global records of daily satellite observations, daily in situ measurements and gridded monthly in situ-based data sets, we identify significant increases in marine heatwaves over the past century. We find that from 1925 to 2016, global average marine heatwave frequency and duration increased by 34% and 17%, respectively, resulting in a 54% increase in annual marine heatwave days globally. Importantly, these trends can largely be explained by increases in mean ocean temperatures, suggesting that we can expect further increases in marine heatwave days under continued global warming.
Origin of vertical orientation in two-dimensional metal halide perovskites and its effect on photovoltaic performance
Authors: Chen Alexander Z. , Shiu Michelle , Ma Jennifer H. , Alpert Matthew R. , Zhang Depei , Foley Benjamin J. , Smilgies Detlef-M. , Lee Seung-Hun , Choi Joshua J.
Published: March 2018

Thin films based on two-dimensional metal halide perovskites have achieved exceptional performance and stability in numerous optoelectronic device applications. Simple solution processing of the 2D perovskite provides opportunities for manufacturing devices at drastically lower cost compared to current commercial technologies. A key to high device performance is to align the 2D perovskite layers, during the solution processing, vertical to the electrodes to achieve efficient charge transport. However, it is yet to be understood how the counter-intuitive vertical orientations of 2D perovskite layers on substrates can be obtained. Here we report a formation mechanism of such vertically orientated 2D perovskite in which the nucleation and growth arise from the liquid–air interface. As a consequence, choice of substrates can be liberal from polymers to metal oxides depending on targeted application. We also demonstrate control over the degree of preferential orientation of the 2D perovskite layers and its drastic impact on device performance.
Cryptic glucocorticoid receptor-binding sites pervade genomic NF-κB response elements
Authors: Hudson William H. , Vera Ian Mitchelle S. de , Nwachukwu Jerome C. , Weikum Emily R. , Herbst Austin G. , Yang Qin , Bain David L. , Nettles Kendall W. , Kojetin Douglas J. , Ortlund Eric A.
Published: March 2018

Glucocorticoids (GCs) are potent repressors of NF-κB activity, making them a preferred choice for treatment of inflammation-driven conditions. Despite the widespread use of GCs in the clinic, current models are inadequate to explain the role of the glucocorticoid receptor (GR) within this critical signaling pathway. GR binding directly to NF-κB itself—tethering in a DNA binding-independent manner—represents the standing model of how GCs inhibit NF-κB-driven transcription. We demonstrate that direct binding of GR to genomic NF-κB response elements (κBREs) mediates GR-driven repression of inflammatory gene expression. We report five crystal structures and solution NMR data of GR DBD-κBRE complexes, which reveal that GR recognizes a cryptic response element between the binding footprints of NF-κB subunits within κBREs. These cryptic sequences exhibit high sequence and functional conservation, suggesting that GR binding to κBREs is an evolutionarily conserved mechanism of controlling the inflammatory response.
A large planetary body inferred from diamond inclusions in a ureilite meteorite
Authors: Nabiei Farhang , Badro James , Dennenwaldt Teresa , Oveisi Emad , Cantoni Marco , Hébert Cécile , El Goresy Ahmed , Barrat Jean-Alix , Gillet Philippe
Published: March 2018

Planetary formation models show that terrestrial planets are formed by the accretion of tens of Moon- to Mars-sized planetary embryos through energetic giant impacts. However, relics of these large proto-planets are yet to be found. Ureilites are one of the main families of achondritic meteorites and their parent body is believed to have been catastrophically disrupted by an impact during the first 10 million years of the solar system. Here we studied a section of the Almahata Sitta ureilite using transmission electron microscopy, where large diamonds were formed at high pressure inside the parent body. We discovered chromite, phosphate, and (Fe,Ni)-sulfide inclusions embedded in diamond. The composition and morphology of the inclusions can only be explained if the formation pressure was higher than 20 GPa. Such pressures suggest that the ureilite parent body was a Mercury- to Mars-sized planetary embryo.
Reduction in global area burned and wildfire emissions since 1930s enhances carbon uptake by land
Authors: Arora Vivek K. , Melton Joe R.
Published: March 2018

The terrestrial biosphere currently absorbs about 30% of anthropogenic CO2 emissions. This carbon uptake over land results primarily from vegetation’s response to increasing atmospheric CO2 but other factors also play a role. Here we show that since the 1930s increasing population densities and cropland area have decreased global area burned, consistent with the charcoal record and recent satellite-based observations. The associated reduced wildfire emissions from increase in cropland area do not enhance carbon uptake since natural vegetation that is spared burning was deforested anyway. However, reduction in fire CO2 emissions due to fire suppression and landscape fragmentation associated with increases in population density is calculated to enhance land carbon uptake by 0.13 Pg C yr−1, or ~19% of the global land carbon uptake (0.7 ± 0.6 Pg C yr−1), for the 1960–2009 period. These results identify reduction in global wildfire CO2 emissions as yet another mechanism that is currently enhancing carbon uptake over land.
Novel, Moon and Mars, partial gravity simulation paradigms and their effects on the balance between cell growth and cell proliferation during early plant development
Authors: Manzano Aránzazu , Herranz Raúl , den Toom Leonardus A. , te Slaa Sjoerd , Borst Guus , Visser Martijn , Medina F. Javier , van Loon Jack J. W. A.
Published: March 2018

Clinostats and Random Positioning Machine (RPM) are used to simulate microgravity, but, for space exploration, we need to know the response of living systems to fractional levels of gravity (partial gravity) as they exist on Moon and Mars. We have developed and compared two different paradigms to simulate partial gravity using the RPM, one by implementing a centrifuge on the RPM (RPMHW), the other by applying specific software protocols to driving the RPM motors (RPMSW). The effects of the simulated partial gravity were tested in plant root meristematic cells, a system with known response to real and simulated microgravity. Seeds of Arabidopsis thaliana were germinated under simulated Moon (0.17 g) and Mars (0.38 g) gravity. In parallel, seeds germinated under simulated microgravity (RPM), or at 1 g control conditions. Fixed root meristematic cells from 4-day grown seedlings were analyzed for cell proliferation rate and rate of ribosome biogenesis using morphometrical methods and molecular markers of the regulation of cell cycle and nucleolar activity. Cell proliferation appeared increased and cell growth was depleted under Moon gravity, compared with the 1 g control. The effects were even higher at the Moon level than at simulated microgravity, indicating that meristematic competence (balance between cell growth and proliferation) is also affected at this gravity level. However, the results at the simulated Mars level were close to the 1 g static control. This suggests that the threshold for sensing and responding to gravity alteration in the root would be at a level intermediate between Moon and Mars gravity. Both partial g simulation strategies seem valid and show similar results at Moon g-levels, but further research is needed, in spaceflight and simulation facilities, especially around and beyond Mars g levels to better understand more precisely the differences and constrains in the use of these facilities for the space biology community.
The spatial and temporal domains of modern ecology
Authors: Estes Lyndon , Elsen Paul R. , Treuer Timothy , Ahmed Labeeb , Caylor Kelly , Chang Jason , Choi Jonathan J. , Ellis Erle C.
Published: March 2018

To understand ecological phenomena, it is necessary to observe their behaviour across multiple spatial and temporal scales. Since this need was first highlighted in the 1980s, technology has opened previously inaccessible scales to observation. To help to determine whether there have been corresponding changes in the scales observed by modern ecologists, we analysed the resolution, extent, interval and duration of observations (excluding experiments) in 348 studies that have been published between 2004 and 2014. We found that observational scales were generally narrow, because ecologists still primarily use conventional field techniques. In the spatial domain, most observations had resolutions ≤1 m2 and extents ≤10,000 ha. In the temporal domain, most observations were either unreplicated or infrequently repeated (>1 month interval) and ≤1 year in duration. Compared with studies conducted before 2004, observational durations and resolutions appear largely unchanged, but intervals have become finer and extents larger. We also found a large gulf between the scales at which phenomena are actually observed and the scales those observations ostensibly represent, raising concerns about observational comprehensiveness. Furthermore, most studies did not clearly report scale, suggesting that it remains a minor concern. Ecologists can better understand the scales represented by observations by incorporating autocorrelation measures, while journals can promote attentiveness to scale by implementing scale-reporting standards.
Application of distribution functions in accurate determination of interdiffusion coefficients
Authors: Wei Ming , Zhang Lijun
Published: March 2018

Diffusion couple technique in combination with the Boltzmann-Matano method is the widely used approach to evaluate the interdiffusion coefficients in the target systems. However, the quality of the evaluated interdiffusion coefficients due to the Boltzmann-Matano method strongly depends on the fitting degree of the utilized continuous function to the discrete experimental composition profiles. In this paper, the application of different types of distribution functions is proposed to solve this problem. For the simple D-c relations, the normal, pseudo-normal, skew normal, pseudo-skew normal distributions can be employed, while for the complex D-c relations, the superposed distributions should be used. Even for the cases with uphill diffusion, the combined superposition of distributions may be chosen. Through validation in several benchmarks and real alloy systems, accurate diffusion coefficients are proved to be successfully obtained by using the distribution functions. It is anticipated that the Boltzmann-Matano method together with the distribution functions may serve as the general solution for determining the accurate interdiffusion coefficients in different materials.
Evidence for Layered Quantized Transport in Dirac Semimetal ZrTe5
Authors: Wang Wei , Zhang Xiaoqian , Xu Huanfeng , Zhao Yafei , Zou Wenqin , He Liang , Xu Yongbing
Published: March 2018

ZrTe5 is an important semiconductor thermoelectric material and a candidate topological insulator. Here we report the observation of Shubnikov-de Hass (SdH) oscillations accompanied by quantized Hall resistance in bulk ZrTe5 crystal, with a mobility of 41,000 cm2V−1s−1. We have found that the quantum oscillations does not originate from the surface states, but from the bulk states. Each single layer ZrTe5 acted like an independent 2D electron system in the quantum Hall regime having the same carrier density and mobilities, while the bulk of the sample exhibits a multilayered quantum Hall effect.
Transparent semiconducting SrTiO3 crystal fabricated by heating treatment with gaseous ammonia and CeO2 powder
Authors: Morimoto Yuka , Nishiyama Junji , Takeda Hiroaki , Tsurumi Takaaki , Hoshina Takuya
Published: March 2018

A transparent semiconducting SrTiO3 single crystal with a resistivity of the order of 103 Ω·cm was fabricated by heating a SrTiO3 single crystal with gaseous ammonia and CeO2 powder. Conductive atomic force microscope (C-AFM) measurement revealed that micro-sized voids were formed and the high conductivity was exhibited only at around the voids. It is considered that the micro-sized voids were caused by the concentrated SrO planar defects, and TiO2-terminated structure with oxygen vacancies contributed to the two-dimensional conduction. In the heating process, the CeO2 powder acted as an oxygen source, and radicals such as NH2 and NH were generated by the reaction of oxygen and ammonia. The radicals may have contributed to the formation of three-dimensional network of the conductive paths consisting of SrO planar defects without the reduction of the bulk components. The electrons were localized on the TiO2-terminated structure, and the volume content of the conductive paths was small compared to the insulating bulk component. Therefore, the crystal was optically transparent and semiconducting.
Structural modelling of the DNAJB6 oligomeric chaperone shows a peptide-binding cleft lined with conserved S/T-residues at the dimer interface
Authors: Söderberg Christopher A. G. , Månsson Cecilia , Bernfur Katja , Rutsdottir Gudrun , Härmark Johan , Rajan Sreekanth , Al-Karadaghi Salam , Rasmussen Morten , Höjrup Peter , Hebert Hans , Emanuelsson Cecilia
Published: March 2018

The remarkably efficient suppression of amyloid fibril formation by the DNAJB6 chaperone is dependent on a set of conserved S/T-residues and an oligomeric structure, features unusual among DNAJ chaperones. We explored the structure of DNAJB6 using a combination of structural methods. Lysine-specific crosslinking mass spectrometry provided distance constraints to select a homology model of the DNAJB6 monomer, which was subsequently used in crosslink-assisted docking to generate a dimer model. A peptide-binding cleft lined with S/T-residues is formed at the monomer-monomer interface. Mixed isotope crosslinking showed that the oligomers are dynamic entities that exchange subunits. The purified protein is well folded, soluble and composed of oligomers with a varying number of subunits according to small-angle X-ray scattering (SAXS). Elongated particles (160 × 120 Å) were detected by electron microscopy and single particle reconstruction resulted in a density map of 20 Å resolution into which the DNAJB6 dimers fit. The structure of the oligomer and the S/T-rich region is of great importance for the understanding of the function of DNAJB6 and how it can bind aggregation-prone peptides and prevent amyloid diseases.
Enterobacter bugandensis: a novel enterobacterial species associated with severe clinical infection
Authors: Pati Niladri Bhusan , Doijad Swapnil Prakash , Schultze Tilman , Mannala Gopala Krishna , Yao Yancheng , Jaiswal Sangeeta , Ryan Daniel , Suar Mrutyunjay , Gwozdzinski Konrad , Bunk Boyke , Mraheil Mobarak Abu , Marahiel Mohamed A. , Hegemann Julian D. , Spröer Cathrin , Goesmann Alexander , Falgenhauer Linda , Hain Torsten , Imirzalioglu Can , Mshana Stephen E. , Overmann Jörg , Chakraborty Trinad
Published: March 2018

Nosocomial pathogens can cause life-threatening infections in neonates and immunocompromised patients. E. bugandensis (EB-247) is a recently described species of Enterobacter, associated with neonatal sepsis. Here we demonstrate that the extended spectrum ß-lactam (ESBL) producing isolate EB-247 is highly virulent in both Galleria mellonella and mouse models of infection. Infection studies in a streptomycin-treated mouse model showed that EB-247 is as efficient as Salmonella Typhimurium in inducing systemic infection and release of proinflammatory cytokines. Sequencing and analysis of the complete genome and plasmid revealed that virulence properties are associated with the chromosome, while antibiotic-resistance genes are exclusively present on a 299 kb IncHI plasmid. EB-247 grew in high concentrations of human serum indicating septicemic potential. Using whole genome-based transcriptome analysis we found 7% of the genome was mobilized for growth in serum. Upregulated genes include those involved in the iron uptake and storage as well as metabolism. The lasso peptide microcin J25 (MccJ25), an inhibitor of iron-uptake and RNA polymerase activity, inhibited EB-247 growth. Our studies indicate that Enterobacter bugandensis is a highly pathogenic species of the genus Enterobacter. Further studies on the colonization and virulence potential of E. bugandensis and its association with septicemic infection is now warranted.
Author Correction: Levels of Faecal Calprotectin and Magnetic Resonance Enterocolonography Correlate with Severity of Small Bowel Crohn’s Disease: A Retrospective Cohort Study
Authors: Ye Lei , Cheng Wei , Chen Bi-qin , Lan Xing , Wang Shao-dong , Wu Xiao-chen , Huang Wei , Wang Fang-yu
Published: March 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Author Correction: Some coral diseases track climate oscillations in the Caribbean
Authors: Randall C. J. , van Woesik R.
Published: March 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Tunable Ampere phase plate for low dose imaging of biomolecular complexes
Authors: Tavabi Amir H. , Beleggia Marco , Migunov Vadim , Savenko Alexey , Öktem Ozan , Dunin-Borkowski Rafal E. , Pozzi Giulio
Published: March 2018

A novel device that can be used as a tunable support-free phase plate for transmission electron microscopy of weakly scattering specimens is described. The device relies on the generation of a controlled phase shift by the magnetic field of a segment of current-carrying wire that is oriented parallel or antiparallel to the electron beam. The validity of the concept is established using both experimental electron holographic measurements and a theoretical model based on Ampere’s law. Computer simulations are used to illustrate the resulting contrast enhancement for studies of biological cells and macromolecules.
Filamentous Virus-based Assembly: Their Oriented Structures and Thermal Diffusivity
Authors: Sawada Toshiki , Murata Yuta , Marubayashi Hironori , Nojima Shuichi , Morikawa Junko , Serizawa Takeshi
Published: March 2018

Organic polymers are generally regarded as thermal insulators because amorphous arrangement of molecular chains reduces the mean free path of heat-conducting phonons. However, recent studies indicated that single chains of polymers with highly oriented structures could have high thermal conductivity than bulk polymers because stretched polymer chains effectively conduct phonons through polymeric covalent bonds. Here, we demonstrated the possibility of non-covalent virus assembly prepared by simple flow-induced methods toward high thermal conductive polymeric materials. Films with high thermal diffusivity composed of non-covalent bond-based assemblies of liquid crystalline filamentous viruses were prepared using a simple flow-induced orientation method. Structural and thermal characterization demonstrated that highly oriented structures of the viruses in the film were attributed to the high thermal diffusivity. Our results will open attractive opportunities for biomolecular-based thermally conductive soft materials even though the assemblies are based on non-covalent bonds.
Transcriptome Profiles Reveal the Crucial Roles of Hormone and Sugar in the Bud Dormancy of Prunus mume
Authors: Zhang Zhiyong , Zhuo XiaoKang , Zhao Kai , Zheng Tangchun , Han Yu , Yuan Cunquan , Zhang Qixiang
Published: March 2018

Bud dormancy transition is a vital developmental process for perennial plant survival. The process is precisely regulated by diverse endogenous genetic factors and environmental cues, but the mechanisms are not yet fully understood. Prunus mume is an ideal crop for bud dormancy analysis because of its early spring-flowering characteristics and small sequenced genome. Here, we analyzed the transcriptome profiles at the three endodormancy stages and natural flush stage using RNA sequencing combined with phytohormone and sugar content measurements. Significant alterations in hormone contents and carbohydrate metabolism have been observed, and α-amylases, Glucan Hydrolase Family 17 and diphosphate-glycosyltransferase family might play crucial roles in the interactions between hormones and sugars. The following hypothetical model for understanding the molecular mechanism of bud dormancy in Prunus mume is proposed: low temperatures exposure induces the significant up-regulation of eight C-repeat binding factor genes, which directly promotes all six dormancy-associated MADS-box genes, resulting in dormancy establishment. The prolonged cold and/or subsequently increasing temperature then decreases the expression levels of these two gene families, which alleviates the inhibition of FLOWERING LOCUS T and reopens the growth-promoting pathway, resulting in dormancy release and the initiation of the bud break process.
Extracting quasi-steady Lagrangian transport patterns from the ocean circulation: An application to the Gulf of Mexico
Authors: Duran R. , Beron-Vera F. J. , Olascoaga M. J.
Published: March 2018

We construct a climatology of Lagrangian coherent structures (LCSs)—the concealed skeleton that shapes transport—with a twelve-year-long data-assimilative simulation of the sea-surface circulation in the Gulf of Mexico (GoM). Computed as time-mean Cauchy–Green strain tensorlines of the climatological velocity, the climatological LCSs (cLCSs) unveil recurrent Lagrangian circulation patterns. The cLCSs strongly constrain the ensemble-mean Lagrangian circulation of the instantaneous model velocity, showing that a climatological velocity can preserve meaningful transport information. The quasi-steady transport patterns revealed by the cLCSs agree well with aspects of the GoM circulation described in several previous observational and numerical studies. For example, the cLCSs identify regions of persistent isolation, and suggest that coastal regions previously identified as high-risk for pollution impact are regions of maximal attraction. We also show that cLCSs are remarkably accurate at identifying transport patterns observed during the Deepwater Horizon and Ixtoc oil spills, and during the Grand LAgrangian Deployment (GLAD) experiment. Thus it is shown that computing cLCSs is an efficient and meaningful way of synthesizing vast amounts of Lagrangian information. The cLCS method confirms previous GoM studies, and contributes to our understanding by revealing the persistent nature of the dynamics and kinematics treated therein.
Differential expression of microRNAs and other small RNAs in muscle tissue of patients with ALS and healthy age-matched controls
Authors: Kovanda Anja , Leonardis Lea , Zidar Janez , Koritnik Blaž , Dolenc-Groselj Leja , Ristic Kovacic Stanislava , Curk Tomaž , Rogelj Boris
Published: March 2018

Amyotrophic lateral sclerosis is a late-onset disorder primarily affecting motor neurons and leading to progressive and lethal skeletal muscle atrophy. Small RNAs, including microRNAs (miRNAs), can serve as important regulators of gene expression and can act both globally and in a tissue-/cell-type-specific manner. In muscle, miRNAs called myomiRs govern important processes and are deregulated in various disorders. Several myomiRs have shown promise for therapeutic use in cellular and animal models of ALS; however, the exact miRNA species differentially expressed in muscle tissue of ALS patients remain unknown. Following small RNA-Seq, we compared the expression of small RNAs in muscle tissue of ALS patients and healthy age-matched controls. The identified snoRNAs, mtRNAs and other small RNAs provide possible molecular links between insulin signaling and ALS. Furthermore, the identified miRNAs are predicted to target proteins that are involved in both normal processes and various muscle disorders and indicate muscle tissue is undergoing active reinnervation/compensatory attempts thus providing targets for further research and therapy development in ALS.
Spindle cell sarcoma: a SEER population-based analysis
Authors: Feng Lei , Wang Meng , Yibulayin Feiluore , Zhang Hao , Yang Yin-Long , Ren Fei , Wushou Alimujiang
Published: March 2018

Due to the substantial limitation of study population, Spindle cell sarcoma (SCS) was unexplored comprehensively. In this study, we investigated the clinical characteristics and disease specific prognostic factors of SCS. 3299 SCS cases were identified and extracted from Surveillance, Epidemiology, and End Results (SEER) database (1973–2017). White people account for 79.1% with median age of 57 years without predominance in any gender. Significant disease specific survival (DSS) and overall survival (OS) were found differentiated in age, T stage, N stage, M stage, AJCC stage, SEER historic stage, tumor locations, surgery, and pathologic grade. In the multivariate Cox analysis, the age >64 years (for DSS, P < 0.001 and for OS, P < 0.001; Reference age ≤64 years), AJCC stage III (for DSS, P = 0.006 and for OS, P = 0.04; Reference: AJCC stage I), and non-surgical treatment (for DSS, P < 0.001 and for OS, P < 0.001; Reference: surgery) were independently associated with worse DSS and OS. In brief, our study demonstrated that SCS mostly found in white people at fifth to seventh decades of life without gender predilection. The patient’s age, AJCC stage, tumor location and surgery were independent prognostic indicators for both DSS and OS of SCS.
Author Correction: Molecular mechanism of K65 acetylation-induced attenuation of Ubc9 and the NDSM interaction
Authors: Naik Mandar T. , Kang Mooseok , Ho Chun-Chen , Liao Pei-Hsin , Hsieh Yung-Lin , Naik Nandita M. , Wang Szu-Huan , Chang Iksoo , Shih Hsiu-Ming , Huang Tai-Huang
Published: March 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Author Correction: Resveratrol Increases Hepatic SHBG Expression through Human Constitutive Androstane Receptor: a new Contribution to the French Paradox
Authors: Saez-Lopez Cristina , Brianso-Llort Laura , Torres-Torronteras J. , Simó Rafael , Hammond Geoffrey L. , Selva David M.
Published: March 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Frequency of Esophageal Eosinophilia in a Pediatric Population from Central Brazil
Authors: Strozzi Daniel , Botacin Marco Aurélio Silveira , Mekdessi Marilia Adriano , Salustiano Luciana Ximenes , Silva Pedro H. de Paula , Minasi Lysa Bernardes , Segundo Gesmar Rodrigues Silva , Cruz Aparecido Divino da
Published: March 2018

Here we report a retrospective cross-sectional study on Esophageal eosinophilia (EsEo) frequency in Brazil, for 2, 425 pediatric patients with symptoms associated with gastroesophageal diseases in 2012. EsEo is defined by ≥15 eosinophils per high power field (400x) and confirmed through histological analyses of esophageal biopsies. Overall, 126 patients had EsEo equating to a frequency of 5.2%. There was a significant difference between the endoscopic features of patients with EsEo, where 10.7% had erosive esophagitis, 3.0% had non-erosive esophagitis and 1% showed normal esophageal mucosa. According to the interaction of the variables in the Classification and Regression Tree Analysis, most patients diagnosed with EsEo were older males with erosive esophagitis. On the other hand, the lowest frequency of EsEo was found among younger females with non-erosive esophagitis/normal mucosa. Environmental conditions, including climate variation and changes, were observed in association with EsEo, supporting a potential role for environmental factors in its pathogenesis. There was an inverse correlation between the number of EsEo, rainfall and humidity. EsEo is a relatively frequent finding in the pediatric population of Brazil with symptoms of gastroesophageal diseases. Both clinical and histological examinations of patients are important for a reliable diagnostic of EsEo cases and to patient care.
Towards Millimeter-wavelength: Transmission-Mode Fresnel-Zone Plate Lens Antennas using Plastic Material Porosity Control in Homogeneous Medium
Authors: Pourahmadazar Javad , Denidni Tayeb A.
Published: March 2018

We present two transmission-mode dielectric Fresnel-Zone Plate Lens (FZPL) antennas for use within the V-band spectrum. The proposed FZPs are realized via pure plastic material using two different additive manufacturing processes. The proposed FZP lenses are designed with half (λ/2) and quarter (λ/4) phase correction rings at 60-GHz with 30λ0 diameter, where λ0 is the free-space wavelength. The permittivity effect for lens sub-zones is controlled by material porosity in cube-shaped structures. The 3D printed zone plate lenses are built using additive manufacturing plastic materials with a thickness of λ0 and constant relative permittivities equal to 2.76 and 3.6. Different types of antenna with cosn-like radiation patterns as lens illuminators are analyzed on the vertical plane of the flat lenses to have a high efficiency over the considered operating band. Simulations and experimental measurements show a reasonably close match, therefore allowing for a reliable predictability.
Personalised drug repositioning for Clear Cell Renal Cell Carcinoma using gene expression
Authors: Koudijs Karel K. M. , Terwisscha van Scheltinga Anton G. T. , Böhringer Stefan , Schimmel Kirsten J. M. , Guchelaar Henk-Jan
Published: March 2018

Reversal of cancer gene expression is predictive of therapeutic potential and can be used to find new indications for existing drugs (drug repositioning). Gene expression reversal potential is currently calculated, in almost all studies, by pre-aggregating all tumour samples into a single group signature or a limited number of molecular subtype signatures. Here, we investigate whether drug repositioning based on individual tumour sample gene expression signatures outperforms the use of tumour group and subtype signatures. The tumour signatures were created using 534 tumour samples and 72 matched normal samples from 530 clear cell renal cell carcinoma (ccRCC) patients. More than 20,000 drug signatures were extracted from the CMAP and LINCS databases. We show that negative enrichment of individual tumour samples correlated (Spearman’s rho = 0.15) much better with the amount of differentially expressed genes in drug signatures than with the tumour group signature (Rho = 0.08) and the 4 tumour subtype signatures (Rho 0.036-0.11). Targeted drugs used against ccRCC, such as sirolimus and temsirolimus, which could not be identified with the pre-aggregated tumour signatures could be recovered using individual sample analysis. Thus, drug repositioning can be personalized by taking into account the gene expression profile of the individual’s tumour sample.